1
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Poding LH, Jägers P, Herlitze S, Huhn M. Diversity and function of fluorescent molecules in marine animals. Biol Rev Camb Philos Soc 2024; 99:1391-1410. [PMID: 38468189 DOI: 10.1111/brv.13072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 02/24/2024] [Accepted: 02/29/2024] [Indexed: 03/13/2024]
Abstract
Fluorescence in marine animals has mainly been studied in Cnidaria but is found in many different phyla such as Annelida, Crustacea, Mollusca, and Chordata. While many fluorescent proteins and molecules have been identified, very little information is available about the biological functions of fluorescence. In this review, we focus on describing the occurrence of fluorescence in marine animals and the behavioural and physiological functions of fluorescent molecules based on experimental approaches. These biological functions of fluorescence range from prey and symbiont attraction, photoprotection, photoenhancement, stress mitigation, mimicry, and aposematism to inter- and intraspecific communication. We provide a comprehensive list of marine taxa that utilise fluorescence, including demonstrated effects on behavioural or physiological responses. We describe the numerous known functions of fluorescence in anthozoans and their underlying molecular mechanisms. We also highlight that other marine taxa should be studied regarding the functions of fluorescence. We suggest that an increase in research effort in this field could contribute to understanding the capacity of marine animals to respond to negative effects of climate change, such as rising sea temperatures and increasing intensities of solar irradiation.
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Affiliation(s)
- Lars H Poding
- Department of General Zoology and Neurobiology, Institute of Biology and Biotechnology, Ruhr-University Bochum, Bochum, 44801, Germany
| | - Peter Jägers
- Department of General Zoology and Neurobiology, Institute of Biology and Biotechnology, Ruhr-University Bochum, Bochum, 44801, Germany
| | - Stefan Herlitze
- Department of General Zoology and Neurobiology, Institute of Biology and Biotechnology, Ruhr-University Bochum, Bochum, 44801, Germany
| | - Mareike Huhn
- Department of General Zoology and Neurobiology, Institute of Biology and Biotechnology, Ruhr-University Bochum, Bochum, 44801, Germany
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2
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Ghosh B, Chatterjee J, Paul RR, Acuña S, Lahiri P, Pal M, Mitra P, Agarwal K. Molecular histopathology of matrix proteins through autofluorescence super-resolution microscopy. Sci Rep 2024; 14:10524. [PMID: 38719976 PMCID: PMC11078950 DOI: 10.1038/s41598-024-61178-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 05/02/2024] [Indexed: 05/12/2024] Open
Abstract
Extracellular matrix diseases like fibrosis are elusive to diagnose early on, to avoid complete loss of organ function or even cancer progression, making early diagnosis crucial. Imaging the matrix densities of proteins like collagen in fixed tissue sections with suitable stains and labels is a standard for diagnosis and staging. However, fine changes in matrix density are difficult to realize by conventional histological staining and microscopy as the matrix fibrils are finer than the resolving capacity of these microscopes. The dyes further blur the outline of the matrix and add a background that bottlenecks high-precision early diagnosis of matrix diseases. Here we demonstrate the multiple signal classification method-MUSICAL-otherwise a computational super-resolution microscopy technique to precisely estimate matrix density in fixed tissue sections using fibril autofluorescence with image stacks acquired on a conventional epifluorescence microscope. We validated the diagnostic and staging performance of the method in extracted collagen fibrils, mouse skin during repair, and pre-cancers in human oral mucosa. The method enables early high-precision label-free diagnosis of matrix-associated fibrotic diseases without needing additional infrastructure or rigorous clinical training.
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Affiliation(s)
- Biswajoy Ghosh
- Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, 721302, India.
- UiT - The Arctic University of Norway, 9019, Tromsø, Norway.
| | | | - Ranjan Rashmi Paul
- Guru Nanak Institute of Dental Sciences and Research, Kolkata, West Bengal, 700114, India
| | | | - Pooja Lahiri
- Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, 721302, India
| | - Mousumi Pal
- Guru Nanak Institute of Dental Sciences and Research, Kolkata, West Bengal, 700114, India
| | - Pabitra Mitra
- Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, 721302, India
| | - Krishna Agarwal
- UiT - The Arctic University of Norway, 9019, Tromsø, Norway.
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3
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Laine RF, Heil HS, Coelho S, Nixon-Abell J, Jimenez A, Wiesner T, Martínez D, Galgani T, Régnier L, Stubb A, Follain G, Webster S, Goyette J, Dauphin A, Salles A, Culley S, Jacquemet G, Hajj B, Leterrier C, Henriques R. High-fidelity 3D live-cell nanoscopy through data-driven enhanced super-resolution radial fluctuation. Nat Methods 2023; 20:1949-1956. [PMID: 37957430 PMCID: PMC10703683 DOI: 10.1038/s41592-023-02057-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 09/29/2023] [Indexed: 11/15/2023]
Abstract
Live-cell super-resolution microscopy enables the imaging of biological structure dynamics below the diffraction limit. Here we present enhanced super-resolution radial fluctuations (eSRRF), substantially improving image fidelity and resolution compared to the original SRRF method. eSRRF incorporates automated parameter optimization based on the data itself, giving insight into the trade-off between resolution and fidelity. We demonstrate eSRRF across a range of imaging modalities and biological systems. Notably, we extend eSRRF to three dimensions by combining it with multifocus microscopy. This realizes live-cell volumetric super-resolution imaging with an acquisition speed of ~1 volume per second. eSRRF provides an accessible super-resolution approach, maximizing information extraction across varied experimental conditions while minimizing artifacts. Its optimal parameter prediction strategy is generalizable, moving toward unbiased and optimized analyses in super-resolution microscopy.
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Affiliation(s)
- Romain F Laine
- Laboratory for Molecular Cell Biology, University College London, London, UK
- The Francis Crick Institute, London, UK
- Micrographia Bio, Translation and Innovation Hub, London, UK
| | - Hannah S Heil
- Optical Cell Biology, Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | - Simao Coelho
- Optical Cell Biology, Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | - Jonathon Nixon-Abell
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
- Cambridge Institute for Medical Research, Cambridge Univeristy, Cambridge, UK
| | - Angélique Jimenez
- Aix-Marseille Université, CNRS, INP UMR7051, NeuroCyto, Marseille, France
| | - Theresa Wiesner
- Aix-Marseille Université, CNRS, INP UMR7051, NeuroCyto, Marseille, France
| | - Damián Martínez
- Optical Cell Biology, Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | - Tommaso Galgani
- Laboratoire Physico-Chimie Curie, Institut Curie, PSL Research University, Sorbonne Université, CNRS UMR168, Paris, France
- Revvity Signals, Tres Cantos, Madrid, Spain
| | - Louise Régnier
- Laboratoire Physico-Chimie Curie, Institut Curie, PSL Research University, Sorbonne Université, CNRS UMR168, Paris, France
| | - Aki Stubb
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
- Department of Cell and Tissue Dynamics, Max Planck Institute for Molecular Biomedicine, Munster, Germany
| | - Gautier Follain
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
- Faculty of Science and Engineering, Cell Biology, Åbo Akademi University, Turku, Finland
| | - Samantha Webster
- EMBL Australia Node in Single Molecule Science, School of Biomedical Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Jesse Goyette
- EMBL Australia Node in Single Molecule Science, School of Biomedical Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Aurelien Dauphin
- Unite Genetique et Biologie du Développement U934, PICT-IBiSA, Institut Curie, INSERM, CNRS, PSL Research University, Paris, France
| | - Audrey Salles
- Institut Pasteur, Université Paris Cité, Unit of Technology and Service Photonic BioImaging (UTechS PBI), C2RT, Paris, France
| | - Siân Culley
- Laboratory for Molecular Cell Biology, University College London, London, UK
- Randall Centre for Cell and Molecular Biophysics, King's College London, Guy's Campus, London, UK
| | - Guillaume Jacquemet
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
- Faculty of Science and Engineering, Cell Biology, Åbo Akademi University, Turku, Finland
- Turku Bioimaging, University of Turku and Åbo Akademi University, Turku, Finland
- InFLAMES Research Flagship Center, Åbo Akademi University, Turku, Finland
| | - Bassam Hajj
- Laboratoire Physico-Chimie Curie, Institut Curie, PSL Research University, Sorbonne Université, CNRS UMR168, Paris, France.
| | | | - Ricardo Henriques
- Laboratory for Molecular Cell Biology, University College London, London, UK.
- The Francis Crick Institute, London, UK.
- Optical Cell Biology, Instituto Gulbenkian de Ciência, Oeiras, Portugal.
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4
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Alva A, Brito-Alarcón E, Linares A, Torres-García E, Hernández HO, Pinto-Cámara R, Martínez D, Hernández-Herrera P, D'Antuono R, Wood C, Guerrero A. Fluorescence fluctuation based super resolution microscopy, basic concepts for an easy start. J Microsc 2022; 288:218-241. [PMID: 35896096 PMCID: PMC10087389 DOI: 10.1111/jmi.13135] [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: 05/06/2022] [Revised: 07/15/2022] [Accepted: 07/20/2022] [Indexed: 11/27/2022]
Abstract
Due to the wave nature of light, optical microscopy has a lower-bound lateral resolution limit of approximately half of the wavelength of visible light, i.e., within the range of 200 to 350 nm. Fluorescence Fluctuation based Super Resolution Microscopy (FF-SRM) is a term used to encompass a collection of image analysis techniques which rely on the statistical processing of temporal variations of the fluorescence signal. FF-SRM aims to reduce the uncertainty of the location of fluorophores within an image, often improving spatial resolution to several tens of nanometers. FF-SRM is suitable for live-cell imaging due to its compatibility with most fluorescent probes and relatively simple instrumental and experimental requirements, which are mostly camera-based epifluorescence instruments. Each FF-SRM approach has strengths and weaknesses, which depend directly on the underlying statistical principles through which enhanced spatial resolution is achieved. In this review, the basic concepts and principles behind a range of FF-SRM methods published to date are described. Their operational parameters are explained and guidance for its selection is provided. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Alma Alva
- Laboratorio Nacional de Microscopía Avanzada, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Eduardo Brito-Alarcón
- Laboratorio Nacional de Microscopía Avanzada, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Alejandro Linares
- Laboratorio Nacional de Microscopía Avanzada, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Esley Torres-García
- Laboratorio Nacional de Microscopía Avanzada, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México.,Centro de Investigación en Ciencias, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, México
| | - Haydee O Hernández
- Posgrado en Ciencia e Ingeniería de la Computación, Universidad Nacional Autónoma de México, México City, México
| | - Raúl Pinto-Cámara
- Laboratorio Nacional de Microscopía Avanzada, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México.,Centro de Investigación en Ciencias, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, México
| | - Damián Martínez
- Laboratorio Nacional de Microscopía Avanzada, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Paul Hernández-Herrera
- Laboratorio Nacional de Microscopía Avanzada, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Rocco D'Antuono
- Crick Advanced Light Microscopy Science and Technology Platform, The Francis Crick Institute, London, UK
| | - Christopher Wood
- Laboratorio Nacional de Microscopía Avanzada, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Adán Guerrero
- Laboratorio Nacional de Microscopía Avanzada, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
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5
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Miao Y, Weiss S, Yi X. PySOFI: an open source Python package for SOFI. BIOPHYSICAL REPORTS 2022; 2:100052. [PMID: 36425773 PMCID: PMC9680711 DOI: 10.1016/j.bpr.2022.100052] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Accepted: 03/25/2022] [Indexed: 06/16/2023]
Abstract
Super-resolution optical fluctuation imaging (SOFI) is a highly democratizable technique that provides optical super-resolution without requirement of sophisticated imaging instruments. Easy-to-use open-source packages for SOFI are important to support the utilization and community adoption of the SOFI method, they also encourage the participation and further development of SOFI by new investigators. In this work, we developed PySOFI, an open-source Python package for SOFI analysis that offers the flexibility to inspect, test, modify, improve, and extend the algorithm. We provide complete documentation for the package and a collection of Jupyter Notebooks to demonstrate the usage of the package. We discuss the architecture of PySOFI and illustrate how to use each functional module. A demonstration on how to extend the PySOFI package with additional modules is also included in the PySOFI package. We expect PySOFI to facilitate efficient adoption, testing, modification, dissemination, and prototyping of new SOFI-relevant algorithms.
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Affiliation(s)
- Yuting Miao
- Department of Chemistry and Biochemistry, University of California, Los Angeles California
| | - Shimon Weiss
- Department of Chemistry and Biochemistry, University of California, Los Angeles California
- Department of Physiology, University of California, Los Angeles California
- Department of Physics, Institute for Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat-Gan, Israel
| | - Xiyu Yi
- Lawrence Livermore National Laboratory, Livermore, California
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6
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Rapid ensemble measurement of protein diffusion and probe blinking dynamics in cells. BIOPHYSICAL REPORTS 2021; 1:100015. [PMID: 36425455 PMCID: PMC9680803 DOI: 10.1016/j.bpr.2021.100015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 08/30/2021] [Indexed: 12/25/2022]
Abstract
We present a fluorescence fluctuation image correlation analysis method that can rapidly and simultaneously measure the diffusion coefficient, photoblinking rates, and fraction of diffusing particles of fluorescent molecules in cells. Unlike other image correlation techniques, we demonstrated that our method could be applied irrespective of a nonuniformly distributed, immobile blinking fluorophore population. This allows us to measure blinking and transport dynamics in complex cell morphologies, a benefit for a range of super-resolution fluorescence imaging approaches that rely on probe emission blinking. Furthermore, we showed that our technique could be applied without directly accounting for photobleaching. We successfully employed our technique on several simulations with realistic EMCCD noise and photobleaching models, as well as on Dronpa-C12-labeled β-actin in living NIH/3T3 and HeLa cells. We found that the diffusion coefficients measured using our method were consistent with previous literature values. We further found that photoblinking rates measured in the live HeLa cells varied as expected with changing excitation power.
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7
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Rossman U, Dadosh T, Eldar YC, Oron D. cSPARCOM: Multi-detector reconstruction by confocal super-resolution correlation microscopy. OPTICS EXPRESS 2021; 29:12772-12786. [PMID: 33985027 DOI: 10.1364/oe.418422] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 03/26/2021] [Indexed: 06/12/2023]
Abstract
Image scanning microscopy (ISM), an upgraded successor of the ubiquitous confocal microscope, facilitates up to two-fold improvement in lateral resolution, and has become an indispensable element in the toolbox of the bio-imaging community. Recently, super-resolution optical fluctuation image scanning microscopy (SOFISM) integrated the analysis of intensity-fluctuations information into the basic ISM architecture, to enhance its resolving power. Both of these techniques typically rely on pixel-reassignment as a fundamental processing step, in which the parallax of different detector elements to the sample is compensated by laterally shifting the point spread function (PSF). Here, we propose an alternative analysis approach, based on the recent high-performing sparsity-based super-resolution correlation microscopy (SPARCOM) method. Through measurements of DNA origami nano-rulers and fixed cells labeled with organic dye, we experimentally show that confocal SPARCOM (cSPARCOM), which circumvents pixel-reassignment altogether, provides enhanced resolution compared to pixel-reassigned based analysis. Thus, cSPARCOM further promotes the effectiveness of ISM, and particularly that of correlation based ISM implementations such as SOFISM, where the PSF deviates significantly from spatial invariance.
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8
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Yi X, Weiss S. Cusp-artifacts in high order superresolution optical fluctuation imaging. BIOMEDICAL OPTICS EXPRESS 2020; 11:554-570. [PMID: 32206387 PMCID: PMC7041480 DOI: 10.1364/boe.382296] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 12/12/2019] [Accepted: 12/13/2019] [Indexed: 05/13/2023]
Abstract
Superresolution optical fluctuation imaging (SOFI) is a simple and affordable super-resolution imaging technique, and attracted a growing community over the past decade. However, the theoretical resolution enhancement of high order SOFI is still not fulfilled. In this study, we identify "cusp artifacts" in high order SOFI images, and show that the high-order cumulants, odd-order moments and balanced-cumulants (bSOFI) are highly vulnerable to cusp artifacts. Our study provides guidelines for developing and screening for fluorescence probes, and improving data acquisition for SOFI. The new insight is important to inspire positive utilization of the cusp artifacts.
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Affiliation(s)
- Xiyu Yi
- Department of Chemistry and Biochemistry, University of California, Los Angeles 90095, USA
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, CA 94550, USA
| | - Shimon Weiss
- Department of Chemistry and Biochemistry, University of California, Los Angeles 90095, USA
- Department of Physiology, University of California, Los Angeles 90095, USA
- California NanoSystems Institute, University of California, Los Angeles 90095, USA
- Department of Physics, Institute for Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat-Gan 52900, Israel
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