1
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Saavedra LA, Mosqueira A, Barrantes FJ. A supervised graph-based deep learning algorithm to detect and quantify clustered particles. NANOSCALE 2024; 16:15308-15318. [PMID: 39082742 DOI: 10.1039/d4nr01944j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/16/2024]
Abstract
Considerable efforts are currently being devoted to characterizing the topography of membrane-embedded proteins using combinations of biophysical and numerical analytical approaches. In this work, we present an end-to-end (i.e., human intervention-independent) algorithm consisting of two concatenated binary Graph Neural Network (GNNs) classifiers with the aim of detecting and quantifying dynamic clustering of particles. As the algorithm only needs simulated data to train the GNNs, it is parameter-independent. The GNN-based algorithm is first tested on datasets based on simulated, albeit biologically realistic data, and validated on actual fluorescence microscopy experimental data. Application of the new GNN method is shown to be faster than other currently used approaches for high-dimensional SMLM datasets, with the additional advantage that it can be implemented on standard desktop computers. Furthermore, GNN models obtained via training procedures are reusable. To the best of our knowledge, this is the first application of GNN-based approaches to the analysis of particle aggregation, with potential applications to the study of nanoscopic particles like the nanoclusters of membrane-associated proteins in live cells.
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Affiliation(s)
- Lucas A Saavedra
- Laboratory of Molecular Neurobiology, Biomedical Research institute (BIOMED), UCA-CONICET, Av. Alicia Moreau de Justo 1600, C1107AFF Buenos Aires, Argentina.
| | - Alejo Mosqueira
- Laboratory of Molecular Neurobiology, Biomedical Research institute (BIOMED), UCA-CONICET, Av. Alicia Moreau de Justo 1600, C1107AFF Buenos Aires, Argentina.
| | - Francisco J Barrantes
- Laboratory of Molecular Neurobiology, Biomedical Research institute (BIOMED), UCA-CONICET, Av. Alicia Moreau de Justo 1600, C1107AFF Buenos Aires, Argentina.
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2
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Baldwin KT, Murai KK, Khakh BS. Astrocyte morphology. Trends Cell Biol 2024; 34:547-565. [PMID: 38180380 DOI: 10.1016/j.tcb.2023.09.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 09/18/2023] [Accepted: 09/29/2023] [Indexed: 01/06/2024]
Abstract
Astrocytes are predominant glial cells that tile the central nervous system (CNS). A cardinal feature of astrocytes is their complex and visually enchanting morphology, referred to as bushy, spongy, and star-like. A central precept of this review is that such complex morphological shapes evolved to allow astrocytes to contact and signal with diverse cells at a range of distances in order to sample, regulate, and contribute to the extracellular milieu, and thus participate widely in cell-cell signaling during physiology and disease. The recent use of improved imaging methods and cell-specific molecular evaluations has revealed new information on the structural organization and molecular underpinnings of astrocyte morphology, the mechanisms of astrocyte morphogenesis, and the contributions to disease states of reduced morphology. These insights have reignited interest in astrocyte morphological complexity as a cornerstone of fundamental glial biology and as a critical substrate for multicellular spatial and physiological interactions in the CNS.
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Affiliation(s)
- Katherine T Baldwin
- Neuroscience Center, University of North Carolina, Chapel Hill, NC 27599, USA; Department of Cell Biology and Physiology, University of North Carolina, Chapel Hill, NC 27599, USA.
| | - Keith K Murai
- Centre for Research in Neuroscience, Department of Neurology and Neurosurgery, Brain Repair and Integrative Neuroscience Program, The Research Institute of the McGill University Health Centre, Montreal General Hospital, 1650 Cedar Avenue, Montreal, QC H3G 1A4, Canada.
| | - Baljit S Khakh
- Department of Physiology, David Geffen School of Medicine, University of California Los Angeles, 10833 Le Conte Avenue, Los Angeles, CA 90034, USA; Department of Neurobiology, David Geffen School of Medicine, University of California Los Angeles, 10833 Le Conte Avenue, Los Angeles, CA 90034, USA.
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3
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Nguyen HD, Abe M. Crucial Roles of Leaving Group and Open-Shell Cation in Photoreaction of (Coumarin-4-yl)methyl Derivatives. J Am Chem Soc 2024; 146:10993-11001. [PMID: 38579283 DOI: 10.1021/jacs.4c02880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2024]
Abstract
Photoreactions of (coumarin-4-yl)methyl derivatives have been extensively studied in many fields of chemistry, including organic synthesis and photoinduced drug delivery systems. The identification of the reaction intermediates involved in the photoreactions is crucial not only for elucidating the reaction mechanism but also for the application of the photoreactions. In this study, the photoreactions of 7-diethylamino(coumarin-4-yl)methyl thioester 1a [-SC(O)CH3], thionoester 1b [-OC(S)CH3], and ester 1c [-OC(O)CH3] were investigated to clarify the intermediary species and their chemical behavior. While a radical pair [i.e., 7-diethylamino(coumarin-4-yl)methyl radical and CH3C(O)S•] plays an important role in the photoreactions of 1a and 1b, an ion pair [i.e., 7-diethylamino(coumarin-4-yl)methyl cation, and CH3CO2-] was the key in the photoreaction of 1c. 18O-isotope-labeling of 1c revealed a negligible recombination process within the ion pair. The unprecedented observation was rationalized by the open-shell character of the 7-diethylamino(coumarin-4-yl)methyl cation, whose formation was confirmed through product analysis and transient absorption spectroscopy.
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Affiliation(s)
- Hai Dang Nguyen
- Department of Chemistry, Graduate School of Advance Science and Engineering, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima 739-8526, Hiroshima, Japan
| | - Manabu Abe
- Department of Chemistry, Graduate School of Advance Science and Engineering, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima 739-8526, Hiroshima, Japan
- Hiroshima Research Center for Photo-Drug-Delivery Systems (Hi-P-DDS), Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima 739-8526, Hiroshima, Japan
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4
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Su B, Gao D, Xin N, Wu K, Yang M, Jiang S, Zhang Y, Ding J, Wu C, Sun J, Wei D, Fan H, Guo Z. Mild synthesis of ultra-bright carbon dots with solvatochromism for rapid lipid droplet monitoring in varied physiological processes. Regen Biomater 2024; 11:rbad109. [PMID: 38404618 PMCID: PMC10884737 DOI: 10.1093/rb/rbad109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 11/21/2023] [Accepted: 12/04/2023] [Indexed: 02/27/2024] Open
Abstract
Lipid droplets (LDs) participating in various cellular activities and are increasingly being emphasized. Fluorescence imaging provides powerful tool for dynamic tracking of LDs, however, most current LDs probes remain inconsistent performance such as low Photoluminescence Quantum Yield (PLQY), poor photostability and tedious washing procedures. Herein, a novel yellow-emissive carbon dot (OT-CD) has been synthesized conveniently with high PLQY up to 90%. Besides, OT-CD exhibits remarkable amphiphilicity and solvatochromic property with lipid-water partition coefficient higher than 2, which is much higher than most LDs probes. These characters enable OT-CD high brightness, stable and wash-free LDs probing, and feasible for in vivo imaging. Then, detailed observation of LDs morphological and polarity variation dynamically in different cellular states were recorded, including ferroptosis and other diseases processes. Furthermore, fast whole imaging of zebrafish and identified LD enrichment in injured liver indicate its further feasibility for in vivo application. In contrast to the reported studies to date, this approach provides a versatile conventional synthesis system for high-performance LDs targeting probes, combing the advantages of easy and high-yield production, as well as robust brightness and stability for long-term imaging, facilitating investigations into organelle interactions and LD-associated diseases.
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Affiliation(s)
- Borui Su
- National Engineering Research Center for Biomaterials, College of Biomedical Engineering, Sichuan University, Chengdu, Sichuan 610064, China
| | - Dong Gao
- National Engineering Research Center for Biomaterials, College of Biomedical Engineering, Sichuan University, Chengdu, Sichuan 610064, China
| | - Nini Xin
- National Engineering Research Center for Biomaterials, College of Biomedical Engineering, Sichuan University, Chengdu, Sichuan 610064, China
| | - Kai Wu
- National Engineering Research Center for Biomaterials, College of Biomedical Engineering, Sichuan University, Chengdu, Sichuan 610064, China
| | - Mei Yang
- National Engineering Research Center for Biomaterials, College of Biomedical Engineering, Sichuan University, Chengdu, Sichuan 610064, China
| | - Shichao Jiang
- National Engineering Research Center for Biomaterials, College of Biomedical Engineering, Sichuan University, Chengdu, Sichuan 610064, China
| | - Yusheng Zhang
- National Engineering Research Center for Biomaterials, College of Biomedical Engineering, Sichuan University, Chengdu, Sichuan 610064, China
| | - Jie Ding
- National Engineering Research Center for Biomaterials, College of Biomedical Engineering, Sichuan University, Chengdu, Sichuan 610064, China
| | - Chengheng Wu
- National Engineering Research Center for Biomaterials, College of Biomedical Engineering, Sichuan University, Chengdu, Sichuan 610064, China
- Institute of Regulatory Science for Medical Devices, Sichuan University, Chengdu, Sichuan 610064, China
| | - Jing Sun
- National Engineering Research Center for Biomaterials, College of Biomedical Engineering, Sichuan University, Chengdu, Sichuan 610064, China
| | - Dan Wei
- National Engineering Research Center for Biomaterials, College of Biomedical Engineering, Sichuan University, Chengdu, Sichuan 610064, China
| | - Hongsong Fan
- National Engineering Research Center for Biomaterials, College of Biomedical Engineering, Sichuan University, Chengdu, Sichuan 610064, China
| | - Zhenzhen Guo
- Department of Gastroenterology, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu 610072, China
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5
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Boyang H, Yangyanqiu W, Wenting R, Chenxin Y, Jian C, Zhanbo Q, Yanjun Y, Qiang Y, Shuwen H. Application and progress of highcontent imaging in molecular biology. Biotechnol J 2023; 18:e2300170. [PMID: 37639283 DOI: 10.1002/biot.202300170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 08/03/2023] [Accepted: 08/22/2023] [Indexed: 08/29/2023]
Abstract
Humans have adopted many different methods to explore matter imaging, among which high content imaging (HCI) could conduct automated imaging analysis of cells while maintaining its structural and functional integrity. Meanwhile, as one of the most important research tools for diagnosing human diseases, HCI is widely used in the frontier of medical research, and its future application has attracted researchers' great interests. Here, the meaning of HCI was briefly explained, the history of optical imaging and the birth of HCI were described, and the experimental methods of HCI were described. Furthermore, the directions of the application of HCI were highlighted in five aspects: protein localization changes, gene identification, chemical and genetic analysis, microbiology, and drug discovery. Most importantly, some challenges and future directions of HCI were discussed, and the application and optimization of HCI were expected to be further explored.
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Affiliation(s)
- Hu Boyang
- Huzhou Hospital of Zhejiang University, Affiliated Central Hospital Huzhou University, Huzhou, China
| | - Wang Yangyanqiu
- Huzhou Hospital of Zhejiang University, Affiliated Central Hospital Huzhou University, Huzhou, China
| | - Rui Wenting
- Huzhou Hospital of Zhejiang University, Affiliated Central Hospital Huzhou University, Huzhou, China
| | - Yan Chenxin
- Shulan International Medical School, Zhejiang Shuren University, Hangzhou, China
| | - Chu Jian
- Fifth Affiliated Clinical Medical College of Zhejiang Chinese Medical University, Huzhou Central Hospital, Huzhou, China
| | - Qu Zhanbo
- Fifth Affiliated Clinical Medical College of Zhejiang Chinese Medical University, Huzhou Central Hospital, Huzhou, China
| | - Yao Yanjun
- Huzhou Hospital of Zhejiang University, Affiliated Central Hospital Huzhou University, Huzhou, China
| | - Yan Qiang
- Huzhou Hospital of Zhejiang University, Affiliated Central Hospital Huzhou University, Huzhou, China
| | - Han Shuwen
- Huzhou Hospital of Zhejiang University, Affiliated Central Hospital Huzhou University, Huzhou, China
- Key Laboratory of Multiomics Research and Clinical Transformation of Digestive Cancer of Huzhou, Huzhou, China
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6
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Wang CF, Krayev AV, El-Khoury PZ. Subnanometer Visualization of Spatially Varying Local Field Resonances that Drive Tip-Enhanced Optical Spectroscopy. NANO LETTERS 2023; 23:9114-9118. [PMID: 37751571 DOI: 10.1021/acs.nanolett.3c03028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/28/2023]
Abstract
Our knowledge of the electromagnetic fields that power modern nanoscale optical measurements, including (non)linear tip-enhanced Raman and photoluminescence, chiefly stems from numerical simulations. Aside from idealized in silico vs heterogeneous (nano)structures in the laboratory, challenges in quantitative descriptions of nanoscale light-matter interactions more generally stem from the very nature of the problem, which lies at the interface of classical and quantum theories. This is particularly the case in ultrahigh spatial resolution measurements that are sensitive to local optical field variations that take place on subnanometer length scales. This work approaches this challenge through extinction-based spectral nanoimaging experiments. We demonstrate <1 nm spatial resolution in hyperspectral extinction measurements that track spatially varying plasmon resonances. We describe the principles behind our experiments and highlight more general implications of our observations.
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Affiliation(s)
- Chih-Feng Wang
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Andrey V Krayev
- Horiba Instruments, Inc., 359 Bel Marin Keys Blvd., Suite 18, Novato, California 94949, United States
| | - Patrick Z El-Khoury
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
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7
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Frawley AT, Leslie KG, Wycisk V, Galiani S, Shrestha D, Eggeling C, Anderson HL. A Photoswitchable Solvatochromic Dye for Probing Membrane Ordering by RESOLFT Super-resolution Microscopy. Chemphyschem 2023; 24:e202300125. [PMID: 36946252 DOI: 10.1002/cphc.202300125] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 03/20/2023] [Accepted: 03/21/2023] [Indexed: 03/23/2023]
Abstract
A switchable solvatochromic fluorescent dyad can be used to map ordering of lipids in vesicle membranes at a resolution better than the diffraction limit. Combining a Nile Red fluorophore with a photochromic spironaphthoxazine quencher allows the fluorescence to be controlled using visible light, via photoswitching and FRET quenching. Synthetic lipid vesicles of varying composition were imaged with an average 2.5-fold resolution enhancement, compared to the confocal images. Ratiometric detection was used to probe the membrane polarity, and domains of different lipid ordering were distinguished within the same membrane.
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Affiliation(s)
- Andrew T Frawley
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford, OX1 3TA, UK
| | - Kathryn G Leslie
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford, OX1 3TA, UK
| | - Virginia Wycisk
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford, OX1 3TA, UK
| | - Silvia Galiani
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Dilip Shrestha
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Christian Eggeling
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK
- Institute of Applied Optics and Biophysics, Friedrich-Schiller-University Jena, Max-Wien-Platz 4, 07743, Jena, Germany
- Leibniz Institute of Photonic Technology e.V., Albert-Einstein-Strasse 9, 07745, Jena, Germany
- Jena Center for Soft Matter (JCSM), Philosophenweg 7, 07743, Jena, Germany
| | - Harry L Anderson
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford, OX1 3TA, UK
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8
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Yang W, Hou L, Luo C. When Super-Resolution Microscopy Meets Microfluidics: Enhanced Biological Imaging and Analysis with Unprecedented Resolution. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2207341. [PMID: 36895074 DOI: 10.1002/smll.202207341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 01/31/2023] [Indexed: 06/08/2023]
Abstract
Super-resolution microscopy is rapidly developed in recent years, allowing biologists to extract more quantitative information on subcellular processes in live cells that is usually not accessible with conventional techniques. However, super-resolution imaging is not fully exploited because of the lack of an appropriate and multifunctional experimental platform. As an important tool in life sciences, microfluidics is capable of cell manipulation and the regulation of the cellular environment because of its superior flexibility and biocompatibility. The combination of microfluidics and super-resolution microscopy revolutionizes the study of complex cellular properties and dynamics, providing valuable insights into cellular structure and biological functions at the single-molecule level. In this perspective, an overview of the main advantages of microfluidic technology that are essential to the performance of super-resolution microscopy are offered. The main benefits of performing super-resolution imaging with microfluidic devices are highlighted and perspectives on the diverse applications that are facilitated by combining these two powerful techniques are provided.
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Affiliation(s)
- Wei Yang
- Wenzhou Institute University of Chinese Academy of Sciences, 1 Jinlian Road, Wenzhou, Zhejiang, 325001, China
| | - Lei Hou
- UMR5298-LP2N, Institut d'Optique and CNRS, Rue François Mitterrand, Talence, 33400, France
| | - Chunxiong Luo
- Wenzhou Institute University of Chinese Academy of Sciences, 1 Jinlian Road, Wenzhou, Zhejiang, 325001, China
- The State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, School of Physics, Peking University, 5 Summer Palace Road, Beijing, 100871, China
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, 5 Summer Palace Road, Beijing, 100871, China
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9
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A general highly efficient synthesis of biocompatible rhodamine dyes and probes for live-cell multicolor nanoscopy. Nat Commun 2023; 14:1306. [PMID: 36894547 PMCID: PMC9998615 DOI: 10.1038/s41467-023-36913-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 02/23/2023] [Indexed: 03/11/2023] Open
Abstract
The development of live-cell fluorescence nanoscopy is powered by the availability of suitable fluorescent probes. Rhodamines are among the best fluorophores for labeling intracellular structures. Isomeric tuning is a powerful method for optimizing the biocompatibility of rhodamine-containing probes without affecting their spectral properties. An efficient synthesis pathway for 4-carboxyrhodamines is still lacking. We present a facile protecting-group-free 4-carboxyrhodamines' synthesis based on the nucleophilic addition of lithium dicarboxybenzenide to the corresponding xanthone. This approach drastically reduces the number of synthesis steps, expands the achievable structural diversity, increases overall yields and permits gram-scale synthesis of the dyes. We synthesize a wide range of symmetrical and unsymmetrical 4-carboxyrhodamines covering the whole visible spectrum and target them to multiple structures in living cells - microtubules, DNA, actin, mitochondria, lysosomes, Halo-tagged and SNAP-tagged proteins. The enhanced permeability fluorescent probes operate at submicromolar concentrations, allowing high-contrast STED and confocal microscopy of living cells and tissues.
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10
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Zhang Y, Zheng Y, Tomassini A, Singh AK, Raymo FM. Photoactivatable BODIPYs for Live-Cell PALM. Molecules 2023; 28:molecules28062447. [PMID: 36985424 PMCID: PMC10057988 DOI: 10.3390/molecules28062447] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 03/03/2023] [Accepted: 03/04/2023] [Indexed: 03/10/2023] Open
Abstract
Photoactivated localization microscopy (PALM) relies on fluorescence photoactivation and single-molecule localization to overcome optical diffraction and reconstruct images of biological samples with spatial resolution at the nanoscale. The implementation of this subdiffraction imaging method, however, requires fluorescent probes with photochemical and photophysical properties specifically engineered to enable the localization of single photoactivated molecules with nanometer precision. The synthetic versatility and outstanding photophysical properties of the borondipyrromethene (BODIPY) chromophore are ideally suited to satisfy these stringent requirements. Specifically, synthetic manipulations of the BODIPY scaffold can be invoked to install photolabile functional groups and photoactivate fluorescence under photochemical control. Additionally, targeting ligands can be incorporated in the resulting photoactivatable fluorophores (PAFs) to label selected subcellular components in live cells. Indeed, photoactivatable BODIPYs have already allowed the sub-diffraction imaging of diverse cellular substructures in live cells using PALM and can evolve into invaluable analytical probes for bioimaging applications.
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Affiliation(s)
- Yang Zhang
- Program of Polymer and Color Chemistry, Department of Textile Engineering, Chemistry and Science, North Carolina State University, Raleigh, NC 27606, USA
- Correspondence: (Y.Z.); (F.M.R.)
| | - Yeting Zheng
- Laboratory for Molecular Photonics, Department of Chemistry, University of Miami, 1301 Memorial Drive, Coral Gables, FL 33146-0431, USA
| | - Andrea Tomassini
- Laboratory for Molecular Photonics, Department of Chemistry, University of Miami, 1301 Memorial Drive, Coral Gables, FL 33146-0431, USA
| | - Ambarish Kumar Singh
- Laboratory for Molecular Photonics, Department of Chemistry, University of Miami, 1301 Memorial Drive, Coral Gables, FL 33146-0431, USA
| | - Françisco M. Raymo
- Laboratory for Molecular Photonics, Department of Chemistry, University of Miami, 1301 Memorial Drive, Coral Gables, FL 33146-0431, USA
- Correspondence: (Y.Z.); (F.M.R.)
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11
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Gong J, Jin Z, Chen H, He J, Zhang Y, Yang X. Super-resolution fluorescence microscopic imaging in pathogenesis and drug treatment of neurological disease. Adv Drug Deliv Rev 2023; 196:114791. [PMID: 37004939 DOI: 10.1016/j.addr.2023.114791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 03/16/2023] [Accepted: 03/19/2023] [Indexed: 04/03/2023]
Abstract
Since super-resolution fluorescence microscopic technology breaks the diffraction limit that has existed for a long time in optical imaging, it can observe the process of synapses formed between nerve cells and the protein aggregation related to neurological disease. Thus, super-resolution fluorescence microscopic imaging has significantly impacted several industries, including drug development and pathogenesis research, and it is anticipated that it will significantly alter the future of life science research. Here, we focus on several typical super-resolution fluorescence microscopic technologies, introducing their benefits and drawbacks, as well as applications in several common neurological diseases, in the hope that their services will be expanded and improved in the pathogenesis and drug treatment of neurological diseases.
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12
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Barrantes FJ. Fluorescence microscopy imaging of a neurotransmitter receptor and its cell membrane lipid milieu. Front Mol Biosci 2022; 9:1014659. [PMID: 36518846 PMCID: PMC9743973 DOI: 10.3389/fmolb.2022.1014659] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 11/01/2022] [Indexed: 05/02/2024] Open
Abstract
Hampered by the diffraction phenomenon, as expressed in 1873 by Abbe, applications of optical microscopy to image biological structures were for a long time limited to resolutions above the ∼200 nm barrier and restricted to the observation of stained specimens. The introduction of fluorescence was a game changer, and since its inception it became the gold standard technique in biological microscopy. The plasma membrane is a tenuous envelope of 4 nm-10 nm in thickness surrounding the cell. Because of its highly versatile spectroscopic properties and availability of suitable instrumentation, fluorescence techniques epitomize the current approach to study this delicate structure and its molecular constituents. The wide spectral range covered by fluorescence, intimately linked to the availability of appropriate intrinsic and extrinsic probes, provides the ability to dissect membrane constituents at the molecular scale in the spatial domain. In addition, the time resolution capabilities of fluorescence methods provide complementary high precision for studying the behavior of membrane molecules in the time domain. This review illustrates the value of various fluorescence techniques to extract information on the topography and motion of plasma membrane receptors. To this end I resort to a paradigmatic membrane-bound neurotransmitter receptor, the nicotinic acetylcholine receptor (nAChR). The structural and dynamic picture emerging from studies of this prototypic pentameric ligand-gated ion channel can be extrapolated not only to other members of this superfamily of ion channels but to other membrane-bound proteins. I also briefly discuss the various emerging techniques in the field of biomembrane labeling with new organic chemistry strategies oriented to applications in fluorescence nanoscopy, the form of fluorescence microscopy that is expanding the depth and scope of interrogation of membrane-associated phenomena.
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Affiliation(s)
- Francisco J. Barrantes
- Biomedical Research Institute (BIOMED), Catholic University of Argentina (UCA)–National Scientific and Technical Research Council (CONICET), Buenos Aires, Argentina
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13
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Ayuso D, Ordonez AF, Smirnova O. Ultrafast chirality: the road to efficient chiral measurements. Phys Chem Chem Phys 2022; 24:26962-26991. [PMID: 36342056 PMCID: PMC9673685 DOI: 10.1039/d2cp01009g] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 07/20/2022] [Indexed: 08/20/2023]
Abstract
Today we are witnessing the electric-dipole revolution in chiral measurements. Here we reflect on its lessons and outcomes, such as the perspective on chiral measurements using the complementary principles of "chiral reagent" and "chiral observer", the hierarchy of scalar, vectorial and tensorial enantio-sensitive observables, the new properties of the chiro-optical response in the ultrafast and non-linear domains, and the geometrical magnetism associated with the chiral response in photoionization. The electric-dipole revolution is a landmark event. It has opened routes to extremely efficient enantio-discrimination with a family of new methods. These methods are governed by the same principles but work in vastly different regimes - from microwaves to optical light; they address all molecular degrees of freedom - electronic, vibrational and rotational, and use flexible detection schemes, i.e. detecting photons or electrons, making them applicable to different chiral phases, from gases to liquids to amorphous solids. The electric-dipole revolution has also enabled enantio-sensitive manipulation of chiral molecules with light. This manipulation includes exciting and controlling ultrafast helical currents in vibronic states of chiral molecules, enantio-sensitive control of populations in electronic, vibronic and rotational molecular states, and opens the way to efficient enantio-separation and enantio-sensitive trapping of chiral molecules. The word "perspective" has two meanings: an "outlook" and a "point of view". In this perspective article, we have tried to cover both meanings.
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Affiliation(s)
- David Ayuso
- Max-Born-Institut, 12489 Berlin, Germany
- Imperial College London, SW7 2AZ London, UK.
| | - Andres F Ordonez
- Max-Born-Institut, 12489 Berlin, Germany
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, 08860 Barcelona, Spain.
| | - Olga Smirnova
- Max-Born-Institut, 12489 Berlin, Germany
- Technische Universität Berlin, 10623 Berlin, Germany.
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14
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Zhang Y, Wang G, Huang P, Sun E, Kweon J, Li Q, Zhe J, Ying LL, Zhang HF. Minimizing Molecular Misidentification in Imaging Low-Abundance Protein Interactions Using Spectroscopic Single-Molecule Localization Microscopy. Anal Chem 2022; 94:13834-13841. [PMID: 36165784 PMCID: PMC9859736 DOI: 10.1021/acs.analchem.2c02417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Super-resolution microscopy can capture spatiotemporal organizations of protein interactions with resolution down to 10 nm; however, the analyses of more than two proteins involving low-abundance protein are challenging because spectral crosstalk and heterogeneities of individual fluorescent labels result in molecular misidentification. Here we developed a deep learning-based imaging analysis method for spectroscopic single-molecule localization microscopy to minimize molecular misidentification in three-color super-resolution imaging. We characterized the 3-fold reduction of molecular misidentification in the new imaging method using pure samples of different photoswitchable fluorophores and visualized three distinct subcellular proteins in U2-OS cell lines. We further validated the protein counts and interactions of TOMM20, DRP1, and SUMO1 in a well-studied biological process, Staurosporine-induced apoptosis, by comparing the imaging results with Western-blot analyses of different subcellular portions.
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Affiliation(s)
- Yang Zhang
- Department of Biomedical Engineering, Northwestern University, Evanston IL, 60208, USA
| | - Gaoxiang Wang
- Department of Biomedical Engineering, Northwestern University, Evanston IL, 60208, USA
- Department of Hematology, Tongji Medical College, Huazhong University of Science and Technology, Wuhan Hubei, 430030, China
| | - Peizhou Huang
- Department of Biomedical Engineering, The State University of New York at Buffalo, Buffalo, NY 14260, USA
| | - Edison Sun
- Department of Biomedical Engineering, Northwestern University, Evanston IL, 60208, USA
| | - Junghun Kweon
- Department of Biomedical Engineering, Northwestern University, Evanston IL, 60208, USA
| | - Qianru Li
- Department of Biomedical Engineering, Northwestern University, Evanston IL, 60208, USA
- Department of Pharmacology, Northwestern University, Chicago IL, 60611, USA
| | - Ji Zhe
- Department of Biomedical Engineering, Northwestern University, Evanston IL, 60208, USA
- Department of Pharmacology, Northwestern University, Chicago IL, 60611, USA
| | - Leslie L. Ying
- Department of Biomedical Engineering, The State University of New York at Buffalo, Buffalo, NY 14260, USA
- Department of Electrical Engineering, The State University of New York at Buffalo, Buffalo, NY 14260, USA
| | - Hao F. Zhang
- Department of Biomedical Engineering, Northwestern University, Evanston IL, 60208, USA
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15
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Jusuf JM, Lew MD. Towards optimal point spread function design for resolving closely spaced emitters in three dimensions. OPTICS EXPRESS 2022; 30:37154-37174. [PMID: 36258632 DOI: 10.1364/oe.472067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 09/12/2022] [Indexed: 06/16/2023]
Abstract
The past decade has brought many innovations in optical design for 3D super-resolution imaging of point-like emitters, but these methods often focus on single-emitter localization precision as a performance metric. Here, we propose a simple heuristic for designing a point spread function (PSF) that allows for precise measurement of the distance between two emitters. We discover that there are two types of PSFs that achieve high performance for resolving emitters in 3D, as quantified by the Cramér-Rao bounds for estimating the separation between two closely spaced emitters. One PSF is very similar to the existing Tetrapod PSFs; the other is a rotating single-spot PSF, which we call the crescent PSF. The latter exhibits excellent performance for localizing single emitters throughout a 1-µm focal volume (localization precisions of 7.3 nm in x, 7.7 nm in y, and 18.3 nm in z using 1000 detected photons), and it distinguishes between one and two closely spaced emitters with superior accuracy (25-53% lower error rates than the best-performing Tetrapod PSF, averaged throughout a 1-µm focal volume). Our study provides additional insights into optimal strategies for encoding 3D spatial information into optical PSFs.
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16
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Furia L, Pelicci S, Scanarini M, Pelicci PG, Faretta M. From Double-Strand Break Recognition to Cell-Cycle Checkpoint Activation: High Content and Resolution Image Cytometry Unmasks 53BP1 Multiple Roles in DNA Damage Response and p53 Action. Int J Mol Sci 2022; 23:ijms231710193. [PMID: 36077590 PMCID: PMC9456172 DOI: 10.3390/ijms231710193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 08/25/2022] [Accepted: 09/02/2022] [Indexed: 11/29/2022] Open
Abstract
53BP1 protein has been isolated in-vitro as a putative p53 interactor. From the discovery of its engagement in the DNA-Damage Response (DDR), its role in sustaining the activity of the p53-regulated transcriptional program has been frequently under-evaluated, even in the case of a specific response to numerous DNA Double-Strand Breaks (DSBs), i.e., exposure to ionizing radiation. The localization of 53BP1 protein constitutes a key to decipher the network of activities exerted in response to stress. We present here an automated-microscopy for image cytometry protocol to analyze the evolution of the DDR, and to demonstrate how 53BP1 moved from damaged sites, where the well-known interaction with the DSB marker γH2A.X takes place, to nucleoplasm, interacting with p53, and enhancing the transcriptional regulation of the guardian of the genome protein. Molecular interactions have been quantitatively described and spatiotemporally localized at the highest spatial resolution by a simultaneous analysis of the impairment of the cell-cycle progression. Thanks to the high statistical sampling of the presented protocol, we provide a detailed quantitative description of the molecular events following the DSBs formation. Single-Molecule Localization Microscopy (SMLM) Analysis finally confirmed the p53–53BP1 interaction on the tens of nanometers scale during the distinct phases of the response.
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Affiliation(s)
- Laura Furia
- Department of Experimental Oncology, European Institute of Oncology IRCCS, 20139 Milan, Italy
| | - Simone Pelicci
- Department of Experimental Oncology, European Institute of Oncology IRCCS, 20139 Milan, Italy
| | - Mirco Scanarini
- Department of Experimental Oncology, European Institute of Oncology IRCCS, 20139 Milan, Italy
| | - Pier Giuseppe Pelicci
- Department of Experimental Oncology, European Institute of Oncology IRCCS, 20139 Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, 20122 Milan, Italy
| | - Mario Faretta
- Department of Experimental Oncology, European Institute of Oncology IRCCS, 20139 Milan, Italy
- Correspondence:
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17
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Baykov S, Tarasenko M, Kotlyarova V, Shetnev A, Zelenkov LE, Boyarskaya IA, Boyarskiy VP. 2‐(1,2,4‐Oxadiazol‐5‐yl)aniline as a New Scaffold for Blue Luminescent Materials. ChemistrySelect 2022. [DOI: 10.1002/slct.202201201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Sergey Baykov
- Institute of Chemistry Saint Petersburg State University Universitetskaya Nab. 7/9 199034 Saint Petersburg Russian Federation
- Research School of Chemistry and Applied Biomedical Sciences Tomsk Polytechnic University 634034 Tomsk Russian Federation
| | - Marina Tarasenko
- Pharmaceutical Technology Transfer Center Yaroslavl State Pedagogical University named after K.D. Ushinsky 108 Respublikanskaya St. 150000 Yaroslavl Russian Federation
| | - Valentina Kotlyarova
- Pharmaceutical Technology Transfer Center Yaroslavl State Pedagogical University named after K.D. Ushinsky 108 Respublikanskaya St. 150000 Yaroslavl Russian Federation
| | - Anton Shetnev
- Pharmaceutical Technology Transfer Center Yaroslavl State Pedagogical University named after K.D. Ushinsky 108 Respublikanskaya St. 150000 Yaroslavl Russian Federation
| | - Lev E. Zelenkov
- Institute of Chemistry Saint Petersburg State University Universitetskaya Nab. 7/9 199034 Saint Petersburg Russian Federation
- ITMO University 191002 Saint Petersburg Russian Federation
| | - Irina A. Boyarskaya
- Institute of Chemistry Saint Petersburg State University Universitetskaya Nab. 7/9 199034 Saint Petersburg Russian Federation
| | - Vadim P. Boyarskiy
- Institute of Chemistry Saint Petersburg State University Universitetskaya Nab. 7/9 199034 Saint Petersburg Russian Federation
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18
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Roßmann K, Akkaya KC, Poc P, Charbonnier C, Eichhorst J, Gonschior H, Valavalkar A, Wendler N, Cordes T, Dietzek-Ivanšić B, Jones B, Lehmann M, Broichhagen J. N-Methyl deuterated rhodamines for protein labelling in sensitive fluorescence microscopy. Chem Sci 2022; 13:8605-8617. [PMID: 35974762 PMCID: PMC9337740 DOI: 10.1039/d1sc06466e] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 06/02/2022] [Indexed: 11/21/2022] Open
Abstract
Rhodamine fluorophores are setting benchmarks in fluorescence microscopy. Herein, we report the deuterium (d12) congeners of tetramethyl(silicon)rhodamine, obtained by isotopic labelling of the four methyl groups, show improved photophysical parameters (i.e. brightness, lifetimes) and reduced chemical bleaching. We explore this finding for SNAP- and Halo-tag labelling in live cells, and highlight enhanced properties in several applications, such as fluorescence activated cell sorting, fluorescence lifetime microscopy, stimulated emission depletion nanoscopy and single-molecule Förster-resonance energy transfer. We finally extend this idea to other dye families and envision deuteration as a generalizable concept to improve existing and to develop new chemical biology probes.
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Affiliation(s)
- Kilian Roßmann
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie Berlin Germany
| | - Kerem C Akkaya
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie Berlin Germany
| | - Pascal Poc
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie Berlin Germany
| | | | - Jenny Eichhorst
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie Berlin Germany
| | - Hannes Gonschior
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie Berlin Germany
| | - Abha Valavalkar
- Leibniz Institute for Photonic Technology Jena e.V. (Leibniz-IPHT), Research Department Functional Interfaces Jena Germany
| | - Nicolas Wendler
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität München Großhaderner Str. 2-4, Planegg-Martinsried 82152 Germany
| | - Thorben Cordes
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität München Großhaderner Str. 2-4, Planegg-Martinsried 82152 Germany
| | - Benjamin Dietzek-Ivanšić
- Leibniz Institute for Photonic Technology Jena e.V. (Leibniz-IPHT), Research Department Functional Interfaces Jena Germany
| | - Ben Jones
- Section of Endocrinology and Investigative Medicine, Imperial College London London W12 0NN UK
| | - Martin Lehmann
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie Berlin Germany
| | - Johannes Broichhagen
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie Berlin Germany
- Department of Chemical Biology, Max Planck Institute for Medical Research Heidelberg Germany
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19
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Cappellari MV, Marcano-García LF, Simoncelli S, Aramendía PF. Determination of association equilibrium constant from single molecule fluorescence localization microscopy. Photochem Photobiol Sci 2022; 21:1751-1760. [PMID: 35749053 DOI: 10.1007/s43630-022-00254-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Accepted: 05/31/2022] [Indexed: 11/26/2022]
Abstract
Single molecule fluorescence localization microscopy provides molecular localization with a precision in the tens of nanometer range in the plane perpendicular to the light propagation. This opens the possibility to count molecules and correlate their locations, starting from a map of the actual positions in a single molecule super resolution image. Considering molecular pair correlation as an indication of interaction, and a way to discern them from free molecules, we describe a method to calculate thermodynamic equilibrium constants. In this work, we use as a test system two complementary homo-oligonucleotides, one strand marked with Cyanine 3.5 and the other with Alexa Fluor 647. Hybridization is controlled by the amount of each strand, temperature, and the ionic force, and measured in steady state emission. The same samples are examined in Stochastic Optical Reconstruction Microscopy (STORM) experiments with split-field simultaneous two-colour detection. The effect of multiblinking, labelling-detection efficiency, and determination of the critical distance for association are discussed. We consistently determine values in STORM coincident with those of the bulk experiment.
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Affiliation(s)
- M Victoria Cappellari
- Centro de Investigaciones en Bionanociencias -''Elizabeth Jares-Erijman'' (CIBION), CONICET, Godoy Cruz 2390, 1425, Ciudad de Buenos Aires, Argentina
| | - Luis F Marcano-García
- Centro de Investigaciones en Bionanociencias -''Elizabeth Jares-Erijman'' (CIBION), CONICET, Godoy Cruz 2390, 1425, Ciudad de Buenos Aires, Argentina
| | - Sabrina Simoncelli
- London Centre for Nanotechnology and Department of Chemistry, University College London, London, WC1H 0AH, UK
| | - Pedro F Aramendía
- Centro de Investigaciones en Bionanociencias -''Elizabeth Jares-Erijman'' (CIBION), CONICET, Godoy Cruz 2390, 1425, Ciudad de Buenos Aires, Argentina.
- Departamento de Química Inorgánica, Analítica y Química Física. Facultad de Ciencias Exactas Y Naturales, Universidad de Buenos Aires, 1428, Ciudad de Buenos Aires, Argentina.
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20
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Adhikari S, Orrit M. Progress and perspectives in single-molecule optical spectroscopy. J Chem Phys 2022; 156:160903. [PMID: 35489995 DOI: 10.1063/5.0087003] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We review some of the progress of single-molecule optical experiments in the past 20 years and propose some perspectives for the coming years. We particularly focus on methodological advances in fluorescence, super-resolution, photothermal contrast, and interferometric scattering and briefly discuss a few of the applications. These advances have enabled the exploration of new emitters and quantum optics; the chemistry and biology of complex heterogeneous systems, nanoparticles, and plasmonics; and the detection and study of non-fluorescing and non-absorbing nano-objects. We conclude by proposing some ideas for future experiments. The field will move toward more and better signals of a broader variety of objects and toward a sharper view of the surprising complexity of the nanoscale world of single (bio-)molecules, nanoparticles, and their nano-environments.
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Affiliation(s)
- Subhasis Adhikari
- Huygens-Kamerlingh Onnes Laboratory, Leiden University, P.O. Box 9504, 2333 CA Leiden, The Netherlands
| | - Michel Orrit
- Huygens-Kamerlingh Onnes Laboratory, Leiden University, P.O. Box 9504, 2333 CA Leiden, The Netherlands
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21
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Gomez Palacios LR, Bracamonte AG. Development of nano- and microdevices for the next generation of biotechnology, wearables and miniaturized instrumentation. RSC Adv 2022; 12:12806-12822. [PMID: 35496334 PMCID: PMC9047444 DOI: 10.1039/d2ra02008d] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 04/15/2022] [Indexed: 12/27/2022] Open
Abstract
This is a short communication based on recent high-impact publications related to how various chemical materials and substrate modifications could be tuned for nano- and microdevices, where their application for high point-of-care bioanalysis and further applications in life science is discussed. Hence, they have allowed different high-impact research topics in a variety of fields, from the control of nanoscale to functional microarchitectures embedded in various support materials to obtain a device for a given application or use. Thus, their incorporation in standard instrumentation is shown, as well as in new optical setups to record different classical and non-classical light, signaling, and energy modes at a variety of wavelengths and energy levels. Moreover, the development of miniaturized instrumentation was also contemplated. In order to develop these different levels of technology, the chemistry, physics and engineering of materials were discussed. In this manner, a number of subjects that allowed the design and manufacture of devices could be found. The following could be mentioned by way of example: (i) nanophotonics; (ii) design, synthesis and tuning of advanced nanomaterials; (iii) classical and non-classical light generation within the near field; (iv) microfluidics and nanofluidics; (v) signal waveguiding; (vi) quantum-, nano- and microcircuits; (vii) materials for nano- and microplatforms, and support substrates and their respective modifications for targeted functionalities. Moreover, nano-optics in in-flow devices and chips for biosensing were discussed, and perspectives on biosensing and single molecule detection (SMD) applications. In this perspective, new insights about precision nanomedicine based on genomics and drug delivery systems were obtained, incorporating new advanced diagnosis methods based on lab-on-particles, labs-on-a-chip, gene therapies, implantable devices, portable miniaturized instrumentation, single molecule detection for biophotonics, and neurophotonics. In this manner, this communication intends to highlight recent reports and developments of nano- and microdevices and further approaches towards the incorporation of developments in nanophotonics and biophotonics in the design of new materials based on different strategies and enhanced techniques and methods. Recent proofs of concept are discussed that could allow new substrates for device manufacturing. Thus, physical phenomena and materials chemistry with accurate control within the nanoscale were introduced into the discussion. In this manner, new potential sources of ideas and strategies for the next generation of technology in many research and development fields are showcased. This is a short communication based on recent high-impact publications related to how various chemical materials and substrate modifications could be tuned for nano- and microdevices, where their application for high point-of-care bioanalysis and further applications in life science is discussed.![]()
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Affiliation(s)
- Luna R Gomez Palacios
- Instituto de Investigaciones en Físico Química de Córdoba (INFIQC), Departamento de Química Orgánica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba (UNC) Ciudad Universitaria 5000 Córdoba Argentina
| | - A Guillermo Bracamonte
- Instituto de Investigaciones en Físico Química de Córdoba (INFIQC), Departamento de Química Orgánica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba (UNC) Ciudad Universitaria 5000 Córdoba Argentina .,Department of Chemistry, University of Victoria (UVic) Vancouver Island V8W 2Y2 British Columbia (BC) Canada.,Département de chimie and Centre d'optique, photonique et laser (COPL), Université Laval Québec (QC) G1V 0A6 Canada
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22
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Brøndsted F, Stains CI. Heteroatom-Substituted Xanthene Fluorophores Enter the Shortwave-Infrared Region. Photochem Photobiol 2022; 98:400-403. [PMID: 34953073 PMCID: PMC8930474 DOI: 10.1111/php.13578] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Accepted: 12/13/2021] [Indexed: 12/18/2022]
Abstract
This article is a highlight of the paper by Ivanic and Schnermann et al. in this issue of Photochemistry and Photobiology (Daly et al. Photochem. Photobiol. 2022). The collaborative team utilized computational approaches to investigate the influence of electron-withdrawing groups at the 10' position of tetramethylrhodamine (TMR). Leveraging this information, the team was able to extend the emission of the TMR scaffold into the shortwave-infrared region (SWIR, 1000-2500 nm) by incorporation of a ketone functional group at the 10' position (Daly et al. Photochem. Photobiol. 2022). This work provides the first example of a TMR derivative with peak SWIR emission (λabs : 862 nm, λem : 1058 nm). The authors utilize the ketone rhodamine scaffold to generate fluorogenic, pH-responsive reporters. This work demonstrates the potential of the classic xanthene scaffold for use as a SWIR reporter, an important step in the ultimate expansion of the repertoire of small-molecule organic fluorophore scaffolds available for deep-tissue imaging applications.
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Affiliation(s)
- Frederik Brøndsted
- Department of Chemistry, University of Virginia, Charlottesville, VA, USA
| | - Cliff I. Stains
- Department of Chemistry, University of Virginia, Charlottesville, VA, USA,University of Virginia Cancer Center, University of Virginia, Charlottesville, VA, USA,Corresponding author: (Cliff I. Stains)
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23
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Boruah A, Saikia BK. Synthesis, Characterization, Properties, and Novel Applications of Fluorescent Nanodiamonds. J Fluoresc 2022; 32:863-885. [PMID: 35230567 DOI: 10.1007/s10895-022-02898-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 02/01/2022] [Indexed: 11/26/2022]
Abstract
In the last few years, fluorescent nanodiamonds (FNDs) have been developed significantly as a new member in the nanocarbon family. The surface of FNDs is embedded with some crystallographic defects containing color centres which surmount the properties of other fluorochromes including up conversion and down conversion nanoparticles, quantum dots, nano tubes, fullerenes, organic dyes, silica etc. Some of the intriguing properties like inevitable photostability, inherent bio-compatibility, outstanding optical and robust mechanical properties, excellent magnetic field, and electric field sensing potentiality make FNDs appealing to some benevolent applications in numerous fields like bio-imaging, delivering drugs, fighting cancer, spin electronics, imaging of magnetic structure at nanoscale and as promising nanometric temperature sensor. The structure of FNDs has certain point defects on the surface among which negatively charged nitrogen vacancy centre (NV-) is the most investigated color centre. The production of NV- fluorescence nanodiamonds is the most challenging task as substitution of carbon atoms is required to create vacancies by causing irradiation from an electron beam which is followed by high temperature annealing. Thus, this review points out the relative advantages of FNDs containing negatively charged nitrogen vacancy centres produced from HPHT method or CVD method with those nanodiamonds produced through detonation process or pulsed laser ablation (PLA) method. The steps involved in the fabrication of FNDs are described along with the major challenges and struggles underwent during the process in this review. This review also summarizes the recent developments made in the functionalization and applications predominantly made in the field of biological science and it is understood that depending on the defect color centres they can exhibit different emitted wavelengths ranging from UV-visible to near infrared with broad or narrow bandwidths. This review also highlights some of the fluorescent NDs that emit stable and strong red or green photoluminescence from the defect centers of NV- which are implanted in the crystal lattice. This critical and extensive review will be useful for the further progress in this futuristic field of FNDs.
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Affiliation(s)
- Anusuya Boruah
- Coal & Energy Group, Materials Science and Technology Division, CSIR-North East Institute of Science and Technology, Jorhat-785006, Assam, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-201002, India
| | - Binoy K Saikia
- Coal & Energy Group, Materials Science and Technology Division, CSIR-North East Institute of Science and Technology, Jorhat-785006, Assam, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-201002, India.
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24
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Bond C, Santiago-Ruiz AN, Tang Q, Lakadamyali M. Technological advances in super-resolution microscopy to study cellular processes. Mol Cell 2022; 82:315-332. [PMID: 35063099 PMCID: PMC8852216 DOI: 10.1016/j.molcel.2021.12.022] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 12/14/2021] [Accepted: 12/16/2021] [Indexed: 01/22/2023]
Abstract
Since its initial demonstration in 2000, far-field super-resolution light microscopy has undergone tremendous technological developments. In parallel, these developments have opened a new window into visualizing the inner life of cells at unprecedented levels of detail. Here, we review the technical details behind the most common implementations of super-resolution microscopy and highlight some of the recent, promising advances in this field.
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Affiliation(s)
- Charles Bond
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Adriana N. Santiago-Ruiz
- Department of Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Qing Tang
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Melike Lakadamyali
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA,Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA,Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA,Correspondence should be sent to M.L.:
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25
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Barr KB, Chiang N, Bertozzi AL, Gilles J, Osher SJ, Weiss PS. Extraction of Hidden Science from Nanoscale Images. THE JOURNAL OF PHYSICAL CHEMISTRY. C, NANOMATERIALS AND INTERFACES 2022; 126:3-13. [PMID: 35633819 PMCID: PMC9135097 DOI: 10.1021/acs.jpcc.1c08712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Scanning probe microscopies and spectroscopies enable investigation of surfaces and even buried interfaces down to the scale of chemical-bonding interactions, and this capability has been enhanced with the support of computational algorithms for data acquisition and image processing to explore physical, chemical, and biological phenomena. Here, we describe how scanning probe techniques have been enhanced by some of these recent algorithmic improvements. One improvement to the data acquisition algorithm is to advance beyond a simple rastering framework by using spirals at constant angular velocity then switching to constant linear velocity, which limits the piezo creep and hysteresis issues seen in traditional acquisition methods. One can also use image-processing techniques to model the distortions that appear from tip motion effects and to make corrections to these images. Another image-processing algorithm we discuss enables researchers to segment images by domains and subdomains, thereby highlighting reactive and interesting disordered sites at domain boundaries. Lastly, we discuss algorithms used to examine the dipole direction of individual molecules and surface domains, hydrogen bonding interactions, and molecular tilt. The computational algorithms used for scanning probe techniques are still improving rapidly and are incorporating machine learning at the next level of iteration. That said, the algorithms are not yet able to perform live adjustments during data recording that could enhance the microscopy and spectroscopic imaging methods significantly.
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Affiliation(s)
- Kristopher B Barr
- California NanoSystems Institute and Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Naihao Chiang
- Department of Chemistry, University of Houston, Houston Texas 77204, United States
| | - Andrea L Bertozzi
- Department of Mathematics, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Jérôme Gilles
- Department of Mathematics and Statistics, San Diego State University, San Diego, California 92182, United States
| | - Stanley J Osher
- Department of Mathematics, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Paul S Weiss
- California NanoSystems Institute, Department of Chemistry and Biochemistry, Department of Bioengineering, and Materials Science and Engineering Department, University of California, Los Angeles, Los Angeles, California 90095, United States
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26
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Xu N, Qiao Q, Liu X, Xu Z. Enhancing Brightness and Photostability of Organic Small Molecular Fluorescent Dyes Through Inhibiting Twisted Intramolecular Charge Transfer (TICT) ※. ACTA CHIMICA SINICA 2022. [DOI: 10.6023/a21120578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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27
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Wang L, Wang S, Tang J, Espinoza VB, Loredo A, Tian Z, Weisman RB, Xiao H. Oxime as a general photocage for the design of visible light photo-activatable fluorophores. Chem Sci 2021; 12:15572-15580. [PMID: 35003586 PMCID: PMC8654061 DOI: 10.1039/d1sc05351e] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 11/21/2021] [Indexed: 12/18/2022] Open
Abstract
Photoactivatable fluorophores have been widely used for tracking molecular and cellular dynamics with subdiffraction resolution. In this work, we have prepared a series of photoactivatable probes using the oxime moiety as a new class of photolabile caging group in which the photoactivation process is mediated by a highly efficient photodeoximation reaction. Incorporation of the oxime caging group into fluorophores results in loss of fluorescence. Upon light irradiation in the presence of air, the oxime-caged fluorophores are oxidized to their carbonyl derivatives, restoring strong fluorophore fluorescence. To demonstrate the utility of these oxime-caged fluorophores, we have created probes that target different organelles for live-cell confocal imaging. We also carried out photoactivated localization microscopy (PALM) imaging under physiological conditions using low-power light activation in the absence of cytotoxic additives. Our studies show that oximes represent a new class of visible-light photocages that can be widely used for cellular imaging, sensing, and photo-controlled molecular release.
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Affiliation(s)
- Lushun Wang
- Department of Chemistry, Rice University 6100 Main Street Houston Texas 77005 USA
| | - Shichao Wang
- Department of Chemistry, Rice University 6100 Main Street Houston Texas 77005 USA
| | - Juan Tang
- Department of Chemistry, Rice University 6100 Main Street Houston Texas 77005 USA
| | - Vanessa B Espinoza
- Department of Chemistry, Rice University 6100 Main Street Houston Texas 77005 USA
| | - Axel Loredo
- Department of Chemistry, Rice University 6100 Main Street Houston Texas 77005 USA
| | - Zeru Tian
- Department of Chemistry, Rice University 6100 Main Street Houston Texas 77005 USA
| | - R Bruce Weisman
- Department of Chemistry, Rice University 6100 Main Street Houston Texas 77005 USA
| | - Han Xiao
- Department of Chemistry, Rice University 6100 Main Street Houston Texas 77005 USA
- Department of Biosciences, Rice University 6100 Main Street Houston Texas 77005 USA
- Department of Bioengineering, Rice University 6100 Main Street Houston Texas 77005 USA
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28
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Barrantes FJ. Fluorescence sensors for imaging membrane lipid domains and cholesterol. CURRENT TOPICS IN MEMBRANES 2021; 88:257-314. [PMID: 34862029 DOI: 10.1016/bs.ctm.2021.09.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Lipid membrane domains are supramolecular lateral heterogeneities of biological membranes. Of nanoscopic dimensions, they constitute specialized hubs used by the cell as transient signaling platforms for a great variety of biologically important mechanisms. Their property to form and dissolve in the bulk lipid bilayer endow them with the ability to engage in highly dynamic processes, and temporarily recruit subpopulations of membrane proteins in reduced nanometric compartments that can coalesce to form larger mesoscale assemblies. Cholesterol is an essential component of these lipid domains; its unique molecular structure is suitable for interacting intricately with crevices and cavities of transmembrane protein surfaces through its rough β face while "talking" to fatty acid acyl chains of glycerophospholipids and sphingolipids via its smooth α face. Progress in the field of membrane domains has been closely associated with innovative improvements in fluorescence microscopy and new fluorescence sensors. These advances enabled the exploration of the biophysical properties of lipids and their supramolecular platforms. Here I review the rationale behind the use of biosensors over the last few decades and their contributions towards elucidation of the in-plane and transbilayer topography of cholesterol-enriched lipid domains and their molecular constituents. The challenges introduced by super-resolution optical microscopy are discussed, as well as possible scenarios for future developments in the field, including virtual ("no staining") staining.
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Affiliation(s)
- Francisco J Barrantes
- Biomedical Research Institute (BIOMED), Catholic University of Argentina (UCA)-National Scientific and Technical Research Council (CONICET), Buenos Aires, Argentina.
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29
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Masullo LA, Szalai AM, Lopez LF, Stefani FD. Fluorescence nanoscopy at the sub-10 nm scale. Biophys Rev 2021; 13:1101-1112. [PMID: 35059030 PMCID: PMC8724505 DOI: 10.1007/s12551-021-00864-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Accepted: 10/20/2021] [Indexed: 12/14/2022] Open
Abstract
Fluorescence nanoscopy represented a breakthrough for the life sciences as it delivers 20-30 nm resolution using far-field fluorescence microscopes. This resolution limit is not fundamental but imposed by the limited photostability of fluorophores under ambient conditions. This has motivated the development of a second generation of fluorescence nanoscopy methods that aim to deliver sub-10 nm resolution, reaching the typical size of structural proteins and thus providing true molecular resolution. In this review, we present common fundamental aspects of these nanoscopies, discuss the key experimental factors that are necessary to fully exploit their capabilities, and discuss their current and future challenges.
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Affiliation(s)
- Luciano A. Masullo
- Centro de Investigaciones en Bionanociencias (CIBION), Consejo Nacional de Investigaciones Científicas Y Técnicas (CONICET), Godoy Cruz 2390, C1425FQD Ciudad Autónoma de Buenos Aires, Argentina
- Departamento de Física, Facultad de Ciencias Exactas Y Naturales, Universidad de Buenos Aires, Güiraldes 2620, C1428EHA Ciudad Autónoma de Buenos Aires, Argentina
| | - Alan M. Szalai
- Centro de Investigaciones en Bionanociencias (CIBION), Consejo Nacional de Investigaciones Científicas Y Técnicas (CONICET), Godoy Cruz 2390, C1425FQD Ciudad Autónoma de Buenos Aires, Argentina
| | - Lucía F. Lopez
- Departamento de Física, Facultad de Ciencias Exactas Y Naturales, Universidad de Buenos Aires, Güiraldes 2620, C1428EHA Ciudad Autónoma de Buenos Aires, Argentina
| | - Fernando D. Stefani
- Centro de Investigaciones en Bionanociencias (CIBION), Consejo Nacional de Investigaciones Científicas Y Técnicas (CONICET), Godoy Cruz 2390, C1425FQD Ciudad Autónoma de Buenos Aires, Argentina
- Departamento de Física, Facultad de Ciencias Exactas Y Naturales, Universidad de Buenos Aires, Güiraldes 2620, C1428EHA Ciudad Autónoma de Buenos Aires, Argentina
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30
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Gagliano G, Nelson T, Saliba N, Vargas-Hernández S, Gustavsson AK. Light Sheet Illumination for 3D Single-Molecule Super-Resolution Imaging of Neuronal Synapses. Front Synaptic Neurosci 2021; 13:761530. [PMID: 34899261 PMCID: PMC8651567 DOI: 10.3389/fnsyn.2021.761530] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 10/27/2021] [Indexed: 01/02/2023] Open
Abstract
The function of the neuronal synapse depends on the dynamics and interactions of individual molecules at the nanoscale. With the development of single-molecule super-resolution microscopy over the last decades, researchers now have a powerful and versatile imaging tool for mapping the molecular mechanisms behind the biological function. However, imaging of thicker samples, such as mammalian cells and tissue, in all three dimensions is still challenging due to increased fluorescence background and imaging volumes. The combination of single-molecule imaging with light sheet illumination is an emerging approach that allows for imaging of biological samples with reduced fluorescence background, photobleaching, and photodamage. In this review, we first present a brief overview of light sheet illumination and previous super-resolution techniques used for imaging of neurons and synapses. We then provide an in-depth technical review of the fundamental concepts and the current state of the art in the fields of three-dimensional single-molecule tracking and super-resolution imaging with light sheet illumination. We review how light sheet illumination can improve single-molecule tracking and super-resolution imaging in individual neurons and synapses, and we discuss emerging perspectives and new innovations that have the potential to enable and improve single-molecule imaging in brain tissue.
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Affiliation(s)
- Gabriella Gagliano
- Department of Chemistry, Rice University, Houston, TX, United States
- Applied Physics Program, Rice University, Houston, TX, United States
- Smalley-Curl Institute, Rice University, Houston, TX, United States
| | - Tyler Nelson
- Department of Chemistry, Rice University, Houston, TX, United States
- Applied Physics Program, Rice University, Houston, TX, United States
- Smalley-Curl Institute, Rice University, Houston, TX, United States
| | - Nahima Saliba
- Department of Chemistry, Rice University, Houston, TX, United States
| | - Sofía Vargas-Hernández
- Department of Chemistry, Rice University, Houston, TX, United States
- Systems, Synthetic, and Physical Biology Program, Rice University, Houston, TX, United States
- Institute of Biosciences & Bioengineering, Rice University, Houston, TX, United States
| | - Anna-Karin Gustavsson
- Department of Chemistry, Rice University, Houston, TX, United States
- Smalley-Curl Institute, Rice University, Houston, TX, United States
- Institute of Biosciences & Bioengineering, Rice University, Houston, TX, United States
- Department of Biosciences, Rice University, Houston, TX, United States
- Laboratory for Nanophotonics, Rice University, Houston, TX, United States
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Abstract
Super-resolution fluorescence microscopy and Förster Resonance Energy Transfer (FRET) form a well-established family of techniques that has provided unique tools to study the dynamic architecture and functionality of biological systems, as well as to investigate nanomaterials. In the last years, the integration of super-resolution methods with FRET measurements has generated advances in two fronts. On the one hand, FRET-based probes have enhanced super-resolution imaging. On the other, the development of super-resolved FRET imaging methods has allowed the visualization of molecular interaction patterns with higher spatial resolution, less averaging and higher dynamic range. Here, we review these advances and discuss future perspectives, including the possible integration of FRET with next generation super-resolution techniques capable of reaching true molecular-scale spatial resolution.
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Affiliation(s)
- Alan M Szalai
- Centro de Investigaciones en Bionanociencias (CIBION), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2390, C1425FQD Ciudad Autónoma de Buenos Aires, Argentina.
| | - Cecilia Zaza
- Centro de Investigaciones en Bionanociencias (CIBION), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2390, C1425FQD Ciudad Autónoma de Buenos Aires, Argentina.
- Departamento de Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Güiraldes 2620, C1428EHA Ciudad Autónoma de Buenos Aires, Argentina
| | - Fernando D Stefani
- Centro de Investigaciones en Bionanociencias (CIBION), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2390, C1425FQD Ciudad Autónoma de Buenos Aires, Argentina.
- Departamento de Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Güiraldes 2620, C1428EHA Ciudad Autónoma de Buenos Aires, Argentina
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32
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Bohrmann‐Linde C, Meuter N, Zeller D, Tausch MW. Teaching Photochemistry: Experimental Approaches and Digital Media. CHEMPHOTOCHEM 2021. [DOI: 10.1002/cptc.202100141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Claudia Bohrmann‐Linde
- Department of Chemical Education University of Wuppertal Gaußstr. 20 42119 Wuppertal Germany
| | - Nico Meuter
- Department of Chemical Education University of Wuppertal Gaußstr. 20 42119 Wuppertal Germany
| | - Diana Zeller
- Department of Chemical Education University of Wuppertal Gaußstr. 20 42119 Wuppertal Germany
| | - Michael W. Tausch
- Department of Chemical Education University of Wuppertal Gaußstr. 20 42119 Wuppertal Germany
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33
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Lardon N, Wang L, Tschanz A, Hoess P, Tran M, D'Este E, Ries J, Johnsson K. Systematic Tuning of Rhodamine Spirocyclization for Super-resolution Microscopy. J Am Chem Soc 2021; 143:14592-14600. [PMID: 34460256 DOI: 10.1021/jacs.1c05004] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Rhodamines are the most important class of fluorophores for applications in live-cell fluorescence microscopy. This is mainly because rhodamines exist in a dynamic equilibrium between a fluorescent zwitterion and a nonfluorescent but cell-permeable spirocyclic form. Different imaging applications require different positions of this dynamic equilibrium, and an adjustment of the equilibrium poses a challenge for the design of suitable probes. We describe here how the conversion of the ortho-carboxy moiety of a given rhodamine into substituted acyl benzenesulfonamides and alkylamides permits the systematic tuning of the equilibrium of spirocyclization with unprecedented accuracy and over a large range. This allows one to transform the same rhodamine into either a highly fluorogenic and cell-permeable probe for live-cell-stimulated emission depletion (STED) microscopy or a spontaneously blinking dye for single-molecule localization microscopy (SMLM). We used this approach to generate differently colored probes optimized for different labeling systems and imaging applications.
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Affiliation(s)
- Nicolas Lardon
- Department of Chemical Biology, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany.,Faculty of Chemistry and Earth Sciences, Heidelberg University, 69120 Heidelberg, Germany
| | - Lu Wang
- Department of Chemical Biology, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany.,Key Laboratory of Smart Drug Delivery, Ministry of Education, School of Pharmacy, Fudan University, Zhangheng Road 826, 201203 Shanghai, China
| | - Aline Tschanz
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany.,Faculty of Biosciences, Collaboration for Joint PhD Degree between EMBL and Heidelberg University, 69120 Heidelberg, Germany
| | - Philipp Hoess
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany.,Faculty of Biosciences, Collaboration for Joint PhD Degree between EMBL and Heidelberg University, 69120 Heidelberg, Germany
| | - Mai Tran
- Department of Chemical Biology, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Elisa D'Este
- Optical Microscopy Facility, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Jonas Ries
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Kai Johnsson
- Department of Chemical Biology, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany.,Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
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34
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Kenath GS, Karanastasis AA, Ullal CK. Super-Resolution Imaging of Spatial Heterogeneities in Model Thermosensitive Hydrogels with Implications for Their Origins. Macromolecules 2021. [DOI: 10.1021/acs.macromol.1c00754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Gopal S. Kenath
- Department of Materials Science and Engineering, Rensselaer Polytechnic Institute, 110 8th Street, Troy, New York 12180, United States
| | - Apostolos A. Karanastasis
- Department of Materials Science and Engineering, Rensselaer Polytechnic Institute, 110 8th Street, Troy, New York 12180, United States
| | - Chaitanya K. Ullal
- Department of Materials Science and Engineering, Rensselaer Polytechnic Institute, 110 8th Street, Troy, New York 12180, United States
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35
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[Comparison and progress review of various super-resolution fluorescence imaging techniques]. Se Pu 2021; 39:1055-1064. [PMID: 34505427 PMCID: PMC9404158 DOI: 10.3724/sp.j.1123.2021.06015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
“Seeing is believing” is the central philosophy of life science research, which runs through the continuous understanding of individual molecules, molecular complexes, molecular dynamic behavior, and the entire molecular network. Living and dynamic molecules are functional in nature; therefore, fluorescence microscopy has emerged as an irreplaceable tool in life science research. However, when fluorescence imaging is performed at the molecular level, some artificial signals may lead to erroneous experimental results. This obstacle is due to the limitation of the optical diffraction limit, and the fluorescence microscope cannot distinguish the target in the diffraction-limited space. Super-resolution fluorescence imaging technology breaks through the diffraction limit, allows visualization of biomolecules at the nanometer scale to the single-molecule level, and allows us to study the structure and dynamic processes of living cells with unprecedented spatial and temporal resolution. It has become a powerful tool for life science research and is gradually being applied to material science, catalytic reaction processes, and photolithography as well. The principle of super-resolution imaging technologies is different; therefore, it has different technical performances, thus limiting their specific technical characteristics and application scope. Current mainstream super-resolution imaging technologies can be classified into three types: structured illumination microscopy (SIM), stimulated emission depletion (STED), and single-molecule localization microscopy (SMLM). These microscopes use different complex technologies, but the strategy is the same and simple, i.e. two adjacent luminous points in a diffraction-limited space can be spatially resolved by time resolution. SIM has been used for three-dimensional real-time imaging in multicellular organisms; however, compared with other technologies, its lower horizontal and vertical resolutions need to be further optimized. STED is limited by its small imaging field of view and high photobleaching; however, the best time resolution can be considered at a high spatial resolution, and it has been proven that three-color STED imaging can be performed. In SMLM super-resolution imaging, the time resolution is affected by the time required to locate all fluorophores, which is closely related to the switching and luminescence properties of the fluorophore. With the improvement in horizontal and vertical resolution of imaging, the image acquisition speed, photobleaching characteristics, and the possibility of multi-color and dynamic imaging have increasingly become the key determinants of super-resolution fluorescence imaging. Thus far, the main use of super-resolution imaging technology has been focused on biological applications for studying structural changes less than 200 nm in dimension. In addition to the combination of structural and morphological characterization with biomolecular detection and identification, super-resolution imaging technology is rapidly expanding into the fields of interaction mapping, multi-target detection, and real-time imaging. In the latter applications, super-resolution imaging technology is particularly advantageous because of more flexible sample staining, higher labeling efficiency, faster and simpler readings, and gentler sample preparation procedures. In this article, we compare the principles of these three technologies and introduce their application progress in biology. We expect the results described herein will help researchers clarify the technical advantages and applicable application directions of different super-resolution imaging technologies, thus facilitating researchers in making reasonable choices in future research.
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Lorizate M, Terrones O, Nieto-Garai JA, Rojo-Bartolomé I, Ciceri D, Morana O, Olazar-Intxausti J, Arboleya A, Martin A, Szynkiewicz M, Calleja-Felipe M, Bernardino de la Serna J, Contreras FX. Super-Resolution Microscopy Using a Bioorthogonal-Based Cholesterol Probe Provides Unprecedented Capabilities for Imaging Nanoscale Lipid Heterogeneity in Living Cells. SMALL METHODS 2021; 5:e2100430. [PMID: 34928061 DOI: 10.1002/smtd.202100430] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 06/26/2021] [Indexed: 06/14/2023]
Abstract
Despite more than 20 years of work since the lipid raft concept was proposed, the existence of these nanostructures remains highly controversial due to the lack of noninvasive methods to investigate their native nanorganization in living unperturbed cells. There is an unmet need for probes for direct imaging of nanoscale membrane dynamics with high spatial and temporal resolution in living cells. In this paper, a bioorthogonal-based cholesterol probe (chol-N3 ) is developed that, combined with nanoscopy, becomes a new powerful method for direct visualization and characterization of lipid raft at unprecedented resolution in living cells. The chol-N3 probe mimics cholesterol in synthetic and cellular membranes without perturbation. When combined with live-cell super-resolution microscopy, chol-N3 demonstrates the existence of cholesterol-rich nanodomains of <50 nm at the plasma membrane of resting living cells. Using this tool, the lipid membrane structure of such subdiffraction limit domains is identified, and the nanoscale spatiotemporal organization of cholesterol in the plasma membrane of living cells reveals multiple cholesterol diffusion modes at different spatial localizations. Finally, imaging across thick organ samples outlines the potential of this new method to address essential biological questions that were previously beyond reach.
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Affiliation(s)
- Maier Lorizate
- Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU) and Instituto Biofisika (UPV/EHU, CSIC), Barrio Sarriena s/n, Leioa, 48940, Spain
| | - Oihana Terrones
- Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, Leioa, 48940, Spain
| | - Jon Ander Nieto-Garai
- Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU) and Instituto Biofisika (UPV/EHU, CSIC), Barrio Sarriena s/n, Leioa, 48940, Spain
- Fundación Biofísica Bizkaia/Biofisika Bizkaia Fundazioa (FBB), Barrio Sarriena s/n, Leioa, 48940, Spain
| | - Iratxe Rojo-Bartolomé
- Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU) and Instituto Biofisika (UPV/EHU, CSIC), Barrio Sarriena s/n, Leioa, 48940, Spain
- Fundación Biofísica Bizkaia/Biofisika Bizkaia Fundazioa (FBB), Barrio Sarriena s/n, Leioa, 48940, Spain
| | - Dalila Ciceri
- Fundación Biofísica Bizkaia/Biofisika Bizkaia Fundazioa (FBB), Barrio Sarriena s/n, Leioa, 48940, Spain
| | - Ornella Morana
- Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU) and Instituto Biofisika (UPV/EHU, CSIC), Barrio Sarriena s/n, Leioa, 48940, Spain
- Fundación Biofísica Bizkaia/Biofisika Bizkaia Fundazioa (FBB), Barrio Sarriena s/n, Leioa, 48940, Spain
| | - June Olazar-Intxausti
- Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, Leioa, 48940, Spain
| | - Aroa Arboleya
- Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU) and Instituto Biofisika (UPV/EHU, CSIC), Barrio Sarriena s/n, Leioa, 48940, Spain
- Fundación Biofísica Bizkaia/Biofisika Bizkaia Fundazioa (FBB), Barrio Sarriena s/n, Leioa, 48940, Spain
| | - Alexia Martin
- National Heart and Lung Institute, Imperial College London, Sir Alexander Fleming Building, London, SW7 2AZ, UK
| | - Marta Szynkiewicz
- Central Laser Facility, Science and Technology Facilities Council, Rutherford Appleton Laboratory, Research Complex at Harwell, Oxford, OX11 0FA, UK
| | - Maria Calleja-Felipe
- Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU) and Instituto Biofisika (UPV/EHU, CSIC), Barrio Sarriena s/n, Leioa, 48940, Spain
| | - Jorge Bernardino de la Serna
- National Heart and Lung Institute, Imperial College London, Sir Alexander Fleming Building, London, SW7 2AZ, UK
- Central Laser Facility, Science and Technology Facilities Council, Rutherford Appleton Laboratory, Research Complex at Harwell, Oxford, OX11 0FA, UK
- NIHR Imperial Biomedical Research Centre, London, SW7 2AZ, UK
| | - F-Xabier Contreras
- Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU) and Instituto Biofisika (UPV/EHU, CSIC), Barrio Sarriena s/n, Leioa, 48940, Spain
- IKERBASQUE, Basque Foundation for Science, Bilbao, 48011, Spain
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Spectroscopic Approach to Correction and Visualisation of Bright-Field Light Transmission Microscopy Biological Data. PHOTONICS 2021. [DOI: 10.3390/photonics8080333] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The most realistic information about a transparent sample such as a live cell can be obtained using bright-field light microscopy. Under high-intensity pulsing LED illumination, we captured a primary 12-bit-per-channel (bpc) response from an observed sample using a bright-field microscope equipped with a high-resolution (4872 × 3248) image sensor. In order to suppress data distortions originating from the light interactions with elements in the optical path, poor sensor reproduction (geometrical defects of the camera sensor and some peculiarities of sensor sensitivity), we propose a spectroscopic approach for the correction of these uncompressed 12 bpc data by simultaneous calibration of all parts of the experimental arrangement. Moreover, the final intensities of the corrected images are proportional to the photon fluxes detected by a camera sensor. It can be visualized in 8 bpc intensity depth after the Least Information Loss compression.
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38
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Abstract
Abstract
This article describes the defining characteristics of photochromic dyes and highlights the subset of properties that are of greatest commercial importance. It outlines the history of the industrial exploitation of photochromic colorants before moving on to discuss current and potential applications. In doing so, a brief tour of key types of photochromic dye is provided.
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Broichhagen J, Kilian N. Chemical Biology Tools To Investigate Malaria Parasites. Chembiochem 2021; 22:2219-2236. [PMID: 33570245 PMCID: PMC8360121 DOI: 10.1002/cbic.202000882] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 02/10/2021] [Indexed: 02/06/2023]
Abstract
Parasitic diseases like malaria tropica have been shaping human evolution and history since the beginning of mankind. After infection, the response of the human host ranges from asymptomatic to severe and may culminate in death. Therefore, proper examination of the parasite's biology is pivotal to deciphering unique molecular, biochemical and cell biological processes, which in turn ensure the identification of treatment strategies, such as potent drug targets and vaccine candidates. However, implementing molecular biology methods for genetic manipulation proves to be difficult for many parasite model organisms. The development of fast and straightforward applicable alternatives, for instance small-molecule probes from the field of chemical biology, is essential. In this review, we will recapitulate the highlights of previous molecular and chemical biology approaches that have already created insight and understanding of the malaria parasite Plasmodium falciparum. We discuss current developments from the field of chemical biology and explore how their application could advance research into this parasite in the future. We anticipate that the described approaches will help to close knowledge gaps in the biology of P. falciparum and we hope that researchers will be inspired to use these methods to gain knowledge - with the aim of ending this devastating disease.
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Affiliation(s)
- Johannes Broichhagen
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)Robert-Roessle-Strasse 1013125BerlinGermany
| | - Nicole Kilian
- Centre for Infectious DiseasesParasitologyHeidelberg University HospitalIm Neuenheimer Feld 32469120HeidelbergGermany
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40
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Abstract
Structured light, which exhibits nontrivial intensity, phase, and polarization patterns in space, has key applications ranging from imaging and 3D micromanipulation to classical and quantum communication. However, to date, its application to molecular chirality has been limited by the weakness of magnetic interactions. Here we structure light's local handedness in space to introduce and realize an enantio-sensitive interferometer for efficient chiral recognition without magnetic interactions, which can be seen as an enantio-sensitive version of Young's double slit experiment. Upon interaction with isotropic chiral media, such chirality-structured light effectively creates chiral emitters of opposite handedness, located at different positions in space. We show that if the distribution of light's handedness breaks left-right symmetry, the interference of these chiral emitters leads to unidirectional bending of the emitted light, in opposite directions in media of opposite handedness, even if the number of the left-handed and right-handed emitters excited in the medium is exactly the same. Our work introduces the concepts of polarization of chirality and chirality-polarized light, exposes the immense potential of sculpting light's local chirality, and offers novel opportunities for efficient chiral discrimination, enantio-sensitive optical molecular fingerprinting and imaging on ultrafast time scales.
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Ghithan JH, Noel JM, Roussel TJ, McCall MA, Alphenaar BW, Mendes SB. Photobleaching reduction in modulated super-resolution microscopy. Microscopy (Oxf) 2021; 70:278-288. [PMID: 33064828 DOI: 10.1093/jmicro/dfaa062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Revised: 10/13/2020] [Accepted: 10/15/2020] [Indexed: 11/13/2022] Open
Abstract
Important breakthroughs in far-field imaging techniques have been made since the first demonstrations of stimulated emission depletion (STED) microscopy. To date, the most straightforward and widespread deployment of STED microscopy has used continuous wave (CW) laser beams for both the excitation and depletion of fluorescence emission. A major drawback of the CW STED imaging technique has been photobleaching effects due to the high optical power needed in the depletion beam to reach sub-diffraction resolution. To overcome this hurdle, we have applied a synchronous detection approach based on modulating the excitation laser beam, while keeping the depletion beam at CW operation, and frequency filtering the collected signal with a lock-in amplifier to record solely the super-resolved fluorescence emission. We demonstrate here that such approach allows an important reduction in the optical power of both laser beams that leads to measurable decreases in photobleaching effects in STED microscopy. We report super-resolution images with relatively low powers for both the excitation and depletion beams. In addition, typical unwanted scattering effects and background signal generated from the depletion beam, which invariably arises from mismatches in refractive index in the material composing the sample, are largely reduced by using the modulated STED approach. The capability of acquiring super-resolution images with relatively low power is quite relevant for studying a variety of samples, but particularly important for biological species as exemplified in this work.
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Affiliation(s)
- Jafar H Ghithan
- University of Louisville, Department of Physics and Astronomy, 215 Eastern Pkwy, Louisville, Kentucky, United States, 40292
| | - Jennifer M Noel
- University of Louisville, Department of Anatomical Sciences and Neurobiology, 511 South Floyd, Louisville, Kentucky, United States, 40202
| | - Thomas J Roussel
- University of Louisville, Department of Bioengineering, J. B. Speed School of Engineering, Louisville, Kentucky, United States, 40292
| | - Maureen A McCall
- University of Louisville, Department of Ophthalmology and Visual Sciences, 301 E. Muhammad Ali Blvd., Louisville, Kentucky, United States, 40202
| | - Bruce W Alphenaar
- University of Louisville, Department of Electrical Engineering, J. B. Speed School of Engineering, Louisville, Kentucky, United States, 40292
| | - Sergio B Mendes
- University of Louisville, Department of Physics and Astronomy, 215 Eastern Pkwy, Louisville, Kentucky, United States, 40292
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Abstract
Optical imaging, which possesses noninvasive and high-resolution features for biomedical imaging, has been used to study various biological samples, from in vitro cells, ex vivo tissue, to in vivo imaging of living organism. Furthermore, optical imaging also covers a very wide scope of spatial scale, from submicron sized organelles to macro-scale live biological samples, enabling it a powerful tool for biomedical studies. Before introducing these superior optical imaging methods to researchers, first of all, it is necessary to present the basic concept of light-matter interactions such as absorption, scattering, and fluorescence, which can be used as the imaging contrast and also affect the imaging quality. And then the working mechanism of various imaging modalities including fluorescence microscopy, confocal microscopy, multiphoton microscopy, super-resolution microscopy, optical coherence tomography (OCT), diffuse optical tomography (DOT), etc. will be presented. Meanwhile, the main features and typical bioimaging applications of these optical imaging technologies are discussed. Finally, the perspective of future optical imaging methods is presented. The aim of this chapter is to introduce the background and principle of optical imaging for grasping the mechanism of advanced optical imaging modalities introduced in the following chapters.
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Fan M, An H, Wang C, Huo S, Wang T, Cui X, Zhang D. STED Imaging the Dynamics of Lysosomes by Dually Fluorogenic Si-Rhodamine. Chemistry 2021; 27:9620-9626. [PMID: 33899976 DOI: 10.1002/chem.202100623] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Indexed: 11/07/2022]
Abstract
Super-resolution microscopy (SRM) imaging of the finite subcellular structures and subtle bioactivities inside organelles delivers abundant cellular information with high fidelity to unravel the intricate biological processes. An ideal fluorescent probe with precise control of fluorescence is critical in SRM technique like stimulated emission depletion (STED). Si-rhodamine was decorated with both targeting group and H+ -receptor, affording the dually fluorogenic Si-rhodamine in which the NIR fluorescence was efficiently controlled by the coalescent of spirolactone-zwitterion equilibrium and PeT mechanism. The dually fluorogenic characters of the probe offer a perfect mutual enhancement in sensitivity, specificity and spatial resolution. Strong fluorescence only released in the existence of targeting protein at acidic lysosomal pH, ensured precisely tracking the dynamic of lysosomal structure and pH in living cells by STED.
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Affiliation(s)
- Mengting Fan
- Department of Chemistry, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai, 200241, P. R. China
| | - Haiyan An
- College of Chemistry and Chemical Engineering, Northwest Normal University, Lanzhou, 730070, P. R. China
- Department of Organic Chemistry, College of Pharmacy, Second Military Medical University, Shanghai, 200433, P. R. China
| | - Chuanfeng Wang
- Department of Chemistry, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai, 200241, P. R. China
| | - Shuhui Huo
- College of Chemistry and Chemical Engineering, Northwest Normal University, Lanzhou, 730070, P. R. China
| | - Ting Wang
- Department of Organic Chemistry, College of Pharmacy, Second Military Medical University, Shanghai, 200433, P. R. China
| | - Xiaoyan Cui
- Department of Chemistry, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai, 200241, P. R. China
| | - Dazhi Zhang
- Department of Organic Chemistry, College of Pharmacy, Second Military Medical University, Shanghai, 200433, P. R. China
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Kell DB. A protet-based, protonic charge transfer model of energy coupling in oxidative and photosynthetic phosphorylation. Adv Microb Physiol 2021; 78:1-177. [PMID: 34147184 DOI: 10.1016/bs.ampbs.2021.01.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Textbooks of biochemistry will explain that the otherwise endergonic reactions of ATP synthesis can be driven by the exergonic reactions of respiratory electron transport, and that these two half-reactions are catalyzed by protein complexes embedded in the same, closed membrane. These views are correct. The textbooks also state that, according to the chemiosmotic coupling hypothesis, a (or the) kinetically and thermodynamically competent intermediate linking the two half-reactions is the electrochemical difference of protons that is in equilibrium with that between the two bulk phases that the coupling membrane serves to separate. This gradient consists of a membrane potential term Δψ and a pH gradient term ΔpH, and is known colloquially as the protonmotive force or pmf. Artificial imposition of a pmf can drive phosphorylation, but only if the pmf exceeds some 150-170mV; to achieve in vivo rates the imposed pmf must reach 200mV. The key question then is 'does the pmf generated by electron transport exceed 200mV, or even 170mV?' The possibly surprising answer, from a great many kinds of experiment and sources of evidence, including direct measurements with microelectrodes, indicates it that it does not. Observable pH changes driven by electron transport are real, and they control various processes; however, compensating ion movements restrict the Δψ component to low values. A protet-based model, that I outline here, can account for all the necessary observations, including all of those inconsistent with chemiosmotic coupling, and provides for a variety of testable hypotheses by which it might be refined.
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Affiliation(s)
- Douglas B Kell
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative, Biology, University of Liverpool, Liverpool, United Kingdom; The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark.
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Szalai AM, Siarry B, Lukin J, Giusti S, Unsain N, Cáceres A, Steiner F, Tinnefeld P, Refojo D, Jovin TM, Stefani FD. Super-resolution Imaging of Energy Transfer by Intensity-Based STED-FRET. NANO LETTERS 2021; 21:2296-2303. [PMID: 33621102 DOI: 10.1021/acs.nanolett.1c00158] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Förster resonance energy transfer (FRET) imaging methods provide unique insight into the spatial distribution of energy transfer and (bio)molecular interaction events, though they deliver average information for an ensemble of events included in a diffraction-limited volume. Coupling super-resolution fluorescence microscopy and FRET has been a challenging and elusive task. Here, we present STED-FRET, a method of general applicability to obtain super-resolved energy transfer images. In addition to higher spatial resolution, STED-FRET provides a more accurate quantification of interaction and has the capacity of suppressing contributions of noninteracting partners, which are otherwise masked by averaging in conventional imaging. The method capabilities were first demonstrated on DNA-origami model systems, verified on uniformly double-labeled microtubules, and then utilized to image biomolecular interactions in the membrane-associated periodic skeleton (MPS) of neurons.
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Affiliation(s)
- Alan M Szalai
- Centro de Investigaciones en Bionanociencias (CIBION), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2390, C1425FQD Ciudad Autónoma de Buenos Aires, Argentina
| | - Bruno Siarry
- Centro de Investigaciones en Bionanociencias (CIBION), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2390, C1425FQD Ciudad Autónoma de Buenos Aires, Argentina
| | - Jerónimo Lukin
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA), CONICET, Partner Institute of the Max Planck Society, Godoy Cruz 2390, C1425FQD Ciudad Autónoma de Buenos Aires, Argentina
| | - Sebastián Giusti
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA), CONICET, Partner Institute of the Max Planck Society, Godoy Cruz 2390, C1425FQD Ciudad Autónoma de Buenos Aires, Argentina
| | - Nicolás Unsain
- Laboratorio de Neurobiología, Instituto de Investigación Médica Mercedes y Martín Ferreyra (INIMEC, CONICET), Universidad Nacional de Córdoba (UNC), Friuli 2434, X5016NST Córdoba, Argentina
- Cátedra de Biología Celular y Molecular, Escuela de Biología, Centro de Biología Celular y Molecular (CeBiCeM, FCEFyN-UNC), Facultad de Ciencias Exactas Físicas y Naturales, Universidad Nacional de Córdoba, X5016NST Córdoba, Argentina
| | - Alfredo Cáceres
- Instituto Universitario de Ciencias Biomédicas Cordoba (IUCBC), Centro de Investigación Medicina Traslacional Severo Amuchástegui (CIMETSA), Friuli 2786, X5016NSW Córdoba, Argentina
| | - Florian Steiner
- Department of Chemistry and Center for NanoScience, Ludwig-Maximilians-Universität München, Butenandtstraße 5-13 Haus E, 81377 München, Germany
| | - Philip Tinnefeld
- Department of Chemistry and Center for NanoScience, Ludwig-Maximilians-Universität München, Butenandtstraße 5-13 Haus E, 81377 München, Germany
| | - Damián Refojo
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA), CONICET, Partner Institute of the Max Planck Society, Godoy Cruz 2390, C1425FQD Ciudad Autónoma de Buenos Aires, Argentina
| | - Thomas M Jovin
- Laboratory of Cellular Dynamics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Fernando D Stefani
- Centro de Investigaciones en Bionanociencias (CIBION), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2390, C1425FQD Ciudad Autónoma de Buenos Aires, Argentina
- Cátedra de Biología Celular y Molecular, Escuela de Biología; Centro de Biología Celular y Molecular (CeBiCeM, FCEFyN - UNC), Facultad de Ciencias Exactas Físicas y Naturales, Universidad Nacional de Córdoba, Vélez Sarsfield 1611, X5016GCA, Córdoba, Argentina
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MINFLUX nanometer-scale 3D imaging and microsecond-range tracking on a common fluorescence microscope. Nat Commun 2021; 12:1478. [PMID: 33674570 PMCID: PMC7935904 DOI: 10.1038/s41467-021-21652-z] [Citation(s) in RCA: 80] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 02/04/2021] [Indexed: 12/13/2022] Open
Abstract
The recently introduced minimal photon fluxes (MINFLUX) concept pushed the resolution of fluorescence microscopy to molecular dimensions. Initial demonstrations relied on custom made, specialized microscopes, raising the question of the method’s general availability. Here, we show that MINFLUX implemented with a standard microscope stand can attain 1–3 nm resolution in three dimensions, rendering fluorescence microscopy with molecule-scale resolution widely applicable. Advances, such as synchronized electro-optical and galvanometric beam steering and a stabilization that locks the sample position to sub-nanometer precision with respect to the stand, ensure nanometer-precise and accurate real-time localization of individually activated fluorophores. In our MINFLUX imaging of cell- and neurobiological samples, ~800 detected photons suffice to attain a localization precision of 2.2 nm, whereas ~2500 photons yield precisions <1 nm (standard deviation). We further demonstrate 3D imaging with localization precision of ~2.4 nm in the focal plane and ~1.9 nm along the optic axis. Localizing with a precision of <20 nm within ~100 µs, we establish this spatio-temporal resolution in single fluorophore tracking and apply it to the diffusion of single labeled lipids in lipid-bilayer model membranes. Minimal photon fluxes (MINFLUX) has enabled molecule-scale resolution in fluorescence microscopy but this had not been shown in standard, broadly applicable microscopy platforms. Here the authors report a solution to allow normal fluorescence microscopy while also providing 1-3 nm 3D resolution.
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47
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Pushing the super-resolution limit: recent improvements in microscopy below the diffraction limit. Biochem Soc Trans 2021; 49:431-439. [PMID: 33599719 DOI: 10.1042/bst20200746] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 12/15/2020] [Accepted: 01/20/2021] [Indexed: 12/12/2022]
Abstract
Super-resolution microscopy has revolutionised the way we observe biological systems. These methods are now a staple of fluorescence microscopy. Researchers have used super-resolution methods in myriad systems to extract nanoscale spatial information on multiple interacting parts. These methods are continually being extended and reimagined to further push their resolving power and achieve truly single protein resolution. Here, we explore the most recent advances at the frontier of the 'super-resolution' limit and what opportunities remain for further improvements in the near future.
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48
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Three-dimensional total-internal reflection fluorescence nanoscopy with nanometric axial resolution by photometric localization of single molecules. Nat Commun 2021; 12:517. [PMID: 33483489 PMCID: PMC7822951 DOI: 10.1038/s41467-020-20863-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 12/17/2020] [Indexed: 01/06/2023] Open
Abstract
Single-molecule localization microscopy enables far-field imaging with lateral resolution in the range of 10 to 20 nanometres, exploiting the fact that the centre position of a single-molecule’s image can be determined with much higher accuracy than the size of that image itself. However, attaining the same level of resolution in the axial (third) dimension remains challenging. Here, we present Supercritical Illumination Microscopy Photometric z-Localization with Enhanced Resolution (SIMPLER), a photometric method to decode the axial position of single molecules in a total internal reflection fluorescence microscope. SIMPLER requires no hardware modification whatsoever to a conventional total internal reflection fluorescence microscope and complements any 2D single-molecule localization microscopy method to deliver 3D images with nearly isotropic nanometric resolution. Performance examples include SIMPLER-direct stochastic optical reconstruction microscopy images of the nuclear pore complex with sub-20 nm axial localization precision and visualization of microtubule cross-sections through SIMPLER-DNA points accumulation for imaging in nanoscale topography with sub-10 nm axial localization precision. Achieving high axial resolution is challenging in single-molecule localization microscopy. Here, the authors present a photometric method to decode the axial position of single molecules in a total internal reflection fluorescence microscope without hardware modification, and show nearly isotropic nanometric resolution.
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49
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Masullo LA, Steiner F, Zähringer J, Lopez LF, Bohlen J, Richter L, Cole F, Tinnefeld P, Stefani FD. Pulsed Interleaved MINFLUX. NANO LETTERS 2021; 21:840-846. [PMID: 33336573 DOI: 10.1021/acs.nanolett.0c04600] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
We introduce p-MINFLUX, a new implementation of the highly photon-efficient single-molecule localization method with a simplified experimental setup and additional fluorescence lifetime information. In contrast to the original MINFLUX implementation, p-MINFLUX uses interleaved laser pulses to deliver the doughnut-shaped excitation foci at a maximum repetition rate. Using both static and dynamic DNA origami model systems, we demonstrate the performance of p-MINFLUX for single-molecule localization nanoscopy and tracking, respectively. p-MINFLUX delivers 1-2 nm localization precision with 2000-1000 photon counts. In addition, p-MINFLUX gives access to the fluorescence lifetime enabling multiplexing and super-resolved lifetime imaging. p-MINFLUX should help to unlock the full potential of innovative single-molecule localization schemes.
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Affiliation(s)
- Luciano A Masullo
- Centro de Investigaciones en Bionanociencias (CIBION), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2390, C1425FQD, Ciudad Autónoma de Buenos Aires, Argentina
- Departamento de Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Güiraldes 2620, C1428EHA, Ciudad Autónoma de Buenos Aires, Argentina
| | - Florian Steiner
- Department of Chemistry and Center for NanoScience, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13 Haus E, 81377 München, Germany
| | - Jonas Zähringer
- Department of Chemistry and Center for NanoScience, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13 Haus E, 81377 München, Germany
| | - Lucía F Lopez
- Centro de Investigaciones en Bionanociencias (CIBION), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2390, C1425FQD, Ciudad Autónoma de Buenos Aires, Argentina
| | - Johann Bohlen
- Department of Chemistry and Center for NanoScience, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13 Haus E, 81377 München, Germany
| | - Lars Richter
- Centro de Investigaciones en Bionanociencias (CIBION), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2390, C1425FQD, Ciudad Autónoma de Buenos Aires, Argentina
- Department of Chemistry and Center for NanoScience, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13 Haus E, 81377 München, Germany
| | - Fiona Cole
- Department of Chemistry and Center for NanoScience, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13 Haus E, 81377 München, Germany
| | - Philip Tinnefeld
- Department of Chemistry and Center for NanoScience, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13 Haus E, 81377 München, Germany
| | - Fernando D Stefani
- Centro de Investigaciones en Bionanociencias (CIBION), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2390, C1425FQD, Ciudad Autónoma de Buenos Aires, Argentina
- Departamento de Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Güiraldes 2620, C1428EHA, Ciudad Autónoma de Buenos Aires, Argentina
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50
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Möckl L, Moerner WE. Super-resolution Microscopy with Single Molecules in Biology and Beyond-Essentials, Current Trends, and Future Challenges. J Am Chem Soc 2020; 142:17828-17844. [PMID: 33034452 PMCID: PMC7582613 DOI: 10.1021/jacs.0c08178] [Citation(s) in RCA: 82] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Indexed: 12/31/2022]
Abstract
Single-molecule super-resolution microscopy has developed from a specialized technique into one of the most versatile and powerful imaging methods of the nanoscale over the past two decades. In this perspective, we provide a brief overview of the historical development of the field, the fundamental concepts, the methodology required to obtain maximum quantitative information, and the current state of the art. Then, we will discuss emerging perspectives and areas where innovation and further improvement are needed. Despite the tremendous progress, the full potential of single-molecule super-resolution microscopy is yet to be realized, which will be enabled by the research ahead of us.
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Affiliation(s)
- Leonhard Möckl
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - W. E. Moerner
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
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