1
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Zhou W, Tao Y, Qiao Q, Xu N, Li J, Wang G, Fang X, Chen J, Liu W, Xu Z. Cell-Impermeable Buffering Fluorogenic Probes for Live-Cell Super-Resolution Imaging of Plasma Membrane Morphology Dynamics. ACS Sens 2024; 9:3170-3177. [PMID: 38859630 DOI: 10.1021/acssensors.4c00486] [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] [Indexed: 06/12/2024]
Abstract
Super-resolution fluorescence imaging has emerged as a potent tool for investigating the nanoscale structure and function of the plasma membrane (PM). Nevertheless, the challenge persists in achieving super-resolution imaging of PM dynamics due to limitations in probe photostability and issues with cell internalization staining. Herein, we report assembly-mediated buffering fluorogenic probes BMP-14 and BMP-16 exhibiting fast PM labeling and extended retention time (over 2 h) on PM. The incorporation of alkyl chains proves effective in promoting the aggregation of BMP-14 and BMP-16 into nonfluorescent nanoparticles to realize fluorogenicity and regulate the buffering capacity to rapidly replace photobleached probes ensuring stable long-term super-resolution imaging of PM. Utilizing these PM-buffering probes, we observed dynamic movements of PM filopodia and continuous shrinkage, leading to the formation of extracellular vesicles (EVs) using structured illumination microscopy (SIM). Furthermore, we discovered two distinct modes of EV fusion: one involving fusion through adjacent lipids and the other through filamentous lipid traction. The entire process of EV fusion outside the PM was dynamically tracked. Additionally, BMP-16 exhibited a unique capability of inducing single-molecule fluorescence blinking when used for cell membrane staining. This property makes BMP-16 suitable for the PAINT imaging of cell membranes.
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Affiliation(s)
- 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
| | - Yi Tao
- 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
| | - Ning 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
| | - 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
| | - Guangying Wang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China
| | - Xiangning Fang
- 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
| | - Jie Chen
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China
| | - Wenjuan Liu
- 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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2
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Chen Q, Li Z, Chen Y, Liu M, Yang Q, Zhu B, Mu J, Feng L, Chen Z. Effects of electron acceptors and donors on anaerobic biodegradation of PAHs in marine sediments. MARINE POLLUTION BULLETIN 2024; 199:115925. [PMID: 38113802 DOI: 10.1016/j.marpolbul.2023.115925] [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: 09/05/2023] [Revised: 12/06/2023] [Accepted: 12/10/2023] [Indexed: 12/21/2023]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are typical organic pollutants accumulated in the environment. PAHs' bioremediation in sediments can be promoted by adding electron acceptor (EA) and electron donor (ED). Bicarbonate and sulfate were chosen as two EAs, and acetate and lactate were selected as two EDs. Six groups of amendments were added into the sediments to access their role in the anaerobic biodegradation of five PAHs, containing phenanthrene, anthracene, fluoranthene, pyrene, and benzo[a]pyrene. The concentrations of PAHs, EAs and EDs, electron transport system activity, and microbial diversity were analyzed during 126-day biodegradation in serum bottles. The HA group (bicarbonate and acetate) achieved the maximum PAH degradation efficiency of 89.67 %, followed by the SL group (sulfate and lactate) with 87.10 %. As the main PAHs degrading bacteria, the abundance of Marinobacter in H group was 8.62 %, and the addition of acetate significantly increased the abundance of Marinobacter in the HA group by 75.65 %.
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Affiliation(s)
- Qingguo Chen
- Zhejiang Key Laboratory of Petrochemical Environmental Pollution, Zhejiang Ocean University, Zhoushan 316022, PR China; National & local Joint Engineering Research Center of Harbor Oil & Gas Storage and Transportation Technology, Zhejiang Ocean University, Zhoushan 316022, PR China
| | - Zhenzhen Li
- Zhejiang Key Laboratory of Petrochemical Environmental Pollution, Zhejiang Ocean University, Zhoushan 316022, PR China; School of Marine Science & Technology, Zhejiang Ocean University, Zhoushan 316022, PR China
| | - Yu Chen
- Zhejiang Key Laboratory of Petrochemical Environmental Pollution, Zhejiang Ocean University, Zhoushan 316022, PR China; School of Marine Science & Technology, Zhejiang Ocean University, Zhoushan 316022, PR China
| | - Mei Liu
- Zhejiang Key Laboratory of Petrochemical Environmental Pollution, Zhejiang Ocean University, Zhoushan 316022, PR China
| | - Qiao Yang
- Zhejiang Key Laboratory of Petrochemical Environmental Pollution, Zhejiang Ocean University, Zhoushan 316022, PR China
| | - Baikang Zhu
- Zhejiang Key Laboratory of Petrochemical Environmental Pollution, Zhejiang Ocean University, Zhoushan 316022, PR China; National & local Joint Engineering Research Center of Harbor Oil & Gas Storage and Transportation Technology, Zhejiang Ocean University, Zhoushan 316022, PR China
| | - Jun Mu
- College of Ecology and Environment, Hainan Tropical Ocean University, Sanya 572022, PR China.
| | - Lijuan Feng
- Zhejiang Key Laboratory of Petrochemical Environmental Pollution, Zhejiang Ocean University, Zhoushan 316022, PR China; National & local Joint Engineering Research Center of Harbor Oil & Gas Storage and Transportation Technology, Zhejiang Ocean University, Zhoushan 316022, PR China
| | - Zhi Chen
- Department of Building, Civil and Environmental Engineering, Faculty of Engineering & Computer Sciences, Concordia University, Montreal, Quebec H3G1M8, Canada
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3
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Herdly L, Tinning PW, Geiser A, Taylor H, Gould GW, van de Linde S. Benchmarking Thiolate-Driven Photoswitching of Cyanine Dyes. J Phys Chem B 2023; 127:732-741. [PMID: 36638265 PMCID: PMC9884076 DOI: 10.1021/acs.jpcb.2c06872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Carbocyanines are among the best performing dyes in single-molecule localization microscopy (SMLM), but their performance critically relies on optimized photoswitching buffers. Here, we study the versatile role of thiols in cyanine photoswitching at varying intensities generated in a single acquisition by a microelectromechanical systems (MEMS) mirror placed in the excitation path. The key metrics we have analyzed as a function of the thiolate concentration are photon budget, on-state and off-state lifetimes and the corresponding impact on image resolution. We show that thiolate acts as a concentration bandpass filter for the maximum achievable resolution and determine a minimum of ∼1 mM is necessary to facilitate SMLM measurements. We also identify a concentration bandwidth of 1-16 mM in which the photoswitching performance can be balanced between high molecular brightness and high off-time to on-time ratios. Furthermore, we monitor the performance of the popular oxygen scavenger system based on glucose and glucose oxidase over time and show simple measures to avoid acidification during prolonged measurements. Finally, the impact of buffer settings is quantitatively tested on the distribution of the glucose transporter protein 4 within the plasma membrane of adipocytes. Our work provides a general strategy for achieving optimal resolution in SMLM with relevance for the development of novel buffers and dyes.
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Affiliation(s)
- Lucas Herdly
- Department
of Physics, SUPA, University of Strathclyde, GlasgowG4 0NG, Scotland, United Kingdom
| | - Peter W. Tinning
- Department
of Physics, SUPA, University of Strathclyde, GlasgowG4 0NG, Scotland, United Kingdom
| | - Angéline Geiser
- Strathclyde
Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, GlasgowG4 0RE, Scotland, United Kingdom
| | - Holly Taylor
- Strathclyde
Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, GlasgowG4 0RE, Scotland, United Kingdom
| | - Gwyn W. Gould
- Strathclyde
Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, GlasgowG4 0RE, Scotland, United Kingdom
| | - Sebastian van de Linde
- Department
of Physics, SUPA, University of Strathclyde, GlasgowG4 0NG, Scotland, United Kingdom,
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4
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Klein T, Sauer M, Ergün S, Karnati S. Direct Stochastic Optical Reconstruction Microscopy (dSTORM) of Peroxisomes. Methods Mol Biol 2023; 2643:85-92. [PMID: 36952179 DOI: 10.1007/978-1-0716-3048-8_6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/27/2023]
Abstract
Peroxisomes are central metabolic organelles whose maturation and function depend on efficient and accurate targeting of peroxisomal membrane proteins (PMPs). Ultrastructural imaging of the PMPs is a quite difficult task as it requires high spatial and temporal resolution. Further, the spatial resolution of conventional light microscopy is limited due to the diffraction of light. However, recent methodological developments in super resolution microscopy showed us to access the nanoscale regimes spatially allowing to elucidate the membrane structures of cell organelles. In this chapter, we present protocols used in our laboratory for the super-resolution imaging of the peroxisomal membrane protein 14 (PEX14p) by direct stochastic optical reconstruction microscopy (dSTORM).
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Affiliation(s)
- Teresa Klein
- Department of Biotechnology and Biophysics, Biocenter, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
| | - Markus Sauer
- Department of Biotechnology and Biophysics, Biocenter, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
| | - Süleyman Ergün
- Institute of Anatomy and Cell Biology, Julius-Maximilians-University Wurzburg, Würzburg, Germany
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5
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Man H, Zhou L, Zhu G, Zheng Y, Ye Z, Huang Z, Teng X, Ai C, Ge G, Xiao Y. Super-Resolution Imaging of Autophagy by a Preferred Pair of Self-Labeling Protein Tags and Fluorescent Ligands. Anal Chem 2022; 94:15057-15066. [PMID: 36262049 DOI: 10.1021/acs.analchem.2c03125] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Autophagy is a core recycling process for homeostasis, with its dysfunction associated with tumorigenesis and various diseases. Yet, its subtle intracellular details are covered due to the limited resolution of conventional microscopies. The major challenge for modern super-resolution microscopy deployment is the lack of a practical labeling system, which could provide robust fluorescence with fidelity in the context of the dynamic autophagy microenvironment. Herein, a representative autophagy marker LC3 protein is selected to develop two hybrid self-labeling systems with tetramethylrhodamine (TMR) fluorophores through SNAP/Halo-tag technologies. A systematic investigation indicated that the match of the LC3-Halo and TMR ligand remarkably outperforms that of LC3-SNAP, as the former Halo system exhibited more robust single-molecule brightness (440 vs 247), total photon numbers (45600 vs 13500), and dwell time of the initial bright state (0.82 vs 0.40 s) than the latter. With the aid of this desirable Halo system, for the first time, live-cell ferritinophagy is monitored with a spatial resolution of ∼50 nm, which disclosed reduced sizes of autophagosomes (∼650 nm, ferritinophagy) than those in nonselective (∼840 nm, mammalian target of rapamycin (mTOR)) and selective autophagy (∼900 nm, mitophagy).
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Affiliation(s)
- Huizi Man
- State Key Laboratory of Fine Chemicals, Frontiers Science Center for Smart Materials Oriented Chemical Engineering, Dalian University of Technology, Dalian 116024, China
| | - Lin Zhou
- State Key Laboratory of Fine Chemicals, Frontiers Science Center for Smart Materials Oriented Chemical Engineering, Dalian University of Technology, Dalian 116024, China
| | - Guanghao Zhu
- Shanghai Frontiers Science Center for TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, 1200 Cailun Road, Shanghai 201203, China
| | - Ying Zheng
- State Key Laboratory of Fine Chemicals, Frontiers Science Center for Smart Materials Oriented Chemical Engineering, Dalian University of Technology, Dalian 116024, China
| | - Zhiwei Ye
- State Key Laboratory of Fine Chemicals, Frontiers Science Center for Smart Materials Oriented Chemical Engineering, Dalian University of Technology, Dalian 116024, China
| | - Zhenlong Huang
- State Key Laboratory of Fine Chemicals, Frontiers Science Center for Smart Materials Oriented Chemical Engineering, Dalian University of Technology, Dalian 116024, China
| | - Xinru Teng
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, Collaborative Innovation Center for Guangxi Ethnic Medicine, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, 15 Yucai Road, Guilin 541004, China
| | - Chunzhi Ai
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, Collaborative Innovation Center for Guangxi Ethnic Medicine, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, 15 Yucai Road, Guilin 541004, China
| | - Guangbo Ge
- Shanghai Frontiers Science Center for TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, 1200 Cailun Road, Shanghai 201203, China
| | - Yi Xiao
- State Key Laboratory of Fine Chemicals, Frontiers Science Center for Smart Materials Oriented Chemical Engineering, Dalian University of Technology, Dalian 116024, China
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Kwon J, Elgawish MS, Shim S. Bleaching-Resistant Super-Resolution Fluorescence Microscopy. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2101817. [PMID: 35088584 PMCID: PMC8948665 DOI: 10.1002/advs.202101817] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Revised: 01/07/2022] [Indexed: 05/08/2023]
Abstract
Photobleaching is the permanent loss of fluorescence after extended exposure to light and is a major limiting factor in super-resolution microscopy (SRM) that restricts spatiotemporal resolution and observation time. Strategies for preventing or overcoming photobleaching in SRM are reviewed developing new probes and chemical environments. Photostabilization strategies are introduced first, which are borrowed from conventional fluorescence microscopy, that are employed in SRM. SRM-specific strategies are then highlighted that exploit the on-off transitions of fluorescence, which is the key mechanism for achieving super-resolution, which are becoming new routes to address photobleaching in SRM. Off states can serve as a shelter from excitation by light or an exit to release a damaged probe and replace it with a fresh one. Such efforts in overcoming the photobleaching limits are anticipated to enhance resolution to molecular scales and to extend the observation time to physiological lifespans.
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Affiliation(s)
- Jiwoong Kwon
- Department of Biophysics and Biophysical ChemistryJohns Hopkins UniversityBaltimoreMD21205USA
| | - Mohamed Saleh Elgawish
- Department of ChemistryKorea UniversitySeoul02841Republic of Korea
- Medicinal Chemistry DepartmentFaculty of PharmacySuez Canal UniversityIsmailia41522Egypt
| | - Sang‐Hee Shim
- Department of ChemistryKorea UniversitySeoul02841Republic of Korea
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7
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Herdly L, Janin P, Bauer R, van de Linde S. Tunable Wide-Field Illumination and Single-Molecule Photoswitching with a Single MEMS Mirror. ACS PHOTONICS 2021; 8:2728-2736. [PMID: 34553004 PMCID: PMC8447260 DOI: 10.1021/acsphotonics.1c00843] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Indexed: 06/13/2023]
Abstract
Homogeneous illumination in single-molecule localization microscopy (SMLM) is key for the quantitative analysis of super-resolution images. Therefore, different approaches for flat-field illumination have been introduced as alternative to the conventional Gaussian illumination. Here, we introduce a single microelectromechanical systems (MEMS) mirror as a tunable and cost-effective device for adapting wide-field illumination in SMLM. In flat-field mode the MEMS allowed for consistent SMLM metrics across the entire field of view. Employing single-molecule photoswitching, we developed a simple yet powerful routine to benchmark different illumination schemes on the basis of local emitter brightness and ON-state lifetime. Moreover, we propose that tuning the MEMS beyond optimal flat-field conditions enables to study the kinetics of photoswitchable fluorophores within a single acquisition.
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Affiliation(s)
- Lucas Herdly
- Department
of Physics, SUPA, University of Strathclyde, Glasgow, Scotland, United Kingdom
| | - Paul Janin
- Department
of Electronic and Electrical Engineering, University of Strathclyde, Glasgow, Scotland, United Kingdom
| | - Ralf Bauer
- Department
of Electronic and Electrical Engineering, University of Strathclyde, Glasgow, Scotland, United Kingdom
| | - Sebastian van de Linde
- Department
of Physics, SUPA, University of Strathclyde, Glasgow, Scotland, United Kingdom
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8
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Xu J, Fan S, Xu L, Maruyama A, Fujitsuka M, Kawai K. Control of Triplet Blinking Using Cyclooctatetraene to Access the Dynamics of Biomolecules at the Single‐Molecule Level. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202101606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Jie Xu
- The Institute of Scientific and Industrial Research (SANKEN) Osaka University Mihogaoka 8-1, Ibaraki Osaka 567-0047 Japan
| | - Shuya Fan
- The Institute of Scientific and Industrial Research (SANKEN) Osaka University Mihogaoka 8-1, Ibaraki Osaka 567-0047 Japan
| | - Lei Xu
- The Institute of Scientific and Industrial Research (SANKEN) Osaka University Mihogaoka 8-1, Ibaraki Osaka 567-0047 Japan
| | - Atsushi Maruyama
- Department of Life Science and Technology Tokyo Institute of Technology 4259 B-57 Nagatsuta, Midori-ku Yokohama Kanagawa 226-8501 Japan
| | - Mamoru Fujitsuka
- The Institute of Scientific and Industrial Research (SANKEN) Osaka University Mihogaoka 8-1, Ibaraki Osaka 567-0047 Japan
| | - Kiyohiko Kawai
- The Institute of Scientific and Industrial Research (SANKEN) Osaka University Mihogaoka 8-1, Ibaraki Osaka 567-0047 Japan
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9
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Xu J, Fan S, Xu L, Maruyama A, Fujitsuka M, Kawai K. Control of Triplet Blinking Using Cyclooctatetraene to Access the Dynamics of Biomolecules at the Single‐Molecule Level. Angew Chem Int Ed Engl 2021; 60:12941-12948. [DOI: 10.1002/anie.202101606] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 03/25/2021] [Indexed: 01/04/2023]
Affiliation(s)
- Jie Xu
- The Institute of Scientific and Industrial Research (SANKEN) Osaka University Mihogaoka 8-1, Ibaraki Osaka 567-0047 Japan
| | - Shuya Fan
- The Institute of Scientific and Industrial Research (SANKEN) Osaka University Mihogaoka 8-1, Ibaraki Osaka 567-0047 Japan
| | - Lei Xu
- The Institute of Scientific and Industrial Research (SANKEN) Osaka University Mihogaoka 8-1, Ibaraki Osaka 567-0047 Japan
| | - Atsushi Maruyama
- Department of Life Science and Technology Tokyo Institute of Technology 4259 B-57 Nagatsuta, Midori-ku Yokohama Kanagawa 226-8501 Japan
| | - Mamoru Fujitsuka
- The Institute of Scientific and Industrial Research (SANKEN) Osaka University Mihogaoka 8-1, Ibaraki Osaka 567-0047 Japan
| | - Kiyohiko Kawai
- The Institute of Scientific and Industrial Research (SANKEN) Osaka University Mihogaoka 8-1, Ibaraki Osaka 567-0047 Japan
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10
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Santos AF, Almeida DRQ, Terra LF, Wailemann RA, Gomes VM, Arini GS, Ravagnani FG, Baptista MS, Labriola L. Fluence Rate Determines PDT Efficiency in Breast Cancer Cells Displaying Different GSH Levels. Photochem Photobiol 2019; 96:658-667. [DOI: 10.1111/php.13182] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 10/25/2019] [Indexed: 12/13/2022]
Affiliation(s)
- Ancély F. Santos
- Department of Biochemistry Chemistry Institute University of Sao Paulo Sao Paulo Brazil
| | | | - Letícia F. Terra
- Department of Biochemistry Chemistry Institute University of Sao Paulo Sao Paulo Brazil
| | | | - Vinícius M. Gomes
- Department of Biochemistry Chemistry Institute University of Sao Paulo Sao Paulo Brazil
| | - Gabriel S. Arini
- Department of Biochemistry Chemistry Institute University of Sao Paulo Sao Paulo Brazil
| | - Felipe G. Ravagnani
- Department of Biochemistry Chemistry Institute University of Sao Paulo Sao Paulo Brazil
| | - Maurício S. Baptista
- Department of Biochemistry Chemistry Institute University of Sao Paulo Sao Paulo Brazil
| | - Leticia Labriola
- Department of Biochemistry Chemistry Institute University of Sao Paulo Sao Paulo Brazil
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11
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A photoelectrochemical biosensor based on fullerene with methylene blue as a sensitizer for ultrasensitive DNA detection. Biosens Bioelectron 2019; 142:111579. [DOI: 10.1016/j.bios.2019.111579] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 08/05/2019] [Accepted: 08/08/2019] [Indexed: 01/19/2023]
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12
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Varga D, Majoros H, Ujfaludi Z, Erdélyi M, Pankotai T. Quantification of DNA damage induced repair focus formation via super-resolution dSTORM localization microscopy. NANOSCALE 2019; 11:14226-14236. [PMID: 31317161 DOI: 10.1039/c9nr03696b] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
In eukaryotic cells, each process, in which DNA is involved, should take place in the context of a chromatin structure. DNA double-strand breaks (DSBs) are one of the most deleterious lesions often leading to chromosomal rearrangement. In response to environmental stresses, cells have developed repair mechanisms to eliminate the DSBs. Upon DSB induction, several factors play roles in chromatin relaxation by catalysing the appropriate histone posttranslational modification (PTM) steps, therefore promoting the access of the repair factors to the DSBs. Among these PTMs, the phosphorylation of the histone variant H2AX at its Ser139 residue (also known as γH2AX) could be observed at the break sites. The structure of a DNA double-strand break induced repair focus has to be organized during the repair as it contributes to the accessibility of specific repair proteins to the damaged site. Our aim was to develop a quantitative approach to analyse the morphology of single repair foci by super-resolution dSTORM microscopy to gain insight into chromatin organization in DNA repair. We have established a specific dSTORM measurement process by developing a new analytical algorithm for gaining quantitative information about chromatin morphology and repair foci topology at an individual γH2AX enriched repair focus. Using this method we quantified single repair foci to show the distribution of γH2AX. The image of individual γH2AX referred to as the Single target Molecule response scatter Plot (SMPlot) was obtained by using high lateral resolution dSTORM images. Determination of the average localization numbers in an SMPlot was one of the key steps of quantitative dSTORM. A repair focus is made up of nanofoci. Such a substructure of repair foci can only be resolved and detected with super-resolution microscopy. Determination of the number of γH2AXs in the nanofoci was another key step of quantitative dSTORM. Additionally, based on our new analysis method, we were able to show the number of nucleosomes in each nanofocus that could allow us to define the possible chromatin structure and the nucleosome density around the break sites. This method is one of the first demonstrations of a single-cell based quantitative measurement of a discrete repair focus, which could provide new opportunities to categorize the spatial organization of nanofoci by parametric determination of topological similarity.
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Affiliation(s)
- Dániel Varga
- University of Szeged, Department of Optics and Quantum Electronics, Hungary.
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13
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Scholz N, Ehmann N, Sachidanandan D, Imig C, Cooper BH, Jahn O, Reim K, Brose N, Meyer J, Lamberty M, Altrichter S, Bormann A, Hallermann S, Pauli M, Heckmann M, Stigloher C, Langenhan T, Kittel RJ. Complexin cooperates with Bruchpilot to tether synaptic vesicles to the active zone cytomatrix. J Cell Biol 2019; 218:1011-1026. [PMID: 30782781 PMCID: PMC6400551 DOI: 10.1083/jcb.201806155] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 12/14/2018] [Accepted: 01/09/2019] [Indexed: 02/06/2023] Open
Abstract
By performing an in vivo screen in Drosophila melanogaster, Scholz, Ehmann, et al. identify Complexin as a functional interaction partner of Bruchpilot. The two proteins mediate a physical attachment of synaptic vesicles to the active zone cytomatrix and promote rapid, sustained synaptic transmission. Information processing by the nervous system depends on neurotransmitter release from synaptic vesicles (SVs) at the presynaptic active zone. Molecular components of the cytomatrix at the active zone (CAZ) regulate the final stages of the SV cycle preceding exocytosis and thereby shape the efficacy and plasticity of synaptic transmission. Part of this regulation is reflected by a physical association of SVs with filamentous CAZ structures via largely unknown protein interactions. The very C-terminal region of Bruchpilot (Brp), a key component of the Drosophila melanogaster CAZ, participates in SV tethering. Here, we identify the conserved SNARE regulator Complexin (Cpx) in an in vivo screen for molecules that link the Brp C terminus to SVs. Brp and Cpx interact genetically and functionally. Both proteins promote SV recruitment to the Drosophila CAZ and counteract short-term synaptic depression. Analyzing SV tethering to active zone ribbons of cpx3 knockout mice supports an evolutionarily conserved role of Cpx upstream of SNARE complex assembly.
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Affiliation(s)
- Nicole Scholz
- Institute of Physiology, Department of Neurophysiology, University of Würzburg, Würzburg, Germany.,Rudolf Schönheimer Institute of Biochemistry, Division of General Biochemistry, Leipzig University, Leipzig, Germany
| | - Nadine Ehmann
- Institute of Physiology, Department of Neurophysiology, University of Würzburg, Würzburg, Germany.,Department of Animal Physiology, Institute of Biology, Leipzig University, Leipzig, Germany.,Carl Ludwig Institute for Physiology, Leipzig University, Leipzig, Germany
| | - Divya Sachidanandan
- Institute of Physiology, Department of Neurophysiology, University of Würzburg, Würzburg, Germany
| | - Cordelia Imig
- Department of Molecular Neurobiology, Max Planck Institute of Experimental Medicine, Göttingen, Germany
| | - Benjamin H Cooper
- Department of Molecular Neurobiology, Max Planck Institute of Experimental Medicine, Göttingen, Germany
| | - Olaf Jahn
- Proteomics Group, Max Planck Institute of Experimental Medicine, Göttingen, Germany
| | - Kerstin Reim
- Department of Molecular Neurobiology, Max Planck Institute of Experimental Medicine, Göttingen, Germany
| | - Nils Brose
- Department of Molecular Neurobiology, Max Planck Institute of Experimental Medicine, Göttingen, Germany
| | - Jutta Meyer
- Department of Molecular Neurobiology, Max Planck Institute of Experimental Medicine, Göttingen, Germany.,Proteomics Group, Max Planck Institute of Experimental Medicine, Göttingen, Germany.,Göttingen Graduate School for Neurosciences, Biophysics and Molecular Biosciences, University of Göttingen, Germany
| | - Marius Lamberty
- Institute of Physiology, Department of Neurophysiology, University of Würzburg, Würzburg, Germany.,Department of Animal Physiology, Institute of Biology, Leipzig University, Leipzig, Germany.,Carl Ludwig Institute for Physiology, Leipzig University, Leipzig, Germany
| | - Steffen Altrichter
- Institute of Physiology, Department of Neurophysiology, University of Würzburg, Würzburg, Germany.,Rudolf Schönheimer Institute of Biochemistry, Division of General Biochemistry, Leipzig University, Leipzig, Germany
| | - Anne Bormann
- Rudolf Schönheimer Institute of Biochemistry, Division of General Biochemistry, Leipzig University, Leipzig, Germany
| | - Stefan Hallermann
- Carl Ludwig Institute for Physiology, Leipzig University, Leipzig, Germany
| | - Martin Pauli
- Institute of Physiology, Department of Neurophysiology, University of Würzburg, Würzburg, Germany
| | - Manfred Heckmann
- Institute of Physiology, Department of Neurophysiology, University of Würzburg, Würzburg, Germany
| | | | - Tobias Langenhan
- Institute of Physiology, Department of Neurophysiology, University of Würzburg, Würzburg, Germany .,Rudolf Schönheimer Institute of Biochemistry, Division of General Biochemistry, Leipzig University, Leipzig, Germany
| | - Robert J Kittel
- Institute of Physiology, Department of Neurophysiology, University of Würzburg, Würzburg, Germany .,Department of Animal Physiology, Institute of Biology, Leipzig University, Leipzig, Germany.,Carl Ludwig Institute for Physiology, Leipzig University, Leipzig, Germany
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14
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Abstract
The past decade has witnessed an explosion in the use of super-resolution fluorescence microscopy methods in biology and other fields. Single-molecule localization microscopy (SMLM) is one of the most widespread of these methods and owes its success in large part to the ability to control the on-off state of fluorophores through various chemical, photochemical, or binding-unbinding mechanisms. We provide here a comprehensive overview of switchable fluorophores in SMLM including a detailed review of all major classes of SMLM fluorophores, and we also address strategies for labeling specimens, considerations for multichannel and live-cell imaging, potential pitfalls, and areas for future development.
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Affiliation(s)
- Honglin Li
- Department of Chemistry, University of Washington, Seattle, Washington, USA, 98195
| | - Joshua C. Vaughan
- Department of Chemistry, University of Washington, Seattle, Washington, USA, 98195
- Department of Physiology and Biophysics, University of Washington, Seattle, Washington, USA, 98195
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15
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Hirvonen LM, Cox S. STORM without enzymatic oxygen scavenging for correlative atomic force and fluorescence superresolution microscopy. Methods Appl Fluoresc 2018; 6:045002. [PMID: 29956675 PMCID: PMC6538533 DOI: 10.1088/2050-6120/aad018] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Superresolution microscopy based on localisation is usually performed in a buffer containing enzymatic oxygen scavenger, which facilitates reversible photoswitching of the dye molecules. This makes correlative fluorescence localisation and atomic force microscopy (AFM) challenging, because enzymatic oxygen scavenging interferes with the AFM cantilevers. Here we report on the blinking kinetics of a new red cyanine dye, iFluor-647, which is similar to the Alexa-647 dye commonly used for superresolution microscopy, but with brightness and blinking properties which are superior to Alexa-647 in a buffer without enzymatic oxygen scavenger. We measure the blinking behaviour of iFluor-647 in buffers with and without enzymatic oxygen scavenger with different thiol concentrations. We then apply this dye for correlative localisation and atomic force microscopy in a buffer without enzymatic oxygen scavenger, which allows acquisition of AFM and superresolution images without buffer change.
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Affiliation(s)
- Liisa M Hirvonen
- Randall Centre for Cell and Molecular Biophysics, King's College London, New Hunt's House, Guy's Campus, London SE1 1UL, United Kingdom
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16
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Tamoto A, Aratani N, Yamada H. Photophysical properties and structural analysis of modified methylene blues as near infrared dyes. J Photochem Photobiol A Chem 2018. [DOI: 10.1016/j.jphotochem.2017.10.031] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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17
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Schücker K, Sauer M, Benavente R. Superresolution imaging of the synaptonemal complex. Methods Cell Biol 2018; 145:335-346. [DOI: 10.1016/bs.mcb.2018.03.033] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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18
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Limpanuparb T, Roongruangsree P, Areekul C. A DFT investigation of the blue bottle experiment: E∘half-cell analysis of autoxidation catalysed by redox indicators. ROYAL SOCIETY OPEN SCIENCE 2017; 4:170708. [PMID: 29291061 PMCID: PMC5717635 DOI: 10.1098/rsos.170708] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 09/05/2017] [Indexed: 06/07/2023]
Abstract
The blue bottle experiment is a collective term for autoxidation reactions catalysed by redox indicators. The reactions are characterized by their repeatable cycle of colour changes when shaken/left to stand and intricate chemical pattern formation. The blue bottle experiment is studied based on calculated solution-phase half-cell reduction potential of related reactions. Our investigation confirms that the reaction in various versions of the blue bottle experiment published to date is mainly the oxidation of an acyloin to a 1,2-dicarbonyl structure. In the light of the calculations, we also propose new non-acyloin reducing agents for the experiment. These results can help guide future experimental studies on the blue bottle experiment.
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Affiliation(s)
- Taweetham Limpanuparb
- Science Division, Mahidol University International College, Mahidol University, Salaya, Nakhon Pathom 73170, Thailand
| | - Pakpong Roongruangsree
- National Nanotechnology Center (NANOTEC), National Science and Technology Development Agency, Khlong Luang, Pathum Thani 12120, Thailand
- Department of Chemical Engineering, McGill University, Quebec H3A 0C5, Canada
| | - Cherprang Areekul
- Science Division, Mahidol University International College, Mahidol University, Salaya, Nakhon Pathom 73170, Thailand
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19
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Abstract
Super-resolution fluorescence imaging by photoactivation or photoswitching of single fluorophores and position determination (single-molecule localization microscopy, SMLM) provides microscopic images with subdiffraction spatial resolution. This technology has enabled new insights into how proteins are organized in a cellular context, with a spatial resolution approaching virtually the molecular level. A unique strength of SMLM is that it delivers molecule-resolved information, along with super-resolved images of cellular structures. This allows quantitative access to cellular structures, for example, how proteins are distributed and organized and how they interact with other biomolecules. Ultimately, it is even possible to determine protein numbers in cells and the number of subunits in a protein complex. SMLM thus has the potential to pave the way toward a better understanding of how cells function at the molecular level. In this review, we describe how SMLM has contributed new knowledge in eukaryotic biology, and we specifically focus on quantitative biological data extracted from SMLM images.
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Affiliation(s)
- Markus Sauer
- Department of Biotechnology & Biophysics, Julius-Maximilian-University of Würzburg , 97074 Würzburg, Germany
| | - Mike Heilemann
- Institute of Physical and Theoretical Chemistry, Goethe-University Frankfurt , 60438 Frankfurt, Germany
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20
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Schubert V. Super-resolution Microscopy - Applications in Plant Cell Research. FRONTIERS IN PLANT SCIENCE 2017; 8:531. [PMID: 28450874 PMCID: PMC5390026 DOI: 10.3389/fpls.2017.00531] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 03/24/2017] [Indexed: 05/10/2023]
Abstract
Most of the present knowledge about cell organization and function is based on molecular and genetic methods as well as cytological investigations. While electron microscopy allows identifying cell substructures until a resolution of ∼1 nm, the resolution of fluorescence microscopy is restricted to ∼200 nm due to the diffraction limit of light. However, the advantage of this technique is the possibility to identify and co-localize specifically labeled structures and molecules. The recently developed super-resolution microscopy techniques, such as Structured Illumination Microscopy, Photoactivated Localization Microscopy, Stochastic Optical Reconstruction Microscopy, and Stimulated Emission Depletion microscopy allow analyzing structures and molecules beyond the diffraction limit of light. Recently, there is an increasing application of these techniques in cell biology. This review evaluates and summarizes especially the data achieved until now in analyzing the organization and function of plant cells, chromosomes and interphase nuclei using super-resolution techniques.
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21
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Photometry unlocks 3D information from 2D localization microscopy data. Nat Methods 2016; 14:41-44. [DOI: 10.1038/nmeth.4073] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Accepted: 10/16/2016] [Indexed: 01/19/2023]
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22
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From single molecules to life: microscopy at the nanoscale. Anal Bioanal Chem 2016; 408:6885-911. [PMID: 27613013 PMCID: PMC5566169 DOI: 10.1007/s00216-016-9781-8] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Revised: 06/30/2016] [Accepted: 07/07/2016] [Indexed: 01/08/2023]
Abstract
Super-resolution microscopy is the term commonly given to fluorescence microscopy techniques with resolutions that are not limited by the diffraction of light. Since their conception a little over a decade ago, these techniques have quickly become the method of choice for many biologists studying structures and processes of single cells at the nanoscale. In this review, we present the three main approaches used to tackle the diffraction barrier of ∼200 nm: stimulated-emission depletion (STED) microscopy, structured illumination microscopy (SIM), and single-molecule localization microscopy (SMLM). We first present a theoretical overview of the techniques and underlying physics, followed by a practical guide to all of the facets involved in designing a super-resolution experiment, including an approachable explanation of the photochemistry involved, labeling methods available, and sample preparation procedures. Finally, we highlight some of the most exciting recent applications of and developments in these techniques, and discuss the outlook for this field. Super-resolution microscopy techniques. Working principles of the common approaches stimulated-emission depletion (STED) microscopy, structured illumination microscopy (SIM), and single-molecule localization microscopy (SMLM). ![]()
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23
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Zhao Q, Li Z, Deng Q, Zhu L, Luo S, Li H. Paired photoelectrocatalytic reactions of glucose driven by a photoelectrochemical fuel cell with assistance of methylene blue. Electrochim Acta 2016. [DOI: 10.1016/j.electacta.2016.05.117] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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24
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Sharma R, Pal M, Mishra KK. Ru(III)-catalyzed oxidation of N-acetyl-L-cysteine by methylene blue in absence and in presence of Cu(II) in acidic medium: influence of solvent and morphology. J Sulphur Chem 2016. [DOI: 10.1080/17415993.2016.1163697] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Ranjana Sharma
- Department of Chemistry, Rani Durgavati University, Jabalpur, MP, India
| | - Mahender Pal
- Department of Chemistry, Rani Durgavati University, Jabalpur, MP, India
| | - K. K. Mishra
- Department of Chemistry, Rani Durgavati University, Jabalpur, MP, India
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25
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Yang Z, Sharma A, Qi J, Peng X, Lee DY, Hu R, Lin D, Qu J, Kim JS. Super-resolution fluorescent materials: an insight into design and bioimaging applications. Chem Soc Rev 2016; 45:4651-67. [DOI: 10.1039/c5cs00875a] [Citation(s) in RCA: 155] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
With the emerging of super-resolution fluorescent imaging microscopy techniques, biological targets below 200 nm in size are successful to be localized clearly and precisely with unprecedented details. In this tutorial review, the fluorescent materials, including organic fluorophores and nanomaterials, utilized in STED, single molecule localized microscopy (PALM/STORM) and SOFI microscopies, together with their working principles are mainly discussed.
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Affiliation(s)
- Zhigang Yang
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province
- College of Optoelectronic Engineering
- Shenzhen University
- Shenzhen
- China
| | - Amit Sharma
- Department of Chemistry
- Korea University
- Seoul 136-701
- Korea
| | - Jing Qi
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province
- College of Optoelectronic Engineering
- Shenzhen University
- Shenzhen
- China
| | - Xiao Peng
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province
- College of Optoelectronic Engineering
- Shenzhen University
- Shenzhen
- China
| | - Dong Yeop Lee
- Department of Chemistry
- Korea University
- Seoul 136-701
- Korea
| | - Rui Hu
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province
- College of Optoelectronic Engineering
- Shenzhen University
- Shenzhen
- China
| | - Danying Lin
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province
- College of Optoelectronic Engineering
- Shenzhen University
- Shenzhen
- China
| | - Junle Qu
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province
- College of Optoelectronic Engineering
- Shenzhen University
- Shenzhen
- China
| | - Jong Seung Kim
- Department of Chemistry
- Korea University
- Seoul 136-701
- Korea
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26
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Winterhoff M, Brühmann S, Franke C, Breitsprecher D, Faix J. Visualization of Actin Assembly and Filament Turnover by In Vitro Multicolor TIRF Microscopy. Methods Mol Biol 2016; 1407:287-306. [PMID: 27271910 DOI: 10.1007/978-1-4939-3480-5_21] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
In response to chemotactic signals, motile cells develop a single protruding front to persistently migrate in direction of the chemotactic gradient. The highly dynamic reorganization of the actin cytoskeleton is an essential part during this process and requires the precise interplay of various actin filament assembly factors and actin-binding proteins (ABPs). Although many ABPs have been implicated in cell migration, as yet only a few of them have been well characterized concerning their specific functions during actin network assembly and disassembly. In this chapter, we describe a versatile method that allows the direct visualization of the assembly of single actin filaments and higher structures in real time by in vitro total internal reflection fluorescence microscopy (TIRF-M) using purified and fluorescently labeled actin and ABPs.
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Affiliation(s)
- Moritz Winterhoff
- Institute for Biophysical Chemistry, Hannover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany
| | - Stefan Brühmann
- Institute for Biophysical Chemistry, Hannover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany
| | - Christof Franke
- Institute for Biophysical Chemistry, Hannover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany
| | | | - Jan Faix
- Institute for Biophysical Chemistry, Hannover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany.
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27
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Light-induced cell damage in live-cell super-resolution microscopy. Sci Rep 2015; 5:15348. [PMID: 26481189 PMCID: PMC4611486 DOI: 10.1038/srep15348] [Citation(s) in RCA: 298] [Impact Index Per Article: 33.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Accepted: 09/22/2015] [Indexed: 12/11/2022] Open
Abstract
Super-resolution microscopy can unravel previously hidden details of cellular structures but requires high irradiation intensities to use the limited photon budget efficiently. Such high photon densities are likely to induce cellular damage in live-cell experiments. We applied single-molecule localization microscopy conditions and tested the influence of irradiation intensity, illumination-mode, wavelength, light-dose, temperature and fluorescence labeling on the survival probability of different cell lines 20–24 hours after irradiation. In addition, we measured the microtubule growth speed after irradiation. The photo-sensitivity is dramatically increased at lower irradiation wavelength. We observed fixation, plasma membrane permeabilization and cytoskeleton destruction upon irradiation with shorter wavelengths. While cells stand light intensities of ~1 kW cm−2 at 640 nm for several minutes, the maximum dose at 405 nm is only ~50 J cm−2, emphasizing red fluorophores for live-cell localization microscopy. We also present strategies to minimize phototoxic factors and maximize the cells ability to cope with higher irradiation intensities.
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28
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Valley CC, Liu S, Lidke DS, Lidke KA. Sequential superresolution imaging of multiple targets using a single fluorophore. PLoS One 2015; 10:e0123941. [PMID: 25860558 PMCID: PMC4393115 DOI: 10.1371/journal.pone.0123941] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Accepted: 03/09/2015] [Indexed: 12/11/2022] Open
Abstract
Fluorescence superresolution (SR) microscopy, or fluorescence nanoscopy, provides nanometer scale detail of cellular structures and allows for imaging of biological processes at the molecular level. Specific SR imaging methods, such as localization-based imaging, rely on stochastic transitions between on (fluorescent) and off (dark) states of fluorophores. Imaging multiple cellular structures using multi-color imaging is complicated and limited by the differing properties of various organic dyes including their fluorescent state duty cycle, photons per switching event, number of fluorescent cycles before irreversible photobleaching, and overall sensitivity to buffer conditions. In addition, multiple color imaging requires consideration of multiple optical paths or chromatic aberration that can lead to differential aberrations that are important at the nanometer scale. Here, we report a method for sequential labeling and imaging that allows for SR imaging of multiple targets using a single fluorophore with negligible cross-talk between images. Using brightfield image correlation to register and overlay multiple image acquisitions with ~10 nm overlay precision in the x-y imaging plane, we have exploited the optimal properties of AlexaFluor647 for dSTORM to image four distinct cellular proteins. We also visualize the changes in co-localization of the epidermal growth factor (EGF) receptor and clathrin upon EGF addition that are consistent with clathrin-mediated endocytosis. These results are the first to demonstrate sequential SR (s-SR) imaging using direct stochastic reconstruction microscopy (dSTORM), and this method for sequential imaging can be applied to any superresolution technique.
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Affiliation(s)
- Christopher C. Valley
- Department of Pathology and Cancer Research and Treatment Center, University of New Mexico, Albuquerque, New Mexico, United States of America
| | - Sheng Liu
- Department of Physics & Astronomy, University of New Mexico, Albuquerque, New Mexico, United States of America
| | - Diane S. Lidke
- Department of Pathology and Cancer Research and Treatment Center, University of New Mexico, Albuquerque, New Mexico, United States of America
| | - Keith A. Lidke
- Department of Physics & Astronomy, University of New Mexico, Albuquerque, New Mexico, United States of America
- * E-mail:
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29
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Quantitative super-resolution imaging of Bruchpilot distinguishes active zone states. Nat Commun 2014; 5:4650. [PMID: 25130366 PMCID: PMC4143948 DOI: 10.1038/ncomms5650] [Citation(s) in RCA: 152] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2014] [Accepted: 07/09/2014] [Indexed: 12/18/2022] Open
Abstract
The precise molecular architecture of synaptic active zones (AZs) gives rise to different structural and functional AZ states that fundamentally shape chemical neurotransmission. However, elucidating the nanoscopic protein arrangement at AZs is impeded by the diffraction-limited resolution of conventional light microscopy. Here we introduce new approaches to quantify endogenous protein organization at single-molecule resolution in situ with super-resolution imaging by direct stochastic optical reconstruction microscopy (dSTORM). Focusing on the Drosophila neuromuscular junction (NMJ), we find that the AZ cytomatrix (CAZ) is composed of units containing ~137 Bruchpilot (Brp) proteins, three quarters of which are organized into about 15 heptameric clusters. We test for a quantitative relationship between CAZ ultrastructure and neurotransmitter release properties by engaging Drosophila mutants and electrophysiology. Our results indicate that the precise nanoscopic organization of Brp distinguishes different physiological AZ states and link functional diversification to a heretofore unrecognized neuronal gradient of the CAZ ultrastructure. Complex molecular interactions occur in the active zone cytomatrix (CAZ) within the presynaptic terminal to regulate synaptic plasticity. Here, the authors use imaging techniques to show that the CAZ is composed of units containing on average 137 Bruchpilot proteins, many of which are arranged into clusters.
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30
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Chozinski TJ, Gagnon LA, Vaughan JC. Twinkle, twinkle little star: photoswitchable fluorophores for super-resolution imaging. FEBS Lett 2014; 588:3603-12. [PMID: 25010263 DOI: 10.1016/j.febslet.2014.06.043] [Citation(s) in RCA: 93] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2014] [Revised: 06/14/2014] [Accepted: 06/16/2014] [Indexed: 01/01/2023]
Abstract
Photoswitchable fluorescent probes are key elements of newly developed super-resolution fluorescence microscopy techniques that enable far-field interrogation of biological systems with a resolution of 50 nm or better. In contrast to most conventional fluorescence imaging techniques, the performance achievable by most super-resolution techniques is critically impacted by the photoswitching properties of the fluorophores. Here we review photoswitchable fluorophores for super-resolution imaging with discussion of the fundamental principles involved, a focus on practical implementation with available tools, and an outlook on future directions.
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Affiliation(s)
| | - Lauren A Gagnon
- Department of Chemistry, University of Washington, Seattle, WA, USA
| | - Joshua C Vaughan
- Department of Chemistry, University of Washington, Seattle, WA, USA; Department of Physiology and Biophysics, University of Washington, Seattle, WA, USA.
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31
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Juette MF, Terry DS, Wasserman MR, Zhou Z, Altman RB, Zheng Q, Blanchard SC. The bright future of single-molecule fluorescence imaging. Curr Opin Chem Biol 2014; 20:103-11. [PMID: 24956235 DOI: 10.1016/j.cbpa.2014.05.010] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2014] [Accepted: 05/09/2014] [Indexed: 11/13/2022]
Abstract
Single-molecule Förster resonance energy transfer (smFRET) is an essential and maturing tool to probe biomolecular interactions and conformational dynamics in vitro and, increasingly, in living cells. Multi-color smFRET enables the correlation of multiple such events and the precise dissection of their order and timing. However, the requirements for good spectral separation, high time resolution, and extended observation times place extraordinary demands on the fluorescent labels used in such experiments. Together with advanced experimental designs and data analysis, the development of long-lasting, non-fluctuating fluorophores is therefore proving key to progress in the field. Recently developed strategies for obtaining ultra-stable organic fluorophores spanning the visible spectrum are underway that will enable multi-color smFRET studies to deliver on their promise of previously unachievable biological insights.
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Affiliation(s)
- Manuel F Juette
- Department of Physiology and Biophysics, Weill Medical College of Cornell University, 1300 York Avenue, New York, NY 10065, United States
| | - Daniel S Terry
- Department of Physiology and Biophysics, Weill Medical College of Cornell University, 1300 York Avenue, New York, NY 10065, United States
| | - Michael R Wasserman
- Department of Physiology and Biophysics, Weill Medical College of Cornell University, 1300 York Avenue, New York, NY 10065, United States
| | - Zhou Zhou
- Department of Physiology and Biophysics, Weill Medical College of Cornell University, 1300 York Avenue, New York, NY 10065, United States
| | - Roger B Altman
- Department of Physiology and Biophysics, Weill Medical College of Cornell University, 1300 York Avenue, New York, NY 10065, United States
| | - Qinsi Zheng
- Department of Physiology and Biophysics, Weill Medical College of Cornell University, 1300 York Avenue, New York, NY 10065, United States; Tri-Institutional Training Program in Chemical Biology, Weill Medical College of Cornell University, 1300 York Avenue, New York, NY 10065, United States
| | - Scott C Blanchard
- Department of Physiology and Biophysics, Weill Medical College of Cornell University, 1300 York Avenue, New York, NY 10065, United States; Tri-Institutional Training Program in Chemical Biology, Weill Medical College of Cornell University, 1300 York Avenue, New York, NY 10065, United States.
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32
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Sauer M. Localization microscopy coming of age: from concepts to biological impact. J Cell Sci 2014; 126:3505-13. [PMID: 23950110 DOI: 10.1242/jcs.123612] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Super-resolution fluorescence imaging by single-molecule photoactivation or photoswitching and position determination (localization microscopy) has the potential to fundamentally revolutionize our understanding of how cellular function is encoded at the molecular level. Among all powerful, high-resolution imaging techniques introduced in recent years, localization microscopy excels because it delivers single-molecule information about molecular distributions, even giving absolute numbers of proteins present in subcellular compartments. This provides insight into biological systems at a molecular level that can yield direct experimental feedback for modeling the complexity of biological interactions. In addition, efficient new labeling methods and strategies to improve localization are emerging that promise to achieve true molecular resolution. This raises localization microscopy as a powerful complementary method for correlative light and electron microscopy experiments.
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Affiliation(s)
- Markus Sauer
- Department of Biotechnology and Biophysics, Julius-Maximilians-University Würzburg, Am Hubland, 97074 Würzburg, Germany.
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33
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Allen JR, Ross ST, Davidson MW. Sample preparation for single molecule localization microscopy. Phys Chem Chem Phys 2014; 15:18771-83. [PMID: 24084850 DOI: 10.1039/c3cp53719f] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Single molecule localization-based optical nanoscopy was introduced in 2006, surpassing traditional diffraction-limited resolutions by an order of magnitude. Seven years later, this superresolution technique is continuing to follow a trend of increasing popularity and pervasiveness, with the proof-of-concept work long finished and commercial implementations now available. However one important aspect that tends to become lost in translation is the importance of proper sample preparation, with very few resources addressing the considerations that must be made when preparing samples for imaging with single molecule level sensitivity. Presented here is a an in-depth analysis of all aspects of sample preparation for single molecule superresolution, including both live and fixed cell preparation, choice of fluorophore, fixation and staining techniques, and imaging buffer considerations.
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Affiliation(s)
- John R Allen
- National High Magnetic Field Laboratory and Department of Biological Science, The Florida State University, 1800 East Paul Dirac Drive, Tallahassee, 32304, Florida, USA.
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34
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Holzmeister P, Gietl A, Tinnefeld P. Geminate recombination as a photoprotection mechanism for fluorescent dyes. Angew Chem Int Ed Engl 2014; 53:5685-8. [PMID: 24715383 DOI: 10.1002/anie.201310300] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2013] [Revised: 01/15/2014] [Indexed: 11/09/2022]
Abstract
Despite common presumption due to fast photodestruction pathways through higher excited states, we show that further improvement of photostability is still achievable with diffusion-limited photoprotection formulas. Single-molecule fluorescence spectroscopy reveals that thiolate ions effectively quench triplet states of dyes by photoinduced electron transfer. Interestingly, this reaction rarely yields a radical anion of the dye, but direct return to the ground state is promoted by an almost instantaneous back electron transfer (geminate recombination). This type of mechanism is not detected for commonly used reductants such as ascorbic acid and trolox. The mechanism avoids the formation of radical cations and improves the photostability of single fluorophores. We find that a combination of β-mercaptoethanol and classical reducing and oxidizing systems yields the best results for several dyes including Atto532 and Alexa568.
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Affiliation(s)
- Phil Holzmeister
- Technische Universität Braunschweig, Institut für physikalische und theoretische Chemie, Hans-Sommer-Strasse 10, 38106 Braunschweig (Germany)
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Holzmeister P, Gietl A, Tinnefeld P. Zwillingsrekombination als Photostabilisierungsmechanismus für Fluoreszenzfarbstoffe. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201310300] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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36
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Mehlitz A, Karunakaran K, Herweg JA, Krohne G, van de Linde S, Rieck E, Sauer M, Rudel T. The chlamydial organism Simkania negevensis forms ER vacuole contact sites and inhibits ER-stress. Cell Microbiol 2014; 16:1224-43. [PMID: 24528559 DOI: 10.1111/cmi.12278] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2013] [Revised: 01/28/2014] [Accepted: 02/05/2014] [Indexed: 01/01/2023]
Abstract
Most intracellular bacterial pathogens reside within membrane-surrounded host-derived vacuoles. Few of these bacteria exploit membranes from the host's endoplasmic reticulum (ER) to form a replicative vacuole. Here, we describe the formation of ER-vacuole contact sites as part of the replicative niche of the chlamydial organism Simkania negevensis. Formation of ER-vacuole contact sites is evolutionary conserved in the distantly related protozoan host Acanthamoeba castellanii. Simkania growth is accompanied by mitochondria associating with the Simkania-containing vacuole (SCV). Super-resolution microscopy as well as 3D reconstruction from electron micrographs of serial ultra-thin sections revealed a single vacuolar system forming extensive ER-SCV contact sites on the Simkania vacuolar surface. Simkania infection induced an ER-stress response, which was later downregulated. Induction of ER-stress with Thapsigargin or Tunicamycin was strongly inhibited in cells infected with Simkania. Inhibition of ER-stress was required for inclusion formation and efficient growth, demonstrating a role of ER-stress in the control of Simkania infection. Thus, Simkania forms extensive ER-SCV contact sites in host species evolutionary as diverse as human and amoeba. Moreover, Simkania is the first bacterial pathogen described to interfere with ER-stress induced signalling to promote infection.
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Affiliation(s)
- Adrian Mehlitz
- University of Wuerzburg, Biocenter, Department of Microbiology, Am Hubland, D-97074, Wuerzburg, Germany
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Zheng Q, Juette MF, Jockusch S, Wasserman MR, Zhou Z, Altman RB, Blanchard SC. Ultra-stable organic fluorophores for single-molecule research. Chem Soc Rev 2014; 43:1044-56. [PMID: 24177677 PMCID: PMC3946787 DOI: 10.1039/c3cs60237k] [Citation(s) in RCA: 252] [Impact Index Per Article: 25.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Fluorescence provides a mechanism for achieving contrast in biological imaging that enables investigations of molecular structure, dynamics, and function at high spatial and temporal resolution. Small-molecule organic fluorophores have proven essential for such efforts and are widely used in advanced applications such as single-molecule and super-resolution microscopy. Yet, organic fluorophores, like all fluorescent species, exhibit instabilities in their emission characteristics, including blinking and photobleaching that limit their utility and performance. Here, we review the photophysics and photochemistry of organic fluorophores as they pertain to mitigating such instabilities, with a specific focus on the development of stabilized fluorophores through derivatization. Self-healing organic fluorophores, wherein the triplet state is intramolecularly quenched by a covalently attached protective agent, exhibit markedly improved photostabilities. We discuss the potential for further enhancements towards the goal of developing "ultra-stable" fluorophores spanning the visible spectrum and how such fluorophores are likely to impact the future of single-molecule research.
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Affiliation(s)
- Qinsi Zheng
- Department of Physiology and Biophysics, Weill Medical College of Cornell University, New York, USA.
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38
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Gillanders F, Giordano L, Díaz SA, Jovin TM, Jares-Erijman EA. Photoswitchable fluorescent diheteroarylethenes: substituent effects on photochromic and solvatochromic properties. Photochem Photobiol Sci 2014; 13:603-12. [PMID: 24496436 DOI: 10.1039/c3pp50374g] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Photoswitchable fluorescent diheteroarylethenes are promising candidates for applications in super-resolution molecular localization fluorescence microscopy thanks to their high quantum yields and fatigue-resistant photoswitching characteristics. We have studied the effect of varying substituents on the photophysical properties of six sulfone derivatives of diheteroarylethenes, which display fluorescence in one (closed form) of two thermally stable photochromic states. Electron-donating substituents displace the absorption and emission spectra towards the red without substantially affecting the fluorescence quantum yields. Furthermore, ethoxybromo, a very electron-donating substituent, stabilizes the excited state of the closed isomer to the extent of almost entirely inhibiting its cycloreversion. Multi-parameter Hammett correlations indicate a relationship between the emission maxima and electron-donating character, providing a useful tool in the design of future photochromic molecules. Most of the synthesized compounds exhibit small bathochromic shifts and shorter fluorescence lifetimes with an increase in solvent polarity. However, the ethoxybromo-substituted fluorescent photochrome is unique in its strong solvatochromic behaviour, constituting a photoactivatable (photochromic), fluorescent and highly solvatochromic small organic compound. The Catalán formalism identified solvent dipolarity as the principal basis of the solvatochromism, reflecting the highly polarized nature of this molecule.
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Affiliation(s)
- Florencia Gillanders
- Laboratory of Cellular Dynamics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany.
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van de Linde S, Sauer M. How to switch a fluorophore: from undesired blinking to controlled photoswitching. Chem Soc Rev 2014; 43:1076-87. [DOI: 10.1039/c3cs60195a] [Citation(s) in RCA: 138] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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Monserrate A, Casado S, Flors C. Correlative Atomic Force Microscopy and Localization-Based Super-Resolution Microscopy: Revealing Labelling and Image Reconstruction Artefacts. Chemphyschem 2013; 15:647-50. [DOI: 10.1002/cphc.201300853] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Indexed: 11/10/2022]
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Zhang B, Liu B, Liao J, Chen G, Tang D. Novel Electrochemical Immunoassay for Quantitative Monitoring of Biotoxin Using Target-Responsive Cargo Release from Mesoporous Silica Nanocontainers. Anal Chem 2013; 85:9245-52. [DOI: 10.1021/ac4019878] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Bing Zhang
- Key Laboratory of Analysis and Detection for Food Safety (Ministry of Education & Fujian Province), Department of Chemistry, Fuzhou University, Fuzhou 350108, People’s Republic of China
| | - Bingqian Liu
- Key Laboratory of Analysis and Detection for Food Safety (Ministry of Education & Fujian Province), Department of Chemistry, Fuzhou University, Fuzhou 350108, People’s Republic of China
| | - Jiayao Liao
- Key
Laboratory on Luminescence and Real-Time Analysis (Ministry of Education),
College of Chemistry, Southwest University, Chongqing 400715, People’s Republic of China
| | - Guonan Chen
- Key Laboratory of Analysis and Detection for Food Safety (Ministry of Education & Fujian Province), Department of Chemistry, Fuzhou University, Fuzhou 350108, People’s Republic of China
| | - Dianping Tang
- Key Laboratory of Analysis and Detection for Food Safety (Ministry of Education & Fujian Province), Department of Chemistry, Fuzhou University, Fuzhou 350108, People’s Republic of China
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