1
|
Noakes F, Smitten KL, Maple LEC, Bernardino de la Serna J, Robertson CC, Pritchard D, Fairbanks SD, Weinstein JA, Smythe CGW, Thomas JA. Phenazine Cations as Anticancer Theranostics †. J Am Chem Soc 2024; 146:12836-12849. [PMID: 38683943 PMCID: PMC11082890 DOI: 10.1021/jacs.4c03491] [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: 03/11/2024] [Revised: 04/17/2024] [Accepted: 04/17/2024] [Indexed: 05/02/2024]
Abstract
The biological properties of two water-soluble organic cations based on polypyridyl structures commonly used as ligands for photoactive transition metal complexes designed to interact with biomolecules are investigated. A cytotoxicity screen employing a small panel of cell lines reveals that both cations show cytotoxicity toward cancer cells but show reduced cytotoxicity to noncancerous HEK293 cells with the more extended system being notably more active. Although it is not a singlet oxygen sensitizer, the more active cation also displayed enhanced potency on irradiation with visible light, making it active at nanomolar concentrations. Using the intrinsic luminescence of the cations, their cellular uptake was investigated in more detail, revealing that the active compound is more readily internalized than its less lipophilic analogue. Colocalization studies with established cell probes reveal that the active cation predominantly localizes within lysosomes and that irradiation leads to the disruption of mitochondrial structure and function. Stimulated emission depletion (STED) nanoscopy and transmission electron microscopy (TEM) imaging reveal that treatment results in distinct lysosomal swelling and extensive cellular vacuolization. Further imaging-based studies confirm that treatment with the active cation induces lysosomal membrane permeabilization, which triggers lysosome-dependent cell-death due to both necrosis and caspase-dependent apoptosis. A preliminary toxicity screen in the Galleria melonella animal model was carried out on both cations and revealed no detectable toxicity up to concentrations of 80 mg/kg. Taken together, these studies indicate that this class of synthetically easy-to-access photoactive compounds offers potential as novel therapeutic leads.
Collapse
Affiliation(s)
- Felicity
F. Noakes
- Department
of Chemistry, The University of Sheffield, Western Bank, Sheffield S3 7HF, U.K.
- Department
of Biomedical Science, The University of
Sheffield, Western Bank, Sheffield S10 2TN, U.K.
| | - Kirsty L. Smitten
- Department
of Chemistry, The University of Sheffield, Western Bank, Sheffield S3 7HF, U.K.
- Department
of Molecular Biology and Biotechnology, The University of Sheffield, Western Bank, Sheffield S10 2TN, U.K.
| | - Laura E. C. Maple
- Department
of Biomedical Science, The University of
Sheffield, Western Bank, Sheffield S10 2TN, U.K.
| | - Jorge Bernardino de la Serna
- National
Heart and Lung Institute, Imperial College
London, London SW7 2AZ, U.K.
- Central
Laser
Facility, Rutherford Appleton Laboratory, Research Complex at Harwell, Science and Technology Facilities Council, Harwell-Oxford, Didcot OX11 0QX, U.K.
| | - Craig C. Robertson
- Department
of Chemistry, The University of Sheffield, Western Bank, Sheffield S3 7HF, U.K.
| | - Dylan Pritchard
- Department
of Chemistry, The University of Sheffield, Western Bank, Sheffield S3 7HF, U.K.
| | - Simon D. Fairbanks
- Department
of Chemistry, The University of Sheffield, Western Bank, Sheffield S3 7HF, U.K.
| | - Julia A. Weinstein
- Department
of Chemistry, The University of Sheffield, Western Bank, Sheffield S3 7HF, U.K.
| | - Carl G. W. Smythe
- Department
of Biomedical Science, The University of
Sheffield, Western Bank, Sheffield S10 2TN, U.K.
| | - Jim A. Thomas
- Department
of Chemistry, The University of Sheffield, Western Bank, Sheffield S3 7HF, U.K.
| |
Collapse
|
2
|
Sekine S, Tarama M, Wada H, Sami MM, Shibata T, Hayashi S. Emergence of periodic circumferential actin cables from the anisotropic fusion of actin nanoclusters during tubulogenesis. Nat Commun 2024; 15:464. [PMID: 38267421 PMCID: PMC10808230 DOI: 10.1038/s41467-023-44684-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 12/29/2023] [Indexed: 01/26/2024] Open
Abstract
The periodic circumferential cytoskeleton supports various tubular tissues. Radial expansion of the tube lumen causes anisotropic tensile stress, which can be exploited as a geometric cue. However, the molecular machinery linking anisotropy to robust circumferential patterning is poorly understood. Here, we aim to reveal the emergent process of circumferential actin cable formation in a Drosophila tracheal tube. During luminal expansion, sporadic actin nanoclusters emerge and exhibit circumferentially biased motion and fusion. RNAi screening reveals the formin family protein, DAAM, as an essential component responding to tissue anisotropy, and non-muscle myosin II as a component required for nanocluster fusion. An agent-based model simulation suggests that crosslinkers play a crucial role in nanocluster formation and cluster-to-cable transition occurs in response to mechanical anisotropy. Altogether, we propose that an actin nanocluster is an organizational unit that responds to stress in the cortical membrane and builds a higher-order cable structure.
Collapse
Affiliation(s)
- Sayaka Sekine
- Laboratory for Morphogenetic Signaling, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan.
- Laboratory for Histogenetic Dynamics, Graduate School of Life Sciences, Tohoku University, Sendai, Japan.
| | - Mitsusuke Tarama
- Laboratory for Physical Biology, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan.
- Department of Physics, Faculty of Science, Kyushu University, Fukuoka, Japan.
| | - Housei Wada
- Laboratory for Morphogenetic Signaling, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan
| | - Mustafa M Sami
- Laboratory for Morphogenetic Signaling, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan
- Physics and Biology Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Tatsuo Shibata
- Laboratory for Physical Biology, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan
| | - Shigeo Hayashi
- Laboratory for Morphogenetic Signaling, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan
- Kobe University Graduate School of Science, Kobe, Japan
| |
Collapse
|
3
|
Sanders S, Jensen Y, Reimer R, Bosse JB. From the beginnings to multidimensional light and electron microscopy of virus morphogenesis. Adv Virus Res 2023; 116:45-88. [PMID: 37524482 DOI: 10.1016/bs.aivir.2023.05.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/02/2023]
Abstract
Individual functional viral morphogenesis events are often dynamic, short, and infrequent and might be obscured by other pathways and dead-end products. Volumetric live cell imaging has become an essential tool for studying viral morphogenesis events. It allows following entire dynamic processes while providing functional evidence that the imaged process is involved in viral production. Moreover, it allows to capture many individual events and allows quantitative analysis. Finally, the correlation of volumetric live-cell data with volumetric electron microscopy (EM) can provide crucial insights into the ultrastructure and mechanisms of viral morphogenesis events. Here, we provide an overview and discussion of suitable imaging methods for volumetric correlative imaging of viral morphogenesis and frame them in a historical summary of their development.
Collapse
Affiliation(s)
- Saskia Sanders
- Department of Virology, Hannover Medical School, Hannover, Germany; Leibniz Institute of Virology (LIV), Hamburg, Germany; Centre for Structural Systems Biology, Hamburg, Germany; Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover, Germany
| | - Yannick Jensen
- Department of Virology, Hannover Medical School, Hannover, Germany; Leibniz Institute of Virology (LIV), Hamburg, Germany; Centre for Structural Systems Biology, Hamburg, Germany; Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover, Germany
| | | | - Jens B Bosse
- Department of Virology, Hannover Medical School, Hannover, Germany; Leibniz Institute of Virology (LIV), Hamburg, Germany; Centre for Structural Systems Biology, Hamburg, Germany; Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover, Germany.
| |
Collapse
|
4
|
Hu K, Hu X, He T, Liu J, Liu S, Zhang J, Tan Y, Yang X, Wang H, Liang Y, Ye J. Structured Illumination Microscopy of Mitochondrial in Mouse Hepatocytes with an Improved Image Reconstruction Algorithm. MICROMACHINES 2023; 14:642. [PMID: 36985049 PMCID: PMC10055965 DOI: 10.3390/mi14030642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 03/04/2023] [Accepted: 03/10/2023] [Indexed: 06/18/2023]
Abstract
In this paper, a structured illumination microscopy (SIM) image reconstruction algorithm combined with notch function (N-SIM) is proposed. This method suppresses the defocus signal in the imaging process by processing the low-frequency signal of the image. The existing super-resolution image reconstruction algorithm produces streak artifacts caused by defocus signal. The experimental results show that the algorithm proposed in our study can well suppress the streak artifacts caused by defocused signals during the imaging process without losing the effective information of the image. The image reconstruction algorithm is used to analyze the mouse hepatocytes, and the image processing tool developed by MATLAB is applied to identify, detect and count the reconstructed images of mitochondria and lipid droplets, respectively. It is found that the mitochondrial activity in oxidative stress induced growth inhibitor 1 (OSGIN1) overexpressed mouse hepatocytes is higher than that in normal cells, and the interaction with lipid droplets is more obvious. This paper provides a reliable subcellular observation platform, which is very meaningful for biomedical work.
Collapse
Affiliation(s)
- Kai Hu
- Sino-German College of Intelligent Manufacturing, Shenzhen Technology University, Shenzhen 518118, China
- Laboratory of Advanced Optical Precision Manufacturing Technology of Guangdong Provincial Higher Education Institute, Shenzhen Technology University, Shenzhen 518118, China
| | - Xuejuan Hu
- Sino-German College of Intelligent Manufacturing, Shenzhen Technology University, Shenzhen 518118, China
- Laboratory of Advanced Optical Precision Manufacturing Technology of Guangdong Provincial Higher Education Institute, Shenzhen Technology University, Shenzhen 518118, China
- College of Physics and Photoelectric Engineering, Shenzhen University, Shenzhen 518060, China
| | - Ting He
- Sino-German College of Intelligent Manufacturing, Shenzhen Technology University, Shenzhen 518118, China
- Laboratory of Advanced Optical Precision Manufacturing Technology of Guangdong Provincial Higher Education Institute, Shenzhen Technology University, Shenzhen 518118, China
- College of Physics and Photoelectric Engineering, Shenzhen University, Shenzhen 518060, China
| | - Jingxin Liu
- College of Pharmacy, Shenzhen Technology University, Shenzhen 518118, China
| | - Shiqian Liu
- Laboratory of Advanced Optical Precision Manufacturing Technology of Guangdong Provincial Higher Education Institute, Shenzhen Technology University, Shenzhen 518118, China
| | - Jiaming Zhang
- Sino-German College of Intelligent Manufacturing, Shenzhen Technology University, Shenzhen 518118, China
- Laboratory of Advanced Optical Precision Manufacturing Technology of Guangdong Provincial Higher Education Institute, Shenzhen Technology University, Shenzhen 518118, China
| | - Yadan Tan
- Sino-German College of Intelligent Manufacturing, Shenzhen Technology University, Shenzhen 518118, China
- Laboratory of Advanced Optical Precision Manufacturing Technology of Guangdong Provincial Higher Education Institute, Shenzhen Technology University, Shenzhen 518118, China
- College of Physics Science and Technology, Guangxi Normal University, Guilin 541001, China
| | - Xiaokun Yang
- Sino-German College of Intelligent Manufacturing, Shenzhen Technology University, Shenzhen 518118, China
- Laboratory of Advanced Optical Precision Manufacturing Technology of Guangdong Provincial Higher Education Institute, Shenzhen Technology University, Shenzhen 518118, China
| | - Hengliang Wang
- Sino-German College of Intelligent Manufacturing, Shenzhen Technology University, Shenzhen 518118, China
- Laboratory of Advanced Optical Precision Manufacturing Technology of Guangdong Provincial Higher Education Institute, Shenzhen Technology University, Shenzhen 518118, China
| | - Yifei Liang
- Sino-German College of Intelligent Manufacturing, Shenzhen Technology University, Shenzhen 518118, China
- Laboratory of Advanced Optical Precision Manufacturing Technology of Guangdong Provincial Higher Education Institute, Shenzhen Technology University, Shenzhen 518118, China
- College of Physics Science and Technology, Guangxi Normal University, Guilin 541001, China
| | - Jianze Ye
- Sino-German College of Intelligent Manufacturing, Shenzhen Technology University, Shenzhen 518118, China
- Laboratory of Advanced Optical Precision Manufacturing Technology of Guangdong Provincial Higher Education Institute, Shenzhen Technology University, Shenzhen 518118, China
| |
Collapse
|
5
|
Kugler E, Bravo I, Durmishi X, Marcotti S, Beqiri S, Carrington A, Stramer B, Mattar P, MacDonald RB. GliaMorph: a modular image analysis toolkit to quantify Müller glial cell morphology. Development 2023; 150:dev201008. [PMID: 36625162 PMCID: PMC10110500 DOI: 10.1242/dev.201008] [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] [Received: 06/08/2022] [Accepted: 01/03/2023] [Indexed: 01/11/2023]
Abstract
Cell morphology is crucial for all cell functions. This is particularly true for glial cells as they rely on complex shape to contact and support neurons. However, methods to quantify complex glial cell shape accurately and reproducibly are lacking. To address this, we developed the image analysis pipeline 'GliaMorph'. GliaMorph is a modular analysis toolkit developed to perform (1) image pre-processing, (2) semi-automatic region-of-interest selection, (3) apicobasal texture analysis, (4) glia segmentation, and (5) cell feature quantification. Müller glia (MG) have a stereotypic shape linked to their maturation and physiological status. Here, we characterized MG on three levels: (1) global image-level, (2) apicobasal texture, and (3) regional apicobasal vertical-to-horizontal alignment. Using GliaMorph, we quantified MG development on a global and single-cell level, showing increased feature elaboration and subcellular morphological rearrangement in the zebrafish retina. As proof of principle, we analysed expression changes in a mouse glaucoma model, identifying subcellular protein localization changes in MG. Together, these data demonstrate that GliaMorph enables an in-depth understanding of MG morphology in the developing and diseased retina.
Collapse
Affiliation(s)
- Elisabeth Kugler
- Institute of Ophthalmology, University College London, 11-43 Bath St, Greater London EC1V 9EL, UK
| | - Isabel Bravo
- Institute of Ophthalmology, University College London, 11-43 Bath St, Greater London EC1V 9EL, UK
| | - Xhuljana Durmishi
- Institute of Ophthalmology, University College London, 11-43 Bath St, Greater London EC1V 9EL, UK
| | - Stefania Marcotti
- Randall Centre for Cell & Molecular Biophysics, King's College London, New Hunt's House, London SE1 1UL, UK
| | - Sara Beqiri
- Institute of Ophthalmology, University College London, 11-43 Bath St, Greater London EC1V 9EL, UK
| | - Alicia Carrington
- Institute of Ophthalmology, University College London, 11-43 Bath St, Greater London EC1V 9EL, UK
| | - Brian Stramer
- Randall Centre for Cell & Molecular Biophysics, King's College London, New Hunt's House, London SE1 1UL, UK
| | - Pierre Mattar
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, K1H 8M5, Canada
- Ottawa Hospital Research Institute (OHRI), Ottawa, ON, K1H 8L6, Canada
| | - Ryan B. MacDonald
- Institute of Ophthalmology, University College London, 11-43 Bath St, Greater London EC1V 9EL, UK
| |
Collapse
|
6
|
SPLIT-PIN software enabling confocal and super-resolution imaging with a virtually closed pinhole. Sci Rep 2023; 13:2741. [PMID: 36792719 PMCID: PMC9931717 DOI: 10.1038/s41598-023-29951-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 02/13/2023] [Indexed: 02/17/2023] Open
Abstract
In point-scanning microscopy, optical sectioning is achieved using a small aperture placed in front of the detector, i.e. the detection pinhole, which rejects the out-of-focus background. The maximum level of optical sectioning is theoretically obtained for the minimum size of the pinhole aperture, but this is normally prevented by the dramatic reduction of the detected signal when the pinhole is closed, leading to a compromise between axial resolution and signal-to-noise ratio. We have recently demonstrated that, instead of closing the pinhole, one can reach a similar level of optical sectioning by tuning the pinhole size in a confocal microscope and by analyzing the resulting image series. The method, consisting in the application of the separation of photons by lifetime tuning (SPLIT) algorithm to series of images acquired with tunable pinhole size, is called SPLIT-pinhole (SPLIT-PIN). Here, we share and describe a SPLIT-PIN software for the processing of series of images acquired at tunable pinhole size, which generates images with reduced out-of-focus background. The software can be used on series of at least two images acquired on available commercial microscopes equipped with a tunable pinhole, including confocal and stimulated emission depletion (STED) microscopes. We demonstrate applicability on different types of imaging modalities: (1) confocal imaging of DNA in a non-adherent cell line; (2) removal of out-of-focus background in super-resolved STED microscopy; (3) imaging of live intestinal organoids stained with a membrane dye.
Collapse
|
7
|
Durand-Smet P, Chevallier A, Colin L, Malivert A, Melogno I, Hamant O. Single-Cell Confinement Methods to Study Plant Cytoskeleton. Methods Mol Biol 2023; 2604:63-75. [PMID: 36773225 DOI: 10.1007/978-1-0716-2867-6_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] [Indexed: 02/12/2023]
Abstract
Progress in cytoskeletal research in animal systems has been accompanied by the development of single-cell systems (e.g., fibroblasts in culture). Single-cell systems exist for plant research, but the presence of a cell wall hinders the possibility to relate cytoskeleton dynamics to changes in cell shape or in mechanical stress pattern. Here we present two protocols to confine wall-less plant protoplasts in microwells with defined geometries. Either protocol might be more or less adapted to the question at hand. For instance, when using microwells made of agarose, the composition of the well can be easily modified to analyze the impact of biochemical cues. When using microwells in a stiff polymer (NOA73), protoplasts can be pressurized, and the wall of the well can be coated with cell wall components. Using both protocols, we could analyze microtubule and actin dynamics in vivo while also revealing the relative contribution of geometry and stress in their self-organization.
Collapse
Affiliation(s)
- Pauline Durand-Smet
- Laboratoire Matière et Systèmes Complexes, Unité Mixte de Recherche 7057, CNRS and Université Paris Cité, Paris cedex 13, France.
| | - Antoine Chevallier
- Laboratoire de Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCBL, INRAE, CNRS, Lyon Cedex 07, France
| | - Léia Colin
- Laboratoire de Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCBL, INRAE, CNRS, Lyon Cedex 07, France
| | - Alice Malivert
- Laboratoire de Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCBL, INRAE, CNRS, Lyon Cedex 07, France
| | - Isaty Melogno
- Laboratoire de Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCBL, INRAE, CNRS, Lyon Cedex 07, France
| | - Olivier Hamant
- Laboratoire de Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCBL, INRAE, CNRS, Lyon Cedex 07, France.
| |
Collapse
|
8
|
Chowdhury J, Ferdous J, Lihavainen J, Albrectsen BR, Lundberg-Felten J. Fluorogenic properties of 4-dimethylaminocinnamaldehyde (DMACA) enable high resolution imaging of cell-wall-bound proanthocyanidins in plant root tissues. FRONTIERS IN PLANT SCIENCE 2023; 13:1060804. [PMID: 36726681 PMCID: PMC9884812 DOI: 10.3389/fpls.2022.1060804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 12/27/2022] [Indexed: 06/18/2023]
Abstract
Proanthocyanidins (PAs) are polymeric phenolic compounds found in plants and used in many industrial applications. Despite strong evidence of herbivore and pathogen resistance-related properties of PAs, their in planta function is not fully understood. Determining the location and dynamics of PAs in plant tissues and cellular compartments is crucial to understand their mode of action. Such an approach requires microscopic localization with fluorescent dyes that specifically bind to PAs. Such dyes have hitherto been lacking. Here, we show that 4-dimethylaminocinnamaldehyde (DMACA) can be used as a PA-specific fluorescent dye that allows localization of PAs at high resolution in cell walls and inside cells using confocal microscopy, revealing features of previously unreported wall-bound PAs. We demonstrate several novel usages of DMACA as a fluorophore by taking advantage of its double staining compatibility with other fluorescent dyes. We illustrate the use of the dye alone and its co-localization with cell wall polymers in different Populus root tissues. The easy-to-use fluorescent staining method, together with its high photostability and compatibility with other fluorogenic dyes, makes DMACA a valuable tool for uncovering the biological function of PAs at a cellular level in plant tissues. DMACA can also be used in other plant tissues than roots, however care needs to be taken when tissues contain compounds that autofluoresce in the red spectral region which can be confounded with the PA-specific DMACA signal.
Collapse
Affiliation(s)
- Jamil Chowdhury
- Umeå Plant Science Center, Department of Plant Physiology, Umeå University, Umeå, Sweden
- Umeå Plant Science Center, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Jannatul Ferdous
- Umeå Plant Science Center, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Jenna Lihavainen
- Umeå Plant Science Center, Department of Plant Physiology, Umeå University, Umeå, Sweden
| | | | - Judith Lundberg-Felten
- Umeå Plant Science Center, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden
| |
Collapse
|
9
|
Lin M, Qiao P, Matschi S, Vasquez M, Ramstein GP, Bourgault R, Mohammadi M, Scanlon MJ, Molina I, Smith LG, Gore MA. Integrating GWAS and TWAS to elucidate the genetic architecture of maize leaf cuticular conductance. PLANT PHYSIOLOGY 2022; 189:2144-2158. [PMID: 35512195 PMCID: PMC9342973 DOI: 10.1093/plphys/kiac198] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 03/28/2022] [Indexed: 05/11/2023]
Abstract
The cuticle, a hydrophobic layer of cutin and waxes synthesized by plant epidermal cells, is the major barrier to water loss when stomata are closed. Dissecting the genetic architecture of natural variation for maize (Zea mays L.) leaf cuticular conductance (gc) is important for identifying genes relevant to improving crop productivity in drought-prone environments. To this end, we performed an integrated genome- and transcriptome-wide association studies (GWAS and TWAS) to identify candidate genes putatively regulating variation in leaf gc. Of the 22 plausible candidate genes identified, 4 were predicted to be involved in cuticle precursor biosynthesis and export, 2 in cell wall modification, 9 in intracellular membrane trafficking, and 7 in the regulation of cuticle development. A gene encoding an INCREASED SALT TOLERANCE1-LIKE1 (ISTL1) protein putatively involved in intracellular protein and membrane trafficking was identified in GWAS and TWAS as the strongest candidate causal gene. A set of maize nested near-isogenic lines that harbor the ISTL1 genomic region from eight donor parents were evaluated for gc, confirming the association between gc and ISTL1 in a haplotype-based association analysis. The findings of this study provide insights into the role of regulatory variation in the development of the maize leaf cuticle and will ultimately assist breeders to develop drought-tolerant maize for target environments.
Collapse
Affiliation(s)
- Meng Lin
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, New York 14853, USA
| | - Pengfei Qiao
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, New York 14853, USA
| | | | - Miguel Vasquez
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, California 92093, USA
| | | | - Richard Bourgault
- Department of Biology, Algoma University, Sault Ste Marie, ON P6A 2G4, Canada
| | - Marc Mohammadi
- Department of Biology, Algoma University, Sault Ste Marie, ON P6A 2G4, Canada
| | - Michael J Scanlon
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, New York 14853, USA
| | - Isabel Molina
- Department of Biology, Algoma University, Sault Ste Marie, ON P6A 2G4, Canada
| | - Laurie G Smith
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, California 92093, USA
| | | |
Collapse
|
10
|
D'Amico M, Di Franco E, Cerutti E, Barresi V, Condorelli D, Diaspro A, Lanzanò L. A phasor-based approach to improve optical sectioning in any confocal microscope with a tunable pinhole. Microsc Res Tech 2022; 85:3207-3216. [PMID: 35686877 PMCID: PMC9542401 DOI: 10.1002/jemt.24178] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 05/26/2022] [Accepted: 05/29/2022] [Indexed: 01/20/2023]
Abstract
Confocal fluorescence microscopy is a well‐established imaging technique capable of generating thin optical sections of biological specimens. Optical sectioning in confocal microscopy is mainly determined by the size of the pinhole, a small aperture placed in front of a point detector. In principle, imaging with a closed pinhole provides the highest degree of optical sectioning. In practice, the dramatic reduction of signal‐to‐noise ratio (SNR) at smaller pinhole sizes makes challenging the use of pinhole sizes significantly smaller than 1 Airy Unit (AU). Here, we introduce a simple method to “virtually” perform confocal imaging at smaller pinhole sizes without the dramatic reduction of SNR. The method is based on the sequential acquisition of multiple confocal images acquired at different pinhole aperture sizes and image processing based on a phasor analysis. The implementation is conceptually similar to separation of photons by lifetime tuning (SPLIT), a technique that exploits the phasor analysis to achieve super‐resolution, and for this reason we call this method SPLIT‐pinhole (SPLIT‐PIN). We show with simulated data that the SPLIT‐PIN image can provide improved optical sectioning (i.e., virtually smaller pinhole size) but better SNR with respect to an image obtained with closed pinhole. For instance, two images acquired at 2 and 1 AU can be combined to obtain a SPLIT‐PIN image with a virtual pinhole size of 0.2 AU but with better SNR. As an example of application to biological imaging, we show that SPLIT‐PIN improves confocal imaging of the apical membrane in an in vitro model of the intestinal epithelium.
Collapse
Affiliation(s)
- Morgana D'Amico
- Department of Physics and Astronomy "Ettore Majorana", University of Catania, Catania, Italy
| | - Elisabetta Di Franco
- Department of Physics and Astronomy "Ettore Majorana", University of Catania, Catania, Italy
| | - Elena Cerutti
- Department of Physics and Astronomy "Ettore Majorana", University of Catania, Catania, Italy.,Nanoscopy, CHT Erzelli, Istituto Italiano di Tecnologia, Genoa, Italy
| | - Vincenza Barresi
- Department of Biomedical and Biotechnological Sciences, Section of Medical Biochemistry, University of Catania, Catania, Italy
| | - Daniele Condorelli
- Department of Biomedical and Biotechnological Sciences, Section of Medical Biochemistry, University of Catania, Catania, Italy
| | - Alberto Diaspro
- Nanoscopy, CHT Erzelli, Istituto Italiano di Tecnologia, Genoa, Italy.,DIFILAB, Department of Physics, University of Genoa, Genoa, Italy
| | - Luca Lanzanò
- Department of Physics and Astronomy "Ettore Majorana", University of Catania, Catania, Italy.,Nanoscopy, CHT Erzelli, Istituto Italiano di Tecnologia, Genoa, Italy
| |
Collapse
|
11
|
Cuny AP, Schlottmann FP, Ewald JC, Pelet S, Schmoller KM. Live cell microscopy: From image to insight. BIOPHYSICS REVIEWS 2022; 3:021302. [PMID: 38505412 PMCID: PMC10903399 DOI: 10.1063/5.0082799] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Accepted: 03/18/2022] [Indexed: 03/21/2024]
Abstract
Live-cell microscopy is a powerful tool that can reveal cellular behavior as well as the underlying molecular processes. A key advantage of microscopy is that by visualizing biological processes, it can provide direct insights. Nevertheless, live-cell imaging can be technically challenging and prone to artifacts. For a successful experiment, many careful decisions are required at all steps from hardware selection to downstream image analysis. Facing these questions can be particularly intimidating due to the requirement for expertise in multiple disciplines, ranging from optics, biophysics, and programming to cell biology. In this review, we aim to summarize the key points that need to be considered when setting up and analyzing a live-cell imaging experiment. While we put a particular focus on yeast, many of the concepts discussed are applicable also to other organisms. In addition, we discuss reporting and data sharing strategies that we think are critical to improve reproducibility in the field.
Collapse
Affiliation(s)
| | - Fabian P. Schlottmann
- Interfaculty Institute of Cell Biology, University of Tuebingen, 72076 Tuebingen, Germany
| | - Jennifer C. Ewald
- Interfaculty Institute of Cell Biology, University of Tuebingen, 72076 Tuebingen, Germany
| | - Serge Pelet
- Department of Fundamental Microbiology, University of Lausanne, 1015 Lausanne, Switzerland
| | | |
Collapse
|
12
|
Ovečka M, Sojka J, Tichá M, Komis G, Basheer J, Marchetti C, Šamajová O, Kuběnová L, Šamaj J. Imaging plant cells and organs with light-sheet and super-resolution microscopy. PLANT PHYSIOLOGY 2022; 188:683-702. [PMID: 35235660 PMCID: PMC8825356 DOI: 10.1093/plphys/kiab349] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Accepted: 07/12/2021] [Indexed: 05/05/2023]
Abstract
The documentation of plant growth and development requires integrative and scalable approaches to investigate and spatiotemporally resolve various dynamic processes at different levels of plant body organization. The present update deals with vigorous developments in mesoscopy, microscopy and nanoscopy methods that have been translated to imaging of plant subcellular compartments, cells, tissues and organs over the past 3 years with the aim to report recent applications and reasonable expectations from current light-sheet fluorescence microscopy (LSFM) and super-resolution microscopy (SRM) modalities. Moreover, the shortcomings and limitations of existing LSFM and SRM are discussed, particularly for their ability to accommodate plant samples and regarding their documentation potential considering spherical aberrations or temporal restrictions prohibiting the dynamic recording of fast cellular processes at the three dimensions. For a more comprehensive description, advances in living or fixed sample preparation methods are also included, supported by an overview of developments in labeling strategies successfully applied in plants. These strategies are practically documented by current applications employing model plant Arabidopsis thaliana (L.) Heynh., but also robust crop species such as Medicago sativa L. and Hordeum vulgare L. Over the past few years, the trend towards designing of integrative microscopic modalities has become apparent and it is expected that in the near future LSFM and SRM will be bridged to achieve broader multiscale plant imaging with a single platform.
Collapse
Affiliation(s)
- Miroslav Ovečka
- Department of Cell Biology, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University Olomouc, Šlechtitelů 27, 783 71 Olomouc, Czech Republic
| | - Jiří Sojka
- Department of Cell Biology, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University Olomouc, Šlechtitelů 27, 783 71 Olomouc, Czech Republic
| | - Michaela Tichá
- Department of Cell Biology, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University Olomouc, Šlechtitelů 27, 783 71 Olomouc, Czech Republic
| | - George Komis
- Department of Cell Biology, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University Olomouc, Šlechtitelů 27, 783 71 Olomouc, Czech Republic
| | - Jasim Basheer
- Department of Cell Biology, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University Olomouc, Šlechtitelů 27, 783 71 Olomouc, Czech Republic
| | - Cintia Marchetti
- Centre of the Region Haná for Biotechnological and Agricultural Research, Czech Advanced Technology and Research Institute, Palacký University Olomouc, Šlechtitelů 27, 783 71 Olomouc, Czech Republic
| | - Olga Šamajová
- Department of Cell Biology, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University Olomouc, Šlechtitelů 27, 783 71 Olomouc, Czech Republic
| | - Lenka Kuběnová
- Department of Cell Biology, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University Olomouc, Šlechtitelů 27, 783 71 Olomouc, Czech Republic
| | - Jozef Šamaj
- Department of Cell Biology, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University Olomouc, Šlechtitelů 27, 783 71 Olomouc, Czech Republic
- Author for communication:
| |
Collapse
|
13
|
McKenna JF. Quantifying the Organization and Dynamics of the Plant Plasma Membrane Across Scales Using Light Microscopy. Methods Mol Biol 2022; 2457:233-251. [PMID: 35349144 DOI: 10.1007/978-1-0716-2132-5_15] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The plant cell surface continuum is composed of the cell wall, plasma membrane, and cytoskeleton. Plasmodesmata are specialized channels in the cell wall allowing intercellular communication and resource distribution. Proteins within these organelles play fundamental roles in development, perception of the external environment, and resource acquisition. Therefore, an understanding of protein dynamics and organization within the membrane and plasmodesmata is of fundamental importance to understanding both how plants develop as well as perceive the myriad of external stimuli they experience and initiate appropriate downstream responses. In this chapter, I will describe protocols for quantifying the dynamics and organization of the plasma membrane and plasmodesmata proteins across scales. The protocols described below allow researchers to determine bulk protein mobility within the membrane using fluorescence recovery after photobleaching (FRAP), imaging, and quantification of nanodomain size (with Airyscan confocal microscopy) and determining the dynamics of these nanodomains at the single particle level using total internal reflection (TIRF) single particle imaging.
Collapse
Affiliation(s)
- Joseph F McKenna
- School of Life Sciences, University of Warwick, Coventry, UK.
- Oxford Brookes University, Gypsy Lane, UK.
| |
Collapse
|
14
|
Dröge F, Noakes FF, Archer SA, Sreedharan S, Raza A, Robertson CC, MacNeil S, Haycock JW, Carson H, Meijer AJHM, Smythe CGW, Bernardino de la Serna J, Dietzek-Ivanšić B, Thomas JA. A Dinuclear Osmium(II) Complex Near-Infrared Nanoscopy Probe for Nuclear DNA. J Am Chem Soc 2021; 143:20442-20453. [PMID: 34808044 DOI: 10.1021/jacs.1c10325] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
With the aim of developing photostable near-infrared cell imaging probes, a convenient route to the synthesis of heteroleptic OsII complexes containing the Os(TAP)2 fragment is reported. This method was used to synthesize the dinuclear OsII complex, [{Os(TAP)2}2tpphz]4+ (where tpphz = tetrapyrido[3,2-a:2',3'-c:3″,2''-h:2‴,3'''-j]phenazine and TAP = 1,4,5,8- tetraazaphenanthrene). Using a combination of resonance Raman and time-resolved absorption spectroscopy, as well as computational studies, the excited state dynamics of the new complex were dissected. These studies revealed that, although the complex has several close lying excited states, its near-infrared, NIR, emission (λmax = 780 nm) is due to a low-lying Os → TAP based 3MCLT state. Cell-based studies revealed that unlike its RuII analogue, the new complex is neither cytotoxic nor photocytotoxic. However, as it is highly photostable as well as live-cell permeant and displays NIR luminescence within the biological optical window, its properties make it an ideal probe for optical microscopy, demonstrated by its use as a super-resolution NIR STED probe for nuclear DNA.
Collapse
Affiliation(s)
- Fabian Dröge
- Institute of Physical Chemistry, Helmholtzweg 4, 07743 Jena, Germany; Institute of Photonic Technology Jena e.V., Albert-Einstein-Straße 9, 07749 Jena, Germany
| | | | | | | | | | | | | | | | | | | | | | - Jorge Bernardino de la Serna
- Central Laser Facility, Rutherford Appleton Laboratory, Research Complex at Harwell, Science and Technology Facilities Council, Harwell-Oxford, Didcot OX11 0QX, United Kingdom; National Heart and Lung Institute, Faculty of Medicine, Imperial College London, Sir Alexander Fleming Building, Exhibition Road, London SW7 2AZ, United Kingdom
| | - Benjamin Dietzek-Ivanšić
- Institute of Physical Chemistry, Helmholtzweg 4, 07743 Jena, Germany; Institute of Photonic Technology Jena e.V., Albert-Einstein-Straße 9, 07749 Jena, Germany
| | | |
Collapse
|
15
|
Haddad TS, Friedl P, Farahani N, Treanor D, Zlobec I, Nagtegaal I. Tutorial: methods for three-dimensional visualization of archival tissue material. Nat Protoc 2021; 16:4945-4962. [PMID: 34716449 DOI: 10.1038/s41596-021-00611-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 08/05/2021] [Indexed: 02/08/2023]
Abstract
Analysis of three-dimensional patient specimens is gaining increasing relevance for understanding the principles of tissue structure as well as the biology and mechanisms underlying disease. New technologies are improving our ability to visualize large volume of tissues with subcellular resolution. One resource often overlooked is archival tissue maintained for decades in hospitals and research archives around the world. Accessing the wealth of information stored within these samples requires the use of appropriate methods. This tutorial introduces the range of sample preparation and microscopy approaches available for three-dimensional visualization of archival tissue. We summarize key aspects of the relevant techniques and common issues encountered when using archival tissue, including registration and antibody penetration. We also discuss analysis pipelines required to process, visualize and analyze the data and criteria to guide decision-making. The methods outlined in this tutorial provide an important and sustainable avenue for validating three-dimensional tissue organization and mechanisms of disease.
Collapse
Affiliation(s)
- Tariq Sami Haddad
- Department of Pathology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands.
| | - Peter Friedl
- Department of Cell Biology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands.,David H. Koch Center for Applied Research of Genitourinary Cancers, Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Cancer GenomiCs.nl (CGC.nl), http://cancergenomics.nl, Utrecht, the Netherlands
| | | | - Darren Treanor
- Leeds Teaching Hospitals NHS Trust, Leeds, UK.,University of Leeds, Leeds, UK.,Department of Clinical Pathology, and Department of Clinical and Experimental Medicine, Linkoping University, Linköping, Sweden.,Center for Medical Imaging Science and Visualization (CMIV), Linköping, Sweden
| | - Inti Zlobec
- Institute of Pathology, University of Bern, Bern, Switzerland
| | - Iris Nagtegaal
- Department of Pathology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| |
Collapse
|
16
|
The Development of Microscopy for Super-Resolution: Confocal Microscopy, and Image Scanning Microscopy. APPLIED SCIENCES-BASEL 2021. [DOI: 10.3390/app11198981] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Optical methods of super-resolution microscopy, such as confocal microscopy, structured illumination, nonlinear microscopy, and image scanning microscopy are reviewed. These methods avoid strong invasive interaction with a sample, allowing the observation of delicate biological samples. The meaning of resolution and the basic principles and different approaches to superresolution are discussed.
Collapse
|
17
|
Korobchevskaya K, Colin-York H, Barbieri L, Fritzsche M. Extended mechanical force measurements using structured illumination microscopy. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2021; 379:20200151. [PMID: 33896200 PMCID: PMC7612033 DOI: 10.1098/rsta.2020.0151] [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] [Accepted: 01/11/2021] [Indexed: 06/12/2023]
Abstract
Quantifying cell generated mechanical forces is key to furthering our understanding of mechanobiology. Traction force microscopy (TFM) is one of the most broadly applied force probing technologies, but its sensitivity is strictly dependent on the spatio-temporal resolution of the underlying imaging system. In previous works, it was demonstrated that increased sampling densities of cell derived forces permitted by super-resolution fluorescence imaging enhanced the sensitivity of the TFM method. However, these recent advances to TFM based on super-resolution techniques were limited to slow acquisition speeds and high illumination powers. Here, we present three novel TFM approaches that, in combination with total internal reflection, structured illumination microscopy and astigmatism, improve the spatial and temporal performance in either two-dimensional or three-dimensional mechanical force quantification, while maintaining low illumination powers. These three techniques can be straightforwardly implemented on a single optical set-up offering a powerful platform to provide new insights into the physiological force generation in a wide range of biological studies. This article is part of the Theo Murphy meeting issue 'Super-resolution structured illumination microscopy (part 1)'.
Collapse
Affiliation(s)
- Kseniya Korobchevskaya
- Kennedy Institute for Rheumatology, Roosevelt Drive, University of Oxford, Oxford, OX3 7LF, United Kingdom
| | - Huw Colin-York
- Kennedy Institute for Rheumatology, Roosevelt Drive, University of Oxford, Oxford, OX3 7LF, United Kingdom
| | - Liliana Barbieri
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Headley Way, Oxford. OX3 9DS, United Kingdom
| | - Marco Fritzsche
- Kennedy Institute for Rheumatology, Roosevelt Drive, University of Oxford, Oxford, OX3 7LF, United Kingdom
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Headley Way, Oxford. OX3 9DS, United Kingdom
- Rosalind Franklin Institute, Harwell Campus, Didcot, OX11 0FA, United Kingdom
| |
Collapse
|
18
|
Restructured Mitochondrial-Nuclear Interaction in Plasmodium falciparum Dormancy and Persister Survival after Artemisinin Exposure. mBio 2021; 12:e0075321. [PMID: 34044591 PMCID: PMC8262848 DOI: 10.1128/mbio.00753-21] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Artemisinin and its semisynthetic derivatives (ART) are fast acting, potent antimalarials; however, their use in malaria treatment is frequently confounded by recrudescences from bloodstream Plasmodium parasites that enter into and later reactivate from a dormant persister state. Here, we provide evidence that the mitochondria of dihydroartemisinin (DHA)-exposed persisters are dramatically altered and enlarged relative to the mitochondria of young, actively replicating ring forms. Restructured mitochondrial-nuclear associations and an altered metabolic state are consistent with stress from reactive oxygen species. New contacts between the mitochondria and nuclei may support communication pathways of mitochondrial retrograde signaling, resulting in transcriptional changes in the nucleus as a survival response. Further characterization of the organelle communication and metabolic dependencies of persisters may suggest strategies to combat recrudescences of malaria after treatment.
Collapse
|
19
|
Siegel N, Brooker G. Single shot holographic super-resolution microscopy. OPTICS EXPRESS 2021; 29:15953-15968. [PMID: 34154169 DOI: 10.1364/oe.424175] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 04/29/2021] [Indexed: 06/13/2023]
Abstract
An exceptionally simple and versatile advance in super-resolution microscopy has been created by adding a new birefringent FINCH holographic lens system including an inexpensive uncooled CMOS camera to a standard microscope. Resolution, after only a single image capture, is equivalent to or better than other more complex popular methods such as SIM, Airyscan and a number of image scanning microscopy methods that boost resolution about two-fold. This new FINCH implementation uniquely works for any objective power and NA and is solid state, fast, and calibration-free. In addition to being as easy to operate and maintain as a standard fluorescence microscope, it can uniquely create super-resolved images with any type or wavelength of light including fluorescence, bioluminescence or reflected light because its principle depends only on emitted light from objects and requires no prior training or knowledge about the sample being imaged. This microscope technique increases the utility and availability of super-resolution microscopy for any user in any research lab.
Collapse
|
20
|
Sims J, Schlögelhofer P, Kurzbauer MT. From Microscopy to Nanoscopy: Defining an Arabidopsis thaliana Meiotic Atlas at the Nanometer Scale. FRONTIERS IN PLANT SCIENCE 2021; 12:672914. [PMID: 34084178 PMCID: PMC8167036 DOI: 10.3389/fpls.2021.672914] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 04/27/2021] [Indexed: 06/12/2023]
Abstract
Visualization of meiotic chromosomes and the proteins involved in meiotic recombination have become essential to study meiosis in many systems including the model plant Arabidopsis thaliana. Recent advances in super-resolution technologies changed how microscopic images are acquired and analyzed. New technologies enable observation of cells and nuclei at a nanometer scale and hold great promise to the field since they allow observing complex meiotic molecular processes with unprecedented detail. Here, we provide an overview of classical and advanced sample preparation and microscopy techniques with an updated Arabidopsis meiotic atlas based on super-resolution microscopy. We review different techniques, focusing on stimulated emission depletion (STED) nanoscopy, to offer researchers guidance for selecting the optimal protocol and equipment to address their scientific question.
Collapse
|
21
|
Kubota R, Tanaka W, Hamachi I. Microscopic Imaging Techniques for Molecular Assemblies: Electron, Atomic Force, and Confocal Microscopies. Chem Rev 2021; 121:14281-14347. [DOI: 10.1021/acs.chemrev.0c01334] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Ryou Kubota
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Wataru Tanaka
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Itaru Hamachi
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
- JST-ERATO, Hamachi Innovative Molecular Technology for Neuroscience, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8530, Japan
| |
Collapse
|
22
|
Barbieri L, Colin-York H, Korobchevskaya K, Li D, Wolfson DL, Karedla N, Schneider F, Ahluwalia BS, Seternes T, Dalmo RA, Dustin ML, Li D, Fritzsche M. Two-dimensional TIRF-SIM-traction force microscopy (2D TIRF-SIM-TFM). Nat Commun 2021; 12:2169. [PMID: 33846317 PMCID: PMC8041833 DOI: 10.1038/s41467-021-22377-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 03/12/2021] [Indexed: 02/01/2023] Open
Abstract
Quantifying small, rapidly evolving forces generated by cells is a major challenge for the understanding of biomechanics and mechanobiology in health and disease. Traction force microscopy remains one of the most broadly applied force probing technologies but typically restricts itself to slow events over seconds and micron-scale displacements. Here, we improve >2-fold spatially and >10-fold temporally the resolution of planar cellular force probing compared to its related conventional modalities by combining fast two-dimensional total internal reflection fluorescence super-resolution structured illumination microscopy and traction force microscopy. This live-cell 2D TIRF-SIM-TFM methodology offers a combination of spatio-temporal resolution enhancement relevant to forces on the nano- and sub-second scales, opening up new aspects of mechanobiology to analysis.
Collapse
Grants
- Biotechnology and Biological Sciences Research Council
- 212343/Z/18/Z Wellcome Trust
- 107457 Wellcome Trust
- 100262/Z/12/Z Wellcome Trust
- Wellcome Trust
- 091911 Wellcome Trust
- Medical Research Council
- L.B. would like to acknowledge funding from the Engineering and Physical Sciences Research Council (EPSRC) and Medical Research Council (EP/L016052/1). M.F., H.C.Y., K.K., and M.L.D. would like to thank the Rosalind Franklin Institute and the Kennedy Trust for Rheumatology Research (KTRR) for support. M.F., F.S., and H.C.Y. thank the Wellcome Trust (212343/Z/18/Z) and EPSRC (EP/S004459/1). M.L.D. also thank the Wellcome Trust for the Principal Research Fellowship awarded to M.D. (100262/Z/12/Z). Di.L. and D.L. are supported by a grant from the Chinese Ministry of Science and Technology (MOST: 2017YFA0505301, 2016YFA0500203), the National Natural Science Foundation of China (NSFC; 91754202, 31827802), and the Youth Innovation Promotion Association of Chinese Academy of Sciences (Grant No. 2020094). N.K. thanks the Alexander von Humboldt Foundation for funding his Feoder Lynen Fellowship. R.A.D acknowledge the Research Council of Norway (grant no. 301401) for funding. The TIRF-SIM platform was built in collaboration with and with funds from Micron (www.micronoxford.com), an Oxford-wide advanced microscopy technology consortium supported by Wellcome Strategic Awards (091911 and 107457) and an MRC/EPSRC/BBSRC next generation imaging award.
Collapse
Affiliation(s)
- Liliana Barbieri
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Huw Colin-York
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Kennedy Institute for Rheumatology, University of Oxford, Oxford, UK
| | | | - Di Li
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Deanna L Wolfson
- Department of Physics and Technology, UiT The Arctic University of Norway, Tromsø, Norway
| | - Narain Karedla
- Kennedy Institute for Rheumatology, University of Oxford, Oxford, UK
- Rosalind Franklin Institute, Didcot, UK
| | - Falk Schneider
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Kennedy Institute for Rheumatology, University of Oxford, Oxford, UK
| | - Balpreet S Ahluwalia
- Department of Physics and Technology, UiT The Arctic University of Norway, Tromsø, Norway
| | - Tore Seternes
- Norwegian College of Fishery Science, UiT The Arctic University of Norway, Tromsø, Norway
| | - Roy A Dalmo
- Norwegian College of Fishery Science, UiT The Arctic University of Norway, Tromsø, Norway
| | - Michael L Dustin
- Kennedy Institute for Rheumatology, University of Oxford, Oxford, UK
| | - Dong Li
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.
| | - Marco Fritzsche
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.
- Kennedy Institute for Rheumatology, University of Oxford, Oxford, UK.
- Rosalind Franklin Institute, Didcot, UK.
| |
Collapse
|
23
|
Kubalová I, Němečková A, Weisshart K, Hřibová E, Schubert V. Comparing Super-Resolution Microscopy Techniques to Analyze Chromosomes. Int J Mol Sci 2021; 22:ijms22041903. [PMID: 33672992 PMCID: PMC7917581 DOI: 10.3390/ijms22041903] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 02/04/2021] [Accepted: 02/10/2021] [Indexed: 12/21/2022] Open
Abstract
The importance of fluorescence light microscopy for understanding cellular and sub-cellular structures and functions is undeniable. However, the resolution is limited by light diffraction (~200–250 nm laterally, ~500–700 nm axially). Meanwhile, super-resolution microscopy, such as structured illumination microscopy (SIM), is being applied more and more to overcome this restriction. Instead, super-resolution by stimulated emission depletion (STED) microscopy achieving a resolution of ~50 nm laterally and ~130 nm axially has not yet frequently been applied in plant cell research due to the required specific sample preparation and stable dye staining. Single-molecule localization microscopy (SMLM) including photoactivated localization microscopy (PALM) has not yet been widely used, although this nanoscopic technique allows even the detection of single molecules. In this study, we compared protein imaging within metaphase chromosomes of barley via conventional wide-field and confocal microscopy, and the sub-diffraction methods SIM, STED, and SMLM. The chromosomes were labeled by DAPI (4′,6-diamidino-2-phenylindol), a DNA-specific dye, and with antibodies against topoisomerase IIα (Topo II), a protein important for correct chromatin condensation. Compared to the diffraction-limited methods, the combination of the three different super-resolution imaging techniques delivered tremendous additional insights into the plant chromosome architecture through the achieved increased resolution.
Collapse
Affiliation(s)
- Ivona Kubalová
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, D-06466 Seeland, Germany;
| | - Alžběta Němečková
- Centre of the Region Hana for Biotechnological and Agricultural Research, Institute of Experimental Botany of the Czech Academy of Sciences, 77900 Olomouc, Czech Republic; (A.N.); (E.H.)
| | | | - Eva Hřibová
- Centre of the Region Hana for Biotechnological and Agricultural Research, Institute of Experimental Botany of the Czech Academy of Sciences, 77900 Olomouc, Czech Republic; (A.N.); (E.H.)
| | - Veit Schubert
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, D-06466 Seeland, Germany;
- Correspondence: ; Tel.: +49-394-825-212
| |
Collapse
|
24
|
Titlow J, Robertson F, Järvelin A, Ish-Horowicz D, Smith C, Gratton E, Davis I. Syncrip/hnRNP Q is required for activity-induced Msp300/Nesprin-1 expression and new synapse formation. J Cell Biol 2020; 219:133707. [PMID: 32040548 PMCID: PMC7055005 DOI: 10.1083/jcb.201903135] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 08/21/2019] [Accepted: 12/12/2019] [Indexed: 01/09/2023] Open
Abstract
Memory and learning involve activity-driven expression of proteins and cytoskeletal reorganization at new synapses, requiring posttranscriptional regulation of localized mRNA a long distance from corresponding nuclei. A key factor expressed early in synapse formation is Msp300/Nesprin-1, which organizes actin filaments around the new synapse. How Msp300 expression is regulated during synaptic plasticity is poorly understood. Here, we show that activity-dependent accumulation of Msp300 in the postsynaptic compartment of the Drosophila larval neuromuscular junction is regulated by the conserved RNA binding protein Syncrip/hnRNP Q. Syncrip (Syp) binds to msp300 transcripts and is essential for plasticity. Single-molecule imaging shows that msp300 is associated with Syp in vivo and forms ribosome-rich granules that contain the translation factor eIF4E. Elevated neural activity alters the dynamics of Syp and the number of msp300:Syp:eIF4E RNP granules at the synapse, suggesting that these particles facilitate translation. These results introduce Syp as an important early acting activity-dependent regulator of a plasticity gene that is strongly associated with human ataxias.
Collapse
Affiliation(s)
- Joshua Titlow
- Department of Biochemistry, University of Oxford, Oxford, UK
| | | | - Aino Järvelin
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - David Ish-Horowicz
- Department of Biochemistry, University of Oxford, Oxford, UK.,Medical Research Council Lab for Molecular Cell Biology, University College London, London, UK
| | - Carlas Smith
- Centre for Neural Circuits and Behaviour, University of Oxford, Oxford, UK
| | - Enrico Gratton
- Laboratory for Fluorescence Dynamics, University of California Irvine, Irvine, CA
| | - Ilan Davis
- Department of Biochemistry, University of Oxford, Oxford, UK
| |
Collapse
|
25
|
Ranjit S, Lanzanò L, Libby AE, Gratton E, Levi M. Advances in fluorescence microscopy techniques to study kidney function. Nat Rev Nephrol 2020; 17:128-144. [PMID: 32948857 DOI: 10.1038/s41581-020-00337-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/30/2020] [Indexed: 02/07/2023]
Abstract
Fluorescence microscopy, in particular immunofluorescence microscopy, has been used extensively for the assessment of kidney function and pathology for both research and diagnostic purposes. The development of confocal microscopy in the 1950s enabled imaging of live cells and intravital imaging of the kidney; however, confocal microscopy is limited by its maximal spatial resolution and depth. More recent advances in fluorescence microscopy techniques have enabled increasingly detailed assessment of kidney structure and provided extraordinary insights into kidney function. For example, nanoscale precise imaging by rapid beam oscillation (nSPIRO) is a super-resolution microscopy technique that was originally developed for functional imaging of kidney microvilli and enables detection of dynamic physiological events in the kidney. A variety of techniques such as fluorescence recovery after photobleaching (FRAP), fluorescence correlation spectroscopy (FCS) and Förster resonance energy transfer (FRET) enable assessment of interaction between proteins. The emergence of other super-resolution techniques, including super-resolution stimulated emission depletion (STED), photoactivated localization microscopy (PALM), stochastic optical reconstruction microscopy (STORM) and structured illumination microscopy (SIM), has enabled functional imaging of cellular and subcellular organelles at ≤50 nm resolution. The deep imaging via emission recovery (DIVER) detector allows deep, label-free and high-sensitivity imaging of second harmonics, enabling assessment of processes such as fibrosis, whereas fluorescence lifetime imaging microscopy (FLIM) enables assessment of metabolic processes.
Collapse
Affiliation(s)
- Suman Ranjit
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, Washington, DC, USA. .,Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California, Irvine, CA, USA.
| | - Luca Lanzanò
- Nanoscopy and NIC@IIT, Istituto Italiano di Tecnologia, Genoa, Italy.,Department of Physics and Astronomy "Ettore Majorana", University of Catania, Catania, Italy
| | - Andrew E Libby
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, Washington, DC, USA
| | - Enrico Gratton
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California, Irvine, CA, USA.
| | - Moshe Levi
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, Washington, DC, USA.
| |
Collapse
|
26
|
Abstract
The light (or optical) microscope is the icon of science. The aphorism "seeing is believing" is often quoted in scientific papers involving microscopy. Unlike many scientific instruments, the light microscope will deliver an image however badly it is set up. Fluorescence microscopy is a widely used research tool across all disciplines of biological and biomedical science. Most universities and research institutions have microscopes, including confocal microscopes. This introductory paper in a series detailing advanced light microscopy techniques explains the foundations of both electron and light microscopy for biologists and life scientists working with the mouse. An explanation is given of how an image is formed. A description is given of how to set up a light microscope, whether it be a brightfield light microscope on the laboratory bench, a widefield fluorescence microscope, or a confocal microscope. These explanations are accompanied by operational protocols. A full explanation on how to set up and adjust a microscope according to the principles of Köhler illumination is given. The importance of Nyquist sampling is discussed. Guidelines are given on how to choose the best microscope to image the particular sample or slide preparation that you are working with. These are the basic principles of microscopy that a researcher must have an understanding of when operating core bioimaging facility instruments, in order to collect high-quality images. © 2020 The Authors. Basic Protocol 1: Setting up Köhler illumination for a brightfield microscope Basic Protocol 2: Aligning the fluorescence bulb and setting up Köhler illumination for a widefield fluorescence microscope Basic Protocol 3: Generic protocol for operating a confocal microscope.
Collapse
Affiliation(s)
- Jeremy Sanderson
- Bioimaging Facility Manager, MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Oxfordshire, UK
| |
Collapse
|
27
|
Jonkman J, Brown CM, Wright GD, Anderson KI, North AJ. Tutorial: guidance for quantitative confocal microscopy. Nat Protoc 2020. [PMID: 32235926 DOI: 10.1038/s41596-020-0313-319] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
When used appropriately, a confocal fluorescence microscope is an excellent tool for making quantitative measurements in cells and tissues. The confocal microscope's ability to block out-of-focus light and thereby perform optical sectioning through a specimen allows the researcher to quantify fluorescence with very high spatial precision. However, generating meaningful data using confocal microscopy requires careful planning and a thorough understanding of the technique. In this tutorial, the researcher is guided through all aspects of acquiring quantitative confocal microscopy images, including optimizing sample preparation for fixed and live cells, choosing the most suitable microscope for a given application and configuring the microscope parameters. Suggestions are offered for planning unbiased and rigorous confocal microscope experiments. Common pitfalls such as photobleaching and cross-talk are addressed, as well as several troubling instrumentation problems that may prevent the acquisition of quantitative data. Finally, guidelines for analyzing and presenting confocal images in a way that maintains the quantitative nature of the data are presented, and statistical analysis is discussed. A visual summary of this tutorial is available as a poster (https://doi.org/10.1038/s41596-020-0307-7).
Collapse
Affiliation(s)
- James Jonkman
- Advanced Optical Microscopy Facility (AOMF), University Health Network, Toronto, Ontario, Canada.
| | - Claire M Brown
- Advanced BioImaging Facility (ABIF), McGill University, Montreal, Quebec, Canada
| | - Graham D Wright
- A*STAR Microscopy Platform (AMP), Skin Research Institute of Singapore, A*STAR, Singapore, Singapore
| | - Kurt I Anderson
- Crick Advanced Light Microscopy Facility (CALM), The Francis Crick Institute, London, UK
| | - Alison J North
- Bio-Imaging Resource Center, The Rockefeller University, New York, NY, USA
| |
Collapse
|
28
|
Tichá M, Hlaváčková K, Hrbáčková M, Ovečka M, Šamajová O, Šamaj J. Super-resolution imaging of microtubules in Medicago sativa. Methods Cell Biol 2020; 160:237-251. [PMID: 32896319 DOI: 10.1016/bs.mcb.2020.03.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Study of microtubules on cellular and subcellular levels is compromised by limited resolution of conventional fluorescence microscopy. However, it is possible to improve Abbe's diffraction-limited resolution by employment of super-resolution microscopy methods. Two of them, described herein, are structured-illumination microscopy (SIM) and Airyscan laser scanning microscopy (AM). Both methods allow high-resolution imaging of cortical microtubules in plant cells, thus contributing to the current knowledge on plant morphogenesis, growth and development. Both SIM and AM provide certain advantages and characteristic features, which are described here. We present immunofluorescence localization methods for microtubules in fixed plant cells achieving high signal efficiency, superb sample stability and sub-diffraction resolution. These protocols were developed for whole-mount immunolabeling of root samples of legume crop species Medicago sativa. They also contain tips for optimal sample preparation of plants germinated from seeds as well as plantlets regenerated from somatic embryos in vitro. We describe in detail all steps of optimized protocols for sample preparation, microtubule immunolabeling and super-resolution imaging.
Collapse
Affiliation(s)
- Michaela Tichá
- Department of Cell Biology, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University Olomouc, Olomouc, Czech Republic
| | - Kateřina Hlaváčková
- Department of Cell Biology, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University Olomouc, Olomouc, Czech Republic
| | - Miroslava Hrbáčková
- Department of Cell Biology, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University Olomouc, Olomouc, Czech Republic
| | - Miroslav Ovečka
- Department of Cell Biology, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University Olomouc, Olomouc, Czech Republic
| | - Olga Šamajová
- Department of Cell Biology, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University Olomouc, Olomouc, Czech Republic
| | - Jozef Šamaj
- Department of Cell Biology, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University Olomouc, Olomouc, Czech Republic.
| |
Collapse
|
29
|
Jonkman J, Brown CM, Wright GD, Anderson KI, North AJ. Tutorial: guidance for quantitative confocal microscopy. Nat Protoc 2020; 15:1585-1611. [DOI: 10.1038/s41596-020-0313-9] [Citation(s) in RCA: 105] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2019] [Accepted: 02/10/2020] [Indexed: 01/04/2023]
|
30
|
Cawte AD, Unrau PJ, Rueda DS. Live cell imaging of single RNA molecules with fluorogenic Mango II arrays. Nat Commun 2020; 11:1283. [PMID: 32152311 PMCID: PMC7062757 DOI: 10.1038/s41467-020-14932-7] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 01/30/2020] [Indexed: 01/19/2023] Open
Abstract
RNA molecules play vital roles in many cellular processes. Visualising their dynamics in live cells at single-molecule resolution is essential to elucidate their role in RNA metabolism. RNA aptamers, such as Spinach and Mango, have recently emerged as a powerful background-free technology for live-cell RNA imaging due to their fluorogenic properties upon ligand binding. Here, we report a novel array of Mango II aptamers for RNA imaging in live and fixed cells with high contrast and single-molecule sensitivity. Direct comparison of Mango II and MS2-tdMCP-mCherry dual-labelled mRNAs show marked improvements in signal to noise ratio using the fluorogenic Mango aptamers. Using both coding (β-actin mRNA) and long non-coding (NEAT1) RNAs, we show that the Mango array does not affect cellular localisation. Additionally, we can track single mRNAs for extended time periods, likely due to bleached fluorophore replacement. This property makes the arrays readily compatible with structured illumination super-resolution microscopy.
Collapse
Affiliation(s)
- Adam D Cawte
- Single Molecule Imaging Group, MRC London Institute of Medical Sciences, Du Cane Rd, London, UK
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, Du Cane Rd, London, UK
| | - Peter J Unrau
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC, Canada.
| | - David S Rueda
- Single Molecule Imaging Group, MRC London Institute of Medical Sciences, Du Cane Rd, London, UK.
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, Du Cane Rd, London, UK.
| |
Collapse
|
31
|
Barlow AM, Mostaço-Guidolin LB, Osei ET, Booth S, Hackett TL. Super resolution measurement of collagen fibers in biological samples: Validation of a commercial solution for multiphoton microscopy. PLoS One 2020; 15:e0229278. [PMID: 32059025 PMCID: PMC7021303 DOI: 10.1371/journal.pone.0229278] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Accepted: 02/03/2020] [Indexed: 01/06/2023] Open
Abstract
Multiphoton microscopy is a powerful, non-invasive technique to image biological specimens. One current limitation of multiphoton microscopy is resolution as many of the biological molecules and structures investigated by research groups are similar in size or smaller than the diffraction limit. To date, the combination of multiphoton and super-resolution imaging has proved technically challenging for biology focused laboratories to implement. Here we validate that the commercial super-resolution Airyscan detector from ZEISS, which is based on image scanning microscopy, can be integrated under warranty with a pulsed multi-photon laser to enable multiphoton microscopy with super-resolution. We demonstrate its biological application in two different imaging modalities, second harmonic generation (SHG) and two-photon excited fluorescence (TPEF), to measure the fibre thicknesses of collagen and elastin molecules surpassing the diffraction limit by a factor of 1.7±0.3x and 1.4±0.3x respectively, in human heart and lung tissues, and 3-dimensional in vitro models. We show that enhanced resolution and signal-to-noise of SHG using the Airyscan compared to traditional GaAs detectors allows for automated and precise measurement of collagen fibres using texture analysis in biological tissues.
Collapse
Affiliation(s)
- Aaron M. Barlow
- Centre for Heart Lung Innovation, St. Paul’s Hospital, Vancouver, BC, Canada
| | - Leila B. Mostaço-Guidolin
- Centre for Heart Lung Innovation, St. Paul’s Hospital, Vancouver, BC, Canada
- Department of Anesthesiology, Pharmacology and Therapeutics, University of British Columbia, Vancouver, BC, Canada
- Department of Systems and Computer Engineering, Carleton University, Ottawa, ON, Canada
| | - Emmanuel T. Osei
- Centre for Heart Lung Innovation, St. Paul’s Hospital, Vancouver, BC, Canada
- Department of Anesthesiology, Pharmacology and Therapeutics, University of British Columbia, Vancouver, BC, Canada
| | - Steven Booth
- Centre for Heart Lung Innovation, St. Paul’s Hospital, Vancouver, BC, Canada
- Department of Anesthesiology, Pharmacology and Therapeutics, University of British Columbia, Vancouver, BC, Canada
| | - Tillie-Louise Hackett
- Centre for Heart Lung Innovation, St. Paul’s Hospital, Vancouver, BC, Canada
- Department of Anesthesiology, Pharmacology and Therapeutics, University of British Columbia, Vancouver, BC, Canada
| |
Collapse
|
32
|
Lorenzo LE, Godin AG, Ferrini F, Bachand K, Plasencia-Fernandez I, Labrecque S, Girard AA, Boudreau D, Kianicka I, Gagnon M, Doyon N, Ribeiro-da-Silva A, De Koninck Y. Enhancing neuronal chloride extrusion rescues α2/α3 GABA A-mediated analgesia in neuropathic pain. Nat Commun 2020; 11:869. [PMID: 32054836 PMCID: PMC7018745 DOI: 10.1038/s41467-019-14154-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 12/16/2019] [Indexed: 02/06/2023] Open
Abstract
Spinal disinhibition has been hypothesized to underlie pain hypersensitivity in neuropathic pain. Apparently contradictory mechanisms have been reported, raising questions on the best target to produce analgesia. Here, we show that nerve injury is associated with a reduction in the number of inhibitory synapses in the spinal dorsal horn. Paradoxically, this is accompanied by a BDNF-TrkB-mediated upregulation of synaptic GABAARs and by an α1-to-α2GABAAR subunit switch, providing a mechanistic rationale for the analgesic action of the α2,3GABAAR benzodiazepine-site ligand L838,417 after nerve injury. Yet, we demonstrate that impaired Cl- extrusion underlies the failure of L838,417 to induce analgesia at high doses due to a resulting collapse in Cl- gradient, dramatically limiting the benzodiazepine therapeutic window. In turn, enhancing KCC2 activity not only potentiated L838,417-induced analgesia, it rescued its analgesic potential at high doses, revealing a novel strategy for analgesia in pathological pain, by combined targeting of the appropriate GABAAR-subtypes and restoring Cl- homeostasis.
Collapse
Affiliation(s)
- Louis-Etienne Lorenzo
- CERVO Brain Research Centre, Quebec Mental Health Institute, Québec, QC, Canada
- Department of Pharmacology & Therapeutics, McGill University, Montreal, QC, Canada
| | - Antoine G Godin
- CERVO Brain Research Centre, Quebec Mental Health Institute, Québec, QC, Canada
- Department of Psychiatry & Neuroscience, Université Laval, Québec, QC, Canada
- Graduate program in Neuroscience, Université Laval, Québec, QC, Canada
| | - Francesco Ferrini
- CERVO Brain Research Centre, Quebec Mental Health Institute, Québec, QC, Canada
- Department of Psychiatry & Neuroscience, Université Laval, Québec, QC, Canada
- Graduate program in Neuroscience, Université Laval, Québec, QC, Canada
- Department of Veterinary Sciences, University of Turin, Turin, Italy
| | - Karine Bachand
- CERVO Brain Research Centre, Quebec Mental Health Institute, Québec, QC, Canada
| | - Isabel Plasencia-Fernandez
- CERVO Brain Research Centre, Quebec Mental Health Institute, Québec, QC, Canada
- Graduate program in Neuroscience, Université Laval, Québec, QC, Canada
| | - Simon Labrecque
- CERVO Brain Research Centre, Quebec Mental Health Institute, Québec, QC, Canada
| | - Alexandre A Girard
- CERVO Brain Research Centre, Quebec Mental Health Institute, Québec, QC, Canada
- Ecole Polytechnique, IP Paris, Palaiseau, France
| | - Dominic Boudreau
- CERVO Brain Research Centre, Quebec Mental Health Institute, Québec, QC, Canada
- Graduate program in Neuroscience, Université Laval, Québec, QC, Canada
| | - Irenej Kianicka
- Chlorion Pharma, Laval, Québec, QC, Canada
- Laurent Pharmaceuticals Inc., Montreal, QC, Canada
| | - Martin Gagnon
- CERVO Brain Research Centre, Quebec Mental Health Institute, Québec, QC, Canada
- Centre for Innovation, University of Otago, Dunedin, New Zealand
| | - Nicolas Doyon
- CERVO Brain Research Centre, Quebec Mental Health Institute, Québec, QC, Canada
- Finite Element Interdisciplinary Research Group (GIREF), Université Laval, Québec, QC, Canada
| | - Alfredo Ribeiro-da-Silva
- Department of Pharmacology & Therapeutics, McGill University, Montreal, QC, Canada
- Department of Anatomy & Cell Biology, McGill University, Montreal, QC, Canada
- Alan Edwards Centre for Research on Pain, McGill University, Montreal, QC, Canada
| | - Yves De Koninck
- CERVO Brain Research Centre, Quebec Mental Health Institute, Québec, QC, Canada.
- Department of Pharmacology & Therapeutics, McGill University, Montreal, QC, Canada.
- Department of Psychiatry & Neuroscience, Université Laval, Québec, QC, Canada.
- Graduate program in Neuroscience, Université Laval, Québec, QC, Canada.
- Alan Edwards Centre for Research on Pain, McGill University, Montreal, QC, Canada.
| |
Collapse
|
33
|
Deroubaix A, Moahla B, Penny C. Monitoring of intracellular localization of Hepatitis B virus P22 protein using Laser Scanning Confocal Microscopy and Airyscan. Microsc Res Tech 2020; 83:499-506. [PMID: 31926041 DOI: 10.1002/jemt.23438] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 12/03/2019] [Accepted: 12/27/2019] [Indexed: 11/09/2022]
Abstract
The aim of this study was to assess nucleo-cytoplasmic protein localization to better understand the exact intracellular localization of viral proteins involved with infections. Having determined the general protein localization of hepatitis B virus P22 precore protein, the aim was to more specifically resolve its intracellular organization. This was done using both laser scanning microscopy and Airyscan techniques. Using a 63× objective, the resolution obtained with Airyscan was increased by 1.5-fold as compared to confocal microscopy (p value <.00001).
Collapse
Affiliation(s)
- Aurélie Deroubaix
- Life Sciences Imaging Facility, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,HVDRU, School of Clinical Medicine, Department of Internal Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Bongani Moahla
- HVDRU, School of Clinical Medicine, Department of Internal Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Clement Penny
- Life Sciences Imaging Facility, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,Oncology Division, School of Clinical Medicine, Department of Internal Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| |
Collapse
|
34
|
Vavrdová T, Křenek P, Ovečka M, Šamajová O, Floková P, Illešová P, Šnaurová R, Šamaj J, Komis G. Complementary Superresolution Visualization of Composite Plant Microtubule Organization and Dynamics. FRONTIERS IN PLANT SCIENCE 2020; 11:693. [PMID: 32582243 PMCID: PMC7290007 DOI: 10.3389/fpls.2020.00693] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Accepted: 05/01/2020] [Indexed: 05/04/2023]
Abstract
Microtubule bundling is an essential mechanism underlying the biased organization of interphase and mitotic microtubular systems of eukaryotes in ordered arrays. Microtubule bundle formation can be exemplified in plants, where the formation of parallel microtubule systems in the cell cortex or the spindle midzone is largely owing to the microtubule crosslinking activity of a family of microtubule associated proteins, designated as MAP65s. Among the nine members of this family in Arabidopsis thaliana, MAP65-1 and MAP65-2 are ubiquitous and functionally redundant. Crosslinked microtubules can form high-order arrays, which are difficult to track using widefield or confocal laser scanning microscopy approaches. Here, we followed spatiotemporal patterns of MAP65-2 localization in hypocotyl cells of Arabidopsis stably expressing fluorescent protein fusions of MAP65-2 and tubulin. To circumvent imaging difficulties arising from the density of cortical microtubule bundles, we use different superresolution approaches including Airyscan confocal laser scanning microscopy (ACLSM), structured illumination microscopy (SIM), total internal reflection SIM (TIRF-SIM), and photoactivation localization microscopy (PALM). We provide insights into spatiotemporal relations between microtubules and MAP65-2 crossbridges by combining SIM and ACLSM. We obtain further details on MAP65-2 distribution by single molecule localization microscopy (SMLM) imaging of either mEos3.2-MAP65-2 stochastic photoconversion, or eGFP-MAP65-2 stochastic emission fluctuations under specific illumination conditions. Time-dependent dynamics of MAP65-2 were tracked at variable time resolution using SIM, TIRF-SIM, and ACLSM and post-acquisition kymograph analysis. ACLSM imaging further allowed to track end-wise dynamics of microtubules labeled with TUA6-GFP and to correlate them with concomitant fluctuations of MAP65-2 tagged with tagRFP. All different microscopy modules examined herein are accompanied by restrictions in either the spatial resolution achieved, or in the frame rates of image acquisition. PALM imaging is compromised by speed of acquisition. This limitation was partially compensated by exploiting emission fluctuations of eGFP which allowed much higher photon counts at substantially smaller time series compared to mEos3.2. SIM, TIRF-SIM, and ACLSM were the methods of choice to follow the dynamics of MAP65-2 in bundles of different complexity. Conclusively, the combination of different superresolution methods allowed for inferences on the distribution and dynamics of MAP65-2 within microtubule bundles of living A. thaliana cells.
Collapse
|
35
|
Somaratne G, Nau F, Ferrua MJ, Singh J, Ye A, Dupont D, Singh RP, Floury J. Characterization of egg white gel microstructure and its relationship with pepsin diffusivity. Food Hydrocoll 2020. [DOI: 10.1016/j.foodhyd.2019.105258] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
|
36
|
Coyle SM, Flaum EM, Li H, Krishnamurthy D, Prakash M. Coupled Active Systems Encode an Emergent Hunting Behavior in the Unicellular Predator Lacrymaria olor. Curr Biol 2019; 29:3838-3850.e3. [PMID: 31679941 PMCID: PMC7511173 DOI: 10.1016/j.cub.2019.09.034] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 07/11/2019] [Accepted: 09/13/2019] [Indexed: 12/23/2022]
Abstract
Many single-celled protists use rapid morphology changes to perform fast animal-like behaviors. To understand how such behaviors are encoded, we analyzed the hunting dynamics of the predatory ciliate Lacrymaria olor, which locates and captures prey using the tip of a slender "neck" that can rapidly extend more than seven times its body length (500 μm from its body) and retract in seconds. By tracking single cells in real-time over hours and analyzing millions of sub-cellular postures, we find that these fast extension-contraction cycles underlie an emergent hunting behavior that comprehensively samples a broad area within the cell's reach. Although this behavior appears complex, we show that it arises naturally as alternating sub-cellular ciliary and contractile activities rearrange the cell's underlying helical cytoskeleton to extend or retract the neck. At short timescales, a retracting neck behaves like an elastic filament under load, such that compression activates a series of buckling modes that reorient the head and scramble its extensile trajectory. At longer timescales, the fundamental length of this filament can change, altering the location in space where these transitions occur. Coupling these fast and slow dynamics together, we present a simple model for how Lacrymaria samples the range of geometries and orientations needed to ensure dense stochastic sampling of the immediate environment when hunting to locate and strike at prey. More generally, coupling active mechanical and chemical signaling systems across different timescales may provide a general strategy by which mechanically encoded emergent cell behaviors can be understood or engineered.
Collapse
Affiliation(s)
- Scott M Coyle
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Eliott M Flaum
- Graduate Program in Biophysics, Stanford University, Stanford, CA 94305, USA
| | - Hongquan Li
- Graduate Program in Electrical Engineering, Stanford University, Stanford, CA 94305, USA
| | - Deepak Krishnamurthy
- Graduate Program in Mechanical Engineering, Stanford University, Stanford, CA 94305, USA
| | - Manu Prakash
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA; Howard Hughes Medical Institute Faculty Scholar, Stanford University, Stanford, CA 94305, USA; Chan Zuckerberg BioHub Investigator, Stanford University, Stanford, CA 94305, USA.
| |
Collapse
|
37
|
Casting a Wider Net: Differentiating between Inner Nuclear Envelope and Outer Nuclear Envelope Transmembrane Proteins. Int J Mol Sci 2019; 20:ijms20215248. [PMID: 31652739 PMCID: PMC6862087 DOI: 10.3390/ijms20215248] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 10/17/2019] [Accepted: 10/18/2019] [Indexed: 12/11/2022] Open
Abstract
The nuclear envelope (NE) surrounds the nucleus with a double membrane in eukaryotic cells. The double membranes are embedded with proteins that are synthesized on the endoplasmic reticulum and often destined specifically for either the outer nuclear membrane (ONM) or the inner nuclear membrane (INM). These nuclear envelope transmembrane proteins (NETs) play important roles in cellular function and participate in transcription, epigenetics, splicing, DNA replication, genome architecture, nuclear structure, nuclear stability, nuclear organization, and nuclear positioning. These vital functions are dependent upon both the correct localization and relative concentrations of NETs on the appropriate membrane of the NE. It is, therefore, important to understand the distribution and abundance of NETs on the NE. This review will evaluate the current tools and methodologies available to address this important topic.
Collapse
|
38
|
Cuentas-Condori A, Mulcahy B, He S, Palumbos S, Zhen M, Miller DM. C. elegans neurons have functional dendritic spines. eLife 2019; 8:e47918. [PMID: 31584430 PMCID: PMC6802951 DOI: 10.7554/elife.47918] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Accepted: 10/03/2019] [Indexed: 12/15/2022] Open
Abstract
Dendritic spines are specialized postsynaptic structures that transduce presynaptic signals, are regulated by neural activity and correlated with learning and memory. Most studies of spine function have focused on the mammalian nervous system. However, spine-like protrusions have been reported in C. elegans (Philbrook et al., 2018), suggesting that the experimental advantages of smaller model organisms could be exploited to study the biology of dendritic spines. Here, we used super-resolution microscopy, electron microscopy, live-cell imaging and genetics to show that C. elegans motor neurons have functional dendritic spines that: (1) are structurally defined by a dynamic actin cytoskeleton; (2) appose presynaptic dense projections; (3) localize ER and ribosomes; (4) display calcium transients triggered by presynaptic activity and propagated by internal Ca++ stores; (5) respond to activity-dependent signals that regulate spine density. These studies provide a solid foundation for a new experimental paradigm that exploits the power of C. elegans genetics and live-cell imaging for fundamental studies of dendritic spine morphogenesis and function.
Collapse
Affiliation(s)
| | - Ben Mulcahy
- Lunenfeld-Tanenbaum Research InstituteUniversity of TorontoTorontoCanada
| | - Siwei He
- Neuroscience ProgramVanderbilt UniversityNashvilleUnited States
| | - Sierra Palumbos
- Neuroscience ProgramVanderbilt UniversityNashvilleUnited States
| | - Mei Zhen
- Lunenfeld-Tanenbaum Research InstituteUniversity of TorontoTorontoCanada
| | - David M Miller
- Department of Cell and Developmental BiologyVanderbilt UniversityNashvilleUnited States
- Neuroscience ProgramVanderbilt UniversityNashvilleUnited States
| |
Collapse
|
39
|
Saliba DG, Céspedes-Donoso PF, Bálint Š, Compeer EB, Korobchevskaya K, Valvo S, Mayya V, Kvalvaag A, Peng Y, Dong T, Tognoli ML, O'Neill E, Bonham S, Fischer R, Kessler BM, Dustin ML. Composition and structure of synaptic ectosomes exporting antigen receptor linked to functional CD40 ligand from helper T cells. eLife 2019; 8:e47528. [PMID: 31469364 PMCID: PMC6748831 DOI: 10.7554/elife.47528] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 08/28/2019] [Indexed: 12/21/2022] Open
Abstract
Planar supported lipid bilayers (PSLB) presenting T cell receptor (TCR) ligands and ICAM-1 induce budding of extracellular microvesicles enriched in functional TCR, defined here as synaptic ectosomes (SE), from helper T cells. SE bind peptide-MHC directly exporting TCR into the synaptic cleft, but incorporation of other effectors is unknown. Here, we utilized bead supported lipid bilayers (BSLB) to capture SE from single immunological synapses (IS), determined SE composition by immunofluorescence flow cytometry and enriched SE for proteomic analysis by particle sorting. We demonstrate selective enrichment of CD40L and ICOS in SE in response to addition of CD40 and ICOSL, respectively, to SLB presenting TCR ligands and ICAM-1. SE are enriched in tetraspanins, BST-2, TCR signaling and ESCRT proteins. Super-resolution microscopy demonstrated that CD40L is present in microclusters within CD81 defined SE that are spatially segregated from TCR/ICOS/BST-2. CD40L+ SE retain the capacity to induce dendritic cell maturation and cytokine production.
Collapse
Affiliation(s)
- David G Saliba
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal SciencesUniversity of OxfordOxfordUnited Kingdom
- Department of Applied Biomedical Science, Faculty of Health ScienceUniversity of MaltaMsidaMalta
| | - Pablo F Céspedes-Donoso
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal SciencesUniversity of OxfordOxfordUnited Kingdom
| | - Štefan Bálint
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal SciencesUniversity of OxfordOxfordUnited Kingdom
| | - Ewoud B Compeer
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal SciencesUniversity of OxfordOxfordUnited Kingdom
| | - Kseniya Korobchevskaya
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal SciencesUniversity of OxfordOxfordUnited Kingdom
| | - Salvatore Valvo
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal SciencesUniversity of OxfordOxfordUnited Kingdom
| | - Viveka Mayya
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal SciencesUniversity of OxfordOxfordUnited Kingdom
| | - Audun Kvalvaag
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal SciencesUniversity of OxfordOxfordUnited Kingdom
| | - Yanchun Peng
- MRC Human Immunology Unit, Weatherall Institute of Molecular MedicineUniversity of OxfordOxfordUnited Kingdom
- Nuffield Department of Medicine, Chinese Academy of Medical Science Oxford InstituteUniversity of OxfordOxfordUnited Kingdom
| | - Tao Dong
- MRC Human Immunology Unit, Weatherall Institute of Molecular MedicineUniversity of OxfordOxfordUnited Kingdom
- Nuffield Department of Medicine, Chinese Academy of Medical Science Oxford InstituteUniversity of OxfordOxfordUnited Kingdom
| | | | - Eric O'Neill
- Department of OncologyUniversity of OxfordOxfordUnited Kingdom
| | - Sarah Bonham
- Discovery Proteomics Facility, Target Discovery Institute, Nuffield Department of MedicineUniversity of OxfordOxfordUnited Kingdom
| | - Roman Fischer
- Discovery Proteomics Facility, Target Discovery Institute, Nuffield Department of MedicineUniversity of OxfordOxfordUnited Kingdom
| | - Benedikt M Kessler
- Discovery Proteomics Facility, Target Discovery Institute, Nuffield Department of MedicineUniversity of OxfordOxfordUnited Kingdom
| | - Michael L Dustin
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal SciencesUniversity of OxfordOxfordUnited Kingdom
| |
Collapse
|
40
|
Image scanning microscopy. Curr Opin Chem Biol 2019; 51:74-83. [DOI: 10.1016/j.cbpa.2019.05.011] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 05/01/2019] [Accepted: 05/13/2019] [Indexed: 12/27/2022]
|
41
|
The cell wall regulates dynamics and size of plasma-membrane nanodomains in Arabidopsis. Proc Natl Acad Sci U S A 2019; 116:12857-12862. [PMID: 31182605 PMCID: PMC6601011 DOI: 10.1073/pnas.1819077116] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Plant plasma-membrane (PM) proteins are involved in several vital processes, such as detection of pathogens, solute transport, and cellular signaling. For these proteins to function effectively there needs to be structure within the PM allowing, for example, proteins in the same signaling cascade to be spatially organized. Here we demonstrate that several proteins with divergent functions are located in clusters of differing size in the membrane using subdiffraction-limited Airyscan confocal microscopy. Single particle tracking reveals that these proteins move at different rates within the membrane. Actin and microtubule cytoskeletons appear to significantly regulate the mobility of one of these proteins (the pathogen receptor FLS2) and we further demonstrate that the cell wall is critical for the regulation of cluster size by quantifying single particle dynamics of proteins with key roles in morphogenesis (PIN3) and pathogen perception (FLS2). We propose a model in which the cell wall and cytoskeleton are pivotal for regulation of protein cluster size and dynamics, thereby contributing to the formation and functionality of membrane nanodomains.
Collapse
|
42
|
Groves NR, McKenna JF, Evans DE, Graumann K, Meier I. A nuclear localization signal targets tail-anchored membrane proteins to the inner nuclear envelope in plants. J Cell Sci 2019; 132:jcs226134. [PMID: 30858196 DOI: 10.1242/jcs.226134] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 02/26/2019] [Indexed: 01/08/2023] Open
Abstract
Protein targeting to the inner nuclear membrane (INM) is one of the least understood protein targeting pathways. INM proteins are important for chromatin organization, nuclear morphology and movement, and meiosis, and have been implicated in human diseases. In opisthokonts, one mechanism for INM targeting is transport factor-mediated trafficking, in which nuclear localization signals (NLSs) function in nuclear import of transmembrane proteins. To explore whether this pathway exists in plants, we fused the SV40 NLS to a plant ER tail-anchored protein and showed that the GFP-tagged fusion protein was significantly enriched at the nuclear envelope (NE) of leaf epidermal cells. Airyscan subdiffraction limited confocal microscopy showed that this protein displays a localization consistent with an INM protein. Nine different monopartite and bipartite NLSs from plants and opisthokonts, fused to a chimeric tail-anchored membrane protein, were all sufficient for NE enrichment, and both monopartite and bipartite NLSs were sufficient for trafficking to the INM. Tolerance for different linker lengths and protein conformations suggests that INM trafficking rules might differ from those in opisthokonts. The INM proteins developed here can be used to target new functionalities to the plant nuclear periphery. This article has an associated First Person interview with the first author of the paper.
Collapse
Affiliation(s)
- Norman R Groves
- Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210, USA
| | - Joseph F McKenna
- Department of Biological and Medical Sciences, Oxford Brookes, Oxford OX3 0BP, UK
| | - David E Evans
- Department of Biological and Medical Sciences, Oxford Brookes, Oxford OX3 0BP, UK
| | - Katja Graumann
- Department of Biological and Medical Sciences, Oxford Brookes, Oxford OX3 0BP, UK
| | - Iris Meier
- Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210, USA
- Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
| |
Collapse
|
43
|
Colin-York H, Li D, Korobchevskaya K, Chang VT, Betzig E, Eggeling C, Fritzsche M. Cytoskeletal actin patterns shape mast cell activation. Commun Biol 2019; 2:93. [PMID: 30854485 PMCID: PMC6405992 DOI: 10.1038/s42003-019-0322-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 01/22/2019] [Indexed: 01/05/2023] Open
Abstract
Activation of immune cells relies on a dynamic actin cytoskeleton. Despite detailed knowledge of molecular actin assembly, the exact processes governing actin organization during activation remain elusive. Using advanced microscopy, we here show that Rat Basophilic Leukemia (RBL) cells, a model mast cell line, employ an orchestrated series of reorganization events within the cortical actin network during activation. In response to IgE antigen-stimulation of FCε receptors (FCεR) at the RBL cell surface, we observed symmetry breaking of the F-actin network and subsequent rapid disassembly of the actin cortex. This was followed by a reassembly process that may be driven by the coordinated transformation of distinct nanoscale F-actin architectures, reminiscent of self-organizing actin patterns. Actin patterns co-localized with zones of Arp2/3 nucleation, while network reassembly was accompanied by myosin-II activity. Strikingly, cortical actin disassembly coincided with zones of granule secretion, suggesting that cytoskeletal actin patterns contribute to orchestrate RBL cell activation. Huw Colin-York et al. use advanced microscopy techniques to show that the cortical actin network within a model mast cell line undergoes a series of reorganizational events at the basal interface during activation. They find that actin patterns co-localize with zones of Arp2/3 nucleation and myosin-II activity accompanies network reassembly.
Collapse
Affiliation(s)
- Huw Colin-York
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Headley Way, Oxford, OX3 9DS, UK
| | - Dong Li
- Howard Hughes Medical Institute, Janelia Research Campus, 19700 Helix Drive, Ashburn, VA, 20147, USA.,National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Kseniya Korobchevskaya
- Kennedy Institute for Rheumatology, University of Oxford, Roosevelt Drive, Oxford, OX3 7LF, UK
| | - Veronica T Chang
- MRC Laboratory of Molecular Biology, University of Cambridge, Cambridge, CB2 0QH, UK
| | - Eric Betzig
- Howard Hughes Medical Institute, Janelia Research Campus, 19700 Helix Drive, Ashburn, VA, 20147, USA
| | - Christian Eggeling
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Headley Way, Oxford, OX3 9DS, UK
| | - Marco Fritzsche
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Headley Way, Oxford, OX3 9DS, UK. .,Kennedy Institute for Rheumatology, University of Oxford, Roosevelt Drive, Oxford, OX3 7LF, UK.
| |
Collapse
|
44
|
Volume expansion and TRPV4 activation regulate stem cell fate in three-dimensional microenvironments. Nat Commun 2019; 10:529. [PMID: 30705265 PMCID: PMC6355972 DOI: 10.1038/s41467-019-08465-x] [Citation(s) in RCA: 122] [Impact Index Per Article: 24.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 01/11/2019] [Indexed: 12/19/2022] Open
Abstract
For mesenchymal stem cells (MSCs) cultured in three dimensional matrices, matrix remodeling is associated with enhanced osteogenic differentiation. However, the mechanism linking matrix remodeling in 3D to osteogenesis of MSCs remains unclear. Here, we find that MSCs in viscoelastic hydrogels exhibit volume expansion during cell spreading, and greater volume expansion is associated with enhanced osteogenesis. Restriction of expansion by either hydrogels with slow stress relaxation or increased osmotic pressure diminishes osteogenesis, independent of cell morphology. Conversely, induced expansion by hypoosmotic pressure accelerates osteogenesis. Volume expansion is mediated by activation of TRPV4 ion channels, and reciprocal feedback between TRPV4 activation and volume expansion controls nuclear localization of RUNX2, but not YAP, to promote osteogenesis. This work demonstrates the role of cell volume in regulating cell fate in 3D culture, and identifies TRPV4 as a molecular sensor of matrix viscoelasticity that regulates osteogenic differentiation. For mesenchymal stem cells (MSCs), matrix remodeling is associated with enhanced osteogenic differentiation. Here authors find that MSCs in viscoelastic hydrogels exhibit volume expansion during cell spreading, and greater volume expansion is associated with enhanced osteogenesis.
Collapse
|
45
|
Schermelleh L, Ferrand A, Huser T, Eggeling C, Sauer M, Biehlmaier O, Drummen GPC. Super-resolution microscopy demystified. Nat Cell Biol 2019; 21:72-84. [PMID: 30602772 DOI: 10.1038/s41556-018-0251-8] [Citation(s) in RCA: 532] [Impact Index Per Article: 106.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2018] [Accepted: 11/12/2018] [Indexed: 02/08/2023]
Abstract
Super-resolution microscopy (SRM) bypasses the diffraction limit, a physical barrier that restricts the optical resolution to roughly 250 nm and was previously thought to be impenetrable. SRM techniques allow the visualization of subcellular organization with unprecedented detail, but also confront biologists with the challenge of selecting the best-suited approach for their particular research question. Here, we provide guidance on how to use SRM techniques advantageously for investigating cellular structures and dynamics to promote new discoveries.
Collapse
Affiliation(s)
- Lothar Schermelleh
- Micron Oxford Advanced Bioimaging Unit, Department of Biochemistry, University of Oxford, Oxford, UK.
| | - Alexia Ferrand
- Imaging Core Facility, Biozentrum, University of Basel, Basel, Switzerland
| | - Thomas Huser
- Biomolecular Photonics, Department of Physics, University of Bielefeld, Bielefeld, Germany
| | - Christian Eggeling
- MRC Human Immunology Unit and Wolfson Imaging Centre Oxford, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Institute for Applied Optics, Friedrich-Schiller-University Jena & Leibniz Institute of Photonic Technology, Jena, Germany
| | - Markus Sauer
- Department of Biotechnology & Biophysics, Biocenter, Julius Maximilian University of Würzburg, Würzburg, Germany
| | - Oliver Biehlmaier
- Imaging Core Facility, Biozentrum, University of Basel, Basel, Switzerland
| | - Gregor P C Drummen
- Advanced Bio-Imaging Program, Bio&Nano Solutions‒LAB3BIO, Bielefeld, Germany.
- ICON-Europe.org, Exxilon Scientific Events, Steinhagen, Germany.
| |
Collapse
|
46
|
Bürgers J, Pavlova I, Rodriguez-Gatica JE, Henneberger C, Oeller M, Ruland JA, Siebrasse JP, Kubitscheck U, Schwarz MK. Light-sheet fluorescence expansion microscopy: fast mapping of neural circuits at super resolution. NEUROPHOTONICS 2019; 6:015005. [PMID: 30796881 PMCID: PMC6368534 DOI: 10.1117/1.nph.6.1.015005] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 01/09/2019] [Indexed: 05/23/2023]
Abstract
The goal of understanding the architecture of neural circuits at the synapse level with a brain-wide perspective has powered the interest in high-speed and large field-of-view volumetric imaging at subcellular resolution. Here, we developed a method combining tissue expansion and light-sheet fluorescence microscopy to allow extended volumetric super resolution high-speed imaging of large mouse brain samples. We demonstrate the capabilities of this method by performing two color fast volumetric super resolution imaging of mouse CA1 and dentate gyrus molecular-, granule cell-, and polymorphic layers. Our method enables an exact evaluation of granule cell and neurite morphology within the context of large cell ensembles spanning several orders of magnitude in resolution. We found that imaging a brain region of 1 mm 3 in super resolution using light-sheet fluorescence expansion microscopy is about 17-fold faster than imaging the same region by a current state-of-the-art high-resolution confocal laser scanning microscope.
Collapse
Affiliation(s)
- Jana Bürgers
- University of Bonn, Institute of Physical and Theoretical Chemistry, Bonn, Germany
| | - Irina Pavlova
- University of Bonn Medical School, Institute of Experimental Epileptology and Cognition Research, Bonn, Germany
| | | | - Christian Henneberger
- University of Bonn Medical School, Institute of Cellular Neurosciences, German Center for Neurodegenerative Diseases, Bonn, Germany
- University College London, Institute of Neurology, London, United Kingdom
| | - Marc Oeller
- University of Bonn, Institute of Physical and Theoretical Chemistry, Bonn, Germany
| | - Jan A. Ruland
- University of Bonn, Institute of Physical and Theoretical Chemistry, Bonn, Germany
| | - Jan P. Siebrasse
- University of Bonn, Institute of Physical and Theoretical Chemistry, Bonn, Germany
| | - Ulrich Kubitscheck
- University of Bonn, Institute of Physical and Theoretical Chemistry, Bonn, Germany
| | - Martin K. Schwarz
- University of Bonn Medical School, Institute of Experimental Epileptology and Cognition Research, Bonn, Germany
| |
Collapse
|
47
|
Ballesteros A, Fenollar-Ferrer C, Swartz KJ. Structural relationship between the putative hair cell mechanotransduction channel TMC1 and TMEM16 proteins. eLife 2018; 7:38433. [PMID: 30063209 PMCID: PMC6067890 DOI: 10.7554/elife.38433] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 07/09/2018] [Indexed: 02/03/2023] Open
Abstract
The hair cell mechanotransduction (MET) channel complex is essential for hearing, yet it's molecular identity and structure remain elusive. The transmembrane channel-like 1 (TMC1) protein localizes to the site of the MET channel, interacts with the tip-link responsible for mechanical gating, and genetic alterations in TMC1 alter MET channel properties and cause deafness, supporting the hypothesis that TMC1 forms the MET channel. We generated a model of TMC1 based on X-ray and cryo-EM structures of TMEM16 proteins, revealing the presence of a large cavity near the protein-lipid interface that also harbors the Beethoven mutation, suggesting that it could function as a permeation pathway. We also find that hair cells are permeable to 3 kDa dextrans, and that dextran permeation requires TMC1/2 proteins and functional MET channels, supporting the presence of a large permeation pathway and the hypothesis that TMC1 is a pore forming subunit of the MET channel complex.
Collapse
Affiliation(s)
- Angela Ballesteros
- Molecular Physiology and Biophysics Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, United States
| | - Cristina Fenollar-Ferrer
- Laboratory of Molecular & Cellular Neurobiology, National Institute of Mental Health, National Institutes of Health, Bethesda, United States.,Laboratory of Molecular Genetics, National Institute of Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, United States.,Molecular Biology and Genetics Section, National Institute of Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, United States
| | - Kenton Jon Swartz
- Molecular Physiology and Biophysics Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, United States
| |
Collapse
|
48
|
Chojnacki J, Eggeling C. Super-resolution fluorescence microscopy studies of human immunodeficiency virus. Retrovirology 2018; 15:41. [PMID: 29884197 PMCID: PMC5994058 DOI: 10.1186/s12977-018-0424-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 05/28/2018] [Indexed: 11/10/2022] Open
Abstract
Super-resolution fluorescence microscopy combines the ability to observe biological processes beyond the diffraction limit of conventional light microscopy with all advantages of the fluorescence readout such as labelling specificity and non-invasive live-cell imaging. Due to their subdiffraction size (< 200 nm) viruses are ideal candidates for super-resolution microscopy studies, and Human Immunodeficiency Virus type 1 (HIV-1) is to date the most studied virus by this technique. This review outlines principles of different super-resolution techniques as well as their advantages and disadvantages for virological studies, especially in the context of live-cell imaging applications. We highlight the findings of super-resolution based HIV-1 studies performed so far, their contributions to the understanding of HIV-1 replication cycle and how the current advances in super-resolution microscopy may open new avenues for future virology research.
Collapse
Affiliation(s)
- Jakub Chojnacki
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK.
| | - Christian Eggeling
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK
- Institute of Applied Optics, Friedrich-Schiller-University Jena, Max-Wien Platz 4, 07743, Jena, Germany
- Leibniz Institute of Photonic Technology e.V., Albert-Einstein-Straße 9, 07745, Jena, Germany
| |
Collapse
|
49
|
Witte R, Andriasyan V, Georgi F, Yakimovich A, Greber UF. Concepts in Light Microscopy of Viruses. Viruses 2018; 10:E202. [PMID: 29670029 PMCID: PMC5923496 DOI: 10.3390/v10040202] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 04/12/2018] [Accepted: 04/16/2018] [Indexed: 12/11/2022] Open
Abstract
Viruses threaten humans, livestock, and plants, and are difficult to combat. Imaging of viruses by light microscopy is key to uncover the nature of known and emerging viruses in the quest for finding new ways to treat viral disease and deepening the understanding of virus–host interactions. Here, we provide an overview of recent technology for imaging cells and viruses by light microscopy, in particular fluorescence microscopy in static and live-cell modes. The review lays out guidelines for how novel fluorescent chemical probes and proteins can be used in light microscopy to illuminate cells, and how they can be used to study virus infections. We discuss advantages and opportunities of confocal and multi-photon microscopy, selective plane illumination microscopy, and super-resolution microscopy. We emphasize the prevalent concepts in image processing and data analyses, and provide an outlook into label-free digital holographic microscopy for virus research.
Collapse
Affiliation(s)
- Robert Witte
- Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland.
| | - Vardan Andriasyan
- Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland.
| | - Fanny Georgi
- Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland.
| | - Artur Yakimovich
- MRC Laboratory for Molecular Cell Biology, University College London, Gower St., London WC1E 6BT, UK.
| | - Urs F Greber
- Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland.
| |
Collapse
|
50
|
Gutu A, Chang F, O'Shea EK. Dynamical localization of a thylakoid membrane binding protein is required for acquisition of photosynthetic competency. Mol Microbiol 2018; 108:16-31. [PMID: 29357135 PMCID: PMC5910887 DOI: 10.1111/mmi.13912] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Accepted: 01/02/2018] [Indexed: 11/29/2022]
Abstract
Vipp1 is highly conserved and essential for photosynthesis, but its function is unclear as it does not participate directly in light-dependent reactions. We analyzed Vipp1 localization in live cyanobacterial cells and show that Vipp1 is highly dynamic, continuously exchanging between a diffuse fraction that is uniformly distributed throughout the cell and a punctate fraction that is concentrated at high curvature regions of the thylakoid located at the cell periphery. Experimentally perturbing the spatial distribution of Vipp1 by relocalizing it to the nucleoid causes a severe growth defect during the transition from non-photosynthetic (dark) to photosynthetic (light) growth. However, the same perturbation of Vipp1 in dark alone or light alone growth conditions causes no growth or thylakoid morphology defects. We propose that the punctuated dynamics of Vipp1 at the cell periphery in regions of high thylakoid curvature enable acquisition of photosynthetic competency, perhaps by facilitating biogenesis of photosynthetic complexes involved in light-dependent reactions of photosynthesis.
Collapse
Affiliation(s)
- Andrian Gutu
- Howard Hughes Medical Institute, Harvard University Faculty of Arts and Sciences Center for Systems Biology, Cambridge, MA 02138, USA.,Department of Molecular and Cellular Biology, Harvard University Faculty of Arts and Sciences, Cambridge, MA 02138, USA.,Department of Chemistry and Chemical Biology, Harvard University Faculty of Arts and Sciences Center for Systems Biology, Cambridge, MA 02138, USA
| | - Frederick Chang
- Department of Molecular and Cellular Biology, Harvard University Faculty of Arts and Sciences, Cambridge, MA 02138, USA
| | - Erin K O'Shea
- Howard Hughes Medical Institute, Harvard University Faculty of Arts and Sciences Center for Systems Biology, Cambridge, MA 02138, USA.,Department of Molecular and Cellular Biology, Harvard University Faculty of Arts and Sciences, Cambridge, MA 02138, USA.,Department of Chemistry and Chemical Biology, Harvard University Faculty of Arts and Sciences Center for Systems Biology, Cambridge, MA 02138, USA
| |
Collapse
|