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Gao Z, Hou S, Deng S, Liang L, Wang F, Guo L, Fang W, Li Q, Kang B, Chen HY, Fan C. Scanning Switch-off Microscopy for Super-Resolution Fluorescence Imaging. NANO LETTERS 2024; 24:12125-12132. [PMID: 39298669 DOI: 10.1021/acs.nanolett.4c02452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/22/2024]
Abstract
Super-resolution (SR) microscopy provides a revolutionary optical imaging approach by breaking the diffraction limit of light, while the commonly required special instrumentation with complex optical setup hampers its popularity. Here, we present a scanning switch-off microscopy (SSM) concept that exploits the omnipresent switch-off response of fluorophores to enable super-resolution imaging using a commercial confocal microscope. We validated the SSM model with theoretical calculations and experiments. An imaging resolution of ∼100 nm was obtained for DNA origami nanostructures and cellular cytoskeletons using fluorescent labels of Alexa 405, Alexa 488, Cy3, and Atto 488. Notably, super-resolution imaging of live cells was realized with SSM, by employing a dronpa fluorescent protein as the fluorescent label. In principle, this SSM method can be applied to any excitation laser scanning-based microscope.
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Affiliation(s)
- Zhaoshuai Gao
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, 200240 Shanghai, China
- School of Chemistry and Chemical Engineering, State Key Laboratory of Analytical Chemistry for Life Science and Collaborative Innovation Center of Chemistry for Life Sciences, Nanjing University, 210023 Nanjing, China
| | - Shangguo Hou
- CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, 201800 Shanghai, China
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, 518055 Shenzhen, China
| | - Suhui Deng
- CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, 201800 Shanghai, China
- School of Information Engineering, Nanchang University, 330031 Nanchang, China
| | - Le Liang
- CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, 201800 Shanghai, China
- The Institute for Advanced Studies, Wuhan University, 430072 Wuhan, China
| | - Fei Wang
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, 200240 Shanghai, China
| | - Linjie Guo
- CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, 201800 Shanghai, China
| | - Weina Fang
- CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, 201800 Shanghai, China
| | - Qian Li
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, 200240 Shanghai, China
| | - Bin Kang
- School of Chemistry and Chemical Engineering, State Key Laboratory of Analytical Chemistry for Life Science and Collaborative Innovation Center of Chemistry for Life Sciences, Nanjing University, 210023 Nanjing, China
| | - Hong-Yuan Chen
- School of Chemistry and Chemical Engineering, State Key Laboratory of Analytical Chemistry for Life Science and Collaborative Innovation Center of Chemistry for Life Sciences, Nanjing University, 210023 Nanjing, China
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, 200240 Shanghai, China
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2
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Lamon S, Yu H, Zhang Q, Gu M. Lanthanide ion-doped upconversion nanoparticles for low-energy super-resolution applications. LIGHT, SCIENCE & APPLICATIONS 2024; 13:252. [PMID: 39277593 PMCID: PMC11401911 DOI: 10.1038/s41377-024-01547-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 05/31/2024] [Accepted: 07/22/2024] [Indexed: 09/17/2024]
Abstract
Energy-intensive technologies and high-precision research require energy-efficient techniques and materials. Lens-based optical microscopy technology is useful for low-energy applications in the life sciences and other fields of technology, but standard techniques cannot achieve applications at the nanoscale because of light diffraction. Far-field super-resolution techniques have broken beyond the light diffraction limit, enabling 3D applications down to the molecular scale and striving to reduce energy use. Typically targeted super-resolution techniques have achieved high resolution, but the high light intensity needed to outperform competing optical transitions in nanomaterials may result in photo-damage and high energy consumption. Great efforts have been made in the development of nanomaterials to improve the resolution and efficiency of these techniques toward low-energy super-resolution applications. Lanthanide ion-doped upconversion nanoparticles that exhibit multiple long-lived excited energy states and emit upconversion luminescence have enabled the development of targeted super-resolution techniques that need low-intensity light. The use of lanthanide ion-doped upconversion nanoparticles in these techniques for emerging low-energy super-resolution applications will have a significant impact on life sciences and other areas of technology. In this review, we describe the dynamics of lanthanide ion-doped upconversion nanoparticles for super-resolution under low-intensity light and their use in targeted super-resolution techniques. We highlight low-energy super-resolution applications of lanthanide ion-doped upconversion nanoparticles, as well as the related research directions and challenges. Our aim is to analyze targeted super-resolution techniques using lanthanide ion-doped upconversion nanoparticles, emphasizing fundamental mechanisms governing transitions in lanthanide ions to surpass the diffraction limit with low-intensity light, and exploring their implications for low-energy nanoscale applications.
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Affiliation(s)
- Simone Lamon
- School of Artificial Intelligence Science and Technology, University of Shanghai for Science and Technology, 200093, Shanghai, China.
- Institute of Photonic Chips, University of Shanghai for Science and Technology, 200093, Shanghai, China.
| | - Haoyi Yu
- School of Artificial Intelligence Science and Technology, University of Shanghai for Science and Technology, 200093, Shanghai, China
- Institute of Photonic Chips, University of Shanghai for Science and Technology, 200093, Shanghai, China
| | - Qiming Zhang
- School of Artificial Intelligence Science and Technology, University of Shanghai for Science and Technology, 200093, Shanghai, China
- Institute of Photonic Chips, University of Shanghai for Science and Technology, 200093, Shanghai, China
| | - Min Gu
- School of Artificial Intelligence Science and Technology, University of Shanghai for Science and Technology, 200093, Shanghai, China.
- Institute of Photonic Chips, University of Shanghai for Science and Technology, 200093, Shanghai, China.
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3
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Zulueta Diaz YDLM, Arnspang EC. Super-resolution microscopy to study membrane nanodomains and transport mechanisms in the plasma membrane. Front Mol Biosci 2024; 11:1455153. [PMID: 39290992 PMCID: PMC11405310 DOI: 10.3389/fmolb.2024.1455153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2024] [Accepted: 08/19/2024] [Indexed: 09/19/2024] Open
Abstract
Biological membranes are complex, heterogeneous, and dynamic systems that play roles in the compartmentalization and protection of cells from the environment. It is still a challenge to elucidate kinetics and real-time transport routes for molecules through biological membranes in live cells. Currently, by developing and employing super-resolution microscopy; increasing evidence indicates channels and transporter nano-organization and dynamics within membranes play an important role in these regulatory mechanisms. Here we review recent advances and discuss the major advantages and disadvantages of using super-resolution microscopy to investigate protein organization and transport within plasma membranes.
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Affiliation(s)
| | - Eva C Arnspang
- Department of Green Technology, SDU Biotechnology, University of Southern Denmark, Odense, Denmark
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4
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Rosen J, Alford S, Allan B, Anand V, Arnon S, Arockiaraj FG, Art J, Bai B, Balasubramaniam GM, Birnbaum T, Bisht NS, Blinder D, Cao L, Chen Q, Chen Z, Dubey V, Egiazarian K, Ercan M, Forbes A, Gopakumar G, Gao Y, Gigan S, Gocłowski P, Gopinath S, Greenbaum A, Horisaki R, Ierodiaconou D, Juodkazis S, Karmakar T, Katkovnik V, Khonina SN, Kner P, Kravets V, Kumar R, Lai Y, Li C, Li J, Li S, Li Y, Liang J, Manavalan G, Mandal AC, Manisha M, Mann C, Marzejon MJ, Moodley C, Morikawa J, Muniraj I, Narbutis D, Ng SH, Nothlawala F, Oh J, Ozcan A, Park Y, Porfirev AP, Potcoava M, Prabhakar S, Pu J, Rai MR, Rogalski M, Ryu M, Choudhary S, Salla GR, Schelkens P, Şener SF, Shevkunov I, Shimobaba T, Singh RK, Singh RP, Stern A, Sun J, Zhou S, Zuo C, Zurawski Z, Tahara T, Tiwari V, Trusiak M, Vinu RV, Volotovskiy SG, Yılmaz H, De Aguiar HB, Ahluwalia BS, Ahmad A. Roadmap on computational methods in optical imaging and holography [invited]. APPLIED PHYSICS. B, LASERS AND OPTICS 2024; 130:166. [PMID: 39220178 PMCID: PMC11362238 DOI: 10.1007/s00340-024-08280-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 07/10/2024] [Indexed: 09/04/2024]
Abstract
Computational methods have been established as cornerstones in optical imaging and holography in recent years. Every year, the dependence of optical imaging and holography on computational methods is increasing significantly to the extent that optical methods and components are being completely and efficiently replaced with computational methods at low cost. This roadmap reviews the current scenario in four major areas namely incoherent digital holography, quantitative phase imaging, imaging through scattering layers, and super-resolution imaging. In addition to registering the perspectives of the modern-day architects of the above research areas, the roadmap also reports some of the latest studies on the topic. Computational codes and pseudocodes are presented for computational methods in a plug-and-play fashion for readers to not only read and understand but also practice the latest algorithms with their data. We believe that this roadmap will be a valuable tool for analyzing the current trends in computational methods to predict and prepare the future of computational methods in optical imaging and holography. Supplementary Information The online version contains supplementary material available at 10.1007/s00340-024-08280-3.
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Affiliation(s)
- Joseph Rosen
- School of Electrical and Computer Engineering, Ben-Gurion University of the Negev, 8410501 Beer-Sheva, Israel
- Institute of Physics, University of Tartu, W. Ostwaldi 1, 50411 Tartu, Estonia
| | - Simon Alford
- Department of Anatomy and Cell Biology, University of Illinois at Chicago, 808 South Wood Street, Chicago, IL 60612 USA
| | - Blake Allan
- Faculty of Science Engineering and Built Environment, Deakin University, Princes Highway, Warrnambool, VIC 3280 Australia
| | - Vijayakumar Anand
- Institute of Physics, University of Tartu, W. Ostwaldi 1, 50411 Tartu, Estonia
- Optical Sciences Center and ARC Training Centre in Surface Engineering for Advanced Materials (SEAM), School of Science, Computing and Engineering Technologies, Optical Sciences Center, Swinburne University of Technology, Hawthorn, Melbourne, VIC 3122 Australia
| | - Shlomi Arnon
- School of Electrical and Computer Engineering, Ben-Gurion University of the Negev, 8410501 Beer-Sheva, Israel
| | - Francis Gracy Arockiaraj
- School of Electrical and Computer Engineering, Ben-Gurion University of the Negev, 8410501 Beer-Sheva, Israel
- Institute of Physics, University of Tartu, W. Ostwaldi 1, 50411 Tartu, Estonia
| | - Jonathan Art
- Department of Anatomy and Cell Biology, University of Illinois at Chicago, 808 South Wood Street, Chicago, IL 60612 USA
| | - Bijie Bai
- Electrical and Computer Engineering Department, Bioengineering Department, California NanoSystems Institute, University of California, Los Angeles (UCLA), Los Angeles, CA USA
| | - Ganesh M. Balasubramaniam
- School of Electrical and Computer Engineering, Ben-Gurion University of the Negev, 8410501 Beer-Sheva, Israel
| | - Tobias Birnbaum
- Department of Electronics and Informatics (ETRO), Vrije Universiteit Brussel VUB), Pleinlaan 2, 1050 Brussel, Belgium
- Swave BV, Gaston Geenslaan 2, 3001 Leuven, Belgium
| | - Nandan S. Bisht
- Applied Optics and Spectroscopy Laboratory, Department of Physics, Soban Singh Jeena University Campus Almora, Almora, Uttarakhand 263601 India
| | - David Blinder
- Department of Electronics and Informatics (ETRO), Vrije Universiteit Brussel VUB), Pleinlaan 2, 1050 Brussel, Belgium
- IMEC, Kapeldreef 75, 3001 Leuven, Belgium
- Graduate School of Engineering, Chiba University, 1-33 Yayoi-cho, Inage-ku, Chiba, Chiba Japan
| | - Liangcai Cao
- Department of Precision Instruments, Tsinghua University, Beijing, 100084 China
| | - Qian Chen
- Jiangsu Key Laboratory of Spectral Imaging and Intelligent Sense, Nanjing, 210094 Jiangsu China
| | - Ziyang Chen
- Fujian Provincial Key Laboratory of Light Propagation and Transformation, College of Information Science and Engineering, Huaqiao University, Xiamen, 361021 Fujian China
| | - Vishesh Dubey
- Department of Physics and Technology, UiT The Arctic University of Norway, 9037 Tromsø, Norway
| | - Karen Egiazarian
- Computational Imaging Group, Faculty of Information Technology and Communication Sciences, Tampere University, 33100 Tampere, Finland
| | - Mert Ercan
- Institute of Materials Science and Nanotechnology, National Nanotechnology Research Center (UNAM), Bilkent University, 06800 Ankara, Turkey
- Department of Physics, Bilkent University, 06800 Ankara, Turkey
| | - Andrew Forbes
- School of Physics, University of the Witwatersrand, Johannesburg, South Africa
| | - G. Gopakumar
- Department of Computer Science and Engineering, Amrita School of Computing, Amrita Vishwa Vidyapeetham, Amritapuri, Vallikavu, Kerala India
| | - Yunhui Gao
- Department of Precision Instruments, Tsinghua University, Beijing, 100084 China
| | - Sylvain Gigan
- Laboratoire Kastler Brossel, Centre National de la Recherche Scientifique (CNRS) UMR 8552, Sorbonne Universite ´, Ecole Normale Supe ´rieure-Paris Sciences et Lettres (PSL) Research University, Collège de France, 24 rue Lhomond, 75005 Paris, France
| | - Paweł Gocłowski
- Department of Physics and Technology, UiT The Arctic University of Norway, 9037 Tromsø, Norway
| | | | - Alon Greenbaum
- Department of Biomedical Engineering, North Carolina State University and University of North Carolina at Chapel Hill, Raleigh, NC 27695 USA
- Comparative Medicine Institute, North Carolina State University, Raleigh, NC 27695 USA
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC 27695 USA
| | - Ryoichi Horisaki
- Graduate School of Information Science and Technology, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656 Japan
| | - Daniel Ierodiaconou
- Faculty of Science Engineering and Built Environment, Deakin University, Princes Highway, Warrnambool, VIC 3280 Australia
| | - Saulius Juodkazis
- Optical Sciences Center and ARC Training Centre in Surface Engineering for Advanced Materials (SEAM), School of Science, Computing and Engineering Technologies, Optical Sciences Center, Swinburne University of Technology, Hawthorn, Melbourne, VIC 3122 Australia
- World Research Hub Initiative (WRHI), Tokyo Institute of Technology, 2-12-1, Ookayama, Tokyo, 152-8550 Japan
| | - Tanushree Karmakar
- Laboratory of Information Photonics and Optical Metrology, Department of Physics, Indian Institute of Technology (Banaras Hindu University), Varanasi, Uttar Pradesh 221005 India
| | - Vladimir Katkovnik
- Computational Imaging Group, Faculty of Information Technology and Communication Sciences, Tampere University, 33100 Tampere, Finland
| | - Svetlana N. Khonina
- IPSI RAS-Branch of the FSRC “Crystallography and Photonics” RAS, 443001 Samara, Russia
- Samara National Research University, 443086 Samara, Russia
| | - Peter Kner
- School of Electrical and Computer Engineering, University of Georgia, Athens, GA 30602 USA
| | - Vladislav Kravets
- School of Electrical and Computer Engineering, Ben-Gurion University of the Negev, 8410501 Beer-Sheva, Israel
| | - Ravi Kumar
- Department of Physics, SRM University – AP, Amaravati, Andhra Pradesh 522502 India
| | - Yingming Lai
- Laboratory of Applied Computational Imaging, Centre Énergie Matériaux Télécommunications, Institut National de la Recherche Scientifique, Université du Québec, Varennes, QC J3X1Pd7 Canada
| | - Chen Li
- Department of Biomedical Engineering, North Carolina State University and University of North Carolina at Chapel Hill, Raleigh, NC 27695 USA
- Comparative Medicine Institute, North Carolina State University, Raleigh, NC 27695 USA
| | - Jiaji Li
- Jiangsu Key Laboratory of Spectral Imaging and Intelligent Sense, Nanjing, 210094 Jiangsu China
- Smart Computational Imaging Laboratory (SCILab), School of Electronic and Optical Engineering, Nanjing University of Science and Technology, Nanjing, 210094 Jiangsu China
- Smart Computational Imaging Research Institute (SCIRI), Nanjing, 210019 Jiangsu China
| | - Shaoheng Li
- School of Electrical and Computer Engineering, University of Georgia, Athens, GA 30602 USA
| | - Yuzhu Li
- Electrical and Computer Engineering Department, Bioengineering Department, California NanoSystems Institute, University of California, Los Angeles (UCLA), Los Angeles, CA USA
| | - Jinyang Liang
- Laboratory of Applied Computational Imaging, Centre Énergie Matériaux Télécommunications, Institut National de la Recherche Scientifique, Université du Québec, Varennes, QC J3X1Pd7 Canada
| | - Gokul Manavalan
- School of Electrical and Computer Engineering, Ben-Gurion University of the Negev, 8410501 Beer-Sheva, Israel
| | - Aditya Chandra Mandal
- Laboratory of Information Photonics and Optical Metrology, Department of Physics, Indian Institute of Technology (Banaras Hindu University), Varanasi, Uttar Pradesh 221005 India
| | - Manisha Manisha
- Laboratory of Information Photonics and Optical Metrology, Department of Physics, Indian Institute of Technology (Banaras Hindu University), Varanasi, Uttar Pradesh 221005 India
| | - Christopher Mann
- Department of Applied Physics and Materials Science, Northern Arizona University, Flagstaff, AZ 86011 USA
- Center for Materials Interfaces in Research and Development, Northern Arizona University, Flagstaff, AZ 86011 USA
| | - Marcin J. Marzejon
- Institute of Micromechanics and Photonics, Warsaw University of Technology, 8 Sw. A. Boboli St., 02-525 Warsaw, Poland
| | - Chané Moodley
- School of Physics, University of the Witwatersrand, Johannesburg, South Africa
| | - Junko Morikawa
- World Research Hub Initiative (WRHI), Tokyo Institute of Technology, 2-12-1, Ookayama, Tokyo, 152-8550 Japan
| | - Inbarasan Muniraj
- LiFE Lab, Department of Electronics and Communication Engineering, Alliance School of Applied Engineering, Alliance University, Bangalore, Karnataka 562106 India
| | - Donatas Narbutis
- Institute of Theoretical Physics and Astronomy, Faculty of Physics, Vilnius University, Sauletekio 9, 10222 Vilnius, Lithuania
| | - Soon Hock Ng
- Optical Sciences Center and ARC Training Centre in Surface Engineering for Advanced Materials (SEAM), School of Science, Computing and Engineering Technologies, Optical Sciences Center, Swinburne University of Technology, Hawthorn, Melbourne, VIC 3122 Australia
| | - Fazilah Nothlawala
- School of Physics, University of the Witwatersrand, Johannesburg, South Africa
| | - Jeonghun Oh
- Department of Physics, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141 South Korea
- KAIST Institute for Health Science and Technology, KAIST, Daejeon, 34141 South Korea
| | - Aydogan Ozcan
- Electrical and Computer Engineering Department, Bioengineering Department, California NanoSystems Institute, University of California, Los Angeles (UCLA), Los Angeles, CA USA
| | - YongKeun Park
- Department of Physics, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141 South Korea
- KAIST Institute for Health Science and Technology, KAIST, Daejeon, 34141 South Korea
- Tomocube Inc., Daejeon, 34051 South Korea
| | - Alexey P. Porfirev
- IPSI RAS-Branch of the FSRC “Crystallography and Photonics” RAS, 443001 Samara, Russia
| | - Mariana Potcoava
- Department of Anatomy and Cell Biology, University of Illinois at Chicago, 808 South Wood Street, Chicago, IL 60612 USA
| | - Shashi Prabhakar
- Quantum Science and Technology Laboratory, Physical Research Laboratory, Navrangpura, Ahmedabad, 380009 India
| | - Jixiong Pu
- Fujian Provincial Key Laboratory of Light Propagation and Transformation, College of Information Science and Engineering, Huaqiao University, Xiamen, 361021 Fujian China
| | - Mani Ratnam Rai
- Department of Biomedical Engineering, North Carolina State University and University of North Carolina at Chapel Hill, Raleigh, NC 27695 USA
- Comparative Medicine Institute, North Carolina State University, Raleigh, NC 27695 USA
| | - Mikołaj Rogalski
- Institute of Micromechanics and Photonics, Warsaw University of Technology, 8 Sw. A. Boboli St., 02-525 Warsaw, Poland
| | - Meguya Ryu
- Research Institute for Material and Chemical Measurement, National Metrology Institute of Japan (AIST), 1-1-1 Umezono, Tsukuba, 305-8563 Japan
| | - Sakshi Choudhary
- Department Chemical Engineering, Ben-Gurion University of the Negev, 8410501 Beer-Shiva, Israel
| | - Gangi Reddy Salla
- Department of Physics, SRM University – AP, Amaravati, Andhra Pradesh 522502 India
| | - Peter Schelkens
- Department of Electronics and Informatics (ETRO), Vrije Universiteit Brussel VUB), Pleinlaan 2, 1050 Brussel, Belgium
- IMEC, Kapeldreef 75, 3001 Leuven, Belgium
| | - Sarp Feykun Şener
- Institute of Materials Science and Nanotechnology, National Nanotechnology Research Center (UNAM), Bilkent University, 06800 Ankara, Turkey
- Department of Physics, Bilkent University, 06800 Ankara, Turkey
| | - Igor Shevkunov
- Computational Imaging Group, Faculty of Information Technology and Communication Sciences, Tampere University, 33100 Tampere, Finland
| | - Tomoyoshi Shimobaba
- Graduate School of Engineering, Chiba University, 1-33 Yayoi-cho, Inage-ku, Chiba, Chiba Japan
| | - Rakesh K. Singh
- Laboratory of Information Photonics and Optical Metrology, Department of Physics, Indian Institute of Technology (Banaras Hindu University), Varanasi, Uttar Pradesh 221005 India
| | - Ravindra P. Singh
- Quantum Science and Technology Laboratory, Physical Research Laboratory, Navrangpura, Ahmedabad, 380009 India
| | - Adrian Stern
- School of Electrical and Computer Engineering, Ben-Gurion University of the Negev, 8410501 Beer-Sheva, Israel
| | - Jiasong Sun
- Jiangsu Key Laboratory of Spectral Imaging and Intelligent Sense, Nanjing, 210094 Jiangsu China
- Smart Computational Imaging Laboratory (SCILab), School of Electronic and Optical Engineering, Nanjing University of Science and Technology, Nanjing, 210094 Jiangsu China
- Smart Computational Imaging Research Institute (SCIRI), Nanjing, 210019 Jiangsu China
| | - Shun Zhou
- Jiangsu Key Laboratory of Spectral Imaging and Intelligent Sense, Nanjing, 210094 Jiangsu China
- Smart Computational Imaging Laboratory (SCILab), School of Electronic and Optical Engineering, Nanjing University of Science and Technology, Nanjing, 210094 Jiangsu China
- Smart Computational Imaging Research Institute (SCIRI), Nanjing, 210019 Jiangsu China
| | - Chao Zuo
- Jiangsu Key Laboratory of Spectral Imaging and Intelligent Sense, Nanjing, 210094 Jiangsu China
- Smart Computational Imaging Laboratory (SCILab), School of Electronic and Optical Engineering, Nanjing University of Science and Technology, Nanjing, 210094 Jiangsu China
- Smart Computational Imaging Research Institute (SCIRI), Nanjing, 210019 Jiangsu China
| | - Zack Zurawski
- Department of Anatomy and Cell Biology, University of Illinois at Chicago, 808 South Wood Street, Chicago, IL 60612 USA
| | - Tatsuki Tahara
- Applied Electromagnetic Research Center, Radio Research Institute, National Institute of Information and Communications Technology (NICT), 4-2-1 Nukuikitamachi, Koganei, Tokyo 184-8795 Japan
| | - Vipin Tiwari
- Institute of Physics, University of Tartu, W. Ostwaldi 1, 50411 Tartu, Estonia
| | - Maciej Trusiak
- Institute of Micromechanics and Photonics, Warsaw University of Technology, 8 Sw. A. Boboli St., 02-525 Warsaw, Poland
| | - R. V. Vinu
- Fujian Provincial Key Laboratory of Light Propagation and Transformation, College of Information Science and Engineering, Huaqiao University, Xiamen, 361021 Fujian China
| | - Sergey G. Volotovskiy
- IPSI RAS-Branch of the FSRC “Crystallography and Photonics” RAS, 443001 Samara, Russia
| | - Hasan Yılmaz
- Institute of Materials Science and Nanotechnology, National Nanotechnology Research Center (UNAM), Bilkent University, 06800 Ankara, Turkey
| | - Hilton Barbosa De Aguiar
- Laboratoire Kastler Brossel, Centre National de la Recherche Scientifique (CNRS) UMR 8552, Sorbonne Universite ´, Ecole Normale Supe ´rieure-Paris Sciences et Lettres (PSL) Research University, Collège de France, 24 rue Lhomond, 75005 Paris, France
| | - Balpreet S. Ahluwalia
- Department of Physics and Technology, UiT The Arctic University of Norway, 9037 Tromsø, Norway
| | - Azeem Ahmad
- Department of Physics and Technology, UiT The Arctic University of Norway, 9037 Tromsø, Norway
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5
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Chang TJ, Yang TT. Multiplexed Nanoscopy via Buffer Exchange. ACS NANO 2024; 18:23445-23456. [PMID: 39143924 PMCID: PMC11363122 DOI: 10.1021/acsnano.4c06829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Revised: 08/06/2024] [Accepted: 08/07/2024] [Indexed: 08/16/2024]
Abstract
Understanding cellular functions, particularly in their intricate complexity, can greatly benefit from the spatial mapping of diverse molecules through multitarget single-molecule localization microscopy (SMLM). Existing methodologies, primarily restricting the encoding dimensions to color and lifetime or requiring cyclic staining, often involve broad chromatic detection, specialized optical configurations, or sophisticated labeling techniques. Here, we propose a simple approach called buffer-exchange stochastic optical reconstruction microscopy (beSTORM), which introduces an additional dimension to differentiate between single molecules irrespective of their spectral properties. This method leverages the distinguishable photoblinking responses to distinct buffer conditions, offering a straightforward yet effective means of fluorophore discrimination. Through buffer exchanges, beSTORM achieves multitarget SMLM imaging with minimal crosstalk. Direct integration with expansion microscopy (ExM) demonstrates its capability to resolve up to six proteins at the molecular level within a single emission color without chromatic aberration. Overall, beSTORM presents a highly compatible imaging platform, promising significant advancements in highly multiplexed nanoscopy for exploring multiple targets in biological systems with nanoscale precision.
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Affiliation(s)
- Ting-Jui
Ben Chang
- Department
of Electrical Engineering, National Taiwan
University, Taipei 10617, Taiwan
- Graduate
Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei 10617, Taiwan
- Department
of Physics, National Taiwan University, Taipei 10617, Taiwan
- Nano
Science and Technology Program, Taiwan International Graduate Program, Academia Sinica and National Taiwan University, Taipei 10617, Taiwan
| | - T. Tony Yang
- Department
of Electrical Engineering, National Taiwan
University, Taipei 10617, Taiwan
- Graduate
Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei 10617, Taiwan
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6
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Li X, Wei SH, Chen M, Xu Q, Jing B, Song HZ. Fiber-integrated quantum microscopy system for cells. OPTICS LETTERS 2024; 49:4561-4564. [PMID: 39146103 DOI: 10.1364/ol.527524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Accepted: 07/21/2024] [Indexed: 08/17/2024]
Abstract
Quantum entanglement serves as an essential resource across various fields, including quantum communication, quantum computing, and quantum precision measurement. Quantum microscope, as one of the significant applications in quantum precision measurement, could bring revolutionary advancements in both signal-to-noise ratio (SNR) and spatial resolution of imaging. Here, we present a quantum microscopy system that relies on a fully fiber-integrated high-performance energy-time entangled light source operating within the near-infrared II (NIR-II) window. Complemented by tailored real-time data acquisition and processing software, we successfully demonstrate the quantum imaging of a standard target, achieving a SNR of 131.51 ± 6.74 and a spatial resolution of 4.75 ± 0.27 µm. Furthermore, we showcase quantum imaging of cancer cells, unveiling the potential of quantum entanglement in biomedical applications. Our fiber-integrated quantum microscope, characterized by high imaging SNR, instantaneous image capture, and analysis capabilities, marks an important step toward the practical application in life sciences.
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7
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Lee LCC, Lo KKW. Shining New Light on Biological Systems: Luminescent Transition Metal Complexes for Bioimaging and Biosensing Applications. Chem Rev 2024; 124:8825-9014. [PMID: 39052606 PMCID: PMC11328004 DOI: 10.1021/acs.chemrev.3c00629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/27/2024]
Abstract
Luminescence imaging is a powerful and versatile technique for investigating cell physiology and pathology in living systems, making significant contributions to life science research and clinical diagnosis. In recent years, luminescent transition metal complexes have gained significant attention for diagnostic and therapeutic applications due to their unique photophysical and photochemical properties. In this Review, we provide a comprehensive overview of the recent development of luminescent transition metal complexes for bioimaging and biosensing applications, with a focus on transition metal centers with a d6, d8, and d10 electronic configuration. We elucidate the structure-property relationships of luminescent transition metal complexes, exploring how their structural characteristics can be manipulated to control their biological behavior such as cellular uptake, localization, biocompatibility, pharmacokinetics, and biodistribution. Furthermore, we introduce the various design strategies that leverage the interesting photophysical properties of luminescent transition metal complexes for a wide variety of biological applications, including autofluorescence-free imaging, multimodal imaging, organelle imaging, biological sensing, microenvironment monitoring, bioorthogonal labeling, bacterial imaging, and cell viability assessment. Finally, we provide insights into the challenges and perspectives of luminescent transition metal complexes for bioimaging and biosensing applications, as well as their use in disease diagnosis and treatment evaluation.
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Affiliation(s)
- Lawrence Cho-Cheung Lee
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong, P. R. China
- Laboratory for Synthetic Chemistry and Chemical Biology Limited, Units 1503-1511, 15/F, Building 17W, Hong Kong Science Park, New Territories, Hong Kong, P. R. China
| | - Kenneth Kam-Wing Lo
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong, P. R. China
- State Key Laboratory of Terahertz and Millimeter Waves, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong, P. R. China
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8
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Jin R, Li Y, Xu Y, Cheng L, Jiang D. Stereoscopic Imaging of Single Molecules at Plasma Membrane of Single Cell Using Photoreduction-Assisted Electrochemistry. RESEARCH (WASHINGTON, D.C.) 2024; 7:0443. [PMID: 39140091 PMCID: PMC11319615 DOI: 10.34133/research.0443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2024] [Accepted: 07/14/2024] [Indexed: 08/15/2024]
Abstract
Stereoscopic imaging of single molecules at the plasma membrane of single cell requires spatial resolutions in 3 dimensions (x-y-z) at 10-nm level, which is rarely achieved using most optical super-resolution microscopies. Here, electrochemical stereoscopic microscopy with a detection limit down to a single molecule is achieved using a photoreduction-assisted cycle inside a 20-nm gel electrolyte nanoball at the tip of a nanopipette. On the basis of the electrochemical oxidation of Ru(bpy)3 2+ into Ru(bpy)3 3+ followed by the reduction of Ru(bpy)3 3+ into Ru(bpy)3 2+ by photogenerated isopropanol radicals, a charge of 1.5 fC is obtained from the cycling electron transfers involving one Ru(bpy)3 2+/3+ molecule. By using the nanopipette to scan the cellular membrane modified with Ru(bpy)3 2+-tagged antibody, the morphology of the cell membrane and the distribution of carcinoembryonic antigen (CEA) on the membrane are electrochemically visualized with a spatial resolution of 14 nm. The resultant stereoscopic image reveals more CEA on membrane protrusions, providing direct evidence to support easy access of membrane CEA to intravenous antibodies. The breakthrough in single-molecule electrochemistry at the cellular level leads to the establishment of high-resolution 3-dimensional single-cell electrochemical microscopy, offering an alternative strategy to remedy the imperfection of stereoscopic visualization in optical microscopes.
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Affiliation(s)
- Rong Jin
- State Key Laboratory of Analytical Chemistry for Life Science and School of Chemistry and Chemical Engineering,
Nanjing University, Nanjing, China
| | - Yu Li
- State Key Laboratory of Analytical Chemistry for Life Science and School of Chemistry and Chemical Engineering,
Nanjing University, Nanjing, China
| | - Yanyan Xu
- State Key Laboratory of Analytical Chemistry for Life Science and School of Chemistry and Chemical Engineering,
Nanjing University, Nanjing, China
| | - Lei Cheng
- College of Engineering and Technology,
Southwest University, Chongqing, China
| | - Dechen Jiang
- State Key Laboratory of Analytical Chemistry for Life Science and School of Chemistry and Chemical Engineering,
Nanjing University, Nanjing, China
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9
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Peng CS, Zhang Y, Liu Q, Marti GE, Huang YWA, Südhof TC, Cui B, Chu S. Nanometer-resolution tracking of single cargo reveals dynein motor mechanisms. Nat Chem Biol 2024:10.1038/s41589-024-01694-2. [PMID: 39090313 DOI: 10.1038/s41589-024-01694-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 07/09/2024] [Indexed: 08/04/2024]
Abstract
Cytoplasmic dynein is essential for intracellular transport. Despite extensive in vitro characterizations, how the dynein motors transport vesicles by processive steps in live cells remains unclear. To dissect the molecular mechanisms of dynein, we develop optical probes that enable long-term single-particle tracking in live cells with high spatiotemporal resolution. We find that the number of active dynein motors transporting cargo switches stochastically between one and five dynein motors during long-range transport in neuronal axons. Our very bright optical probes allow the observation of individual molecular steps. Strikingly, these measurements reveal that the dwell times between steps are controlled by two temperature-dependent rate constants in which two ATP molecules are hydrolyzed sequentially during each dynein step. Thus, our observations uncover a previously unknown chemomechanical cycle of dynein-mediated cargo transport in living cells.
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Affiliation(s)
- Chunte Sam Peng
- Department of Physics, Stanford University, Stanford, CA, USA
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA, USA
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Yunxiang Zhang
- Department of Physics, Stanford University, Stanford, CA, USA
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA, USA
- Department of Chemistry and Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Fudan University, Shanghai, China
| | - Qian Liu
- Department of Physics, Stanford University, Stanford, CA, USA
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA, USA
- Department of Chemistry and Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Fudan University, Shanghai, China
| | - G Edward Marti
- Department of Physics, Stanford University, Stanford, CA, USA
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA, USA
| | - Yu-Wen Alvin Huang
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI, USA
| | - Thomas C Südhof
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
| | - Bianxiao Cui
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | - Steven Chu
- Department of Physics, Stanford University, Stanford, CA, USA.
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA, USA.
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10
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Wang LM, Kim J, Han KY. Highly sensitive volumetric single-molecule imaging. NANOPHOTONICS 2024; 13:3805-3814. [PMID: 39224784 PMCID: PMC11366074 DOI: 10.1515/nanoph-2024-0152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Accepted: 07/02/2024] [Indexed: 09/04/2024]
Abstract
Volumetric subcellular imaging has long been essential for studying structures and dynamics in cells and tissues. However, due to limited imaging speed and depth of field, it has been challenging to perform live-cell imaging and single-particle tracking. Here we report a 2.5D fluorescence microscopy combined with highly inclined illumination beams, which significantly reduce not only the image acquisition time but also the out-of-focus background by ∼2-fold compared to epi-illumination. Instead of sequential z-scanning, our method projects a certain depth of volumetric information onto a 2D plane in a single shot using multi-layered glass for incoherent wavefront splitting, enabling high photon detection efficiency. We apply our method to multi-color immunofluorescence imaging and volumetric super-resolution imaging, covering ∼3-4 µm thickness of samples without z-scanning. Additionally, we demonstrate that our approach can substantially extend the observation time of single-particle tracking in living cells.
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Affiliation(s)
- Le-Mei Wang
- CREOL, The College of Optics and Photonics, University of Central Florida, Orlando, FL, USA
| | - Jiah Kim
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Kyu Young Han
- CREOL, The College of Optics and Photonics, University of Central Florida, Orlando, FL, USA
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11
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Ur Rahman H, Khan E, Muhammad M, Khan M, Ahmad Bhat M, Shahzada Khan G, Ali N. Antioxidant and Antibacterial Screening and Hg(II) Sensing, Activities of Cu(II)pyridine-2,6-dicarboxylate Complexes. ChemistryOpen 2024:e202400089. [PMID: 39051714 DOI: 10.1002/open.202400089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 05/18/2024] [Indexed: 07/27/2024] Open
Abstract
In this study five different complexes of Cu(II) were synthesized for the purpose of environmentally notorious mercury sensing and preliminary biological screening. Pyridine-2,6-dicarboxylic acid (also known as dipicolinic acid, and abbreviated as H2DPA), 3-phenyl pyrazole (3-ppz), 4-iodo-1H-pyrazole (4-ipz), 4-nitropyrazole (4-npz), 4-bromopyrazole (4-bpz), and 4-chloropyrazole (4-cpz) were chosen as potential ligands. The synthesized complexes labelled as 1-5, namely [Cu(DPA)(3-ppz)], [Cu(DPA)(4-ipz)], [Cu(DPA)(4-npz)], [Cu(DPA)(4-bpz)], [Cu(DPA)(4-cpz)], were proposed based on spectroscopic data (FTIR, TGA, and UV-visible spectroscopy). These complexes feature C=O functionalities that are not involved in coordination and may be used for further applications. The isolated complexes were utilized for detecting Hg(II) ions in water samples. Various concentrations of Hg(II) ions were prepared for detection purposes, and changes in absorption concerning complexes 1-5 were determined using UV-Visible spectroscopy. It was found that complexes 3 and 4 exhibit efficient sensing abilities towards Hg(II) ions. The antibacterial activities of complexes 1-5 were assessed against S. typhi and E. coli. The complexes 1 and 3 displayed good antibacterial activities against S. typhi (13.67, and 13.56 mm, respectively) while complexes 1, 2 and 4 were found to be efficient against E. coli (11.6, 12.66, 11.31 mm, respectively). The absorption maxima of 2,2-diphenyl-1-picryhydrazyl (DPPH) at 517 nm, considerably shifted upon addition of complexes 1-5. The results reveal that the complexes possess potential free radical scavenging abilities.
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Affiliation(s)
- Hameed Ur Rahman
- Department of Chemistry, University of Malakand, 18800, Chakdara, Dir (Lower), Khyber, Pakhtunkhwa, Pakistan
| | - Ezzat Khan
- Department of Chemistry, University of Malakand, 18800, Chakdara, Dir (Lower), Khyber, Pakhtunkhwa, Pakistan
- Department of Chemistry, College of Science, University of Bahrain, Main Campus, 32038, Sakhir, Kingdom of Bahrain
| | - Mian Muhammad
- Department of Chemistry, University of Malakand, 18800, Chakdara, Dir (Lower), Khyber, Pakhtunkhwa, Pakistan
| | - Maaz Khan
- Department of Chemistry, University of Malakand, 18800, Chakdara, Dir (Lower), Khyber, Pakhtunkhwa, Pakistan
| | - Mashooq Ahmad Bhat
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, 11451, Riyadh, Saudi Arabia
| | - Gul Shahzada Khan
- Department of Chemistry, College of Science, University of Bahrain, Main Campus, 32038, Sakhir, Kingdom of Bahrain
| | - Nisar Ali
- Key Laboratory for Palygorskite Science and Applied Technology of Jiangsu Province, Faculty of Chemical Engineering, National and Local Joint Engineering Research Centre for Deep Utilization Technology of Rock-Salt Resource, Huaiyin Institute of Technology, 223003, Huaian, China
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12
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Chen J, Du Y, Hou H, Li W, Sun C, Liang F, Wang H. Unveiling the Correlation Between the Membrane Assembly of P-gp and Drug Resistance in Multiple Myeloma Using Super-Resolution Fluorescence Imaging. Anal Chem 2024; 96:11673-11681. [PMID: 38994836 DOI: 10.1021/acs.analchem.4c00093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/13/2024]
Abstract
Drug resistance in multiple myeloma (MM) poses a significant challenge to treatment efficacy, primarily attributed to P-glycoprotein (P-gp) dysfunction. This study delves into the elusive spatial organization of P-gp, aiming to enhance our understanding of its role in MM drug resistance by exploring the intricate relationship between molecular function and spatial arrangement. Employing super-resolution imaging of P-gp with the inhibitor probe Tariquidar-TAMR labeling on MM cell membranes, the research uncovered a more pronounced clustering distribution of P-gp in drug-resistant cells (MM1R) compared to drug-sensitive counterparts (MM1S). Further exploration revealed the clustering distribution of P-gp was heightened as cellular drug resistance increased in hypoxic condition, directly emphasizing the strong correlation between P-gp cluster morphology and drug resistance. Additionally, stable P-gp cluster formation was influenced by cross-linking of membrane carbohydrates, and disrupting these glycoprotein clusters could reduce cellular drug resistance, suggesting that altering distribution patterns of P-gp can modulate drug responsiveness. Finally, dexamethasone (Dex) treatment was revealed to enhance P-gp clustering distribution, particularly in MM1S cells, indicating that change degree in P-gp distribution correlate with the modifiable space of cellular drug responsiveness. This study provides insights into the correlation between P-gp assembly and cellular drug responsiveness, deepening our understanding of functional changes in MM drug resistance and offering valuable perspectives for overcoming this challenge.
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Affiliation(s)
- Junling Chen
- School of Chemistry & Chemical Engineering, Wuhan University of Science and Technology, 947 Heping Street, Wuhan, Hubei 430081, China
| | - Yuwei Du
- School of Chemistry & Chemical Engineering, Wuhan University of Science and Technology, 947 Heping Street, Wuhan, Hubei 430081, China
| | - Hao Hou
- School of Chemistry & Chemical Engineering, Wuhan University of Science and Technology, 947 Heping Street, Wuhan, Hubei 430081, China
| | - WenFeng Li
- School of Chemistry & Chemical Engineering, Wuhan University of Science and Technology, 947 Heping Street, Wuhan, Hubei 430081, China
| | - Chunyan Sun
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Dadao, Wuhan 430022, China
| | - Feng Liang
- School of Chemistry & Chemical Engineering, Wuhan University of Science and Technology, 947 Heping Street, Wuhan, Hubei 430081, China
| | - Hongda Wang
- State Key Laboratory of Electroanalytical Chemistry, Research Center of Biomembranomics, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, 5625 Renmin Street, Changchun, Jilin 130022, China
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13
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Ye Z, Harrington B, Pickel AD. Optical super-resolution nanothermometry via stimulated emission depletion imaging of upconverting nanoparticles. SCIENCE ADVANCES 2024; 10:eado6268. [PMID: 39018395 PMCID: PMC466949 DOI: 10.1126/sciadv.ado6268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Accepted: 06/13/2024] [Indexed: 07/19/2024]
Abstract
From engineering improved device performance to unraveling the breakdown of classical heat transfer laws, far-field optical temperature mapping with nanoscale spatial resolution would benefit diverse areas. However, these attributes are traditionally in opposition because conventional far-field optical temperature mapping techniques are inherently diffraction limited. Optical super-resolution imaging techniques revolutionized biological imaging, but such approaches have yet to be applied to thermometry. Here, we demonstrate a super-resolution nanothermometry technique based on highly doped upconverting nanoparticles (UCNPs) that enable stimulated emission depletion (STED) super-resolution imaging. We identify a ratiometric thermometry signal and maintain imaging resolution better than ~120 nm for the relevant spectral bands. We also form self-assembled UCNP monolayers and multilayers and implement a detection scheme with scan times >0.25 μm2/min. We further show that STED nanothermometry reveals a temperature gradient across a joule-heated microstructure that is undetectable with diffraction limited thermometry, indicating the potential of this technique to uncover local temperature variation in wide-ranging practical applications.
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Affiliation(s)
- Ziyang Ye
- Materials Science Program, University of Rochester, Rochester, NY 14627, USA
| | - Benjamin Harrington
- Materials Science Program, University of Rochester, Rochester, NY 14627, USA
| | - Andrea D. Pickel
- Materials Science Program, University of Rochester, Rochester, NY 14627, USA
- Department of Mechanical Engineering, University of Rochester, Rochester, NY 14627, USA
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14
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Zheng Y, Ye Z, Zhang X, Xiao Y. Photo-uncaging Triggers on Self-Blinking to Control Single-Molecule Fluorescence Kinetics for Super-resolution Imaging. ACS NANO 2024; 18:18477-18484. [PMID: 38941491 DOI: 10.1021/acsnano.4c03809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/30/2024]
Abstract
Super-resolution imaging, especially a single-molecule localization approach, has raised a fluorophore engineering revolution chasing sparse single-molecule dark-bright blinking transforms. Yet, it is a challenge to structurally devise fluorophores manipulating the single-molecule blinking kinetics. In this pursuit, we have developed a triggering strategy by innovatively integrating the photoactivatable nitroso-caging strategy into self-blinking sulfonamide to form a nitroso-caged sulfonamide rhodamine (NOSR). Our fluorophore demonstrated controllable self-blinking events upon phototriggered caging unit release. This exceptional blink kinetics improved the super-resolution imaging integrity on microtubules compared to self-blinking analogues. With the aid of paramount single-molecule fluorescence kinetics, we successfully reconstructed the ring structure of nuclear pores and the axial morphology of mitochondrial outer membranes. We foresee that our synthetic approach of photoactivation and self-blinking would facilitate rhodamine devising for super-resolution imaging.
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Affiliation(s)
- Ying Zheng
- State Key Laboratory of Fine Chemicals, Frontiers Science Center for Smart Materials Oriented Chemical Engineering, Dalian University of Technology, Linggong Road 2, Dalian 116024, China
- College of Medical Laboratory, Dalian Medical University, Dalian 116044, China
| | - Zhiwei Ye
- State Key Laboratory of Fine Chemicals, Frontiers Science Center for Smart Materials Oriented Chemical Engineering, Dalian University of Technology, Linggong Road 2, Dalian 116024, China
| | - Xue Zhang
- State Key Laboratory of Fine Chemicals, Frontiers Science Center for Smart Materials Oriented Chemical Engineering, Dalian University of Technology, Linggong Road 2, Dalian 116024, China
| | - Yi Xiao
- State Key Laboratory of Fine Chemicals, Frontiers Science Center for Smart Materials Oriented Chemical Engineering, Dalian University of Technology, Linggong Road 2, Dalian 116024, China
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15
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Liu J, Li Y, Chen T, Zhang F, Xu F. Machine Learning for Single-Molecule Localization Microscopy: From Data Analysis to Quantification. Anal Chem 2024; 96:11103-11114. [PMID: 38946062 DOI: 10.1021/acs.analchem.3c05857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Single-molecule localization microscopy (SMLM) is a versatile tool for realizing nanoscale imaging with visible light and providing unprecedented opportunities to observe bioprocesses. The integration of machine learning with SMLM enhances data analysis by improving efficiency and accuracy. This tutorial aims to provide a comprehensive overview of the data analysis process and theoretical aspects of SMLM, while also highlighting the typical applications of machine learning in this field. By leveraging advanced analytical techniques, SMLM is becoming a powerful quantitative analysis tool for biological research.
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Affiliation(s)
- Jianli Liu
- School of Medical Technology, Beijing Institute of Technology, Beijing 100081, China
| | - Yumian Li
- Advanced Research Institute of Multidisciplinary Science, Beijing Institute of Technology, Beijing 100081, China
- School of Optics and Photonics, Beijing Institute of Technology, Beijing 100081, China
| | - Tailong Chen
- Advanced Research Institute of Multidisciplinary Science, Beijing Institute of Technology, Beijing 100081, China
- School of Optics and Photonics, Beijing Institute of Technology, Beijing 100081, China
| | - Fa Zhang
- School of Medical Technology, Beijing Institute of Technology, Beijing 100081, China
| | - Fan Xu
- Advanced Research Institute of Multidisciplinary Science, Beijing Institute of Technology, Beijing 100081, China
- School of Optics and Photonics, Beijing Institute of Technology, Beijing 100081, China
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16
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Knežević S, Han D, Liu B, Jiang D, Sojic N. Electrochemiluminescence Microscopy. Angew Chem Int Ed Engl 2024; 63:e202407588. [PMID: 38742673 DOI: 10.1002/anie.202407588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Revised: 05/13/2024] [Accepted: 05/13/2024] [Indexed: 05/16/2024]
Abstract
Electrochemiluminescence (ECL) is rapidly evolving from an analytical method into an optical microscopy. The orthogonality of the electrochemical trigger and the optical readout distinguishes it from classic microscopy and electrochemical techniques, owing to its near-zero background, remarkable sensitivity, and absence of photobleaching and phototoxicity. In this minireview, we summarize the recent advances in ECL imaging technology, emphasizing original configurations which enable the imaging of biological entities and the improvement of the analytical properties by increasing the complexity and multiplexing of bioassays. Additionally, mapping the (electro)chemical reactivity in space provides valuable information on nanomaterials and facilitates deciphering ECL mechanisms for improving their performances in diagnostics and (electro)catalysis. Finally, we highlight the recent achievements in imaging at the ultimate limits of single molecules, single photons or single chemical reactions, and the current challenges to translate the ECL imaging advances to other fields such as material science, catalysis and biology.
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Affiliation(s)
- Sara Knežević
- Univ. Bordeaux, CNRS, Bordeaux INP, ISM, UMR 5255, ENSCBP, 33607, Pessac, France
| | - Dongni Han
- State Key Laboratory of Analytical Chemistry for Life Science and School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu, 210023, China
| | - Baohong Liu
- Department of Chemistry, State Key Laboratory of Molecular Engineering of Polymers, Fudan University, Shanghai, 200433, China
| | - Dechen Jiang
- State Key Laboratory of Analytical Chemistry for Life Science and School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu, 210023, China
| | - Neso Sojic
- Univ. Bordeaux, CNRS, Bordeaux INP, ISM, UMR 5255, ENSCBP, 33607, Pessac, France
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17
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Chen S, Wang J, Guan D, Tan B, Zhai T, Yang L, Han Y, Liu Y, Liu Q, Zhang Y. Near-Infrared Spontaneously Blinking Fluorophores for Live Cell Super-Resolution Imaging with Minimized Phototoxicity. Anal Chem 2024; 96:10860-10869. [PMID: 38889184 DOI: 10.1021/acs.analchem.4c02445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/20/2024]
Abstract
Single-molecule localization microscopy (SMLM) requires high-intensity laser irradiation, typically exceeding kW/cm2, to yield a sufficient photon count. However, this intense visible light exposure incurs substantial cellular toxicity, hindering its use in living cells. Here, we developed a class of near-infrared (NIR) spontaneously blinking fluorophores for SMLM. These NIR fluorophores are a combination of rhodamine spirolactams and merocyanine derivatives, where the rhodamine spirolactam component converts between a bright and dark state based on pH-dependent spirocyclization and merocyanine derivatives shift the excitation wavelength into the infrared. Single-molecule characterizations demonstrated their potential for SMLM. At a moderate power density of 3.93 kW/cm2, these probes exhibit duty cycle as low as 0.18% and an emission rate as high as 26,700 photons/s. Phototoxicity assessment under single-molecule imaging conditions reveals that NIR illumination (721 nm) minimizes harm to living cells. Employing these NIR fluorophores, we successfully captured time-lapse super-resolution tracking of mitochondria at a Fourier ring correlation (FRC) resolution of 69.4 nm and reconstructed the ultrastructures of endoplasmic reticulum (ER) in living cells.
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Affiliation(s)
- Song Chen
- Department of Chemistry and Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Fudan University, Shanghai 200438, China
| | - Jing Wang
- Department of Chemistry and Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Fudan University, Shanghai 200438, China
| | - Daoming Guan
- Department of Chemistry and Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Fudan University, Shanghai 200438, China
| | - Baojin Tan
- School of Engineering, China Pharmaceutical University, Nanjing 211198, China
| | - Tianli Zhai
- Department of Chemistry and Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Fudan University, Shanghai 200438, China
| | - Lu Yang
- Department of Chemistry and Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Fudan University, Shanghai 200438, China
| | - Yuheng Han
- School of Engineering, China Pharmaceutical University, Nanjing 211198, China
| | - Yi Liu
- School of Engineering, China Pharmaceutical University, Nanjing 211198, China
| | - Qian Liu
- Department of Chemistry and Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Fudan University, Shanghai 200438, China
| | - Yunxiang Zhang
- Department of Chemistry and Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Fudan University, Shanghai 200438, China
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18
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Liu J, Tan YY, Zheng W, Wang Y, Ju LA, Su QP. Nanoscale insights into hematology: super-resolved imaging on blood cell structure, function, and pathology. J Nanobiotechnology 2024; 22:363. [PMID: 38910248 PMCID: PMC11194919 DOI: 10.1186/s12951-024-02605-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Accepted: 05/30/2024] [Indexed: 06/25/2024] Open
Abstract
Fluorescence nanoscopy, also known as super-resolution microscopy, has transcended the conventional resolution barriers and enabled visualization of biological samples at nanometric resolutions. A series of super-resolution techniques have been developed and applied to investigate the molecular distribution, organization, and interactions in blood cells, as well as the underlying mechanisms of blood-cell-associated diseases. In this review, we provide an overview of various fluorescence nanoscopy technologies, outlining their current development stage and the challenges they are facing in terms of functionality and practicality. We specifically explore how these innovations have propelled forward the analysis of thrombocytes (platelets), erythrocytes (red blood cells) and leukocytes (white blood cells), shedding light on the nanoscale arrangement of subcellular components and molecular interactions. We spotlight novel biomarkers uncovered by fluorescence nanoscopy for disease diagnosis, such as thrombocytopathies, malignancies, and infectious diseases. Furthermore, we discuss the technological hurdles and chart out prospective avenues for future research directions. This review aims to underscore the significant contributions of fluorescence nanoscopy to the field of blood cell analysis and disease diagnosis, poised to revolutionize our approach to exploring, understanding, and managing disease at the molecular level.
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Affiliation(s)
- Jinghan Liu
- School of Biomedical Engineering, University of Technology Sydney, Sydney, NSW, 2007, Australia
| | - Yuping Yolanda Tan
- Charles Perkins Centre, The University of Sydney, Camperdown, NSW, 2006, Australia
- Heart Research Institute, Newtown, NSW, 2042, Australia
| | - Wen Zheng
- School of Biomedical Engineering, University of Technology Sydney, Sydney, NSW, 2007, Australia
| | - Yao Wang
- School of Biomedical Engineering, The University of Sydney, Darlington, NSW, 2008, Australia
| | - Lining Arnold Ju
- School of Biomedical Engineering, The University of Sydney, Darlington, NSW, 2008, Australia
- Charles Perkins Centre, The University of Sydney, Camperdown, NSW, 2006, Australia
- Heart Research Institute, Newtown, NSW, 2042, Australia
| | - Qian Peter Su
- School of Biomedical Engineering, University of Technology Sydney, Sydney, NSW, 2007, Australia.
- Heart Research Institute, Newtown, NSW, 2042, Australia.
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19
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Ohno N, Karube F, Fujiyama F. Volume electron microscopy for genetically and molecularly defined neural circuits. Neurosci Res 2024:S0168-0102(24)00074-9. [PMID: 38914208 DOI: 10.1016/j.neures.2024.06.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2024] [Revised: 06/03/2024] [Accepted: 06/09/2024] [Indexed: 06/26/2024]
Abstract
The brain networks responsible for adaptive behavioral changes are based on the physical connections between neurons. Light and electron microscopy have long been used to study neural projections and the physical connections between neurons. Volume electron microscopy has recently expanded its scale of analysis due to methodological advances, resulting in complete wiring maps of neurites in a large volume of brain tissues and even entire nervous systems in a growing number of species. However, structural approaches frequently suffer from inherent limitations in which elements in images are identified solely by morphological criteria. Recently, an increasing number of tools and technologies have been developed to characterize cells and cellular components in the context of molecules and gene expression. These advancements include newly developed probes for visualization in electron microscopic images as well as correlative integration methods for the same elements across multiple microscopic modalities. Such approaches advance our understanding of interactions between specific neurons and circuits and may help to elucidate novel aspects of the basal ganglia network involving dopamine neurons. These advancements are expected to reveal mechanisms for processing adaptive changes in specific neural circuits that modulate brain functions.
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Affiliation(s)
- Nobuhiko Ohno
- Department of Anatomy, Division of Histology and Cell Biology, Jichi Medical University, Japan; Division of Ultrastructural Research, National Institute for Physiological Sciences, Japan.
| | - Fuyuki Karube
- Laboratory of Histology and Cytology, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, Japan
| | - Fumino Fujiyama
- Laboratory of Histology and Cytology, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, Japan
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20
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Teixeira P, Galland R, Chevrollier A. Super-resolution microscopies, technological breakthrough to decipher mitochondrial structure and dynamic. Semin Cell Dev Biol 2024; 159-160:38-51. [PMID: 38310707 DOI: 10.1016/j.semcdb.2024.01.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 01/08/2024] [Accepted: 01/25/2024] [Indexed: 02/06/2024]
Abstract
Mitochondria are complex organelles with an outer membrane enveloping a second inner membrane that creates a vast matrix space partitioned by pockets or cristae that join the peripheral inner membrane with several thin junctions. Several micrometres long, mitochondria are generally close to 300 nm in diameter, with membrane layers separated by a few tens of nanometres. Ultrastructural data from electron microscopy revealed the structure of these mitochondria, while conventional optical microscopy revealed their extraordinary dynamics through fusion, fission, and migration processes but its limited resolution power restricted the possibility to go further. By overcoming the limits of light diffraction, Super-Resolution Microscopy (SRM) now offers the potential to establish the links between the ultrastructure and remodelling of mitochondrial membranes, leading to major advances in our understanding of mitochondria's structure-function. Here we review the contributions of SRM imaging to our understanding of the relationship between mitochondrial structure and function. What are the hopes for these new imaging approaches which are particularly important for mitochondrial pathologies?
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Affiliation(s)
- Pauline Teixeira
- Univ. Angers, INSERM, CNRS, MITOVASC, Equipe MITOLAB, SFR ICAT, F-49000 Angers, France
| | - Rémi Galland
- Univ. Bordeaux, CNRS, Interdisciplinary Institute for Neuroscience, IINS, UMR 5297, F-33000 Bordeaux, France
| | - Arnaud Chevrollier
- Univ. Angers, INSERM, CNRS, MITOVASC, Equipe MITOLAB, SFR ICAT, F-49000 Angers, France.
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21
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Gao Z, Han K, Hua X, Liu W, Jia S. hydroSIM: super-resolution speckle illumination microscopy with a hydrogel diffuser. BIOMEDICAL OPTICS EXPRESS 2024; 15:3574-3585. [PMID: 38867780 PMCID: PMC11166422 DOI: 10.1364/boe.521521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 03/27/2024] [Accepted: 04/18/2024] [Indexed: 06/14/2024]
Abstract
Super-resolution microscopy has emerged as an indispensable methodology for probing the intricacies of cellular biology. Structured illumination microscopy (SIM), in particular, offers an advantageous balance of spatial and temporal resolution, allowing for visualizing cellular processes with minimal disruption to biological specimens. However, the broader adoption of SIM remains hampered by the complexity of instrumentation and alignment. Here, we introduce speckle-illumination super-resolution microscopy using hydrogel diffusers (hydroSIM). The study utilizes the high scattering and optical transmissive properties of hydrogel materials and realizes a remarkably simplified approach to plug-in super-resolution imaging via a common epi-fluorescence platform. We demonstrate the hydroSIM system using various phantom and biological samples, and the results exhibited effective 3D resolution doubling, optical sectioning, and high contrast. We foresee hydroSIM, a cost-effective, biocompatible, and user-accessible super-resolution methodology, to significantly advance a wide range of biomedical imaging and applications.
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Affiliation(s)
- Zijun Gao
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30332, USA
- Parker H. Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
- School of Materials Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Keyi Han
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30332, USA
| | - Xuanwen Hua
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30332, USA
| | - Wenhao Liu
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30332, USA
| | - Shu Jia
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30332, USA
- Parker H. Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
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22
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Steves MA, He C, Xu K. Single-Molecule Spectroscopy and Super-Resolution Mapping of Physicochemical Parameters in Living Cells. Annu Rev Phys Chem 2024; 75:163-183. [PMID: 38360526 DOI: 10.1146/annurev-physchem-070623-034225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2024]
Abstract
By superlocalizing the positions of millions of single molecules over many camera frames, a class of super-resolution fluorescence microscopy methods known as single-molecule localization microscopy (SMLM) has revolutionized how we understand subcellular structures over the past decade. In this review, we highlight emerging studies that transcend the outstanding structural (shape) information offered by SMLM to extract and map physicochemical parameters in living mammalian cells at single-molecule and super-resolution levels. By encoding/decoding high-dimensional information-such as emission and excitation spectra, motion, polarization, fluorescence lifetime, and beyond-for every molecule, and mass accumulating these measurements for millions of molecules, such multidimensional and multifunctional super-resolution approaches open new windows into intracellular architectures and dynamics, as well as their underlying biophysical rules, far beyond the diffraction limit.
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Affiliation(s)
- Megan A Steves
- Department of Chemistry, University of California, Berkeley, California, USA;
| | - Changdong He
- Department of Chemistry, University of California, Berkeley, California, USA;
| | - Ke Xu
- Department of Chemistry, University of California, Berkeley, California, USA;
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23
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Cha HJ, He C, Glover DJ, Xu K, Clark DS. STORM Super-Resolution Visualization of Self-Assembled γPFD Chaperone Ultrastructures in Methanocaldococcus jannaschii. NANO LETTERS 2024; 24:6078-6083. [PMID: 38723608 PMCID: PMC11117396 DOI: 10.1021/acs.nanolett.4c01043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 05/04/2024] [Accepted: 05/07/2024] [Indexed: 05/23/2024]
Abstract
Gamma-prefoldin (γPFD), a unique chaperone found in the extremely thermophilic methanogen Methanocaldococcus jannaschii, self-assembles into filaments in vitro, which so far have been observed using transmission electron microscopy and cryo-electron microscopy. Utilizing three-dimensional stochastic optical reconstruction microscopy (3D-STORM), here we achieve ∼20 nm resolution by precisely locating individual fluorescent molecules, hence resolving γPFD ultrastructure both in vitro and in vivo. Through CF647 NHS ester labeling, we first demonstrate the accurate visualization of filaments and bundles with purified γPFD. Next, by implementing immunofluorescence labeling after creating a 3xFLAG-tagged γPFD strain, we successfully visualize γPFD in M. jannaschii cells. Through 3D-STORM and two-color STORM imaging with DNA, we show the widespread distribution of filamentous γPFD structures within the cell. These findings provide valuable insights into the structure and localization of γPFD, opening up possibilities for studying intriguing nanoscale components not only in archaea but also in other microorganisms.
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Affiliation(s)
- Hee-Jeong Cha
- Department
of Chemical and Biomolecular Engineering, University of California—Berkeley, Berkeley, California 94720, United States
| | - Changdong He
- Department
of Chemistry, University of California—Berkeley, Berkeley, California 94720, United States
| | - Dominic J. Glover
- School
of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Ke Xu
- Department
of Chemistry, University of California—Berkeley, Berkeley, California 94720, United States
- Molecular
Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, United States
| | - Douglas S. Clark
- Department
of Chemical and Biomolecular Engineering, University of California—Berkeley, Berkeley, California 94720, United States
- Molecular
Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, United States
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24
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Cao X, Li M, Li Q, Fan C, Sun J, Gao Z. Single-molecule localization microscopy at 2.4-fold resolution improvement with optical lattice pattern illumination. OPTICS EXPRESS 2024; 32:20218-20229. [PMID: 38859137 DOI: 10.1364/oe.514937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 03/27/2024] [Indexed: 06/12/2024]
Abstract
Traditional camera-based single-molecule localization microscopy (SMLM), with its high imaging resolution and localization throughput, has made significant advancements in biological and chemical researches. However, due to the limitation of the fluorescence signal-to-noise ratio (SNR) of a single molecule, its resolution is difficult to reach to 5 nm. Optical lattice produces a nondiffracting beam pattern that holds the potential to enhance microscope performance through its high contrast and penetration depth. Here, we propose a new method named LatticeFLUX which utilizes the wide-field optical lattice pattern illumination for individual molecule excitation and localization. We calculated the Cramér-Rao lower bound of LatticeFLUX resolution and proved that our method can improve the single molecule localization precision by 2.4 times compared with the traditional SMLM. We propose a scheme using 9-frame localization, which solves the problem of uneven lattice light illumination. Based on the experimental single-molecule fluorescence SNR, we coded the image reconstruction software to further verify the resolution enhancement capability of LatticeFLUX on simulated punctate DNA origami, line pairs, and cytoskeleton. LatticeFLUX confirms the feasibility of using 2D structured light illumination to obtain high single-molecule localization precision under high localization throughput. It paves the way for further implementation of ultra-high resolution full 3D structured-light-illuminated SMLM.
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25
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Zhang Y, Xu Z, Xiao Y, Jiang H, Zuo X, Li X, Fang X. Structural mechanisms for binding and activation of a contact-quenched fluorophore by RhoBAST. Nat Commun 2024; 15:4206. [PMID: 38760339 PMCID: PMC11101630 DOI: 10.1038/s41467-024-48478-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Accepted: 04/29/2024] [Indexed: 05/19/2024] Open
Abstract
The fluorescent light-up aptamer RhoBAST, which binds and activates the fluorophore-quencher conjugate tetramethylrhodamine-dinitroaniline with high affinity, super high brightness, remarkable photostability, and fast exchange kinetics, exhibits excellent performance in super-resolution RNA imaging. Here we determine the co-crystal structure of RhoBAST in complex with tetramethylrhodamine-dinitroaniline to elucidate the molecular basis for ligand binding and fluorescence activation. The structure exhibits an asymmetric "A"-like architecture for RhoBAST with a semi-open binding pocket harboring the xanthene of tetramethylrhodamine at the tip, while the dinitroaniline quencher stacks over the phenyl of tetramethylrhodamine instead of being fully released. Molecular dynamics simulations show highly heterogeneous conformational ensembles with the contact-but-unstacked fluorophore-quencher conformation for both free and bound tetramethylrhodamine-dinitroaniline being predominant. The simulations also show that, upon RNA binding, the fraction of xanthene-dinitroaniline stacked conformation significantly decreases in free tetramethylrhodamine-dinitroaniline. This highlights the importance of releasing dinitroaniline from xanthene tetramethylrhodamine to unquench the RhoBAST-tetramethylrhodamine-dinitroaniline complex. Using SAXS and ITC, we characterized the magnesium dependency of the folding and binding mode of RhoBAST in solution and indicated its strong structural robustness. The structures and binding modes of relevant fluorescent light-up aptamers are compared, providing mechanistic insights for rational design and optimization of this important fluorescent light-up aptamer-ligand system.
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Affiliation(s)
- Yufan Zhang
- Key Laboratory of RNA Science and Engineering, Institute of Biophysics Chinese Academy of Sciences, Beijing, China
| | - Zhonghe Xu
- Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, China
| | - Yu Xiao
- Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, China
| | - Haodong Jiang
- Institute of Zoology, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China
| | - Xiaobing Zuo
- X-ray Science Division, Argonne National Laboratory, Lemont, IL, USA
| | - Xing Li
- Institute of Zoology, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China.
| | - Xianyang Fang
- Key Laboratory of RNA Science and Engineering, Institute of Biophysics Chinese Academy of Sciences, Beijing, China.
- Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, China.
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26
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An K, Qiao Q, Zhou W, Jiang W, Li J, Xu Z. Stable Super-Resolution Imaging of Cell Membrane Nanoscale Subcompartment Dynamics with a Buffering Cyanine Dye. Anal Chem 2024; 96:5985-5991. [PMID: 38557031 DOI: 10.1021/acs.analchem.4c00342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Super-resolution fluorescence imaging is a crucial method for visualizing the dynamics of the cell membrane involved in various physiological and pathological processes. This requires bright fluorescent dyes with excellent photostability and labeling stability to enable long-term imaging. In this context, we introduce a buffering-strategy-based cyanine dye, SA-Cy5, designed to identify and label carbonic anhydrase IX (CA IX) located in the cell membrane. The unique feature of SA-Cy5 lies in its ability to overcome photobleaching. When the dye on the cell membrane undergoes photobleaching, it is rapidly replaced by an intact probe from the buffer pool outside the cell membrane. This dynamic replacement ensures that the fluorescence intensity on the cell membrane remains stable over time. Under the super-resolution structured illumination microscopy (SIM), the cell membrane can be continuously imaged for 60 min with a time resolution of 20 s. This extended imaging period allows for the observation of substructural dynamics of the cell membrane, including the growth and fusion of filamentous pseudopodia and the fusion of vesicles. Additionally, this buffering strategy introduces a novel approach to address the issue of poor photostability associated with the cyanine dyes.
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Affiliation(s)
- Kai An
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qinglong Qiao
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China
| | - Wei Zhou
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China
| | - Wenchao Jiang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jin Li
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China
| | - Zhaochao Xu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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27
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Bashir S, Aiman A, Chaudhary AA, Khan N, Ahanger IA, Sami N, Almugri EA, Ali MA, Khan SUD, Shahid M, Basir SF, Hassan MI, Islam A. Probing protein aggregation through spectroscopic insights and multimodal approaches: A comprehensive review for counteracting neurodegenerative disorders. Heliyon 2024; 10:e27949. [PMID: 38689955 PMCID: PMC11059433 DOI: 10.1016/j.heliyon.2024.e27949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 03/01/2024] [Accepted: 03/08/2024] [Indexed: 05/02/2024] Open
Abstract
Aberrant accumulation of protein misfolding can cause aggregation and fibrillation and is one of the primary characteristic features of neurodegenerative diseases. Because they are disordered, misfolded, and aggregated proteins pose a significant setback in drug designing. The structural study of intermediate steps in these kinds of aggregated proteins will allow us to determine the conformational changes as well as the probable pathways encompassing various neurodegenerative disorders. The analysis of protein aggregates involved in neurodegenerative diseases relies on a diverse toolkit of biophysical techniques, encompassing both morphological and non-morphological methods. Additionally, Thioflavin T (ThT) assays and Circular Dichroism (CD) spectroscopy facilitate investigations into aggregation kinetics and secondary structure alterations. The collective application of these biophysical techniques empowers researchers to comprehensively unravel the intricate nature of protein aggregates associated with neurodegeneration. Furthermore, the topics covered in this review have summed up a handful of well-established techniques used for the structural analysis of protein aggregation. This multifaceted approach advances our fundamental understanding of the underlying mechanisms driving neurodegenerative diseases and informs potential therapeutic strategies.
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Affiliation(s)
- Sania Bashir
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India
| | - Ayesha Aiman
- Department of Biosciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India
| | - Anis Ahmad Chaudhary
- Department of Biology, College of Science, Imam Mohammad Ibn Saud Islamic University, Riyadh, Saudi Arabia
| | - Nashrah Khan
- Department of Biosciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India
| | - Ishfaq Ahmad Ahanger
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India
| | - Neha Sami
- Department of Biosciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India
| | - Eman Abdullah Almugri
- Department of Biology, College of Science, Imam Mohammad Ibn Saud Islamic University, Riyadh, Saudi Arabia
| | - Mohamed A.M. Ali
- Department of Biology, College of Science, Imam Mohammad Ibn Saud Islamic University, Riyadh, Saudi Arabia
- Department of Biochemistry, Faculty of Science, Ain Shams University, Abbassia, 11566, Cairo, Egypt
| | - Salah-Ud-Din Khan
- Department of Biochemistry, College of Medicine, Imam Mohammad Ibn Saud Islamic Universi-ty (IMSIU), Riyadh, 11623, Saudi Arabia
| | - Mohammad Shahid
- Department of Basic Medical Sciences, College of Medicine, Prince Sattam Bin Abdulaziz University, AlKharj, 11942, Saudi Arabia
| | - Seemi Farhat Basir
- Department of Biosciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India
| | - Md Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India
| | - Asimul Islam
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India
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28
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Lizana L, Schwartz YB. The scales, mechanisms, and dynamics of the genome architecture. SCIENCE ADVANCES 2024; 10:eadm8167. [PMID: 38598632 PMCID: PMC11006219 DOI: 10.1126/sciadv.adm8167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 03/06/2024] [Indexed: 04/12/2024]
Abstract
Even when split into several chromosomes, DNA molecules that make up our genome are too long to fit into the cell nuclei unless massively folded. Such folding must accommodate the need for timely access to selected parts of the genome by transcription factors, RNA polymerases, and DNA replication machinery. Here, we review our current understanding of the genome folding inside the interphase nuclei. We consider the resulting genome architecture at three scales with a particular focus on the intermediate (meso) scale and summarize the insights gained from recent experimental observations and diverse computational models.
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Affiliation(s)
- Ludvig Lizana
- Integrated Science Lab, Department of Physics, Umeå University, Umeå, Sweden
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29
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F Shida J, Ma K, Toll HW, Salinas O, Ma X, Peng CS. Multicolor Long-Term Single-Particle Tracking Using 10 nm Upconverting Nanoparticles. NANO LETTERS 2024; 24:4194-4201. [PMID: 38497588 DOI: 10.1021/acs.nanolett.4c00207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Single-particle tracking (SPT) is a powerful technique to unveil molecular behaviors crucial to the understanding of many biological processes, but it is limited by factors such as probe photostability and spectral orthogonality. To overcome these limitations, we develop upconverting nanoparticles (UCNPs), which are photostable over several hours at the single-particle level, enabling long-term multicolor SPT. We investigate the brightness of core-shell UCNPs as a function of inert shell thickness to minimize particle size while maintaining sufficient signal for SPT. We explore different rare-earth dopants to optimize for the brightest probes and find that UCNPs doped with 2% Tm3+/30% Yb3+, 10% Er3+/90% Yb3+, and 15% Tm3+/85% Yb3+ represent the optimal probes for blue, green, and near-infrared emission, respectively. The multiplexed 10 nm probes enable three-color single-particle tracking on live HeLa cells for tens of minutes using a single, near-infrared excitation source. These photostable and multiplexed probes open new avenues for numerous biological applications.
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Affiliation(s)
- João F Shida
- Department of Chemistry, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts 02139, United States
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02139, United States
| | - Kaibo Ma
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02139, United States
| | - Harrison W Toll
- Department of Chemistry, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts 02139, United States
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02139, United States
| | - Omar Salinas
- Department of Chemistry, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts 02139, United States
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02139, United States
| | - Xiaojie Ma
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02139, United States
| | - Chunte Sam Peng
- Department of Chemistry, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts 02139, United States
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02139, United States
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30
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Li M. Harnessing atomic force microscopy-based single-cell analysis to advance physical oncology. Microsc Res Tech 2024; 87:631-659. [PMID: 38053519 DOI: 10.1002/jemt.24467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 11/21/2023] [Accepted: 11/23/2023] [Indexed: 12/07/2023]
Abstract
Single-cell analysis is an emerging and promising frontier in the field of life sciences, which is expected to facilitate the exploration of fundamental laws of physiological and pathological processes. Single-cell analysis allows experimental access to cell-to-cell heterogeneity to reveal the distinctive behaviors of individual cells, offering novel opportunities to dissect the complexity of severe human diseases such as cancers. Among the single-cell analysis tools, atomic force microscopy (AFM) is a powerful and versatile one which is able to nondestructively image the fine topographies and quantitatively measure multiple mechanical properties of single living cancer cells in their native states under aqueous conditions with unprecedented spatiotemporal resolution. Over the past few decades, AFM has been widely utilized to detect the structural and mechanical behaviors of individual cancer cells during the process of tumor formation, invasion, and metastasis, yielding numerous unique insights into tumor pathogenesis from the biomechanical perspective and contributing much to the field of cancer mechanobiology. Here, the achievements of AFM-based analysis of single cancer cells to advance physical oncology are comprehensively summarized, and challenges and future perspectives are also discussed. RESEARCH HIGHLIGHTS: Achievements of AFM in characterizing the structural and mechanical behaviors of single cancer cells are summarized, and future directions are discussed. AFM is not only capable of visualizing cellular fine structures, but can also measure multiple cellular mechanical properties as well as cell-generated mechanical forces. There is still plenty of room for harnessing AFM-based single-cell analysis to advance physical oncology.
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Affiliation(s)
- Mi Li
- State Key Laboratory of Robotics, Shenyang Institute of Automation, Chinese Academy of Sciences, Shenyang, China
- Institutes for Robotics and Intelligent Manufacturing, Chinese Academy of Sciences, Shenyang, China
- University of Chinese Academy of Sciences, Beijing, China
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31
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Wu ZH, Zhu X, Yang Q, Zagranyarski Y, Mishra K, Strickfaden H, Wong RP, Basché T, Koynov K, Bonn M, Li C, Liu X, Müllen K. Near-Infrared Perylenecarboximide Fluorophores for Live-Cell Super-Resolution Imaging. J Am Chem Soc 2024; 146:7135-7139. [PMID: 38441879 PMCID: PMC10958508 DOI: 10.1021/jacs.3c13368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 02/28/2024] [Accepted: 02/29/2024] [Indexed: 03/08/2024]
Abstract
Organic near-infrared (NIR) photoblinking fluorophores are highly desirable for live-cell super-resolution imaging based on single-molecule localization microscopy (SMLM). Herein we introduce a novel small chromophore, PMIP, through the fusion of perylenecarboximide with 2,2-dimetheylpyrimidine. PMIP exhibits an emission maximum at 732 nm with a high fluorescence quantum yield of 60% in the wavelength range of 700-1000 nm and excellent photoblinking without any additives. With resorcinol-functionalized PMIP (PMIP-OH), NIR SMLM imaging of lysosomes is demonstrated for the first time in living mammalian cells under physiological conditions. Moreover, metabolically labeled nascent DNA is site-specifically detected using azido-functionalized PMIP (PMIP-N3) via click chemistry, thereby enabling the super-resolution imaging of nascent DNA in phosphate-buffered saline with a 9-fold improvement in spatial resolution. These results indicate the potential of PMIP-based NIR blinking fluorophores for biological applications of SMLM.
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Affiliation(s)
- Ze-Hua Wu
- Max
Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
- Department
of Chemistry, Johannes Gutenberg-University, 55099 Mainz, Germany
| | - Xingfu Zhu
- Max
Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Qiqi Yang
- Max
Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Yulian Zagranyarski
- Max
Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Krishna Mishra
- Department
of Chemistry, Johannes Gutenberg-University, 55099 Mainz, Germany
| | | | - Ronald P. Wong
- Institute
of Molecular Biology (IMB), Ackermannweg 4, 55128 Mainz, Germany
| | - Thomas Basché
- Department
of Chemistry, Johannes Gutenberg-University, 55099 Mainz, Germany
| | - Kaloian Koynov
- Max
Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Mischa Bonn
- Max
Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Chen Li
- Max
Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Xiaomin Liu
- Max
Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Klaus Müllen
- Max
Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
- Department
of Chemistry, Johannes Gutenberg-University, 55099 Mainz, Germany
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32
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Zhang Y, He Z, Tong X, Garrett DC, Cao R, Wang LV. Quantum imaging of biological organisms through spatial and polarization entanglement. SCIENCE ADVANCES 2024; 10:eadk1495. [PMID: 38457506 PMCID: PMC10923495 DOI: 10.1126/sciadv.adk1495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 02/06/2024] [Indexed: 03/10/2024]
Abstract
Quantum imaging holds potential benefits over classical imaging but has faced challenges such as poor signal-to-noise ratios, low resolvable pixel counts, difficulty in imaging biological organisms, and inability to quantify full birefringence properties. Here, we introduce quantum imaging by coincidence from entanglement (ICE), using spatially and polarization-entangled photon pairs to overcome these challenges. With spatial entanglement, ICE offers higher signal-to-noise ratios, greater resolvable pixel counts, and the ability to image biological organisms. With polarization entanglement, ICE provides quantitative quantum birefringence imaging capability, where both the phase retardation and the principal refractive index axis angle of an object can be remotely and instantly quantified without changing the polarization states of the photons incident on the object. Furthermore, ICE enables 25 times greater suppression of stray light than classical imaging. ICE has the potential to pave the way for quantum imaging in diverse fields, such as life sciences and remote sensing.
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Affiliation(s)
| | | | | | - David C. Garrett
- Caltech Optical Imaging Laboratory, Andrew and Peggy Cherng Department of Medical Engineering, Department of Electrical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Rui Cao
- Caltech Optical Imaging Laboratory, Andrew and Peggy Cherng Department of Medical Engineering, Department of Electrical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Lihong V. Wang
- Caltech Optical Imaging Laboratory, Andrew and Peggy Cherng Department of Medical Engineering, Department of Electrical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
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33
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Xu D, Gu Y, Lu J, Xu L, Wang W, Dong B. Deep-learning-assisted spectroscopic single-molecule localization microscopy based on spectrum-to-spectrum denoising. NANOSCALE 2024. [PMID: 38407360 DOI: 10.1039/d3nr05870k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Spectroscopic single-molecule localization microscopy (sSMLM) simultaneously captures spatial localizations and spectral signatures, providing the ability of multiplexed and functional subcellular imaging applications. However, extracting accurate spectral information in sSMLM remains challenging due to the poor signal-to-noise ratio (SNR) of spectral images set by a limited photon budget from single-molecule fluorescence emission and inherent electronic noise during the image acquisition using digital cameras. Here, we report a novel spectrum-to-spectrum (Spec2Spec) framework, a self-supervised deep-learning network that can significantly suppress the noise and accurately recover low SNR emission spectra from a single-molecule localization event. A training strategy of Spec2Spec was designed for sSMLM data by exploiting correlated spectral information in spatially adjacent pixels, which contain independent noise. By validating the qualitative and quantitative performance of Spec2Spec on simulated and experimental sSMLM data, we demonstrated that Spec2Spec can improve the SNR and the structure similarity index measure (SSIM) of single-molecule spectra by about 6-fold and 3-fold, respectively, further facilitating 94.6% spectral classification accuracy and nearly 100% data utilization ratio in dual-color sSMLM imaging.
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Affiliation(s)
- Dandan Xu
- Academy for Engineering and Technology, Yiwu Research Institute, Fudan University, Shanghai 200433, China.
| | - Yuanjie Gu
- Academy for Engineering and Technology, Yiwu Research Institute, Fudan University, Shanghai 200433, China.
| | - Jun Lu
- Academy for Engineering and Technology, Yiwu Research Institute, Fudan University, Shanghai 200433, China.
| | - Lei Xu
- Academy for Engineering and Technology, Yiwu Research Institute, Fudan University, Shanghai 200433, China.
| | - Wei Wang
- Changchun Institute of Optics, Fine Mechanics and Physics, Chinese Academy of Sciences, Changchun 130033, China
| | - Biqin Dong
- Academy for Engineering and Technology, Yiwu Research Institute, Fudan University, Shanghai 200433, China.
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34
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Kozma E, Kele P. Bioorthogonal Reactions in Bioimaging. Top Curr Chem (Cham) 2024; 382:7. [PMID: 38400853 PMCID: PMC10894152 DOI: 10.1007/s41061-024-00452-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 01/22/2024] [Indexed: 02/26/2024]
Abstract
Visualization of biomolecules in their native environment or imaging-aided understanding of more complex biomolecular processes are one of the focus areas of chemical biology research, which requires selective, often site-specific labeling of targets. This challenging task is effectively addressed by bioorthogonal chemistry tools in combination with advanced synthetic biology methods. Today, the smart combination of the elements of the bioorthogonal toolbox allows selective installation of multiple markers to selected targets, enabling multicolor or multimodal imaging of biomolecules. Furthermore, recent developments in bioorthogonally applicable probe design that meet the growing demands of superresolution microscopy enable more complex questions to be addressed. These novel, advanced probes enable highly sensitive, low-background, single- or multiphoton imaging of biological species and events in live organisms at resolutions comparable to the size of the biomolecule of interest. Herein, the latest developments in bioorthogonal fluorescent probe design and labeling schemes will be discussed in the context of in cellulo/in vivo (multicolor and/or superresolved) imaging schemes. The second part focuses on the importance of genetically engineered minimal bioorthogonal tags, with a particular interest in site-specific protein tagging applications to answer biological questions.
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Affiliation(s)
- Eszter Kozma
- Chemical Biology Research Group, Institute of Organic Chemistry, HUN-REN Research Centre for Natural Sciences, Magyar Tudósok Krt. 2, Budapest, 1117, Hungary
| | - Péter Kele
- Chemical Biology Research Group, Institute of Organic Chemistry, HUN-REN Research Centre for Natural Sciences, Magyar Tudósok Krt. 2, Budapest, 1117, Hungary.
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35
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Matsuzaki T, Kawamura R, Yamamoto A, Takahashi H, Fujii M, Togo S, Yoneyama Y, Hakuno F, Takahashi SI, Suganuma M, Nakabayashi S, Sharma S, Gimzewski JK, Yoshikawa HY. Advanced Interferometry with 3-D Structured Illumination Reveals the Surface Fine Structure of Complex Biospecimens. J Phys Chem Lett 2024; 15:1097-1104. [PMID: 38262433 DOI: 10.1021/acs.jpclett.3c02767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2024]
Abstract
Interference reflection microscopy (IRM) is a powerful, label-free technique to visualize the surface structure of biospecimens. However, stray light outside a focal plane obscures the surface fine structures beyond the diffraction limit (dxy ≈ 200 nm). Here, we developed an advanced interferometry approach to visualize the surface fine structure of complex biospecimens, ranging from protein assemblies to single cells. Compared to 2-D, our unique 3-D structure illumination introduced to IRM enabled successful visualization of fine structures and the dynamics of protein crystal growth under lateral (dx-y ≈ 110 nm) and axial (dx-z ≤ 5 nm) resolutions and dynamical adhesion of microtubule fiber networks with lateral resolution (dx-y ≈ 120 nm), 10 times greater than unstructured IRM (dx-y ≈ 1000 nm). Simultaneous reflection/fluorescence imaging provides new physical fingerprints for studying complex biospecimens and biological processes such as myogenic differentiation and highlights the potential use of advanced interferometry to study key nanostructures of complex biospecimens.
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Affiliation(s)
- Takahisa Matsuzaki
- Department of Applied Physics, Graduate School of Engineering, Osaka University, 2-1, Yamadaoka, Suita 565-0871, Japan
- Center for Future Innovation, Graduate School of Engineering, Osaka University, 2-1, Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Ryuzo Kawamura
- Department of Chemistry, Saitama University, 255 Shimo-Okubo, Sakura-Ku, Saitama 338-8570, Japan
| | - Akihisa Yamamoto
- Center for Integrative Medicine and Physics, Institute for Advanced Study, Kyoto University, Kyoto 606-8501, Japan
| | - Hozumi Takahashi
- Department of Applied Physics, Graduate School of Engineering, Osaka University, 2-1, Yamadaoka, Suita 565-0871, Japan
| | - Mai Fujii
- Department of Chemistry, Saitama University, 255 Shimo-Okubo, Sakura-Ku, Saitama 338-8570, Japan
| | - Shodai Togo
- Department of Chemistry, Saitama University, 255 Shimo-Okubo, Sakura-Ku, Saitama 338-8570, Japan
| | - Yosuke Yoneyama
- Institute of Research, Tokyo Medical and Dental University (TMDU), 1-5-45 Yushima, bunkyo-Ku, Tokyo 113-8510, Japan
| | - Fumihiko Hakuno
- Institute of Research, Tokyo Medical and Dental University (TMDU), 1-5-45 Yushima, bunkyo-Ku, Tokyo 113-8510, Japan
| | - Shin-Ichiro Takahashi
- Departments of Animal Sciences and Applied Biological Chemistry, Graduate School of Agriculture and Life Sciences, The University of Tokyo, Bunkyo-Ku, Tokyo 113-8657, Japan
| | - Masami Suganuma
- Division of Strategic Research and Development, Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-Ku, Saitama 338-8570, Japan
| | - Seiichiro Nakabayashi
- Division of Strategic Research and Development, Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-Ku, Saitama 338-8570, Japan
| | - Shivani Sharma
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, California 90095, United States
- Pathology & Laboratory Medicine, David Geffen School of Medicine, Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - James K Gimzewski
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, California 90095, United States
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095-1569, United States
- WPI Center for Materials Nanoarchitectonics (MANA), National Institute for Materials Science (NIMS), Tsukuba 305-0044, Japan
| | - Hiroshi Y Yoshikawa
- Department of Applied Physics, Graduate School of Engineering, Osaka University, 2-1, Yamadaoka, Suita 565-0871, Japan
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36
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Farkas D, Szikora S, Jijumon AS, Polgár TF, Patai R, Tóth MÁ, Bugyi B, Gajdos T, Bíró P, Novák T, Erdélyi M, Mihály J. Peripheral thickening of the sarcomeres and pointed end elongation of the thin filaments are both promoted by SALS and its formin interaction partners. PLoS Genet 2024; 20:e1011117. [PMID: 38198522 PMCID: PMC10805286 DOI: 10.1371/journal.pgen.1011117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Revised: 01/23/2024] [Accepted: 12/27/2023] [Indexed: 01/12/2024] Open
Abstract
During striated muscle development the first periodically repeated units appear in the premyofibrils, consisting of immature sarcomeres that must undergo a substantial growth both in length and width, to reach their final size. Here we report that, beyond its well established role in sarcomere elongation, the Sarcomere length short (SALS) protein is involved in Z-disc formation and peripheral growth of the sarcomeres. Our protein localization data and loss-of-function studies in the Drosophila indirect flight muscle strongly suggest that radial growth of the sarcomeres is initiated at the Z-disc. As to thin filament elongation, we used a powerful nanoscopy approach to reveal that SALS is subject to a major conformational change during sarcomere development, which might be critical to stop pointed end elongation in the adult muscles. In addition, we demonstrate that the roles of SALS in sarcomere elongation and radial growth are both dependent on formin type of actin assembly factors. Unexpectedly, when SALS is present in excess amounts, it promotes the formation of actin aggregates highly resembling the ones described in nemaline myopathy patients. Collectively, these findings helped to shed light on the complex mechanisms of SALS during the coordinated elongation and thickening of the sarcomeres, and resulted in the discovery of a potential nemaline myopathy model, suitable for the identification of genetic and small molecule inhibitors.
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Affiliation(s)
- Dávid Farkas
- Institute of Genetics, Biological Research Centre, Szeged, Hungary
| | - Szilárd Szikora
- Institute of Genetics, Biological Research Centre, Szeged, Hungary
| | - A S Jijumon
- Institute of Genetics, Biological Research Centre, Szeged, Hungary
| | - Tamás F Polgár
- Institute of Biophysics, Biological Research Centre, Szeged, Hungary
- Doctoral School of Theoretical Medicine, University of Szeged, Szeged, Hungary
| | - Roland Patai
- Institute of Biophysics, Biological Research Centre, Szeged, Hungary
| | - Mónika Ágnes Tóth
- University of Pécs, Medical School, Department of Biophysics, Pécs, Hungary
| | - Beáta Bugyi
- University of Pécs, Medical School, Department of Biophysics, Pécs, Hungary
| | - Tamás Gajdos
- Department of Optics and Quantum Electronics, University of Szeged, Szeged, Hungary
| | - Péter Bíró
- Department of Optics and Quantum Electronics, University of Szeged, Szeged, Hungary
| | - Tibor Novák
- Department of Optics and Quantum Electronics, University of Szeged, Szeged, Hungary
| | - Miklós Erdélyi
- Department of Optics and Quantum Electronics, University of Szeged, Szeged, Hungary
| | - József Mihály
- Institute of Genetics, Biological Research Centre, Szeged, Hungary
- University of Szeged, Department of Genetics, Szeged, Hungary
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37
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Sun N, Jia Y, Bai S, Yang Y, Dai L, Li J. Spatial mapping and quantitative evaluation of protein corona on PEGylated mesoporous silica particles by super-resolution fluorescence microscopy. J Colloid Interface Sci 2024; 653:351-358. [PMID: 37717435 DOI: 10.1016/j.jcis.2023.09.067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 09/01/2023] [Accepted: 09/10/2023] [Indexed: 09/19/2023]
Abstract
Nanoparticles (NPs) adsorb serum proteins when exposed to biological fluids, forming a dynamic protein corona that has a profound impact on their overall biological profile and fate. Polyethylene glycol (PEG) modification is the most widely used strategy to mitigate and inhibit protein corona formation. Nevertheless, the accurate mapping and quantification of PEG inhibition effects on protein corona formation have scarcely been reported. Herein, we demonstrate the direct observation and quantification of protein corona adsorbed onto PEGylated mesoporous silica particles by direct stochastic optical reconstruction microscopy (dSTORM). The variation tendency of protein penetration depth in terms of PEG molecular weights and incubated time is investigated for the first time. The maximum penetration depths present slight increase with the prolonged incubation time, while they tend to remarkably decrease with increased chain length of modified PEG. Moreover, the co-localization of preformed protein corona with lysosomes and the destination of adsorbed protein are demonstrated. Our method provides important technical characterization information and in-depth understanding of protein corona adsorbed onto PEGylated mesoporous silica particles. This shines new light on the behaviors of silica materials in cells and may promote their practical applications in biomedicine.
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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
| | - 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, China
| | - Yang Yang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology, 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, China.
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38
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Shrestha P, Yang D, Ward A, Shih WM, Wong WP. Mapping Single-Molecule Protein Complexes in 3D with DNA Nanoswitch Calipers. J Am Chem Soc 2023; 145:27916-27921. [PMID: 38096567 PMCID: PMC10755700 DOI: 10.1021/jacs.3c10262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 12/11/2023] [Accepted: 12/12/2023] [Indexed: 12/26/2023]
Abstract
The ability to accurately map the 3D geometry of single-molecule complexes in trace samples is a challenging goal that would lead to new insights into molecular mechanics and provide an approach for single-molecule structural proteomics. To enable this, we have developed a high-resolution force spectroscopy method capable of measuring multiple distances between labeled sites in natively folded protein complexes. Our approach combines reconfigurable nanoscale devices, we call DNA nanoswitch calipers, with a force-based barcoding system to distinguish each measurement location. We demonstrate our approach by reconstructing the tetrahedral geometry of biotin-binding sites in natively folded streptavidin, with 1.5-2.5 Å agreement with previously reported structures.
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Affiliation(s)
- Prakash Shrestha
- Program
in Cellular and Molecular Medicine, Boston
Children’s Hospital, Boston, Massachusetts 02115, United States
- Wyss
Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02215, United States
- Department
of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Darren Yang
- Program
in Cellular and Molecular Medicine, Boston
Children’s Hospital, Boston, Massachusetts 02115, United States
- Wyss
Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02215, United States
- Department
of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Andrew Ward
- Program
in Cellular and Molecular Medicine, Boston
Children’s Hospital, Boston, Massachusetts 02115, United States
- Wyss
Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02215, United States
| | - William M. Shih
- Wyss
Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02215, United States
- Department
of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
- Department
of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Wesley P. Wong
- Program
in Cellular and Molecular Medicine, Boston
Children’s Hospital, Boston, Massachusetts 02115, United States
- Wyss
Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02215, United States
- Department
of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts 02115, United States
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39
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Ci Y, Han K, Kong J, Huang S, Yang Y, Qin C, Shi L. Flavivirus Concentrates Host ER in Main Replication Compartments to Facilitate Replication. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2305093. [PMID: 37888856 PMCID: PMC10754076 DOI: 10.1002/advs.202305093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Indexed: 10/28/2023]
Abstract
Flavivirus remodels the host endoplasmic reticulum (ER) to generate replication compartments (RCs) as the fundamental structures to accommodate viral replication. Here, a centralized replication mode of flavivirus is reported, i.e., flavivirus concentrates host ER in perinuclear main replication compartments (MRCs) for efficient replication. Superresolution live-cell imaging demonstrated that flavivirus MRCs formed via a series of events, including multisite ER clustering, growth and merging of ER clusters, directional movement, and convergence in the perinuclear region. The dynamic activities of viral RCs are driven by nonstructural (NS) proteins and are independent of microtubules and actin. Moreover, disrupting MRCs formation by small molecule compounds inhibited flavivirus replication. Overall, the findings reveal unprecedented insight into dynamic ER reorganization by flavivirus and identify a new inhibition strategy.
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Affiliation(s)
- Yali Ci
- State Key Laboratory of Common Mechanism Research for Major DiseasesInstitute of Basic Medical SciencesChinese Academy of Medical Sciences and School of Basic MedicinePeking Union Medical CollegeBeijing100005China
- Department of Biochemistry and Molecular BiologyInstitute of Basic Medical SciencesChinese Academy of Medical Sciences and School of Basic MedicinePeking Union Medical CollegeBeijing100005China
| | - Kai Han
- State Key Laboratory of Common Mechanism Research for Major DiseasesInstitute of Basic Medical SciencesChinese Academy of Medical Sciences and School of Basic MedicinePeking Union Medical CollegeBeijing100005China
- Department of Biochemistry and Molecular BiologyInstitute of Basic Medical SciencesChinese Academy of Medical Sciences and School of Basic MedicinePeking Union Medical CollegeBeijing100005China
| | - Jie Kong
- State Key Laboratory of Common Mechanism Research for Major DiseasesInstitute of Basic Medical SciencesChinese Academy of Medical Sciences and School of Basic MedicinePeking Union Medical CollegeBeijing100005China
| | - Shuhan Huang
- State Key Laboratory of Common Mechanism Research for Major DiseasesInstitute of Basic Medical SciencesChinese Academy of Medical Sciences and School of Basic MedicinePeking Union Medical CollegeBeijing100005China
- Department of Biochemistry and Molecular BiologyInstitute of Basic Medical SciencesChinese Academy of Medical Sciences and School of Basic MedicinePeking Union Medical CollegeBeijing100005China
| | - Yang Yang
- State Key Laboratory of Common Mechanism Research for Major DiseasesInstitute of Basic Medical SciencesChinese Academy of Medical Sciences and School of Basic MedicinePeking Union Medical CollegeBeijing100005China
- Department of Biochemistry and Molecular BiologyInstitute of Basic Medical SciencesChinese Academy of Medical Sciences and School of Basic MedicinePeking Union Medical CollegeBeijing100005China
| | - Cheng‐Feng Qin
- State Key Laboratory of Pathogen and BiosecurityBeijing Institute of Microbiology and EpidemiologyBeijing100071China
| | - Lei Shi
- State Key Laboratory of Common Mechanism Research for Major DiseasesInstitute of Basic Medical SciencesChinese Academy of Medical Sciences and School of Basic MedicinePeking Union Medical CollegeBeijing100005China
- Department of Biochemistry and Molecular BiologyInstitute of Basic Medical SciencesChinese Academy of Medical Sciences and School of Basic MedicinePeking Union Medical CollegeBeijing100005China
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40
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Astratov VN, Sahel YB, Eldar YC, Huang L, Ozcan A, Zheludev N, Zhao J, Burns Z, Liu Z, Narimanov E, Goswami N, Popescu G, Pfitzner E, Kukura P, Hsiao YT, Hsieh CL, Abbey B, Diaspro A, LeGratiet A, Bianchini P, Shaked NT, Simon B, Verrier N, Debailleul M, Haeberlé O, Wang S, Liu M, Bai Y, Cheng JX, Kariman BS, Fujita K, Sinvani M, Zalevsky Z, Li X, Huang GJ, Chu SW, Tzang O, Hershkovitz D, Cheshnovsky O, Huttunen MJ, Stanciu SG, Smolyaninova VN, Smolyaninov II, Leonhardt U, Sahebdivan S, Wang Z, Luk’yanchuk B, Wu L, Maslov AV, Jin B, Simovski CR, Perrin S, Montgomery P, Lecler S. Roadmap on Label-Free Super-Resolution Imaging. LASER & PHOTONICS REVIEWS 2023; 17:2200029. [PMID: 38883699 PMCID: PMC11178318 DOI: 10.1002/lpor.202200029] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Indexed: 06/18/2024]
Abstract
Label-free super-resolution (LFSR) imaging relies on light-scattering processes in nanoscale objects without a need for fluorescent (FL) staining required in super-resolved FL microscopy. The objectives of this Roadmap are to present a comprehensive vision of the developments, the state-of-the-art in this field, and to discuss the resolution boundaries and hurdles which need to be overcome to break the classical diffraction limit of the LFSR imaging. The scope of this Roadmap spans from the advanced interference detection techniques, where the diffraction-limited lateral resolution is combined with unsurpassed axial and temporal resolution, to techniques with true lateral super-resolution capability which are based on understanding resolution as an information science problem, on using novel structured illumination, near-field scanning, and nonlinear optics approaches, and on designing superlenses based on nanoplasmonics, metamaterials, transformation optics, and microsphere-assisted approaches. To this end, this Roadmap brings under the same umbrella researchers from the physics and biomedical optics communities in which such studies have often been developing separately. The ultimate intent of this paper is to create a vision for the current and future developments of LFSR imaging based on its physical mechanisms and to create a great opening for the series of articles in this field.
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Affiliation(s)
- Vasily N. Astratov
- Department of Physics and Optical Science, University of North Carolina at Charlotte, Charlotte, North Carolina 28223-0001, USA
| | - Yair Ben Sahel
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Yonina C. Eldar
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Luzhe Huang
- Electrical and Computer Engineering Department, University of California, Los Angeles, California 90095, USA
- Bioengineering Department, University of California, Los Angeles, California 90095, USA
- California Nano Systems Institute (CNSI), University of California, Los Angeles, California 90095, USA
| | - Aydogan Ozcan
- Electrical and Computer Engineering Department, University of California, Los Angeles, California 90095, USA
- Bioengineering Department, University of California, Los Angeles, California 90095, USA
- California Nano Systems Institute (CNSI), University of California, Los Angeles, California 90095, USA
- David Geffen School of Medicine, University of California, Los Angeles, California 90095, USA
| | - Nikolay Zheludev
- Optoelectronics Research Centre, University of Southampton, Southampton, SO17 1BJ, UK
- Centre for Disruptive Photonic Technologies, The Photonics Institute, School of Physical and Mathematical Sciences, Nanyang Technological University, 637371, Singapore
| | - Junxiang Zhao
- Department of Electrical and Computer Engineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA
| | - Zachary Burns
- Department of Electrical and Computer Engineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA
| | - Zhaowei Liu
- Department of Electrical and Computer Engineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA
- Material Science and Engineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA
| | - Evgenii Narimanov
- School of Electrical Engineering, and Birck Nanotechnology Center, Purdue University, West Lafayette, Indiana 47907, USA
| | - Neha Goswami
- Quantitative Light Imaging Laboratory, Beckman Institute of Advanced Science and Technology, University of Illinois at Urbana-Champaign, Illinois 61801, USA
| | - Gabriel Popescu
- Quantitative Light Imaging Laboratory, Beckman Institute of Advanced Science and Technology, University of Illinois at Urbana-Champaign, Illinois 61801, USA
| | - Emanuel Pfitzner
- Department of Chemistry, University of Oxford, Oxford OX1 3QZ, United Kingdom
| | - Philipp Kukura
- Department of Chemistry, University of Oxford, Oxford OX1 3QZ, United Kingdom
| | - Yi-Teng Hsiao
- Institute of Atomic and Molecular Sciences (IAMS), Academia Sinica 1, Roosevelt Rd. Sec. 4, Taipei 10617 Taiwan
| | - Chia-Lung Hsieh
- Institute of Atomic and Molecular Sciences (IAMS), Academia Sinica 1, Roosevelt Rd. Sec. 4, Taipei 10617 Taiwan
| | - Brian Abbey
- Australian Research Council Centre of Excellence for Advanced Molecular Imaging, La Trobe University, Melbourne, Victoria, Australia
- Department of Chemistry and Physics, La Trobe Institute for Molecular Science (LIMS), La Trobe University, Melbourne, Victoria, Australia
| | - Alberto Diaspro
- Optical Nanoscopy and NIC@IIT, CHT, Istituto Italiano di Tecnologia, Via Enrico Melen 83B, 16152 Genoa, Italy
- DIFILAB, Department of Physics, University of Genoa, Via Dodecaneso 33, 16146 Genoa, Italy
| | - Aymeric LeGratiet
- Optical Nanoscopy and NIC@IIT, CHT, Istituto Italiano di Tecnologia, Via Enrico Melen 83B, 16152 Genoa, Italy
- Université de Rennes, CNRS, Institut FOTON - UMR 6082, F-22305 Lannion, France
| | - Paolo Bianchini
- Optical Nanoscopy and NIC@IIT, CHT, Istituto Italiano di Tecnologia, Via Enrico Melen 83B, 16152 Genoa, Italy
- DIFILAB, Department of Physics, University of Genoa, Via Dodecaneso 33, 16146 Genoa, Italy
| | - Natan T. Shaked
- Tel Aviv University, Faculty of Engineering, Department of Biomedical Engineering, Tel Aviv 6997801, Israel
| | - Bertrand Simon
- LP2N, Institut d’Optique Graduate School, CNRS UMR 5298, Université de Bordeaux, Talence France
| | - Nicolas Verrier
- IRIMAS UR UHA 7499, Université de Haute-Alsace, Mulhouse, France
| | | | - Olivier Haeberlé
- IRIMAS UR UHA 7499, Université de Haute-Alsace, Mulhouse, France
| | - Sheng Wang
- School of Physics and Technology, Wuhan University, China
- Wuhan Institute of Quantum Technology, China
| | - Mengkun Liu
- Department of Physics and Astronomy, Stony Brook University, USA
- National Synchrotron Light Source II, Brookhaven National Laboratory, USA
| | - Yeran Bai
- Boston University Photonics Center, Boston, MA 02215, USA
| | - Ji-Xin Cheng
- Boston University Photonics Center, Boston, MA 02215, USA
| | - Behjat S. Kariman
- Optical Nanoscopy and NIC@IIT, CHT, Istituto Italiano di Tecnologia, Via Enrico Melen 83B, 16152 Genoa, Italy
- DIFILAB, Department of Physics, University of Genoa, Via Dodecaneso 33, 16146 Genoa, Italy
| | - Katsumasa Fujita
- Department of Applied Physics and the Advanced Photonics and Biosensing Open Innovation Laboratory (AIST); and the Transdimensional Life Imaging Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Osaka, Japan
| | - Moshe Sinvani
- Faculty of Engineering and the Nano-Technology Center, Bar-Ilan University, Ramat Gan, 52900 Israel
| | - Zeev Zalevsky
- Faculty of Engineering and the Nano-Technology Center, Bar-Ilan University, Ramat Gan, 52900 Israel
| | - Xiangping Li
- Guangdong Provincial Key Laboratory of Optical Fiber Sensing and Communications, Institute of Photonics Technology, Jinan University, Guangzhou 510632, China
| | - Guan-Jie Huang
- Department of Physics and Molecular Imaging Center, National Taiwan University, Taipei 10617, Taiwan
- Brain Research Center, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Shi-Wei Chu
- Department of Physics and Molecular Imaging Center, National Taiwan University, Taipei 10617, Taiwan
- Brain Research Center, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Omer Tzang
- School of Chemistry, The Sackler faculty of Exact Sciences, and the Center for Light matter Interactions, and the Tel Aviv University Center for Nanoscience and Nanotechnology, Tel Aviv 69978, Israel
| | - Dror Hershkovitz
- School of Chemistry, The Sackler faculty of Exact Sciences, and the Center for Light matter Interactions, and the Tel Aviv University Center for Nanoscience and Nanotechnology, Tel Aviv 69978, Israel
| | - Ori Cheshnovsky
- School of Chemistry, The Sackler faculty of Exact Sciences, and the Center for Light matter Interactions, and the Tel Aviv University Center for Nanoscience and Nanotechnology, Tel Aviv 69978, Israel
| | - Mikko J. Huttunen
- Laboratory of Photonics, Physics Unit, Tampere University, FI-33014, Tampere, Finland
| | - Stefan G. Stanciu
- Center for Microscopy – Microanalysis and Information Processing, Politehnica University of Bucharest, 313 Splaiul Independentei, 060042, Bucharest, Romania
| | - Vera N. Smolyaninova
- Department of Physics Astronomy and Geosciences, Towson University, 8000 York Rd., Towson, MD 21252, USA
| | - Igor I. Smolyaninov
- Department of Electrical and Computer Engineering, University of Maryland, College Park, MD 20742, USA
| | - Ulf Leonhardt
- Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Sahar Sahebdivan
- EMTensor GmbH, TechGate, Donau-City-Strasse 1, 1220 Wien, Austria
| | - Zengbo Wang
- School of Computer Science and Electronic Engineering, Bangor University, Bangor, LL57 1UT, United Kingdom
| | - Boris Luk’yanchuk
- Faculty of Physics, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Limin Wu
- Department of Materials Science and State Key Laboratory of Molecular Engineering of Polymers, Fudan University, Shanghai 200433, China
| | - Alexey V. Maslov
- Department of Radiophysics, University of Nizhny Novgorod, Nizhny Novgorod, 603022, Russia
| | - Boya Jin
- Department of Physics and Optical Science, University of North Carolina at Charlotte, Charlotte, North Carolina 28223-0001, USA
| | - Constantin R. Simovski
- Department of Electronics and Nano-Engineering, Aalto University, FI-00076, Espoo, Finland
- Faculty of Physics and Engineering, ITMO University, 199034, St-Petersburg, Russia
| | - Stephane Perrin
- ICube Research Institute, University of Strasbourg - CNRS - INSA de Strasbourg, 300 Bd. Sébastien Brant, 67412 Illkirch, France
| | - Paul Montgomery
- ICube Research Institute, University of Strasbourg - CNRS - INSA de Strasbourg, 300 Bd. Sébastien Brant, 67412 Illkirch, France
| | - Sylvain Lecler
- ICube Research Institute, University of Strasbourg - CNRS - INSA de Strasbourg, 300 Bd. Sébastien Brant, 67412 Illkirch, France
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41
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Wu X, Barner-Kowollik C. Fluorescence-readout as a powerful macromolecular characterisation tool. Chem Sci 2023; 14:12815-12849. [PMID: 38023522 PMCID: PMC10664555 DOI: 10.1039/d3sc04052f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 10/10/2023] [Indexed: 12/01/2023] Open
Abstract
The last few decades have witnessed significant progress in synthetic macromolecular chemistry, which can provide access to diverse macromolecules with varying structural complexities, topology and functionalities, bringing us closer to the aim of controlling soft matter material properties with molecular precision. To reach this goal, the development of advanced analytical techniques, allowing for micro-, molecular level and real-time investigation, is essential. Due to their appealing features, including high sensitivity, large contrast, fast and real-time response, as well as non-invasive characteristics, fluorescence-based techniques have emerged as a powerful tool for macromolecular characterisation to provide detailed information and give new and deep insights beyond those offered by commonly applied analytical methods. Herein, we critically examine how fluorescence phenomena, principles and techniques can be effectively exploited to characterise macromolecules and soft matter materials and to further unravel their constitution, by highlighting representative examples of recent advances across major areas of polymer and materials science, ranging from polymer molecular weight and conversion, architecture, conformation to polymer self-assembly to surfaces, gels and 3D printing. Finally, we discuss the opportunities for fluorescence-readout to further advance the development of macromolecules, leading to the design of polymers and soft matter materials with pre-determined and adaptable properties.
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Affiliation(s)
- Xingyu Wu
- School of Chemistry and Physics, Centre for Materials Science, Queensland University of Technology (QUT) 2 George Street Brisbane QLD 4000 Australia
| | - Christopher Barner-Kowollik
- School of Chemistry and Physics, Centre for Materials Science, Queensland University of Technology (QUT) 2 George Street Brisbane QLD 4000 Australia
- Institute of Nanotechnology (INT), Karlsruhe Institute of Technology (KIT) Hermann-von-Helmholtz-Platz 1 76344 Eggenstein-Leopoldshafen Germany
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42
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Xu L, Kan S, Yu X, Liu Y, Fu Y, Peng Y, Liang Y, Cen Y, Zhu C, Jiang W. Deep learning enables stochastic optical reconstruction microscopy-like superresolution image reconstruction from conventional microscopy. iScience 2023; 26:108145. [PMID: 37867953 PMCID: PMC10587619 DOI: 10.1016/j.isci.2023.108145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 08/05/2023] [Accepted: 10/02/2023] [Indexed: 10/24/2023] Open
Abstract
Despite its remarkable potential for transforming low-resolution images, deep learning faces significant challenges in achieving high-quality superresolution microscopy imaging from wide-field (conventional) microscopy. Here, we present X-Microscopy, a computational tool comprising two deep learning subnets, UR-Net-8 and X-Net, which enables STORM-like superresolution microscopy image reconstruction from wide-field images with input-size flexibility. X-Microscopy was trained using samples of various subcellular structures, including cytoskeletal filaments, dot-like, beehive-like, and nanocluster-like structures, to generate prediction models capable of producing images of comparable quality to STORM-like images. In addition to enabling multicolour superresolution image reconstructions, X-Microscopy also facilitates superresolution image reconstruction from different conventional microscopic systems. The capabilities of X-Microscopy offer promising prospects for making superresolution microscopy accessible to a broader range of users, going beyond the confines of well-equipped laboratories.
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Affiliation(s)
- Lei Xu
- Department of Etiology and Carcinogenesis and State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
- Key Laboratory of Molecular and Cellular Systems Biology, College of Life Sciences, Tianjin Normal University, Tianjin 300387, China
| | - Shichao Kan
- School of Computer Science and Engineering, Central South University, Changsha, Hunan 410083, China
| | - Xiying Yu
- Department of Etiology and Carcinogenesis and State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Ye Liu
- HAMD (Ningbo) Intelligent Medical Technology Co., Ltd, Ningbo 315194, China
| | - Yuxia Fu
- Department of Etiology and Carcinogenesis and State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Yiqiang Peng
- HAMD (Ningbo) Intelligent Medical Technology Co., Ltd, Ningbo 315194, China
| | - Yanhui Liang
- HAMD (Ningbo) Intelligent Medical Technology Co., Ltd, Ningbo 315194, China
| | - Yigang Cen
- Institute of Information Science, Beijing Jiaotong University, Beijing 100044, China
| | - Changjun Zhu
- Key Laboratory of Molecular and Cellular Systems Biology, College of Life Sciences, Tianjin Normal University, Tianjin 300387, China
| | - Wei Jiang
- Department of Etiology and Carcinogenesis and State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
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43
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Duan X, Zhang M, Zhang YH. Organic fluorescent probes for live-cell super-resolution imaging. FRONTIERS OF OPTOELECTRONICS 2023; 16:34. [PMID: 37946039 PMCID: PMC10635970 DOI: 10.1007/s12200-023-00090-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Accepted: 10/25/2023] [Indexed: 11/12/2023]
Abstract
The development of super-resolution technology has made it possible to investigate the ultrastructure of intracellular organelles by fluorescence microscopy, which has greatly facilitated the development of life sciences and biomedicine. To realize super-resolution imaging of living cells, both advanced imaging systems and excellent fluorescent probes are required. Traditional fluorescent probes have good availability, but that is not the case for probes for live-cell super-resolution imaging. In this review, we first introduce the principles of various super-resolution technologies and their probe requirements, then summarize the existing designs and delivery strategies of super-resolution probes for live-cell imaging, and finally provide a brief conclusion and overview of the future.
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Affiliation(s)
- Xinxin Duan
- Britton Chance Center for Biomedical Photonics, MoE Key Laboratory for Biomedical Photonics, Advanced Biomedical Imaging Facility-Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Meng Zhang
- Britton Chance Center for Biomedical Photonics, MoE Key Laboratory for Biomedical Photonics, Advanced Biomedical Imaging Facility-Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Yu-Hui Zhang
- Britton Chance Center for Biomedical Photonics, MoE Key Laboratory for Biomedical Photonics, Advanced Biomedical Imaging Facility-Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, 430074, China.
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44
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He C, Wu CY, Li W, Xu K. Multidimensional Super-Resolution Microscopy Unveils Nanoscale Surface Aggregates in the Aging of FUS Condensates. J Am Chem Soc 2023; 145:24240-24248. [PMID: 37782826 PMCID: PMC10691933 DOI: 10.1021/jacs.3c08674] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
The intracellular liquid-liquid phase separation (LLPS) of biomolecules gives rise to condensates that act as membrane-less organelles with vital functions. FUS, an RNA-binding protein, natively forms condensates through LLPS and further provides a model system for the often disease-linked liquid-to-solid transition of biomolecular condensates during aging. However, the mechanism of such maturation processes, as well as the structural and physical properties of the system, remains unclear, partly attributable to difficulties in resolving the internal structures of the micrometer-sized condensates with diffraction-limited optical microscopy. Harnessing a set of multidimensional super-resolution microscopy tools that uniquely map out local physicochemical parameters through single-molecule spectroscopy, here, we uncover nanoscale heterogeneities in FUS condensates and elucidate their evolution over aging. Through spectrally resolved single-molecule localization microscopy (SR-SMLM) with a solvatochromic dye, we unveil distinct hydrophobic nanodomains at the condensate surface. Through SMLM with a fluorogenic amyloid probe, we identify these nanodomains as amyloid aggregates. Through single-molecule displacement/diffusivity mapping (SMdM), we show that such nanoaggregates drastically impede local diffusion. Notably, upon aging or mechanical shears, these nanoaggregates progressively expand on the condensate surface, thus leading to a growing low-diffusivity shell while leaving the condensate interior diffusion-permitting. Together, beyond uncovering fascinating structural arrangements and aging mechanisms in the single-component FUS condensates, the demonstrated synergy of multidimensional super-resolution approaches in this study opens new paths for understanding LLPS systems at the nanoscale.
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Affiliation(s)
- Changdong He
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Chun Ying Wu
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Wan Li
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Ke Xu
- Department of Chemistry, University of California, Berkeley, California 94720, United States
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45
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Jeong S, Kim J, Koh D, Lee JC. Simultaneously enhancing the resolution and signal-to-background ratio in STED optical nanoscopy via differential depletion. OPTICS EXPRESS 2023; 31:37549-37563. [PMID: 38017882 DOI: 10.1364/oe.505430] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 10/08/2023] [Indexed: 11/30/2023]
Abstract
STED (stimulated emission depletion) far-field optical nanoscopy achieves resolution beyond the diffraction limit by depleting fluorescence at the periphery of excitation with a donut-shaped depletion laser. What is traded off with the superior resolution of STED nanoscopy is the unwanted elevation of structured background noise which hampers the quality of STED images. Here, we alleviate the background noise problem by adopting the differential stimulated emission depletion (diffSTED) approach. In diffSTED nanoscopy, signals obtained with different depletion strengths are compared and properly subtracted to remove two major background noise sources in STED nanoscopy. We show via simulations that by using diffSTED nanoscopy, background noise is significantly decreased, and the image contrast is improved. In addition, we show by simulation and analytical calculation that diffSTED improves resolution simultaneously. We assess the effect of different parameters, such as the STED beam intensity, depletion intensity ratio of two STED beams, and the subtraction factor, on the signal-to-background ratio (SBR) and the resolution of diffSTED nanoscopy. We introduce a logical algorithm to determine the optimal subtraction factor and the depletion intensity ratio. DiffSTED nanoscopy is a versatile technique that can be readily applied to any STED system without requiring any hardware modifications. We predict the wide applicability of diffSTED for its enhanced resolution, improved SBR, and easiness of implementation.
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46
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Tanaka H, Funahashi J, Hirano T. Live-cell imaging of endocytosed synaptophysin around individual hippocampal presynaptic active zones. Front Cell Neurosci 2023; 17:1277729. [PMID: 37927445 PMCID: PMC10620501 DOI: 10.3389/fncel.2023.1277729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 10/06/2023] [Indexed: 11/07/2023] Open
Abstract
In presynaptic terminals 4 types of endocytosis, kiss-and-run, clathrin-mediated, bulk and ultrafast endocytosis have been reported to maintain repetitive exocytosis of neurotransmitter. However, detailed characteristics and relative contribution of each type of endocytosis still need to be determined. Our previous live-cell imaging study demonstrated individual exocytosis events of synaptic vesicle within an active-zone-like membrane (AZLM) formed on glass using synaptophysin tagged with a pH-sensitive fluorescent protein. On the other hand, individual endocytosis events of postsynaptic receptors were recorded with a rapid extracellular pH exchange method. Combining these methods, here we live-cell imaged endocytosed synaptophysin with total internal reflection fluorescence microscopy in rat hippocampal culture preparations. Clathrin-dependent and -independent endocytosis, which was seemingly bulk endocytosis, occurred within several seconds after electrical stimulation at multiple locations around AZLM at room temperature, with the locations varying trial to trial. The contribution of clathrin-independent endocytosis was more prominent when the number of stimulation pulses was large. The skewness of synaptophysin distribution in intracellular vesicles became smaller after addition of a clathrin inhibitor, which suggests that clathrin-dependent endocytosis concentrates synaptophysin. Ultrafast endocytosis was evident immediately after stimulation only at near physiological temperature and was the predominant endocytosis when the number of stimulation pulses was small.
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Affiliation(s)
- Hiromitsu Tanaka
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto, Japan
- Department of Developmental Biology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Junichiro Funahashi
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Tomoo Hirano
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto, Japan
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47
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Fazel M, Grussmayer KS, Ferdman B, Radenovic A, Shechtman Y, Enderlein J, Pressé S. Fluorescence Microscopy: a statistics-optics perspective. ARXIV 2023:arXiv:2304.01456v3. [PMID: 37064525 PMCID: PMC10104198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
Fundamental properties of light unavoidably impose features on images collected using fluorescence microscopes. Modeling these features is ever more important in quantitatively interpreting microscopy images collected at scales on par or smaller than light's wavelength. Here we review the optics responsible for generating fluorescent images, fluorophore properties, microscopy modalities leveraging properties of both light and fluorophores, in addition to the necessarily probabilistic modeling tools imposed by the stochastic nature of light and measurement.
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Affiliation(s)
- Mohamadreza Fazel
- Department of Physics, Arizona State University, Tempe, Arizona, USA
- Center for Biological Physics, Arizona State University, Tempe, Arizona, USA
| | - Kristin S Grussmayer
- Department of Bionanoscience, Faculty of Applied Science and Kavli Institute for Nanoscience, Delft University of Technology, Delft, Netherlands
| | - Boris Ferdman
- Russel Berrie Nanotechnology Institute and Department of Biomedical Engineering, Technion - Israel Institute of Technology, Haifa, Israel
| | - Aleksandra Radenovic
- Laboratory of Nanoscale Biology, Institute of Bioengineering, Ecole Polytechnique Federale de Lausanne (EPFL), Lausanne, Switzerland
| | - Yoav Shechtman
- Russel Berrie Nanotechnology Institute and Department of Biomedical Engineering, Technion - Israel Institute of Technology, Haifa, Israel
| | - Jörg Enderlein
- III. Institute of Physics - Biophysics, Georg August University, Göttingen, Germany
| | - Steve Pressé
- Department of Physics, Arizona State University, Tempe, Arizona, USA
- Center for Biological Physics, Arizona State University, Tempe, Arizona, USA
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48
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Samanta S, Lai K, Wu F, Liu Y, Cai S, Yang X, Qu J, Yang Z. Xanthene, cyanine, oxazine and BODIPY: the four pillars of the fluorophore empire for super-resolution bioimaging. Chem Soc Rev 2023; 52:7197-7261. [PMID: 37743716 DOI: 10.1039/d2cs00905f] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
In the realm of biological research, the invention of super-resolution microscopy (SRM) has enabled the visualization of ultrafine sub-cellular structures and their functions in live cells at the nano-scale level, beyond the diffraction limit, which has opened up a new window for advanced biomedical studies to unravel the complex unknown details of physiological disorders at the sub-cellular level with unprecedented resolution and clarity. However, most of the SRM techniques are highly reliant on the personalized special photophysical features of the fluorophores. In recent times, there has been an unprecedented surge in the development of robust new fluorophore systems with personalized features for various super-resolution imaging techniques. To date, xanthene, cyanine, oxazine and BODIPY cores have been authoritatively utilized as the basic fluorophore units in most of the small-molecule-based organic fluorescent probe designing strategies for SRM owing to their excellent photophysical characteristics and easy synthetic acquiescence. Since the future of next-generation SRM studies will be decided by the availability of advanced fluorescent probes and these four fluorescent building blocks will play an important role in progressive new fluorophore design, there is an urgent need to review the recent advancements in designing fluorophores for different SRM methods based on these fluorescent dye cores. This review article not only includes a comprehensive discussion about the recent developments in designing fluorescent probes for various SRM techniques based on these four important fluorophore building blocks with special emphasis on their effective integration into live cell super-resolution bio-imaging applications but also critically evaluates the background of each of the fluorescent dye cores to highlight their merits and demerits towards developing newer fluorescent probes for SRM.
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Affiliation(s)
- Soham Samanta
- Center for Biomedical Optics and Photonics & Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China.
| | - Kaitao Lai
- Center for Biomedical Optics and Photonics & Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China.
| | - Feihu Wu
- Center for Biomedical Optics and Photonics & Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China.
| | - Yingchao Liu
- Center for Biomedical Optics and Photonics & Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China.
| | - Songtao Cai
- Center for Biomedical Optics and Photonics & Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China.
| | - Xusan Yang
- Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China
| | - Junle Qu
- Center for Biomedical Optics and Photonics & Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China.
| | - Zhigang Yang
- Center for Biomedical Optics and Photonics & Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China.
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49
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Aktalay A, Khan TA, Bossi ML, Belov VN, Hell SW. Photoactivatable Carbo- and Silicon-Rhodamines and Their Application in MINFLUX Nanoscopy. Angew Chem Int Ed Engl 2023; 62:e202302781. [PMID: 37555720 DOI: 10.1002/anie.202302781] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 08/05/2023] [Accepted: 08/08/2023] [Indexed: 08/10/2023]
Abstract
New photoactivatable fluorescent dyes (rhodamine, carbo- and silicon-rhodamines [SiR]) with emission ranging from green to far red have been prepared, and their photophysical properties studied. The photocleavable 2-nitrobenzyloxycarbonyl unit with an alpha-carboxyl group as a branching point and additional functionality was attached to a polycyclic and lipophilic fluorescent dye. The photoactivatable probes having the HaloTagTM amine (O2) ligand bound with a dye core were obtained and applied for live-cell staining in stable cell lines incorporating Vimentin (VIM) or Nuclear Pore Complex Protein NUP96 fused with the HaloTag. The probes were applied in 2D (VIM, NUP96) and 3D (VIM) MINFLUX nanoscopy, as well as in superresolution fluorescence microscopy with single fluorophore activation (VIM, live-cell labeling). Images of VIM and NUPs labeled with different dyes were acquired and their apparent dimensions and shapes assessed on a lower single-digit nanometer scale. Applicability and performance of the photoactivatable dye derivatives were evaluated in terms of photoactivation rate, labeling and detection efficiency, number of detected photons per molecule and other parameters related to MINFLUX nanoscopy.
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Affiliation(s)
- Ayse Aktalay
- Department of Optical Nanoscopy, Max Planck Institute for Medical Research (MPI-MR), Jahnstraße 29, 69120, Heidelberg, Germany
| | - Taukeer A Khan
- Department of NanoBiophotonics, Max Planck Institute for Multidisciplinary Sciences (MPI-NAT), Am Fassberg 11, 37077, Göttingen, Germany
| | - Mariano L Bossi
- Department of Optical Nanoscopy, Max Planck Institute for Medical Research (MPI-MR), Jahnstraße 29, 69120, Heidelberg, Germany
| | - Vladimir N Belov
- Department of NanoBiophotonics, Max Planck Institute for Multidisciplinary Sciences (MPI-NAT), Am Fassberg 11, 37077, Göttingen, Germany
| | - Stefan W Hell
- Department of Optical Nanoscopy, Max Planck Institute for Medical Research (MPI-MR), Jahnstraße 29, 69120, Heidelberg, Germany
- Department of NanoBiophotonics, Max Planck Institute for Multidisciplinary Sciences (MPI-NAT), Am Fassberg 11, 37077, Göttingen, Germany
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50
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Han Y, Tu S, Gong W, Tao W, Tang M, Wei Y, Kuang C, Liu X, Zhang YH, Hao X. Three-dimensional multi-color optical nanoscopy at sub-10-nm resolution based on small-molecule organic probes. CELL REPORTS METHODS 2023; 3:100556. [PMID: 37751692 PMCID: PMC10545905 DOI: 10.1016/j.crmeth.2023.100556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 06/07/2023] [Accepted: 07/18/2023] [Indexed: 09/28/2023]
Abstract
Achieving nanometer-scale resolution remains challenging in expansion microscopy due to photon loss. To address this concern, here we develop a multi-color expansion stimulated emission depletion technique based on small-molecule probes to realize high labeling density and intensity. Our method substantially lowers the barrier to visualizing diverse intracellular proteins and their interactions in three dimensions. It enables us to achieve sub-10-nm resolution in structures such as microfilaments, lysosomes, and mitochondria, providing new insights into cell biology.
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Affiliation(s)
- Yubing Han
- College of Optical Science and Engineering, Zhejiang University, Hangzhou, Zhejiang 310027, China; Britton Chance Center for Biomedical Photonics-MoE Key Laboratory for Biomedical Photonics, Advanced Biomedical Imaging Facility-Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China.
| | - Shijie Tu
- College of Optical Science and Engineering, Zhejiang University, Hangzhou, Zhejiang 310027, China
| | - Wenwen Gong
- College of Optical Science and Engineering, Zhejiang University, Hangzhou, Zhejiang 310027, China; Institute of Pharmacology, College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, P.R. China
| | - Wenli Tao
- College of Optical Science and Engineering, Zhejiang University, Hangzhou, Zhejiang 310027, China
| | - Mingwei Tang
- College of Optical Science and Engineering, Zhejiang University, Hangzhou, Zhejiang 310027, China
| | - Yunfei Wei
- Britton Chance Center for Biomedical Photonics-MoE Key Laboratory for Biomedical Photonics, Advanced Biomedical Imaging Facility-Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Cuifang Kuang
- College of Optical Science and Engineering, Zhejiang University, Hangzhou, Zhejiang 310027, China; Ningbo Research Institute, Zhejiang University, Ningbo, Zhejiang 315100, China
| | - Xu Liu
- College of Optical Science and Engineering, Zhejiang University, Hangzhou, Zhejiang 310027, China; Ningbo Research Institute, Zhejiang University, Ningbo, Zhejiang 315100, China.
| | - Yu-Hui Zhang
- Britton Chance Center for Biomedical Photonics-MoE Key Laboratory for Biomedical Photonics, Advanced Biomedical Imaging Facility-Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China.
| | - Xiang Hao
- College of Optical Science and Engineering, Zhejiang University, Hangzhou, Zhejiang 310027, China.
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