1
|
Zhang H, Lesnov GD, Subach OM, Zhang W, Kuzmicheva TP, Vlaskina AV, Samygina VR, Chen L, Ye X, Nikolaeva AY, Gabdulkhakov A, Papadaki S, Qin W, Borshchevskiy V, Perfilov MM, Gavrikov AS, Drobizhev M, Mishin AS, Piatkevich KD, Subach FV. Bright and stable monomeric green fluorescent protein derived from StayGold. Nat Methods 2024; 21:657-665. [PMID: 38409224 DOI: 10.1038/s41592-024-02203-y] [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: 07/20/2023] [Accepted: 01/31/2024] [Indexed: 02/28/2024]
Abstract
The high brightness and photostability of the green fluorescent protein StayGold make it a particularly attractive probe for long-term live-cell imaging; however, its dimeric nature precludes its application as a fluorescent tag for some proteins. Here, we report the development and crystal structures of a monomeric variant of StayGold, named mBaoJin, which preserves the beneficial properties of its precursor, while serving as a tag for structural proteins and membranes. Systematic benchmarking of mBaoJin against popular green fluorescent proteins and other recently introduced monomeric and pseudomonomeric derivatives of StayGold established mBaoJin as a bright and photostable fluorescent protein, exhibiting rapid maturation and high pH/chemical stability. mBaoJin was also demonstrated for super-resolution, long-term live-cell imaging and expansion microscopy. We further showed the applicability of mBaoJin for neuronal labeling in model organisms, including Caenorhabditis elegans and mice.
Collapse
Affiliation(s)
- Hanbin Zhang
- School of Life Sciences, Westlake University, Hangzhou, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, China
| | - Gleb D Lesnov
- Complex of NBICS Technologies, National Research Center 'Kurchatov Institute', Moscow, Russia
| | - Oksana M Subach
- Complex of NBICS Technologies, National Research Center 'Kurchatov Institute', Moscow, Russia
| | - Wenhao Zhang
- School of Life Sciences, Westlake University, Hangzhou, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, China
| | - Tatyana P Kuzmicheva
- Complex of NBICS Technologies, National Research Center 'Kurchatov Institute', Moscow, Russia
| | - Anna V Vlaskina
- Complex of NBICS Technologies, National Research Center 'Kurchatov Institute', Moscow, Russia
| | - Valeriya R Samygina
- Complex of NBICS Technologies, National Research Center 'Kurchatov Institute', Moscow, Russia
- Institute of Crystallography of Federal Research Scientific Center 'Crystallography and Photonics' of the Russian Academy of Sciences, Moscow, Russia
| | - Liangyi Chen
- Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
- PKU-IDG/McGovern Institute for Brain Research, Beijing, China
| | - Xianxin Ye
- Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| | - Alena Yu Nikolaeva
- Complex of NBICS Technologies, National Research Center 'Kurchatov Institute', Moscow, Russia
| | - Azat Gabdulkhakov
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Russia
| | - Stavrini Papadaki
- School of Life Sciences, Westlake University, Hangzhou, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, China
| | - Wenming Qin
- National Facility for Protein Science in Shanghai, Shanghai Advanced Research Institute CAS, Shanghai, China
| | | | - Maxim M Perfilov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Alexey S Gavrikov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Mikhail Drobizhev
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, USA
| | - Alexander S Mishin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Kiryl D Piatkevich
- School of Life Sciences, Westlake University, Hangzhou, China.
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China.
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, China.
| | - Fedor V Subach
- Complex of NBICS Technologies, National Research Center 'Kurchatov Institute', Moscow, Russia.
| |
Collapse
|
2
|
Heydecker M, Shitara A, Chen D, Tran D, Masedunskas A, Tora M, Ebrahim S, Appaduray MA, Galeano Niño JL, Bhardwaj A, Narayan K, Hardeman EC, Gunning PW, Weigert R. Spatial and Temporal Coordination of Force-generating Actin-based Modules Drives Membrane Remodeling In Vivo. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.04.569944. [PMID: 38168275 PMCID: PMC10760165 DOI: 10.1101/2023.12.04.569944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Membrane remodeling drives a broad spectrum of cellular functions, and it is regulated through mechanical forces exerted on the membrane by cytoplasmic complexes. Here, we investigate how actin filaments dynamically tune their structure to control the active transfer of membranes between cellular compartments with distinct compositions and biophysical properties. Using intravital subcellular microscopy in live rodents we show that: a lattice composed of linear filaments stabilizes the granule membrane after fusion with the plasma membrane; and a network of branched filaments linked to the membranes by Ezrin, a regulator of membrane tension, initiates and drives to completion the integration step. Our results highlight how the actin cytoskeleton tunes its structure to adapt to dynamic changes in the biophysical properties of membranes.
Collapse
|
3
|
Cheng T. Single-molecule localization microscopy based on denoising, interpolation and local maxima. Microscopy (Oxf) 2023; 72:336-342. [PMID: 36412750 DOI: 10.1093/jmicro/dfac065] [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: 09/05/2022] [Revised: 11/05/2022] [Accepted: 11/21/2022] [Indexed: 08/05/2023] Open
Abstract
A single fluorescent molecule is highly likely to be located at the center pixel position of a raw image diffused spot in an ideal situation. Even if the molecule and the center pixel position do not completely overlap, they are very close. A single-molecule localization method based on denoising, interpolation and local maxima (DIL) is proposed. The low-resolution raw image is denoised and interpolated, and a new image with a pixel size equal to that of the super-resolution image is attained. The local maxima of the new image are extracted. With this method, it is found that the local maxima positions can be regarded as the fluorescent molecule positions. Simulation results demonstrate that the DIL single-molecule localization accuracy reaches ∼18 nm when the Gaussian noise variance is equal to 0.01. Experimental results demonstrate that the DIL localization methodology is comparable to the Gaussian fitting algorithm and is faster.
Collapse
Affiliation(s)
- Tao Cheng
- School of Mechanical and Automotive Engineering, Guangxi University of Science and Technology, No. 268 Avenue Donghuan, Chengzhong District, Liuzhou, Guangxi 545006, P. R. China
| |
Collapse
|
4
|
Kikuchi K, Adair LD, Lin J, New EJ, Kaur A. Photochemical Mechanisms of Fluorophores Employed in Single-Molecule Localization Microscopy. Angew Chem Int Ed Engl 2023; 62:e202204745. [PMID: 36177530 PMCID: PMC10100239 DOI: 10.1002/anie.202204745] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Indexed: 02/02/2023]
Abstract
Decoding cellular processes requires visualization of the spatial distribution and dynamic interactions of biomolecules. It is therefore not surprising that innovations in imaging technologies have facilitated advances in biomedical research. The advent of super-resolution imaging technologies has empowered biomedical researchers with the ability to answer long-standing questions about cellular processes at an entirely new level. Fluorescent probes greatly enhance the specificity and resolution of super-resolution imaging experiments. Here, we introduce key super-resolution imaging technologies, with a brief discussion on single-molecule localization microscopy (SMLM). We evaluate the chemistry and photochemical mechanisms of fluorescent probes employed in SMLM. This Review provides guidance on the identification and adoption of fluorescent probes in single molecule localization microscopy to inspire the design of next-generation fluorescent probes amenable to single-molecule imaging.
Collapse
Affiliation(s)
- Kai Kikuchi
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, Melbourne, VIC 305, Australia.,School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia.,The University of Sydney Nano Institute, The University of Sydney, Sydney, NSW 2006, Australia
| | - Liam D Adair
- The University of Sydney Nano Institute, The University of Sydney, Sydney, NSW 2006, Australia.,School of Chemistry, The University of Sydney, Sydney, NSW 2006, Australia.,Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, NSW 2006, Australia
| | - Jiarun Lin
- The University of Sydney Nano Institute, The University of Sydney, Sydney, NSW 2006, Australia.,School of Chemistry, The University of Sydney, Sydney, NSW 2006, Australia
| | - Elizabeth J New
- The University of Sydney Nano Institute, The University of Sydney, Sydney, NSW 2006, Australia.,School of Chemistry, The University of Sydney, Sydney, NSW 2006, Australia.,Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, NSW 2006, Australia
| | - Amandeep Kaur
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, Melbourne, VIC 305, Australia.,School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia.,The University of Sydney Nano Institute, The University of Sydney, Sydney, NSW 2006, Australia
| |
Collapse
|
5
|
Pramanik SK, Sreedharan S, Tiwari R, Dutta S, Kandoth N, Barman S, Aderinto SO, Chattopadhyay S, Das A, Thomas JA. Nanoparticles for super-resolution microscopy: intracellular delivery and molecular targeting. Chem Soc Rev 2022; 51:9882-9916. [PMID: 36420611 DOI: 10.1039/d1cs00605c] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Following an overview of the approaches and techniques used to acheive super-resolution microscopy, this review presents the advantages supplied by nanoparticle based probes for these applications. The various clases of nanoparticles that have been developed toward these goals are then critically described and these discussions are illustrated with a variety of examples from the recent literature.
Collapse
Affiliation(s)
- Sumit Kumar Pramanik
- CSIR - Central Salt and Marine Chemicals Research Institute, Gijubhai Badheka Marg, Bhavnagar, Gujarat 364002, India.
| | - Sreejesh Sreedharan
- Human Science Research Centre, University of Derby, Kedleston road, DE22 1GB, UK
| | - Rajeshwari Tiwari
- CSIR - Central Salt and Marine Chemicals Research Institute, Gijubhai Badheka Marg, Bhavnagar, Gujarat 364002, India.
| | - Sourav Dutta
- Department of Chemical Sciences and Centre for Advanced Functional Materials, Indian Institute of Science Education and Research, Kolkata, West Bengal, India.
| | - Noufal Kandoth
- Department of Chemical Sciences and Centre for Advanced Functional Materials, Indian Institute of Science Education and Research, Kolkata, West Bengal, India.
| | - Surajit Barman
- Department of Chemical Sciences and Centre for Advanced Functional Materials, Indian Institute of Science Education and Research, Kolkata, West Bengal, India.
| | - Stephen O Aderinto
- Department of Chemistry, University of Sheffield, Western Bank, Sheffield, S3 7HF, UK.
| | - Samit Chattopadhyay
- Department of Biological Sciences, BITS-Pilani, K K Birla Goa Campus, NH 17B, Zuarinagar, Goa 403726, India.
| | - Amitava Das
- Department of Chemical Sciences and Centre for Advanced Functional Materials, Indian Institute of Science Education and Research, Kolkata, West Bengal, India.
| | - Jim A Thomas
- Department of Chemistry, University of Sheffield, Western Bank, Sheffield, S3 7HF, UK.
| |
Collapse
|
6
|
Direct observation of heterogeneous formation of amyloid spherulites in real-time by super-resolution microscopy. Commun Biol 2022; 5:850. [PMID: 35987792 PMCID: PMC9392779 DOI: 10.1038/s42003-022-03810-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 08/05/2022] [Indexed: 12/14/2022] Open
Abstract
Protein misfolding in the form of fibrils or spherulites is involved in a spectrum of pathological abnormalities. Our current understanding of protein aggregation mechanisms has primarily relied on the use of spectrometric methods to determine the average growth rates and diffraction-limited microscopes with low temporal resolution to observe the large-scale morphologies of intermediates. We developed a REal-time kinetics via binding and Photobleaching LOcalization Microscopy (REPLOM) super-resolution method to directly observe and quantify the existence and abundance of diverse aggregate morphologies of human insulin, below the diffraction limit and extract their heterogeneous growth kinetics. Our results revealed that even the growth of microscopically identical aggregates, e.g., amyloid spherulites, may follow distinct pathways. Specifically, spherulites do not exclusively grow isotropically but, surprisingly, may also grow anisotropically, following similar pathways as reported for minerals and polymers. Combining our technique with machine learning approaches, we associated growth rates to specific morphological transitions and provided energy barriers and the energy landscape at the level of single aggregate morphology. Our unifying framework for the detection and analysis of spherulite growth can be extended to other self-assembled systems characterized by a high degree of heterogeneity, disentangling the broad spectrum of diverse morphologies at the single-molecule level. Real-time super-resolution microscopy analysis reveals the growth kinetics, morphology, and abundance of human insulin amyloid spherulites with different growth pathways.
Collapse
|
7
|
Tao C, Jia D. Super-Resolution Reconstruction Based on BM3D and Compressed Sensing. Microscopy (Oxf) 2022; 71:283-288. [PMID: 35707877 DOI: 10.1093/jmicro/dfac029] [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: 04/06/2022] [Revised: 05/11/2022] [Accepted: 06/14/2022] [Indexed: 11/13/2022] Open
Abstract
In the various papers published in the field of super-resolution microscopy, denoising of raw images based on Block-matching and 3D filtering (BM3D) was rarely reported. BM3D for blocks of different sizes was studied. The denoising ability is related to block sizes. The larger the block is, the better the denoising effect is. When the block size is bigger than 40, the good denoising effect can be achieved. Denoising has great influence on the super-resolution reconstruction effect and the reconstruction time. Better super-resolution reconstruction and shorter reconstruction time can be achieved after denoising. Using compressed sensing, only 20 raw images are needed for super-resolution reconstruction. The temporal resolution is less than half a second. The spatial resolution is also greatly improved.
Collapse
Affiliation(s)
- Cheng Tao
- School of Mechanical and Automotive Engineering, Guangxi University of Science and Technology, Liuzhou, 545006, P R China
| | - Dongdong Jia
- School of Mechanical and Automotive Engineering, Guangxi University of Science and Technology, Liuzhou, 545006, P R China
| |
Collapse
|
8
|
DeSalvo GA, Hoy GR, Kogan IM, Li JZ, Palmer ET, Luz-Ricca E, de Gialluly PS, Wustholz KL. Blinking-Based Multiplexing: A New Approach for Differentiating Spectrally Overlapped Emitters. J Phys Chem Lett 2022; 13:5056-5060. [PMID: 35652798 DOI: 10.1021/acs.jpclett.2c01252] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Multicolor single-molecule imaging is widely applied to answer questions in biology and materials science. However, most studies rely on spectrally distinct fluorescent probes or time-intensive sequential imaging strategies to multiplex. Here, we introduce blinking-based multiplexing (BBM), a simple approach to differentiate spectrally overlapped emitters based solely on their intrinsic blinking dynamics. The blinking dynamics of hundreds of rhodamine 6G and CdSe/ZnS quantum dots on glass are obtained using the same acquisition settings and analyzed with a change point detection algorithm. Although substantial blinking heterogeneity is observed, the analysis yields a blinking metric with 93.5% classification accuracy. We further show that BBM with up to 96.6% accuracy is achieved by using a deep learning algorithm for classification. This proof-of-concept study demonstrates that a single emitter can be accurately classified based on its intrinsic blinking dynamics and without the need to probe its spectral color.
Collapse
Affiliation(s)
- Grace A DeSalvo
- Department of Chemistry, William & Mary, P.O. Box 8795, Williamsburg, Virginia 23187, United States
| | - Grayson R Hoy
- Department of Chemistry, William & Mary, P.O. Box 8795, Williamsburg, Virginia 23187, United States
| | - Isabelle M Kogan
- Department of Chemistry, William & Mary, P.O. Box 8795, Williamsburg, Virginia 23187, United States
| | - John Z Li
- Department of Chemistry, William & Mary, P.O. Box 8795, Williamsburg, Virginia 23187, United States
| | - Elise T Palmer
- Department of Chemistry, William & Mary, P.O. Box 8795, Williamsburg, Virginia 23187, United States
| | - Emilio Luz-Ricca
- Department of Chemistry, William & Mary, P.O. Box 8795, Williamsburg, Virginia 23187, United States
| | - Paul Scemama de Gialluly
- Department of Chemistry, William & Mary, P.O. Box 8795, Williamsburg, Virginia 23187, United States
| | - Kristin L Wustholz
- Department of Chemistry, William & Mary, P.O. Box 8795, Williamsburg, Virginia 23187, United States
| |
Collapse
|
9
|
Mukherjee S, Gardner MK. Centromere Tension Measurement in Budding Yeast Mitosis. Methods Mol Biol 2022; 2415:199-210. [PMID: 34972956 PMCID: PMC9800073 DOI: 10.1007/978-1-0716-1904-9_15] [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: 01/03/2023]
Abstract
During budding yeast mitosis, duplicated chromosomes are aligned at the center of the metaphase mitotic spindle, and the centromeres are stretched by forces generated within the mitotic spindle. In response to these stretching forces, mechanical tension builds up in the centromeric chromatin. The magnitude of this tension is detected by the cell to signal the attachment configuration of the sister chromosomes: a high tension signal would indicate that sister chromosomes are properly attached to opposite spindle poles, while a low tension signal could indicate the lack of a bipolar attachment. A low tension signal drives the cell to correct improper attachments in metaphase, thus preventing potential errors in anaphase chromosome segregation. In this paper, we describe a microscopy-based method to directly measure the magnitude of centromere tension in budding yeast metaphase spindles. The advantage of this method is that quantitative tension estimates are obtained without perturbing spindle and/or chromosome structure and as cells progress normally through mitosis.
Collapse
Affiliation(s)
- Soumya Mukherjee
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN, USA
| | - Melissa K Gardner
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN, USA.
| |
Collapse
|
10
|
Mukherjee S, Thomas C, Wilson R, Simmerman E, Hung ST, Jimenez R. Characterizing Dark State Kinetics and Single Molecule Fluorescence of FusionRed and FusionRed-MQ at Low Irradiances. Phys Chem Chem Phys 2022; 24:14310-14323. [DOI: 10.1039/d2cp00889k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The presence of dark states causes fluorescence intermittency of single molecules due to transitions between “on” and “off” states. Genetically encodable markers such as fluorescent proteins (FPs) exhibit dark states...
Collapse
|
11
|
Dong F, An J, Zhang J, Yin J, Guo W, Wang D, Feng F, Huang S, Zhang J, Cheng H. Blinking Acoustic Nanodroplets Enable Fast Super-resolution Ultrasound Imaging. ACS NANO 2021; 15:16913-16923. [PMID: 34647449 DOI: 10.1021/acsnano.1c07896] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The advent of localization-based super-resolution ultrasound (SRUS) imaging creates a vista for precision vasculature and hemodynamic measurements in brain science, cardiovascular diseases, and cancer. As blinking fluorophores are crucial to super-resolution optical imaging, blinking acoustic contrast agents enabling ultrasound localization microscopy have been highly sought, but only with limited success. Here we report on the discovery and characterization of a type of blinking acoustic nanodroplets (BANDs) ideal for SRUS. BANDs of 200-500 nm diameters comprise a perfluorocarbon-filled core and a shell of DSPC, Pluronic F68, and DSPE-PEG2000. When driven by clinically safe acoustic pulses (MI < 1.9) provided by a diagnostic ultrasound transducer, BANDs underwent reversible vaporization and reliquefaction, manifesting as "blinks", at rates of up to 5 kHz. By sparse activation of perfluorohexane-filled BANDs-C6 at high concentrations, only 100 frames of ultrasound imaging were sufficient to reconstruct super-resolution images of a no-flow tube through either cumulative localization or temporal radiality autocorrelation. Furthermore, the use of high-density BANDs-C6-4 (1 × 108/mL) with a 1:9 admixture of perfluorohexane and perfluorobutane supported the fast SRUS imaging of muscle vasculature in live animals, at 64 μm resolution requiring only 100 frames per layer. We anticipate that the BANDs developed here will greatly boost the application of SRUS in both basic science and clinical settings.
Collapse
Affiliation(s)
- Feihong Dong
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
- State Key Laboratory of Membrane Biology, National Biomedical Imaging Center, Peking-Tsinghua Center for Life Sciences, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing 100871, China
| | - Jian An
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Jiabin Zhang
- State Key Laboratory of Membrane Biology, National Biomedical Imaging Center, Peking-Tsinghua Center for Life Sciences, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing 100871, China
| | - Jingyi Yin
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Wenyu Guo
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Di Wang
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Feng Feng
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Shuo Huang
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Jue Zhang
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
- College of Engineering, Peking University, Beijing 100871, China
- National Biomedical Imaging Center, Peking University, Beijing 100871, China
| | - Heping Cheng
- State Key Laboratory of Membrane Biology, National Biomedical Imaging Center, Peking-Tsinghua Center for Life Sciences, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing 100871, China
- National Biomedical Imaging Center, Peking University, Beijing 100871, China
- Research Unit of Mitochondria in Brain Diseases, Chinese Academy of Medical Sciences, PKU-Nanjing Institute of Translational Medicine, Nanjing 211899, China
| |
Collapse
|
12
|
Jiang Y, Chen H, Men X, Sun Z, Yuan Z, Zhang X, Chiu DT, Wu C, McNeill J. Multimode Time-Resolved Superresolution Microscopy Revealing Chain Packing and Anisotropic Single Carrier Transport in Conjugated Polymer Nanowires. NANO LETTERS 2021; 21:4255-4261. [PMID: 33733782 DOI: 10.1021/acs.nanolett.1c00405] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Here, we developed a novel, multimode superresolution method to perform full-scale structural mapping and measure the energy landscape for single carrier transport along conjugated polymer nanowires. Through quenching of the local emission, the motion of a single photogenerated hole was tracked using blinking-assisted localization microscopy. Then, utilizing binding and unbinding dynamics of quenchers onto the nanowires, local emission spectra were collected sequentially and assembled to create a superresolution map of emission sites throughout the structure. The hole polaron trajectories were overlaid with the superresolution maps to correlate structures with charge transport properties. Using this method, we compared the efficiency of inter- and intrachain hole transport inside the nanowires and for the first time directly measured the depth of carrier traps originated from torsional disorder and chemical defects.
Collapse
Affiliation(s)
- Yifei Jiang
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Haobin Chen
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
- Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Xiaoju Men
- Faculty of Health Science, University of Macau, Taipa 999078, Macau
| | - Zezhou Sun
- Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Zhen Yuan
- Faculty of Health Science, University of Macau, Taipa 999078, Macau
| | - Xuanjun Zhang
- Faculty of Health Science, University of Macau, Taipa 999078, Macau
| | - Daniel T Chiu
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Changfeng Wu
- Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Jason McNeill
- Department of Chemistry, Clemson University, Clemson, South Carolina 29634, United States
| |
Collapse
|
13
|
Miriklis EL, Rozario AM, Rothenberg E, Bell TDM, Whelan DR. Understanding DNA organization, damage, and repair with super-resolution fluorescence microscopy. Methods Appl Fluoresc 2021; 9. [PMID: 33765677 DOI: 10.1088/2050-6120/abf239] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Accepted: 03/25/2021] [Indexed: 11/12/2022]
Abstract
Super-resolution microscopy (SRM) comprises a suite of techniques well-suited to probing the nanoscale landscape of genomic function and dysfunction. Offering the specificity and sensitivity that has made conventional fluorescence microscopy a cornerstone technique of biological research, SRM allows for spatial resolutions as good as 10 nanometers. Moreover, single molecule localization microscopies (SMLMs) enable examination of individual molecular targets and nanofoci allowing for the characterization of subpopulations within a single cell. This review describes how key advances in both SRM techniques and sample preparation have enabled unprecedented insights into DNA structure and function, and highlights many of these new discoveries. Ongoing development and application of these novel, highly interdisciplinary SRM assays will continue to expand the toolbox available for research into the nanoscale genomic landscape.
Collapse
Affiliation(s)
| | | | - Eli Rothenberg
- Department of Biochemistry and Molecular Pharmacology, Perlmutter Cancer Center, New York University School of Medicine, New York, NY, United States of America
| | - Toby D M Bell
- School of Chemistry, Monash University, Clayton, VIC, Australia
| | - Donna R Whelan
- Department of Pharmacy and Biomedical Sciences, La Trobe Institute for Molecular Science, La Trobe University, Bendigo, VIC, Australia
| |
Collapse
|
14
|
Dankovich TM, Rizzoli SO. Challenges facing quantitative large-scale optical super-resolution, and some simple solutions. iScience 2021; 24:102134. [PMID: 33665555 PMCID: PMC7898072 DOI: 10.1016/j.isci.2021.102134] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Optical super-resolution microscopy (SRM) has enabled biologists to visualize cellular structures with near-molecular resolution, giving unprecedented access to details about the amounts, sizes, and spatial distributions of macromolecules in the cell. Precisely quantifying these molecular details requires large datasets of high-quality, reproducible SRM images. In this review, we discuss the unique set of challenges facing quantitative SRM, giving particular attention to the shortcomings of conventional specimen preparation techniques and the necessity for optimal labeling of molecular targets. We further discuss the obstacles to scaling SRM methods, such as lengthy image acquisition and complex SRM data analysis. For each of these challenges, we review the recent advances in the field that circumvent these pitfalls and provide practical advice to biologists for optimizing SRM experiments.
Collapse
Affiliation(s)
- Tal M. Dankovich
- University Medical Center Göttingen, Institute for Neuro- and Sensory Physiology, Göttingen 37073, Germany
- International Max Planck Research School for Neuroscience, Göttingen, Germany
| | - Silvio O. Rizzoli
- University Medical Center Göttingen, Institute for Neuro- and Sensory Physiology, Göttingen 37073, Germany
- Biostructural Imaging of Neurodegeneration (BIN) Center & Multiscale Bioimaging Excellence Center, Göttingen 37075, Germany
| |
Collapse
|
15
|
Xing J, Chen S, Becker S, Yu JY, Cogswell C. ℓ 1-regularized maximum likelihood estimation with focused-spot illumination quadruples the diffraction-limited resolution in fluorescence microscopy. OPTICS EXPRESS 2020; 28:39413-39429. [PMID: 33379491 DOI: 10.1364/oe.411574] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 12/04/2020] [Indexed: 06/12/2023]
Abstract
Super-resolution fluorescence microscopy has proven to be a useful tool in biological studies. To achieve more than two-fold resolution improvement over the diffraction limit, existing methods require exploitation of the physical properties of the fluorophores. Recently, it has been demonstrated that achieving more than two-fold resolution improvement without such exploitation is possible using only a focused illumination spot and numerical post-processing. However, how the achievable resolution is affected by the processing step has not been thoroughly investigated. In this paper, we focus on the processing aspect of this emerging super-resolution microscopy technique. Based on a careful examination of the dominant noise source and the available prior information in the image, we find that if a processing scheme is appropriate for the dominant noise model in the image and can utilize the prior information in the form of sparsity, improved accuracy can be expected. Based on simulation results, we identify an improved processing scheme and apply it in a real-world experiment to super-resolve a known calibration sample. We show an improved super-resolution of 60nm, approximately four times beyond the conventional diffraction-limited resolution.
Collapse
|
16
|
|
17
|
Hermon K, Schidorsky S, Razvag Y, Yakovian O, Sherman E. Time-correlated single molecule localization microscopy enhances resolution and fidelity. Sci Rep 2020; 10:16212. [PMID: 33004828 PMCID: PMC7529757 DOI: 10.1038/s41598-020-72812-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 09/07/2020] [Indexed: 11/29/2022] Open
Abstract
Single-molecule-localization-microscopy (SMLM) enables superresolution imaging of biological samples down to ~ 10–20 nm and in single molecule detail. However, common SMLM reconstruction largely disregards information embedded in the entire intensity trajectories of individual emitters. Here, we develop and demonstrate an approach, termed time-correlated-SMLM (tcSMLM), that uses such information for enhancing SMLM reconstruction. Specifically, tcSMLM is shown to increase the spatial resolution and fidelity of SMLM reconstruction of both simulated and experimental data; esp. upon acquisition under stringent conditions of low SNR, high acquisition rate and high density of emitters. We further provide detailed guidelines and optimization procedures for effectively applying tcSMLM to data of choice. Importantly, our approach can be readily added in tandem to multiple SMLM and related superresolution reconstruction algorithms. Thus, we expect that our approach will become an effective and readily accessible tool for enhancing SMLM and superresolution imaging.
Collapse
Affiliation(s)
- Kobi Hermon
- Racah Institute of Physics, The Hebrew University, 91904, Jerusalem, Israel
| | - Shachar Schidorsky
- Racah Institute of Physics, The Hebrew University, 91904, Jerusalem, Israel
| | - Yair Razvag
- Racah Institute of Physics, The Hebrew University, 91904, Jerusalem, Israel
| | - Oren Yakovian
- Racah Institute of Physics, The Hebrew University, 91904, Jerusalem, Israel
| | - Eilon Sherman
- Racah Institute of Physics, The Hebrew University, 91904, Jerusalem, Israel.
| |
Collapse
|
18
|
Ma Y, Ye Z, Zhang C, Wang X, Li HW, Wong MS, Luo HB, Xiao L. Deep Red Blinking Fluorophore for Nanoscopic Imaging and Inhibition of β-Amyloid Peptide Fibrillation. ACS NANO 2020; 14:11341-11351. [PMID: 32857496 DOI: 10.1021/acsnano.0c03400] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Deposition and aggregation of β-amyloid (Aβ) peptides are demonstrated to be closely related to the pathogenesis of Alzheimer's disease (AD). Development of functional molecules capable of visualizing Aβ1-40 aggregates with nanoscale resolution and even modulating Aβ assembly has attracted great attention recently. In this work, we use monocyanine fluorophore as the lead structure to develop a set of deep red carbazole-based cyanine molecules, which can specifically bind with Aβ1-40 fibril via electrostatic and van der Waals interactions. Spectroscopic and microscopic characterizations demonstrate that one of these fluorophores, (E)-1-(2-(2-methoxyethoxy)ethyl)-4-(2-(9-methyl-9H-carbazol-3-yl)vinyl) quinolinium iodide (me-slg) can bind to Aβ1-40 aggregates with strong fluorescence enhancement. The photophysical properties of me-slg at the single-molecule level, including low "on/off" duty cycle, high photon output, and sufficient switching cycles, enable real-time nanoscopic imaging of Aβ1-40 aggregates. Morphology-dependent toxic effect of Aβ1-40 aggregates toward PC12 cells is unveiled from in situ nanoscopic fluorescence imaging. In addition, me-slg displays a strong inhibitory effect on Aβ1-40 fibrillation in a low inhibitor-protein ratio (e.g., I:P = 0.2). A noticeably reduced cytotoxic effect of Aβ1-40 after the addition of me-slg is also confirmed. These results afford promising applications in the design of a nanoscopic imaging probe for amyloid fibril as well as the development of inhibitors to modulate the fibrillation process.
Collapse
Affiliation(s)
- Yuanyuan Ma
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Zhongju Ye
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Chen Zhang
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Xueli Wang
- Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong SAR, China
| | - Hung-Wing Li
- Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong SAR, China
| | - Man Shing Wong
- Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong SAR, China
| | - Hai-Bin Luo
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Lehui Xiao
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, College of Chemistry, Nankai University, Tianjin 300071, China
| |
Collapse
|
19
|
Jiang Y, Hu Q, Chen H, Zhang J, Chiu DT, McNeill J. Dual‐Mode Superresolution Imaging Using Charge Transfer Dynamics in Semiconducting Polymer Dots. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202006348] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Yifei Jiang
- Department of Chemistry Clemson University Clemson SC 29634 USA
- Department of Chemistry University of Washington Seattle WA 98195 USA
| | - Qiongzheng Hu
- Department of Chemistry University of Washington Seattle WA 98195 USA
| | - Haobin Chen
- Department of Chemistry University of Washington Seattle WA 98195 USA
| | - Jicheng Zhang
- Department of Chemistry University of Washington Seattle WA 98195 USA
| | - Daniel T. Chiu
- Department of Chemistry University of Washington Seattle WA 98195 USA
| | - Jason McNeill
- Department of Chemistry Clemson University Clemson SC 29634 USA
| |
Collapse
|
20
|
Jiang Y, Hu Q, Chen H, Zhang J, Chiu DT, McNeill J. Dual-Mode Superresolution Imaging Using Charge Transfer Dynamics in Semiconducting Polymer Dots. Angew Chem Int Ed Engl 2020; 59:16173-16180. [PMID: 32521111 PMCID: PMC7811208 DOI: 10.1002/anie.202006348] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 06/09/2020] [Indexed: 11/08/2022]
Abstract
In a conjugated polymer-based single-particle heterojunction, stochastic fluctuations of the photogenerated hole population lead to spontaneous fluorescence switching. We found that 405 nm irradiation can induce charge recombination and activate the single-particle emission. Based on these phenomena, we developed a novel class of semiconducting polymer dots that can operate in two superresolution imaging modes. The spontaneous switching mode offers efficient imaging of large areas, with <10 nm localization precision, while the photoactivation/deactivation mode offers slower imaging, with further improved localization precision (ca. 1 nm), showing advantages in resolving small structures that require high spatial resolution. Superresolution imaging of microtubules and clathrin-coated pits was demonstrated, under both modes. The excellent localization precision and versatile imaging options provided by these nanoparticles offer clear advantages for imaging of various biological systems.
Collapse
Affiliation(s)
- Yifei Jiang
- Department of Chemistry, Clemson University, Clemson, SC, 29634, USA
- Department of Chemistry, University of Washington, Seattle, WA, 98195, USA
| | - Qiongzheng Hu
- Department of Chemistry, University of Washington, Seattle, WA, 98195, USA
| | - Haobin Chen
- Department of Chemistry, University of Washington, Seattle, WA, 98195, USA
| | - Jicheng Zhang
- Department of Chemistry, University of Washington, Seattle, WA, 98195, USA
| | - Daniel T Chiu
- Department of Chemistry, University of Washington, Seattle, WA, 98195, USA
| | - Jason McNeill
- Department of Chemistry, Clemson University, Clemson, SC, 29634, USA
| |
Collapse
|
21
|
Jang S, Kim M, Shim S. Reductively Caged, Photoactivatable DNA‐PAINT for High‐Throughput Super‐resolution Microscopy. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201915377] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Soohyun Jang
- Center for Molecular Spectroscopy and Dynamics Institute for Basic Science (IBS) Anam-ro 145, Sungbuk-gu Seoul 02841 Republic of Korea
- Department of Chemistry Korea University Anam-ro 145, Sungbuk-gu Seoul 02841 Republic of Korea
| | - Mingi Kim
- Department of Chemistry Korea University Anam-ro 145, Sungbuk-gu Seoul 02841 Republic of Korea
| | - Sang‐Hee Shim
- Center for Molecular Spectroscopy and Dynamics Institute for Basic Science (IBS) Anam-ro 145, Sungbuk-gu Seoul 02841 Republic of Korea
- Department of Chemistry Korea University Anam-ro 145, Sungbuk-gu Seoul 02841 Republic of Korea
| |
Collapse
|
22
|
Abstract
Recent advances in super-resolution (sub-diffraction limited) microscopy have yielded remarkable insights into the nanoscale architecture and behavior of cells. In addition to the capacity to provide sub 100 nm resolution, these technologies offer unique quantitative opportunities with particular relevance to platelet and megakaryocyte biology. In this review, we provide a short introduction to modern super-resolution microscopy, its applications in the field of platelet and megakaryocyte biology, and emerging quantitative approaches which will allow for unprecedented insights into the biology of these unique cell types.
Collapse
Affiliation(s)
- Abdullah O Khan
- Institute of Cardiovascular Sciences, College of Medical and Dental Science, University of Birmingham , Birmingham, UK
| | - Jeremy A Pike
- Institute of Cardiovascular Sciences, College of Medical and Dental Science, University of Birmingham , Birmingham, UK.,Centre of Membrane Proteins and Receptors, Universities of Birmingham and Nottingham , UK
| |
Collapse
|
23
|
Jang S, Kim M, Shim S. Reductively Caged, Photoactivatable DNA‐PAINT for High‐Throughput Super‐resolution Microscopy. Angew Chem Int Ed Engl 2020; 59:11758-11762. [DOI: 10.1002/anie.201915377] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 02/13/2020] [Indexed: 01/17/2023]
Affiliation(s)
- Soohyun Jang
- Center for Molecular Spectroscopy and Dynamics Institute for Basic Science (IBS) Anam-ro 145, Sungbuk-gu Seoul 02841 Republic of Korea
- Department of Chemistry Korea University Anam-ro 145, Sungbuk-gu Seoul 02841 Republic of Korea
| | - Mingi Kim
- Department of Chemistry Korea University Anam-ro 145, Sungbuk-gu Seoul 02841 Republic of Korea
| | - Sang‐Hee Shim
- Center for Molecular Spectroscopy and Dynamics Institute for Basic Science (IBS) Anam-ro 145, Sungbuk-gu Seoul 02841 Republic of Korea
- Department of Chemistry Korea University Anam-ro 145, Sungbuk-gu Seoul 02841 Republic of Korea
| |
Collapse
|
24
|
Lu M, Kaminski CF, Schierle GSK. Advanced fluorescence imaging of in situ protein aggregation. Phys Biol 2020; 17:021001. [DOI: 10.1088/1478-3975/ab694e] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
|
25
|
Chakraborty C, Thompson S, Lyons VJ, Snoeyink C, Pappas D. Modulation and study of photoblinking behavior in dye doped silver-silica core-shell nanoparticles for localization super-resolution microscopy. NANOTECHNOLOGY 2019; 30:455704. [PMID: 31357181 PMCID: PMC7278086 DOI: 10.1088/1361-6528/ab368d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Blinking of fluorescent nanoparticles is a compelling phenomenon with widely debated mechanisms. The ability to inhibit or control blinking is important for applications in the field of optical, semiconductor and fluorescent imaging. Self-blinking nanomaterials are also attractive labels for localization-based super-resolution microscopy. In this work, we have synthesized silver core silica nanoparticles (Ag@SiO2) doped with Rhodamine 110 and studied the parameters that affect blinking. We found that under nitrogen rich conditions the nanoparticles shifted towards higher duty cycles. Also, it was found that hydrated nanoparticles showed a less drastic response to nitrogen rich conditions as compared to dried nanoparticles, indicating that surrounding matrix played a role in the response of nanoparticles to molecular oxygen. Further, the blinking is not a multi-body phenomena, super-resolution localization combined with intensity histogram analysis confirmed that single particles are emitting.
Collapse
Affiliation(s)
- Chumki Chakraborty
- Department of Mechanical Engineering, Texas Tech University, Lubbock, TX 79409, United States of America
- Both authors contributed equally to this work
| | - S Thompson
- Department of Chemistry, Texas Tech University, Lubbock, TX 79409, United States of America
- Both authors contributed equally to this work
| | - Veronica J Lyons
- Department of Chemistry, Texas Tech University, Lubbock, TX 79409, United States of America
| | - Craig Snoeyink
- Department of Mechanical Engineering, University at Buffalo, Buffalo, NY 14260, United States of America
| | - Dimitri Pappas
- Department of Chemistry, Texas Tech University, Lubbock, TX 79409, United States of America
| |
Collapse
|
26
|
Ye Z, Wei L, Geng X, Wang X, Li Z, Xiao L. Mitochondrion-Specific Blinking Fluorescent Bioprobe for Nanoscopic Monitoring of Mitophagy. ACS NANO 2019; 13:11593-11602. [PMID: 31592641 DOI: 10.1021/acsnano.9b05354] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Dynamic changes of mitochondrial morphology play an important role in cellular metabolism. Real-time monitoring mitochondrial ultrastructural dynamics at nanometer-scale resolution is crucially desired for further understanding of the mitochondria-based cellular function. In this work, we introduce a fluorescent carbon dot, which can selectively target mitochondria in live cells (named as MitoCD). MitoCD can effectively accumulate in mitochondria regardless of the decrease or vanishing of mitochondrial membrane potential (MMP), enabling the exploration of MMP-independent mitochondrial process. Moreover, the MitoCD is a thiol-based reaction-free probe that target mitochondria without consuming the thiol groups from mitochondrial proteins. Additionally, the MitoCD possesses good photophysical properties under physiological conditions, such as burst-like blinking, high photon counts, and low "on"/"off" ratio, which are specifically suitable for localization-based nanoscopic imaging. According to the optical microscopic imaging results, dynamical fission and fusion processes from mitochondria have been observed in live cells. During mitophagy, it is found that reticular formation of the mitochondria gradually collapsed, and then a portion of mitochondria split and vanished. Owing to the attractive biological and special photophysical properties, this probe displays promising application in a variety of super-resolution based biological studies and will provide deep insight in mitochondrial metabolism.
Collapse
Affiliation(s)
- Zhongju Ye
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, College of Chemistry , Nankai University , Tianjin 300071 , China
| | - Lin Wei
- College of Chemistry and Chemical Engineering , Hunan Normal University , Changsha 410081 , China
| | - Xin Geng
- College of Chemistry and Molecular Engineering , Zhengzhou University , Zhengzhou 450001 , China
| | - Xin Wang
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, College of Chemistry , Nankai University , Tianjin 300071 , China
| | - Zhaohui Li
- College of Chemistry and Molecular Engineering , Zhengzhou University , Zhengzhou 450001 , China
| | - Lehui Xiao
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, College of Chemistry , Nankai University , Tianjin 300071 , China
| |
Collapse
|
27
|
Khan AO, White CW, Pike JA, Yule J, Slater A, Hill SJ, Poulter NS, Thomas SG, Morgan NV. Optimised insert design for improved single-molecule imaging and quantification through CRISPR-Cas9 mediated knock-in. Sci Rep 2019; 9:14219. [PMID: 31578415 PMCID: PMC6775134 DOI: 10.1038/s41598-019-50733-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Accepted: 09/18/2019] [Indexed: 12/29/2022] Open
Abstract
The use of CRISPR-Cas9 genome editing to introduce endogenously expressed tags has the potential to address a number of the classical limitations of single molecule localisation microscopy. In this work we present the first systematic comparison of inserts introduced through CRISPR-knock in, with the aim of optimising this approach for single molecule imaging. We show that more highly monomeric and codon optimised variants of mEos result in improved expression at the TubA1B locus, despite the use of identical guides, homology templates, and selection strategies. We apply this approach to target the G protein-coupled receptor (GPCR) CXCR4 and show a further insert dependent effect on expression and protein function. Finally, we show that compared to over-expressed CXCR4, endogenously labelled samples allow for accurate single molecule quantification on ligand treatment. This suggests that despite the complications evident in CRISPR mediated labelling, the development of CRISPR-PALM has substantial quantitative benefits.
Collapse
Affiliation(s)
- Abdullah O Khan
- Institute of Cardiovascular Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK.
| | - Carl W White
- Centre of Membrane and Protein and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, UK
- Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, UK
- Molecular Endocrinology and Pharmacology, Harry Perkins Institute of Medical Research, Nedlands, WA, Australia
- Centre for Medical Research, The University of Western Australia, Crawley, WA, Australia
| | - Jeremy A Pike
- Institute of Cardiovascular Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
- Centre of Membrane and Protein and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, UK
| | - Jack Yule
- Institute of Cardiovascular Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
- Centre of Membrane and Protein and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, UK
| | - Alexandre Slater
- Institute of Cardiovascular Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Stephen J Hill
- Centre of Membrane and Protein and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, UK
- Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Natalie S Poulter
- Institute of Cardiovascular Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
- Centre of Membrane and Protein and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, UK
| | - Steven G Thomas
- Institute of Cardiovascular Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK.
- Centre of Membrane and Protein and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, UK.
| | - Neil V Morgan
- Institute of Cardiovascular Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK.
| |
Collapse
|
28
|
Dynamic polyhedral actomyosin lattices remodel micron-scale curved membranes during exocytosis in live mice. Nat Cell Biol 2019; 21:933-939. [PMID: 31358965 DOI: 10.1038/s41556-019-0365-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Accepted: 06/25/2019] [Indexed: 01/10/2023]
Abstract
Actomyosin networks, the cell's major force production machineries, remodel cellular membranes during myriad dynamic processes1,2 by assembling into various architectures with distinct force generation properties3,4. While linear and branched actomyosin architectures are well characterized in cell-culture and cell-free systems3, it is not known how actin and myosin networks form and function to remodel membranes in complex three-dimensional mammalian tissues. Here, we use four-dimensional spinning-disc confocal microscopy with image deconvolution to acquire macromolecular-scale detail of dynamic actomyosin networks in exocrine glands of live mice. We address how actin and myosin organize around large membrane-bound secretory vesicles and generate the forces required to complete exocytosis5-7. We find that actin and non-muscle myosin II (NMII) assemble into previously undescribed polyhedral-like lattices around the vesicle membrane. The NMII lattice comprises bipolar minifilaments8-10 as well as non-canonical three-legged configurations. Using photobleaching and pharmacological perturbations in vivo, we show that actomyosin contractility and actin polymerization together push on the underlying vesicle membrane to overcome the energy barrier and complete exocytosis7. Our imaging approach thus unveils a force-generating actomyosin lattice that regulates secretion in the exocrine organs of live animals.
Collapse
|
29
|
Mishin AS, Lukyanov KA. Live-Cell Super-resolution Fluorescence Microscopy. BIOCHEMISTRY (MOSCOW) 2019; 84:S19-S31. [PMID: 31213193 DOI: 10.1134/s0006297919140025] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Super-resolution fluorescence microscopy (nanoscopy) enables imaging with a spatial resolution much higher than the diffraction limit of optical microscopy. However, the methods of fluorescence nanoscopy are still poorly suitable for studying living cells. In this review, we describe some of methods for nanoscopy and specific fluorescent labeling aimed to decrease the damaging effects of light illumination on live samples.
Collapse
Affiliation(s)
- A S Mishin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia.
| | - K A Lukyanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
| |
Collapse
|
30
|
Ye Z, Wei L, Li Y, Xiao L. Efficient Modulation of β-Amyloid Peptide Fibrillation with Polymer Nanoparticles Revealed by Super-Resolution Optical Microscopy. Anal Chem 2019; 91:8582-8590. [PMID: 31148450 DOI: 10.1021/acs.analchem.9b01877] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
β-Amyloid peptide (Aβ) aggregation is the essential hallmark of neurodegenerative disorders such as Alzheimer's disease. Efficient inhibitors are highly desired for the prevention of Aβ assembly that has been considered as the primary therapeutic strategy for neurodegenerative diseases. Apart from this, visualization of the aggregates and morphology at high spatial resolution is widely considered of crucial significance on biological treatment. In this work, we have developed small-sized (with diameter of ∼4.7 nm) and positively charged fluorescent conjugated polymer nanoparticles (CPNPs) with strong inhibition effect on Aβ1-40 peptides fibrillation. Interestingly, the CPNPs also possess excellent photophysical properties, including high photon counts, robust blinking, and repetitive fluorescence switching, that are especially suitable for localization-based super-resolution imaging. Spatial resolution of ∼20 nm for these blinking CPNPs is readily achieved. According to the optical microscopic results, it was found that binding of CPNPs to the terminal of seed fibrils can effectively inhibit the fibrillation process. Owing to these attractive biological and unique photophysical properties, the small-sized CPNPs show high potential in a variety of super-resolution based biological applications.
Collapse
Affiliation(s)
- Zhongju Ye
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, College of Chemistry , Nankai University , Tianjin , 300071 , China
| | - Lin Wei
- Key Laboratory of Phytochemical R&D of Hunan Province, College of Chemistry and Chemical Engineering , Hunan Normal University , Changsha , 410081 , China
| | - Yiliang Li
- Department of Rehabilitation Medicine , The Affiliated Baoan Hospital of Southern Medical University, The Second Affiliated Hospital of Shenzhen University, The People's Hospital of Baoan Shenzhen , Shenzhen , 510530 , China
| | - Lehui Xiao
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, College of Chemistry , Nankai University , Tianjin , 300071 , China
| |
Collapse
|
31
|
Lu CH, Tang WC, Liu YT, Chang SW, Wu FCM, Chen CY, Tsai YC, Yang SM, Kuo CW, Okada Y, Hwu YK, Chen P, Chen BC. Lightsheet localization microscopy enables fast, large-scale, and three-dimensional super-resolution imaging. Commun Biol 2019; 2:177. [PMID: 31098410 PMCID: PMC6509110 DOI: 10.1038/s42003-019-0403-9] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Accepted: 03/26/2019] [Indexed: 01/08/2023] Open
Abstract
Recent advances in super-resolution microscopy allow the localization of single molecules within individual cells but not within multiple whole cells due to weak signals from single molecules and slow acquisition process for point accumulation to reconstruct super-resolution images. Here, we report a fast, large-scale, and three-dimensional super-resolution fluorescence microscope based on single-wavelength Bessel lightsheet to selectively illuminate spontaneous blinking fluorophores tagged to the proteins of interest in space. Critical parameters such as labeling density, excitation power, and exposure time were systematically optimized resulting in a maximum imaging speed of 2.7 × 104 µm3 s-1. Fourier ring correlation analysis revealed a reconstructed image with a lateral resolution of ~75 nm through the accumulation of 250 image volumes on immobilized samples within 15 min. Hence, the designed system could open new insights into the discovery of complex biological structures and live 3D localization imaging.
Collapse
Affiliation(s)
- Chieh-Han Lu
- Research Center for Applied Sciences, Academia Sinica, Taipei, 11529 Taiwan
| | - Wei-Chun Tang
- Research Center for Applied Sciences, Academia Sinica, Taipei, 11529 Taiwan
| | - Yen-Ting Liu
- Research Center for Applied Sciences, Academia Sinica, Taipei, 11529 Taiwan
| | - Shu-Wei Chang
- Research Center for Applied Sciences, Academia Sinica, Taipei, 11529 Taiwan
| | | | - Chin-Yi Chen
- Research Center for Applied Sciences, Academia Sinica, Taipei, 11529 Taiwan
| | - Yun-Chi Tsai
- Research Center for Applied Sciences, Academia Sinica, Taipei, 11529 Taiwan
| | - Shun-Min Yang
- Institute of Physics, Academia Sinica, Taipei, 11529 Taiwan
| | - Chiung-Wen Kuo
- Research Center for Applied Sciences, Academia Sinica, Taipei, 11529 Taiwan
| | - Yasushi Okada
- Laboratory for Cell Polarity Regulation, Center for Biosystems Dynamics Research, RIKEN, Suita, Osaka, 565-0874 Japan
- Department of Physics, Universal Biology Institute and International Research Center for Neurointelligence, The University of Tokyo, Tokyo, 113-0033 Japan
| | - Yeu-Kuang Hwu
- Institute of Physics, Academia Sinica, Taipei, 11529 Taiwan
| | - Peilin Chen
- Research Center for Applied Sciences, Academia Sinica, Taipei, 11529 Taiwan
| | - Bi-Chang Chen
- Research Center for Applied Sciences, Academia Sinica, Taipei, 11529 Taiwan
- Brain Research Center, National Tsing Hua University, Hsinchu, 30013 Taiwan
| |
Collapse
|
32
|
Nemukhin AV, Grigorenko BL, Khrenova MG, Krylov AI. Computational Challenges in Modeling of Representative Bioimaging Proteins: GFP-Like Proteins, Flavoproteins, and Phytochromes. J Phys Chem B 2019; 123:6133-6149. [DOI: 10.1021/acs.jpcb.9b00591] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Alexander V. Nemukhin
- Department of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russia
- Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow 119334, Russia
| | - Bella L. Grigorenko
- Department of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russia
- Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow 119334, Russia
| | - Maria G. Khrenova
- Department of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russia
- Federal Research Center of Biotechnology, Bach Institute of Biochemistry, Russian Academy of Sciences, Moscow 119071, Russian
| | - Anna I. Krylov
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-0482, United States
| |
Collapse
|
33
|
Klusmeier N, Schnittler HJ, Seebach J. A Novel Microscopic Assay Reveals Heterogeneous Regulation of Local Endothelial Barrier Function. Biophys J 2019; 116:1547-1559. [PMID: 30878197 PMCID: PMC6486479 DOI: 10.1016/j.bpj.2019.02.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 02/11/2019] [Accepted: 02/13/2019] [Indexed: 12/27/2022] Open
Abstract
Blood vessels are covered with endothelial cells on their inner surfaces, forming a selective and semipermeable barrier between the blood and the underlying tissue. Many pathological processes, such as inflammation or cancer metastasis, are accompanied by an increased vascular permeability. Progress in live cell imaging techniques has recently revealed that the structure of endothelial cell contacts is constantly reorganized and that endothelial junctions display high heterogeneities at a subcellular level even within one cell. Although it is assumed that this dynamic remodeling is associated with a local change in endothelial barrier function, a direct proof is missing mainly because of a lack of appropriate experimental techniques. Here, we describe a new assay to dynamically measure local endothelial barrier function with a lateral resolution of ∼15 μm and a temporal resolution of 1 min. In this setup, fluorescence-labeled molecules are added to the apical compartment of an endothelial monolayer, and the penetration of molecules from the apical to the basal compartment is recorded by total internal reflection fluorescence microscopy utilizing the generated evanescent field. With this technique, we found a remarkable heterogeneity in the local permeability for albumin within confluent endothelial cell layers. In regions with low permeability, stimulation with the proinflammatory agent histamine results in a transient increase in paracellular permeability. The effect showed a high variability along the contact of one individual cell, indicating a local regulation of endothelial barrier function. In regions with high basal permeability, histamine had no obvious effect. In contrast, the barrier-enhancing drug forskolin reduces the permeability for albumin and dextran uniformly along the cell junctions. Because this new approach can be readily combined with other live cell imaging techniques, it will contribute to a better understanding of the mechanisms underlying subcellular junctional reorganization during wound healing, inflammation, and angiogenesis.
Collapse
Affiliation(s)
- Nadine Klusmeier
- Institute of Anatomy and Vascular Biology, Westfälische Wilhelms-Universität Münster, Münster, Germany
| | - Hans-Joachim Schnittler
- Institute of Anatomy and Vascular Biology, Westfälische Wilhelms-Universität Münster, Münster, Germany
| | - Jochen Seebach
- Institute of Anatomy and Vascular Biology, Westfälische Wilhelms-Universität Münster, Münster, Germany.
| |
Collapse
|
34
|
Stehr F, Stein J, Schueder F, Schwille P, Jungmann R. Flat-top TIRF illumination boosts DNA-PAINT imaging and quantification. Nat Commun 2019; 10:1268. [PMID: 30894522 PMCID: PMC6426843 DOI: 10.1038/s41467-019-09064-6] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 02/19/2019] [Indexed: 11/09/2022] Open
Abstract
Super-resolution (SR) techniques have extended the optical resolution down to a few nanometers. However, quantitative treatment of SR data remains challenging due to its complex dependence on a manifold of experimental parameters. Among the different SR variants, DNA-PAINT is relatively straightforward to implement, since it achieves the necessary ‘blinking’ without the use of rather complex optical or chemical activation schemes. However, it still suffers from image and quantification artifacts caused by inhomogeneous optical excitation. Here we demonstrate that several experimental challenges can be alleviated by introducing a segment-wise analysis approach and ultimately overcome by implementing a flat-top illumination profile for TIRF microscopy using a commercially-available beam-shaping device. The improvements with regards to homogeneous spatial resolution and precise kinetic information over the whole field-of-view were quantitatively assayed using DNA origami and cell samples. Our findings open the door to high-throughput DNA-PAINT studies with thus far unprecedented accuracy for quantitative data interpretation. The use of TIRF microscopy for DNA-PAINT experiments is limited by inhomogeneous illumination. Here the authors show that quantitative analysis of single-molecule TIRF experiments can be improved by using a segment-wise analysis approach and overcome by using a beam-shaping device to give a flat-top illumination profile.
Collapse
Affiliation(s)
- Florian Stehr
- Max Planck Institute of Biochemistry, 82152, Martinsried, Munich, Germany
| | - Johannes Stein
- Max Planck Institute of Biochemistry, 82152, Martinsried, Munich, Germany
| | - Florian Schueder
- Max Planck Institute of Biochemistry, 82152, Martinsried, Munich, Germany.,Faculty of Physics and Center for Nanoscience, Ludwig Maximilian University, 80539, Munich, Germany
| | - Petra Schwille
- Max Planck Institute of Biochemistry, 82152, Martinsried, Munich, Germany.
| | - Ralf Jungmann
- Max Planck Institute of Biochemistry, 82152, Martinsried, Munich, Germany. .,Faculty of Physics and Center for Nanoscience, Ludwig Maximilian University, 80539, Munich, Germany.
| |
Collapse
|
35
|
Halabi EA, Pinotsi D, Rivera-Fuentes P. Photoregulated fluxional fluorophores for live-cell super-resolution microscopy with no apparent photobleaching. Nat Commun 2019; 10:1232. [PMID: 30874551 PMCID: PMC6420572 DOI: 10.1038/s41467-019-09217-7] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 02/25/2019] [Indexed: 01/13/2023] Open
Abstract
Photoswitchable molecules have multiple applications in the physical and life sciences because their properties can be modulated with light. Fluxional molecules, which undergo rapid degenerate rearrangements in the electronic ground state, also exhibit switching behavior. The stochastic nature of fluxional switching, however, has hampered its application in the development of functional molecules and materials. Here we combine photoswitching and fluxionality to develop a fluorophore that enables very long (>30 min) time-lapse single-molecule localization microscopy in living cells with minimal phototoxicity and no apparent photobleaching. These long time-lapse experiments allow us to track intracellular organelles with unprecedented spatiotemporal resolution, revealing new information of the three-dimensional compartmentalization of synaptic vesicle trafficking in live human neurons. Super-resolution microscopy with spontaneously blinking dyes is dependent on pH and polarity of the medium. Here the authors introduce a photoactivatable fluxional fluorophore for live cell imaging that allows control over the fraction of spontaneously blinking molecules independently of medium properties.
Collapse
Affiliation(s)
- Elias A Halabi
- Laboratory of Organic Chemistry, ETH Zurich, Zurich, 8093, Switzerland
| | - Dorothea Pinotsi
- Scientific Center for Optical and Electron Microscopy, ETH Zurich, Zurich, 8093, Switzerland
| | | |
Collapse
|
36
|
Mamode Cassim A, Gouguet P, Gronnier J, Laurent N, Germain V, Grison M, Boutté Y, Gerbeau-Pissot P, Simon-Plas F, Mongrand S. Plant lipids: Key players of plasma membrane organization and function. Prog Lipid Res 2018; 73:1-27. [PMID: 30465788 DOI: 10.1016/j.plipres.2018.11.002] [Citation(s) in RCA: 124] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 11/07/2018] [Accepted: 11/09/2018] [Indexed: 12/29/2022]
Abstract
The plasma membrane (PM) is the biological membrane that separates the interior of all cells from the outside. The PM is constituted of a huge diversity of proteins and lipids. In this review, we will update the diversity of molecular species of lipids found in plant PM. We will further discuss how lipids govern global properties of the plant PM, explaining that plant lipids are unevenly distributed and are able to organize PM in domains. From that observation, it emerges a complex picture showing a spatial and multiscale segregation of PM components. Finally, we will discuss how lipids are key players in the function of PM in plants, with a particular focus on plant-microbe interaction, transport and hormone signaling, abiotic stress responses, plasmodesmata function. The last chapter is dedicated to the methods that the plant membrane biology community needs to develop to get a comprehensive understanding of membrane organization in plants.
Collapse
Affiliation(s)
- Adiilah Mamode Cassim
- Laboratoire de Biogenèse Membranaire (LBM), CNRS, University of Bordeaux, UMR 5200, F-33882 Villenave d'Ornon, France
| | - Paul Gouguet
- Laboratoire de Biogenèse Membranaire (LBM), CNRS, University of Bordeaux, UMR 5200, F-33882 Villenave d'Ornon, France
| | - Julien Gronnier
- Laboratoire de Biogenèse Membranaire (LBM), CNRS, University of Bordeaux, UMR 5200, F-33882 Villenave d'Ornon, France
| | - Nelson Laurent
- Agroécologie, AgroSup Dijon, INRA, University of Bourgogne Franche-Comté, F-21000 Dijon, ERL 6003 CNRS, Dijon, France
| | - Véronique Germain
- Laboratoire de Biogenèse Membranaire (LBM), CNRS, University of Bordeaux, UMR 5200, F-33882 Villenave d'Ornon, France
| | - Magali Grison
- Laboratoire de Biogenèse Membranaire (LBM), CNRS, University of Bordeaux, UMR 5200, F-33882 Villenave d'Ornon, France
| | - Yohann Boutté
- Laboratoire de Biogenèse Membranaire (LBM), CNRS, University of Bordeaux, UMR 5200, F-33882 Villenave d'Ornon, France
| | - Patricia Gerbeau-Pissot
- Agroécologie, AgroSup Dijon, INRA, University of Bourgogne Franche-Comté, F-21000 Dijon, ERL 6003 CNRS, Dijon, France
| | - Françoise Simon-Plas
- Agroécologie, AgroSup Dijon, INRA, University of Bourgogne Franche-Comté, F-21000 Dijon, ERL 6003 CNRS, Dijon, France.
| | - Sébastien Mongrand
- Laboratoire de Biogenèse Membranaire (LBM), CNRS, University of Bordeaux, UMR 5200, F-33882 Villenave d'Ornon, France.
| |
Collapse
|
37
|
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.
Collapse
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
| |
Collapse
|
38
|
Marsh RJ, Pfisterer K, Bennett P, Hirvonen LM, Gautel M, Jones GE, Cox S. Artifact-free high-density localization microscopy analysis. Nat Methods 2018; 15:689-692. [DOI: 10.1038/s41592-018-0072-5] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Accepted: 06/08/2018] [Indexed: 11/09/2022]
|
39
|
Orth A, Ghosh RN, Wilson ER, Doughney T, Brown H, Reineck P, Thompson JG, Gibson BC. Super-multiplexed fluorescence microscopy via photostability contrast. BIOMEDICAL OPTICS EXPRESS 2018; 9:2943-2954. [PMID: 29984077 PMCID: PMC6033574 DOI: 10.1364/boe.9.002943] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Revised: 05/24/2018] [Accepted: 05/26/2018] [Indexed: 05/21/2023]
Abstract
Fluorescence microscopy is widely used to observe and quantify the inner workings of the cell. Traditionally, multiple types of cellular structures or biomolecules are visualized simultaneously in a sample by using spectrally distinct fluorescent labels. The wide emission spectra of most fluorophores limits spectral multiplexing to four or five labels in a standard fluorescence microscope. Further multiplexing requires another dimension of contrast. Here, we show that photostability differences can be used to distinguish between fluorescent labels. By combining photobleaching characteristics with a novel unmixing algorithm, we resolve up to three fluorescent labels in a single spectral channel and unmix fluorescent labels with nearly identical emission spectra. We apply our technique to organic dyes, autofluorescent biomolecules and fluorescent proteins. Our approach has the potential to triple the multiplexing capabilities of any digital widefield or confocal fluorescence microscope with no additional hardware, making it readily accessible to a wide range of researchers.
Collapse
Affiliation(s)
- Antony Orth
- ARC Centre of Excellence for Nanoscale BioPhotonics, School of Science, RMIT University, Melbourne, VIC 3001, Australia
| | - Richik N. Ghosh
- Thermo Fisher Scientific, 100 Technology Drive, Pittsburgh, PA 15219, USA
| | - Emma R. Wilson
- ARC Centre of Excellence for Nanoscale BioPhotonics, School of Science, RMIT University, Melbourne, VIC 3001, Australia
| | - Timothy Doughney
- ARC Centre of Excellence for Nanoscale BioPhotonics, School of Science, RMIT University, Melbourne, VIC 3001, Australia
- Defence Science and Technology Group, Cyber and Electronic Warfare Division, Edinburgh, SA 5111, Australia
| | - Hannah Brown
- ARC Centre of Excellence for Nanoscale BioPhotonics, Robinson Research Institute, Institute for Photonics and Sensing, Adelaide Medical School, The University of Adelaide, Adelaide, SA 5005, Australia
| | - Philipp Reineck
- ARC Centre of Excellence for Nanoscale BioPhotonics, School of Science, RMIT University, Melbourne, VIC 3001, Australia
| | - Jeremy G. Thompson
- ARC Centre of Excellence for Nanoscale BioPhotonics, Robinson Research Institute, Institute for Photonics and Sensing, Adelaide Medical School, The University of Adelaide, Adelaide, SA 5005, Australia
| | - Brant C. Gibson
- ARC Centre of Excellence for Nanoscale BioPhotonics, School of Science, RMIT University, Melbourne, VIC 3001, Australia
| |
Collapse
|
40
|
Baddeley D, Bewersdorf J. Biological Insight from Super-Resolution Microscopy: What We Can Learn from Localization-Based Images. Annu Rev Biochem 2018; 87:965-989. [PMID: 29272143 DOI: 10.1146/annurev-biochem-060815-014801] [Citation(s) in RCA: 121] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Super-resolution optical imaging based on the switching and localization of individual fluorescent molecules [photoactivated localization microscopy (PALM), stochastic optical reconstruction microscopy (STORM), etc.] has evolved remarkably over the last decade. Originally driven by pushing technological limits, it has become a tool of biological discovery. The initial demand for impressive pictures showing well-studied biological structures has been replaced by a need for quantitative, reliable data providing dependable evidence for specific unresolved biological hypotheses. In this review, we highlight applications that showcase this development, identify the features that led to their success, and discuss remaining challenges and difficulties. In this context, we consider the complex topic of defining resolution for this imaging modality and address some of the more common analytical methods used with this data.
Collapse
Affiliation(s)
- David Baddeley
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06520, USA; , .,Auckland Bioengineering Institute, University of Auckland, Auckland 1010, New Zealand
| | - Joerg Bewersdorf
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06520, USA; , .,Department of Biomedical Engineering, Yale University, New Haven, Connecticut 06520, USA
| |
Collapse
|
41
|
Variable number of TMC1-dependent mechanotransducer channels underlie tonotopic conductance gradients in the cochlea. Nat Commun 2018; 9:2185. [PMID: 29872055 PMCID: PMC5988745 DOI: 10.1038/s41467-018-04589-8] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 04/16/2018] [Indexed: 11/25/2022] Open
Abstract
Functional mechanoelectrical transduction (MET) channels of cochlear hair cells require the presence of transmembrane channel-like protein isoforms TMC1 or TMC2. We show that TMCs are required for normal stereociliary bundle development and distinctively influence channel properties. TMC1-dependent channels have larger single-channel conductance and in outer hair cells (OHCs) support a tonotopic apex-to-base conductance gradient. Each MET channel complex exhibits multiple conductance states in ~50 pS increments, basal MET channels having more large-conductance levels. Using mice expressing fluorescently tagged TMCs, we show a three-fold increase in number of TMC1 molecules per stereocilium tip from cochlear apex to base, mirroring the channel conductance gradient in OHCs. Single-molecule photobleaching indicates the number of TMC1 molecules per MET complex changes from ~8 at the apex to ~20 at base. The results suggest there are varying numbers of channels per MET complex, each requiring multiple TMC1 molecules, and together operating in a coordinated or cooperative manner. Mechanoelectrical transduction channel (MET) current found in stereocilia of hair cells matures over the first postnatal week. Here the authors look at the contribution of transmembrane channel-like protein 1 and 2 (TMC1 and TMC2) to MET current during development of tonotopic gradients.
Collapse
|
42
|
Zhao J, Krystofiak ES, Ballesteros A, Cui R, Van Itallie CM, Anderson JM, Fenollar-Ferrer C, Kachar B. Multiple claudin-claudin cis interfaces are required for tight junction strand formation and inherent flexibility. Commun Biol 2018; 1:50. [PMID: 30271933 PMCID: PMC6123731 DOI: 10.1038/s42003-018-0051-5] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Accepted: 04/03/2018] [Indexed: 02/07/2023] Open
Abstract
Tight junctions consist of a network of sealing strands that create selective ion permeability barriers between adjoining epithelial or endothelial cells. The current model for tight junction strands consists of paired rows of claudins (Cldn) coupled by a cis interface (X-1) derived from crystalline Cldn15. Here we show that tight junction strands exhibit a broad range of lateral bending, indicating diversity in cis interactions. By combining protein–protein docking, coevolutionary analysis, molecular dynamics, and a mutagenesis screen, we identify a new Cldn–Cldn cis interface (Cis-1) that shares interacting residues with X-1 but has an ~ 17° lateral rotation between monomers. In addition, we found that a missense mutation in a Cldn14 that causes deafness and contributes stronger to Cis-1 than to X-1 prevents strand formation in cultured cells. Our results suggest that Cis-1 contributes to the inherent structural flexibility of tight junction strands and is required for maintaining permeability barrier function and hearing. Jun Zhao, Evan S. Krystofiak, and colleagues identified a new cis interface (Cis-1) essential for the formation of normal tight junctions. This study suggests that Cis-1 contributes to maintaining structural flexibility of tight junction strands for proper ion balance and hearing.
Collapse
Affiliation(s)
- Jun Zhao
- Laboratory of Cell Structure and Dynamics, National Institute on Deafness and Other Communication Disorders, 35A Convent Drive, Bethesda, MD, 20892, USA.,Cancer and Inflammation Program, National Cancer Institute, Frederick, MD, 21702, USA
| | - Evan S Krystofiak
- Laboratory of Cell Structure and Dynamics, National Institute on Deafness and Other Communication Disorders, 35A Convent Drive, Bethesda, MD, 20892, USA
| | - Angela Ballesteros
- Laboratory of Cell Structure and Dynamics, National Institute on Deafness and Other Communication Disorders, 35A Convent Drive, Bethesda, MD, 20892, USA.,Molecular Physiology and Biophysics Section, National Institute of Neurological Disorders and Stroke, Bethesda, MD, 20892, USA
| | - Runjia Cui
- Laboratory of Cell Structure and Dynamics, National Institute on Deafness and Other Communication Disorders, 35A Convent Drive, Bethesda, MD, 20892, USA
| | - Christina M Van Itallie
- Laboratory of Tight Junction Structure and Function, National Heart, Lung, and Blood Institute, 50 South Drive, Bethesda, MD, 20892, USA
| | - James M Anderson
- Laboratory of Tight Junction Structure and Function, National Heart, Lung, and Blood Institute, 50 South Drive, Bethesda, MD, 20892, USA
| | - Cristina Fenollar-Ferrer
- Computational Structural Biology Unit, National Institute of Neurological Disorders and Stroke, 35 Convent Drive, Bethesda, MD, 20892, USA. .,Laboratory of Molecular & Cellular Neurobiology, National Institute of Mental Health, 35 Convent Drive, Bethesda, MD, 20892, USA.
| | - Bechara Kachar
- Laboratory of Cell Structure and Dynamics, National Institute on Deafness and Other Communication Disorders, 35A Convent Drive, Bethesda, MD, 20892, USA.
| |
Collapse
|
43
|
|
44
|
Deep learning massively accelerates super-resolution localization microscopy. Nat Biotechnol 2018; 36:460-468. [PMID: 29658943 DOI: 10.1038/nbt.4106] [Citation(s) in RCA: 280] [Impact Index Per Article: 46.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 02/16/2018] [Indexed: 02/07/2023]
Abstract
The speed of super-resolution microscopy methods based on single-molecule localization, for example, PALM and STORM, is limited by the need to record many thousands of frames with a small number of observed molecules in each. Here, we present ANNA-PALM, a computational strategy that uses artificial neural networks to reconstruct super-resolution views from sparse, rapidly acquired localization images and/or widefield images. Simulations and experimental imaging of microtubules, nuclear pores, and mitochondria show that high-quality, super-resolution images can be reconstructed from up to two orders of magnitude fewer frames than usually needed, without compromising spatial resolution. Super-resolution reconstructions are even possible from widefield images alone, though adding localization data improves image quality. We demonstrate super-resolution imaging of >1,000 fields of view containing >1,000 cells in ∼3 h, yielding an image spanning spatial scales from ∼20 nm to ∼2 mm. The drastic reduction in acquisition time and sample irradiation afforded by ANNA-PALM enables faster and gentler high-throughput and live-cell super-resolution imaging.
Collapse
|
45
|
Yu JY, Becker SR, Folberth J, Wallin BF, Chen S, Cogswell CJ. Achieving superresolution with illumination-enhanced sparsity. OPTICS EXPRESS 2018; 26:9850-9865. [PMID: 29715931 DOI: 10.1364/oe.26.009850] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Recent advances in superresolution fluorescence microscopy have been limited by a belief that surpassing two-fold resolution enhancement of the Rayleigh resolution limit requires stimulated emission or the fluorophore to undergo state transitions. Here we demonstrate a new superresolution method that requires only image acquisitions with a focused illumination spot and computational post-processing. The proposed method utilizes the focused illumination spot to effectively reduce the object size and enhance the object sparsity and consequently increases the resolution and accuracy through nonlinear image post-processing. This method clearly resolves 70nm resolution test objects emitting ~530nm light with a 1.4 numerical aperture (NA) objective, and, when imaging through a 0.5NA objective, exhibits high spatial frequencies comparable to a 1.4NA widefield image, both demonstrating a resolution enhancement above two-fold of the Rayleigh resolution limit. More importantly, we examine how the resolution increases with photon numbers, and show that the more-than-two-fold enhancement is achievable with realistic photon budgets.
Collapse
|
46
|
Yadav R, Lu HP. Revealing dynamically-organized receptor ion channel clusters in live cells by a correlated electric recording and super-resolution single-molecule imaging approach. Phys Chem Chem Phys 2018. [PMID: 29517089 DOI: 10.1039/c7cp08030a] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The N-methyl-d-aspartate (NMDA) receptor ion-channel is activated by the binding of ligands, along with the application of action potential, important for synaptic transmission and memory functions. Despite substantial knowledge of the structure and function, the gating mechanism of the NMDA receptor ion channel for electric on-off signals is still a topic of debate. We investigate the NMDA receptor partition distribution and the associated channel's open-close electric signal trajectories using a combined approach of correlating single-molecule fluorescence photo-bleaching, single-molecule super-resolution imaging, and single-channel electric patch-clamp recording. Identifying the compositions of NMDA receptors, their spatial organization and distributions over live cell membranes, we observe that NMDA receptors are organized inhomogeneously: nearly half of the receptor proteins are individually dispersed; whereas others exist in heterogeneous clusters of around 50 nm in size as well as co-localized within the diffraction limited imaging area. We demonstrate that inhomogeneous interactions and partitions of the NMDA receptors can be a cause of the heterogeneous gating mechanism of NMDA receptors in living cells. Furthermore, comparing the imaging results with the ion-channel electric current recording, we propose that the clustered NMDA receptors may be responsible for the variation in the current amplitude observed in the on-off two-state ion-channel electric signal trajectories. Our findings shed new light on the fundamental structure-function mechanism of NMDA receptors and present a conceptual advancement of the ion-channel mechanism in living cells.
Collapse
Affiliation(s)
- Rajeev Yadav
- Center for Photochemical Sciences, Department of Chemistry, Bowling Green State University, Bowling Green, Ohio 43403, USA.
| | - H Peter Lu
- Center for Photochemical Sciences, Department of Chemistry, Bowling Green State University, Bowling Green, Ohio 43403, USA.
| |
Collapse
|
47
|
Park G, Chakkarapani SK, Ju S, Ahn S, Kang SH. Super-resolution morphological dissemination of intercalating dye in single DNA molecules via binding activated localization microscopy. CHINESE CHEM LETT 2018. [DOI: 10.1016/j.cclet.2017.08.018] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
48
|
Miller H, Zhou Z, Shepherd J, Wollman AJM, Leake MC. Single-molecule techniques in biophysics: a review of the progress in methods and applications. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2018; 81:024601. [PMID: 28869217 DOI: 10.1088/1361-6633/aa8a02] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Single-molecule biophysics has transformed our understanding of biology, but also of the physics of life. More exotic than simple soft matter, biomatter lives far from thermal equilibrium, covering multiple lengths from the nanoscale of single molecules to up to several orders of magnitude higher in cells, tissues and organisms. Biomolecules are often characterized by underlying instability: multiple metastable free energy states exist, separated by levels of just a few multiples of the thermal energy scale k B T, where k B is the Boltzmann constant and T absolute temperature, implying complex inter-conversion kinetics in the relatively hot, wet environment of active biological matter. A key benefit of single-molecule biophysics techniques is their ability to probe heterogeneity of free energy states across a molecular population, too challenging in general for conventional ensemble average approaches. Parallel developments in experimental and computational techniques have catalysed the birth of multiplexed, correlative techniques to tackle previously intractable biological questions. Experimentally, progress has been driven by improvements in sensitivity and speed of detectors, and the stability and efficiency of light sources, probes and microfluidics. We discuss the motivation and requirements for these recent experiments, including the underpinning mathematics. These methods are broadly divided into tools which detect molecules and those which manipulate them. For the former we discuss the progress of super-resolution microscopy, transformative for addressing many longstanding questions in the life sciences, and for the latter we include progress in 'force spectroscopy' techniques that mechanically perturb molecules. We also consider in silico progress of single-molecule computational physics, and how simulation and experimentation may be drawn together to give a more complete understanding. Increasingly, combinatorial techniques are now used, including correlative atomic force microscopy and fluorescence imaging, to probe questions closer to native physiological behaviour. We identify the trade-offs, limitations and applications of these techniques, and discuss exciting new directions.
Collapse
Affiliation(s)
- Helen Miller
- Clarendon Laboratory, Department of Physics, University of Oxford, Oxford, OX1 3PU, United Kingdom
| | | | | | | | | |
Collapse
|
49
|
Siebert S, Ickstadt K, Schäfer M, Radon Y, Verveer PJ. Comparison of clustering approaches with application to dual colour protein data. IET Syst Biol 2018; 12:7-17. [PMID: 29337285 PMCID: PMC8687232 DOI: 10.1049/iet-syb.2017.0019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Cells communicate with their environment via proteins, located at the plasma membrane separating the interior of a cell from its surroundings. The spatial distribution of these proteins in the plasma membrane under different physiological conditions is of importance, since this may influence their signal transmission properties. In this study, the authors compare different methods such as hierarchical clustering, extensible Markov models and the gammics method for analysing such a spatial distribution. The methods are examined in a simulation study to determine their optimal use. Afterwards, they analyse experimental imaging data and extend these methods to simulate dual colour data.
Collapse
Affiliation(s)
- Sabrina Siebert
- Faculty of Statistics, TU Dortmund University, Dortmund, Germany.
| | - Katja Ickstadt
- Faculty of Statistics, TU Dortmund University, Dortmund, Germany
| | - Martin Schäfer
- Chair of Mathematical Optimization, Mathematical Institute, Heinrich Heine University, Düsseldorf, Germany
| | - Yvonne Radon
- Max-Planck-Institute Dortmund, Dortmund, Germany
| | | |
Collapse
|
50
|
Sezgin E. Super-resolution optical microscopy for studying membrane structure and dynamics. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2017; 29:273001. [PMID: 28481213 PMCID: PMC5952331 DOI: 10.1088/1361-648x/aa7185] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Investigation of cell membrane structure and dynamics requires high spatial and temporal resolution. The spatial resolution of conventional light microscopy is limited due to the diffraction of light. However, recent developments in microscopy enabled us to access the nano-scale regime spatially, thus to elucidate the nanoscopic structures in the cellular membranes. In this review, we will explain the resolution limit, address the working principles of the most commonly used super-resolution microscopy techniques and summarise their recent applications in the biomembrane field.
Collapse
Affiliation(s)
- Erdinc Sezgin
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, OX39DS, United Kingdom
| |
Collapse
|