1
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Zhang C, Tian Z, Chen R, Rowan F, Qiu K, Sun Y, Guan JL, Diao J. Advanced imaging techniques for tracking drug dynamics at the subcellular level. Adv Drug Deliv Rev 2023; 199:114978. [PMID: 37385544 PMCID: PMC10527994 DOI: 10.1016/j.addr.2023.114978] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 06/17/2023] [Accepted: 06/26/2023] [Indexed: 07/01/2023]
Abstract
Optical microscopes are an important imaging tool that have effectively advanced the development of modern biomedicine. In recent years, super-resolution microscopy (SRM) has become one of the most popular techniques in the life sciences, especially in the field of living cell imaging. SRM has been used to solve many problems in basic biological research and has great potential in clinical application. In particular, the use of SRM to study drug delivery and kinetics at the subcellular level enables researchers to better study drugs' mechanisms of action and to assess the efficacy of their targets in vivo. The purpose of this paper is to review the recent advances in SRM and to highlight some of its applications in assessing subcellular drug dynamics.
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Affiliation(s)
- Chengying Zhang
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Zhiqi Tian
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Rui Chen
- Department of Chemistry, University of Cincinnati, Cincinnati, OH 45221, USA
| | - Fiona Rowan
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Kangqiang Qiu
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Yujie Sun
- Department of Chemistry, University of Cincinnati, Cincinnati, OH 45221, USA
| | - Jun-Lin Guan
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Jiajie Diao
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA.
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2
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Sun N, Jia Y, Bai S, Li Q, Dai L, Li J. The power of super-resolution microscopy in modern biomedical science. Adv Colloid Interface Sci 2023; 314:102880. [PMID: 36965225 DOI: 10.1016/j.cis.2023.102880] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 03/08/2023] [Accepted: 03/08/2023] [Indexed: 03/14/2023]
Abstract
Super-resolution microscopy (SRM) technology that breaks the diffraction limit has revolutionized the field of cell biology since its appearance, which enables researchers to visualize cellular structures with nanometric resolution, multiple colors and single-molecule sensitivity. With the flourishing development of hardware and the availability of novel fluorescent probes, the impact of SRM has already gone beyond cell biology and extended to nanomedicine, material science and nanotechnology, and remarkably boosted important breakthroughs in these fields. In this review, we will mainly highlight the power of SRM in modern biomedical science, discussing how these SRM techniques revolutionize the way we understand cell structures, biomaterials assembly and how assembled biomaterials interact with cellular organelles, and finally their promotion to the clinical pre-diagnosis. Moreover, we also provide an outlook on the current technical challenges and future improvement direction of SRM. We hope this review can provide useful information, inspire new ideas and propel the development both from the perspective of SRM techniques and from the perspective of SRM's applications.
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Affiliation(s)
- Nan Sun
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Lab of Colloid, Interface and Chemical Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China; University of Chinese Academy of Sciences, Beijing 100049
| | - Yi Jia
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Lab of Colloid, Interface and Chemical Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China.
| | - Shiwei Bai
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Lab of Colloid, Interface and Chemical Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China; University of Chinese Academy of Sciences, Beijing 100049
| | - Qi Li
- State Key Laboratory of Biochemical Engineering Institute of Process Engineering Chinese Academy of Sciences, Beijing 100190, China
| | - Luru Dai
- Wenzhou Institute and Wenzhou Key Laboratory of Biophysics, University of Chinese Academy of Sciences, Wenzhou, Zhejiang 325001, China
| | - Junbai Li
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Lab of Colloid, Interface and Chemical Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China; University of Chinese Academy of Sciences, Beijing 100049.
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3
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Curtin N, Garre M, Wu D, O’Shea DF. Identifying STEDable BF 2-Azadipyrromethene Fluorophores. Molecules 2023; 28:molecules28031415. [PMID: 36771082 PMCID: PMC9919209 DOI: 10.3390/molecules28031415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 01/28/2023] [Accepted: 01/30/2023] [Indexed: 02/05/2023] Open
Abstract
BF2-azadipyrromethenes are highly versatile fluorophores used for cellular and in vivo imaging in the near-infrared and far-red regions of the spectrum. As of yet, their use in conjunction with super-resolution imaging methodologies has not been explored. In this report, a series of structurally related BF2-azadipyrromethenes has been examined for their suitability for use with stimulated emission depletion (STED) nanoscopy. The potential for STED imaging was initially evaluated using aqueous solutions of fluorophores as an effective predictor of fluorophore suitability. For live cell STED imaging in both 2D and 3D, several far-red emitting BF2-azadipyrromethenes were successfully employed. Image resolution below the diffraction limit of a confocal microscope was demonstrated through measurement of distinct intracellular features including the nuclear membrane, nuclear lamina invaginations, the endoplasmic reticulum, and vacuoles. As the STED ability of BF2-azadipyrromethene fluorophores has now been established, their use with this super-resolution method may be expected to increase in the future.
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4
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Chan CY, Han S, Wang X, Guo X, Wu LG. Visualization of Exo- and Endocytosis Membrane Dynamics with Super-Resolution STED Microscopy. Methods Mol Biol 2023; 2565:77-87. [PMID: 36205888 DOI: 10.1007/978-1-0716-2671-9_6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Recent advances in stimulated emission depletion (STED) microscopy offer an unparalleled avenue to study membrane dynamics of exo- and endocytosis, such as fusion pore opening, pore expansion, constriction, and closure, as well as the membrane transformation from flat-shaped to round-shaped vesicles in real time. Here we depict a method of using the state-of-the-art STED microscopy to image these membrane dynamics in bovine chromaffin cells. This method can potentially be applied to study other membrane structure dynamics in other cell model system.
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Affiliation(s)
- Chung Yu Chan
- National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA.
| | - Sue Han
- National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
| | - Xin Wang
- National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
| | - Xiaoli Guo
- National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
| | - Ling-Gang Wu
- National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA.
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5
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Wang Y, Soto Rodriguez PED, Woythe L, Sánchez S, Samitier J, Zijlstra P, Albertazzi L. Multicolor Super-Resolution Microscopy of Protein Corona on Single Nanoparticles. ACS APPLIED MATERIALS & INTERFACES 2022; 14:37345-37355. [PMID: 35961006 PMCID: PMC9412947 DOI: 10.1021/acsami.2c06975] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 08/04/2022] [Indexed: 06/15/2023]
Abstract
Nanoparticles represent a promising class of material for nanomedicine and molecular biosensing. The formation of a protein corona due to nonspecific particle-protein interactions is a determining factor for the biological fate of nanoparticles in vivo and strongly impacts the performance of nanoparticles when used as biosensors. Nonspecific interactions are usually highly heterogeneous, yet little is known about the heterogeneity of the protein corona that may lead to inter- and intraparticle differences in composition and protein distribution. Here, we present a super-resolution microscopic approach to study the protein corona on single silica nanoparticles and subsequent cellular interactions using multicolor stimulated emission depletion (STED) microscopy. We demonstrate that STED resolves structural features of protein corona on single particles including the distribution on the particle surface and the degree of protein internalization in porous particles. Using multicolor measurements of multiple labeled protein species, we determine the composition of the protein corona at the single-particle level. We quantify particle-to-particle differences in the composition and find that the composition is considerably influenced by the particle geometry. In a subsequent cellular uptake measurement, we demonstrate multicolor STED of protein corona on single particles internalized by cells. Our study shows that STED microscopy opens the window toward mechanistic understanding of protein coronas and aids in the rational design of nanoparticles as nanomedicines and biosensors.
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Affiliation(s)
- Yuyang Wang
- Department
of Applied Physics and Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, 5612AZ Eindhoven, The Netherlands
| | - Paul E. D. Soto Rodriguez
- Institute
for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
| | - Laura Woythe
- Department
of Biomedical Engineering and Institute for Complex Molecular Systems
(ICMS), Eindhoven University of Technology, 5612AZ Eindhoven, The Netherlands
| | - Samuel Sánchez
- Institute
for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
- Institució
Catalana de Recerca i Estudis Avançats (ICREA), Passeige Lluís Companys 23, 08010 Barcelona, Spain
| | - Josep Samitier
- Institute
for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
- Department
of Electronics and Biomedical Engineering, University of Barcelona (UB), 08028 Barcelona, Spain
- Biomedical
Research Networking Center in Bioengineering, Biomaterials, and Nanomedicine (CIBER-BBN), 28029 Madrid, Spain
| | - Peter Zijlstra
- Department
of Applied Physics and Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, 5612AZ Eindhoven, The Netherlands
| | - Lorenzo Albertazzi
- Institute
for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
- Department
of Biomedical Engineering and Institute for Complex Molecular Systems
(ICMS), Eindhoven University of Technology, 5612AZ Eindhoven, The Netherlands
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6
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Radius measurement via super-resolution microscopy enables the development of a variable radii proximity labeling platform. Proc Natl Acad Sci U S A 2022; 119:e2203027119. [PMID: 35914173 PMCID: PMC9371666 DOI: 10.1073/pnas.2203027119] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
The elucidation of protein interaction networks is critical to understanding fundamental biology as well as developing new therapeutics. Proximity labeling platforms (PLPs) are state-of-the-art technologies that enable the discovery and delineation of biomolecular networks through the identification of protein-protein interactions. These platforms work via catalytic generation of reactive probes at a biological region of interest; these probes then diffuse through solution and covalently "tag" proximal biomolecules. The physical distance that the probes diffuse determines the effective labeling radius of the PLP and is a critical parameter that influences the scale and resolution of interactome mapping. As such, by expanding the degrees of labeling resolution offered by PLPs, it is possible to better capture the various size scales of interactomes. At present, however, there is little quantitative understanding of the labeling radii of different PLPs. Here, we report the development of a superresolution microscopy-based assay for the direct quantification of PLP labeling radii. Using this assay, we provide direct extracellular measurements of the labeling radii of state-of-the-art antibody-targeted PLPs, including the peroxidase-based phenoxy radical platform (269 ± 41 nm) and the high-resolution iridium-catalyzed µMap technology (54 ± 12 nm). Last, we apply these insights to the development of a molecular diffusion-based approach to tuning PLP resolution and introduce a new aryl-azide-based µMap platform with an intermediate labeling radius (80 ± 28 nm).
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7
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Refractive Bi-Conic Axicon (Volcone) for Polarization Conversion of Monochromatic Radiation. PHOTONICS 2022. [DOI: 10.3390/photonics9060421] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
A new element is proposed for producing an azimuthally polarized beam with a vortex phase dependence. The element is formed by two conical surfaces in such a way that the optical element resembles a mountain with a crater on top, like a volcano (volcanic cone is volcone). The element in the form of a refractive bi-conic axicon is fabricated by diamond turning, in which an internal conical cavity is made. Polarization conversion in this optical element occurs on the inner surface due to the refraction of beams at the Brewster angle. The outer surface is used to collimate the converted beam, which significantly distinguishes the proposed element from previously proposed approaches. The paper describes a method for calculating the path of beams through a refractive bi-conic axicon, taking into account phase and polarization conversions. In the case of incident circularly polarized radiation, azimuthally polarized ring-shape beam radiation is generated at the output. The proposed element is experimentally made of polymethyl methacrylate on a CNC milling machine. The experiment demonstrates the effectiveness of the proposed element.
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8
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Shan H, Dai H, Chen X. Monitoring Various Bioactivities at the Molecular, Cellular, Tissue, and Organism Levels via Biological Lasers. SENSORS (BASEL, SWITZERLAND) 2022; 22:3149. [PMID: 35590841 PMCID: PMC9102053 DOI: 10.3390/s22093149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 04/16/2022] [Accepted: 04/18/2022] [Indexed: 06/15/2023]
Abstract
The laser is considered one of the greatest inventions of the 20th century. Biolasers employ high signal-to-noise ratio lasing emission rather than regular fluorescence as the sensing signal, directional out-coupling of lasing and excellent biocompatibility. Meanwhile, biolasers can also be micro-sized or smaller lasers with embedded/integrated biological materials. This article presents the progress in biolasers, focusing on the work done over the past years, including the molecular, cellular, tissue, and organism levels. Furthermore, biolasers have been utilized and explored for broad applications in biosensing, labeling, tracking, bioimaging, and biomedical development due to a number of unique advantages. Finally, we provide the possible directions of biolasers and their applications in the future.
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Affiliation(s)
- Hongrui Shan
- State Key Laboratory of Advanced Optical Communication Systems and Networks, School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai 200240, China; (H.S.); (H.D.)
| | - Hailang Dai
- State Key Laboratory of Advanced Optical Communication Systems and Networks, School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai 200240, China; (H.S.); (H.D.)
| | - Xianfeng Chen
- State Key Laboratory of Advanced Optical Communication Systems and Networks, School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai 200240, China; (H.S.); (H.D.)
- Collaborative Innovation Center of Light Manipulations and Applications, Shandong Normal University, Jinan 250358, China
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9
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Storti B, Carlotti B, Chiellini G, Ruglioni M, Salvadori T, Scotto M, Elisei F, Diaspro A, Bianchini P, Bizzarri R. An Efficient Aequorea victoria Green Fluorescent Protein for Stimulated Emission Depletion Super-Resolution Microscopy. Int J Mol Sci 2022; 23:ijms23052482. [PMID: 35269626 PMCID: PMC8910729 DOI: 10.3390/ijms23052482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 02/18/2022] [Accepted: 02/22/2022] [Indexed: 11/16/2022] Open
Abstract
In spite of their value as genetically encodable reporters for imaging in living systems, fluorescent proteins have been used sporadically for stimulated emission depletion (STED) super-resolution imaging, owing to their moderate photophysical resistance, which does not enable reaching resolutions as high as for synthetic dyes. By a rational approach combining steady-state and ultrafast spectroscopy with gated STED imaging in living and fixed cells, we here demonstrate that F99S/M153T/V163A GFP (c3GFP) represents an efficient genetic reporter for STED, on account of no excited state absorption at depletion wavelengths <600 nm and a long emission lifetime. This makes c3GFP a valuable alternative to more common, but less photostable, EGFP and YFP/Citrine mutants for STED imaging studies targeting the green-yellow region of the optical spectrum.
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Affiliation(s)
- Barbara Storti
- NEST, Scuola Normale Superiore and Istituto Nanoscienze-CNR, Piazza San Silvestro 12, 56127 Pisa, Italy;
- Correspondence:
| | - Benedetta Carlotti
- Department of Chemistry, Biology and Biotechnology and CEMIN, University of Perugia, Via Elce di Sotto 8, 06123 Perugia, Italy; (B.C.); (F.E.)
| | - Grazia Chiellini
- Department of Surgical, Medical and Molecular Pathology and Critical Care Medicine, University of Pisa, Via Roma 65, 56126 Pisa, Italy; (G.C.); (M.R.); (T.S.)
| | - Martina Ruglioni
- Department of Surgical, Medical and Molecular Pathology and Critical Care Medicine, University of Pisa, Via Roma 65, 56126 Pisa, Italy; (G.C.); (M.R.); (T.S.)
| | - Tiziano Salvadori
- Department of Surgical, Medical and Molecular Pathology and Critical Care Medicine, University of Pisa, Via Roma 65, 56126 Pisa, Italy; (G.C.); (M.R.); (T.S.)
| | - Marco Scotto
- Nanoscopy, CHT, Istituto Italiano di Tecnologia, Via E. Melen 83, 16152 Genova, Italy; (M.S.); (A.D.); (P.B.)
| | - Fausto Elisei
- Department of Chemistry, Biology and Biotechnology and CEMIN, University of Perugia, Via Elce di Sotto 8, 06123 Perugia, Italy; (B.C.); (F.E.)
| | - Alberto Diaspro
- Nanoscopy, CHT, Istituto Italiano di Tecnologia, Via E. Melen 83, 16152 Genova, Italy; (M.S.); (A.D.); (P.B.)
- DIFILAB, Dipartimento di Fisica, Università degli Studi di Genova, Via Dodecaneso 33, 16146 Genova, Italy
| | - Paolo Bianchini
- Nanoscopy, CHT, Istituto Italiano di Tecnologia, Via E. Melen 83, 16152 Genova, Italy; (M.S.); (A.D.); (P.B.)
| | - Ranieri Bizzarri
- NEST, Scuola Normale Superiore and Istituto Nanoscienze-CNR, Piazza San Silvestro 12, 56127 Pisa, Italy;
- Department of Surgical, Medical and Molecular Pathology and Critical Care Medicine, University of Pisa, Via Roma 65, 56126 Pisa, Italy; (G.C.); (M.R.); (T.S.)
- Nanoscopy, CHT, Istituto Italiano di Tecnologia, Via E. Melen 83, 16152 Genova, Italy; (M.S.); (A.D.); (P.B.)
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10
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Jeong S, Widengren J, Lee JC. Fluorescent Probes for STED Optical Nanoscopy. NANOMATERIALS (BASEL, SWITZERLAND) 2021; 12:21. [PMID: 35009972 PMCID: PMC8746377 DOI: 10.3390/nano12010021] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 12/17/2021] [Accepted: 12/17/2021] [Indexed: 06/14/2023]
Abstract
Progress in developing fluorescent probes, such as fluorescent proteins, organic dyes, and fluorescent nanoparticles, is inseparable from the advancement in optical fluorescence microscopy. Super-resolution microscopy, or optical nanoscopy, overcame the far-field optical resolution limit, known as Abbe's diffraction limit, by taking advantage of the photophysical properties of fluorescent probes. Therefore, fluorescent probes for super-resolution microscopy should meet the new requirements in the probes' photophysical and photochemical properties. STED optical nanoscopy achieves super-resolution by depleting excited fluorophores at the periphery of an excitation laser beam using a depletion beam with a hollow core. An ideal fluorescent probe for STED nanoscopy must meet specific photophysical and photochemical properties, including high photostability, depletability at the depletion wavelength, low adverse excitability, and biocompatibility. This review introduces the requirements of fluorescent probes for STED nanoscopy and discusses the recent progress in the development of fluorescent probes, such as fluorescent proteins, organic dyes, and fluorescent nanoparticles, for the STED nanoscopy. The strengths and the limitations of the fluorescent probes are analyzed in detail.
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Affiliation(s)
- Sejoo Jeong
- Department of New Biology, Daegu Gyeongbuk Institute of Science & Technology, Daegu 42988, Korea;
| | - Jerker Widengren
- Experimental Biomolecular Physics, Department of Applied Physics, Royal Institute of Technology (KTH), Stockholm 10691, Sweden;
| | - Jong-Chan Lee
- Department of New Biology, Daegu Gyeongbuk Institute of Science & Technology, Daegu 42988, Korea;
- New Biology Research Center, Daegu Gyeongbuk Institute of Science & Technology, Daegu 42988, Korea
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11
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Levchenko SM, Pliss A, Peng X, Prasad PN, Qu J. Fluorescence lifetime imaging for studying DNA compaction and gene activities. LIGHT, SCIENCE & APPLICATIONS 2021; 10:224. [PMID: 34728612 PMCID: PMC8563720 DOI: 10.1038/s41377-021-00664-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 10/04/2021] [Accepted: 10/18/2021] [Indexed: 05/04/2023]
Abstract
Optical imaging is a most useful and widespread technique for the investigation of the structure and function of the cellular genomes. However, an analysis of immensely convoluted and irregularly compacted DNA polymer is highly challenging even by modern super-resolution microscopy approaches. Here we propose fluorescence lifetime imaging (FLIM) for the advancement of studies of genomic structure including DNA compaction, replication as well as monitoring of gene expression. The proposed FLIM assay employs two independent mechanisms for DNA compaction sensing. One mechanism relies on the inverse quadratic relation between the fluorescence lifetimes of fluorescence probes incorporated into DNA and their local refractive index, variable due to DNA compaction density. Another mechanism is based on the Förster resonance energy transfer (FRET) process between the donor and the acceptor fluorophores, both incorporated into DNA. Both these proposed mechanisms were validated in cultured cells. The obtained data unravel a significant difference in compaction of the gene-rich and gene-poor pools of genomic DNA. We show that the gene-rich DNA is loosely compacted compared to the dense DNA domains devoid of active genes.
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Affiliation(s)
- Svitlana M Levchenko
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen, Guangdong, 518060, China
- Department of Cell Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387, Krakow, Poland
| | - Artem Pliss
- Institute for Lasers, Photonics and Biophotonics, University at Buffalo, State University of New York, Buffalo, NY, 14260-3000, USA
| | - Xiao Peng
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen, Guangdong, 518060, China
| | - Paras N Prasad
- Institute for Lasers, Photonics and Biophotonics, University at Buffalo, State University of New York, Buffalo, NY, 14260-3000, USA.
| | - Junle Qu
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen, Guangdong, 518060, China.
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12
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Stiekema M, Ramaekers FCS, Kapsokalyvas D, van Zandvoort MAMJ, Veltrop RJA, Broers JLV. Super-Resolution Imaging of the A- and B-Type Lamin Networks: A Comparative Study of Different Fluorescence Labeling Procedures. Int J Mol Sci 2021; 22:ijms221910194. [PMID: 34638534 PMCID: PMC8508656 DOI: 10.3390/ijms221910194] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 09/13/2021] [Accepted: 09/14/2021] [Indexed: 12/31/2022] Open
Abstract
A- and B-type lamins are type V intermediate filament proteins. Mutations in the genes encoding these lamins cause rare diseases, collectively called laminopathies. A fraction of the cells obtained from laminopathy patients show aberrations in the localization of each lamin subtype, which may represent only the minority of the lamina disorganization. To get a better insight into more delicate and more abundant lamina abnormalities, the lamin network can be studied using super-resolution microscopy. We compared confocal scanning laser microscopy and stimulated emission depletion (STED) microscopy in combination with different fluorescence labeling approaches for the study of the lamin network. We demonstrate the suitability of an immunofluorescence staining approach when using STED microscopy, by determining the lamin layer thickness and the degree of lamin A and B1 colocalization as detected in fixed fibroblasts (co-)stained with lamin antibodies or (co-)transfected with EGFP/YFP lamin constructs. This revealed that immunofluorescence staining of cells does not lead to consequent changes in the detected lamin layer thickness, nor does it influence the degree of colocalization of lamin A and B1, when compared to the transfection approach. Studying laminopathy patient dermal fibroblasts (LMNA c.1130G>T (p.(Arg377Leu)) variant) confirmed the suitability of immunofluorescence protocols in STED microscopy, which circumvents the need for less convenient transfection steps. Furthermore, we found a significant decrease in lamin A/C and B1 colocalization in these patient fibroblasts, compared to normal human dermal fibroblasts. We conclude that super-resolution light microscopy combined with immunofluorescence protocols provides a potential tool to detect structural lamina differences between normal and laminopathy patient fibroblasts.
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Affiliation(s)
- Merel Stiekema
- Department of Genetics and Cell Biology, Maastricht University Medical Centre, 6200 MD Maastricht, The Netherlands; (M.S.); (F.C.S.R.); (D.K.); (M.A.M.J.v.Z.)
- GROW-School for Oncology and Developmental Biology, Maastricht University Medical Centre, 6200 MD Maastricht, The Netherlands
| | - Frans C. S. Ramaekers
- Department of Genetics and Cell Biology, Maastricht University Medical Centre, 6200 MD Maastricht, The Netherlands; (M.S.); (F.C.S.R.); (D.K.); (M.A.M.J.v.Z.)
- GROW-School for Oncology and Developmental Biology, Maastricht University Medical Centre, 6200 MD Maastricht, The Netherlands
| | - Dimitrios Kapsokalyvas
- Department of Genetics and Cell Biology, Maastricht University Medical Centre, 6200 MD Maastricht, The Netherlands; (M.S.); (F.C.S.R.); (D.K.); (M.A.M.J.v.Z.)
- Interdisciplinary Center for Clinical Research, IZKF, RWTH Aachen University, 52074 Aachen, Germany
| | - Marc A. M. J. van Zandvoort
- Department of Genetics and Cell Biology, Maastricht University Medical Centre, 6200 MD Maastricht, The Netherlands; (M.S.); (F.C.S.R.); (D.K.); (M.A.M.J.v.Z.)
- GROW-School for Oncology and Developmental Biology, Maastricht University Medical Centre, 6200 MD Maastricht, The Netherlands
- CARIM-School for Cardiovascular Diseases, Maastricht University Medical Centre, 6200 MD Maastricht, The Netherlands
- Institute for Molecular Cardiovascular Research IMCAR, RWTH Aachen University, 52074 Aachen, Germany
| | - Rogier J. A. Veltrop
- Institute for Molecular Cardiovascular Research IMCAR, RWTH Aachen University, 52074 Aachen, Germany
- Department of Biochemistry, Cardiovascular Research Institute Maastricht, Maastricht University, 6200 MD Maastricht, The Netherlands;
| | - Jos L. V. Broers
- Department of Genetics and Cell Biology, Maastricht University Medical Centre, 6200 MD Maastricht, The Netherlands; (M.S.); (F.C.S.R.); (D.K.); (M.A.M.J.v.Z.)
- GROW-School for Oncology and Developmental Biology, Maastricht University Medical Centre, 6200 MD Maastricht, The Netherlands
- CARIM-School for Cardiovascular Diseases, Maastricht University Medical Centre, 6200 MD Maastricht, The Netherlands
- Correspondence: ; Tel.: +31-433881366
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13
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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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14
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Åberg C. Kinetics of nanoparticle uptake into and distribution in human cells. NANOSCALE ADVANCES 2021; 3:2196-2212. [PMID: 36133761 PMCID: PMC9416924 DOI: 10.1039/d0na00716a] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 03/12/2021] [Indexed: 05/17/2023]
Abstract
Whether one wishes to optimise drug delivery using nano-sized carriers or avoid hazard posed by engineered nanomaterials, the kinetics of nanoparticle uptake into human cells and their subsequent intracellular distribution is key. Unique properties of the nanoscale implies that such nanoparticles are taken up and trafficked in a different fashion compared to molecular species. In this review, we discuss in detail how to describe the kinetics of nanoparticle uptake and intracellular distribution, using previous studies for illustration. We also cover the extracellular kinetics, particle degradation, endosomal escape and cell division, ending with an outlook on the future of kinetic studies.
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Affiliation(s)
- Christoffer Åberg
- Groningen Research Institute of Pharmacy, University of Groningen Antonius Deusinglaan 1 9713AV Groningen The Netherlands
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15
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Predicting the membrane permeability of organic fluorescent probes by the deep neural network based lipophilicity descriptor DeepFl-LogP. Sci Rep 2021; 11:6991. [PMID: 33772099 PMCID: PMC7997998 DOI: 10.1038/s41598-021-86460-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 03/16/2021] [Indexed: 01/17/2023] Open
Abstract
Light microscopy has become an indispensable tool for the life sciences, as it enables the rapid acquisition of three-dimensional images from the interior of living cells/tissues. Over the last decades, super-resolution light microscopy techniques have been developed, which allow a resolution up to an order of magnitude higher than that of conventional light microscopy. Those techniques require labelling of cellular structures with fluorescent probes exhibiting specific properties, which are supplied from outside and therefore have to surpass cell membranes. Currently, major efforts are undertaken to develop probes which can surpass cell membranes and exhibit the photophysical properties required for super-resolution imaging. However, the process of probe development is still based on a tedious and time consuming manual screening. An accurate computer based model that enables the prediction of the cell permeability based on their chemical structure would therefore be an invaluable asset for the development of fluorescent probes. Unfortunately, current models, which are based on multiple molecular descriptors, are not well suited for this task as they require high effort in the usage and exhibit moderate accuracy in their prediction. Here, we present a novel fragment based lipophilicity descriptor DeepFL-LogP, which was developed on the basis of a deep neural network. DeepFL-LogP exhibits excellent correlation with the experimental partition coefficient reference data (R2 = 0.892 and MSE = 0.359) of drug-like substances. Further a simple threshold permeability model on the basis of this descriptor allows to categorize the permeability of fluorescent probes with 96% accuracy. This novel descriptor is expected to largely simplify and speed up the development process for novel cell permeable fluorophores.
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16
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Kubalová I, Němečková A, Weisshart K, Hřibová E, Schubert V. Comparing Super-Resolution Microscopy Techniques to Analyze Chromosomes. Int J Mol Sci 2021; 22:ijms22041903. [PMID: 33672992 PMCID: PMC7917581 DOI: 10.3390/ijms22041903] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 02/04/2021] [Accepted: 02/10/2021] [Indexed: 12/21/2022] Open
Abstract
The importance of fluorescence light microscopy for understanding cellular and sub-cellular structures and functions is undeniable. However, the resolution is limited by light diffraction (~200–250 nm laterally, ~500–700 nm axially). Meanwhile, super-resolution microscopy, such as structured illumination microscopy (SIM), is being applied more and more to overcome this restriction. Instead, super-resolution by stimulated emission depletion (STED) microscopy achieving a resolution of ~50 nm laterally and ~130 nm axially has not yet frequently been applied in plant cell research due to the required specific sample preparation and stable dye staining. Single-molecule localization microscopy (SMLM) including photoactivated localization microscopy (PALM) has not yet been widely used, although this nanoscopic technique allows even the detection of single molecules. In this study, we compared protein imaging within metaphase chromosomes of barley via conventional wide-field and confocal microscopy, and the sub-diffraction methods SIM, STED, and SMLM. The chromosomes were labeled by DAPI (4′,6-diamidino-2-phenylindol), a DNA-specific dye, and with antibodies against topoisomerase IIα (Topo II), a protein important for correct chromatin condensation. Compared to the diffraction-limited methods, the combination of the three different super-resolution imaging techniques delivered tremendous additional insights into the plant chromosome architecture through the achieved increased resolution.
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Affiliation(s)
- Ivona Kubalová
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, D-06466 Seeland, Germany;
| | - Alžběta Němečková
- Centre of the Region Hana for Biotechnological and Agricultural Research, Institute of Experimental Botany of the Czech Academy of Sciences, 77900 Olomouc, Czech Republic; (A.N.); (E.H.)
| | | | - Eva Hřibová
- Centre of the Region Hana for Biotechnological and Agricultural Research, Institute of Experimental Botany of the Czech Academy of Sciences, 77900 Olomouc, Czech Republic; (A.N.); (E.H.)
| | - Veit Schubert
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, D-06466 Seeland, Germany;
- Correspondence: ; Tel.: +49-394-825-212
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17
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Török G, Cserép GB, Telek A, Arany D, Váradi M, Homolya L, Kellermayer M, Kele P, Németh K. Large Stokes-shift bioorthogonal probes for STED, 2P-STED and multi-color STED nanoscopy. Methods Appl Fluoresc 2021; 9:015006. [PMID: 33427202 DOI: 10.1088/2050-6120/abb363] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Synthesis and multiple STED imaging applications of four, red-emitting (610-670 nm), tetrazine-functionalized fluorescent probes (CBRD = Chemical Biology Research group Dye 1-4) with large Stokes-shift is presented. Present studies revealed the super-resolution microscopy applicability of the probes as demonstrated through bioorthogonal labeling scheme of cytoskeletal proteins actin and keratin-19, and mitochondrial protein TOMM20. Furthermore, super-resolved images of insulin receptors in live-cell bioorthogonal labeling schemes through a genetically encoded cyclooctynylated non-canonical amino acid are also presented. The large Stokes-shifts and the wide spectral bands of the probes enabled the use of two common depletion lasers (660 nm and 775 nm). The probes were also found suitable for super-resolution microscopy in combination with two-photon excitation (2P-STED) resulting in improved spatial resolution. One of the dyes was also used together with two commercial dyes in the three-color STED imaging of intracellular structures.
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Affiliation(s)
- György Török
- Chemical Biology Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, Magyar tudósok krt. 2., H-1117 Budapest, Hungary. Department of Biophysics and Radiation Biology, Semmelweis University, Tűzoltó u. 37-47., H-1094 Budapest, Hungary. Laboratory of Molecular Cell Biology, Institute of Enzymology, Research Centre for Natural Sciences, Magyar tudósok krt. 2., H-1117 Budapest, Hungary
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18
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Xu Y, Xu R, Wang Z, Zhou Y, Shen Q, Ji W, Dang D, Meng L, Tang BZ. Recent advances in luminescent materials for super-resolution imaging via stimulated emission depletion nanoscopy. Chem Soc Rev 2021; 50:667-690. [DOI: 10.1039/d0cs00676a] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Recent progress on STED fluorophores for super-resolution imaging and also their characteristics are outlined here, thus providing some guidelines to select proper probes and even develop new materials for super-resolution imaging via STED nanoscopy.
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Affiliation(s)
- Yanzi Xu
- School of Chemistry
- Xi'an Key Laboratory of Sustainable Energy Material Chemistry
- MOE Key Laboratory for Non-equilibrium Synthesis and Modulation of Condensed Matter
- Xi'an Jiao Tong University
- Xi'an 710049
| | - Ruohan Xu
- School of Chemistry
- Xi'an Key Laboratory of Sustainable Energy Material Chemistry
- MOE Key Laboratory for Non-equilibrium Synthesis and Modulation of Condensed Matter
- Xi'an Jiao Tong University
- Xi'an 710049
| | - Zhi Wang
- School of Chemistry
- Xi'an Key Laboratory of Sustainable Energy Material Chemistry
- MOE Key Laboratory for Non-equilibrium Synthesis and Modulation of Condensed Matter
- Xi'an Jiao Tong University
- Xi'an 710049
| | - Yu Zhou
- Instrumental Analysis Center
- Xi'an Jiao Tong University
- Xi'an
- P. R. China
| | - Qifei Shen
- School of Chemistry
- Xi'an Key Laboratory of Sustainable Energy Material Chemistry
- MOE Key Laboratory for Non-equilibrium Synthesis and Modulation of Condensed Matter
- Xi'an Jiao Tong University
- Xi'an 710049
| | - Wenchen Ji
- Department of Orthopedics
- the First Affiliated Hospital of Xi’an Jiaotong University
- P. R. China
| | - Dongfeng Dang
- School of Chemistry
- Xi'an Key Laboratory of Sustainable Energy Material Chemistry
- MOE Key Laboratory for Non-equilibrium Synthesis and Modulation of Condensed Matter
- Xi'an Jiao Tong University
- Xi'an 710049
| | - Lingjie Meng
- School of Chemistry
- Xi'an Key Laboratory of Sustainable Energy Material Chemistry
- MOE Key Laboratory for Non-equilibrium Synthesis and Modulation of Condensed Matter
- Xi'an Jiao Tong University
- Xi'an 710049
| | - Ben Zhong Tang
- Department of Chemistry
- The Hong Kong University of Science and Technology
- Clear Water Bay
- Kowloon
- P. R. China
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19
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Lucidi M, Hristu R, Nichele L, Stanciu GA, Tranca DE, Holban AM, Visca P, Stanciu SG, Cincotti G. STED nanoscopy of KK114-stained pathogenic bacteria. JOURNAL OF BIOPHOTONICS 2020; 13:e202000097. [PMID: 32483852 DOI: 10.1002/jbio.202000097] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 05/11/2020] [Accepted: 05/27/2020] [Indexed: 06/11/2023]
Abstract
Super-resolution microscopy techniques can provide answers to still pending questions on prokaryotic organisms but are yet to be used at their full potential for this purpose. To address this, we evaluate the ability of the rhodamine-like KK114 dye to label various types of bacteria, to enable imaging of fine structural details with stimulated emission depletion microscopy (STED). We assessed fluorescent labeling with KK114 for eleven Gram-positive and Gram-negative bacterial species and observed that this contrast agent binds to their cell membranes. Significant differences in the labeling outputs were noticed across the tested bacterial species, but importantly, KK114-staining allowed the observation of subtle nanometric cell details in some cases. For example, a helix pattern resembling a cytoskeleton arrangement was detected in Bacillus subtilis. Furthermore, we found that KK114 easily penetrates the membrane of bacterial microorganism that lost their viability, which can be useful to discriminate between living and dead cells.
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Affiliation(s)
| | - Radu Hristu
- Center for Microscopy - Microanalysis and Information Processing, University Politehnica of Bucharest, Bucharest, Romania
| | | | - George A Stanciu
- Center for Microscopy - Microanalysis and Information Processing, University Politehnica of Bucharest, Bucharest, Romania
| | - Denis E Tranca
- Center for Microscopy - Microanalysis and Information Processing, University Politehnica of Bucharest, Bucharest, Romania
| | - Alina Maria Holban
- Microbiology and Immunology Department, Faculty of Biology, University of Bucharest, Bucharest, Romania
| | - Paolo Visca
- Department of Sciences, University Roma Tre, Rome, Italy
| | - Stefan G Stanciu
- Center for Microscopy - Microanalysis and Information Processing, University Politehnica of Bucharest, Bucharest, Romania
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20
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Wu Y, Ruan H, Dong Z, Zhao R, Yu J, Tang X, Kou X, Zhang X, Wu M, Luo F, Yuan J, Fang X. Fluorescent Polymer Dot-Based Multicolor Stimulated Emission Depletion Nanoscopy with a Single Laser Beam Pair for Cellular Tracking. Anal Chem 2020; 92:12088-12096. [PMID: 32867488 DOI: 10.1021/acs.analchem.0c02821] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Stimulated emission depletion (STED) nanoscopy provides subdiffraction resolution while preserving the benefits of fluorescence confocal microscopy in live-cell imaging. However, there are several challenges for multicolor STED nanoscopy, including sophisticated microscopy architectures, fast photobleaching, and cross talk of fluorescent probes. Here, we introduce two types of nanoscale fluorescent semiconducting polymer dots (Pdots) with different emission wavelengths: CNPPV (poly[2-methoxy-5-(2-ethylhexyloxy)-1,4-(1-cyanovinylene-1,4-phenylene)]) Pdots and PDFDP (poly[{9,9-dihexyl-2,7-bis(1-cyanovinylene)fluorene}-alt-co-{2,5-bis (N,N'-diphenylamino)-1,4-phenylene}]) Pdots, for dual-color STED bioimaging and cellular tracking. Besides bright fluorescence, strong photostability, and easy bioconjugation, these Pdots have large Stokes shifts, which make it possible to share both excitation and depletion beams, thus requiring only a single pair of laser beams for the dual-color STED imaging. Long-term tracking of cellular organelles by the Pdots has been achieved in living cells, and the dynamic interaction of endosomes derived from clathrin-mediated and caveolae-mediated endocytic pathways has been monitored for the first time to propose their interaction models. These results demonstrate the promise of Pdots as excellent probes for live-cell multicolor STED nanoscopy.
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Affiliation(s)
- Yayun Wu
- Key Laboratory of Molecular Nanostructure and Nanotechnology, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hefei Ruan
- Key Laboratory of Molecular Nanostructure and Nanotechnology, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Zaizai Dong
- Key Laboratory of Molecular Nanostructure and Nanotechnology, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Rong Zhao
- Key Laboratory of Molecular Nanostructure and Nanotechnology, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jianqiang Yu
- Key Laboratory of Molecular Nanostructure and Nanotechnology, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Xiaojun Tang
- Key Laboratory of Molecular Nanostructure and Nanotechnology, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Xiaolong Kou
- Key Laboratory of Molecular Nanostructure and Nanotechnology, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Xing Zhang
- Key Laboratory of Molecular Nanostructure and Nanotechnology, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Manchen Wu
- Key Laboratory of Molecular Nanostructure and Nanotechnology, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fang Luo
- Key Laboratory of Molecular Nanostructure and Nanotechnology, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jinghe Yuan
- Key Laboratory of Molecular Nanostructure and Nanotechnology, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Xiaohong Fang
- Key Laboratory of Molecular Nanostructure and Nanotechnology, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China.,University of Chinese Academy of Sciences, Beijing 100049, China.,Institute of Cancer and Basic Medicine, Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
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21
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Lemon WC, McDole K. Live-cell imaging in the era of too many microscopes. Curr Opin Cell Biol 2020; 66:34-42. [PMID: 32470820 DOI: 10.1016/j.ceb.2020.04.008] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 04/14/2020] [Accepted: 04/15/2020] [Indexed: 01/04/2023]
Abstract
At the time of this writing, searching Google Scholar for 'light-sheet microscopy' returns almost 8500 results; over three-quarters of which were published in the last 5 years alone. Searching for other advanced imaging methods in the last 5 years yields similar results: 'super-resolution microscopy' (>16 000), 'single-molecule imaging' (almost 10 000), SPIM (Single Plane Illumination Microscopy, 5000), and 'lattice light-sheet' (1300). The explosion of new imaging methods has also produced a dizzying menagerie of acronyms, with over 100 different species of 'light-sheet' alone, from SPIM to UM (Ultra microscopy) to SiMView (Simultaneous MultiView) to iSPIM (inclined SPIM, not to be confused with iSPIM, inverted SPIM). How then is the average biologist, without an advanced degree in physics, optics, or computer science supposed to make heads or tails of which method is best suited for their needs? Let us also not forget the plight of the optical physicist, who at best might need help with obtaining healthy samples and keeping them that way, or at worst may not realize the impact their newest technique could have for biologists. This review will not attempt to solve all these problems, but instead highlight some of the most recent, successful mergers between biology and advanced imaging technologies, as well as hopefully provide some guidance for anyone interested in journeying into the world of live-cell imaging.
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Affiliation(s)
- William C Lemon
- Howard Hughes Medical Institute, Janelia Farm Research Campus, Ashburn, VA, USA
| | - Katie McDole
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, CB2 0QH, UK.
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22
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Potapova TA, Unruh JR, Yu Z, Rancati G, Li H, Stampfer MR, Gerton JL. Superresolution microscopy reveals linkages between ribosomal DNA on heterologous chromosomes. J Cell Biol 2019; 218:2492-2513. [PMID: 31270138 PMCID: PMC6683752 DOI: 10.1083/jcb.201810166] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 03/14/2019] [Accepted: 06/03/2019] [Indexed: 12/15/2022] Open
Abstract
Potapova et al. use superresolution microscopy to describe linkages between ribosomal DNA on heterologous human chromosomes whose formation depends on the transcription factor UBF and topoisomerase II. Linkages persist in the absence of cohesion but require topoisomerase II for resolution. The spatial organization of the genome is enigmatic. Direct evidence of physical contacts between chromosomes and their visualization at nanoscale resolution has been limited. We used superresolution microscopy to demonstrate that ribosomal DNA (rDNA) can form linkages between chromosomes. We observed rDNA linkages in many different human cell types and demonstrated their resolution in anaphase. rDNA linkages are coated by the transcription factor UBF and their formation depends on UBF, indicating that they regularly occur between transcriptionally active loci. Overexpression of c-Myc increases rDNA transcription and the frequency of rDNA linkages, further suggesting that their formation depends on active transcription. Linkages persist in the absence of cohesion, but inhibition of topoisomerase II prevents their resolution in anaphase. We propose that linkages are topological intertwines occurring between transcriptionally active rDNA loci spatially colocated in the same nucleolar compartment. Our findings suggest that active DNA loci engage in physical interchromosomal connections that are an integral and pervasive feature of genome organization.
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Affiliation(s)
| | - Jay R Unruh
- Stowers Institute for Medical Research, Kansas City, MO
| | - Zulin Yu
- Stowers Institute for Medical Research, Kansas City, MO
| | - Giulia Rancati
- Institute of Medical Biology, Agency for Science, Technology and Research, Singapore
| | - Hua Li
- Stowers Institute for Medical Research, Kansas City, MO
| | - Martha R Stampfer
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA
| | - Jennifer L Gerton
- Stowers Institute for Medical Research, Kansas City, MO .,Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS
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23
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Wollweber M, Roth B. Raman Sensing and Its Multimodal Combination with Optoacoustics and OCT for Applications in the Life Sciences. SENSORS (BASEL, SWITZERLAND) 2019; 19:E2387. [PMID: 31137716 PMCID: PMC6566696 DOI: 10.3390/s19102387] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 05/10/2019] [Accepted: 05/15/2019] [Indexed: 12/29/2022]
Abstract
Currently, many optical modalities are being investigated, applied, and further developed for non-invasive analysis and sensing in the life sciences. To befit the complexity of the study objects and questions in this field, the combination of two or more modalities is attempted. We review our work on multimodal sensing concepts for applications ranging from non-invasive quantification of biomolecules in the living organism to supporting medical diagnosis showing the combined capabilities of Raman spectroscopy, optical coherence tomography, and optoacoustics.
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Affiliation(s)
- Merve Wollweber
- Laser Zentrum Hannover e.V., Industrial and Biomedical Optics Department, Hollerithallee 8, 30419 Hannover, Germany.
- Hannover Centre for Optical Technologies, Leibniz University Hannover, Nienburger Str. 17, 30167 Hannover, Germany.
| | - Bernhard Roth
- Hannover Centre for Optical Technologies, Leibniz University Hannover, Nienburger Str. 17, 30167 Hannover, Germany.
- Cluster of Excellence PhoenixD, Leibniz University Hannover, Welfengarten 1, 30167 Hannover, Germany.
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24
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Wirth R, Gao P, Nienhaus GU, Sunbul M, Jäschke A. SiRA: A Silicon Rhodamine-Binding Aptamer for Live-Cell Super-Resolution RNA Imaging. J Am Chem Soc 2019; 141:7562-7571. [PMID: 30986047 DOI: 10.1021/jacs.9b02697] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Although genetically encoded light-up RNA aptamers have become promising tools for visualizing and tracking RNAs in living cells, aptamer/ligand pairs that emit in the far-red and near-infrared (NIR) regions are still rare. In this work, we developed a light-up RNA aptamer that binds silicon rhodamines (SiRs). SiRs are photostable, NIR-emitting fluorophores that change their open-closed equilibrium between the noncolored spirolactone and the fluorescent zwitterion in response to their environment. This property is responsible for their high cell permeability and fluorogenic behavior. Aptamers binding to SiR were in vitro selected from a combinatorial RNA library. Sequencing, bioinformatic analysis, truncation, and mutational studies revealed a 50-nucleotide minimal aptamer, SiRA, which binds with nanomolar affinity to the target SiR. In addition to silicon rhodamines, SiRA binds structurally related rhodamines and carborhodamines, making it a versatile tool spanning the far-red region of the spectrum. Photophysical characterization showed that SiRA is remarkably resistant to photobleaching and constitutes the brightest far-red light-up aptamer system known to date owing to its favorable features: a fluorescence quantum yield of 0.98 and an extinction coefficient of 86 000 M-1cm-1. Using the SiRA system, we visualized the expression of RNAs in bacteria in no-wash live-cell imaging experiments and also report stimulated emission depletion (STED) super-resolution microscopy images of aptamer-based, fluorescently labeled mRNA in live cells. This work represents, to our knowledge, the first application of the popular SiR dyes and of intramolecular spirocyclization as a means of background reduction in the field of aptamer-based RNA imaging. We anticipate a high potential for this novel RNA labeling tool to address biological questions.
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Affiliation(s)
- Regina Wirth
- Institute of Pharmacy and Molecular Biotechnology (IPMB) , Heidelberg University , 69120 Heidelberg , Germany
| | - Peng Gao
- Institute of Applied Physics (APH) , Karlsruhe Institute of Technology (KIT) , Wolfgang-Gaede-Straße 1 , D-76131 Karlsruhe , Germany.,Institute of Nanotechnology (INT) , Karlsruhe Institute of Technology (KIT) , D-76344 Eggenstein-Leopoldshafen , Germany
| | - G Ulrich Nienhaus
- Institute of Applied Physics (APH) , Karlsruhe Institute of Technology (KIT) , Wolfgang-Gaede-Straße 1 , D-76131 Karlsruhe , Germany.,Institute of Nanotechnology (INT) , Karlsruhe Institute of Technology (KIT) , D-76344 Eggenstein-Leopoldshafen , Germany.,Institute of Toxicology and Genetics (ITG) , Karlsruhe Institute of Technology (KIT) , D-76344 Eggenstein-Leopoldshafen , Germany.,Department of Physics , University of Illinois at Urbana-Champaign , 1110 West Green Street , Urbana , Illinois 61801 , United States
| | - Murat Sunbul
- Institute of Pharmacy and Molecular Biotechnology (IPMB) , Heidelberg University , 69120 Heidelberg , Germany
| | - Andres Jäschke
- Institute of Pharmacy and Molecular Biotechnology (IPMB) , Heidelberg University , 69120 Heidelberg , Germany
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25
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Chen S, Wang J, Xin B, Yang Y, Ma Y, Zhou Y, Yuan L, Huang Z, Yuan Q. Direct Observation of Nanoparticles within Cells at Subcellular Levels by Super-Resolution Fluorescence Imaging. Anal Chem 2019; 91:5747-5752. [PMID: 30938156 DOI: 10.1021/acs.analchem.8b05919] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Direct observation of nanoparticles with high spatial resolution at subcellular levels is of great importance to understand the nanotoxicology and promote the biomedical applications of nanoparticles. Super-resolution fluorescence microscopy can break the diffraction resolution limit to achieve spatial resolution of tens of nanometers, making it ideal for highly accurate observation of nanoparticles in the cellular world. In this study, we introduced the employment of super-resolution fluorescence imaging for monitoring nanoparticles within cells. Carbocyanine dyes Alexa Flour 647 labeled mesoporous silica nanoparticles (designated as MSNs-AF647) were constructed as the super-resolution imaging nanoplatform in this work as proof of concept. The MSNs-AF647 were incubated with Hela cells, and the nanoparticles within cells were further monitored by super-resolution fluorescence microscopy. The fluorescence images of MSNs-AF647 within cells captured with the super-resolution fluorescence microscopy showed a much higher spatial resolution than that obtained using conventional fluorescence microscopy, showing that super-resolution fluorescence images can provide more accurate information to locate the nanoparticles at the subcellular levels. Moreover, other functional molecules can be easily loaded into the MSNs-AF647 super-resolution imaging nanoplatform, which suggested that super-resolution fluorescence imaging can further be applied to various bioimaging-related areas, such as imaging-guided therapy, with the aid of the MSNs-AF647 nanoplatform. This study demonstrates that super-resolution fluorescence microscopy offers a highly accurate method to study nanoparticles in the cellular world. We anticipate this strategy may further be applied to research areas such as studying the nanotoxicology and optimization of nanoparticle-based bioprobes or drugs by designing new nanostructured materials with multifunctional properties based on MSNs-AF647.
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Affiliation(s)
- Shasha Chen
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences , Wuhan University , Wuhan 430072 , PR China
| | - Jie Wang
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences , Wuhan University , Wuhan 430072 , PR China
| | - Bo Xin
- Wuhan National Laboratory for Optoelectronics , Huazhong University of Science and Technology , Wuhan 430074 , PR China
| | - Yanbing Yang
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences , Wuhan University , Wuhan 430072 , PR China
| | - Yurou Ma
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences , Wuhan University , Wuhan 430072 , PR China
| | - Yu Zhou
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences , Wuhan University , Wuhan 430072 , PR China
| | - Liangjie Yuan
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences , Wuhan University , Wuhan 430072 , PR China
| | - Zhenli Huang
- Wuhan National Laboratory for Optoelectronics , Huazhong University of Science and Technology , Wuhan 430074 , PR China
| | - Quan Yuan
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences , Wuhan University , Wuhan 430072 , PR China
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Du Y, Pan J, Choi JH. A review on optical imaging of DNA nanostructures and dynamic processes. Methods Appl Fluoresc 2019; 7:012002. [PMID: 30523978 DOI: 10.1088/2050-6120/aaed11] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
DNA self-assembly offers a powerful means to construct complex nanostructures and program dynamic molecular processes such as strand displacement. DNA nanosystems pack high structural complexity in a small scale (typically, <100 nm) and span dynamic features over long periods of time, which bring new challenges for characterizations. The spatial and temporal features of DNA nanosystems require novel experimental methods capable of high resolution imaging over long time periods. This article reviews recent advances in optical imaging methods for characterizing self-assembled DNA nanosystems, with particular emphasis on super-resolved fluorescence microscopy. Several advanced strategies are developed to obtain accurate and detailed images of intricate DNA nanogeometries and to perform precise tracking of molecular motions in dynamic processes. We present state-of-the-art instruments and imaging strategies including localization microscopy and spectral imaging. We discuss how they are used in biological studies and biomedical applications, and also provide current challenges and future outlook. Overall, this review serves as a practical guide in optical microscopy for the field of DNA nanotechnology.
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Affiliation(s)
- Yancheng Du
- School of Mechanical Engineering, Purdue University, West Lafayette, IN 47907
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27
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Ji H, Ruan Y, Ebendorff-Heidepriem H, Vahid SA, Monro T. A six-strut suspended core fiber for cylindrical vector mode generation and propagation. OPTICS EXPRESS 2018; 26:32037-32047. [PMID: 30650782 DOI: 10.1364/oe.26.032037] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 11/09/2018] [Indexed: 06/09/2023]
Abstract
We report fabrication and simulation of an F2 glass six-strut suspended core fiber (SCF) with small effective core diameter of 2.5 μm for cylindrical vector (CV) modes generation and propagation. Simulation results show that the fiber has a large effective refractive index difference in the order of 10-4-10-3 between the first higher-order CV modes, including TE01, HE21even and odd and TM01 modes. TE01 and TM01 were experimentally generated and were evaluated as having high purity of 82 percent and 85 percent, respectively. The results demonstrate that the SCF is a competitive waveguide candidate for selectable CV mode generation and propagation.
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28
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Sutanto H, van Sloun B, Schönleitner P, van Zandvoort MAMJ, Antoons G, Heijman J. The Subcellular Distribution of Ryanodine Receptors and L-Type Ca 2+ Channels Modulates Ca 2+-Transient Properties and Spontaneous Ca 2+-Release Events in Atrial Cardiomyocytes. Front Physiol 2018; 9:1108. [PMID: 30166973 PMCID: PMC6107030 DOI: 10.3389/fphys.2018.01108] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 07/23/2018] [Indexed: 11/13/2022] Open
Abstract
Spontaneous Ca2+-release events (SCaEs) from the sarcoplasmic reticulum play crucial roles in the initiation of cardiac arrhythmias by promoting triggered activity. However, the subcellular determinants of these SCaEs remain incompletely understood. Structural differences between atrial and ventricular cardiomyocytes, e.g., regarding the density of T-tubular membrane invaginations, may influence cardiomyocyte Ca2+-handling and the distribution of cardiac ryanodine receptors (RyR2) has recently been shown to undergo remodeling in atrial fibrillation. These data suggest that the subcellular distribution of Ca2+-handling proteins influences proarrhythmic Ca2+-handling abnormalities. Here, we employ computational modeling to provide an in-depth analysis of the impact of variations in subcellular RyR2 and L-type Ca2+-channel distributions on Ca2+-transient properties and SCaEs in a human atrial cardiomyocyte model. We incorporate experimentally observed RyR2 expression patterns and various configurations of axial tubules in a previously published model of the human atrial cardiomyocyte. We identify an increased SCaE incidence for larger heterogeneity in RyR2 expression, in which SCaEs preferentially arise from regions of high local RyR2 expression. Furthermore, we show that the propagation of Ca2+ waves is modulated by the distance between RyR2 bands, as well as the presence of experimentally observed RyR2 clusters between bands near the lateral membranes. We also show that incorporation of axial tubules in various amounts and locations reduces Ca2+-transient time to peak. Furthermore, selective hyperphosphorylation of RyR2 around axial tubules increases the number of spontaneous waves. Finally, we present a novel model of the human atrial cardiomyocyte with physiological RyR2 and L-type Ca2+-channel distributions that reproduces experimentally observed Ca2+-handling properties. Taken together, these results significantly enhance our understanding of the structure-function relationship in cardiomyocytes, identifying that RyR2 and L-type Ca2+-channel distributions have a major impact on systolic Ca2+ transients and SCaEs.
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Affiliation(s)
- Henry Sutanto
- Department of Cardiology, CARIM School for Cardiovascular Diseases, Maastricht University, Maastricht, Netherlands
| | - Bart van Sloun
- Department of Cardiology, CARIM School for Cardiovascular Diseases, Maastricht University, Maastricht, Netherlands
| | - Patrick Schönleitner
- Department of Physiology, CARIM School for Cardiovascular Diseases, Maastricht University, Maastricht, Netherlands
| | | | - Gudrun Antoons
- Department of Physiology, CARIM School for Cardiovascular Diseases, Maastricht University, Maastricht, Netherlands
| | - Jordi Heijman
- Department of Cardiology, CARIM School for Cardiovascular Diseases, Maastricht University, Maastricht, Netherlands
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29
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Wang C, Fukazawa A, Tanabe Y, Inai N, Yokogawa D, Yamaguchi S. Water-Soluble Phospholo[3,2-b
]phosphole-P
,P
′-Dioxide-Based Fluorescent Dyes with High Photostability. Chem Asian J 2018; 13:1616-1624. [DOI: 10.1002/asia.201800533] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Indexed: 12/16/2022]
Affiliation(s)
- Chenguang Wang
- Institute of Transformative Bio-Molecules (WPI-ITbM); Nagoya University; Furo-cho, Chikusa-ku Nagoya 464-8602 Japan
| | - Aiko Fukazawa
- Department of Chemistry; Graduate School of Science and Integrated Research Consortium on Chemical Sciences (IRCCS); Nagoya University; Furo-cho, Chikusa-ku Nagoya 464-8602 Japan
| | - Yoshiyuki Tanabe
- Department of Chemistry; Graduate School of Science and Integrated Research Consortium on Chemical Sciences (IRCCS); Nagoya University; Furo-cho, Chikusa-ku Nagoya 464-8602 Japan
| | - Naoto Inai
- Department of Chemistry; Graduate School of Science and Integrated Research Consortium on Chemical Sciences (IRCCS); Nagoya University; Furo-cho, Chikusa-ku Nagoya 464-8602 Japan
| | - Daisuke Yokogawa
- Institute of Transformative Bio-Molecules (WPI-ITbM); Nagoya University; Furo-cho, Chikusa-ku Nagoya 464-8602 Japan
- Department of Chemistry; Graduate School of Science and Integrated Research Consortium on Chemical Sciences (IRCCS); Nagoya University; Furo-cho, Chikusa-ku Nagoya 464-8602 Japan
| | - Shigehiro Yamaguchi
- Institute of Transformative Bio-Molecules (WPI-ITbM); Nagoya University; Furo-cho, Chikusa-ku Nagoya 464-8602 Japan
- Department of Chemistry; Graduate School of Science and Integrated Research Consortium on Chemical Sciences (IRCCS); Nagoya University; Furo-cho, Chikusa-ku Nagoya 464-8602 Japan
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30
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Witte R, Andriasyan V, Georgi F, Yakimovich A, Greber UF. Concepts in Light Microscopy of Viruses. Viruses 2018; 10:E202. [PMID: 29670029 PMCID: PMC5923496 DOI: 10.3390/v10040202] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 04/12/2018] [Accepted: 04/16/2018] [Indexed: 12/11/2022] Open
Abstract
Viruses threaten humans, livestock, and plants, and are difficult to combat. Imaging of viruses by light microscopy is key to uncover the nature of known and emerging viruses in the quest for finding new ways to treat viral disease and deepening the understanding of virus–host interactions. Here, we provide an overview of recent technology for imaging cells and viruses by light microscopy, in particular fluorescence microscopy in static and live-cell modes. The review lays out guidelines for how novel fluorescent chemical probes and proteins can be used in light microscopy to illuminate cells, and how they can be used to study virus infections. We discuss advantages and opportunities of confocal and multi-photon microscopy, selective plane illumination microscopy, and super-resolution microscopy. We emphasize the prevalent concepts in image processing and data analyses, and provide an outlook into label-free digital holographic microscopy for virus research.
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Affiliation(s)
- Robert Witte
- Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland.
| | - Vardan Andriasyan
- Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland.
| | - Fanny Georgi
- Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland.
| | - Artur Yakimovich
- MRC Laboratory for Molecular Cell Biology, University College London, Gower St., London WC1E 6BT, UK.
| | - Urs F Greber
- Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland.
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31
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Zhang X, Sisamakis E, Sozanski K, Holyst R. Nanoscopic Approach to Quantification of Equilibrium and Rate Constants of Complex Formation at Single-Molecule Level. J Phys Chem Lett 2017; 8:5785-5791. [PMID: 29131951 DOI: 10.1021/acs.jpclett.7b02742] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Equilibrium and rate constants are key descriptors of complex-formation processes in a variety of chemical and biological reactions. However, these parameters are difficult to quantify, especially in the locally confined, heterogeneous, and dynamically changing living matter. Herein, we address this challenge by combining stimulated emission depletion (STED) nanoscopy with fluorescence correlation spectroscopy (FCS). STED reduces the length-scale of observation to tens of nanometres (2D)/attoliters (3D) and the time-scale to microseconds, with direct, gradual control. This allows one to distinguish diffusional and binding processes of complex-formation, even at reaction rates higher by an order of magnitude than in confocal FCS. We provide analytical autocorrelation formulas for probes undergoing diffusion-reaction processes under STED condition. We support the theoretical analysis of experimental STED-FCS data on a model system of dye-micelle, where we retrieve the equilibrium and rates constants. Our work paves a promising way toward quantitative characterization of molecular interactions in vivo.
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Affiliation(s)
- Xuzhu Zhang
- Department of Soft Condensed Matter, Institute of Physical Chemistry, Polish Academy of Sciences , 01-224 Warsaw, Poland
| | | | - Krzysztof Sozanski
- Department of Soft Condensed Matter, Institute of Physical Chemistry, Polish Academy of Sciences , 01-224 Warsaw, Poland
| | - Robert Holyst
- Department of Soft Condensed Matter, Institute of Physical Chemistry, Polish Academy of Sciences , 01-224 Warsaw, Poland
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32
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Cofré A, Vargas A, Torres-Ruiz FA, Campos J, Lizana A, Sánchez-López MM, Moreno I. Dual polarization split lenses. OPTICS EXPRESS 2017; 25:23773-23783. [PMID: 29041328 DOI: 10.1364/oe.25.023773] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Accepted: 07/27/2017] [Indexed: 06/07/2023]
Abstract
We report the realization of polarization sensitive split lens configurations. While split lenses can be used to easily generate different types of controlled structured light patterns, their realization has been limited so far to scalar beams. Here we propose and experimentally demonstrate their generalization to vectorial split lenses, leading to light patterns with customized intensity and state of polarization. We demonstrate how these polarization split lenses can be experimentally implemented by means of an optical system using two liquid crystal spatial light modulators, each one phase modulating one orthogonal polarization component. As a result, we demonstrate the experimental generation of vectorial beams with different shapes generated with these dual polarization split lenses. Excellent experimental results are provided in each case. The proposed technique is a simple method to generate structured light beams with polarization diversity, with potential applications in polarimetry, customized illuminators or quantum optics.
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33
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Ivask A, Mitchell AJ, Malysheva A, Voelcker NH, Lombi E. Methodologies and approaches for the analysis of cell-nanoparticle interactions. WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY 2017; 10:e1486. [DOI: 10.1002/wnan.1486] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Revised: 06/12/2017] [Accepted: 06/20/2017] [Indexed: 01/09/2023]
Affiliation(s)
- Angela Ivask
- Laboratory of Environmental Toxicology; National Institute of Chemical Physics and Biophysics; Tallinn Estonia
- Future Industries Institute; University of South Australia; Mawson Lakes Australia
| | - Andrew J. Mitchell
- Materials Characterisation and Fabrication Platform; University of Melbourne; Melbourne Australia
| | - Anzhela Malysheva
- Future Industries Institute; University of South Australia; Mawson Lakes Australia
| | - Nicolas H. Voelcker
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences; Monash University; Parkville Australia
| | - Enzo Lombi
- Future Industries Institute; University of South Australia; Mawson Lakes Australia
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34
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Lévesque É, Bechara WS, Constantineau-Forget L, Pelletier G, Rachel NM, Pelletier JN, Charette AB. General C-H Arylation Strategy for the Synthesis of Tunable Visible Light-Emitting Benzo[a]imidazo[2,1,5-c,d]indolizine Fluorophores. J Org Chem 2017; 82:5046-5067. [PMID: 28441020 DOI: 10.1021/acs.joc.6b02928] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Herein we report the discovery of the benzo[a]imidazo[2,1,5-c,d]indolizine motif displaying tunable emission covering most of the visible spectrum. The polycyclic core is obtained from readily available amides via a chemoselective process involving Tf2O-mediated amide cyclodehydration, followed by intramolecular C-H arylation. Additionally, these fluorescent heterocycles are easily functionalized using electrophilic reagents, enabling divergent access to varied substitution. The effects of said substitution on the compounds' photophysical properties were rationalized by density functional theory calculations. For some compounds, emission wavelengths are directly correlated to the substituent's Hammett constants. Easily introduced nonconjugated reactive functional groups allow the labeling of biomolecules without modification of emissive properties. This work provides a straightforward platform for the synthesis of new moderately bright fluorescent dyes remarkable for their chemical stability, predictability, and unusually high excitation-emission differential.
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Affiliation(s)
- Éric Lévesque
- Centre in Green Chemistry and Catalysis, Faculty of Arts and Sciences, Department of Chemistry, Université de Montréal , P.O. Box 6128, Station Downtown, Montréal, Québec H3C 3J7, Canada
| | - William S Bechara
- Centre in Green Chemistry and Catalysis, Faculty of Arts and Sciences, Department of Chemistry, Université de Montréal , P.O. Box 6128, Station Downtown, Montréal, Québec H3C 3J7, Canada
| | - Léa Constantineau-Forget
- Centre in Green Chemistry and Catalysis, Faculty of Arts and Sciences, Department of Chemistry, Université de Montréal , P.O. Box 6128, Station Downtown, Montréal, Québec H3C 3J7, Canada
| | - Guillaume Pelletier
- Centre in Green Chemistry and Catalysis, Faculty of Arts and Sciences, Department of Chemistry, Université de Montréal , P.O. Box 6128, Station Downtown, Montréal, Québec H3C 3J7, Canada
| | - Natalie M Rachel
- Centre in Green Chemistry and Catalysis, Faculty of Arts and Sciences, Department of Chemistry, Université de Montréal , P.O. Box 6128, Station Downtown, Montréal, Québec H3C 3J7, Canada
| | - Joelle N Pelletier
- Centre in Green Chemistry and Catalysis, Faculty of Arts and Sciences, Department of Chemistry, Université de Montréal , P.O. Box 6128, Station Downtown, Montréal, Québec H3C 3J7, Canada
| | - André B Charette
- Centre in Green Chemistry and Catalysis, Faculty of Arts and Sciences, Department of Chemistry, Université de Montréal , P.O. Box 6128, Station Downtown, Montréal, Québec H3C 3J7, Canada
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35
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Demmerle J, Innocent C, North AJ, Ball G, Müller M, Miron E, Matsuda A, Dobbie IM, Markaki Y, Schermelleh L. Strategic and practical guidelines for successful structured illumination microscopy. Nat Protoc 2017; 12:988-1010. [DOI: 10.1038/nprot.2017.019] [Citation(s) in RCA: 191] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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36
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Affiliation(s)
- Hans Blom
- Royal Institute of Technology (KTH), Dept Applied Physics, SciLifeLab, 17165 Solna, Sweden
| | - Jerker Widengren
- Royal Institute of Technology (KTH), Dept Applied Physics, Albanova Univ Center, 10691 Stockholm, Sweden
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37
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Wang L, Ta H, Ullal C, Wang F, Wang C, Dong G. Aptamer functionalized silver clusters for STED microscopy. RSC Adv 2017. [DOI: 10.1039/c6ra26991e] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Novel STED probe was prepared through aptamer functionalized silver clusters, which preserve specific affinity with smaller size and more photostability.
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Affiliation(s)
- Lan Wang
- Laboratory of Environmental Sciences and Technology
- Key Laboratory of Functional Materials and Devices for Special Environments
- Xinjiang Technical Institute of Physics & Chemistry
- Chinese Academy of Sciences
- Urumqi 830011
| | - Haisen Ta
- Department of NanoBiophotonics
- Max Planck Institute for Biophysical Chemistry
- Göttingen 37077
- Germany
| | - Chaitanya Ullal
- Department of Materials Science and Engineering
- Rensselaer Polytechnic Institute
- Troy
- USA
| | - Fu Wang
- Laboratory of Environmental Sciences and Technology
- Key Laboratory of Functional Materials and Devices for Special Environments
- Xinjiang Technical Institute of Physics & Chemistry
- Chinese Academy of Sciences
- Urumqi 830011
| | - Chuanyi Wang
- Laboratory of Environmental Sciences and Technology
- Key Laboratory of Functional Materials and Devices for Special Environments
- Xinjiang Technical Institute of Physics & Chemistry
- Chinese Academy of Sciences
- Urumqi 830011
| | - Guohui Dong
- Laboratory of Environmental Sciences and Technology
- Key Laboratory of Functional Materials and Devices for Special Environments
- Xinjiang Technical Institute of Physics & Chemistry
- Chinese Academy of Sciences
- Urumqi 830011
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38
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Allodi MA, Dahlberg PD, Mazuski RJ, Davis HC, Otto JP, Engel GS. Optical resonance imaging: An optical analog to MRI with sub-diffraction-limited capabilities. ACS PHOTONICS 2016; 3:2445-2452. [PMID: 28451625 PMCID: PMC5403159 DOI: 10.1021/acsphotonics.6b00694] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
We propose here optical resonance imaging (ORI), a direct optical analog to magnetic resonance imaging (MRI). The proposed pulse sequence for ORI maps space to time and recovers an image from a heterodyne-detected third-order nonlinear photon echo measurement. As opposed to traditional photon echo measurements, the third pulse in the ORI pulse sequence has significant pulse-front tilt that acts as a temporal gradient. This gradient couples space to time by stimulating the emission of a photon echo signal from different lateral spatial locations of a sample at different times, providing a widefield ultrafast microscopy. We circumvent the diffraction limit of the optics by mapping the lateral spatial coordinate of the sample with the emission time of the signal, which can be measured to high precision using interferometric heterodyne detection. This technique is thus an optical analog of MRI, where magnetic-field gradients are used to localize the spin-echo emission to a point below the diffraction limit of the radio-frequency wave used. We calculate the expected ORI signal using 15 fs pulses and 87° of pulse-front tilt, collected using f/2 optics and find a two-point resolution 275 nm using 800 nm light that satisfies the Rayleigh criterion. We also derive a general equation for resolution in optical resonance imaging that indicates that there is a possibility of superresolution imaging using this technique. The photon echo sequence also enables spectroscopic determination of the input and output energy. The technique thus correlates the input energy with the final position and energy of the exciton.
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Affiliation(s)
- Marco A Allodi
- Department of Chemistry, The Institute for Biophysical Dynamics, The James Franck Institute, The University of Chicago, Chicago, IL, 60637, USA
| | - Peter D Dahlberg
- Graduate Program in Biophysical Sciences, The University of Chicago, Chicago, IL, 60637, USA
| | - Richard J Mazuski
- Department of Chemistry, The Institute for Biophysical Dynamics, The James Franck Institute, The University of Chicago, Chicago, IL, 60637, USA
| | - Hunter C Davis
- Department of Chemistry, The Institute for Biophysical Dynamics, The James Franck Institute, The University of Chicago, Chicago, IL, 60637, USA
| | - John P Otto
- Department of Chemistry, The Institute for Biophysical Dynamics, The James Franck Institute, The University of Chicago, Chicago, IL, 60637, USA
| | - Gregory S Engel
- Department of Chemistry, The Institute for Biophysical Dynamics, The James Franck Institute, The University of Chicago, Chicago, IL, 60637, USA
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Rowlett VW, Margolin W. The bacterial divisome: ready for its close-up. Philos Trans R Soc Lond B Biol Sci 2016; 370:rstb.2015.0028. [PMID: 26370940 DOI: 10.1098/rstb.2015.0028] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Bacterial cells divide by targeting a transmembrane protein machine to the division site and regulating its assembly and disassembly so that cytokinesis occurs at the correct time in the cell cycle. The structure and dynamics of this machine (divisome) in bacterial model systems are coming more clearly into focus, thanks to incisive cell biology methods in combination with biochemical and genetic approaches. The main conserved structural element of the machine is the tubulin homologue FtsZ, which assembles into a circumferential ring at the division site that is stabilized and anchored to the inner surface of the cytoplasmic membrane by FtsZ-binding proteins. Once this ring is in place, it recruits a series of transmembrane proteins that ultimately trigger cytokinesis. This review will survey the methods used to characterize the structure of the bacterial divisome, focusing mainly on the Escherichia coli model system, as well as the challenges that remain. These methods include recent super-resolution microscopy, cryo-electron tomography and synthetic reconstitution.
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Affiliation(s)
- Veronica W Rowlett
- Microbiology and Molecular Genetics, University of Texas Medical School at Houston, 6431 Fannin, Houston, TX 77030, USA
| | - William Margolin
- Microbiology and Molecular Genetics, University of Texas Medical School at Houston, 6431 Fannin, Houston, TX 77030, USA
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40
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Superresolution imaging of telomeres with continuous wave stimulated emission depletion (STED) microscope. Sci China Chem 2016. [DOI: 10.1007/s11426-016-0020-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Abstract
The majority of studies of the living cell rely on capturing images using fluorescence microscopy. Unfortunately, for centuries, diffraction of light was limiting the spatial resolution in the optical microscope: structural and molecular details much finer than about half the wavelength of visible light (~200 nm) could not be visualized, imposing significant limitations on this otherwise so promising method. The surpassing of this resolution limit in far-field microscopy is currently one of the most momentous developments for studying the living cell, as the move from microscopy to super-resolution microscopy or 'nanoscopy' offers opportunities to study problems in biophysical and biomedical research at a new level of detail. This review describes the principles and modalities of present fluorescence nanoscopes, as well as their potential for biophysical and cellular experiments. All the existing nanoscopy variants separate neighboring features by transiently preparing their fluorescent molecules in states of different emission characteristics in order to make the features discernible. Usually these are fluorescent 'on' and 'off' states causing the adjacent molecules to emit sequentially in time. Each of the variants can in principle reach molecular spatial resolution and has its own advantages and disadvantages. Some require specific transitions and states that can be found only in certain fluorophore subfamilies, such as photoswitchable fluorophores, while other variants can be realized with standard fluorescent labels. Similar to conventional far-field microscopy, nanoscopy can be utilized for dynamical, multi-color and three-dimensional imaging of fixed and live cells, tissues or organisms. Lens-based fluorescence nanoscopy is poised for a high impact on future developments in the life sciences, with the potential to help solve long-standing quests in different areas of scientific research.
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Reindl J, Drexler GA, Girst S, Greubel C, Siebenwirth C, Drexler SE, Dollinger G, Friedl AA. Nanoscopic exclusion between Rad51 and 53BP1 after ion irradiation in human HeLa cells. Phys Biol 2015; 12:066005. [DOI: 10.1088/1478-3975/12/6/066005] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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Wang C, Fukazawa A, Taki M, Sato Y, Higashiyama T, Yamaguchi S. A Phosphole Oxide Based Fluorescent Dye with Exceptional Resistance to Photobleaching: A Practical Tool for Continuous Imaging in STED Microscopy. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201507939] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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Subdiffraction localization of a nanostructured photosensitizer in bacterial cells. Sci Rep 2015; 5:15564. [PMID: 26494535 PMCID: PMC4616064 DOI: 10.1038/srep15564] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Accepted: 09/24/2015] [Indexed: 12/17/2022] Open
Abstract
Antibacterial treatments based on photosensitized production of reactive oxygen species is a promising approach to address local microbial infections. Given the small size of bacterial cells, identification of the sites of binding of the photosensitizing molecules is a difficult issue to address with conventional microscopy. We show that the excited state properties of the naturally occurring photosensitizer hypericin can be exploited to perform STED microscopy on bacteria incubated with the complex between hypericin and apomyoglobin, a self-assembled nanostructure that confers very good bioavailability to the photosensitizer. Hypericin fluorescence is mostly localized at the bacterial wall, and accumulates at the polar regions of the cell and at sites of cell wall growth. While these features are shared by Gram-negative and Gram-positive bacteria, only the latter are effectively photoinactivated by light exposure.
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Wang C, Fukazawa A, Taki M, Sato Y, Higashiyama T, Yamaguchi S. A Phosphole Oxide Based Fluorescent Dye with Exceptional Resistance to Photobleaching: A Practical Tool for Continuous Imaging in STED Microscopy. Angew Chem Int Ed Engl 2015; 54:15213-7. [PMID: 26493944 DOI: 10.1002/anie.201507939] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Indexed: 12/26/2022]
Abstract
The development of stimulated emission depletion (STED) microscopy represented a major breakthrough in cellular and molecular biology. However, the intense laser beams required for both excitation and STED usually provoke rapid photobleaching of fluorescent molecular probes, which significantly limits the performance and practical utility of STED microscopy. We herein developed a photoresistant fluorescent dye C-Naphox as a practical tool for STED imaging. With excitation using either a λ=405 or 488 nm laser in protic solvents, C-Naphox exhibited an intense red/orange fluorescence (quantum yield ΦF >0.7) with a large Stokes shift (circa 5900 cm(-1) ). Even after irradiation with a Xe lamp (300 W, λex =460 nm, full width at half maximum (FWHM)=11 nm) for 12 hours, 99.5 % of C-Naphox remained intact. The high photoresistance of C-Naphox allowed repeated STED imaging of HeLa cells. Even after recording 50 STED images, 83 % of the initial fluorescence intensity persisted.
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Affiliation(s)
- Chenguang Wang
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Furo, Chikusa, Nagoya 464-8602 (Japan)
| | - Aiko Fukazawa
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo, Chikusa, Nagoya 464-8602 (Japan).
| | - Masayasu Taki
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Furo, Chikusa, Nagoya 464-8602 (Japan).
| | - Yoshikatsu Sato
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Furo, Chikusa, Nagoya 464-8602 (Japan)
| | - Tetsuya Higashiyama
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Furo, Chikusa, Nagoya 464-8602 (Japan). .,Division of Biological Science, Graduate School of Science, Nagoya University, Furo, Chikusa, Nagoya 464-8602 (Japan).
| | - Shigehiro Yamaguchi
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Furo, Chikusa, Nagoya 464-8602 (Japan). .,Department of Chemistry, Graduate School of Science, Nagoya University, Furo, Chikusa, Nagoya 464-8602 (Japan).
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Sednev MV, Belov VN, Hell SW. Fluorescent dyes with large Stokes shifts for super-resolution optical microscopy of biological objects: a review. Methods Appl Fluoresc 2015; 3:042004. [DOI: 10.1088/2050-6120/3/4/042004] [Citation(s) in RCA: 130] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Søndergaard RV, Christensen NM, Henriksen JR, Kumar EKP, Almdal K, Andresen TL. Facing the Design Challenges of Particle-Based Nanosensors for Metabolite Quantification in Living Cells. Chem Rev 2015; 115:8344-78. [PMID: 26244372 DOI: 10.1021/cr400636x] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Rikke V Søndergaard
- Department of Micro- and Nanotechnology, Technical University of Denmark , Produktionstorvet 423, 2800 Lyngby, Denmark
| | - Nynne M Christensen
- Department of Micro- and Nanotechnology, Technical University of Denmark , Produktionstorvet 423, 2800 Lyngby, Denmark
| | - Jonas R Henriksen
- Department of Micro- and Nanotechnology, Technical University of Denmark , Produktionstorvet 423, 2800 Lyngby, Denmark
| | - E K Pramod Kumar
- Department of Micro- and Nanotechnology, Technical University of Denmark , Produktionstorvet 423, 2800 Lyngby, Denmark
| | - Kristoffer Almdal
- Department of Micro- and Nanotechnology, Technical University of Denmark , Produktionstorvet 423, 2800 Lyngby, Denmark
| | - Thomas L Andresen
- Department of Micro- and Nanotechnology, Technical University of Denmark , Produktionstorvet 423, 2800 Lyngby, Denmark
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Uno SN, Tiwari DK, Kamiya M, Arai Y, Nagai T, Urano Y. A guide to use photocontrollable fluorescent proteins and synthetic smart fluorophores for nanoscopy. Microscopy (Oxf) 2015; 64:263-77. [PMID: 26152215 DOI: 10.1093/jmicro/dfv037] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2015] [Accepted: 06/12/2015] [Indexed: 12/28/2022] Open
Abstract
Recent advances in nanoscopy, which breaks the diffraction barrier and can visualize structures smaller than the diffraction limit in cells, have encouraged biologists to investigate cellular processes at molecular resolution. Since nanoscopy depends not only on special optics but also on 'smart' photophysical properties of photocontrollable fluorescent probes, including photoactivatability, photoswitchability and repeated blinking, it is important for biologists to understand the advantages and disadvantages of fluorescent probes and to choose appropriate ones for their specific requirements. Here, we summarize the characteristics of currently available fluorescent probes based on both proteins and synthetic compounds applicable to nanoscopy and provide a guideline for selecting optimal probes for specific applications.
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Affiliation(s)
- Shin-Nosuke Uno
- Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Dhermendra K Tiwari
- The Institute of Scientific and Industrial Research, Osaka University, Mihogaoka 8-1, Ibaraki, Osaka 567-0047, Japan
| | - Mako Kamiya
- Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan PRESTO, Japan Science and Technology Agency, Saitama, Japan
| | - Yoshiyuki Arai
- The Institute of Scientific and Industrial Research, Osaka University, Mihogaoka 8-1, Ibaraki, Osaka 567-0047, Japan
| | - Takeharu Nagai
- The Institute of Scientific and Industrial Research, Osaka University, Mihogaoka 8-1, Ibaraki, Osaka 567-0047, Japan
| | - Yasuteru Urano
- Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
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Abstract
The increasing interest in "seeing" the molecular environment in biological systems has led to the recent quest for breaking the diffraction barrier in far-field fluorescence microscopy. The first nanoscopy method successfully applied to conventional biological probes was stimulated emission depletion microscopy (STED). It is based on a physical principle that instantly delivers diffraction-unlimited images, with no need for further computational processing: the excitation laser beam is overlaid with a doughnut-shaped depleting beam that switches off previously excited fluorophores, thereby resulting in what is effectively a smaller imaging volume. In this chapter we give an overview of several applications of STED microscopy to biological questions. We explain technical aspects of sample preparation and image acquisition that will help in obtaining good diffraction-unlimited pictures. We also present embedding techniques adapted for ultrathin sectioning, which allow optimal 3D resolutions in virtually all biological preparations.
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Affiliation(s)
- Natalia H Revelo
- Department of Neuro- and Sensory Physiology, University Medical Center Göttingen, Humboldtallee 23, Göttingen, Germany,
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