1
|
Sedeh AB, Kobitski A, Dai S, Eroğlu-Kayıkçı S, Nienhaus K, Hilbert L, Nienhaus GU. Stimulated emission double depletion nanoscopy with background correction at the single-pixel level. OPTICS LETTERS 2023; 48:5791-5794. [PMID: 37910760 DOI: 10.1364/ol.502001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 10/12/2023] [Indexed: 11/03/2023]
Abstract
Fluorescence microscopy images are inevitably tainted by background contributions including emission from out-of-focus planes, scattered light, and detector noise. In stimulated emission depletion (STED) nanoscopy, an additional, method-specific background arises from incomplete depletion and re-excitation by the depletion beam. Various approaches have been proposed to remove the background from a STED image, some of which rely on the acquisition of a separate background image that is subtracted from the STED image with a weighting factor. Using stimulated emission double depletion (STEDD) nanoscopy, we observed that the weighting factor varies locally in densely labeled samples, so that background removal with a single (global) weighting factor generates local image artifacts due to incorrect background subtraction. Here we present an algorithm that computes the optimal weighting factor at the single-pixel level, yielding a difference image with excellent suppression of low-frequency background.
Collapse
|
2
|
Zhu J, Wu F, Li C, Mao J, Wang Y, Zhou X, Xie H, Wen C. Application of Single Extracellular Vesicle Analysis Techniques. Int J Nanomedicine 2023; 18:5365-5376. [PMID: 37750091 PMCID: PMC10518151 DOI: 10.2147/ijn.s421342] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 09/12/2023] [Indexed: 09/27/2023] Open
Abstract
Extracellular vesicles (EVs) are lipid containers that are actively released by cells and contain complex molecular cargoes. These cargoes include abundant material such as genomes and proteins from cells of origin. They are involved in intercellular communication and various pathological processes, showing excellent potential for diagnosing and treating diseases. Given the significant heterogeneity of EVs in complex physiopathological processes, unveiling their composition is essential to understanding their function. Bulk detection methods have been previously used to analyze EVs, but they often mask their heterogeneity, leading to the loss of valuable information. To overcome this limitation, single extracellular vesicle (SEV) analysis techniques have been developed and advanced. These techniques allow for analyzing EVs' physical information and biometric molecules at the SEV level. This paper reviews recent advances in SEV detection methods and summarizes some clinical applications for SEV detection strategies.
Collapse
Affiliation(s)
- Junquan Zhu
- Department of Pediatrics, The Second Xiangya Hospital, Central South University, Changsha, People’s Republic of China
| | - Feifeng Wu
- Department of Pediatrics, The Second Xiangya Hospital, Central South University, Changsha, People’s Republic of China
| | - Cuifang Li
- Department of Pediatrics, The Second Xiangya Hospital, Central South University, Changsha, People’s Republic of China
| | - Jueyi Mao
- Department of Pediatrics, The Second Xiangya Hospital, Central South University, Changsha, People’s Republic of China
| | - Yang Wang
- Department of Pediatrics, The Second Xiangya Hospital, Central South University, Changsha, People’s Republic of China
| | - Xin Zhou
- Department of Pediatrics, The Second Xiangya Hospital, Central South University, Changsha, People’s Republic of China
| | - Haotian Xie
- Department of Pediatrics, The Second Xiangya Hospital, Central South University, Changsha, People’s Republic of China
| | - Chuan Wen
- Department of Pediatrics, The Second Xiangya Hospital, Central South University, Changsha, People’s Republic of China
| |
Collapse
|
3
|
Cooper C, Thompson RCA, Clode PL. Investigating parasites in three dimensions: trends in volume microscopy. Trends Parasitol 2023; 39:668-681. [PMID: 37302958 DOI: 10.1016/j.pt.2023.05.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 05/17/2023] [Accepted: 05/17/2023] [Indexed: 06/13/2023]
Abstract
To best understand parasite, host, and vector morphologies, host-parasite interactions, and to develop new drug and vaccine targets, structural data should, ideally, be obtained and visualised in three dimensions (3D). Recently, there has been a significant uptake of available 3D volume microscopy techniques that allow collection of data across centimetre (cm) to Angstrom (Å) scales by utilising light, X-ray, electron, and ion sources. Here, we present and discuss microscopy tools available for the collection of 3D structural data, focussing on electron microscopy-based techniques. We highlight their strengths and limitations, such that parasitologists can identify techniques best suited to answer their research questions. Additionally, we review the importance of volume microscopy to the advancement of the field of parasitology.
Collapse
Affiliation(s)
- Crystal Cooper
- Centre for Microscopy, Characterisation, and Analysis, University of Western Australia, Stirling Hwy, Crawley, WA 6009, Australia.
| | - R C Andrew Thompson
- School of Veterinary and Life Sciences, Murdoch University, 90 South Street, Murdoch, WA 6150, Australia
| | - Peta L Clode
- Centre for Microscopy, Characterisation, and Analysis, University of Western Australia, Stirling Hwy, Crawley, WA 6009, Australia; School of Biological Sciences, University of Western Australia, Stirling Hwy, Crawley, WA 6009, Australia
| |
Collapse
|
4
|
Englert D, Burger EM, Grün F, Verma MS, Lackner J, Lampe M, Bühler B, Schokolowski J, Nienhaus GU, Jäschke A, Sunbul M. Fast-exchanging spirocyclic rhodamine probes for aptamer-based super-resolution RNA imaging. Nat Commun 2023; 14:3879. [PMID: 37391423 PMCID: PMC10313827 DOI: 10.1038/s41467-023-39611-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 06/22/2023] [Indexed: 07/02/2023] Open
Abstract
Live-cell RNA imaging with high spatial and temporal resolution remains a major challenge. Here we report the development of RhoBAST:SpyRho, a fluorescent light-up aptamer (FLAP) system ideally suited for visualizing RNAs in live or fixed cells with various advanced fluorescence microscopy modalities. Overcoming problems associated with low cell permeability, brightness, fluorogenicity, and signal-to-background ratio of previous fluorophores, we design a novel probe, SpyRho (Spirocyclic Rhodamine), which tightly binds to the RhoBAST aptamer. High brightness and fluorogenicity is achieved by shifting the equilibrium between spirolactam and quinoid. With its high affinity and fast ligand exchange, RhoBAST:SpyRho is a superb system for both super-resolution SMLM and STED imaging. Its excellent performance in SMLM and the first reported super-resolved STED images of specifically labeled RNA in live mammalian cells represent significant advances over other FLAPs. The versatility of RhoBAST:SpyRho is further demonstrated by imaging endogenous chromosomal loci and proteins.
Collapse
Affiliation(s)
- Daniel Englert
- Institute of Pharmacy and Molecular Biotechnology (IPMB), Heidelberg University, Heidelberg, Germany
| | - Eva-Maria Burger
- Institute of Pharmacy and Molecular Biotechnology (IPMB), Heidelberg University, Heidelberg, Germany
| | - Franziska Grün
- Institute of Pharmacy and Molecular Biotechnology (IPMB), Heidelberg University, Heidelberg, Germany
| | - Mrigank S Verma
- Institute of Applied Physics (APH), Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
| | - Jens Lackner
- Institute of Applied Physics (APH), Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
| | - Marko Lampe
- Advanced Light Microscopy Facility, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Bastian Bühler
- Institute of Pharmacy and Molecular Biotechnology (IPMB), Heidelberg University, Heidelberg, Germany
| | - Janin Schokolowski
- Institute of Pharmacy and Molecular Biotechnology (IPMB), Heidelberg University, Heidelberg, Germany
| | - G Ulrich Nienhaus
- Institute of Applied Physics (APH), Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany.
- Institute of Nanotechnology (INT), Karlsruhe Institute of Technology (KIT), Eggenstein-Leopoldshafen, Germany.
- Institute of Biological and Chemical Systems (IBCS), Karlsruhe Institute of Technology (KIT), Eggenstein-Leopoldshafen, Germany.
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
| | - Andres Jäschke
- Institute of Pharmacy and Molecular Biotechnology (IPMB), Heidelberg University, Heidelberg, Germany.
| | - Murat Sunbul
- Institute of Pharmacy and Molecular Biotechnology (IPMB), Heidelberg University, Heidelberg, Germany.
| |
Collapse
|
5
|
Nienhaus K, Nienhaus GU. Mechanistic Understanding of Protein Corona Formation around Nanoparticles: Old Puzzles and New Insights. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023:e2301663. [PMID: 37010040 DOI: 10.1002/smll.202301663] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 03/14/2023] [Indexed: 06/19/2023]
Abstract
Although a wide variety of nanoparticles (NPs) have been engineered for use as disease markers or drug delivery agents, the number of nanomedicines in clinical use has hitherto remained small. A key obstacle in nanomedicine development is the lack of a deep mechanistic understanding of NP interactions in the bio-environment. Here, the focus is on the biomolecular adsorption layer (protein corona), which quickly enshrouds a pristine NP exposed to a biofluid and modifies the way the NP interacts with the bio-environment. After a brief introduction of NPs for nanomedicine, proteins, and their mutual interactions, research aimed at addressing fundamental properties of the protein corona, specifically its mono-/multilayer structure, reversibility and irreversibility, time dependence, as well as its role in NP agglomeration, is critically reviewed. It becomes quite evident that the knowledge of the protein corona is still fragmented, and conflicting results on fundamental issues call for further mechanistic studies. The article concludes with a discussion of future research directions that should be taken to advance the understanding of the protein corona around NPs. This knowledge will provide NP developers with the predictive power to account for these interactions in the design of efficacious nanomedicines.
Collapse
Affiliation(s)
- Karin Nienhaus
- Institute of Applied Physics, Karlsruhe Institute of Technology, 76049, Karlsruhe, Germany
| | - Gerd Ulrich Nienhaus
- Institute of Applied Physics, Karlsruhe Institute of Technology, 76049, Karlsruhe, Germany
- Institute of Nanotechnology, Karlsruhe Institute of Technology, 76021, Karlsruhe, Germany
- Institute of Biological and Chemical Systems, Karlsruhe Institute of Technology, 76021, Karlsruhe, Germany
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| |
Collapse
|
6
|
Nienhaus K, Nienhaus GU. Genetically encodable fluorescent protein markers in advanced optical imaging. Methods Appl Fluoresc 2022; 10. [PMID: 35767981 DOI: 10.1088/2050-6120/ac7d3f] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 06/29/2022] [Indexed: 11/12/2022]
Abstract
Optical fluorescence microscopy plays a pivotal role in the exploration of biological structure and dynamics, especially on live specimens. Progress in the field relies, on the one hand, on technical advances in imaging and data processing and, on the other hand, on progress in fluorescent marker technologies. Among these, genetically encodable fluorescent proteins (FPs) are invaluable tools, as they allow facile labeling of live cells, tissues or organisms, as these produce the FP markers all by themselves after introduction of a suitable gene. Here we cover FP markers from the GFP family of proteins as well as tetrapyrrole-binding proteins, which further complement the FP toolbox in important ways. A broad range of FP variants have been endowed, by using protein engineering, with photophysical properties that are essential for specific fluorescence microscopy techniques, notably those offering nanoscale image resolution. We briefly introduce various advanced imaging methods and show how they utilize the distinct properties of the FP markers in exciting imaging applications, with the aim to guide researchers toward the design of powerful imaging experiments that are optimally suited to address their biological questions.
Collapse
Affiliation(s)
- Karin Nienhaus
- Institute of Applied Physics, Karlsruhe Institute of Technology, Wolfgang Gaede Str. 1, Karlsruhe, 76131, GERMANY
| | - Gerd Ulrich Nienhaus
- Karlsruhe Institute of Technology, Wolfgang Gaede Str. 1, Karlsruhe, 76131, GERMANY
| |
Collapse
|
7
|
Ma R, Štefl M, Nienhaus GU. Single molecule localization-based analysis of clathrin-coated pit and caveolar dynamics. NANOSCALE HORIZONS 2022; 7:385-395. [PMID: 35289830 DOI: 10.1039/d2nh00008c] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Clathrin-coated pits and caveolae are nanoscale invaginations of the plasma membrane of cells, forming through the assembly of membrane coat and accessory proteins in a tightly regulated process. We have analyzed the development of these membrane coat structures with high spatial and temporal resolution and sensitivity using super-resolution single-molecule localization microscopy (SMLM) on live cells. To this end, we developed a sophisticated clustering and data analysis workflow that automatically extracts the relevant information from SMLM image sequences taken on live cells. We quantified lifetime distributions of clathrin-coated and caveolar structures, and analyzed their growth dynamics. Moreover, we observed hotspots in the plasma membrane where coat structures appear repeatedly. The stunningly similar temporal development of clathrin-coated and caveolar structures suggests that key accessory proteins, some of which are shared between the two types of membrane coat structures, orchestrate the temporal evolution of these complex architectures.
Collapse
Affiliation(s)
- Rui Ma
- Institute of Applied Physics (APH), Karlsruhe Institute of Technology (KIT), Wolfgang Gaede-Strasse 1, 76131 Karlsruhe, Germany.
| | - Martin Štefl
- Institute of Applied Physics (APH), Karlsruhe Institute of Technology (KIT), Wolfgang Gaede-Strasse 1, 76131 Karlsruhe, Germany.
| | - Gerd Ulrich Nienhaus
- Institute of Applied Physics (APH), Karlsruhe Institute of Technology (KIT), Wolfgang Gaede-Strasse 1, 76131 Karlsruhe, Germany.
- Institute of Nanotechnology (INT), Karlsruhe Institute of Technology (KIT), PO Box 3640, 76021 Karlsruhe, Germany
- Institute of Biological and Chemical Systems (IBCS), Karlsruhe Institute of Technology (KIT), PO Box 3640, 76021 Karlsruhe, Germany
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| |
Collapse
|
8
|
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.
Collapse
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
| |
Collapse
|
9
|
Computerized fluorescence microscopy of microbial cells. World J Microbiol Biotechnol 2021; 37:189. [PMID: 34617135 DOI: 10.1007/s11274-021-03159-3] [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: 07/27/2021] [Accepted: 09/30/2021] [Indexed: 10/20/2022]
Abstract
The upgrading of fluorescence microscopy by the introduction of computer technologies has led to the creation of a new methodology, computerized fluorescence microscopy (CFM). CFM improves subjective visualization and combines it with objective quantitative analysis of the microscopic data. CFM has opened up two fundamentally new opportunities for studying microorganisms. The first is the quantitative measurement of the fluorescence parameters of the targeted fluorophores in association with certain structures of individual cells. The second is the expansion of the boundaries of visualization/resolution of intracellular components beyond the "diffraction limit" of light microscopy into the nanometer range. This enables to obtain unique information about the localization and dynamics of intracellular processes at the molecular level. The purpose of this review is to demonstrate the potential of CFM in the study of fundamental aspects of the structural and functional organization of microbial cells. The basics of computer processing and analysis of digital images are briefly described. The fluorescent molecules used in CFM with an emphasis on fluorescent proteins are characterized. The main methods of super-resolution microscopy (nanoscopy) are presented. The capabilities of various CFM methods for exploring microbial cells at the subcellular level are illustrated by the examples of various studies on yeast and bacteria.
Collapse
|
10
|
Bordanaba-Florit G, Royo F, Kruglik SG, Falcón-Pérez JM. Using single-vesicle technologies to unravel the heterogeneity of extracellular vesicles. Nat Protoc 2021; 16:3163-3185. [PMID: 34135505 DOI: 10.1038/s41596-021-00551-z] [Citation(s) in RCA: 114] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 03/31/2021] [Indexed: 12/12/2022]
Abstract
Extracellular vesicles (EVs) are heterogeneous lipid containers with a complex molecular cargo comprising several populations with unique roles in biological processes. These vesicles are closely associated with specific physiological features, which makes them invaluable in the detection and monitoring of various diseases. EVs play a key role in pathophysiological processes by actively triggering genetic or metabolic responses. However, the heterogeneity of their structure and composition hinders their application in medical diagnosis and therapies. This diversity makes it difficult to establish their exact physiological roles, and the functions and composition of different EV (sub)populations. Ensemble averaging approaches currently employed for EV characterization, such as western blotting or 'omics' technologies, tend to obscure rather than reveal these heterogeneities. Recent developments in single-vesicle analysis have made it possible to overcome these limitations and have facilitated the development of practical clinical applications. In this review, we discuss the benefits and challenges inherent to the current methods for the analysis of single vesicles and review the contribution of these approaches to the understanding of EV biology. We describe the contributions of these recent technological advances to the characterization and phenotyping of EVs, examination of the role of EVs in cell-to-cell communication pathways and the identification and validation of EVs as disease biomarkers. Finally, we discuss the potential of innovative single-vesicle imaging and analysis methodologies using microfluidic devices, which promise to deliver rapid and effective basic and practical applications for minimally invasive prognosis systems.
Collapse
Affiliation(s)
- Guillermo Bordanaba-Florit
- Exosomes Laboratory, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Derio, Spain.
| | - Félix Royo
- Exosomes Laboratory, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Derio, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (Ciberehd), Madrid, Spain
| | - Sergei G Kruglik
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, Laboratoire Jean Perrin, Paris, France
| | - Juan M Falcón-Pérez
- Exosomes Laboratory, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Derio, Spain. .,Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (Ciberehd), Madrid, Spain. .,Ikerbasque, Basque Foundation for Science, Bilbao, Spain.
| |
Collapse
|
11
|
Nienhaus K, Nienhaus GU. Fluorescent proteins of the EosFP clade: intriguing marker tools with multiple photoactivation modes for advanced microscopy. RSC Chem Biol 2021; 2:796-814. [PMID: 34458811 PMCID: PMC8341165 DOI: 10.1039/d1cb00014d] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 03/27/2021] [Indexed: 02/04/2023] Open
Abstract
Optical fluorescence microscopy has taken center stage in the exploration of biological structure and dynamics, especially on live specimens, and super-resolution imaging methods continue to deliver exciting new insights into the molecular foundations of life. Progress in the field, however, crucially hinges on advances in fluorescent marker technology. Among these, fluorescent proteins (FPs) of the GFP family are advantageous because they are genetically encodable, so that live cells, tissues or organisms can produce these markers all by themselves. A subclass of them, photoactivatable FPs, allow for control of their fluorescence emission by light irradiation, enabling pulse-chase imaging and super-resolution microscopy. In this review, we discuss FP variants of the EosFP clade that have been optimized by amino acid sequence modification to serve as markers for various imaging techniques. In general, two different modes of photoactivation are found, reversible photoswitching between a fluorescent and a nonfluorescent state and irreversible green-to red photoconversion. First, we describe their basic structural and optical properties. We then summarize recent research aimed at elucidating the photochemical processes underlying photoactivation. Finally, we briefly introduce various advanced imaging methods facilitated by specific EosFP variants, and show some exciting sample applications.
Collapse
Affiliation(s)
- Karin Nienhaus
- Institute of Applied Physics, Karlsruhe Institute of Technology 76049 Karlsruhe Germany
| | - Gerd Ulrich Nienhaus
- Institute of Applied Physics, Karlsruhe Institute of Technology 76049 Karlsruhe Germany
- Institute of Nanotechnology, Karlsruhe Institute of Technology 76021 Karlsruhe Germany
- Institute of Biological and Chemical Systems, Karlsruhe Institute of Technology 76021 Karlsruhe Germany
- Department of Physics, University of Illinois at Urbana-Champaign Urbana IL 61801 USA
| |
Collapse
|
12
|
Hüpfel M, Yu. Kobitski A, Zhang W, Nienhaus GU. Wavelet-based background and noise subtraction for fluorescence microscopy images. BIOMEDICAL OPTICS EXPRESS 2021; 12:969-980. [PMID: 33680553 PMCID: PMC7901331 DOI: 10.1364/boe.413181] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 12/27/2020] [Accepted: 01/15/2021] [Indexed: 05/20/2023]
Abstract
Fluorescence microscopy images are inevitably contaminated by background intensity contributions. Fluorescence from out-of-focus planes and scattered light are important sources of slowly varying, low spatial frequency background, whereas background varying from pixel to pixel (high frequency noise) is introduced by the detection system. Here we present a powerful, easy-to-use software, wavelet-based background and noise subtraction (WBNS), which effectively removes both of these components. To assess its performance, we apply WBNS to synthetic images and compare the results quantitatively with the ground truth and with images processed by other background removal algorithms. We further evaluate WBNS on real images taken with a light-sheet microscope and a super-resolution stimulated emission depletion microscope. For both cases, we compare the WBNS algorithm with hardware-based background removal techniques and present a quantitative assessment of the results. WBNS shows an excellent performance in all these applications and significantly enhances the visual appearance of fluorescence images. Moreover, it may serve as a pre-processing step for further quantitative analysis.
Collapse
Affiliation(s)
- Manuel Hüpfel
- Institute of Applied Physics, Karlsruhe Institute of Technology (KIT), Wolfgang-Gaede-Str. 1, 76131 Karlsruhe, Germany
| | - Andrei Yu. Kobitski
- Institute of Applied Physics, Karlsruhe Institute of Technology (KIT), Wolfgang-Gaede-Str. 1, 76131 Karlsruhe, Germany
| | - Weichun Zhang
- Institute of Applied Physics, Karlsruhe Institute of Technology (KIT), Wolfgang-Gaede-Str. 1, 76131 Karlsruhe, Germany
| | - G. Ulrich Nienhaus
- Institute of Applied Physics, Karlsruhe Institute of Technology (KIT), Wolfgang-Gaede-Str. 1, 76131 Karlsruhe, Germany
- Institute of Nanotechnology, Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
- Institute of Biological and Chemical Systems, Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
- Department of Physics, University of Illinois at Urbana-Champaign, 1110 W. Green Street, Urbana, IL 61801, USA
| |
Collapse
|
13
|
Brownian motion-based nanoparticle sizing-A powerful approach for in situ analysis of nanoparticle-protein interactions. Biointerphases 2020; 15:061201. [PMID: 33356335 DOI: 10.1116/6.0000438] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
A key hurdle toward effective application of nanoparticles (NPs) in biomedicine is still the incomplete understanding of the biomolecular adsorption layer, the so-called protein corona, which inevitably forms around NPs when they are immersed in a biofluid. NP sizing techniques via the analysis of Brownian motions offer a powerful way to measure the thickness of the protein corona in situ. Here, the fundamentals of three techniques, dynamic light scattering, fluorescence correlation spectroscopy, and nanoparticle tracking analysis are briefly summarized. Then, experimental procedures for the determination of binding curves are presented in a tutorial fashion. Nanoparticle sizing experiments are illustrated with a selection of recent results on the interactions of transferrin with hydrophilic and hydrophobic polystyrene nanoparticles, and key insights gained from this work are discussed.
Collapse
|
14
|
Guthrie DA, Klein Herenbrink C, Lycas MD, Ku T, Bonifazi A, DeVree BT, Mathiasen S, Javitch JA, Grimm JB, Lavis L, Gether U, Newman AH. Novel Fluorescent Ligands Enable Single-Molecule Localization Microscopy of the Dopamine Transporter. ACS Chem Neurosci 2020; 11:3288-3300. [PMID: 32926777 DOI: 10.1021/acschemneuro.0c00397] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The dopamine transporter (DAT) is critical for spatiotemporal control of dopaminergic neurotransmission and is the target for therapeutic agents, including ADHD medications, and abused substances, such as cocaine. Here, we develop new fluorescently labeled ligands that bind DAT with high affinity and enable single-molecule detection of the transporter. The cocaine analogue MFZ2-12 (1) was conjugated to novel rhodamine-based Janelia Fluorophores (JF549 and JF646). High affinity binding of the resulting ligands to DAT was demonstrated by potent inhibition of [3H]dopamine uptake in DAT transfected CAD cells and by competition radioligand binding experiments on rat striatal membranes. Visualization of binding was substantiated by confocal or TIRF microscopy revealing selective binding of the analogues to DAT transfected CAD cells. Single particle tracking experiments were performed with JF549-conjugated DG3-80 (3) and JF646-conjugated DG4-91 (4) on DAT transfected CAD cells enabling quantification and categorization of the dynamic behavior of DAT into four distinct motion classes (immobile, confined, Brownian, and directed). Finally, we show that the ligands can be used in direct stochastic optical reconstruction microscopy (dSTORM) experiments permitting further analyses of DAT distribution on the nanoscale. In summary, these novel fluorescent ligands are promising new tools for studying DAT localization and regulation with single-molecule resolution.
Collapse
Affiliation(s)
- Daryl A. Guthrie
- Medicinal Chemistry Section, Molecular Targets and Medications Discovery Branch, National Institute on Drug Abuse-Intramural Research Program, National Institutes of Health, 333 Cassell Drive, Baltimore, Maryland 21224, United States,
| | - Carmen Klein Herenbrink
- Department of Neuroscience, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen N, Denmark
| | - Matthew Domenic Lycas
- Department of Neuroscience, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen N, Denmark
| | - Therese Ku
- Medicinal Chemistry Section, Molecular Targets and Medications Discovery Branch, National Institute on Drug Abuse-Intramural Research Program, National Institutes of Health, 333 Cassell Drive, Baltimore, Maryland 21224, United States,
| | - Alessandro Bonifazi
- Medicinal Chemistry Section, Molecular Targets and Medications Discovery Branch, National Institute on Drug Abuse-Intramural Research Program, National Institutes of Health, 333 Cassell Drive, Baltimore, Maryland 21224, United States,
| | - Brian T. DeVree
- Department of Neuroscience, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen N, Denmark
| | - Signe Mathiasen
- Department of Psychiatry, Columbia University Vagelos College of Physicians & Surgeon and Division of Molecular Therapeutics, New York State Psychiatric Institute, New York, New York 10032, United States
| | - Jonathan A. Javitch
- Department of Psychiatry, Columbia University Vagelos College of Physicians & Surgeon and Division of Molecular Therapeutics, New York State Psychiatric Institute, New York, New York 10032, United States
| | - Jonathan B. Grimm
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, Virginia 20147, United States
| | - Luke Lavis
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, Virginia 20147, United States
| | - Ulrik Gether
- Department of Neuroscience, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen N, Denmark
| | - Amy Hauck Newman
- Medicinal Chemistry Section, Molecular Targets and Medications Discovery Branch, National Institute on Drug Abuse-Intramural Research Program, National Institutes of Health, 333 Cassell Drive, Baltimore, Maryland 21224, United States,
| |
Collapse
|
15
|
Schubert V, Neumann P, Marques A, Heckmann S, Macas J, Pedrosa-Harand A, Schubert I, Jang TS, Houben A. Super-Resolution Microscopy Reveals Diversity of Plant Centromere Architecture. Int J Mol Sci 2020; 21:E3488. [PMID: 32429054 PMCID: PMC7278974 DOI: 10.3390/ijms21103488] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 05/11/2020] [Accepted: 05/11/2020] [Indexed: 12/20/2022] Open
Abstract
Centromeres are essential for proper chromosome segregation to the daughter cells during mitosis and meiosis. Chromosomes of most eukaryotes studied so far have regional centromeres that form primary constrictions on metaphase chromosomes. These monocentric chromosomes vary from point centromeres to so-called "meta-polycentromeres", with multiple centromere domains in an extended primary constriction, as identified in Pisum and Lathyrus species. However, in various animal and plant lineages centromeres are distributed along almost the entire chromosome length. Therefore, they are called holocentromeres. In holocentric plants, centromere-specific proteins, at which spindle fibers usually attach, are arranged contiguously (line-like), in clusters along the chromosomes or in bands. Here, we summarize findings of ultrastructural investigations using immunolabeling with centromere-specific antibodies and super-resolution microscopy to demonstrate the structural diversity of plant centromeres. A classification of the different centromere types has been suggested based on the distribution of spindle attachment sites. Based on these findings we discuss the possible evolution and advantages of holocentricity, and potential strategies to segregate holocentric chromosomes correctly.
Collapse
Affiliation(s)
- Veit Schubert
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466 Seeland, Germany; (S.H.); (I.S.); (A.H.)
| | - Pavel Neumann
- Biology Centre, Czech Academy of Sciences, 37005 České Budějovice, Czech Republic; (P.N.); (J.M.); (T.-S.J.)
| | - André Marques
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany;
| | - Stefan Heckmann
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466 Seeland, Germany; (S.H.); (I.S.); (A.H.)
| | - Jiri Macas
- Biology Centre, Czech Academy of Sciences, 37005 České Budějovice, Czech Republic; (P.N.); (J.M.); (T.-S.J.)
| | - Andrea Pedrosa-Harand
- Department of Botany, Federal University of Pernambuco (UFPE), Recife 50670-901, Pernambuco, Brazil;
| | - Ingo Schubert
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466 Seeland, Germany; (S.H.); (I.S.); (A.H.)
| | - Tae-Soo Jang
- Biology Centre, Czech Academy of Sciences, 37005 České Budějovice, Czech Republic; (P.N.); (J.M.); (T.-S.J.)
- Department of Biological Sciences, Chungnam National University, Daejeon 34134, Korea
| | - Andreas Houben
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466 Seeland, Germany; (S.H.); (I.S.); (A.H.)
| |
Collapse
|
16
|
Roy D, Steinkühler J, Zhao Z, Lipowsky R, Dimova R. Mechanical Tension of Biomembranes Can Be Measured by Super Resolution (STED) Microscopy of Force-Induced Nanotubes. NANO LETTERS 2020; 20:3185-3191. [PMID: 32320255 PMCID: PMC7304919 DOI: 10.1021/acs.nanolett.9b05232] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 04/20/2020] [Indexed: 05/26/2023]
Abstract
Membrane tension modulates the morphology of plasma-membrane tubular protrusions in cells but is difficult to measure. Here, we propose to use microscopy imaging to assess the membrane tension. We report direct measurement of membrane nanotube diameters with unprecedented resolution using stimulated emission depletion (STED) microscopy. For this purpose, we integrated an optical tweezers setup in a commercial microscope equipped for STED imaging and established micropipette aspiration of giant vesicles. Membrane nanotubes were pulled from the vesicles at specific membrane tension imposed by the aspiration pipet. Tube diameters calculated from the applied tension using the membrane curvature elasticity model are in excellent agreement with data measured directly with STED. Our approach can be extended to cellular membranes and will then allow us to estimate the mechanical membrane tension within the force-induced nanotubes.
Collapse
|
17
|
Morozumi A, Kamiya M, Uno SN, Umezawa K, Kojima R, Yoshihara T, Tobita S, Urano Y. Spontaneously Blinking Fluorophores Based on Nucleophilic Addition/Dissociation of Intracellular Glutathione for Live-Cell Super-resolution Imaging. J Am Chem Soc 2020; 142:9625-9633. [PMID: 32343567 DOI: 10.1021/jacs.0c00451] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Single-molecule localization microscopy (SMLM) allows the reconstruction of super-resolution images but generally requires prior intense laser irradiation and in some cases additives to induce blinking of conventional fluorophores. We previously introduced a spontaneously blinking rhodamine fluorophore based on an intramolecular spirocyclization reaction for live-cell SMLM under physiological conditions. Here, we report a novel principle of spontaneous blinking in living cells, which utilizes reversible ground-state nucleophilic attack of intracellular glutathione (GSH) upon a xanthene fluorophore. Structural optimization afforded two pyronine fluorophores with different colors, both of which exhibit equilibrium (between the fluorescent dissociated form and the nonfluorescent GSH adduct form) and blinking kinetics that enable SMLM of microtubules or mitochondria in living cells. Furthermore, by using spontaneously blinking fluorophores working in the near-infrared (NIR) and green ranges, we succeeded in dual-color live-cell SMLM without the need for optimization of the imaging medium.
Collapse
Affiliation(s)
| | - Mako Kamiya
- PRESTO, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | | | | | - Ryosuke Kojima
- PRESTO, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Toshitada Yoshihara
- Graduate School of Science and Technology, Gunma University, 1-5-1 Tenjin-cho, Kiryu-shi, Gunma 376-8515, Japan
| | - Seiji Tobita
- Graduate School of Science and Technology, Gunma University, 1-5-1 Tenjin-cho, Kiryu-shi, Gunma 376-8515, Japan
| | - Yasuteru Urano
- AMED-CREST, Japan Agency for Medical Research and Development, 1-7-1 Otemachi, Chiyoda-ku, Tokyo 100-0004, Japan
| |
Collapse
|
18
|
Wirth R, Gao P, Nienhaus GU, Sunbul M, Jäschke A. Confocal and Super-resolution Imaging of RNA in Live Bacteria Using a Fluorogenic Silicon Rhodamine-binding Aptamer. Bio Protoc 2020; 10:e3603. [PMID: 33659569 DOI: 10.21769/bioprotoc.3603] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 01/15/2020] [Accepted: 02/13/2020] [Indexed: 12/15/2022] Open
Abstract
Genetically encoded light-up RNA aptamers have been shown to be promising tools for the visualization of RNAs in living cells, helping us to advance our understanding of the broad and complex life of RNA. Although a handful of light-up aptamers spanning the visible wavelength region have been developed, none of them have yet been reported to be compatible with advanced super-resolution techniques, mainly due to poor photophysical properties of their small-molecule fluorogens. Here, we describe a detailed protocol for fluorescence microscopy of mRNA in live bacteria using the recently reported fluorogenic silicon rhodamine binding aptamer (SiRA) featuring excellent photophysical properties. Notably, with SiRA, we demonstrated the first aptamer-based RNA visualization using super-resolution (STED) microscopy. This imaging method can be especially valuable for visualization of RNA in prokaryotes since the size of a bacterium is only a few times greater than the optical resolution of a conventional microscope.
Collapse
Affiliation(s)
- Regina Wirth
- Institute of Pharmacy and Molecular Biotechnology (IPMB), Heidelberg University, 69120 Heidelberg, Germany
| | - Peng Gao
- Institute of Applied Physics (APH), Karlsruhe Institute of Technology (KIT), Wolfgang-Gaede-Str. 1, 76131 Karlsruhe, Germany.,Institute of Nanotechnology (INT), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - G Ulrich Nienhaus
- Institute of Applied Physics (APH), Karlsruhe Institute of Technology (KIT), Wolfgang-Gaede-Str. 1, 76131 Karlsruhe, Germany.,Institute of Nanotechnology (INT), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany.,Institute of Toxicology and Genetics (ITG), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany.,Department of Physics, University of Illinois at Urbana-Champaign, 1110 West Green Street, Urbana, Illinois 61801, United States
| | - Murat Sunbul
- Institute of Pharmacy and Molecular Biotechnology (IPMB), Heidelberg University, 69120 Heidelberg, Germany
| | - Andres Jäschke
- Institute of Pharmacy and Molecular Biotechnology (IPMB), Heidelberg University, 69120 Heidelberg, Germany
| |
Collapse
|
19
|
Xu M, Liu J, Sun J, Xu X, Hu Y, Liu B. Optical Microscopy and Electron Microscopy for the Morphological Evaluation of Tendons: A Mini Review. Orthop Surg 2020; 12:366-371. [PMID: 32096911 PMCID: PMC7189050 DOI: 10.1111/os.12637] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Accepted: 01/20/2020] [Indexed: 12/17/2022] Open
Abstract
The morphological characteristics of tendons have been thoroughly evaluated via microscopy. Optical microscopy and electron microscopy are the most commonly used techniques for tendon tissue observation. According to the principles of both microscopy types, preparation and evaluation methods vary. Simple optical microscopy is commonly used in the observation of cells and extracellular matrix, and many stains, including hematoxylin–eosin, Van Gieson, Prussian blue, Alcian blue, and toluidine blue, are used for evaluating cells, collagen fiber arrangement, and noncollagenous proteins. Histological scoring systems have been used in many studies for semi‐quantification. Scanning electron microscopy (SEM) and transmission electron microscopy (TEM) are the most commonly used electron microscopy types, and special consideration is needed for the fixation and embedding protocols. Glutaraldehyde followed by osmium is most commonly used in the chemical fixation of tendon tissue, followed by epoxy resin embedment. Longitudinal sections captured in SEM images show the arrangement of collagen fibrils and the cells and lipid drops among them, while cross sections captured in TEM images show the diameter and distribution of collagen fibrils. SEM and TEM are used together for comprehensive evaluations. This mini review is focused on the preparation methodology and related evaluation indexes for the morphological evaluation of tendons.
Collapse
Affiliation(s)
- Mingyou Xu
- Graduate School, Tianjin Medical University, Tianjin, China.,Department of Orthopedic Oncology, Tianjin Hospital, Tianjin, China
| | - Jie Liu
- Graduate School, Tianjin Medical University, Tianjin, China
| | - Jiayi Sun
- Center for Medical Device Evaluation NMPA, Beijing, China
| | - Xinrong Xu
- Analytical and Testing Center, South China University of Technology, Guangzhou, China
| | - Yongcheng Hu
- Department of Orthopedic Oncology, Tianjin Hospital, Tianjin, China
| | - Bin Liu
- Center for Medical Device Evaluation NMPA, Beijing, China
| |
Collapse
|
20
|
Tachibana R, Kamiya M, Morozumi A, Miyazaki Y, Fujioka H, Nanjo A, Kojima R, Komatsu T, Ueno T, Hanaoka K, Yoshihara T, Tobita S, Urano Y. Design of spontaneously blinking fluorophores for live-cell super-resolution imaging based on quantum-chemical calculations. Chem Commun (Camb) 2020; 56:13173-13176. [DOI: 10.1039/d0cc05126h] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Spontaneously blinking fluorophores are powerful tools for live-cell super-resolution imaging under physiological conditions.
Collapse
|
21
|
Li CC, Li Y, Zhang Y, Zhang CY. Single-molecule fluorescence resonance energy transfer and its biomedical applications. Trends Analyt Chem 2020. [DOI: 10.1016/j.trac.2019.115753] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
|
22
|
Abstract
AbstractThe dynamics of proteins in solution includes a variety of processes, such as backbone and side-chain fluctuations, interdomain motions, as well as global rotational and translational (i.e. center of mass) diffusion. Since protein dynamics is related to protein function and essential transport processes, a detailed mechanistic understanding and monitoring of protein dynamics in solution is highly desirable. The hierarchical character of protein dynamics requires experimental tools addressing a broad range of time- and length scales. We discuss how different techniques contribute to a comprehensive picture of protein dynamics, and focus in particular on results from neutron spectroscopy. We outline the underlying principles and review available instrumentation as well as related analysis frameworks.
Collapse
|
23
|
Luo H, Wang G, Yuan L. A special three-layer step-index fiber for building compact STED systems. Sci Rep 2019; 9:8455. [PMID: 31186490 PMCID: PMC6560122 DOI: 10.1038/s41598-019-44905-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 05/23/2019] [Indexed: 11/09/2022] Open
Abstract
Up to now, most of stimulated-emission-depletion (STED) systems were lens-based bulky systems. Exchanging some spatial light paths with optical fiber components will make the systems more flexible and will benefit various fields. A big problem to achieve this goal is that the STED beam generated by the traditional method of bulky systems cannot be maintained in an optical fiber due to its birefringence. In this article, we will introduce a type of special optical fiber. With the special fiber, a dark hollow beam with doughnut-shaped focal spot and a concentric beam with Gaussian-shaped focal spot can be generated at the same time. Parameters of a sample and a compact STED system based on it are demonstrated.
Collapse
Affiliation(s)
- Hao Luo
- Key Laboratory of In-Fiber Integrated Optics, Ministry of Education, College of Science, Harbin Engineering University, Harbin, 150001, People's Republic of China
| | - Guiren Wang
- Department of Mechanical Engineering and Biomedical Engineering Program, University of South Carolina, Columbia, SC, 29208, USA
| | - Libo Yuan
- Photonics Research Center, Guilin University of Electronics Technology, Guilin, 541004, People's Republic of China.
| |
Collapse
|
24
|
Nienhaus K, Nienhaus GU. Towards a molecular-level understanding of the protein corona around nanoparticles – Recent advances and persisting challenges. CURRENT OPINION IN BIOMEDICAL ENGINEERING 2019. [DOI: 10.1016/j.cobme.2019.01.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
|
25
|
Wang H, Ma R, Nienhaus K, Nienhaus GU. Formation of a Monolayer Protein Corona around Polystyrene Nanoparticles and Implications for Nanoparticle Agglomeration. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2019; 15:e1900974. [PMID: 31021510 DOI: 10.1002/smll.201900974] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 04/08/2019] [Indexed: 05/23/2023]
Abstract
Nanoparticle (NP) interactions with cells and organisms are mediated by a biomolecular adsorption layer, the so-called "protein corona." An in-depth understanding of the corona is a prerequisite to successful and safe application of NPs in biology and medicine. In this work, earlier in situ investigations on small NPs are extended to large polystyrene (PS) NPs of up to 100 nm diameter, using human transferrin (Tf) and human serum albumin (HSA) as model proteins. Direct NP sizing experiments reveal a reversibly bound monolayer protein shell (under saturating conditions) on hydrophilic, carboxyl-functionalized (PS-COOH) NPs, as was earlier observed for much smaller NPs. In contrast, protein binding on hydrophobic, sulfated (PS-OSO3 H) NPs in solvent of low ionic strength is completely irreversible; nevertheless, the thickness of the observed protein corona again corresponds to a protein monolayer. Under conditions of reduced charge repulsion (higher ionic strength), the NPs are colloidally unstable and form large clusters below a certain protein-NP stoichiometric ratio, indicating that the adsorbed proteins induce NP agglomeration. This comprehensive characterization of the persistent protein corona on PS-OSO3 H NPs by nanoparticle sizing and quantitative fluorescence microscopy/nanoscopy reveals mechanistic aspects of molecular interactions occurring during exposure of NPs to biofluids.
Collapse
Affiliation(s)
- Haixia Wang
- Institute of Applied Physics, Karlsruhe Institute of Technology (KIT), 76131, Karlsruhe, Germany
- Institute of Nanotechnology, Karlsruhe Institute of Technology (KIT), 76344, Eggenstein-Leopoldshafen, Germany
| | - Rui Ma
- Institute of Applied Physics, Karlsruhe Institute of Technology (KIT), 76131, Karlsruhe, Germany
| | - Karin Nienhaus
- Institute of Applied Physics, Karlsruhe Institute of Technology (KIT), 76131, Karlsruhe, Germany
| | - Gerd Ulrich Nienhaus
- Institute of Applied Physics, Karlsruhe Institute of Technology (KIT), 76131, Karlsruhe, Germany
- Institute of Nanotechnology, Karlsruhe Institute of Technology (KIT), 76344, Eggenstein-Leopoldshafen, Germany
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology (KIT), 76344, Eggenstein-Leopoldshafen, Germany
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| |
Collapse
|
26
|
Wirth R, Gao P, Nienhaus GU, Sunbul M, Jäschke A. SiRA: A Silicon Rhodamine-Binding Aptamer for Live-Cell Super-Resolution RNA Imaging. J Am Chem Soc 2019; 141:7562-7571. [PMID: 30986047 DOI: 10.1021/jacs.9b02697] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Although genetically encoded light-up RNA aptamers have become promising tools for visualizing and tracking RNAs in living cells, aptamer/ligand pairs that emit in the far-red and near-infrared (NIR) regions are still rare. In this work, we developed a light-up RNA aptamer that binds silicon rhodamines (SiRs). SiRs are photostable, NIR-emitting fluorophores that change their open-closed equilibrium between the noncolored spirolactone and the fluorescent zwitterion in response to their environment. This property is responsible for their high cell permeability and fluorogenic behavior. Aptamers binding to SiR were in vitro selected from a combinatorial RNA library. Sequencing, bioinformatic analysis, truncation, and mutational studies revealed a 50-nucleotide minimal aptamer, SiRA, which binds with nanomolar affinity to the target SiR. In addition to silicon rhodamines, SiRA binds structurally related rhodamines and carborhodamines, making it a versatile tool spanning the far-red region of the spectrum. Photophysical characterization showed that SiRA is remarkably resistant to photobleaching and constitutes the brightest far-red light-up aptamer system known to date owing to its favorable features: a fluorescence quantum yield of 0.98 and an extinction coefficient of 86 000 M-1cm-1. Using the SiRA system, we visualized the expression of RNAs in bacteria in no-wash live-cell imaging experiments and also report stimulated emission depletion (STED) super-resolution microscopy images of aptamer-based, fluorescently labeled mRNA in live cells. This work represents, to our knowledge, the first application of the popular SiR dyes and of intramolecular spirocyclization as a means of background reduction in the field of aptamer-based RNA imaging. We anticipate a high potential for this novel RNA labeling tool to address biological questions.
Collapse
Affiliation(s)
- Regina Wirth
- Institute of Pharmacy and Molecular Biotechnology (IPMB) , Heidelberg University , 69120 Heidelberg , Germany
| | - Peng Gao
- Institute of Applied Physics (APH) , Karlsruhe Institute of Technology (KIT) , Wolfgang-Gaede-Straße 1 , D-76131 Karlsruhe , Germany.,Institute of Nanotechnology (INT) , Karlsruhe Institute of Technology (KIT) , D-76344 Eggenstein-Leopoldshafen , Germany
| | - G Ulrich Nienhaus
- Institute of Applied Physics (APH) , Karlsruhe Institute of Technology (KIT) , Wolfgang-Gaede-Straße 1 , D-76131 Karlsruhe , Germany.,Institute of Nanotechnology (INT) , Karlsruhe Institute of Technology (KIT) , D-76344 Eggenstein-Leopoldshafen , Germany.,Institute of Toxicology and Genetics (ITG) , Karlsruhe Institute of Technology (KIT) , D-76344 Eggenstein-Leopoldshafen , Germany.,Department of Physics , University of Illinois at Urbana-Champaign , 1110 West Green Street , Urbana , Illinois 61801 , United States
| | - Murat Sunbul
- Institute of Pharmacy and Molecular Biotechnology (IPMB) , Heidelberg University , 69120 Heidelberg , Germany
| | - Andres Jäschke
- Institute of Pharmacy and Molecular Biotechnology (IPMB) , Heidelberg University , 69120 Heidelberg , Germany
| |
Collapse
|
27
|
Zheng J, Zuo C, Gao P, Nienhaus GU. Dual-mode phase and fluorescence imaging with a confocal laser scanning microscope. OPTICS LETTERS 2018; 43:5689-5692. [PMID: 30439929 DOI: 10.1364/ol.43.005689] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 10/19/2018] [Indexed: 06/09/2023]
Abstract
We present dual-mode phase and fluorescence imaging in a confocal laser scanning microscopy (CLSM) system. For phase imaging, the depth of field of the CLSM system is extended by fast axial scanning with a tunable acoustic gradient index of refraction lens. Under transillumination, intensity images of the sample are recorded at a few different defocusing distances. The phase image is reconstructed from these intensity images by using the transport-of-intensity equation. The 3D fluorescence image is obtained by confocal scanning. The dual-mode images with pixel-to-pixel correspondence yield complementary quantitative structural and functional information. Combination of the two imaging modalities enables standalone determination of the refractive index of live cells.
Collapse
|
28
|
Smith PJ, Darzynkiewicz Z, Errington RJ. Nuclear cytometry and chromatin organization. Cytometry A 2018; 93:771-784. [PMID: 30144297 DOI: 10.1002/cyto.a.23521] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 05/25/2018] [Accepted: 06/13/2018] [Indexed: 12/18/2022]
Abstract
The nuclear-targeting chemical probe, for the detection and quantification of DNA within cells, has been a mainstay of cytometry-from the colorimetric Feulgen stain to smart fluorescent agents with tuned functionality. The level of nuclear structure and function at which the probe aims to readout, or indeed at which a DNA-targeted drug acts, is shadowed by a wide range of detection modalities and analytical methods. These methods are invariably limited in terms of the resolution attainable versus the volume occupied by targeted chromatin structures. The scalar challenge arises from the need to understand the extent and different levels of compaction of genomic DNA and how such structures can be re-modeled, reported, or even perturbed by both probes and drugs. Nuclear cytometry can report on the complex levels of chromatin order, disorder, disassembly, and even active disruption by probes and drugs. Nuclear probes can report defining features of clinical and therapeutic interest as in NETosis and other cell death processes. New cytometric approaches continue to bridge the scalar challenges of analyzing chromatin organization. Advances in super-resolution microscopy address the resolution and depth of analysis issues in cellular systems. Typical of recent insights into chromatin organization enabled by exploiting a DNA interacting probe is ChromEM tomography (ChromEMT). ChromEMT uses the unique properties of the anthraquinone-based cytometric dye DRAQ5™ to reveal that local and global 3D chromatin structures effect differences in compaction. The focus of this review is nuclear and chromatin cytometry, with linked reference to DNA targeting probes and drugs as exemplified by the anthracenediones.
Collapse
Affiliation(s)
- Paul J Smith
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Cardiff, CF14 4XN, UK
| | - Zbigniew Darzynkiewicz
- Department of Pathology, Brander Cancer Research Institute, New York Medical College, Valhalla, New York, 10595
| | - Rachel J Errington
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Cardiff, CF14 4XN, UK
| |
Collapse
|
29
|
Baroux C, Schubert V. Technical Review: Microscopy and Image Processing Tools to Analyze Plant Chromatin: Practical Considerations. Methods Mol Biol 2018; 1675:537-589. [PMID: 29052212 DOI: 10.1007/978-1-4939-7318-7_31] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/28/2023]
Abstract
In situ nucleus and chromatin analyses rely on microscopy imaging that benefits from versatile, efficient fluorescent probes and proteins for static or live imaging. Yet the broad choice in imaging instruments offered to the user poses orientation problems. Which imaging instrument should be used for which purpose? What are the main caveats and what are the considerations to best exploit each instrument's ability to obtain informative and high-quality images? How to infer quantitative information on chromatin or nuclear organization from microscopy images? In this review, we present an overview of common, fluorescence-based microscopy systems and discuss recently developed super-resolution microscopy systems, which are able to bridge the resolution gap between common fluorescence microscopy and electron microscopy. We briefly present their basic principles and discuss their possible applications in the field, while providing experience-based recommendations to guide the user toward best-possible imaging. In addition to raw data acquisition methods, we discuss commercial and noncommercial processing tools required for optimal image presentation and signal evaluation in two and three dimensions.
Collapse
Affiliation(s)
- Célia Baroux
- Department of Plant and Microbial Biology, Zürich-Basel Plant Science Center, University of Zürich, Zollikerstrasse 107, 8008, Zürich, Switzerland.
| | - Veit Schubert
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466, Seeland, Germany
| |
Collapse
|
30
|
Abstract
Overcoming Abbe's diffraction limit has been a challenging task and one of great interest for biological investigations. The emergence of fluorescence nanoscopy circumvents the diffraction barrier with nearly limitless power for optical microscopy, which enables investigations of the microscopic world in the 1-100 nm range. Proposed variants, such as expansion microscopy (ExM), stimulated emission depletion microscopy (STED), and Airyscan, are innovative in three aspects: sampling, illumination, and detection. These techniques show increasing strength in bioimaging subcellular structures. In this Perspective, we highlight advances in and prospects of fluorescence nanoscopy.
Collapse
Affiliation(s)
- Chuankang Li
- State Key Laboratory of Modern Optical Instrumentation, College of Optical Science and Engineering , Zhejiang University , Hangzhou 310027 , China
| | - Cuifang Kuang
- State Key Laboratory of Modern Optical Instrumentation, College of Optical Science and Engineering , Zhejiang University , Hangzhou 310027 , China
- Collaborative Innovation Center of Extreme Optics , Shanxi University , Taiyuan 030006 , China
| | - Xu Liu
- State Key Laboratory of Modern Optical Instrumentation, College of Optical Science and Engineering , Zhejiang University , Hangzhou 310027 , China
- Collaborative Innovation Center of Extreme Optics , Shanxi University , Taiyuan 030006 , China
| |
Collapse
|
31
|
Wang S, Chen X, Chang L, Ding M, Xue R, Duan H, Sun Y. GMars-T Enabling Multimodal Subdiffraction Structural and Functional Fluorescence Imaging in Live Cells. Anal Chem 2018; 90:6626-6634. [PMID: 29722976 DOI: 10.1021/acs.analchem.8b00418] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Fluorescent probes with multimodal and multilevel imaging capabilities are highly valuable as imaging with such probes not only can obtain new layers of information but also enable cross-validation of results under different experimental conditions. In recent years, the development of genetically encoded reversibly photoswitchable fluorescent proteins (RSFPs) has greatly promoted the application of various kinds of live-cell nanoscopy approaches, including reversible saturable optical fluorescence transitions (RESOLFT) and stochastic optical fluctuation imaging (SOFI). However, these two classes of live-cell nanoscopy approaches require different optical characteristics of specific RSFPs. In this work, we developed GMars-T, a monomeric bright green RSFP which can satisfy both RESOLFT and photochromic SOFI (pcSOFI) imaging in live cells. We further generated biosensor based on bimolecular fluorescence complementation (BiFC) of GMars-T which offers high specificity and sensitivity in detecting and visualizing various protein-protein interactions (PPIs) in different subcellular compartments under physiological conditions (e.g., 37 °C) in live mammalian cells. Thus, the newly developed GMars-T can serve as both structural imaging probe with multimodal super-resolution imaging capability and functional imaging probe for reporting PPIs with high specificity and sensitivity based on its derived biosensor.
Collapse
Affiliation(s)
- Sheng Wang
- State Key Laboratory of Membrane Biology, Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences , Peking University , Beijing 100871 , China
| | - Xuanze Chen
- State Key Laboratory of Membrane Biology, Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences , Peking University , Beijing 100871 , China.,Department of Biomedical Engineering, College of Engineering , Peking University , Beijing 100871 , China.,Cowin Venture Shanghai 200040 , China
| | - Lei Chang
- State Key Laboratory of Membrane Biology, Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences , Peking University , Beijing 100871 , China
| | - Miao Ding
- State Key Laboratory of Membrane Biology, Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences , Peking University , Beijing 100871 , China
| | - Ruiying Xue
- State Key Laboratory of Membrane Biology, Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences , Peking University , Beijing 100871 , China
| | - Haifeng Duan
- State Key Laboratory of Membrane Biology, Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences , Peking University , Beijing 100871 , China
| | - Yujie Sun
- State Key Laboratory of Membrane Biology, Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences , Peking University , Beijing 100871 , China
| |
Collapse
|
32
|
Wackett LP, Robinson SL. The future of environmental microbiology: a perspective. Environ Microbiol 2018; 20:1988-1990. [PMID: 29727058 DOI: 10.1111/1462-2920.14256] [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)
- Lawrence P Wackett
- Department of Biochemistry, Molecular Biology, and Biophysics; Department of Microbiology; BioTechnology Institute, University of Minnesota, Saint Paul, MN 55108, USA
| | - Serina L Robinson
- Department of Biochemistry, Molecular Biology, and Biophysics; Department of Microbiology; BioTechnology Institute, University of Minnesota, Saint Paul, MN 55108, USA
| |
Collapse
|
33
|
Zhou L, Obhof T, Schneider K, Feldbrügge M, Nienhaus GU, Kämper J. Cytoplasmic Transport Machinery of the SPF27 Homologue Num1 in Ustilago maydis. Sci Rep 2018; 8:3611. [PMID: 29483520 PMCID: PMC5832149 DOI: 10.1038/s41598-018-21628-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 02/07/2018] [Indexed: 01/15/2023] Open
Abstract
In the phytopathogenic basidiomycete Ustilago maydis, the Num1 protein has a pivotal function in hyphal morphogenesis. Num1 functions as a core component of the spliceosome-associated Prp19/CDC5 complex (NTC). The interaction of Num1 with the kinesin motor Kin1 suggests a connection between a component of the splicing machinery and cytoplasmic trafficking processes. Previously it was shown that Num1 localizes predominantly in the nucleus; however, due to the diffraction-limited spatial resolution of conventional optical microscopy, it was not possible to attribute the localization to specific structures within the cytoplasm. We have now employed super-resolution localization microscopy to visualize Num1 in the cytoplasm by fusing it to a tandem dimeric Eos fluorescent protein (tdEosFP). The Num1 protein is localized within the cytoplasm with an enhanced density in the vicinity of microtubules. Num1 movement is found predominantly close to the nucleus. Movement is dependent on its interaction partner Kin1, but independent of Kin3. Our results provide strong evidence that, in addition to its involvement in splicing in the nucleus, Num1 has an additional functional role in the cytosol connected to the Kin1 motor protein.
Collapse
Affiliation(s)
- Lu Zhou
- Institute of Applied Physics, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany.,Institute of Nanotechnology, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
| | - Theresa Obhof
- Department of Genetics, Institute of Applied Biosciences, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
| | - Karina Schneider
- Department of Genetics, Institute of Applied Biosciences, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
| | - Michael Feldbrügge
- Institute of Microbiology, Cluster of Excellence on Plant Sciences, Heinrich-Heine-University, Düsseldorf, Germany
| | - G Ulrich Nienhaus
- Institute of Applied Physics, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany. .,Institute of Nanotechnology, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany. .,Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, USA. .,Institute of Toxicology and Genetics, Karlsruhe Institute of Technology (KIT), Eggenstein-Leopoldshafen, Germany.
| | - Jörg Kämper
- Department of Genetics, Institute of Applied Biosciences, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany.
| |
Collapse
|
34
|
Beloqui A, Kobitski AY, Nienhaus GU, Delaittre G. A simple route to highly active single-enzyme nanogels. Chem Sci 2018; 9:1006-1013. [PMID: 29675147 PMCID: PMC5883864 DOI: 10.1039/c7sc04438k] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Accepted: 11/30/2017] [Indexed: 11/25/2022] Open
Abstract
We have established a simple one-step synthesis of single-enzyme nanogels (SENs), i.e., nanobiocatalysts consisting of an enzyme molecule embedded in a hydrophilic, polymeric crosslinked nanostructure, as a most attractive approach to enhance the stability of enzymes. In contrast to earlier protocols, we demonstrate here that the addition of a small amount of sucrose makes the nanogel formation equally effective as earlier two-step protocols requiring enzyme pre-modification. This provides the dual advantage of skipping a synthetic step and preserving the surface chemistry of the enzymes, hence their native structure. Enzymes encapsulated in this way exhibit a high catalytic activity, similar to that of the free enzymes, in a markedly widened pH range. With our method, the thickness of the hydrogel layer can be finely tuned by careful adjustment of reaction parameters. This is most important because the shell thickness strongly affects both enzyme activity and stability, as we observe for a wide selection of proteins. Finally, a single-molecule analysis by means of two-color confocal fluorescence coincidence analysis confirms that our encapsulation method is highly efficient and suppresses the occurrence of nanoparticles lacking an enzyme molecule. The proposed method is therefore highly attractive for biocatalysis applications, ensuring a high activity and stability of the enzymes.
Collapse
Affiliation(s)
- Ana Beloqui
- Institute of Toxicology and Genetics , Karlsruhe Institute of Technology (KIT) , Hermann-von-Helmholtz-Platz 1 , 76344 Eggenstein-Leopoldshafen , Germany . ;
- Preparative Macromolecular Chemistry , Institute for Technical Chemistry and Polymer Chemistry , Karlsruhe Institute of Technology (KIT) , Engesserstrasse 15 , 76131 Karlsruhe , Germany
| | - Andrei Yu Kobitski
- Institute of Applied Physics , Karlsruhe Institute of Technology (KIT) , Wolfgang-Gaede-Strasse 1 , 76131 Karlsruhe , Germany
| | - Gerd Ulrich Nienhaus
- Institute of Toxicology and Genetics , Karlsruhe Institute of Technology (KIT) , Hermann-von-Helmholtz-Platz 1 , 76344 Eggenstein-Leopoldshafen , Germany . ;
- Institute of Applied Physics , Karlsruhe Institute of Technology (KIT) , Wolfgang-Gaede-Strasse 1 , 76131 Karlsruhe , Germany
- Institute of Nanotechnology , Karlsruhe Institute of Technology (KIT) , Hermann-von-Helmholtz-Platz 1 , 76344 Eggenstein-Leopoldshafen , Germany
- Department of Physics , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , USA
| | - Guillaume Delaittre
- Institute of Toxicology and Genetics , Karlsruhe Institute of Technology (KIT) , Hermann-von-Helmholtz-Platz 1 , 76344 Eggenstein-Leopoldshafen , Germany . ;
- Preparative Macromolecular Chemistry , Institute for Technical Chemistry and Polymer Chemistry , Karlsruhe Institute of Technology (KIT) , Engesserstrasse 15 , 76131 Karlsruhe , Germany
| |
Collapse
|
35
|
Lee J, Park S, Kang W, Hohng S. Accelerated super-resolution imaging with FRET-PAINT. Mol Brain 2017; 10:63. [PMID: 29284498 PMCID: PMC5747120 DOI: 10.1186/s13041-017-0344-5] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 12/20/2017] [Indexed: 12/25/2022] Open
Abstract
Super-resolution fluorescence microscopy in the current form is hard to be used to image the neural connectivity of thick tissue samples due to problems such as slow imaging speed, severe photobleaching of fluorescent probes, and high background noise. Recently developed DNA-PAINT solved the photobleaching problem, but its imaging speed is extremely low. We report accelerated super-resolution fluorescence microscopy named FRET-PAINT. Compared to conventional DNA-PAINT, the imaging speed of the microscopy increases up to ~30-fold. As demonstrations, we show that 25-50 second imaging time is long enough to provide super-resolution reconstruction of microtubules and mitochondria of COS-7 cells.
Collapse
Affiliation(s)
- Jongjin Lee
- Department of Physics and Astronomy, Seoul National University, Seoul, 08826, Republic of Korea.,National Center for Creative Research Initiatives, Seoul National University, Seoul, 08826, Republic of Korea
| | - Sangjun Park
- Department of Physics and Astronomy, Seoul National University, Seoul, 08826, Republic of Korea.,National Center for Creative Research Initiatives, Seoul National University, Seoul, 08826, Republic of Korea
| | - Wooyoung Kang
- Department of Physics and Astronomy, Seoul National University, Seoul, 08826, Republic of Korea.,National Center for Creative Research Initiatives, Seoul National University, Seoul, 08826, Republic of Korea
| | - Sungchul Hohng
- Department of Physics and Astronomy, Seoul National University, Seoul, 08826, Republic of Korea. .,National Center for Creative Research Initiatives, Seoul National University, Seoul, 08826, Republic of Korea. .,Institute of Applied Physics, Seoul National University, Seoul, 08826, Republic of Korea.
| |
Collapse
|
36
|
Super-resolution microscopy reveals functional organization of dopamine transporters into cholesterol and neuronal activity-dependent nanodomains. Nat Commun 2017; 8:740. [PMID: 28963530 PMCID: PMC5622129 DOI: 10.1038/s41467-017-00790-3] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Accepted: 07/27/2017] [Indexed: 01/13/2023] Open
Abstract
Dopamine regulates reward, cognition, and locomotor functions. By mediating rapid reuptake of extracellular dopamine, the dopamine transporter is critical for spatiotemporal control of dopaminergic neurotransmission. Here, we use super-resolution imaging to show that the dopamine transporter is dynamically sequestrated into cholesterol-dependent nanodomains in the plasma membrane of presynaptic varicosities and neuronal projections of dopaminergic neurons. Stochastic optical reconstruction microscopy reveals irregular dopamine transporter nanodomains (∼70 nm mean diameter) that were highly sensitive to cholesterol depletion. Live photoactivated localization microscopy shows a similar dopamine transporter membrane organization in live heterologous cells. In neurons, dual-color dSTORM shows that tyrosine hydroxylase and vesicular monoamine transporter-2 are distinctively localized adjacent to, but not overlapping with, the dopamine transporter nanodomains. The molecular organization of the dopamine transporter in nanodomains is reversibly reduced by short-term activation of NMDA-type ionotropic glutamate receptors, implicating dopamine transporter nanodomain distribution as a potential mechanism to modulate dopaminergic neurotransmission in response to excitatory input.The dopamine transporter (DAT) has a crucial role in the regulation of neurotransmission. Here, the authors use super-resolution imaging to show that DAT clusters into cholesterol-dependent membrane regions that are reversibly regulated by ionotropic glutamate receptors activation.
Collapse
|
37
|
Thédié D, Berardozzi R, Adam V, Bourgeois D. Photoswitching of Green mEos2 by Intense 561 nm Light Perturbs Efficient Green-to-Red Photoconversion in Localization Microscopy. J Phys Chem Lett 2017; 8:4424-4430. [PMID: 28850784 DOI: 10.1021/acs.jpclett.7b01701] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Green-to-red photoconvertible fluorescent proteins (PCFPs) such as mEos2 and its derivatives are widely used in PhotoActivated Localization Microscopy (PALM). However, the complex photophysics of these genetically encoded markers complicates the quantitative analysis of PALM data. Here, we show that intense 561 nm light (∼1 kW/cm2) typically used to localize single red molecules considerably affects the green-state photophysics of mEos2 by populating at least two reversible dark states. These dark states retard green-to-red photoconversion through a shelving effect, although one of them is rapidly depopulated by 405 nm light illumination. Multiple mEos2 switching and irreversible photobleaching is thus induced by yellow/green and violet photons before green-to-red photoconversion occurs, contributing to explain the apparent limited signaling efficiency of this PCFP. Our data reveals that the photophysics of PCFPs of anthozoan origin is substantially more complex than previously thought, and suggests that intense 561 nm laser light should be used with care, notably for quantitative or fast PALM approaches.
Collapse
Affiliation(s)
- Daniel Thédié
- Institut de Biologie Structurale, CNRS, Université Grenoble Alpes, CEA, IBS, 38044 Grenoble, France
| | - Romain Berardozzi
- Institut de Biologie Structurale, CNRS, Université Grenoble Alpes, CEA, IBS, 38044 Grenoble, France
| | - Virgile Adam
- Institut de Biologie Structurale, CNRS, Université Grenoble Alpes, CEA, IBS, 38044 Grenoble, France
| | - Dominique Bourgeois
- Institut de Biologie Structurale, CNRS, Université Grenoble Alpes, CEA, IBS, 38044 Grenoble, France
| |
Collapse
|
38
|
Wachter RM. Photoconvertible Fluorescent Proteins and the Role of Dynamics in Protein Evolution. Int J Mol Sci 2017; 18:ijms18081792. [PMID: 32962314 PMCID: PMC5578180 DOI: 10.3390/ijms18081792] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Revised: 08/11/2017] [Accepted: 08/17/2017] [Indexed: 12/12/2022] Open
Abstract
Photoconvertible fluorescent proteins (pcFPs) constitute a large group of fluorescent proteins related to green fluorescent protein (GFP) that, when exposed to blue light, bear the capability of irreversibly switching their emission color from green to red. Not surprisingly, this fascinating class of FPs has found numerous applications, in particular for the visualization of biological processes. A detailed understanding of the photoconversion mechanism appears indispensable in the design of improved variants for applications such as super-resolution imaging. In this article, recent work is reviewed that involves using pcFPs as a model system for studying protein dynamics. Evidence has been provided that the evolution of pcFPs from a green ancestor involved the natural selection for altered dynamical features of the beta-barrel fold. It appears that photoconversion may be the outcome of a long-range positional shift of a fold-anchoring region. A relatively stiff, rigid element appears to have migrated away from the chromophore-bearing section to the opposite edge of the barrel, thereby endowing pcFPs with increased active site flexibility while keeping the fold intact. In this way, the stage was set for the coupling of light absorption with subsequent chemical transformations. The emerging mechanistic model suggests that highly specific dynamic motions are linked to key chemical steps, preparing the system for a concerted deprotonation and β-elimination reaction that enlarges the chromophore's π-conjugation to generate red color.
Collapse
Affiliation(s)
- Rebekka M Wachter
- School of Molecular Sciences and Center for Bioenergy and Photosynthesis, Arizona State University, Tempe, AZ 85287, USA
| |
Collapse
|
39
|
Cox H, Georgiades P, Xu H, Waigh TA, Lu JR. Self-Assembly of Mesoscopic Peptide Surfactant Fibrils Investigated by STORM Super-Resolution Fluorescence Microscopy. Biomacromolecules 2017; 18:3481-3491. [PMID: 28570040 DOI: 10.1021/acs.biomac.7b00465] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
| | | | - Hai Xu
- Centre
for Bioengineering and Biotechnology, China University of Petroleum (East China), 66 Changjiang West Road, Qingdao 266555, China
| | | | | |
Collapse
|
40
|
Bourgeois D. Deciphering Structural Photophysics of Fluorescent Proteins by Kinetic Crystallography. Int J Mol Sci 2017; 18:ijms18061187. [PMID: 28574447 PMCID: PMC5486010 DOI: 10.3390/ijms18061187] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Revised: 05/24/2017] [Accepted: 05/26/2017] [Indexed: 01/02/2023] Open
Abstract
Because they enable labeling of biological samples in a genetically-encoded manner, Fluorescent Proteins (FPs) have revolutionized life sciences. Photo-transformable fluorescent proteins (PTFPs), in particular, recently attracted wide interest, as their fluorescence state can be actively modulated by light, a property central to the emergence of super-resolution microscopy. PTFPs, however, exhibit highly complex photophysical behaviours that are still poorly understood, hampering the rational engineering of variants with improved performances. We show that kinetic crystallography combined with in crystallo optical spectroscopy, modeling approaches and single-molecule measurements constitutes a powerful tool to decipher processes such as photoactivation, photoconversion, photoswitching, photoblinking and photobleaching. Besides potential applications for the design of enhanced PTFPs, these investigations provide fundamental insight into photoactivated protein dynamics.
Collapse
Affiliation(s)
- Dominique Bourgeois
- Institut de Biologie Structurale, Univ. Grenoble Alpes, CNRS, CEA, CNRS, IBS, F-38000 Grenoble, France.
| |
Collapse
|
41
|
High-numerical-aperture cryogenic light microscopy for increased precision of superresolution reconstructions. Proc Natl Acad Sci U S A 2017; 114:3832-3836. [PMID: 28348224 DOI: 10.1073/pnas.1618206114] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Superresolution microscopy has fundamentally altered our ability to resolve subcellular proteins, but improving on these techniques to study dense structures composed of single-molecule-sized elements has been a challenge. One possible approach to enhance superresolution precision is to use cryogenic fluorescent imaging, reported to reduce fluorescent protein bleaching rates, thereby increasing the precision of superresolution imaging. Here, we describe an approach to cryogenic photoactivated localization microscopy (cPALM) that permits the use of a room-temperature high-numerical-aperture objective lens to image frozen samples in their native state. We find that cPALM increases photon yields and show that this approach can be used to enhance the effective resolution of two photoactivatable/switchable fluorophore-labeled structures in the same frozen sample. This higher resolution, two-color extension of the cPALM technique will expand the accessibility of this approach to a range of laboratories interested in more precise reconstructions of complex subcellular targets.
Collapse
|
42
|
Gao P, Nienhaus GU. Precise background subtraction in stimulated emission double depletion nanoscopy. OPTICS LETTERS 2017; 42:831-834. [PMID: 28198876 DOI: 10.1364/ol.42.000831] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Accepted: 01/26/2017] [Indexed: 06/06/2023]
Abstract
Low-resolution background in stimulated emission depletion (STED) nanoscopy can arise from incomplete depletion or re-excitation by the STED beam. We have recently introduced stimulated emission double depletion (STEDD), a technique to efficiently suppress this background. In STEDD, the conventional, doughnut-shaped STED pulse, which depletes excited fluorophores outside the center of the focal region, is followed by a second Gaussian STED pulse, which specifically depletes the central region. The background is removed by calculating a weighted difference of photon events collected before and after the second STED pulse. Here, we present a simple, yet powerful, method to determine the weight factor, which depends on the fluorescence decay, from a direct analysis of the acquired data. We vary the weight factor to identify its optimal value as the one for which the weight of high-frequency components in the spectrum of the acquired STEDD image is maximized. This strategy is also applicable to other differential approaches for background suppression in imaging.
Collapse
|
43
|
Barr VA, Yi J, Samelson LE. Super-resolution Analysis of TCR-Dependent Signaling: Single-Molecule Localization Microscopy. Methods Mol Biol 2017; 1584:183-206. [PMID: 28255704 PMCID: PMC6676910 DOI: 10.1007/978-1-4939-6881-7_13] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Single-molecule localization microscopy (SMLM) comprises methods that produce super-resolution images from molecular locations of single molecules. These techniques mathematically determine the center of a diffraction-limited spot produced by a fluorescent molecule, which represents the most likely location of the molecule. Only a small cohort of well-separated molecules is visualized in a single image, and then many images are obtained from a single sample. The localizations from all the images are combined to produce a super-resolution picture of the sample. Here we describe the application of two methods, photoactivation localization microscopy (PALM) and direct stochastic optical reconstruction microscopy (dSTORM), to the study of signaling microclusters in T cells.
Collapse
Affiliation(s)
- Valarie A Barr
- Laboratory of Cellular and Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, 20892-4256, USA
| | - Jason Yi
- Laboratory of Cellular and Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, 20892-4256, USA
| | - Lawrence E Samelson
- Laboratory of Cellular and Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, 20892-4256, USA.
| |
Collapse
|
44
|
Ryan J, Gerhold AR, Boudreau V, Smith L, Maddox PS. Introduction to Modern Methods in Light Microscopy. Methods Mol Biol 2017; 1563:1-15. [PMID: 28324598 DOI: 10.1007/978-1-4939-6810-7_1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
For centuries, light microscopy has been a key method in biological research, from the early work of Robert Hooke describing biological organisms as cells, to the latest in live-cell and single-molecule systems. Here, we introduce some of the key concepts related to the development and implementation of modern microscopy techniques. We briefly discuss the basics of optics in the microscope, super-resolution imaging, quantitative image analysis, live-cell imaging, and provide an outlook on active research areas pertaining to light microscopy.
Collapse
Affiliation(s)
- Joel Ryan
- LMU Munich, Biocenter Martinsried, Grosshadernerstr. 2, 82152, Martinsried, Munich, Germany
| | - Abby R Gerhold
- Institute for Research in Immunology and Cancer, Université de Montréal, Montreal, QC, Canada
| | - Vincent Boudreau
- University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Lydia Smith
- University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Paul S Maddox
- Department of Biology, University of North Carolina at Chapel Hill, 4358 Genome Sciences Building, Chapel Hill, NC, 27599, USA.
| |
Collapse
|
45
|
Schubert V. Super-resolution Microscopy - Applications in Plant Cell Research. FRONTIERS IN PLANT SCIENCE 2017; 8:531. [PMID: 28450874 PMCID: PMC5390026 DOI: 10.3389/fpls.2017.00531] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 03/24/2017] [Indexed: 05/10/2023]
Abstract
Most of the present knowledge about cell organization and function is based on molecular and genetic methods as well as cytological investigations. While electron microscopy allows identifying cell substructures until a resolution of ∼1 nm, the resolution of fluorescence microscopy is restricted to ∼200 nm due to the diffraction limit of light. However, the advantage of this technique is the possibility to identify and co-localize specifically labeled structures and molecules. The recently developed super-resolution microscopy techniques, such as Structured Illumination Microscopy, Photoactivated Localization Microscopy, Stochastic Optical Reconstruction Microscopy, and Stimulated Emission Depletion microscopy allow analyzing structures and molecules beyond the diffraction limit of light. Recently, there is an increasing application of these techniques in cell biology. This review evaluates and summarizes especially the data achieved until now in analyzing the organization and function of plant cells, chromosomes and interphase nuclei using super-resolution techniques.
Collapse
|
46
|
Barr VA, Sherman E, Yi J, Akpan I, Rouquette-Jazdanian AK, Samelson LE. Development of nanoscale structure in LAT-based signaling complexes. J Cell Sci 2016; 129:4548-4562. [PMID: 27875277 PMCID: PMC5201021 DOI: 10.1242/jcs.194886] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 11/04/2016] [Indexed: 12/30/2022] Open
Abstract
The adapter molecule linker for activation of T cells (LAT) plays a crucial role in forming signaling complexes induced by stimulation of the T cell receptor (TCR). These multi-molecular complexes are dynamic structures that activate highly regulated signaling pathways. Previously, we have demonstrated nanoscale structure in LAT-based complexes where the adapter SLP-76 (also known as LCP2) localizes to the periphery of LAT clusters. In this study, we show that initially LAT and SLP-76 are randomly dispersed throughout the clusters that form upon TCR engagement. The segregation of LAT and SLP-76 develops near the end of the spreading process. The local concentration of LAT also increases at the same time. Both changes require TCR activation and an intact actin cytoskeleton. These results demonstrate that the nanoscale organization of LAT-based signaling complexes is dynamic and indicates that different kinds of LAT-based complexes appear at different times during T cell activation.
Collapse
Affiliation(s)
- Valarie A Barr
- Laboratory of Cellular and Molecular Biology, CCR, NCI, NIH, Bethesda, MD 20892, USA
| | - Eilon Sherman
- Racah Institute of Physics, The Hebrew University, Jerusalem 91904, Israel
| | - Jason Yi
- Laboratory of Cellular and Molecular Biology, CCR, NCI, NIH, Bethesda, MD 20892, USA
| | - Itoro Akpan
- Laboratory of Cellular and Molecular Biology, CCR, NCI, NIH, Bethesda, MD 20892, USA
| | | | - Lawrence E Samelson
- Laboratory of Cellular and Molecular Biology, CCR, NCI, NIH, Bethesda, MD 20892, USA
| |
Collapse
|
47
|
Lychagov VV, Shemetov AA, Jimenez R, Verkhusha VV. Microfluidic System for In-Flow Reversible Photoswitching of Near-Infrared Fluorescent Proteins. Anal Chem 2016; 88:11821-11829. [PMID: 27807973 DOI: 10.1021/acs.analchem.6b03499] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
We have developed a microfluidic flow cytometry system to screen reversibly photoswitchable fluorescent proteins for contrast and stability of reversible photoconversion between high- and low-fluorescent states. A two-color array of 20 excitation and deactivation beams generated with diffractive optics was combined with a serpentine microfluidic channel geometry designed to provide five cycles of photoswitching with real-time calculation of photoconversion fluorescence contrast. The characteristics of photoswitching in-flow as a function of excitation and deactivation beam fluence, flow speed, and protein concentration were studied with droplets of the bacterial phytochrome from Deinococcus radiodurans (DrBphP), which is weakly fluorescent in the near-infrared (NIR) spectral range. In agreement with measurements on stationary droplets and HeLa S3 mammalian cells expressing DrBphP, optimized operation of the flow system provided up to 50% photoconversion contrast in-flow at a droplet rate of few hertz and a coefficient of variation (CV) of up to 2% over 10 000 events. The methods for calibrating the brightness and photoswitching measurements in microfluidic flow established here provide a basis for screening of cell-based libraries of reversibly switchable NIR fluorescent proteins.
Collapse
Affiliation(s)
| | | | | | - Vladislav V Verkhusha
- Department of Biochemistry and Developmental Biology, Faculty of Medicine, University of Helsinki , Helsinki 00029, Finland
| |
Collapse
|
48
|
Lam F, Cladière D, Guillaume C, Wassmann K, Bolte S. Super-resolution for everybody: An image processing workflow to obtain high-resolution images with a standard confocal microscope. Methods 2016; 115:17-27. [PMID: 27826080 DOI: 10.1016/j.ymeth.2016.11.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Revised: 11/02/2016] [Accepted: 11/04/2016] [Indexed: 11/29/2022] Open
Abstract
In the presented work we aimed at improving confocal imaging to obtain highest possible resolution in thick biological samples, such as the mouse oocyte. We therefore developed an image processing workflow that allows improving the lateral and axial resolution of a standard confocal microscope. Our workflow comprises refractive index matching, the optimization of microscope hardware parameters and image restoration by deconvolution. We compare two different deconvolution algorithms, evaluate the necessity of denoising and establish the optimal image restoration procedure. We validate our workflow by imaging sub resolution fluorescent beads and measuring the maximum lateral and axial resolution of the confocal system. Subsequently, we apply the parameters to the imaging and data restoration of fluorescently labelled meiotic spindles of mouse oocytes. We measure a resolution increase of approximately 2-fold in the lateral and 3-fold in the axial direction throughout a depth of 60μm. This demonstrates that with our optimized workflow we reach a resolution that is comparable to 3D-SIM-imaging, but with better depth penetration for confocal images of beads and the biological sample.
Collapse
Affiliation(s)
- France Lam
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Core Facilities - Institut de Biologie Paris Seine (IBPS), 75005 Paris, France
| | - Damien Cladière
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Laboratory of Developmental Biology - Institut de Biologie Paris Seine (IBPS), 75005 Paris, France
| | - Cyndélia Guillaume
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Core Facilities - Institut de Biologie Paris Seine (IBPS), 75005 Paris, France
| | - Katja Wassmann
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Laboratory of Developmental Biology - Institut de Biologie Paris Seine (IBPS), 75005 Paris, France
| | - Susanne Bolte
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Core Facilities - Institut de Biologie Paris Seine (IBPS), 75005 Paris, France.
| |
Collapse
|
49
|
Wang F, Bélanger E, Paquet ME, Côté DC, De Koninck Y. Probing pain pathways with light. Neuroscience 2016; 338:248-271. [PMID: 27702648 DOI: 10.1016/j.neuroscience.2016.09.035] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Revised: 09/19/2016] [Accepted: 09/20/2016] [Indexed: 02/06/2023]
Abstract
We have witnessed an accelerated growth of photonics technologies in recent years to enable not only monitoring the activity of specific neurons, while animals are performing certain types of behavior, but also testing whether specific cells, circuits, and regions are sufficient or necessary for initiating, maintaining, or altering this or that behavior. Compared to other sensory systems, however, such as the visual or olfactory system, photonics applications in pain research are only beginning to emerge. One reason pain studies have lagged behind is that many of the techniques originally developed cannot be directly implemented to study key relay sites within pain pathways, such as the skin, dorsal root ganglia, spinal cord, and brainstem. This is due, in part, to difficulties in accessing these structures with light. Here we review a number of recent advances in design and delivery of light-sensitive molecular probes (sensors and actuators) into pain relay circuits to help decipher their structural and functional organization. We then discuss several challenges that have hampered hardware access to specific structures including light scattering, tissue movement and geometries. We review a number of strategies to circumvent these challenges, by delivering light into, and collecting it from the different key sites to unravel how nociceptive signals are encoded at each level of the neuraxis. We conclude with an outlook on novel imaging modalities for label-free chemical detection and opportunities for multimodal interrogation in vivo. While many challenges remain, these advances offer unprecedented opportunities to bridge cellular approaches with context-relevant behavioral testing, an essential step toward improving translation of basic research findings into clinical applications.
Collapse
Affiliation(s)
- Feng Wang
- Institut universitaire en santé mentale de Québec, Université Laval, Québec, QC, Canada
| | - Erik Bélanger
- Institut universitaire en santé mentale de Québec, Université Laval, Québec, QC, Canada; Centre d'optique, photonique et laser, Université Laval, Québec, QC, Canada
| | - Marie-Eve Paquet
- Institut universitaire en santé mentale de Québec, Université Laval, Québec, QC, Canada; Département de biochimie, microbiologie et bioinformatique, Université Laval, Québec, QC, Canada
| | - Daniel C Côté
- Institut universitaire en santé mentale de Québec, Université Laval, Québec, QC, Canada; Centre d'optique, photonique et laser, Université Laval, Québec, QC, Canada; Département de physique, de génie physique et d'optique, Université Laval, Québec, QC, Canada
| | - Yves De Koninck
- Institut universitaire en santé mentale de Québec, Université Laval, Québec, QC, Canada; Centre d'optique, photonique et laser, Université Laval, Québec, QC, Canada; Département de psychiatrie et neurosciences, Université Laval, Québec, QC, Canada.
| |
Collapse
|
50
|
Johnson CK, Harms GS. Tracking and localization of calmodulin in live cells. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2016; 1863:2017-26. [DOI: 10.1016/j.bbamcr.2016.04.021] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Revised: 04/19/2016] [Accepted: 04/20/2016] [Indexed: 01/20/2023]
|