1
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Illand A, Jouchet P, Fort E, Lévêque-Fort S. Flexible implementation of modulated localisation microscopy based on DMD. J Microsc 2024; 295:21-32. [PMID: 38353429 DOI: 10.1111/jmi.13274] [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: 12/03/2023] [Revised: 01/25/2024] [Accepted: 01/25/2024] [Indexed: 06/19/2024]
Abstract
Localisation microscopy of individual molecules allows one to bypass the diffraction limit, revealing cellular organisation on a nanometric scale. This method, which relies on spatial analysis of the signal emitted by molecules, is often limited to the observation of biological objects at shallow depths, or with very few aberrations. The introduction of a temporal parameter into the localisation process through a time-modulated excitation was recently proposed to address these limitations. This method, called ModLoc, is demonstrated here with an alternative flexible strategy. In this implementation, to encode the time-modulated excitation a digital micromirror device (DMD) is used in combination with a fast demodulation approach, and provides a twofold enhancement in localisation precision. Layout: Nowadays, we can use an optical microscope to observe how proteins are organised in 3D within a cell at the nanoscale. By carefully controlling the emission of molecules in both space and time, we can overcome the limitations set by the diffraction limit. This allows us to pinpoint the exact location of molecules more precisely. However, the usual spatial analysis method limits observations to shallow depths or causing low distortion of optical waves. To overcome these restrictions, a recent approach introduces a temporal element to the localisation process. This involves changing the illumination over time to enhance the precision of localisation. This method, known as ModLoc, is showcased here using a flexible and alternative strategy. In this setup, a matrix of micrometric mirrors, working together with a fast demodulation optical module, is used to encode and decode the time-modulated information. This combination results in a twofold improvement in localisation precision.
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Affiliation(s)
- Abigail Illand
- Institut des Sciences Moléculaires d'Orsay, Université Paris Saclay, CNRS UMR8214, Orsay, France
| | - Pierre Jouchet
- Institut des Sciences Moléculaires d'Orsay, Université Paris Saclay, CNRS UMR8214, Orsay, France
| | - Emmanuel Fort
- Institut Langevin, ESPCI Paris, Université PSL, CNRS, Paris, France
| | - Sandrine Lévêque-Fort
- Institut des Sciences Moléculaires d'Orsay, Université Paris Saclay, CNRS UMR8214, Orsay, France
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2
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Lujan P, Garcia-Cabau C, Wakana Y, Vera Lillo J, Rodilla-Ramírez C, Sugiura H, Malhotra V, Salvatella X, Garcia-Parajo MF, Campelo F. Sorting of secretory proteins at the trans-Golgi network by human TGN46. eLife 2024; 12:RP91708. [PMID: 38466628 DOI: 10.7554/elife.91708] [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] [Indexed: 03/13/2024] Open
Abstract
Secretory proteins are sorted at the trans-Golgi network (TGN) for export into specific transport carriers. However, the molecular players involved in this fundamental process remain largely elusive. Here, we identified the human transmembrane protein TGN46 as a receptor for the export of secretory cargo protein PAUF in CARTS - a class of protein kinase D-dependent TGN-to-plasma membrane carriers. We show that TGN46 is necessary for cargo sorting and loading into nascent carriers at the TGN. By combining quantitative fluorescence microscopy and mutagenesis approaches, we further discovered that the lumenal domain of TGN46 encodes for its cargo sorting function. In summary, our results define a cellular function of TGN46 in sorting secretory proteins for export from the TGN.
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Affiliation(s)
- Pablo Lujan
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Carla Garcia-Cabau
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Yuichi Wakana
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Tokyo, Japan
| | - Javier Vera Lillo
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Carmen Rodilla-Ramírez
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Hideaki Sugiura
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Tokyo, Japan
| | - Vivek Malhotra
- Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Xavier Salvatella
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Maria F Garcia-Parajo
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Felix Campelo
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, Barcelona, Spain
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3
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Seabury AG, Khodabocus AJ, Kogan IM, Hoy GR, DeSalvo GA, Wustholz KL. Blinking characteristics of organic fluorophores for blink-based multiplexing. Commun Chem 2024; 7:18. [PMID: 38280979 PMCID: PMC10821931 DOI: 10.1038/s42004-024-01106-5] [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: 09/20/2023] [Accepted: 01/12/2024] [Indexed: 01/29/2024] Open
Abstract
Single-molecule fluorescence experiments have transformed our understanding of complex materials and biological systems. Whether single molecules are used to report on their nano-environment or provide for localization, understanding their blinking dynamics (i.e., stochastic fluctuations in emission intensity under continuous illumination) is paramount. We recently demonstrated another use for blinking dynamics called blink-based multiplexing (BBM), where individual emitters are classified using a single excitation laser based on blinking dynamics, rather than color. This study elucidates the structure-activity relationships governing BBM performance in a series of model rhodamine, BODIPY, and anthraquinone fluorophores that undergo different photo-physical and-chemical processes during blinking. Change point detection and multinomial logistic regression analyses show that BBM can leverage spectral fluctuations, electron and proton transfer kinetics, as well as photostability for molecular classification-even within the context of a shared blinking mechanism. In doing so, we demonstrate two- and three-color BBM with ≥ 93% accuracy using spectrally-overlapped fluorophores.
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Affiliation(s)
| | | | | | - Grayson R Hoy
- Chemistry Department, William & Mary, Williamsburg, VA, USA
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4
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Zhang YP, Lobanova E, Emin D, Lobanov SV, Kouli A, Williams-Gray CH, Klenerman D. Imaging Protein Aggregates in Parkinson's Disease Serum Using Aptamer-Assisted Single-Molecule Pull-Down. Anal Chem 2023; 95:15254-15263. [PMID: 37782556 PMCID: PMC10585954 DOI: 10.1021/acs.analchem.3c02515] [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: 06/10/2023] [Accepted: 09/18/2023] [Indexed: 10/04/2023]
Abstract
The formation of soluble α-synuclein (α-syn) and amyloid-β (Aβ) aggregates is associated with the development of Parkinson's disease (PD). Current methods mainly focus on the measurement of the aggregate concentration and are unable to determine their heterogeneous size and shape, which potentially also change during the development of PD due to increased protein aggregation. In this work, we introduce aptamer-assisted single-molecule pull-down (APSiMPull) combined with super-resolution fluorescence imaging of α-syn and Aβ aggregates in human serum from early PD patients and age-matched controls. Our diffraction-limited imaging results indicate that the proportion of α-syn aggregates (α-syn/(α-syn+Aβ)) can be used to distinguish PD and control groups with an area under the curve (AUC) of 0.85. Further, super resolution fluorescence imaging reveals that PD serums have a higher portion of larger and rounder α-syn aggregates than controls. Little difference was observed for Aβ aggregates. Combining these two metrics, we constructed a new biomarker and achieved an AUC of 0.90. The combination of the aggregate number and morphology provides a new approach to early PD diagnosis.
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Affiliation(s)
- Yu P. Zhang
- Department
of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
- UK
Dementia Research Institute at Cambridge, Cambridge CB2 0XY, United Kingdom
| | - Evgeniia Lobanova
- Department
of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
- UK
Dementia Research Institute at Cambridge, Cambridge CB2 0XY, United Kingdom
| | - Derya Emin
- Department
of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
- UK
Dementia Research Institute at Cambridge, Cambridge CB2 0XY, United Kingdom
| | - Sergey V. Lobanov
- Medical
Research Council Centre for Neuropsychiatric Genetics and Genomics, Cardiff University, Cardiff CF24 4HQ, United Kingdom
| | - Antonina Kouli
- Department
of Clinical Neurosciences, University of
Cambridge, Cambridge CB2 0PY, United Kingdom
| | | | - David Klenerman
- Department
of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
- UK
Dementia Research Institute at Cambridge, Cambridge CB2 0XY, United Kingdom
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5
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Feng J, Yao Y, Wang Q, Han X, Deng X, Cao Y, Chen X, Zhou M, Zhao C. Exosomes: Potential key players towards novel therapeutic options in diabetic wounds. Biomed Pharmacother 2023; 166:115297. [PMID: 37562235 DOI: 10.1016/j.biopha.2023.115297] [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: 06/08/2023] [Revised: 07/31/2023] [Accepted: 08/05/2023] [Indexed: 08/12/2023] Open
Abstract
Diabetic wounds are usually difficult to heal, and wounds in foot in particular are often aggravated by infection, trauma, diabetic neuropathy, peripheral vascular disease and other factors, resulting in serious foot ulcers. The pathogenesis and clinical manifestations of diabetic wounds are complicated, and there is still a lack of objective and in-depth laboratory diagnosis and classification standards. Exosomes are nanoscale vesicles containing DNA, mRNA, microRNA, cyclic RNA, metabolites, lipids, cytoplasm and cell surface proteins, etc., which are involved in intercellular communication and play a crucial role in vascular regeneration, tissue repair and inflammation regulation in the process of diabetic wound healing. Here, we discussed exosomes of different cellular origins, such as diabetic wound-related fibroblasts (DWAF), adipose stem cells (ASCs), mesenchymal stem cells (MSCs), immune cells, platelets, human amniotic epithelial cells (hAECs), epidermal stem cells (ESCs), and their various molecular components. They exhibit multiple therapeutic effects during diabetic wound healing, including promoting cell proliferation and migration associated with wound healing, regulating macrophage polarization to inhibit inflammatory responses, promoting nerve repair, and promoting vascular renewal and accelerating wound vascularization. In addition, exosomes can be designed to deliver different therapeutic loads and have the ability to deliver them to the desired target. Therefore, exosomes may become an innovative target for precision therapeutics in diabetic wounds. In this review, we summarize the latest research on the role of exosomes in the healing of diabetic wound by regulating the pathogenesis of diabetic wounds, and discuss their potential applications in the precision treatment of diabetic wounds.
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Affiliation(s)
- Jiawei Feng
- Shanghai Traditional Chinese Medicine Integrated Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200082, China
| | - Yichen Yao
- Institute for Interdisciplinary Medicine Sciences, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China; School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Qixue Wang
- Institute for Interdisciplinary Medicine Sciences, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Xiaozhou Han
- Shanghai Traditional Chinese Medicine Integrated Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200082, China
| | - Xiaofei Deng
- Shanghai Traditional Chinese Medicine Integrated Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200082, China
| | - Yemin Cao
- Shanghai Traditional Chinese Medicine Integrated Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200082, China
| | - Xinghua Chen
- Jinshan Hospital Afflicted to Fudan University, Shanghai, China.
| | - Mingmei Zhou
- Institute for Interdisciplinary Medicine Sciences, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China.
| | - Cheng Zhao
- Shanghai Traditional Chinese Medicine Integrated Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200082, China.
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6
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Cosma MP, Neguembor MV. The magic of unraveling genome architecture and function. Cell Rep 2023; 42:112361. [PMID: 37059093 DOI: 10.1016/j.celrep.2023.112361] [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: 12/06/2022] [Revised: 02/20/2023] [Accepted: 03/22/2023] [Indexed: 04/16/2023] Open
Abstract
Over the last decades, technological breakthroughs in super-resolution microscopy have allowed us to reach molecular resolution and design experiments of unprecedented complexity. Investigating how chromatin is folded in 3D, from the nucleosome level up to the entire genome, is becoming possible by "magic" (imaging genomic), i.e., the combination of imaging and genomic approaches. This offers endless opportunities to delve into the relationship between genome structure and function. Here, we review recently achieved objectives and the conceptual and technical challenges the field of genome architecture is currently undertaking. We discuss what we have learned so far and where we are heading. We elucidate how the different super-resolution microscopy approaches and, more specifically, live-cell imaging have contributed to the understanding of genome folding. Moreover, we discuss how future technical developments could address remaining open questions.
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Affiliation(s)
- Maria Pia Cosma
- Medical Research Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, 106 Zhongshan Er Road, Yuexiu District, 510080 Guangzhou, China; Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Dr Aiguader 88, 08003 Barcelona, Spain; ICREA, Pg. Lluís Companys 23, 08010 Barcelona, Spain.
| | - Maria Victoria Neguembor
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain.
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7
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Yang Y, Xie Y, Zhang F. Second near-infrared window fluorescence nanoprobes for deep-tissue in vivo multiplexed bioimaging. Adv Drug Deliv Rev 2023; 193:114697. [PMID: 36641080 DOI: 10.1016/j.addr.2023.114697] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 12/25/2022] [Accepted: 01/09/2023] [Indexed: 01/13/2023]
Abstract
In vivo multiplexed bioimaging in the second near-infrared window (NIR-II, 1000-1700 nm), owing to its superiorities of simultaneous multi-channel (multicolor) observations for multiple intrinsic biomarkers, high sensitivity, deeper penetration and high spatiotemporal resolution, and high throughput, has been a growing technology in fundamental medical diagnosis and clinical applications. Among several NIR-II nanoprobes for multiplexed bioimaging, the inorganic nanoprobes based on quantum dots (QDs) and lanthanide downconversion nanoparticles (DCNPs), as well as organic fluorophores based on donor-acceptor-donor (D-A-D) chromophores, polymethine dyes, and lanthanide complexes are extensively suitable for intravital imaging and diagnosis of disease, exhibiting excellent accomplishments. Here, we summarize recent advances in NIR-II-emitted nanoprobes for intravital multiplexed bioimaging. Furthermore, the current challenges and potential opportunities in designing novel long-wavelength nanoprobes for deep-tissue intravital multiplexed bioimaging are discussed.
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Affiliation(s)
- Yanling Yang
- State Key Laboratory of Analytical Chemistry for Life Science, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023 China
| | - Yang Xie
- Department of Orthopaedic Surgery, Changhai Hospital, Second Military Medical University, Shanghai 200433, China.
| | - Fan Zhang
- Department of Chemistry, State Key Laboratory of Molecular Engineering of Polymers and iChem, Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Fudan University, Shanghai 200433 China; College of Energy Materials and Chemistry, Inner Mongolia University, Hohhot 010021, China.
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8
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Wu W, Luo S, Fan C, Yang T, Zhang S, Meng W, Xu T, Ji W, Gu L. Tetra-color superresolution microscopy based on excitation spectral demixing. LIGHT, SCIENCE & APPLICATIONS 2023; 12:9. [PMID: 36588110 PMCID: PMC9806106 DOI: 10.1038/s41377-022-01054-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 11/29/2022] [Accepted: 12/02/2022] [Indexed: 05/09/2023]
Abstract
Multicolor imaging allows protein colocalizations and organelle interactions to be studied in biological research, which is especially important for single-molecule localization microscopy (SMLM). Here, we propose a multicolor method called excitation-resolved stochastic optical reconstruction microscopy (ExR-STORM). The method, which is based on the excitation spectrum of fluorescent dyes, successfully separated four spectrally very close far-red organic fluorophores utilizing three excitation lasers with cross-talk of less than 3%. Dyes that are only 5 nm apart in the emission spectrum were resolved, resulting in negligible chromatic aberrations. This method was extended to three-dimensional (3D) imaging by combining the astigmatic method, providing a powerful tool for resolving 3D morphologies at the nanoscale.
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Affiliation(s)
- Wanyan Wu
- Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
- College of Life Science, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shihang Luo
- Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
- College of Life Science, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chunyan Fan
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Tianjie Yang
- Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
- School of Future Technology, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shuwen Zhang
- Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Wenxiang Meng
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Tao Xu
- Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.
- College of Life Science, University of Chinese Academy of Sciences, Beijing, 100049, China.
- School of Future Technology, University of Chinese Academy of Sciences, Beijing, 100049, China.
- Bioland Laboratory, Guangzhou, 510005, China.
- Guangzhou Laboratory, Guangzhou, 510030, China.
| | - Wei Ji
- Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.
- College of Life Science, University of Chinese Academy of Sciences, Beijing, 100049, China.
- Bioland Laboratory, Guangzhou, 510005, China.
| | - Lusheng Gu
- Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.
- College of Life Science, University of Chinese Academy of Sciences, Beijing, 100049, China.
- Bioland Laboratory, Guangzhou, 510005, China.
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9
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Golmohammadzadeh M, Sexton DL, Parmar S, Tocheva EI. Advanced imaging techniques: Microscopy. ADVANCES IN APPLIED MICROBIOLOGY 2023; 122:1-25. [PMID: 37085191 DOI: 10.1016/bs.aambs.2023.01.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/02/2023]
Abstract
For decades, bacteria were thought of as "bags" of enzymes, lacking organelles and significant subcellular structures. This stood in sharp contrast with eukaryotes, where intracellular compartmentalization and the role of large-scale order had been known for a long time. However, the emerging field of Bacterial Cell Biology has established that bacteria are in fact highly organized, with most macromolecular components having specific subcellular locations that can change depending on the cell's physiological state (Barry & Gitai, 2011; Lenz & Søgaard-Andersen, 2011; Thanbichler & Shapiro, 2008). For example, we now know that many processes in bacteria are orchestrated by cytoskeletal proteins, which polymerize into surprisingly diverse superstructures, such as rings, sheets, and tread-milling rods (Pilhofer & Jensen, 2013). These superstructures connect individual proteins, macromolecular assemblies, and even two neighboring cells, to affect essential higher-order processes including cell division, DNA segregation, and motility. Understanding these processes requires resolving the in vivo dynamics and ultrastructure at different functional stages of the cell, at macromolecular resolution and in 3-dimensions (3D). Fluorescence light microscopy (fLM) of tagged proteins is highly valuable for investigating protein localization and dynamics, and the resolution power of transmission electron microscopy (TEM) is required to elucidate the structure of macromolecular complexes in vivo and in vitro. This chapter summarizes the most recent advances in LM and TEM approaches that have revolutionized our knowledge and understanding of the microbial world.
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Affiliation(s)
- Mona Golmohammadzadeh
- Department of Microbiology and Immunology, Life Sciences Institute, Health Sciences Mall, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Danielle L Sexton
- Department of Microbiology and Immunology, Life Sciences Institute, Health Sciences Mall, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Shweta Parmar
- Department of Microbiology and Immunology, Life Sciences Institute, Health Sciences Mall, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Elitza I Tocheva
- Department of Microbiology and Immunology, Life Sciences Institute, Health Sciences Mall, The University of British Columbia, Vancouver, British Columbia, Canada.
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10
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Shahhosseini M, Beshay PE, Akbari E, Roki N, Lucas CR, Avendano A, Song JW, Castro CE. Multiplexed Detection of Molecular Interactions with DNA Origami Engineered Cells in 3D Collagen Matrices. ACS APPLIED MATERIALS & INTERFACES 2022; 14:55307-55319. [PMID: 36509424 PMCID: PMC9785045 DOI: 10.1021/acsami.2c07971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 09/29/2022] [Indexed: 06/17/2023]
Abstract
The interactions of cells with signaling molecules present in their local microenvironment maintain cell proliferation, differentiation, and spatial organization and mediate progression of diseases such as metabolic disorders and cancer. Real-time monitoring of the interactions between cells and their extracellular ligands in a three-dimensional (3D) microenvironment can inform detection and understanding of cell processes and the development of effective therapeutic agents. DNA origami technology allows for the design and fabrication of biocompatible and 3D functional nanodevices via molecular self-assembly for various applications including molecular sensing. Here, we report a robust method to monitor live cell interactions with molecules in their surrounding environment in a 3D tissue model using a microfluidic device. We used a DNA origami cell sensing platform (CSP) to detect two specific nucleic acid sequences on the membrane of B cells and dendritic cells. We further demonstrated real-time detection of biomolecules with the DNA sensing platform on the surface of dendritic cells in a 3D microfluidic tissue model. Our results establish the integration of live cells with membranes engineered with DNA nanodevices into microfluidic chips as a highly capable biosensor approach to investigate subcellular interactions in physiologically relevant 3D environments under controlled biomolecular transport.
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Affiliation(s)
- Melika Shahhosseini
- Department
of Mechanical and Aerospace Engineering, The Ohio State University, 201 West 19th Avenue, Columbus, Ohio 43210, United States
| | - Peter E. Beshay
- Department
of Mechanical and Aerospace Engineering, The Ohio State University, 201 West 19th Avenue, Columbus, Ohio 43210, United States
| | - Ehsan Akbari
- Biophysics
Graduate Program, The Ohio State University, Columbus, Ohio 43210, United States
| | - Niksa Roki
- Department
of Mechanical and Aerospace Engineering, The Ohio State University, 201 West 19th Avenue, Columbus, Ohio 43210, United States
- Comprehensive
Cancer Center, The Ohio State University, Columbus, Ohio 43210 United States
| | - Christopher R. Lucas
- Department
of Mechanical and Aerospace Engineering, The Ohio State University, 201 West 19th Avenue, Columbus, Ohio 43210, United States
- Comprehensive
Cancer Center, The Ohio State University, Columbus, Ohio 43210 United States
| | - Alex Avendano
- Department
of Biomedical Engineering, The Ohio State
University, Columbus, Ohio 43210, United States
| | - Jonathan W. Song
- Department
of Mechanical and Aerospace Engineering, The Ohio State University, 201 West 19th Avenue, Columbus, Ohio 43210, United States
- Comprehensive
Cancer Center, The Ohio State University, Columbus, Ohio 43210 United States
| | - Carlos E. Castro
- Department
of Mechanical and Aerospace Engineering, The Ohio State University, 201 West 19th Avenue, Columbus, Ohio 43210, United States
- Biophysics
Graduate Program, The Ohio State University, Columbus, Ohio 43210, United States
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11
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Neguembor MV, Arcon JP, Buitrago D, Lema R, Walther J, Garate X, Martin L, Romero P, AlHaj Abed J, Gut M, Blanc J, Lakadamyali M, Wu CT, Brun Heath I, Orozco M, Dans PD, Cosma MP. MiOS, an integrated imaging and computational strategy to model gene folding with nucleosome resolution. Nat Struct Mol Biol 2022; 29:1011-1023. [PMID: 36220894 PMCID: PMC9627188 DOI: 10.1038/s41594-022-00839-y] [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: 01/31/2022] [Accepted: 08/23/2022] [Indexed: 11/06/2022]
Abstract
The linear sequence of DNA provides invaluable information about genes and their regulatory elements along chromosomes. However, to fully understand gene function and regulation, we need to dissect how genes physically fold in the three-dimensional nuclear space. Here we describe immuno-OligoSTORM, an imaging strategy that reveals the distribution of nucleosomes within specific genes in super-resolution, through the simultaneous visualization of DNA and histones. We combine immuno-OligoSTORM with restraint-based and coarse-grained modeling approaches to integrate super-resolution imaging data with Hi-C contact frequencies and deconvoluted micrococcal nuclease-sequencing information. The resulting method, called Modeling immuno-OligoSTORM, allows quantitative modeling of genes with nucleosome resolution and provides information about chromatin accessibility for regulatory factors, such as RNA polymerase II. With Modeling immuno-OligoSTORM, we explore intercellular variability, transcriptional-dependent gene conformation, and folding of housekeeping and pluripotency-related genes in human pluripotent and differentiated cells, thereby obtaining the highest degree of data integration achieved so far to our knowledge.
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Affiliation(s)
- Maria Victoria Neguembor
- Center for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain.
| | - Juan Pablo Arcon
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Diana Buitrago
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology, Barcelona, Spain
- Departamento de Física y Matemáticas, Universidad Autónoma de Manizales, Manizales, Colombia
| | - Rafael Lema
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Jürgen Walther
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Ximena Garate
- Center for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Laura Martin
- Center for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Pablo Romero
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology, Barcelona, Spain
| | | | - Marta Gut
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Julie Blanc
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Melike Lakadamyali
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Chao-Ting Wu
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Isabelle Brun Heath
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Modesto Orozco
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology, Barcelona, Spain.
- Faculty of Biology, University of Barcelona, Barcelona, Spain.
- ICREA, Barcelona, Spain.
| | - Pablo D Dans
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology, Barcelona, Spain.
- Department of Biological Sciences, CENUR Litoral Norte, Universidad de la República (UdelaR), Salto, Uruguay.
- Bioinformatics Unit, Institut Pasteur de Montevideo, Montevideo, Uruguay.
| | - Maria Pia Cosma
- Center for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain.
- Universitat Pompeu Fabra (UPF), Barcelona, Spain.
- ICREA, Barcelona, Spain.
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.
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12
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Gimber N, Strauss S, Jungmann R, Schmoranzer J. Simultaneous Multicolor DNA-PAINT without Sequential Fluid Exchange Using Spectral Demixing. NANO LETTERS 2022; 22:2682-2690. [PMID: 35290738 PMCID: PMC9011399 DOI: 10.1021/acs.nanolett.1c04520] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 02/21/2022] [Indexed: 05/19/2023]
Abstract
Several variants of multicolor single-molecule localization microscopy (SMLM) have been developed to resolve the spatial relationship of nanoscale structures in biological samples. The oligonucleotide-based SMLM approach "DNA-PAINT" robustly achieves nanometer localization precision and can be used to count binding sites within nanostructures. However, multicolor DNA-PAINT has primarily been realized by "Exchange-PAINT", which requires sequential exchange of the imaging solution and thus leads to extended acquisition times. To alleviate the need for fluid exchange and to speed up the acquisition of current multichannel DNA-PAINT, we here present a novel approach that combines DNA-PAINT with simultaneous multicolor acquisition using spectral demixing (SD). By using newly designed probes and a novel multichannel registration procedure, we achieve simultaneous multicolor SD-DNA-PAINT with minimal crosstalk. We demonstrate high localization precision (3-6 nm) and multicolor registration of dual- and triple-color SD-DNA-PAINT by resolving patterns on DNA origami nanostructures and cellular structures.
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Affiliation(s)
- Niclas Gimber
- Advanced
Medical Bioimaging Core Facility, Charité-Universitätsmedizin, 10117 Berlin, Germany
- . Phone +49 30 450 536331
| | - Sebastian Strauss
- Faculty
of Physics and Center for Nanoscience, Ludwig
Maximilian University, 80799 Munich, Germany
- Max
Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Ralf Jungmann
- Faculty
of Physics and Center for Nanoscience, Ludwig
Maximilian University, 80799 Munich, Germany
- Max
Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Jan Schmoranzer
- Advanced
Medical Bioimaging Core Facility, Charité-Universitätsmedizin, 10117 Berlin, Germany
- . Phone +49
30 450 536331
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13
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Acuña-Rodriguez JP, Mena-Vega JP, Argüello-Miranda O. Live-cell fluorescence spectral imaging as a data science challenge. Biophys Rev 2022; 14:579-597. [PMID: 35528031 PMCID: PMC9043069 DOI: 10.1007/s12551-022-00941-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 03/09/2022] [Indexed: 12/13/2022] Open
Abstract
Live-cell fluorescence spectral imaging is an evolving modality of microscopy that uses specific properties of fluorophores, such as excitation or emission spectra, to detect multiple molecules and structures in intact cells. The main challenge of analyzing live-cell fluorescence spectral imaging data is the precise quantification of fluorescent molecules despite the weak signals and high noise found when imaging living cells under non-phototoxic conditions. Beyond the optimization of fluorophores and microscopy setups, quantifying multiple fluorophores requires algorithms that separate or unmix the contributions of the numerous fluorescent signals recorded at the single pixel level. This review aims to provide both the experimental scientist and the data analyst with a straightforward description of the evolution of spectral unmixing algorithms for fluorescence live-cell imaging. We show how the initial systems of linear equations used to determine the concentration of fluorophores in a pixel progressively evolved into matrix factorization, clustering, and deep learning approaches. We outline potential future trends on combining fluorescence spectral imaging with label-free detection methods, fluorescence lifetime imaging, and deep learning image analysis.
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Affiliation(s)
- Jessy Pamela Acuña-Rodriguez
- grid.412889.e0000 0004 1937 0706Center for Geophysical Research (CIGEFI), University of Costa Rica, San Pedro, San José Costa Rica
- grid.412889.e0000 0004 1937 0706School of Physics, University of Costa Rica, 2060 San Pedro, San José Costa Rica
| | - Jean Paul Mena-Vega
- grid.412889.e0000 0004 1937 0706School of Physics, University of Costa Rica, 2060 San Pedro, San José Costa Rica
| | - Orlando Argüello-Miranda
- grid.40803.3f0000 0001 2173 6074Department of Plant and Microbial Biology, North Carolina State University, 112 DERIEUX PLACE, Raleigh, NC 27695-7612 USA
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14
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Filbrun SL, Zhao F, Chen K, Huang TX, Yang M, Cheng X, Dong B, Fang N. Imaging Dynamic Processes in Multiple Dimensions and Length Scales. Annu Rev Phys Chem 2022; 73:377-402. [PMID: 35119943 DOI: 10.1146/annurev-physchem-090519-034100] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Optical microscopy has become an invaluable tool for investigating complex samples. Over the years, many advances to optical microscopes have been made that have allowed us to uncover new insights into the samples studied. Dynamic changes in biological and chemical systems are of utmost importance to study. To probe these samples, multidimensional approaches have been developed to acquire a fuller understanding of the system of interest. These dimensions include the spatial information, such as the three-dimensional coordinates and orientation of the optical probes, and additional chemical and physical properties through combining microscopy with various spectroscopic techniques. In this review, we survey the field of multidimensional microscopy and provide an outlook on the field and challenges that may arise. Expected final online publication date for the Annual Review of Physical Chemistry, Volume 73 is April 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Seth L Filbrun
- Department of Chemistry, Georgia State University, Atlanta, Georgia, USA
| | - Fei Zhao
- Department of Chemistry, Georgia State University, Atlanta, Georgia, USA
| | - Kuangcai Chen
- Department of Chemistry, Georgia State University, Atlanta, Georgia, USA.,Imaging Core Facility, Georgia State University, Atlanta, Georgia, USA
| | - Teng-Xiang Huang
- Department of Chemistry, Georgia State University, Atlanta, Georgia, USA
| | - Meek Yang
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas, USA;
| | - Xiaodong Cheng
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen Key Laboratory of Analytical Molecular Nanotechnology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian, China; ,
| | - Bin Dong
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas, USA;
| | - Ning Fang
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen Key Laboratory of Analytical Molecular Nanotechnology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian, China; ,
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15
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Oleksiievets N, Sargsyan Y, Thiele JC, Mougios N, Sograte-Idrissi S, Nevskyi O, Gregor I, Opazo F, Thoms S, Enderlein J, Tsukanov R. Fluorescence lifetime DNA-PAINT for multiplexed super-resolution imaging of cells. Commun Biol 2022; 5:38. [PMID: 35017652 PMCID: PMC8752799 DOI: 10.1038/s42003-021-02976-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 12/08/2021] [Indexed: 11/08/2022] Open
Abstract
DNA point accumulation for imaging in nanoscale topography (DNA-PAINT) is a powerful super-resolution technique highly suitable for multi-target (multiplexing) bio-imaging. However, multiplexed imaging of cells is still challenging due to the dense and sticky environment inside a cell. Here, we combine fluorescence lifetime imaging microscopy (FLIM) with DNA-PAINT and use the lifetime information as a multiplexing parameter for targets identification. In contrast to Exchange-PAINT, fluorescence lifetime PAINT (FL-PAINT) can image multiple targets simultaneously and does not require any fluid exchange, thus leaving the sample undisturbed and making the use of flow chambers/microfluidic systems unnecessary. We demonstrate the potential of FL-PAINT by simultaneous imaging of up to three targets in a cell using both wide-field FLIM and 3D time-resolved confocal laser scanning microscopy (CLSM). FL-PAINT can be readily combined with other existing techniques of multiplexed imaging and is therefore a perfect candidate for high-throughput multi-target bio-imaging.
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Affiliation(s)
- Nazar Oleksiievets
- III. Institute of Physics - Biophysics, Georg August University, 37077, Göttingen, Germany
| | - Yelena Sargsyan
- Department of Child and Adolescent Health, University Medical Center Göttingen, 37073, Göttingen, Germany
| | - Jan Christoph Thiele
- III. Institute of Physics - Biophysics, Georg August University, 37077, Göttingen, Germany
| | - Nikolaos Mougios
- Institute of Neuro- and Sensory Physiology, University Medical Center Göttingen, 37073, Göttingen, Germany
- Center for Biostructural Imaging of Neurodegeneration (BIN), University Medical Center Göttingen, 37075, Göttingen, Germany
| | - Shama Sograte-Idrissi
- Institute of Neuro- and Sensory Physiology, University Medical Center Göttingen, 37073, Göttingen, Germany
- Center for Biostructural Imaging of Neurodegeneration (BIN), University Medical Center Göttingen, 37075, Göttingen, Germany
| | - Oleksii Nevskyi
- III. Institute of Physics - Biophysics, Georg August University, 37077, Göttingen, Germany
| | - Ingo Gregor
- III. Institute of Physics - Biophysics, Georg August University, 37077, Göttingen, Germany
| | - Felipe Opazo
- Institute of Neuro- and Sensory Physiology, University Medical Center Göttingen, 37073, Göttingen, Germany
- Center for Biostructural Imaging of Neurodegeneration (BIN), University Medical Center Göttingen, 37075, Göttingen, Germany
- NanoTag Biotechnologies GmbH, 37079, Göttingen, Germany
| | - Sven Thoms
- Department of Child and Adolescent Health, University Medical Center Göttingen, 37073, Göttingen, Germany
- Biochemistry and Molecular Medicine, Medical School, Bielefeld University, 33615, Bielefeld, Germany
| | - Jörg Enderlein
- III. Institute of Physics - Biophysics, Georg August University, 37077, Göttingen, Germany.
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), Georg August University, Göttingen, Germany.
| | - Roman Tsukanov
- III. Institute of Physics - Biophysics, Georg August University, 37077, Göttingen, Germany.
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16
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Huang D, Haddad L, Rahman F, Palma M, Sapelkin A. Engineering a DNA origami mediated multicolour quantum dot platform for sub-diffraction spectral separation imaging. RSC Adv 2022; 12:23778-23785. [PMID: 36093241 PMCID: PMC9394590 DOI: 10.1039/d2ra04316e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 08/04/2022] [Indexed: 12/04/2022] Open
Abstract
The validation of super-resolution optical imaging techniques requires well-defined reference samples that can be used repeatedly and reliably as model standards. Here, we engineer a DNA origami scaffold-mediated multicolour quantum dot hybrid nanostructure and test it using a recently proposed Quantum Dot-based spectral separation technique. We show that multivalent DNA structures offer a robust and precise nanoscale quantum dot placement scaffold, while the spectral resolution method provides relatively simple and fast image acquisition capabilities using any standard confocal or fluorescence microscope capable of spectral signal separation and a single excitation laser wavelength. The validation of super-resolution optical imaging techniques requires well-defined reference samples that can be used repeatedly and reliably as model standards.![]()
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Affiliation(s)
- Da Huang
- Department of Chemistry, Queen Mary University of London, London E1 4NS, UK
| | - Lucy Haddad
- Department of Physics and Astronomy, Queen Mary University of London, London E1 4NS, UK
| | - Fahmida Rahman
- Department of Physics and Astronomy, Queen Mary University of London, London E1 4NS, UK
| | - Matteo Palma
- Department of Chemistry, Queen Mary University of London, London E1 4NS, UK
| | - Andrei Sapelkin
- Department of Physics and Astronomy, Queen Mary University of London, London E1 4NS, UK
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17
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Liu B, Liao J, Song Y, Chen C, Ding L, Lu J, Zhou J, Wang F. Multiplexed structured illumination super-resolution imaging with lifetime-engineered upconversion nanoparticles. NANOSCALE ADVANCES 2021; 4:30-38. [PMID: 36132948 PMCID: PMC9419758 DOI: 10.1039/d1na00765c] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Accepted: 11/02/2021] [Indexed: 05/05/2023]
Abstract
The emerging optical multiplexing within nanoscale shows super-capacity in encoding information by using lifetime fingerprints from luminescent nanoparticles. However, the optical diffraction limit compromises the decoding accuracy and throughput of the nanoparticles during conventional widefield imaging. This, in turn, challenges the quality of nanoparticles to afford the modulated excitation condition and further retain the multiplexed optical fingerprints for super-resolution multiplexing. Here we report a tailor-made multiplexed super-resolution imaging method using the lifetime-engineered upconversion nanoparticles. We demonstrate that the nanoparticles are bright, uniform, and stable under structured illumination, which supports a lateral resolution of 185 nm, less than 1/4th of the excitation wavelength. We further develop a deep learning algorithm to coordinate with super-resolution images for more accurate decoding compared to a numeric algorithm. We demonstrate a three-channel super-resolution imaging based optical multiplexing with decoding accuracies above 93% for each channel and larger than 60% accuracy for potential seven-channel multiplexing. The improved resolution provides high throughput by resolving the particles within the diffraction-limited spots, which enables higher multiplexing capacity in space. This lifetime multiplexing super-resolution method opens a new horizon for handling the growing amount of information content, disease source, and security risk in modern society.
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Affiliation(s)
- Baolei Liu
- Institute for Biomedical Materials and Devices (IBMD), Faculty of Science, University of Technology Sydney NSW 2007 Australia
- School of Electrical and Data Engineering, Faculty of Engineering and IT, University of Technology Sydney NSW 2007 Australia
| | - Jiayan Liao
- Institute for Biomedical Materials and Devices (IBMD), Faculty of Science, University of Technology Sydney NSW 2007 Australia
| | - Yiliao Song
- Centre for Artificial Intelligence, Faculty of Engineering and IT, University of Technology Sydney NSW 2007 Australia
| | - Chaohao Chen
- Institute for Biomedical Materials and Devices (IBMD), Faculty of Science, University of Technology Sydney NSW 2007 Australia
| | - Lei Ding
- Institute for Biomedical Materials and Devices (IBMD), Faculty of Science, University of Technology Sydney NSW 2007 Australia
| | - Jie Lu
- Centre for Artificial Intelligence, Faculty of Engineering and IT, University of Technology Sydney NSW 2007 Australia
| | - Jiajia Zhou
- Institute for Biomedical Materials and Devices (IBMD), Faculty of Science, University of Technology Sydney NSW 2007 Australia
| | - Fan Wang
- Institute for Biomedical Materials and Devices (IBMD), Faculty of Science, University of Technology Sydney NSW 2007 Australia
- School of Electrical and Data Engineering, Faculty of Engineering and IT, University of Technology Sydney NSW 2007 Australia
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18
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Kierzek M, Deal PE, Miller EW, Mukherjee S, Wachten D, Baumann A, Kaupp UB, Strünker T, Brenker C. Simultaneous recording of multiple cellular signaling events by frequency- and spectrally-tuned multiplexing of fluorescent probes. eLife 2021; 10:e63129. [PMID: 34859780 PMCID: PMC8700268 DOI: 10.7554/elife.63129] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 12/01/2021] [Indexed: 12/21/2022] Open
Abstract
Fluorescent probes that change their spectral properties upon binding to small biomolecules, ions, or changes in the membrane potential (Vm) are invaluable tools to study cellular signaling pathways. Here, we introduce a novel technique for simultaneous recording of multiple probes at millisecond time resolution: frequency- and spectrally-tuned multiplexing (FASTM). Different from present multiplexing approaches, FASTM uses phase-sensitive signal detection, which renders various combinations of common probes for Vm and ions accessible for multiplexing. Using kinetic stopped-flow fluorimetry, we show that FASTM allows simultaneous recording of rapid changes in Ca2+, pH, Na+, and Vm with high sensitivity and minimal crosstalk. FASTM is also suited for multiplexing using single-cell microscopy and genetically encoded FRET biosensors. Moreover, FASTM is compatible with optochemical tools to study signaling using light. Finally, we show that the exceptional time resolution of FASTM also allows resolving rapid chemical reactions. Altogether, FASTM opens new opportunities for interrogating cellular signaling.
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Affiliation(s)
- Michelina Kierzek
- Centre of Reproductive Medicine and Andrology, University of MünsterMünsterGermany
- CiM-IMPRS Graduate School, University of MünsterMünsterGermany
| | - Parker E Deal
- Department of Chemistry, University of California, BerkeleyBerkeleyUnited States
| | - Evan W Miller
- Department of Chemistry, University of California, BerkeleyBerkeleyUnited States
- Department of Molecular & Cell Biology, University of California, BerkeleyBerkeleyUnited States
- Helen Wills Neuroscience Institute, University of California, BerkeleyBerkeleyUnited States
| | - Shatanik Mukherjee
- Molecular Sensory Systems, Center of Advanced European Studies and ResearchBonnGermany
| | - Dagmar Wachten
- Institute of Innate Immunity, Department of Biophysical Imaging, Medical Faculty, University of BonnBonnGermany
| | - Arnd Baumann
- Institute of Biological Information Processing (IBI-1), Research Center JülichJülichGermany
| | - U Benjamin Kaupp
- Life & Medical Sciences Institute (LIMES), University of BonnBonnGermany
| | - Timo Strünker
- Centre of Reproductive Medicine and Andrology, University of MünsterMünsterGermany
- Cells in Motion Interfaculty Centre, University of MünsterMünsterGermany
| | - Christoph Brenker
- Centre of Reproductive Medicine and Andrology, University of MünsterMünsterGermany
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19
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Dorozynska K, Ek S, Kornienko V, Andersson D, Andersson A, Ehn A, Kristensson E. Snapshot multicolor fluorescence imaging using double multiplexing of excitation and emission on a single detector. Sci Rep 2021; 11:20454. [PMID: 34650144 PMCID: PMC8517015 DOI: 10.1038/s41598-021-99670-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 09/27/2021] [Indexed: 12/02/2022] Open
Abstract
Fluorescence-based multispectral imaging of rapidly moving or dynamic samples requires both fast two-dimensional data acquisition as well as sufficient spectral sensitivity for species separation. As the number of fluorophores in the experiment increases, meeting both these requirements becomes technically challenging. Although several solutions for fast imaging of multiple fluorophores exist, they all have one main restriction; they rely solely on spectrally resolving either the excitation- or the emission characteristics of the fluorophores. This inability directly limits how many fluorophores existing methods can simultaneously distinguish. Here we present a snapshot multispectral imaging approach that not only senses the excitation and emission characteristics of the probed fluorophores but also all cross term combinations of excitation and emission. To the best of the authors’ knowledge, this is the only snapshot multispectral imaging method that has this ability, allowing us to even sense and differentiate between light of equal wavelengths emitted from the same fluorescing species but where the signal components stem from different excitation sources. The current implementation of the technique allows us to simultaneously gather 24 different spectral images on a single detector, from which we demonstrate the ability to visualize and distinguish up to nine fluorophores within the visible wavelength range.
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Affiliation(s)
| | - Simon Ek
- Department of Combustion Physics, Lund University, 22363, Lund, Sweden
| | - Vassily Kornienko
- Department of Combustion Physics, Lund University, 22363, Lund, Sweden
| | - David Andersson
- Department of Combustion Physics, Lund University, 22363, Lund, Sweden
| | | | - Andreas Ehn
- Department of Combustion Physics, Lund University, 22363, Lund, Sweden
| | - Elias Kristensson
- Department of Combustion Physics, Lund University, 22363, Lund, Sweden.
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20
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Wang Y, Kuang W, Shang M, Huang ZL. Two-color super-resolution localization microscopy via joint encoding of emitter location and color. OPTICS EXPRESS 2021; 29:34797-34809. [PMID: 34809261 DOI: 10.1364/oe.440706] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 10/04/2021] [Indexed: 06/13/2023]
Abstract
Multi-color super-resolution localization microscopy (SRLM) provides great opportunities for studying the structural and functional details of biological samples. However, current multi-color SRLM methods either suffer from medium to high crosstalk, or require a dedicated optical system and a complicated image analysis procedure. To address these problems, here we propose a completely different method to realize multi-color SRLM. This method is built upon a customized RGBW camera with a repeated pattern of filtered (Red, Green, Blue and Near-infrared) and unfiltered (White) pixels. With a new insight that RGBW camera is advantageous for color recognition instead of color reproduction, we developed a joint encoding scheme of emitter location and color. By combing this RGBW camera with the joint encoding scheme and a simple optical set-up, we demonstrated two-color SRLM with ∼20 nm resolution and < 2% crosstalk (which is comparable to the best-reported values). This study significantly reduces the complexity of two-color SRLM (and potentially multi-color SRLM), and thus offers good opportunities for general biomedical research laboratories to use multi-color SRLM, which is currently mastered only by well-trained researchers.
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21
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Wensel TG, Potter VL, Moye A, Zhang Z, Robichaux MA. Structure and dynamics of photoreceptor sensory cilia. Pflugers Arch 2021; 473:1517-1537. [PMID: 34050409 PMCID: PMC11216635 DOI: 10.1007/s00424-021-02564-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 04/07/2021] [Accepted: 04/08/2021] [Indexed: 02/06/2023]
Abstract
The rod and cone photoreceptor cells of the vertebrate retina have highly specialized structures that enable them to carry out their function of light detection over a broad range of illumination intensities with optimized spatial and temporal resolution. Most prominent are their unusually large sensory cilia, consisting of outer segments packed with photosensitive disc membranes, a connecting cilium with many features reminiscent of the primary cilium transition zone, and a pair of centrioles forming a basal body which serves as the platform upon which the ciliary axoneme is assembled. These structures form a highway through which an enormous flux of material moves on a daily basis to sustain the continual turnover of outer segment discs and the energetic demands of phototransduction. After decades of study, the details of the fine structure and distribution of molecular components of these structures are still incompletely understood, but recent advances in cellular imaging techniques and animal models of inherited ciliary defects are yielding important new insights. This knowledge informs our understanding both of the mechanisms of trafficking and assembly and of the pathophysiological mechanisms of human blinding ciliopathies.
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Affiliation(s)
- Theodore G Wensel
- Vera and Marrs McLean Department of Biochemistry and Molecular Biology and Developmental Biology Graduate Program, Baylor College of Medicine, Houston, TX, 77030, USA.
| | - Valencia L Potter
- Vera and Marrs McLean Department of Biochemistry and Molecular Biology and Developmental Biology Graduate Program, Baylor College of Medicine, Houston, TX, 77030, USA
- Medical Scientist Training Program (MSTP), Baylor College of Medicine, Houston, TX, 77030, USA
| | - Abigail Moye
- Vera and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Zhixian Zhang
- Vera and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Michael A Robichaux
- Departments of Ophthalmology and Biochemistry, West Virginia University, Morgantown, WV, USA
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22
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van Wee R, Filius M, Joo C. Completing the canvas: advances and challenges for DNA-PAINT super-resolution imaging. Trends Biochem Sci 2021; 46:918-930. [PMID: 34247944 DOI: 10.1016/j.tibs.2021.05.010] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 05/16/2021] [Accepted: 05/31/2021] [Indexed: 01/02/2023]
Abstract
Single-molecule localization microscopy (SMLM) is a potent tool to examine biological systems with unprecedented resolution, enabling the investigation of increasingly smaller structures. At the forefront of these developments is DNA-based point accumulation for imaging in nanoscale topography (DNA-PAINT), which exploits the stochastic and transient binding of fluorescently labeled DNA probes. In its early stages the implementation of DNA-PAINT was burdened by low-throughput, excessive acquisition time, and difficult integration with live-cell imaging. However, recent advances are addressing these challenges and expanding the range of applications of DNA-PAINT. We review the current state of the art of DNA-PAINT in light of these advances and contemplate what further developments remain indispensable to realize live-cell imaging.
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Affiliation(s)
- Raman van Wee
- Department of BioNanoScience, Kavli Institute of Nanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Mike Filius
- Department of BioNanoScience, Kavli Institute of Nanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Chirlmin Joo
- Department of BioNanoScience, Kavli Institute of Nanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands.
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23
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DNA hybridisation kinetics using single-molecule fluorescence imaging. Essays Biochem 2021; 65:27-36. [PMID: 33491734 PMCID: PMC8056036 DOI: 10.1042/ebc20200040] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 12/17/2020] [Accepted: 12/21/2020] [Indexed: 01/05/2023]
Abstract
Deoxyribonucleic acid (DNA) hybridisation plays a key role in many biological processes and nucleic acid biotechnologies, yet surprisingly there are many aspects about the process which are still unknown. Prior to the invention of single-molecule microscopy, DNA hybridisation experiments were conducted at the ensemble level, and thus it was impossible to directly observe individual hybridisation events and understand fully the kinetics of DNA hybridisation. In this mini-review, recent single-molecule fluorescence-based studies of DNA hybridisation are discussed, particularly for short nucleic acids, to gain more insight into the kinetics of DNA hybridisation. As well as looking at single-molecule studies of intrinsic and extrinsic factors affecting DNA hybridisation kinetics, the influence of the methods used to detect hybridisation of single DNAs is considered. Understanding the kinetics of DNA hybridisation not only gives insight into an important biological process but also allows for further advancements in the growing field of nucleic acid biotechnology.
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24
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Repeat DNA-PAINT suppresses background and non-specific signals in optical nanoscopy. Nat Commun 2021; 12:501. [PMID: 33479249 PMCID: PMC7820506 DOI: 10.1038/s41467-020-20686-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 12/10/2020] [Indexed: 11/26/2022] Open
Abstract
DNA-PAINT is a versatile optical super-resolution technique relying on the transient binding of fluorescent DNA ‘imagers’ to target epitopes. Its performance in biological samples is often constrained by strong background signals and non-specific binding events, both exacerbated by high imager concentrations. Here we describe Repeat DNA-PAINT, a method that enables a substantial reduction in imager concentration, thus suppressing spurious signals. Additionally, Repeat DNA-PAINT reduces photoinduced target-site loss and can accelerate sampling, all without affecting spatial resolution. DNA-PAINT is a super-resolution imaging technique which suffers from high background signals and non-specific binding. Here the authors report Repeat DNA-PAINT which is capable of supressing background noise and preventing photoinduced site loss, as well as decreasing the time taken for the sampling process.
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Lelek M, Gyparaki MT, Beliu G, Schueder F, Griffié J, Manley S, Jungmann R, Sauer M, Lakadamyali M, Zimmer C. Single-molecule localization microscopy. NATURE REVIEWS. METHODS PRIMERS 2021; 1:39. [PMID: 35663461 PMCID: PMC9160414 DOI: 10.1038/s43586-021-00038-x] [Citation(s) in RCA: 258] [Impact Index Per Article: 86.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/01/2023]
Abstract
Single-molecule localization microscopy (SMLM) describes a family of powerful imaging techniques that dramatically improve spatial resolution over standard, diffraction-limited microscopy techniques and can image biological structures at the molecular scale. In SMLM, individual fluorescent molecules are computationally localized from diffraction-limited image sequences and the localizations are used to generate a super-resolution image or a time course of super-resolution images, or to define molecular trajectories. In this Primer, we introduce the basic principles of SMLM techniques before describing the main experimental considerations when performing SMLM, including fluorescent labelling, sample preparation, hardware requirements and image acquisition in fixed and live cells. We then explain how low-resolution image sequences are computationally processed to reconstruct super-resolution images and/or extract quantitative information, and highlight a selection of biological discoveries enabled by SMLM and closely related methods. We discuss some of the main limitations and potential artefacts of SMLM, as well as ways to alleviate them. Finally, we present an outlook on advanced techniques and promising new developments in the fast-evolving field of SMLM. We hope that this Primer will be a useful reference for both newcomers and practitioners of SMLM.
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Affiliation(s)
- Mickaël Lelek
- Imaging and Modeling Unit, Department of Computational
Biology, Institut Pasteur, Paris, France
- CNRS, UMR 3691, Paris, France
| | - Melina T. Gyparaki
- Department of Biology, University of Pennsylvania,
Philadelphia, PA, USA
| | - Gerti Beliu
- Department of Biotechnology and Biophysics Biocenter,
University of Würzburg, Würzburg, Germany
| | - Florian Schueder
- Faculty of Physics and Center for Nanoscience, Ludwig
Maximilian University, Munich, Germany
- Max Planck Institute of Biochemistry, Martinsried,
Germany
| | - Juliette Griffié
- Laboratory of Experimental Biophysics, Institute of
Physics, École Polytechnique Fédérale de Lausanne (EPFL),
Lausanne, Switzerland
| | - Suliana Manley
- Laboratory of Experimental Biophysics, Institute of
Physics, École Polytechnique Fédérale de Lausanne (EPFL),
Lausanne, Switzerland
- ;
;
;
;
| | - Ralf Jungmann
- Faculty of Physics and Center for Nanoscience, Ludwig
Maximilian University, Munich, Germany
- Max Planck Institute of Biochemistry, Martinsried,
Germany
- ;
;
;
;
| | - Markus Sauer
- Department of Biotechnology and Biophysics Biocenter,
University of Würzburg, Würzburg, Germany
- ;
;
;
;
| | - Melike Lakadamyali
- Department of Physiology, Perelman School of Medicine,
University of Pennsylvania, Philadelphia, PA, USA
- Department of Cell and Developmental Biology, Perelman
School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Epigenetics Institute, Perelman School of Medicine,
University of Pennsylvania, Philadelphia, PA, USA
- ;
;
;
;
| | - Christophe Zimmer
- Imaging and Modeling Unit, Department of Computational
Biology, Institut Pasteur, Paris, France
- CNRS, UMR 3691, Paris, France
- ;
;
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;
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26
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Cosco ED, Spearman AL, Ramakrishnan S, Lingg JGP, Saccomano M, Pengshung M, Arús BA, Wong KCY, Glasl S, Ntziachristos V, Warmer M, McLaughlin RR, Bruns OT, Sletten EM. Shortwave infrared polymethine fluorophores matched to excitation lasers enable non-invasive, multicolour in vivo imaging in real time. Nat Chem 2020; 12:1123-1130. [PMID: 33077925 PMCID: PMC7680456 DOI: 10.1038/s41557-020-00554-5] [Citation(s) in RCA: 136] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Accepted: 08/17/2020] [Indexed: 01/06/2023]
Abstract
High-resolution, multiplexed experiments are a staple in cellular imaging. Analogous experiments in animals are challenging, however, due to substantial scattering and autofluorescence in tissue at visible (350-700 nm) and near-infrared (700-1,000 nm) wavelengths. Here, we enable real-time, non-invasive multicolour imaging experiments in animals through the design of optical contrast agents for the shortwave infrared (SWIR, 1,000-2,000 nm) region and complementary advances in imaging technologies. We developed tunable, SWIR-emissive flavylium polymethine dyes and established relationships between structure and photophysical properties for this class of bright SWIR contrast agents. In parallel, we designed an imaging system with variable near-infrared/SWIR excitation and single-channel detection, facilitating video-rate multicolour SWIR imaging for optically guided surgery and imaging of awake and moving mice with multiplexed detection. Optimized dyes matched to 980 nm and 1,064 nm lasers, combined with the clinically approved indocyanine green, enabled real-time, three-colour imaging with high temporal and spatial resolutions.
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Affiliation(s)
- Emily D Cosco
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA
- Helmholtz Pioneer Campus, Helmholtz Zentrum München, Neuherberg, Germany
| | - Anthony L Spearman
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - Shyam Ramakrishnan
- Helmholtz Pioneer Campus, Helmholtz Zentrum München, Neuherberg, Germany
| | - Jakob G P Lingg
- Helmholtz Pioneer Campus, Helmholtz Zentrum München, Neuherberg, Germany
| | - Mara Saccomano
- Helmholtz Pioneer Campus, Helmholtz Zentrum München, Neuherberg, Germany
| | - Monica Pengshung
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - Bernardo A Arús
- Helmholtz Pioneer Campus, Helmholtz Zentrum München, Neuherberg, Germany
| | - Kelly C Y Wong
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - Sarah Glasl
- Institute of Biomedical Imaging, Helmholtz Zentrum München, Neuherberg, Germany
| | | | - Martin Warmer
- Helmholtz Pioneer Campus, Helmholtz Zentrum München, Neuherberg, Germany
| | - Ryan R McLaughlin
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - Oliver T Bruns
- Helmholtz Pioneer Campus, Helmholtz Zentrum München, Neuherberg, Germany.
| | - Ellen M Sletten
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA.
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27
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Thomsen J, Sletfjerding MB, Jensen SB, Stella S, Paul B, Malle MG, Montoya G, Petersen TC, Hatzakis NS. DeepFRET, a software for rapid and automated single-molecule FRET data classification using deep learning. eLife 2020; 9:e60404. [PMID: 33138911 PMCID: PMC7609065 DOI: 10.7554/elife.60404] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 10/02/2020] [Indexed: 12/20/2022] Open
Abstract
Single-molecule Förster Resonance energy transfer (smFRET) is an adaptable method for studying the structure and dynamics of biomolecules. The development of high throughput methodologies and the growth of commercial instrumentation have outpaced the development of rapid, standardized, and automated methodologies to objectively analyze the wealth of produced data. Here we present DeepFRET, an automated, open-source standalone solution based on deep learning, where the only crucial human intervention in transiting from raw microscope images to histograms of biomolecule behavior, is a user-adjustable quality threshold. Integrating standard features of smFRET analysis, DeepFRET consequently outputs the common kinetic information metrics. Its classification accuracy on ground truth data reached >95% outperforming human operators and commonly used threshold, only requiring ~1% of the time. Its precise and rapid operation on real data demonstrates DeepFRET's capacity to objectively quantify biomolecular dynamics and the potential to contribute to benchmarking smFRET for dynamic structural biology.
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Affiliation(s)
- Johannes Thomsen
- Department of Chemistry and Nanoscience Centre, University of CopenhagenCopenhagenDenmark
| | | | - Simon Bo Jensen
- Department of Chemistry and Nanoscience Centre, University of CopenhagenCopenhagenDenmark
| | - Stefano Stella
- Structural Molecular Biology Group, Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences, University of CopenhagenCopenhagenDenmark
| | - Bijoya Paul
- Structural Molecular Biology Group, Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences, University of CopenhagenCopenhagenDenmark
| | - Mette Galsgaard Malle
- Department of Chemistry and Nanoscience Centre, University of CopenhagenCopenhagenDenmark
| | - Guillermo Montoya
- Structural Molecular Biology Group, Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences, University of CopenhagenCopenhagenDenmark
| | | | - Nikos S Hatzakis
- Department of Chemistry and Nanoscience Centre, University of CopenhagenCopenhagenDenmark
- Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences, University of CopenhagenCopenhagenDenmark
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28
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Thiele JC, Helmerich DA, Oleksiievets N, Tsukanov R, Butkevich E, Sauer M, Nevskyi O, Enderlein J. Confocal Fluorescence-Lifetime Single-Molecule Localization Microscopy. ACS NANO 2020; 14:14190-14200. [PMID: 33035050 DOI: 10.1021/acsnano.0c07322] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Fluorescence lifetime imaging microscopy is an important technique that adds another dimension to intensity and color acquired by conventional microscopy. In particular, it allows for multiplexing fluorescent labels that have otherwise similar spectral properties. Currently, the only super-resolution technique that is capable of recording super-resolved images with lifetime information is stimulated emission depletion microscopy. In contrast, all single-molecule localization microscopy (SMLM) techniques that employ wide-field cameras completely lack the lifetime dimension. Here, we combine fluorescence-lifetime confocal laser-scanning microscopy with SMLM for realizing single-molecule localization-based fluorescence-lifetime super-resolution imaging. Besides yielding images with a spatial resolution much beyond the diffraction limit, it determines the fluorescence lifetime of all localized molecules. We validate our technique by applying it to direct stochastic optical reconstruction microscopy and points accumulation for imaging in nanoscale topography imaging of fixed cells, and we demonstrate its multiplexing capability on samples with two different labels that differ only by fluorescence lifetime but not by their spectral properties.
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Affiliation(s)
- Jan Christoph Thiele
- III. Institute of Physics-Biophysics, Georg August University, Göttingen 37077, Germany
| | - Dominic A Helmerich
- Department of Biotechnology and Biophysics, Biocenter, University of Würzburg, Am Hubland, Würzburg 97074, Germany
| | - Nazar Oleksiievets
- III. Institute of Physics-Biophysics, Georg August University, Göttingen 37077, Germany
| | - Roman Tsukanov
- III. Institute of Physics-Biophysics, Georg August University, Göttingen 37077, Germany
| | - Eugenia Butkevich
- III. Institute of Physics-Biophysics, Georg August University, Göttingen 37077, Germany
| | - Markus Sauer
- Department of Biotechnology and Biophysics, Biocenter, University of Würzburg, Am Hubland, Würzburg 97074, Germany
| | - Oleksii Nevskyi
- III. Institute of Physics-Biophysics, Georg August University, Göttingen 37077, Germany
| | - Jörg Enderlein
- III. Institute of Physics-Biophysics, Georg August University, Göttingen 37077, Germany
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), Georg August University, Göttingen 37077, Germany
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29
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García-Calvo J, Maillard J, Fureraj I, Strakova K, Colom A, Mercier V, Roux A, Vauthey E, Sakai N, Fürstenberg A, Matile S. Fluorescent Membrane Tension Probes for Super-Resolution Microscopy: Combining Mechanosensitive Cascade Switching with Dynamic-Covalent Ketone Chemistry. J Am Chem Soc 2020; 142:12034-12038. [PMID: 32609500 DOI: 10.1021/jacs.0c04942] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
We report the design, synthesis, and evaluation of fluorescent flipper probes for single-molecule super-resolution imaging of membrane tension in living cells. Reversible switching from bright-state ketones to dark-state hydrates, hemiacetals, and hemithioacetals is demonstrated for twisted and planarized mechanophores in solution and membranes. Broadband femtosecond fluorescence up-conversion spectroscopy evinces ultrafast chalcogen-bonding cascade switching in the excited state in solution. According to fluorescence lifetime imaging microscopy, the new flippers image membrane tension in live cells with record red shifts and photostability. Single-molecule localization microscopy with the new tension probes resolves membranes well below the diffraction limit.
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Affiliation(s)
- José García-Calvo
- School of Chemistry and Biochemistry, University of Geneva, Geneva 1211, Switzerland
| | - Jimmy Maillard
- School of Chemistry and Biochemistry, University of Geneva, Geneva 1211, Switzerland
| | - Ina Fureraj
- School of Chemistry and Biochemistry, University of Geneva, Geneva 1211, Switzerland
| | - Karolina Strakova
- School of Chemistry and Biochemistry, University of Geneva, Geneva 1211, Switzerland
| | - Adai Colom
- School of Chemistry and Biochemistry, University of Geneva, Geneva 1211, Switzerland
| | - Vincent Mercier
- School of Chemistry and Biochemistry, University of Geneva, Geneva 1211, Switzerland
| | - Aurelien Roux
- School of Chemistry and Biochemistry, University of Geneva, Geneva 1211, Switzerland
| | - Eric Vauthey
- School of Chemistry and Biochemistry, University of Geneva, Geneva 1211, Switzerland
| | - Naomi Sakai
- School of Chemistry and Biochemistry, University of Geneva, Geneva 1211, Switzerland
| | - Alexandre Fürstenberg
- School of Chemistry and Biochemistry, University of Geneva, Geneva 1211, Switzerland
| | - Stefan Matile
- School of Chemistry and Biochemistry, University of Geneva, Geneva 1211, Switzerland
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30
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Pandey S, Bodas D. High-quality quantum dots for multiplexed bioimaging: A critical review. Adv Colloid Interface Sci 2020; 278:102137. [PMID: 32171116 DOI: 10.1016/j.cis.2020.102137] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 03/02/2020] [Accepted: 03/04/2020] [Indexed: 11/18/2022]
Abstract
Bioimaging done using two or more fluorophores possessing different emission wavelengths can be termed as a multicolor/multiplexed bioimaging technique. Traditionally, images are captured sequentially using multiple fluorophores having specific excitation and emission. For this purpose, multifunctional nanoprobes, such as organic fluorophores, metallic nanoparticles, semiconductor quantum dots, and carbon dots (CDs) are used. Among these fluorophores, quantum dots (QDs) have emerged as an ideal probe for multiplexed bioimaging due to their unique property of size tunable emission. However, the usage of quantum dots in bioimaging is limited due to their toxicity. Furthermore, the reproducibility of optical properties is cynical. These desirable properties, along with enhancement in quantum efficiency, photostability, fluorescence lifetime, etc. can be achieved by stringent control over synthesis parameters. This review summarizes the desirable properties and synthesis methods of such superior QDs followed by their application in multiplexed imaging.
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Affiliation(s)
- Sulaxna Pandey
- Nanobioscience group, Agharkar Research Institute, GG Agarkar Road, Pune 411 004, India; Savitribai Phule Pune University, Ganeshkhind Road, Pune 411 007, India
| | - Dhananjay Bodas
- Nanobioscience group, Agharkar Research Institute, GG Agarkar Road, Pune 411 004, India; Savitribai Phule Pune University, Ganeshkhind Road, Pune 411 007, India.
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31
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Lakadamyali M, Cosma MP. Visualizing the genome in high resolution challenges our textbook understanding. Nat Methods 2020; 17:371-379. [DOI: 10.1038/s41592-020-0758-3] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 01/22/2020] [Indexed: 12/29/2022]
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32
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Sil P, Mateos N, Nath S, Buschow S, Manzo C, Suzuki KGN, Fujiwara T, Kusumi A, Garcia-Parajo MF, Mayor S. Dynamic actin-mediated nano-scale clustering of CD44 regulates its meso-scale organization at the plasma membrane. Mol Biol Cell 2019; 31:561-579. [PMID: 31577524 PMCID: PMC7202065 DOI: 10.1091/mbc.e18-11-0715] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Transmembrane adhesion receptors at the cell surface, such as CD44, are often equipped with modules to interact with the extracellular matrix (ECM) and the intracellular cytoskeletal machinery. CD44 has been recently shown to compartmentalize the membrane into domains by acting as membrane pickets, facilitating the function of signaling receptors. While spatial organization and diffusion studies of membrane proteins are usually conducted separately, here we combine observations of organization and diffusion by using high spatio-temporal resolution imaging on living cells to reveal a hierarchical organization of CD44. CD44 is present in a meso-scale meshwork pattern where it exhibits enhanced confinement and is enriched in nanoclusters of CD44 along its boundaries. This nanoclustering is orchestrated by the underlying cortical actin dynamics. Interaction with actin is mediated by specific segments of the intracellular domain. This influences the organization of the protein at the nano-scale, generating a selective requirement for formin over Arp2/3-based actin-nucleation machinery. The extracellular domain and its interaction with elements of ECM do not influence the meso-scale organization, but may serve to reposition the meshwork with respect to the ECM. Taken together, our results capture the hierarchical nature of CD44 organization at the cell surface, with active cytoskeleton-templated nanoclusters localized to a meso-scale meshwork pattern.
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Affiliation(s)
- Parijat Sil
- National Centre for Biological Sciences (NCBS)
| | - Nicolas Mateos
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, Barcelona 08860, Spain
| | - Sangeeta Nath
- Institute of Stem Cell and Regenerative Medicine.,Manipal Institute of Regenerative Medicine, Manipal Academy of Higher Education, Bangalore 560065, India
| | - Sonja Buschow
- Department of Gastroenterology and Hepatology, Erasmus University Medical Center Rotterdam, Rotterdam 3015 GD Rotterdam, The Netherlands
| | - Carlo Manzo
- Facultat de Ciències i Tecnologia, Universitat de Vic-Universitat Central de Catalunya, Vic 08500, Spain
| | - Kenichi G N Suzuki
- Centre for Highly Advanced Integration of Nano and Life Sciences (G-CHAIN), Gifu University, Gifu 501-1193, Japan.,Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Kyoto 606-8501, Japan
| | - Takahiro Fujiwara
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Kyoto 606-8501, Japan
| | - Akihiro Kusumi
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Kyoto 606-8501, Japan.,Okinawa Institute of Science and Technology, Graduate University, Okinawa 904-0412, Japan
| | - Maria F Garcia-Parajo
- Institute of Stem Cell and Regenerative Medicine.,Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain
| | - Satyajit Mayor
- National Centre for Biological Sciences (NCBS).,Institute of Stem Cell and Regenerative Medicine
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