1
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Jahnke K, Struve N, Hofmann D, Gote MJ, Bach M, Kriegs M, Hausmann M. Formation of EGFRwt/EGFRvIII homo- and hetero-dimers in glioblastoma cells as detected by single molecule localization microscopy. NANOSCALE 2024; 16:15240-15255. [PMID: 39073345 DOI: 10.1039/d4nr01570c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
Super-resolution microscopy has been used to show the formation of receptor clusters and adapted lipid organization of cell membranes for many members of the ErbB receptor family. The clustering behaviour depends on the receptor size and shape, possibly ligand binding or expression activity. Using single molecule localization microscopy (SMLM), we also showed this typical clustering for the epidermal growth factor receptor variant III (EGFRvIII) in glioblastoma multiforme (GBM) cells. EGFRvIII is co-expressed with the wild type (EGFRwt) and both receptors are assumed to preferentially form hetero-dimers leading to transactivation and elevated oncogenic EGFR-signalling in GBM cells. Here, we analysed EGFRvIII and EGFRwt co-localization using our already described model system of the glioblastoma cell line DKMG, displaying endogenous EGFRvIII expression. Using EGFRvIII and EGFRwt specific antibodies, EGFR localization and their potential for dimerization in a given membrane cluster were analysed by dual colour SMLM supported by novel approaches of mathematic evaluations including Ripley statistics, persistent homology and similarity algorithms. Surprisingly, cluster analysis, Ripley point-to-point distance statistics for cluster geometry and persistent homology comparing cluster topology, revealed that both EGFRvIII and EGFRwt do primarily not form hetero-dimers but the results support the hypothesis that they tend to form homo-dimers. The ratio of homo-dimers obtained by this calculation was significantly higher (>5σ, standard deviation) than expected from randomly arranged points. In comparison, hetero-dimer formation was only slightly increased. We confirmed these data by immunoprecipitation, which show no co-precipitation of EGFRvIII and EGFRwt. Furthermore, we showed that the topology of the clusters was more similar among the same type than among the different types of receptors. Taken together, these data indicate that EGFRvIII does induce oncogenic signalling by homo-dimerisation and not preferentially by hetero-dimer formation with EGFRwt. These data offer a new perspective on EGFRvIII signalling which will lead to a better understanding of this tumour associated receptor variant in GBM.
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Affiliation(s)
- Kevin Jahnke
- Kirchhoff-Institute for Physics, Heidelberg University, Im Neuenheimer Feld 227, 69120 Heidelberg, Germany.
| | - Nina Struve
- Department of Radiotherapy & Radiation Oncology, University Medical Center Hamburg - Eppendorf, Martinistr. 52, 20246 Hamburg, Germany.
| | - Daniel Hofmann
- Kirchhoff-Institute for Physics, Heidelberg University, Im Neuenheimer Feld 227, 69120 Heidelberg, Germany.
| | - Martin Julius Gote
- Kirchhoff-Institute for Physics, Heidelberg University, Im Neuenheimer Feld 227, 69120 Heidelberg, Germany.
| | - Margund Bach
- Kirchhoff-Institute for Physics, Heidelberg University, Im Neuenheimer Feld 227, 69120 Heidelberg, Germany.
| | - Malte Kriegs
- Department of Radiotherapy & Radiation Oncology, University Medical Center Hamburg - Eppendorf, Martinistr. 52, 20246 Hamburg, Germany.
| | - Michael Hausmann
- Kirchhoff-Institute for Physics, Heidelberg University, Im Neuenheimer Feld 227, 69120 Heidelberg, Germany.
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2
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Power RM, Tschanz A, Zimmermann T, Ries J. Build and operation of a custom 3D, multicolor, single-molecule localization microscope. Nat Protoc 2024; 19:2467-2525. [PMID: 38702387 DOI: 10.1038/s41596-024-00989-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 02/19/2024] [Indexed: 05/06/2024]
Abstract
Single-molecule localization microscopy (SMLM) enables imaging scientists to visualize biological structures with unprecedented resolution. Particularly powerful implementations of SMLM are capable of three-dimensional, multicolor and high-throughput imaging and can yield key biological insights. However, widespread access to these technologies is limited, primarily by the cost of commercial options and complexity of de novo development of custom systems. Here we provide a comprehensive guide for interested researchers who wish to establish a high-end, custom-built SMLM setup in their laboratories. We detail the initial configuration and subsequent assembly of the SMLM, including the instructions for the alignment of all the optical pathways, the software and hardware integration, and the operation of the instrument. We describe the validation steps, including the preparation and imaging of test and biological samples with structures of well-defined geometries, and assist the user in troubleshooting and benchmarking the system's performance. Additionally, we provide a walkthrough of the reconstruction of a super-resolved dataset from acquired raw images using the Super-resolution Microscopy Analysis Platform. Depending on the instrument configuration, the cost of the components is in the range US$95,000-180,000, similar to other open-source advanced SMLMs, and substantially lower than the cost of a commercial instrument. A builder with some experience of optical systems is expected to require 4-8 months from the start of the system construction to attain high-quality three-dimensional and multicolor biological images.
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Affiliation(s)
- Rory M Power
- EMBL Imaging Centre, EMBL Heidelberg, Heidelberg, Germany.
| | - Aline Tschanz
- Cell Biology and Biophysics Unit, EMBL Heidelberg, Heidelberg, Germany
| | - Timo Zimmermann
- EMBL Imaging Centre, EMBL Heidelberg, Heidelberg, Germany
- Cell Biology and Biophysics Unit, EMBL Heidelberg, Heidelberg, Germany
| | - Jonas Ries
- Cell Biology and Biophysics Unit, EMBL Heidelberg, Heidelberg, Germany.
- Max Perutz Labs, Vienna Biocenter Campus, Vienna, Austria.
- University of Vienna, Center for Molecular Biology, Department of Structural and Computational Biology, Vienna, Austria.
- University of Vienna, Faculty of Physics, Vienna, Austria.
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3
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Campbell KR, Hallada LP, Huang YS, Solecki DJ. From Blur to Brilliance: The Ascendance of Advanced Microscopy in Neuronal Cell Biology. Annu Rev Neurosci 2024; 47:235-253. [PMID: 38608643 DOI: 10.1146/annurev-neuro-111020-090208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/14/2024]
Abstract
The intricate network of the brain's neurons and synapses poses unparalleled challenges for research, distinct from other biological studies. This is particularly true when dissecting how neurons and their functional units work at a cell biological level. While traditional microscopy has been foundational, it was unable to reveal the deeper complexities of neural interactions. However, an imaging renaissance has transformed our capabilities. Advancements in light and electron microscopy, combined with correlative imaging, now achieve unprecedented resolutions, uncovering the most nuanced neural structures. Maximizing these tools requires more than just technical proficiency. It is crucial to align research aims, allocate resources wisely, and analyze data effectively. At the heart of this evolution is interdisciplinary collaboration, where various experts come together to translate detailed imagery into significant biological insights. This review navigates the latest developments in microscopy, underscoring both the promise of and prerequisites for bending this powerful tool set to understanding neuronal cell biology.
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Affiliation(s)
- Kirby R Campbell
- Neuronal Cell Biology Division, Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA;
| | - Liam P Hallada
- St. Jude Graduate School of Biomedical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
- Neuronal Cell Biology Division, Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA;
| | - Yu-Shan Huang
- Neuronal Cell Biology Division, Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA;
| | - David J Solecki
- Neuronal Cell Biology Division, Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA;
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4
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DʼEste E, Lukinavičius G, Lincoln R, Opazo F, Fornasiero EF. Advancing cell biology with nanoscale fluorescence imaging: essential practical considerations. Trends Cell Biol 2024; 34:671-684. [PMID: 38184400 DOI: 10.1016/j.tcb.2023.12.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 12/06/2023] [Accepted: 12/11/2023] [Indexed: 01/08/2024]
Abstract
Recently, biologists have gained access to several far-field fluorescence nanoscopy (FN) technologies that allow the observation of cellular components with ~20 nm resolution. FN is revolutionizing cell biology by enabling the visualization of previously inaccessible subcellular details. While technological advances in microscopy are critical to the field, optimal sample preparation and labeling are equally important and often overlooked in FN experiments. In this review, we provide an overview of the methodological and experimental factors that must be considered when performing FN. We present key concepts related to the selection of affinity-based labels, dyes, multiplexing, live cell imaging approaches, and quantitative microscopy. Consideration of these factors greatly enhances the effectiveness of FN, making it an exquisite tool for numerous biological applications.
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Affiliation(s)
- Elisa DʼEste
- Optical Microscopy Facility, Max Planck Institute for Medical Research, Heidelberg 69120, Germany.
| | - Gražvydas Lukinavičius
- Chromatin Labelling and Imaging Group, Department of NanoBiophotonics, Max Planck Institute for Multidisciplinary Sciences, Göttingen 37077, Germany.
| | - Richard Lincoln
- Department of Optical Nanoscopy, Max Planck Institute for Medical Research, Heidelberg 69120, Germany.
| | - Felipe Opazo
- Institute of Neuro- and Sensory Physiology, University Medical Center Göttingen (UMG), Göttingen 37073, Germany; Center for Biostructural Imaging of Neurodegeneration (BIN), University Medical Center, Göttingen 37075, Germany; NanoTag Biotechnologies GmbH, Göttingen 37079, Germany.
| | - Eugenio F Fornasiero
- Institute of Neuro- and Sensory Physiology, University Medical Center Göttingen (UMG), Göttingen 37073, Germany; Department of Life Sciences, University of Trieste, Trieste 34127, Italy.
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5
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Moya Muñoz GG, Brix O, Klocke P, Harris PD, Luna Piedra JR, Wendler ND, Lerner E, Zijlstra N, Cordes T. Single-molecule detection and super-resolution imaging with a portable and adaptable 3D-printed microscopy platform (Brick-MIC). BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.29.573596. [PMID: 38234760 PMCID: PMC10793419 DOI: 10.1101/2023.12.29.573596] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
Over the past decades, single-molecule and super-resolution microscopy have advanced and represent essential tools for life science research. There is,however, a growing gap between the state-of-the-art and what is accessible to biologists, biochemists, medical researchers or labs with financial constraints. To bridge this gap, we introduce Brick-MIC, a versatile and affordable open-source 3D-printed micro-spectroscopy and imaging platform. Brick-MIC enables the integration of various fluorescence imaging techniques with single-molecule resolution within a single platform and exchange between different modalities within minutes. We here present variants of Brick-MIC that facilitate single-molecule fluorescence detection, fluorescence correlation spectroscopy and super-resolution imaging (STORM and PAINT). Detailed descriptions of the hardware and software components, as well as data analysis routines are provided, to allow non-optics specialist to operate their own Brick-MIC with minimal effort and investments. We foresee that our affordable, flexible, and opensource Brick-MIC platform will be a valuable tool for many laboratories worldwide.
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Affiliation(s)
- Gabriel G. Moya Muñoz
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians Universität München, Planegg-Martinsried, Germany
| | - Oliver Brix
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians Universität München, Planegg-Martinsried, Germany
| | - Philipp Klocke
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians Universität München, Planegg-Martinsried, Germany
| | - Paul D. Harris
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Faculty of Mathematics Science, The Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Jorge R. Luna Piedra
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians Universität München, Planegg-Martinsried, Germany
| | - Nicolas D. Wendler
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians Universität München, Planegg-Martinsried, Germany
| | - Eitan Lerner
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Faculty of Mathematics Science, The Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
- The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Niels Zijlstra
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians Universität München, Planegg-Martinsried, Germany
| | - Thorben Cordes
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians Universität München, Planegg-Martinsried, Germany
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6
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Lakadamyali M. From feulgen to modern methods: marking a century of DNA imaging advances. Histochem Cell Biol 2024; 162:13-22. [PMID: 38753186 PMCID: PMC11227465 DOI: 10.1007/s00418-024-02291-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/18/2024] [Indexed: 07/07/2024]
Abstract
The mystery of how human DNA is compactly packaged into a nucleus-a space a hundred thousand times smaller-while still allowing for the regulation of gene function, has long been one of the greatest enigmas in cell biology. This puzzle is gradually being solved, thanks in part to the advent of new technologies. Among these, innovative genome-labeling techniques combined with high-resolution imaging methods have been pivotal. These methods facilitate the visualization of DNA within intact nuclei and have significantly contributed to our current understanding of genome organization. This review will explore various labeling and imaging approaches that are revolutionizing our understanding of the three-dimensional organization of the genome, shedding light on the relationship between its structure and function.
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Affiliation(s)
- Melike Lakadamyali
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA.
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA.
- Perelman School of Medicine, Epigenetics Institute, University of Pennsylvania, Philadelphia, USA.
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7
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Budiarta M, Streit M, Beliu G. Site-specific protein labeling strategies for super-resolution microscopy. Curr Opin Chem Biol 2024; 80:102445. [PMID: 38490137 DOI: 10.1016/j.cbpa.2024.102445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Revised: 02/28/2024] [Accepted: 02/28/2024] [Indexed: 03/17/2024]
Abstract
Super-resolution microscopy (SRM) has transformed our understanding of proteins' subcellular organization and revealed cellular details down to nanometers, far beyond conventional microscopy. While localization precision is independent of the number of fluorophores attached to a biomolecule, labeling density is a decisive factor for resolving complex biological structures. The average distance between adjacent fluorophores should be less than half the desired spatial resolution for optimal clarity. While this was not a major limitation in recent decades, the success of modern microscopy approaching molecular resolution down to the single-digit nanometer range will depend heavily on advancements in fluorescence labeling. This review highlights recent advances and challenges in labeling strategies for SRM, focusing on site-specific labeling technologies. These advancements are crucial for improving SRM precision and expanding our understanding of molecular interactions.
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Affiliation(s)
- Made Budiarta
- Rudolf Virchow Center, Research Center for Integrative and Translational Bioimaging, University of Würzburg, 97080 Würzburg, Germany
| | - Marcel Streit
- Rudolf Virchow Center, Research Center for Integrative and Translational Bioimaging, University of Würzburg, 97080 Würzburg, Germany
| | - Gerti Beliu
- Rudolf Virchow Center, Research Center for Integrative and Translational Bioimaging, University of Würzburg, 97080 Würzburg, Germany; Interdisciplinary Institute for Neuroscience, University of Bordeaux, CNRS, UMR 5297, 33076 Bordeaux, France.
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8
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Martinez-Sarmiento JA, Cosma MP, Lakadamyali M. Dissecting gene activation and chromatin remodeling dynamics in single human cells undergoing reprogramming. Cell Rep 2024; 43:114170. [PMID: 38700983 PMCID: PMC11195307 DOI: 10.1016/j.celrep.2024.114170] [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: 08/09/2023] [Revised: 03/08/2024] [Accepted: 04/15/2024] [Indexed: 05/05/2024] Open
Abstract
During cell fate transitions, cells remodel their transcriptome, chromatin, and epigenome; however, it has been difficult to determine the temporal dynamics and cause-effect relationship between these changes at the single-cell level. Here, we employ the heterokaryon-mediated reprogramming system as a single-cell model to dissect key temporal events during early stages of pluripotency conversion using super-resolution imaging. We reveal that, following heterokaryon formation, the somatic nucleus undergoes global chromatin decompaction and removal of repressive histone modifications H3K9me3 and H3K27me3 without acquisition of active modifications H3K4me3 and H3K9ac. The pluripotency gene OCT4 (POU5F1) shows nascent and mature RNA transcription within the first 24 h after cell fusion without requiring an initial open chromatin configuration at its locus. NANOG, conversely, has significant nascent RNA transcription only at 48 h after cell fusion but, strikingly, exhibits genomic reopening early on. These findings suggest that the temporal relationship between chromatin compaction and gene activation during cellular reprogramming is gene context dependent.
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Affiliation(s)
- Jose A Martinez-Sarmiento
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Maria Pia Cosma
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain; ICREA, 08010 Barcelona, Spain; Medical Research Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, 510080 Guangzhou, China.
| | - Melike Lakadamyali
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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9
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Sharma A, Yadav A, Nandy A, Ghatak S. Insight into the Functional Dynamics and Challenges of Exosomes in Pharmaceutical Innovation and Precision Medicine. Pharmaceutics 2024; 16:709. [PMID: 38931833 PMCID: PMC11206934 DOI: 10.3390/pharmaceutics16060709] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2024] [Revised: 05/13/2024] [Accepted: 05/16/2024] [Indexed: 06/28/2024] Open
Abstract
Of all the numerous nanosized extracellular vesicles released by a cell, the endosomal-originated exosomes are increasingly recognized as potential therapeutics, owing to their inherent stability, low immunogenicity, and targeted delivery capabilities. This review critically evaluates the transformative potential of exosome-based modalities across pharmaceutical and precision medicine landscapes. Because of their precise targeted biomolecular cargo delivery, exosomes are posited as ideal candidates in drug delivery, enhancing regenerative medicine strategies, and advancing diagnostic technologies. Despite the significant market growth projections of exosome therapy, its utilization is encumbered by substantial scientific and regulatory challenges. These include the lack of universally accepted protocols for exosome isolation and the complexities associated with navigating the regulatory environment, particularly the guidelines set forth by the U.S. Food and Drug Administration (FDA). This review presents a comprehensive overview of current research trajectories aimed at addressing these impediments and discusses prospective advancements that could substantiate the clinical translation of exosomal therapies. By providing a comprehensive analysis of both the capabilities and hurdles inherent to exosome therapeutic applications, this article aims to inform and direct future research paradigms, thereby fostering the integration of exosomal systems into mainstream clinical practice.
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Affiliation(s)
| | | | | | - Subhadip Ghatak
- McGowan Institute for Regenerative Medicine, Department of Surgery, University of Pittsburgh, Pittsburgh, PA 15219, USA; (A.S.); (A.Y.); (A.N.)
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10
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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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11
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Shin M, Seo M, Lee K, Yoon K. Super-resolution techniques for biomedical applications and challenges. Biomed Eng Lett 2024; 14:465-496. [PMID: 38645589 PMCID: PMC11026337 DOI: 10.1007/s13534-024-00365-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 02/12/2024] [Accepted: 02/18/2024] [Indexed: 04/23/2024] Open
Abstract
Super-resolution (SR) techniques have revolutionized the field of biomedical applications by detailing the structures at resolutions beyond the limits of imaging or measuring tools. These techniques have been applied in various biomedical applications, including microscopy, magnetic resonance imaging (MRI), computed tomography (CT), X-ray, electroencephalogram (EEG), ultrasound, etc. SR methods are categorized into two main types: traditional non-learning-based methods and modern learning-based approaches. In both applications, SR methodologies have been effectively utilized on biomedical images, enhancing the visualization of complex biological structures. Additionally, these methods have been employed on biomedical data, leading to improvements in computational precision and efficiency for biomedical simulations. The use of SR techniques has resulted in more detailed and accurate analyses in diagnostics and research, essential for early disease detection and treatment planning. However, challenges such as computational demands, data interpretation complexities, and the lack of unified high-quality data persist. The article emphasizes these issues, underscoring the need for ongoing development in SR technologies to further improve biomedical research and patient care outcomes.
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Affiliation(s)
- Minwoo Shin
- School of Mathematics and Computing (Computational Science and Engineering), Yonsei University, 50 Yonsei-Ro, Seodaemun-Gu, Seoul, 03722 Republic of Korea
| | - Minjee Seo
- School of Mathematics and Computing (Computational Science and Engineering), Yonsei University, 50 Yonsei-Ro, Seodaemun-Gu, Seoul, 03722 Republic of Korea
| | - Kyunghyun Lee
- School of Mathematics and Computing (Computational Science and Engineering), Yonsei University, 50 Yonsei-Ro, Seodaemun-Gu, Seoul, 03722 Republic of Korea
| | - Kyungho Yoon
- School of Mathematics and Computing (Computational Science and Engineering), Yonsei University, 50 Yonsei-Ro, Seodaemun-Gu, Seoul, 03722 Republic of Korea
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12
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Santiago-Ruiz AN, Hugelier S, Bond CR, Lee EB, Lakadamyali M. Super-Resolution Imaging Uncovers Nanoscale Tau Aggregate Hyperphosphorylation Patterns in Human Alzheimer's Disease Brain Tissue. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.24.590893. [PMID: 38712162 PMCID: PMC11071528 DOI: 10.1101/2024.04.24.590893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Tau aggregation plays a critical role in Alzheimer's Disease (AD), where tau neurofibrillary tangles (NFTs) are a key pathological hallmark. While much attention has been given to NFTs, emerging evidence underscores nano-sized pre-NFT tau aggregates as potentially toxic entities in AD. By leveraging DNA-PAINT super-resolution microscopy, we visualized and quantified nanoscale tau aggregates (nano-aggregates) in human postmortem brain tissues from intermediate and advanced AD, and Primary Age-Related Tauopathy (PART). Nano-aggregates were predominant across cases, with AD exhibiting a higher burden compared to PART. Hyperphosphorylated tau residues (p-T231, p-T181, and p-S202/T205) were present within nano-aggregates across all AD Braak stages and PART. Moreover, nano-aggregates displayed morphological differences between PART and AD, and exhibited distinct hyperphosphorylation patterns in advanced AD. These findings suggest that changes in nano-aggregate morphology and hyperphosphorylation patterns may exacerbate tau aggregation and AD progression. The ability to detect and profile nanoscale tau aggregates in human brain tissue opens new avenues for studying the molecular underpinnings of tauopathies.
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13
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Carsten A, Wolters M, Aepfelbacher M. Super-resolution fluorescence microscopy for investigating bacterial cell biology. Mol Microbiol 2024; 121:646-658. [PMID: 38041391 DOI: 10.1111/mmi.15203] [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: 08/04/2023] [Revised: 11/13/2023] [Accepted: 11/16/2023] [Indexed: 12/03/2023]
Abstract
Super-resolution fluorescence microscopy technologies developed over the past two decades have pushed the resolution limit for fluorescently labeled molecules into the nanometer range. These technologies have the potential to study bacterial structures, for example, macromolecular assemblies such as secretion systems, with single-molecule resolution on a millisecond time scale. Here we review recent applications of super-resolution fluorescence microscopy with a focus on bacterial secretion systems. We also describe MINFLUX fluorescence nanoscopy, a relatively new technique that promises to one day produce molecular movies of molecular machines in action.
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Affiliation(s)
- Alexander Carsten
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg Eppendorf, Hamburg, Germany
| | - Manuel Wolters
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg Eppendorf, Hamburg, Germany
| | - Martin Aepfelbacher
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg Eppendorf, Hamburg, Germany
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14
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Bond C, Hugelier S, Xing J, Sorokina EM, Lakadamyali M. Multiplexed DNA-PAINT Imaging of the Heterogeneity of Late Endosome/Lysosome Protein Composition. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.18.585634. [PMID: 38562776 PMCID: PMC10983937 DOI: 10.1101/2024.03.18.585634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Late endosomes/lysosomes (LELs) are crucial for numerous physiological processes and their dysfunction is linked to many diseases. Proteomic analyses have identified hundreds of LEL proteins, however, whether these proteins are uniformly present on each LEL, or if there are cell-type dependent LEL sub-populations with unique protein compositions is unclear. We employed a quantitative, multiplexed DNA-PAINT super-resolution approach to examine the distribution of six key LEL proteins (LAMP1, LAMP2, CD63, TMEM192, NPC1 and LAMTOR4) on individual LELs. While LAMP1 and LAMP2 were abundant across LELs, marking a common population, most analyzed proteins were associated with specific LEL subpopulations. Our multiplexed imaging approach identified up to eight different LEL subpopulations based on their unique membrane protein composition. Additionally, our analysis of the spatial relationships between these subpopulations and mitochondria revealed a cell-type specific tendency for NPC1-positive LELs to be closely positioned to mitochondria. Our approach will be broadly applicable to determining organelle heterogeneity with single organelle resolution in many biological contexts. Summary This study develops a multiplexed and quantitative DNA-PAINT super-resolution imaging pipeline to investigate the distribution of late endosomal/lysosomal (LEL) proteins across individual LELs, revealing cell-type specific LEL sub-populations with unique protein compositions, offering insights into organelle heterogeneity at single-organelle resolution.
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15
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Sharma N, Jung M, Mishra PK, Mun JY, Rhee HW. FLEX: genetically encodable enzymatic fluorescence signal amplification using engineered peroxidase. Cell Chem Biol 2024; 31:S2451-9456(24)00081-3. [PMID: 38513646 DOI: 10.1016/j.chembiol.2024.02.007] [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: 07/31/2023] [Revised: 11/30/2023] [Accepted: 02/22/2024] [Indexed: 03/23/2024]
Abstract
Fluorescent tagging of biomolecules enables their sensitive detection during separation and determining their subcellular location. In this context, peroxidase-based reactions are actively utilized for signal amplification. To harness this potential, we developed a genetically encodable enzymatic fluorescence signal amplification method using APEX (FLEX). We synthesized a fluorescent probe, Jenfluor triazole (JFT1), which effectively amplifies and restricts fluorescence signals under fixed conditions, enabling fluorescence-based detection of subcellularly localized electron-rich metabolites. Moreover, JFT1 exhibited stable fluorescence signals even under osmium-treated and polymer-embedded conditions, which supported findings from correlative light and electron microscopy (CLEM) using APEX. Using various APEX-conjugated proteins of interest (POIs) targeted to different organelles, we successfully visualized their localization through FLEX imaging while effectively preserving organelle ultrastructures. FLEX provides insights into dynamic lysosome-mitochondria interactions upon exposure to chemical stressors. Overall, FLEX holds significant promise as a sensitive and versatile system for fluorescently detecting APEX2-POIs in multiscale biological samples.
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Affiliation(s)
- Nirmali Sharma
- Department of Chemistry, Seoul National University, Seoul 08826, Korea; Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Korea
| | - Minkyo Jung
- Neural Circuits Research Group, Korea Brain Research Institute, Daegu 41062, Republic of Korea
| | | | - Ji Young Mun
- Neural Circuits Research Group, Korea Brain Research Institute, Daegu 41062, Republic of Korea.
| | - Hyun-Woo Rhee
- Department of Chemistry, Seoul National University, Seoul 08826, Korea; School of Biological Sciences, Seoul National University, Seoul 08826, Korea.
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16
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Gong D, Cai C, Strahilevitz E, Chen J, Scherer NF. Easily scalable multi-color DMD-based structured illumination microscopy. OPTICS LETTERS 2024; 49:77-80. [PMID: 38134158 DOI: 10.1364/ol.507599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 12/04/2023] [Indexed: 12/24/2023]
Abstract
Structured illumination microscopy (SIM) achieves super-resolution imaging using a series of phase-shifted sinusoidal illumination patterns to down-modulate high spatial-frequency information of samples. Digital micromirror devices (DMDs) have been increasingly used to generate SIM illumination patterns due to their high speed and moderate cost. However, a DMD micromirror array's blazed grating structure causes strong angular dispersion for different wavelengths of light, thus severely hampering its application in multicolor imaging. We developed a multi-color DMD-SIM setup that employs a diffraction grating to compensate the DMD's dispersion and demonstrate super-resolution SIM imaging of both fluorescent beads and live cells samples with four color channels. This simple but effective approach can be readily scaled to more color channels, thereby greatly expanding the application of SIM in the study of complex multi-component structures and dynamics in soft matter systems.
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17
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Leisten ED, Woods AC, Wong YC. Super-resolution microscopy: Insights into mitochondria-lysosome crosstalk in health and disease. J Cell Biol 2023; 222:e202305032. [PMID: 37917024 PMCID: PMC10621667 DOI: 10.1083/jcb.202305032] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2023] Open
Abstract
Live super-resolution microscopy has allowed for new insights into recently identified mitochondria-lysosome contact sites, which mediate crosstalk between mitochondria and lysosomes, including co-regulation of Rab7 GTP hydrolysis and Drp1 GTP hydrolysis. Here, we highlight recent findings and future perspectives on this dynamic pathway and its roles in health and disease.
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Affiliation(s)
- Eric D. Leisten
- Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Abby C. Woods
- Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Yvette C. Wong
- Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
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18
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Gong D, Scherer NF. Tandem aberration correction optics (TACO) in wide-field structured illumination microscopy. BIOMEDICAL OPTICS EXPRESS 2023; 14:6381-6396. [PMID: 38420301 PMCID: PMC10898552 DOI: 10.1364/boe.503801] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 11/08/2023] [Accepted: 11/09/2023] [Indexed: 03/02/2024]
Abstract
Structured illumination microscopy (SIM) is a powerful super-resolution imaging technique that uses patterned illumination to down-modulate high spatial-frequency information of samples. However, the presence of spatially-dependent aberrations can severely disrupt the illumination pattern, limiting the quality of SIM imaging. Conventional adaptive optics (AO) techniques that employ wavefront correctors at the pupil plane are not capable of effectively correcting these spatially-dependent aberrations. We introduce the Tandem Aberration Correction Optics (TACO) approach that combines both pupil AO and conjugate AO for aberration correction in SIM. TACO incorporates a deformable mirror (DM) for pupil AO in the detection path to correct for global aberrations, while a spatial light modulator (SLM) is placed at the plane conjugate to the aberration source near the sample plane, termed conjugate AO, to compensate spatially-varying aberrations in the illumination path. Our numerical simulations and experimental results show that the TACO approach can recover the illumination pattern close to an ideal condition, even when severely misshaped by aberrations, resulting in high-quality super-resolution SIM reconstruction. The TACO approach resolves a critical traditional shortcoming of aberration correction for structured illumination. This advance significantly expands the application of SIM imaging in the study of complex, particularly biological, samples and should be effective in other wide-field microscopies.
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Affiliation(s)
- Daozheng Gong
- Graduate Program in Biophysical Sciences, University of Chicago, Chicago, IL 60637, USA
- Institute for Biophysical Dynamics, University of Chicago, Chicago, IL 60637, USA
| | - Norbert F. Scherer
- Institute for Biophysical Dynamics, University of Chicago, Chicago, IL 60637, USA
- Department of Chemistry, University of Chicago, Chicago, IL 60637, USA
- James Franck Institute, University of Chicago, Chicago, IL 60637, USA
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19
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Duan X, Zhang M, Zhang YH. Organic fluorescent probes for live-cell super-resolution imaging. FRONTIERS OF OPTOELECTRONICS 2023; 16:34. [PMID: 37946039 PMCID: PMC10635970 DOI: 10.1007/s12200-023-00090-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Accepted: 10/25/2023] [Indexed: 11/12/2023]
Abstract
The development of super-resolution technology has made it possible to investigate the ultrastructure of intracellular organelles by fluorescence microscopy, which has greatly facilitated the development of life sciences and biomedicine. To realize super-resolution imaging of living cells, both advanced imaging systems and excellent fluorescent probes are required. Traditional fluorescent probes have good availability, but that is not the case for probes for live-cell super-resolution imaging. In this review, we first introduce the principles of various super-resolution technologies and their probe requirements, then summarize the existing designs and delivery strategies of super-resolution probes for live-cell imaging, and finally provide a brief conclusion and overview of the future.
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Affiliation(s)
- Xinxin Duan
- Britton Chance Center for Biomedical Photonics, MoE Key Laboratory for Biomedical Photonics, Advanced Biomedical Imaging Facility-Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Meng Zhang
- Britton Chance Center for Biomedical Photonics, MoE Key Laboratory for Biomedical Photonics, Advanced Biomedical Imaging Facility-Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Yu-Hui Zhang
- Britton Chance Center for Biomedical Photonics, MoE Key Laboratory for Biomedical Photonics, Advanced Biomedical Imaging Facility-Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, 430074, China.
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20
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Tadesse K, Mandracchia B, Yoon K, Han K, Jia S. Three-dimensional multifocal scanning microscopy for super-resolution cell and tissue imaging. OPTICS EXPRESS 2023; 31:38550-38559. [PMID: 38017958 DOI: 10.1364/oe.501100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 10/24/2023] [Indexed: 11/30/2023]
Abstract
Recent advancements in image-scanning microscopy have significantly enriched super-resolution biological research, providing deeper insights into cellular structures and processes. However, current image-scanning techniques often require complex instrumentation and alignment, constraining their broader applicability in cell biological discovery and convenient, cost-effective integration into commonly used frameworks like epi-fluorescence microscopes. Here, we introduce three-dimensional multifocal scanning microscopy (3D-MSM) for super-resolution imaging of cells and tissue with substantially reduced instrumental complexity. This method harnesses the inherent 3D movement of specimens to achieve stationary, multi-focal excitation and super-resolution microscopy through a standard epi-fluorescence platform. We validated the system using a range of phantom, single-cell, and tissue specimens. The combined strengths of structured illumination, confocal detection, and epi-fluorescence setup result in two-fold resolution improvement in all three dimensions, effective optical sectioning, scalable volume acquisition, and compatibility with general imaging and sample protocols. We anticipate that 3D-MSM will pave a promising path for future super-resolution investigations in cell and tissue biology.
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21
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Zhao B, Mertz J. Resolution enhancement with deblurring by pixel reassignment. ADVANCED PHOTONICS 2023; 5:066004. [PMID: 38884067 PMCID: PMC11178354 DOI: 10.1117/1.ap.5.6.066004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/18/2024]
Abstract
Improving the spatial resolution of a fluorescence microscope has been an ongoing challenge in the imaging community. To address this challenge, a variety of approaches have been taken, ranging from instrumentation development to image postprocessing. An example of the latter is deconvolution, where images are numerically deblurred based on a knowledge of the microscope point spread function. However, deconvolution can easily lead to noise-amplification artifacts. Deblurring by postprocessing can also lead to negativities or fail to conserve local linearity between sample and image. We describe here a simple image deblurring algorithm based on pixel reassignment that inherently avoids such artifacts and can be applied to general microscope modalities and fluorophore types. Our algorithm helps distinguish nearby fluorophores, even when these are separated by distances smaller than the conventional resolution limit, helping facilitate, for example, the application of single-molecule localization microscopy in dense samples. We demonstrate the versatility and performance of our algorithm under a variety of imaging conditions.
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Affiliation(s)
- Bingying Zhao
- Boston University, Department of Electrical and Computer Engineering, Boston, Massachusetts, United States
| | - Jerome Mertz
- Boston University, Department of Biomedical Engineering, Boston, Massachusetts, United States
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22
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Jain P, Geisler C, Leitz D, Udachin V, Nagorny S, Weingartz T, Adams J, Schmidt A, Rembe C, Egner A. Super-resolution Reflection Microscopy via Absorbance Modulation. ACS NANOSCIENCE AU 2023; 3:375-380. [PMID: 37868228 PMCID: PMC10588435 DOI: 10.1021/acsnanoscienceau.3c00013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/18/2023] [Revised: 06/02/2023] [Accepted: 06/08/2023] [Indexed: 10/24/2023]
Abstract
In recent years, fluorescence microscopy has been revolutionized. Reversible switching of fluorophores has enabled circumventing the limits imposed by diffraction. Thus, resolution down to the molecular scale became possible. However, to the best of our knowledge, the application of the principles underlying super-resolution fluorescence microscopy to reflection microscopy has not been experimentally demonstrated. Here, we present the first evidence that this is indeed possible. A layer of photochromic molecules referred to as the absorbance modulation layer (AML) is applied to a sample under investigation. The AML-coated sample is then sequentially illuminated with a one-dimensional (1D) focal intensity distribution (similar to the transverse laser mode TEM01) at wavelength λ1 = 325 nm to create a subwavelength aperture within the AML, followed by illumination with a Gaussian focal spot at λ2 = 633 nm for high-resolution imaging. Using this method, called absorbance modulation imaging (AMI) in reflection, we demonstrate a 2.4-fold resolution enhancement over the diffraction limit for a numerical aperture (NA) of 0.65 and wavelength (λ) of 633 nm.
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Affiliation(s)
- Parul Jain
- Department
of Optical Nanoscopy, Institute for Nanophotonics
Göttingen e.V., 37077 Göttingen, Germany
| | - Claudia Geisler
- Department
of Optical Nanoscopy, Institute for Nanophotonics
Göttingen e.V., 37077 Göttingen, Germany
| | - Dennis Leitz
- Institute
of Electrical Information Technology, Clausthal
University of Technology, 38678 Clausthal-Zellerfeld, Germany
| | - Viktor Udachin
- Clausthal
Center of Materials Technology, Clausthal
University of Technology, 38678 Clausthal-Zellerfeld, Germany
| | - Sven Nagorny
- Institute
of Organic Chemistry, Clausthal University
of Technology, 38678 Clausthal-Zellerfeld, Germany
| | - Thea Weingartz
- Institute
of Organic Chemistry, Clausthal University
of Technology, 38678 Clausthal-Zellerfeld, Germany
| | - Jörg Adams
- Institute
of Physical Chemistry, Clausthal University
of Technology, 38678 Clausthal-Zellerfeld, Germany
| | - Andreas Schmidt
- Institute
of Organic Chemistry, Clausthal University
of Technology, 38678 Clausthal-Zellerfeld, Germany
| | - Christian Rembe
- Institute
of Electrical Information Technology, Clausthal
University of Technology, 38678 Clausthal-Zellerfeld, Germany
| | - Alexander Egner
- Department
of Optical Nanoscopy, Institute for Nanophotonics
Göttingen e.V., 37077 Göttingen, Germany
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23
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Zhao B, Mertz J. Resolution enhancement with deblurring by pixel reassignment (DPR). BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.24.550382. [PMID: 37546886 PMCID: PMC10402078 DOI: 10.1101/2023.07.24.550382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
Improving the spatial resolution of a fluorescence microscope has been an ongoing challenge in the imaging community. To address this challenge, a variety of approaches have been taken, ranging from instrumentation development to image post-processing. An example of the latter is deconvolution, where images are numerically deblurred based on a knowledge of the microscope point spread function. However, deconvolution can easily lead to noise-amplification artifacts. Deblurring by post-processing can also lead to negativities or fail to conserve local linearity between sample and image. We describe here a simple image deblurring algorithm based on pixel reassignment that inherently avoids such artifacts and can be applied to general microscope modalities and fluorophore types. Our algorithm helps distinguish nearby fluorophores even when these are separated by distances smaller than the conventional resolution limit, helping facilitate, for example, the application of single-molecule localization microscopy in dense samples. We demonstrate the versatility and performance of our algorithm under a variety of imaging conditions.
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Affiliation(s)
- Bingying Zhao
- Department of Electrical and Computer Engineering, Boston University, MA 02215
| | - Jerome Mertz
- Department of Biomedical Engineering, Boston University, MA 02215
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24
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Xu Z, Foster JB, Lashley R, Wang X, Benson E, Kidd G, Lin CLG. Impact of a pyridazine derivative on tripartite synapse ultrastructure in hippocampus: a three-dimensional analysis. Front Cell Neurosci 2023; 17:1229731. [PMID: 37671169 PMCID: PMC10476950 DOI: 10.3389/fncel.2023.1229731] [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: 05/26/2023] [Accepted: 07/24/2023] [Indexed: 09/07/2023] Open
Abstract
Introduction We previously discovered a pyridazine derivative compound series that can improve cognitive functions in mouse models of Alzheimer's disease. One of the advanced compounds from this series, LDN/OSU-0215111-M3, was selected as the preclinical development candidate. This compound activates local protein translation at the perisynaptic astrocytic process (PAP) and enhances synaptic plasticity sequentially. While biochemical evidence supports the hypothesis that the compound enhances the structural plasticity of the tripartite synapse, its direct structural impact has not been investigated. Methods Volume electron microscopy was used to study the hippocampal tripartite synapse three-dimensional structure in 3-month-old wild-type FVB/NJ mice after LDN/OSU-0215111-M3 treatment. Results LDN/OSU-0215111-M3 increased the size of tertiary apical dendrites, the volume of mushroom spines, the proportion of mushroom spines containing spine apparatus, and alterations in the spine distribution across the surface area of tertiary dendrites. Compound also increased the number of the PAP interacting with the mushroom spines as well as the size of the PAP in contact with the spines. Furthermore, proteomic analysis of the isolated synaptic terminals indicated an increase in dendritic and synaptic proteins as well as suggested a possible involvement of the phospholipase D signaling pathway. To further validate that LDN/OSU-0215111-M3 altered synaptic function, electrophysiological studies showed increased long-term potentiation following compound treatment. Discussion This study provides direct evidence that pyridazine derivatives enhance the structural and functional plasticity of the tripartite synapse.
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Affiliation(s)
- Zan Xu
- Department of Neuroscience, College of Medicine, The Ohio State University, Columbus, OH, United States
| | - Joshua B. Foster
- Department of Neuroscience, College of Medicine, The Ohio State University, Columbus, OH, United States
| | - Rashelle Lashley
- Department of Neuroscience, College of Medicine, The Ohio State University, Columbus, OH, United States
| | - Xueqin Wang
- Department of Neuroscience, College of Medicine, The Ohio State University, Columbus, OH, United States
| | - Emily Benson
- Department of Neuroscience, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, United States
| | - Grahame Kidd
- Department of Neuroscience, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, United States
| | - Chien-liang Glenn Lin
- Department of Neuroscience, College of Medicine, The Ohio State University, Columbus, OH, United States
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25
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Marin Z, Fuentes LA, Bewersdorf J, Baddeley D. Extracting nanoscale membrane morphology from single-molecule localizations. Biophys J 2023; 122:3022-3030. [PMID: 37355772 PMCID: PMC10432223 DOI: 10.1016/j.bpj.2023.06.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 05/17/2023] [Accepted: 06/15/2023] [Indexed: 06/26/2023] Open
Abstract
Membrane surface reconstruction at the nanometer scale is required for understanding mechanisms of subcellular shape change. This historically has been the domain of electron microscopy, but extraction of surfaces from specific labels is a difficult task in this imaging modality. Existing methods for extracting surfaces from fluorescence microscopy have poor resolution or require high-quality super-resolution data that are manually cleaned and curated. Here, we present NanoWrap, a new method for extracting surfaces from generalized single-molecule localization microscopy data. This makes it possible to study the shape of specifically labeled membranous structures inside cells. We validate NanoWrap using simulations and demonstrate its reconstruction capabilities on single-molecule localization microscopy data of the endoplasmic reticulum and mitochondria. NanoWrap is implemented in the open-source Python Microscopy Environment.
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Affiliation(s)
- Zach Marin
- Auckland Bioengineering Institute, University of Auckland, Auckland, New Zealand; Department of Cell Biology, Yale University School of Medicine, New Haven, Connecticut; Department of Biomedical Engineering, Yale University, New Haven, Connecticut
| | - Lukas A Fuentes
- Department of Cell Biology, Yale University School of Medicine, New Haven, Connecticut
| | - Joerg Bewersdorf
- Department of Cell Biology, Yale University School of Medicine, New Haven, Connecticut; Department of Biomedical Engineering, Yale University, New Haven, Connecticut; Department of Physics, Yale University, New Haven, Connecticut
| | - David Baddeley
- Auckland Bioengineering Institute, University of Auckland, Auckland, New Zealand; Department of Cell Biology, Yale University School of Medicine, New Haven, Connecticut.
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26
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Leonard TA, Loose M, Martens S. The membrane surface as a platform that organizes cellular and biochemical processes. Dev Cell 2023; 58:1315-1332. [PMID: 37419118 DOI: 10.1016/j.devcel.2023.06.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 04/22/2023] [Accepted: 06/08/2023] [Indexed: 07/09/2023]
Abstract
Membranes are essential for life. They act as semi-permeable boundaries that define cells and organelles. In addition, their surfaces actively participate in biochemical reaction networks, where they confine proteins, align reaction partners, and directly control enzymatic activities. Membrane-localized reactions shape cellular membranes, define the identity of organelles, compartmentalize biochemical processes, and can even be the source of signaling gradients that originate at the plasma membrane and reach into the cytoplasm and nucleus. The membrane surface is, therefore, an essential platform upon which myriad cellular processes are scaffolded. In this review, we summarize our current understanding of the biophysics and biochemistry of membrane-localized reactions with particular focus on insights derived from reconstituted and cellular systems. We discuss how the interplay of cellular factors results in their self-organization, condensation, assembly, and activity, and the emergent properties derived from them.
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Affiliation(s)
- Thomas A Leonard
- Max Perutz Labs, Vienna Biocenter Campus (VBC), Dr. Bohr-Gasse 9, 1030, Vienna, Austria; Medical University of Vienna, Center for Medical Biochemistry, Dr. Bohr-Gasse 9, 1030, Vienna, Austria.
| | - Martin Loose
- Institute of Science and Technology Austria, Am Campus 1, 3400 Klosterneuburg, Austria.
| | - Sascha Martens
- Max Perutz Labs, Vienna Biocenter Campus (VBC), Dr. Bohr-Gasse 9, 1030, Vienna, Austria; University of Vienna, Center for Molecular Biology, Department of Biochemistry and Cell Biology, Dr. Bohr-Gasse 9, 1030, Vienna, Austria.
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27
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Wang J, Zhao Y, Nie G. Intelligent nanomaterials for cancer therapy: recent progresses and future possibilities. MEDICAL REVIEW (2021) 2023; 3:321-342. [PMID: 38235406 PMCID: PMC10790212 DOI: 10.1515/mr-2023-0028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 08/15/2023] [Indexed: 01/19/2024]
Abstract
Intelligent nanomedicine is currently one of the most active frontiers in cancer therapy development. Empowered by the recent progresses of nanobiotechnology, a new generation of multifunctional nanotherapeutics and imaging platforms has remarkably improved our capability to cope with the highly heterogeneous and complicated nature of cancer. With rationally designed multifunctionality and programmable assembly of functional subunits, the in vivo behaviors of intelligent nanosystems have become increasingly tunable, making them more efficient in performing sophisticated actions in physiological and pathological microenvironments. In recent years, intelligent nanomaterial-based theranostic platforms have showed great potential in tumor-targeted delivery, biological barrier circumvention, multi-responsive tumor sensing and drug release, as well as convergence with precise medication approaches such as personalized tumor vaccines. On the other hand, the increasing system complexity of anti-cancer nanomedicines also pose significant challenges in characterization, monitoring and clinical use, requesting a more comprehensive and dynamic understanding of nano-bio interactions. This review aims to briefly summarize the recent progresses achieved by intelligent nanomaterials in tumor-targeted drug delivery, tumor immunotherapy and temporospatially specific tumor imaging, as well as important advances of our knowledge on their interaction with biological systems. In the perspective of clinical translation, we have further discussed the major possibilities provided by disease-oriented development of anti-cancer nanomaterials, highlighting the critical importance clinically-oriented system design.
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Affiliation(s)
- Jing Wang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center of Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, China
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing, China
| | - Yuliang Zhao
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center of Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, China
- GBA Research Innovation Institute for Nanotechnology, Guangzhou, Guangdong Province, China
| | - Guangjun Nie
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center of Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, China
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing, China
- GBA Research Innovation Institute for Nanotechnology, Guangzhou, Guangdong Province, China
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28
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Nagao M, Seto H. Neutron scattering studies on dynamics of lipid membranes. BIOPHYSICS REVIEWS 2023; 4:021306. [PMID: 38504928 PMCID: PMC10903442 DOI: 10.1063/5.0144544] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 05/01/2023] [Indexed: 03/21/2024]
Abstract
Neutron scattering methods are powerful tools for the study of the structure and dynamics of lipid bilayers in length scales from sub Å to tens to hundreds nm and the time scales from sub ps to μs. These techniques also are nondestructive and, perhaps most importantly, require no additives to label samples. Because the neutron scattering intensities are very different for hydrogen- and deuterium-containing molecules, one can replace the hydrogen atoms in a molecule with deuterium to prepare on demand neutron scattering contrast without significantly altering the physical properties of the samples. Moreover, recent advances in neutron scattering techniques, membrane dynamics theories, analysis tools, and sample preparation technologies allow researchers to study various aspects of lipid bilayer dynamics. In this review, we focus on the dynamics of individual lipids and collective membrane dynamics as well as the dynamics of hydration water.
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Affiliation(s)
| | - Hideki Seto
- Institute of Materials Structure Science, High Energy Accelerator Research Organization, Tsukuba, Ibaraki 305-0801, Japan
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Arnould B, Quillin AL, Heemstra JM. Tracking the Message: Applying Single Molecule Localization Microscopy to Cellular RNA Imaging. Chembiochem 2023; 24:e202300049. [PMID: 36857087 PMCID: PMC10192057 DOI: 10.1002/cbic.202300049] [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: 01/20/2023] [Revised: 02/28/2023] [Accepted: 03/01/2023] [Indexed: 03/02/2023]
Abstract
RNA function is increasingly appreciated to be more complex than merely communicating between DNA sequence and protein structure. RNA localization has emerged as a key contributor to the intricate roles RNA plays in the cell, and the link between dysregulated spatiotemporal localization and disease warrants an exploration beyond sequence and structure. However, the tools needed to visualize RNA with precise resolution are lacking in comparison to methods available for studying proteins. In the past decade, many techniques have been developed for imaging RNA, and in parallel super resolution and single-molecule techniques have enabled imaging of single molecules in cells. Of these methods, single molecule localization microscopy (SMLM) has shown significant promise for probing RNA localization. In this review, we highlight current approaches that allow super resolution imaging of specific RNA transcripts and summarize challenges and future opportunities for developing innovative RNA labeling methods that leverage the power of SMLM.
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Affiliation(s)
- Benoît Arnould
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Alexandria L Quillin
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Jennifer M Heemstra
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA
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Hugelier S, Kim H, Gyparaki MT, Bond C, Tang Q, Santiago-Ruiz AN, Porta S, Lakadamyali M. ECLiPSE: A Versatile Classification Technique for Structural and Morphological Analysis of Super-Resolution Microscopy Data. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.10.540077. [PMID: 37215010 PMCID: PMC10197633 DOI: 10.1101/2023.05.10.540077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
We introduce a new automated machine learning analysis pipeline to precisely classify cellular structures captured through single molecule localization microscopy, which we call ECLiPSE (Enhanced Classification of Localized Pointclouds by Shape Extraction). ECLiPSE leverages 67 comprehensive shape descriptors encompassing geometric, boundary, skeleton and other properties, the majority of which are directly extracted from the localizations to accurately characterize individual structures. We validate ECLiPSE through unsupervised and supervised classification on a dataset featuring five distinct cellular structures, achieving exceptionally high classification accuracies nearing 100%. Moreover, we demonstrate the versatility of our approach by applying it to two novel biological applications: quantifying the clearance of tau protein aggregates, a critical marker for neurodegenerative diseases, and differentiating between two distinct morphological features (morphotypes) of TAR DNA-binding protein 43 proteinopathy, potentially associated to different TDP-43 strains, each exhibiting unique seeding and spreading properties. We anticipate that this versatile approach will significantly enhance the way we study cellular structures across various biological contexts, elucidating their roles in disease development and progression.
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Abstract
Super-resolution fluorescence microscopy allows the investigation of cellular structures at nanoscale resolution using light. Current developments in super-resolution microscopy have focused on reliable quantification of the underlying biological data. In this review, we first describe the basic principles of super-resolution microscopy techniques such as stimulated emission depletion (STED) microscopy and single-molecule localization microscopy (SMLM), and then give a broad overview of methodological developments to quantify super-resolution data, particularly those geared toward SMLM data. We cover commonly used techniques such as spatial point pattern analysis, colocalization, and protein copy number quantification but also describe more advanced techniques such as structural modeling, single-particle tracking, and biosensing. Finally, we provide an outlook on exciting new research directions to which quantitative super-resolution microscopy might be applied.
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Affiliation(s)
- Siewert Hugelier
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA; , ,
| | - P L Colosi
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA; , ,
| | - Melike Lakadamyali
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA; , ,
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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Girard-Dias W, Augusto I, V. A. Fernandes T, G. Pascutti P, de Souza W, Miranda K. A spatially resolved elemental nanodomain organization within acidocalcisomes in Trypanosoma cruzi. Proc Natl Acad Sci U S A 2023; 120:e2300942120. [PMID: 37036984 PMCID: PMC10120040 DOI: 10.1073/pnas.2300942120] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 03/06/2023] [Indexed: 04/12/2023] Open
Abstract
How are ions distributed in the three-dimensional (3D) volume confined in a nanoscale compartment? Regulation of ionic flow in the intracellular milieu has been explained by different theoretical models and experimentally demonstrated for several compartments with microscale dimensions. Most of these models predict a homogeneous distribution of ions seconds or milliseconds after an initial diffusion step formed at the ion translocation site, leaving open questions when it comes to ion/element distribution in spaces/compartments with nanoscale dimensions. Due to the influence of compartment size on the regulation of ionic flow, theoretical variations of classical models have been proposed, suggesting heterogeneous distributions of ions/elements within nanoscale compartments. Nonetheless, such assumptions have not been fully proven for the 3D volume of an organelle. In this work, we used a combination of cutting-edge electron microscopy techniques to map the 3D distribution of diffusible elements within the whole volume of acidocalcisomes in trypanosomes. Cryofixed cells were analyzed by scanning transmission electron microscopy tomography combined with elemental mapping using a high-performance setup of X-ray detectors. Results showed the existence of elemental nanodomains within the acidocalcisomes, where cationic elements display a self-excluding pattern. These were validated by Pearson correlation analysis and in silico molecular dynamic simulations. Formation of element domains within the 3D space of an organelle is demonstrated. Distribution patterns that support the electrodiffusion theory proposed for nanophysiology models have been found. The experimental pipeline shown here can be applied to a variety of models where ion mobilization plays a crucial role in physiological processes.
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Affiliation(s)
- Wendell Girard-Dias
- Laboratório de Ultraestrutura Celular Hertha Meyer, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro21941-902, Brazil
- Centro Nacional de Biologia Estrutural e Bioimagem, Universidade Federal do Rio de Janeiro, Rio de Janeiro21941-902, Brazil
- Instituto Nacional de Ciência e Tecnologia em Biologia Estrutural e Bioimagem - Universidade Federal do Rio de Janeiro, Rio de Janeiro21941-902, Brazil
- Plataforma de Microscopia Eletrônica Rudolf Barth, Instituto Oswaldo Cruz - Fiocruz, Rio de Janeiro21041-250, Brazil
| | - Ingrid Augusto
- Laboratório de Ultraestrutura Celular Hertha Meyer, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro21941-902, Brazil
- Centro Nacional de Biologia Estrutural e Bioimagem, Universidade Federal do Rio de Janeiro, Rio de Janeiro21941-902, Brazil
- Instituto Nacional de Ciência e Tecnologia em Biologia Estrutural e Bioimagem - Universidade Federal do Rio de Janeiro, Rio de Janeiro21941-902, Brazil
| | - Tácio V. A. Fernandes
- Laboratório de Modelagem e Dinâmica Molecular, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro21941-902, Brazil
- Instituto de Tecnologia de Fármacos (Farmanguinhos), Fiocruz, Rio de Janeiro22775-903, Brazil
| | - Pedro G. Pascutti
- Laboratório de Modelagem e Dinâmica Molecular, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro21941-902, Brazil
| | - Wanderley de Souza
- Laboratório de Ultraestrutura Celular Hertha Meyer, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro21941-902, Brazil
- Centro Nacional de Biologia Estrutural e Bioimagem, Universidade Federal do Rio de Janeiro, Rio de Janeiro21941-902, Brazil
- Instituto Nacional de Ciência e Tecnologia em Biologia Estrutural e Bioimagem - Universidade Federal do Rio de Janeiro, Rio de Janeiro21941-902, Brazil
- Centro Multiusuário para Análise de Fenômenos Biomédicos, Universidade do Estado do Amazonas, Amazonas69065-001, Brazil
| | - Kildare Miranda
- Laboratório de Ultraestrutura Celular Hertha Meyer, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro21941-902, Brazil
- Centro Nacional de Biologia Estrutural e Bioimagem, Universidade Federal do Rio de Janeiro, Rio de Janeiro21941-902, Brazil
- Instituto Nacional de Ciência e Tecnologia em Biologia Estrutural e Bioimagem - Universidade Federal do Rio de Janeiro, Rio de Janeiro21941-902, Brazil
- Centro Multiusuário para Análise de Fenômenos Biomédicos, Universidade do Estado do Amazonas, Amazonas69065-001, Brazil
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Kylies D, Zimmermann M, Haas F, Schwerk M, Kuehl M, Brehler M, Czogalla J, Hernandez LC, Konczalla L, Okabayashi Y, Menzel J, Edenhofer I, Mezher S, Aypek H, Dumoulin B, Wu H, Hofmann S, Kretz O, Wanner N, Tomas NM, Krasemann S, Glatzel M, Kuppe C, Kramann R, Banjanin B, Schneider RK, Urbschat C, Arck P, Gagliani N, van Zandvoort M, Wiech T, Grahammer F, Sáez PJ, Wong MN, Bonn S, Huber TB, Puelles VG. Expansion-enhanced super-resolution radial fluctuations enable nanoscale molecular profiling of pathology specimens. NATURE NANOTECHNOLOGY 2023; 18:336-342. [PMID: 37037895 PMCID: PMC10115634 DOI: 10.1038/s41565-023-01328-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 01/13/2023] [Indexed: 06/19/2023]
Abstract
Expansion microscopy physically enlarges biological specimens to achieve nanoscale resolution using diffraction-limited microscopy systems1. However, optimal performance is usually reached using laser-based systems (for example, confocal microscopy), restricting its broad applicability in clinical pathology, as most centres have access only to light-emitting diode (LED)-based widefield systems. As a possible alternative, a computational method for image resolution enhancement, namely, super-resolution radial fluctuations (SRRF)2,3, has recently been developed. However, this method has not been explored in pathology specimens to date, because on its own, it does not achieve sufficient resolution for routine clinical use. Here, we report expansion-enhanced super-resolution radial fluctuations (ExSRRF), a simple, robust, scalable and accessible workflow that provides a resolution of up to 25 nm using LED-based widefield microscopy. ExSRRF enables molecular profiling of subcellular structures from archival formalin-fixed paraffin-embedded tissues in complex clinical and experimental specimens, including ischaemic, degenerative, neoplastic, genetic and immune-mediated disorders. Furthermore, as examples of its potential application to experimental and clinical pathology, we show that ExSRRF can be used to identify and quantify classical features of endoplasmic reticulum stress in the murine ischaemic kidney and diagnostic ultrastructural features in human kidney biopsies.
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Affiliation(s)
- Dominik Kylies
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Research Center On Rare Kidney Diseases (RECORD), University Hospital Erlangen, Erlangen, Germany
| | - Marina Zimmermann
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Institute of Medical Systems Biology, Center for Biomedical AI (bAIome), Center for Molecular Neurobiology Hamburg (ZMNH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Fabian Haas
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Maria Schwerk
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Malte Kuehl
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Institute of Medical Systems Biology, Center for Biomedical AI (bAIome), Center for Molecular Neurobiology Hamburg (ZMNH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Michael Brehler
- Institute of Medical Systems Biology, Center for Biomedical AI (bAIome), Center for Molecular Neurobiology Hamburg (ZMNH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Jan Czogalla
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Lola C Hernandez
- Cell Communication and Migration Laboratory, Department of Biochemistry and Molecular Cell Biology (IBMZ), Center for Experimental Medicine, Hamburg, Germany
| | - Leonie Konczalla
- Department of General, Visceral and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Mildred Scheel Cancer Career Center HaTriCS4, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Yusuke Okabayashi
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Division of Nephrology and Hypertension, Department of Internal Medicine, The Jikei University School of Medicine, Tokyo, Japan
| | | | - Ilka Edenhofer
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Sam Mezher
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Hande Aypek
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Bernhard Dumoulin
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Hui Wu
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Smilla Hofmann
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Oliver Kretz
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Nicola Wanner
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Nicola M Tomas
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Susanne Krasemann
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Markus Glatzel
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Christoph Kuppe
- Institute of Experimental Medicine and Systems Biology and Division of Nephrology and Clinical Immunology, RWTH Aachen University Medical Faculty, Aachen, Germany
| | - Rafael Kramann
- Institute of Experimental Medicine and Systems Biology and Division of Nephrology and Clinical Immunology, RWTH Aachen University Medical Faculty, Aachen, Germany
| | - Bella Banjanin
- Department of Developmental Biology, Erasmus Medical Center, Rotterdam, The Netherlands
- Oncode Institute, Erasmus Medical Center Cancer Institute, Rotterdam, The Netherlands
| | - Rebekka K Schneider
- Department of Developmental Biology, Erasmus Medical Center, Rotterdam, The Netherlands
- Oncode Institute, Erasmus Medical Center Cancer Institute, Rotterdam, The Netherlands
- Institute for Cell and Tumor Biology, RWTH Aachen University, Aachen, Germany
| | - Christopher Urbschat
- Department of Obstetrics and Fetal Medicine, Division of Experimental Feto-Maternal Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Petra Arck
- Department of Obstetrics and Fetal Medicine, Division of Experimental Feto-Maternal Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Nicola Gagliani
- Department of General, Visceral and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- I. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Marc van Zandvoort
- Department of Genetics and Cell Biology, Maastricht University, School for Oncology and Reproduction GROW, School for Mental Health and Neuroscience MHeNS, and School for Cardiovascular Diseases CARIM, Maastricht University, Maastricht, The Netherlands
- Institute for Molecular Cardiovascular Research (IMCAR), RWTH Aachen University, Aachen, Germany
| | - Thorsten Wiech
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Florian Grahammer
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Pablo J Sáez
- Cell Communication and Migration Laboratory, Department of Biochemistry and Molecular Cell Biology (IBMZ), Center for Experimental Medicine, Hamburg, Germany
| | - Milagros N Wong
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Department of Pathology, Aarhus University Hospital, Aarhus, Denmark
| | - Stefan Bonn
- Institute of Medical Systems Biology, Center for Biomedical AI (bAIome), Center for Molecular Neurobiology Hamburg (ZMNH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Tobias B Huber
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Victor G Puelles
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
- Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark.
- Department of Pathology, Aarhus University Hospital, Aarhus, Denmark.
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Burgers TCQ, Vlijm R. Fluorescence-based super-resolution-microscopy strategies for chromatin studies. Chromosoma 2023:10.1007/s00412-023-00792-9. [PMID: 37000292 PMCID: PMC10356683 DOI: 10.1007/s00412-023-00792-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 02/28/2023] [Accepted: 03/16/2023] [Indexed: 04/01/2023]
Abstract
Super-resolution microscopy (SRM) is a prime tool to study chromatin organisation at near biomolecular resolution in the native cellular environment. With fluorescent labels DNA, chromatin-associated proteins and specific epigenetic states can be identified with high molecular specificity. The aim of this review is to introduce the field of diffraction-unlimited SRM to enable an informed selection of the most suitable SRM method for a specific chromatin-related research question. We will explain both diffraction-unlimited approaches (coordinate-targeted and stochastic-localisation-based) and list their characteristic spatio-temporal resolutions, live-cell compatibility, image-processing, and ability for multi-colour imaging. As the increase in resolution, compared to, e.g. confocal microscopy, leads to a central role of the sample quality, important considerations for sample preparation and concrete examples of labelling strategies applicable to chromatin research are discussed. To illustrate how SRM-based methods can significantly improve our understanding of chromatin functioning, and to serve as an inspiring starting point for future work, we conclude with examples of recent applications of SRM in chromatin research.
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Affiliation(s)
- Thomas C Q Burgers
- Molecular Biophysics, Zernike Institute for Advanced Materials, Rijksuniversiteit Groningen, Groningen, the Netherlands
| | - Rifka Vlijm
- Molecular Biophysics, Zernike Institute for Advanced Materials, Rijksuniversiteit Groningen, Groningen, the Netherlands.
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Marin Z, Fuentes LA, Bewersdorf J, Baddeley D. Extracting nanoscale membrane morphology from single-molecule localizations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.26.525798. [PMID: 36945449 PMCID: PMC10028748 DOI: 10.1101/2023.01.26.525798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Membrane surface reconstruction at the nanometer scale is required for understanding mechanisms of subcellular shape change. This historically has been the domain of electron microscopy, but extraction of surfaces from specific labels is a difficult task in this imaging modality. Existing methods for extracting surfaces from fluorescence microscopy have poor resolution or require high-quality super-resolution data that is manually cleaned and curated. Here we present a new method for extracting surfaces from generalized single-molecule localization microscopy (SMLM) data. This makes it possible to study the shape of specifically-labelled membraneous structures inside of cells. We validate our method using simulations and demonstrate its reconstruction capabilities on SMLM data of the endoplasmic reticulum and mitochondria. Our method is implemented in the open-source Python Microscopy Environment. SIGNIFICANCE We introduce a novel tool for reconstruction of subcellular membrane surfaces from single-molecule localization microscopy data and use it to visualize and quantify local shape and membrane-membrane interactions. We benchmark its performance on simulated data and demonstrate its fidelity to experimental data.
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Vanslembrouck B, Chen JH, Larabell C, van Hengel J. Microscopic Visualization of Cell-Cell Adhesion Complexes at Micro and Nanoscale. Front Cell Dev Biol 2022; 10:819534. [PMID: 35517500 PMCID: PMC9065677 DOI: 10.3389/fcell.2022.819534] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Accepted: 03/21/2022] [Indexed: 12/25/2022] Open
Abstract
Considerable progress has been made in our knowledge of the morphological and functional varieties of anchoring junctions. Cell-cell adhesion contacts consist of discrete junctional structures responsible for the mechanical coupling of cytoskeletons and allow the transmission of mechanical signals across the cell collective. The three main adhesion complexes are adherens junctions, tight junctions, and desmosomes. Microscopy has played a fundamental role in understanding these adhesion complexes on different levels in both physiological and pathological conditions. In this review, we discuss the main light and electron microscopy techniques used to unravel the structure and composition of the three cell-cell contacts in epithelial and endothelial cells. It functions as a guide to pick the appropriate imaging technique(s) for the adhesion complexes of interest. We also point out the latest techniques that have emerged. At the end, we discuss the problems investigators encounter during their cell-cell adhesion research using microscopic techniques.
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Affiliation(s)
- Bieke Vanslembrouck
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
- Department of Anatomy, University of San Francisco, San Francisco, CA, United States
- *Correspondence: Bieke Vanslembrouck, ; Jolanda van Hengel,
| | - Jian-hua Chen
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
- Department of Anatomy, University of San Francisco, San Francisco, CA, United States
| | - Carolyn Larabell
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
- Department of Anatomy, University of San Francisco, San Francisco, CA, United States
| | - Jolanda van Hengel
- Medical Cell Biology Research Group, Department of Human Structure and Repair, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
- *Correspondence: Bieke Vanslembrouck, ; Jolanda van Hengel,
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Prakash K, Diederich B, Heintzmann R, Schermelleh L. Super-resolution microscopy: a brief history and new avenues. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2022; 380:20210110. [PMID: 35152764 PMCID: PMC8841785 DOI: 10.1098/rsta.2021.0110] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 01/18/2022] [Indexed: 05/03/2023]
Abstract
Super-resolution microscopy (SRM) is a fast-developing field that encompasses fluorescence imaging techniques with the capability to resolve objects below the classical diffraction limit of optical resolution. Acknowledged with the Nobel prize in 2014, numerous SRM methods have meanwhile evolved and are being widely applied in biomedical research, all with specific strengths and shortcomings. While some techniques are capable of nanometre-scale molecular resolution, others are geared towards volumetric three-dimensional multi-colour or fast live-cell imaging. In this editorial review, we pick on the latest trends in the field. We start with a brief historical overview of both conceptual and commercial developments. Next, we highlight important parameters for imaging successfully with a particular super-resolution modality. Finally, we discuss the importance of reproducibility and quality control and the significance of open-source tools in microscopy. This article is part of the Theo Murphy meeting issue 'Super-resolution structured illumination microscopy (part 2)'.
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Affiliation(s)
- Kirti Prakash
- Integrated Pathology Unit, Centre for Molecular Pathology, The Royal Marsden Trust and Institute of Cancer Research, Sutton SM2 5NG, UK
| | - Benedict Diederich
- Leibniz Institute for Photonic Technology, Albert-Einstein-Strasse 9, 07745 Jena, Germany
| | - Rainer Heintzmann
- Leibniz Institute for Photonic Technology, Albert-Einstein-Strasse 9, 07745 Jena, Germany
- Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich-Schiller-University, Helmholtzweg 4, 07743 Jena, Germany
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