1
|
Banerjee C, Mehra D, Song D, Mancebo A, Park JM, Kim DH, Puchner EM. ULK1 forms distinct oligomeric states and nanoscopic structures during autophagy initiation. SCIENCE ADVANCES 2023; 9:eadh4094. [PMID: 37774021 PMCID: PMC10541014 DOI: 10.1126/sciadv.adh4094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 08/30/2023] [Indexed: 10/01/2023]
Abstract
Autophagy induction involves extensive molecular and membrane reorganization. Despite substantial progress, the mechanism underlying autophagy initiation remains poorly understood. Here, we used quantitative photoactivated localization microscopy with single-molecule sensitivity to analyze the nanoscopic distribution of endogenous ULK1, the kinase that triggers autophagy. Under amino acid starvation, ULK1 formed large clusters containing up to 161 molecules at the endoplasmic reticulum. Cross-correlation analysis revealed that ULK1 clusters engaging in autophagosome formation require 30 or more molecules. The ULK1 structures with more than the threshold number contained varying levels of Atg13, Atg14, Atg16, LC3B, GEC1, and WIPI2. We found that ULK1 activity is dispensable for the initial clustering of ULK1, but necessary for the subsequent expansion of the clusters, which involves interaction with Atg14, Atg16, and LC3B and relies on Vps34 activity. This quantitative analysis at the single-molecule level has provided unprecedented insights into the behavior of ULK1 during autophagy initiation.
Collapse
Affiliation(s)
- Chiranjib Banerjee
- School of Physics and Astronomy, University of Minnesota, Twin Cities, Minneapolis, MN, USA
| | - Dushyant Mehra
- School of Physics and Astronomy, University of Minnesota, Twin Cities, Minneapolis, MN, USA
- Department of Biomedical Engineering and Physiology, Mayo Clinic, Rochester, MN, USA
| | - Daihyun Song
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Twin Cities, Minneapolis, MN, USA
| | - Angel Mancebo
- School of Physics and Astronomy, University of Minnesota, Twin Cities, Minneapolis, MN, USA
| | - Ji-Man Park
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Twin Cities, Minneapolis, MN, USA
| | - Do-Hyung Kim
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Twin Cities, Minneapolis, MN, USA
| | - Elias M. Puchner
- School of Physics and Astronomy, University of Minnesota, Twin Cities, Minneapolis, MN, USA
| |
Collapse
|
2
|
Riachy L, Ferrand T, Chasserot-Golaz S, Galas L, Alexandre S, Montero-Hadjadje M. Advanced Imaging Approaches to Reveal Molecular Mechanisms Governing Neuroendocrine Secretion. Neuroendocrinology 2023; 113:107-119. [PMID: 34915491 DOI: 10.1159/000521457] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 12/09/2021] [Indexed: 11/19/2022]
Abstract
Identification of the molecular mechanisms governing neuroendocrine secretion and resulting intercellular communication is one of the great challenges of cell biology to better understand organism physiology and neurosecretion disruption-related pathologies such as hypertension, neurodegenerative, or metabolic diseases. To visualize molecule distribution and dynamics at the nanoscale, many imaging approaches have been developed and are still emerging. In this review, we provide an overview of the pioneering studies using transmission electron microscopy, atomic force microscopy, total internal reflection microscopy, and super-resolution microscopy in neuroendocrine cells to visualize molecular mechanisms driving neurosecretion processes, including exocytosis and associated fusion pores, endocytosis and associated recycling vesicles, and protein-protein or protein-lipid interactions. Furthermore, the potential and the challenges of these different advanced imaging approaches for application in the study of neuroendocrine cell biology are discussed, aiming to guide researchers to select the best approach for their specific purpose around the crucial but not yet fully understood neurosecretion process.
Collapse
Affiliation(s)
- Lina Riachy
- Laboratoire de Différenciation et Communication Neuronale et Neuroendocrine, Institut de Recherche et d'Innovation Biomédicale de Normandie, Normandie University, UNIROUEN, INSERM, U1239, Rouen, France
| | - Thomas Ferrand
- Laboratoire de Différenciation et Communication Neuronale et Neuroendocrine, Institut de Recherche et d'Innovation Biomédicale de Normandie, Normandie University, UNIROUEN, INSERM, U1239, Rouen, France
| | - Sylvette Chasserot-Golaz
- Institut des Neurosciences Cellulaires et Intégratives, Centre National de la Recherche Scientifique, Strasbourg University, Strasbourg, France
| | - Ludovic Galas
- Normandie University, UNIROUEN, INSERM, PRIMACEN, Rouen, France
| | - Stéphane Alexandre
- Polymères, Biopolymères, Surfaces Laboratory, CNRS, Normandie University, UNIROUEN, UMR 6270, Rouen, France
| | - Maité Montero-Hadjadje
- Laboratoire de Différenciation et Communication Neuronale et Neuroendocrine, Institut de Recherche et d'Innovation Biomédicale de Normandie, Normandie University, UNIROUEN, INSERM, U1239, Rouen, France
| |
Collapse
|
3
|
Padilla-Parra S. Next-generation single virus tracking. Nat Methods 2022; 19:1524-1525. [PMID: 36357693 DOI: 10.1038/s41592-022-01670-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Sergi Padilla-Parra
- Department of Infectious Diseases, Faculty of Life Sciences & Medicine, King's College London, London, UK. .,Randall Division of Cell and Molecular Biophysics, King's College London, London, UK.
| |
Collapse
|
4
|
Superresolution microscopy localizes endogenous Dvl2 to Wnt signaling-responsive biomolecular condensates. Proc Natl Acad Sci U S A 2022; 119:e2122476119. [PMID: 35867833 PMCID: PMC9335300 DOI: 10.1073/pnas.2122476119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Wnt signaling governs cell fate and tissue polarity across species. The Dishevelled proteins are central to Wnt signaling cascades. Wnt-mediated multiprotein complexes such as the “signalosome” and the “destruction complex” have been proposed to represent biomolecular condensates. These nonmembranous, specialized compartments have been suggested to form through liquid–liquid phase separation and ensure correctly proceeding physiological reactions. Although biomolecular condensates have increasingly been studied, key questions remain regarding, for example, their architecture and physiological regulation. Here, superresolution microscopy after endogenous labeling of Dishevelled-2 gives insights into protein functions and Wnt signaling at physiological levels. It reveals the distinct molecular architecture of endogenous Wnt condensates at single-molecule resolution and illustrates close interactions at the centrosome. During organismal development, homeostasis, and disease, Dishevelled (Dvl) proteins act as key signaling factors in beta-catenin–dependent and beta-catenin–independent Wnt pathways. While their importance for signal transmission has been genetically demonstrated in many organisms, our mechanistic understanding is still limited. Previous studies using overexpressed proteins showed Dvl localization to large, punctate-like cytoplasmic structures that are dependent on its DIX domain. To study Dvl’s role in Wnt signaling, we genome engineered an endogenously expressed Dvl2 protein tagged with an mEos3.2 fluorescent protein for superresolution imaging. First, we demonstrate the functionality and specificity of the fusion protein in beta-catenin–dependent and beta-catenin–independent signaling using multiple independent assays. We performed live-cell imaging of Dvl2 to analyze the dynamic formation of the supramolecular cytoplasmic Dvl2_mEos3.2 condensates. While overexpression of Dvl2_mEos3.2 mimics the previously reported formation of abundant large “puncta,” supramolecular condensate formation at physiological protein levels is only observed in a subset of cells with approximately one per cell. We show that, in these condensates, Dvl2 colocalizes with Wnt pathway components at gamma-tubulin and CEP164-positive centrosomal structures and that the localization of Dvl2 to these condensates is Wnt dependent. Single-molecule localization microscopy using photoactivated localization microscopy (PALM) of mEos3.2 in combination with DNA-PAINT demonstrates the organization and repetitive patterns of these condensates in a cell cycle–dependent manner. Our results indicate that the localization of Dvl2 in supramolecular condensates is coordinated dynamically and dependent on cell state and Wnt signaling levels. Our study highlights the formation of endogenous and physiologically regulated biomolecular condensates in the Wnt pathways at single-molecule resolution.
Collapse
|
5
|
CRISPR/Cas9 Genome Editing vs. Over-Expression for Fluorescent Extracellular Vesicle-Labeling: A Quantitative Analysis. Int J Mol Sci 2021; 23:ijms23010282. [PMID: 35008709 PMCID: PMC8745383 DOI: 10.3390/ijms23010282] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Revised: 12/22/2021] [Accepted: 12/24/2021] [Indexed: 12/12/2022] Open
Abstract
Over-expression of fluorescently-labeled markers for extracellular vesicles is frequently used to visualize vesicle up-take and transport. EVs that are labeled by over-expression show considerable heterogeneity regarding the number of fluorophores on single particles, which could potentially bias tracking and up-take studies in favor of more strongly-labeled particles. To avoid the potential artefacts that are caused by over-expression, we developed a genome editing approach for the fluorescent labeling of the extracellular vesicle marker CD63 with green fluorescent protein using the CRISPR/Cas9 technology. Using single-molecule sensitive fluorescence microscopy, we quantitatively compared the degree of labeling of secreted small extracellular vesicles from conventional over-expression and the CRISPR/Cas9 approach with true single-particle measurements. With our analysis, we can demonstrate a larger fraction of single-GFP-labeled EVs in the EVs that were isolated from CRISPR/Cas9-modified cells (83%) compared to EVs that were isolated from GFP-CD63 over-expressing cells (36%). Despite only single-GFP-labeling, CRISPR-EVs can be detected and discriminated from auto-fluorescence after their up-take into cells. To demonstrate the flexibility of the CRISPR/Cas9 genome editing method, we fluorescently labeled EVs using the HaloTag® with lipid membrane permeable dye, JaneliaFluor® 646, which allowed us to perform 3D-localization microscopy of single EVs taken up by the cultured cells.
Collapse
|
6
|
Osuga M, Nishimura T, Suetsugu S. Development of a green reversibly photoswitchable variant of Eos fluorescent protein with fixation resistance. Mol Biol Cell 2021; 32:br7. [PMID: 34495704 PMCID: PMC8693962 DOI: 10.1091/mbc.e21-01-0044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 08/23/2021] [Accepted: 09/01/2021] [Indexed: 11/11/2022] Open
Abstract
Superresolution microscopy determines the localization of fluorescent proteins with high precision, beyond the diffraction limit of light. Superresolution microscopic techniques include photoactivated localization microscopy (PALM), which can localize a single protein by the stochastic activation of its fluorescence. In the determination of single-molecule localization by PALM, the number of molecules that can be analyzed per image is limited. Thus, many images are required to reconstruct the localization of numerous molecules in the cell. However, most fluorescent proteins lose their fluorescence upon fixation. Here, we combined the amino acid substitutions of two Eos protein derivatives, Skylan-S and mEos4b, which are a green reversibly photoswitchable fluorescent protein (RSFP) and a fixation-resistant green-to-red photoconvertible fluorescent protein, respectively, resulting in the fixation-resistant Skylan-S (frSkylan-S), a green RSFP. The frSkylan-S protein is inactivated by excitation light and reactivated by irradiation with violet light, and retained more fluorescence after aldehyde fixation than Skylan-S. The qualities of the frSkylan-S fusion proteins were sufficiently high in PALM observations, as examined using α-tubulin and clathrin light chain. Furthermore, frSkylan-S can be combined with antibody staining for multicolor imaging. Therefore, frSkylan-S is a green fluorescent protein suitable for PALM imaging under aldehyde-fixation conditions.
Collapse
Affiliation(s)
- Mitsuo Osuga
- Nara Institute of Science and Technology, Ikoma 630-0192, Japan
| | | | - Shiro Suetsugu
- Nara Institute of Science and Technology, Ikoma 630-0192, Japan
| |
Collapse
|
7
|
Single-Protein Tracking to Study Protein Interactions During Integrin-Based Migration. Methods Mol Biol 2021; 2217:85-113. [PMID: 33215379 DOI: 10.1007/978-1-0716-0962-0_8] [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: 12/03/2022]
Abstract
Cell migration is a complex biophysical process which involves the coordination of molecular assemblies including integrin-dependent adhesions, signaling networks and force-generating cytoskeletal structures incorporating both actin polymerization and myosin activity. During the last decades, proteomic studies have generated impressive protein-protein interaction maps, although the subcellular location, duration, strength, sequence, and nature of these interactions are still concealed. In this chapter we describe how recent developments in superresolution microscopy (SRM) and single-protein tracking (SPT) start to unravel protein interactions and actions in subcellular molecular assemblies driving cell migration.
Collapse
|
8
|
Khan AO, Slater A, Maclachlan A, Nicolson PLR, Pike JA, Reyat JS, Yule J, Stapley R, Rayes J, Thomas SG, Morgan NV. Post-translational polymodification of β1-tubulin regulates motor protein localisation in platelet production and function. Haematologica 2020; 107:243-259. [PMID: 33327716 PMCID: PMC8719104 DOI: 10.3324/haematol.2020.270793] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Indexed: 11/17/2022] Open
Abstract
In specialized cells, the expression of specific tubulin isoforms and their subsequent post-translational modifications drive and coordinate unique morphologies and behaviors. The mechanisms by which b1-tubulin, the platelet and megakaryocyte (MK) lineage restricted tubulin isoform, drives platelet production and function remains poorly understood. We investigated the roles of two key post-translational tubulin polymodifications (polyglutamylation and polyglycylation) on these processes using a cohort of thrombocytopenic patients, human induced pluripotent stem cell derived MK, and healthy human donor platelets. We find distinct patterns of polymodification in MK and platelets, mediated by the antagonistic activities of the cell specific expression of tubulin tyrosine ligase like enzymes and cytosolic carboxypeptidase enzymes. The resulting microtubule patterning spatially regulates motor proteins to drive proplatelet formation in megakaryocytes, and the cytoskeletal reorganization required for thrombus formation. This work is the first to show a reversible system of polymodification by which different cell specific functions are achieved.
Collapse
Affiliation(s)
- Abdullah O Khan
- Institute of Cardiovascular Sciences, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham, UK, B15 2TT.
| | - Alexandre Slater
- Institute of Cardiovascular Sciences, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham, UK, B15 2TT
| | - Annabel Maclachlan
- Institute of Cardiovascular Sciences, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham, UK, B15 2TT
| | - Phillip L R Nicolson
- Institute of Cardiovascular Sciences, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham, UK, B15 2TT
| | - Jeremy A Pike
- Institute of Cardiovascular Sciences, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham, UK, B15 2TT; Centre of Membrane and Protein and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands
| | - Jasmeet S Reyat
- Institute of Cardiovascular Sciences, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham, UK, B15 2TT
| | - Jack Yule
- Centre of Membrane and Protein and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands
| | - Rachel Stapley
- Institute of Cardiovascular Sciences, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham, UK, B15 2TT
| | - Julie Rayes
- Institute of Cardiovascular Sciences, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham, UK, B15 2TT
| | - Steven G Thomas
- Institute of Cardiovascular Sciences, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham, UK, B15 2TT; Centre of Membrane and Protein and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands
| | - Neil V Morgan
- Institute of Cardiovascular Sciences, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham, UK, B15 2TT.
| |
Collapse
|
9
|
Baldering TN, Karathanasis C, Harwardt MLIE, Freund P, Meurer M, Rahm JV, Knop M, Dietz MS, Heilemann M. CRISPR/Cas12a-mediated labeling of MET receptor enables quantitative single-molecule imaging of endogenous protein organization and dynamics. iScience 2020; 24:101895. [PMID: 33364584 PMCID: PMC7753144 DOI: 10.1016/j.isci.2020.101895] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 11/12/2020] [Accepted: 12/02/2020] [Indexed: 12/31/2022] Open
Abstract
Single-molecule localization microscopy (SMLM) reports on protein organization in cells with near-molecular resolution and in combination with stoichiometric labeling enables protein counting. Fluorescent proteins allow stoichiometric labeling of cellular proteins; however, most methods either lead to overexpression or are complex and time demanding. We introduce CRISPR/Cas12a for simple and efficient tagging of endogenous proteins with a photoactivatable protein for quantitative SMLM and single-particle tracking. We constructed a HEK293T cell line with the receptor tyrosine kinase MET tagged with mEos4b and demonstrate full functionality. We determine the oligomeric state of MET with quantitative SMLM and find a reorganization from monomeric to dimeric MET upon ligand stimulation. In addition, we measured the mobility of single MET receptors in vivo in resting and ligand-treated cells. The combination of CRISPR/Cas12a-assisted endogenous protein labeling and super-resolution microscopy represents a powerful tool for cell biological research with molecular resolution. CRISPR/Cas12a enables endogenous protein labeling for super-resolution microscopy HEK293T cells were generated with MET endogenously labeled with mEos4b Quantitative PALM microscopy reports efficient dimerization of MET receptor Single-particle tracking shows increased MET immobilization upon ligand treatment
Collapse
Affiliation(s)
- Tim N Baldering
- Single Molecule Biophysics, Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue Str. 7, 60438 Frankfurt, Germany
| | - Christos Karathanasis
- Single Molecule Biophysics, Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue Str. 7, 60438 Frankfurt, Germany
| | - Marie-Lena I E Harwardt
- Single Molecule Biophysics, Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue Str. 7, 60438 Frankfurt, Germany
| | - Petra Freund
- Single Molecule Biophysics, Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue Str. 7, 60438 Frankfurt, Germany
| | - Matthias Meurer
- Center for Molecular Biology of Heidelberg University (ZMBH), 69120 Heidelberg, Germany
| | - Johanna V Rahm
- Single Molecule Biophysics, Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue Str. 7, 60438 Frankfurt, Germany
| | - Michael Knop
- Center for Molecular Biology of Heidelberg University (ZMBH), 69120 Heidelberg, Germany.,German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Marina S Dietz
- Single Molecule Biophysics, Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue Str. 7, 60438 Frankfurt, Germany
| | - Mike Heilemann
- Single Molecule Biophysics, Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue Str. 7, 60438 Frankfurt, Germany
| |
Collapse
|
10
|
Sapoznik E, Chang BJ, Huh J, Ju RJ, Azarova EV, Pohlkamp T, Welf ES, Broadbent D, Carisey AF, Stehbens SJ, Lee KM, Marín A, Hanker AB, Schmidt JC, Arteaga CL, Yang B, Kobayashi Y, Tata PR, Kruithoff R, Doubrovinski K, Shepherd DP, Millett-Sikking A, York AG, Dean KM, Fiolka RP. A versatile oblique plane microscope for large-scale and high-resolution imaging of subcellular dynamics. eLife 2020; 9:e57681. [PMID: 33179596 PMCID: PMC7707824 DOI: 10.7554/elife.57681] [Citation(s) in RCA: 82] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 11/09/2020] [Indexed: 12/31/2022] Open
Abstract
We present an oblique plane microscope (OPM) that uses a bespoke glass-tipped tertiary objective to improve the resolution, field of view, and usability over previous variants. Owing to its high numerical aperture optics, this microscope achieves lateral and axial resolutions that are comparable to the square illumination mode of lattice light-sheet microscopy, but in a user friendly and versatile format. Given this performance, we demonstrate high-resolution imaging of clathrin-mediated endocytosis, vimentin, the endoplasmic reticulum, membrane dynamics, and Natural Killer-mediated cytotoxicity. Furthermore, we image biological phenomena that would be otherwise challenging or impossible to perform in a traditional light-sheet microscope geometry, including cell migration through confined spaces within a microfluidic device, subcellular photoactivation of Rac1, diffusion of cytoplasmic rheological tracers at a volumetric rate of 14 Hz, and large field of view imaging of neurons, developing embryos, and centimeter-scale tissue sections.
Collapse
Affiliation(s)
- Etai Sapoznik
- Department of Cell Biology, University of Texas Southwestern Medical CenterDallasUnited States
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical CenterDallasUnited States
| | - Bo-Jui Chang
- Department of Cell Biology, University of Texas Southwestern Medical CenterDallasUnited States
| | - Jaewon Huh
- Department of Cell Biology, University of Texas Southwestern Medical CenterDallasUnited States
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical CenterDallasUnited States
| | - Robert J Ju
- Institute for Molecular Bioscience, University of QueenslandQueenslandAustralia
| | - Evgenia V Azarova
- Department of Cell Biology, University of Texas Southwestern Medical CenterDallasUnited States
| | - Theresa Pohlkamp
- Department of Molecular Genetics, University of Texas Southwestern Medical CenterDallasUnited States
| | - Erik S Welf
- Department of Cell Biology, University of Texas Southwestern Medical CenterDallasUnited States
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical CenterDallasUnited States
| | - David Broadbent
- Institute for Quantitative Health Sciences and Engineering, Michigan State UniversityEast LansingUnited States
| | - Alexandre F Carisey
- William T. Shearer Center for Human Immunobiology, Baylor College of Medicine and Texas Children’s HospitalHoustonUnited States
| | - Samantha J Stehbens
- Institute for Molecular Bioscience, University of QueenslandQueenslandAustralia
| | - Kyung-Min Lee
- Harold C. Simmons Comprehensive Cancer Center and the Department of Internal Medicine, University of Texas Southwestern Medical CenterDallasUnited States
| | - Arnaldo Marín
- Harold C. Simmons Comprehensive Cancer Center and the Department of Internal Medicine, University of Texas Southwestern Medical CenterDallasUnited States
- Department of Basic and Clinical Oncology, Faculty of Medicine, University of ChileSantiagoChile
| | - Ariella B Hanker
- Harold C. Simmons Comprehensive Cancer Center and the Department of Internal Medicine, University of Texas Southwestern Medical CenterDallasUnited States
| | - Jens C Schmidt
- Institute for Quantitative Health Sciences and Engineering, Michigan State UniversityEast LansingUnited States
- Department of Obstetrics, Gynecology, and Reproductive Biology, Michigan State UniversityEast LansingUnited States
| | - Carlos L Arteaga
- Harold C. Simmons Comprehensive Cancer Center and the Department of Internal Medicine, University of Texas Southwestern Medical CenterDallasUnited States
| | - Bin Yang
- Chan Zuckerberg BiohubSan FranciscoUnited States
| | - Yoshihiko Kobayashi
- Department of Cell Biology, Duke University School of MedicineDurhamUnited States
| | | | - Rory Kruithoff
- Center for Biological Physics and Department of Physics, Arizona State UniversityTempeUnited States
| | - Konstantin Doubrovinski
- Department of Cell Biology, University of Texas Southwestern Medical CenterDallasUnited States
- Cecil H. and Ida Green Comprehensive Center for Molecular, Computational and Systems Biology, University of Texas Southwestern Medical CenterDallasUnited States
| | - Douglas P Shepherd
- Center for Biological Physics and Department of Physics, Arizona State UniversityTempeUnited States
| | | | - Andrew G York
- Calico Life Sciences LLCSouth San FranciscoUnited States
| | - Kevin M Dean
- Department of Cell Biology, University of Texas Southwestern Medical CenterDallasUnited States
| | - Reto P Fiolka
- Department of Cell Biology, University of Texas Southwestern Medical CenterDallasUnited States
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical CenterDallasUnited States
| |
Collapse
|
11
|
Pike JA, Khan AO, Pallini C, Thomas SG, Mund M, Ries J, Poulter NS, Styles IB. Topological data analysis quantifies biological nano-structure from single molecule localization microscopy. Bioinformatics 2020; 36:1614-1621. [PMID: 31626286 PMCID: PMC7162425 DOI: 10.1093/bioinformatics/btz788] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 09/03/2019] [Accepted: 10/17/2019] [Indexed: 01/23/2023] Open
Abstract
Motivation Localization microscopy data is represented by a set of spatial coordinates, each corresponding to a single detection, that form a point cloud. This can be analyzed either by rendering an image from these coordinates, or by analyzing the point cloud directly. Analysis of this type has focused on clustering detections into distinct groups which produces measurements such as cluster area, but has limited capacity to quantify complex molecular organization and nano-structure. Results We present a segmentation protocol which, through the application of persistence-based clustering, is capable of probing densely packed structures which vary in scale. An increase in segmentation performance over state-of-the-art methods is demonstrated. Moreover we employ persistent homology to move beyond clustering, and quantify the topological structure within data. This provides new information about the preserved shapes formed by molecular architecture. Our methods are flexible and we demonstrate this by applying them to receptor clustering in platelets, nuclear pore components, endocytic proteins and microtubule networks. Both 2D and 3D implementations are provided within RSMLM, an R package for pointillist-based analysis and batch processing of localization microscopy data. Availability and implementation RSMLM has been released under the GNU General Public License v3.0 and is available at https://github.com/JeremyPike/RSMLM. Tutorials for this library implemented as Binder ready Jupyter notebooks are available at https://github.com/JeremyPike/RSMLM-tutorials. Supplementary information Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- Jeremy A Pike
- Centre of Membrane Proteins and Receptors (COMPARE), Universities of Birmingham and Nottingham, Midlands, UK.,Institute of Cardiovascular Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Abdullah O Khan
- Centre of Membrane Proteins and Receptors (COMPARE), Universities of Birmingham and Nottingham, Midlands, UK.,Institute of Cardiovascular Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Chiara Pallini
- Centre of Membrane Proteins and Receptors (COMPARE), Universities of Birmingham and Nottingham, Midlands, UK.,Institute of Cardiovascular Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Steven G Thomas
- Centre of Membrane Proteins and Receptors (COMPARE), Universities of Birmingham and Nottingham, Midlands, UK.,Institute of Cardiovascular Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Markus Mund
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Heidelberg 69117, Germany.,Department of Biochemistry, University of Geneva, 1211 Geneva 4, Switzerland
| | - Jonas Ries
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Heidelberg 69117, Germany
| | - Natalie S Poulter
- Centre of Membrane Proteins and Receptors (COMPARE), Universities of Birmingham and Nottingham, Midlands, UK.,Institute of Cardiovascular Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Iain B Styles
- Centre of Membrane Proteins and Receptors (COMPARE), Universities of Birmingham and Nottingham, Midlands, UK.,School of Computer Science, University of Birmingham, Birmingham B15 2TT, UK
| |
Collapse
|
12
|
Li Y, Yi J, Liu W, Liu Y, Liu J. Gaining insight into cellular cardiac physiology using single particle tracking. J Mol Cell Cardiol 2020; 148:63-77. [PMID: 32871158 DOI: 10.1016/j.yjmcc.2020.08.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 08/18/2020] [Accepted: 08/20/2020] [Indexed: 11/29/2022]
Abstract
Single particle tracking (SPT) is a robust technique to monitor single-molecule behaviors in living cells directly. By this approach, we can uncover the potential biological significance of particle dynamics by statistically characterizing individual molecular behaviors. SPT provides valuable information at the single-molecule level, that could be obscured by simple averaging that is inherent to conventional ensemble measurements. Here, we give a brief introduction to SPT including the commonly used optical implementations, fluorescence labeling strategies, and data analysis methods. We then focus on how SPT has been harnessed to decipher myocardial function. In this context, SPT has provided novel insight into the lateral diffusion of signal receptors and ion channels, the dynamic organization of cardiac nanodomains, subunit composition and stoichiometry of cardiac ion channels, myosin movement along actin filaments, the kinetic features of transcription factors involved in cardiac remodeling, and the intercellular communication by nanotubes. Finally, we speculate on the prospects and challenges of applying SPT to future questions regarding cellular cardiac physiology using SPT.
Collapse
Affiliation(s)
- Ying Li
- School of Basic Medical Sciences, Shenzhen University Health Science Center, Shenzhen, 518060, China.
| | - Jing Yi
- School of Basic Medical Sciences, Shenzhen University Health Science Center, Shenzhen, 518060, China.
| | - Wenjuan Liu
- School of Basic Medical Sciences, Shenzhen University Health Science Center, Shenzhen, 518060, China.
| | - Yun Liu
- The Seventh Affiliated Hospital, Sun Yat-sen University, Guangdong Province, China.
| | - Jie Liu
- School of Basic Medical Sciences, Shenzhen University Health Science Center, Shenzhen, 518060, China.
| |
Collapse
|
13
|
Abstract
Recent advances in super-resolution (sub-diffraction limited) microscopy have yielded remarkable insights into the nanoscale architecture and behavior of cells. In addition to the capacity to provide sub 100 nm resolution, these technologies offer unique quantitative opportunities with particular relevance to platelet and megakaryocyte biology. In this review, we provide a short introduction to modern super-resolution microscopy, its applications in the field of platelet and megakaryocyte biology, and emerging quantitative approaches which will allow for unprecedented insights into the biology of these unique cell types.
Collapse
Affiliation(s)
- Abdullah O Khan
- Institute of Cardiovascular Sciences, College of Medical and Dental Science, University of Birmingham , Birmingham, UK
| | - Jeremy A Pike
- Institute of Cardiovascular Sciences, College of Medical and Dental Science, University of Birmingham , Birmingham, UK.,Centre of Membrane Proteins and Receptors, Universities of Birmingham and Nottingham , UK
| |
Collapse
|
14
|
Tosheva KL, Yuan Y, Matos Pereira P, Culley S, Henriques R. Between life and death: strategies to reduce phototoxicity in super-resolution microscopy. JOURNAL OF PHYSICS D: APPLIED PHYSICS 2020; 53:163001. [PMID: 33994582 PMCID: PMC8114953 DOI: 10.1088/1361-6463/ab6b95] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 11/01/2019] [Accepted: 01/14/2020] [Indexed: 05/23/2023]
Abstract
Super-resolution microscopy (SRM) enables non-invasive, molecule-specific imaging of the internal structure and dynamics of cells with sub-diffraction limit spatial resolution. One of its major limitations is the requirement for high-intensity illumination, generating considerable cellular phototoxicity. This factor considerably limits the capacity for live-cell observations, particularly for extended periods of time. Here, we give an overview of new developments in hardware, software and probe chemistry aiming to reduce phototoxicity. Additionally, we discuss how the choice of biological model and sample environment impacts the capacity for live-cell observations.
Collapse
Affiliation(s)
- Kalina L Tosheva
- MRC Laboratory for Molecular Cell Biology, University College London, London, United Kingdom
| | - Yue Yuan
- MRC Laboratory for Molecular Cell Biology, University College London, London, United Kingdom
| | | | - Siân Culley
- MRC Laboratory for Molecular Cell Biology, University College London, London, United Kingdom
- The Francis Crick Institute, London, United Kingdom
| | - Ricardo Henriques
- MRC Laboratory for Molecular Cell Biology, University College London, London, United Kingdom
- The Francis Crick Institute, London, United Kingdom
| |
Collapse
|
15
|
Francia V, Montizaan D, Salvati A. Interactions at the cell membrane and pathways of internalization of nano-sized materials for nanomedicine. BEILSTEIN JOURNAL OF NANOTECHNOLOGY 2020; 11:338-353. [PMID: 32117671 PMCID: PMC7034226 DOI: 10.3762/bjnano.11.25] [Citation(s) in RCA: 72] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 01/27/2020] [Indexed: 05/17/2023]
Abstract
Nano-sized materials have great potential as drug carriers for nanomedicine applications. Thanks to their size, they can exploit the cellular machinery to enter cells and be trafficked intracellularly, thus they can be used to overcome some of the cellular barriers to drug delivery. Nano-sized drug carriers of very different properties can be prepared, and their surface can be modified by the addition of targeting moieties to recognize specific cells. However, it is still difficult to understand how the material properties affect the subsequent interactions and outcomes at cellular level. As a consequence of this, designing targeted drugs remains a major challenge in drug delivery. Within this context, we discuss the current understanding of the initial steps in the interactions of nano-sized materials with cells in relation to nanomedicine applications. In particular, we focus on the difficult interplay between the initial adhesion of nano-sized materials to the cell surface, the potential recognition by cell receptors, and the subsequent mechanisms cells use to internalize them. The factors affecting these initial events are discussed. Then, we briefly describe the different pathways of endocytosis in cells and illustrate with some examples the challenges in understanding how nanomaterial properties, such as size, charge, and shape, affect the mechanisms cells use for their internalization. Technical difficulties in characterizing these mechanisms are presented. A better understanding of the first interactions of nano-sized materials with cells will help to design nanomedicines with improved targeting.
Collapse
Affiliation(s)
- Valentina Francia
- Groningen Research Institute of Pharmacy, University of Groningen, 9713AV Groningen, Netherlands
| | - Daphne Montizaan
- Groningen Research Institute of Pharmacy, University of Groningen, 9713AV Groningen, Netherlands
| | - Anna Salvati
- Groningen Research Institute of Pharmacy, University of Groningen, 9713AV Groningen, Netherlands
| |
Collapse
|
16
|
Khan AO, White CW, Pike JA, Yule J, Slater A, Hill SJ, Poulter NS, Thomas SG, Morgan NV. Optimised insert design for improved single-molecule imaging and quantification through CRISPR-Cas9 mediated knock-in. Sci Rep 2019; 9:14219. [PMID: 31578415 PMCID: PMC6775134 DOI: 10.1038/s41598-019-50733-9] [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: 04/05/2019] [Accepted: 09/18/2019] [Indexed: 12/29/2022] Open
Abstract
The use of CRISPR-Cas9 genome editing to introduce endogenously expressed tags has the potential to address a number of the classical limitations of single molecule localisation microscopy. In this work we present the first systematic comparison of inserts introduced through CRISPR-knock in, with the aim of optimising this approach for single molecule imaging. We show that more highly monomeric and codon optimised variants of mEos result in improved expression at the TubA1B locus, despite the use of identical guides, homology templates, and selection strategies. We apply this approach to target the G protein-coupled receptor (GPCR) CXCR4 and show a further insert dependent effect on expression and protein function. Finally, we show that compared to over-expressed CXCR4, endogenously labelled samples allow for accurate single molecule quantification on ligand treatment. This suggests that despite the complications evident in CRISPR mediated labelling, the development of CRISPR-PALM has substantial quantitative benefits.
Collapse
Affiliation(s)
- Abdullah O Khan
- Institute of Cardiovascular Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK.
| | - Carl W White
- Centre of Membrane and Protein and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, UK
- Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, UK
- Molecular Endocrinology and Pharmacology, Harry Perkins Institute of Medical Research, Nedlands, WA, Australia
- Centre for Medical Research, The University of Western Australia, Crawley, WA, Australia
| | - Jeremy A Pike
- Institute of Cardiovascular Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
- Centre of Membrane and Protein and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, UK
| | - Jack Yule
- Institute of Cardiovascular Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
- Centre of Membrane and Protein and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, UK
| | - Alexandre Slater
- Institute of Cardiovascular Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Stephen J Hill
- Centre of Membrane and Protein and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, UK
- Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Natalie S Poulter
- Institute of Cardiovascular Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
- Centre of Membrane and Protein and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, UK
| | - Steven G Thomas
- Institute of Cardiovascular Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK.
- Centre of Membrane and Protein and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, UK.
| | - Neil V Morgan
- Institute of Cardiovascular Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK.
| |
Collapse
|
17
|
Nishida-Aoki N, Gujral TS. Emerging approaches to study cell-cell interactions in tumor microenvironment. Oncotarget 2019; 10:785-797. [PMID: 30774780 PMCID: PMC6366828 DOI: 10.18632/oncotarget.26585] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 12/27/2018] [Indexed: 01/19/2023] Open
Abstract
Cell-cell interactions are of crucial importance for tissue formation, homeostasis, regeneration processes, and immune response. Recent studies underlined contribution of cell-cell interaction in tumor microenvironment (TME) for tumor progression and metastasis. Cancer cells modify the host cells to tumor-supportive traits, and the modified host cells contribute to tumor progression by interacting with cancer cells and further modifying other normal cells. However, the complex interaction networks of cancer cells and host cells remained largely unknown. Recent advances in high throughput microscopy and single cells-based molecular analyses have unlocked a new era for studying cell-cell interactions in the complex tissue microenvironment at the resolution of a single cell. Here, we review various model systems and emerging experimental approaches that are used to study cell-cell interactions focusing on the studies of TME. We discuss strengths and weaknesses of each model system and each experimental approach, and how upcoming approaches can solve current fundamental questions of cell-cell interactions in TME.
Collapse
Affiliation(s)
- Nao Nishida-Aoki
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Taranjit S. Gujral
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| |
Collapse
|
18
|
Ghosh D, Venkataramani P, Nandi S, Bhattacharjee S. CRISPR-Cas9 a boon or bane: the bumpy road ahead to cancer therapeutics. Cancer Cell Int 2019; 19:12. [PMID: 30636933 PMCID: PMC6325665 DOI: 10.1186/s12935-019-0726-0] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Accepted: 01/02/2019] [Indexed: 12/13/2022] Open
Abstract
Genome editing allows for the precise manipulation of DNA sequences in a cell making this technology essential for understanding gene function. CRISPR/Cas9 is a targeted genome-editing platform derived from bacterial adaptive immune system and has been repurposed into a genome-editing tool. The RNA-guided DNA endonuclease, Cas9 can be easily programmed to target new sites by altering its guide RNA sequence, making this technology easier, more efficient, scalable and an indispensable tool in biological research. This technology has helped genetically engineer animal models to understand disease mechanisms and elucidate molecular details that can be exploited for improved therapeutic outcomes. In this review, we describe the CRISPR-Cas9 gene-editing mechanism, CRISPR-screening methods, therapeutic targeting of CRISPR in animal models and in cancer immunotherapy. We also discuss the ongoing clinical trials using this tool, limitations of this tool that might impede the clinical applicability of CRISPR-Cas9 and future directions for developing effective CRISPR-Cas9 delivery systems that may improve cancer therapeutics.
Collapse
Affiliation(s)
- Debarati Ghosh
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY USA
| | | | - Saikat Nandi
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY USA
| | | |
Collapse
|
19
|
Zwetsloot AJ, Tut G, Straube A. Measuring microtubule dynamics. Essays Biochem 2018; 62:725-735. [PMID: 30287587 PMCID: PMC6281472 DOI: 10.1042/ebc20180035] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Revised: 08/31/2018] [Accepted: 09/04/2018] [Indexed: 12/31/2022]
Abstract
Microtubules are key players in cellular self-organization, acting as structural scaffolds, cellular highways, force generators and signalling platforms. Microtubules are polar filaments that undergo dynamic instability, i.e. transition between phases of growth and shrinkage. This allows microtubules to explore the inner space of the cell, generate pushing and pulling forces and remodel themselves into arrays with different geometry and function such as the mitotic spindle. To do this, eukaryotic cells employ an arsenal of regulatory proteins to control microtubule dynamics spatially and temporally. Plants and microorganisms have developed secondary metabolites that perturb microtubule dynamics, many of which are in active use as cancer chemotherapeutics and anti-inflammatory drugs. Here, we summarize the methods used to visualize microtubules and to measure the parameters of dynamic instability to study both microtubule regulatory proteins and the action of small molecules interfering with microtubule assembly and/or disassembly.
Collapse
Affiliation(s)
- Alexander James Zwetsloot
- Centre for Mechanochemical Cell Biology, University of Warwick, Coventry, CV4 7AL, U.K
- MRC Doctoral Training Partnership, University of Warwick, Coventry, CV4 7AL, U.K
| | - Gokhan Tut
- Centre for Mechanochemical Cell Biology, University of Warwick, Coventry, CV4 7AL, U.K
- MRC Doctoral Training Partnership, University of Warwick, Coventry, CV4 7AL, U.K
| | - Anne Straube
- Centre for Mechanochemical Cell Biology, University of Warwick, Coventry, CV4 7AL, U.K.
- Division of Biomedical Sciences, Warwick Medical School, Coventry, CV4 7AL, U.K
| |
Collapse
|
20
|
Culley S, Tosheva KL, Matos Pereira P, Henriques R. SRRF: Universal live-cell super-resolution microscopy. Int J Biochem Cell Biol 2018; 101:74-79. [PMID: 29852248 PMCID: PMC6025290 DOI: 10.1016/j.biocel.2018.05.014] [Citation(s) in RCA: 91] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Revised: 05/21/2018] [Accepted: 05/23/2018] [Indexed: 11/30/2022]
Abstract
Super-resolution microscopy techniques break the diffraction limit of conventional optical microscopy to achieve resolutions approaching tens of nanometres. The major advantage of such techniques is that they provide resolutions close to those obtainable with electron microscopy while maintaining the benefits of light microscopy such as a wide palette of high specificity molecular labels, straightforward sample preparation and live-cell compatibility. Despite this, the application of super-resolution microscopy to dynamic, living samples has thus far been limited and often requires specialised, complex hardware. Here we demonstrate how a novel analytical approach, Super-Resolution Radial Fluctuations (SRRF), is able to make live-cell super-resolution microscopy accessible to a wider range of researchers. We show its applicability to live samples expressing GFP using commercial confocal as well as laser- and LED-based widefield microscopes, with the latter achieving long-term timelapse imaging with minimal photobleaching.
Collapse
Affiliation(s)
- Siân Culley
- MRC Laboratory for Molecular Cell Biology, University College London, Gower Street, London WC1E 6BT, UK; Department of Cell and Developmental Biology, University College London, Gower Street, London, WC1E 6BT, UK; The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Kalina L Tosheva
- MRC Laboratory for Molecular Cell Biology, University College London, Gower Street, London WC1E 6BT, UK; Department of Cell and Developmental Biology, University College London, Gower Street, London, WC1E 6BT, UK
| | - Pedro Matos Pereira
- MRC Laboratory for Molecular Cell Biology, University College London, Gower Street, London WC1E 6BT, UK; Department of Cell and Developmental Biology, University College London, Gower Street, London, WC1E 6BT, UK; The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Ricardo Henriques
- MRC Laboratory for Molecular Cell Biology, University College London, Gower Street, London WC1E 6BT, UK; Department of Cell and Developmental Biology, University College London, Gower Street, London, WC1E 6BT, UK; The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.
| |
Collapse
|
21
|
Banerjee S, Maurya S, Roy R. Single-molecule fluorescence imaging: Generating insights into molecular interactions in virology. J Biosci 2018; 43:519-540. [PMID: 30002270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Single-molecule fluorescence methods remain a challenging yet information-rich set of techniques that allow one to probe the dynamics, stoichiometry and conformation of biomolecules one molecule at a time. Viruses are small (nanometers) in size, can achieve cellular infections with a small number of virions and their lifecycle is inherently heterogeneous with a large number of structural and functional intermediates. Single-molecule measurements that reveal the complete distribution of properties rather than the average can hence reveal new insights into virus infections and biology that are inaccessible otherwise. This article highlights some of the methods and recent applications of single-molecule fluorescence in the field of virology. Here, we have focused on new findings in virus-cell interaction, virus cell entry and transport, viral membrane fusion, genome release, replication, translation, assembly, genome packaging, egress and interaction with host immune proteins that underline the advantage of single-molecule approach to the question at hand. Finally, we discuss the challenges, outlook and potential areas for improvement and future use of single-molecule fluorescence that could further aid our understanding of viruses.
Collapse
Affiliation(s)
- Sunaina Banerjee
- Molecular Biophysics Unit, Indian Institute of Science, Bengaluru, India
| | | | | |
Collapse
|
22
|
Schulze H, Stegner D. Imaging platelet biogenesis in vivo. Res Pract Thromb Haemost 2018; 2:461-468. [PMID: 30046750 PMCID: PMC6046590 DOI: 10.1002/rth2.12112] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 04/21/2018] [Indexed: 12/11/2022] Open
Abstract
In this review paper, we give a historical perspective of the development of imaging modalities to visualize platelet biogenesis and how this contributed to our current understanding of megakaryopoiesis and thrombopoiesis. We provide some insight how distinct in vivo and in situ imaging methods, including ultramicrographs, have contributed to the current concepts of platelet formation. The onset of intravital microscopy into the mouse bone marrow has markedly modified and challenged our thinking of platelet biogenesis during the last decade. Finally, we discuss ongoing work, which was presented at the recent International Society on Thrombosis and Haemostasis (ISTH) meeting.
Collapse
Affiliation(s)
- Harald Schulze
- Institute of Experimental BiomedicineUniversity Hospital WürzburgWürzburgGermany
| | - David Stegner
- Institute of Experimental BiomedicineUniversity Hospital WürzburgWürzburgGermany
| |
Collapse
|
23
|
Single-molecule fluorescence imaging: Generating insights into molecular interactions in virology. J Biosci 2018. [DOI: 10.1007/s12038-018-9769-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
|
24
|
Ward R, Sundaramurthi H, Di Giacomo V, Kennedy BN. Enhancing Understanding of the Visual Cycle by Applying CRISPR/Cas9 Gene Editing in Zebrafish. Front Cell Dev Biol 2018; 6:37. [PMID: 29696141 PMCID: PMC5904205 DOI: 10.3389/fcell.2018.00037] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Accepted: 03/19/2018] [Indexed: 01/23/2023] Open
Abstract
During the vertebrate visual cycle, all-trans-retinal is exported from photoreceptors to the adjacent RPE or Müller glia wherein 11-cis-retinal is regenerated. The 11-cis chromophore is returned to photoreceptors, forming light-sensitive visual pigments with opsin GPCRs. Dysfunction of this process perturbs phototransduction because functional visual pigment cannot be generated. Mutations in visual cycle genes can result in monogenic inherited forms of blindness. Though key enzymatic processes are well characterized, questions remain as to the physiological role of visual cycle proteins in different retinal cell types, functional domains of these proteins in retinoid biochemistry and in vivo pathogenesis of disease mutations. Significant progress is needed to develop effective and accessible treatments for inherited blindness arising from mutations in visual cycle genes. Here, we review opportunities to apply gene editing technology to two crucial visual cycle components, RPE65 and CRALBP. Expressed exclusively in the human RPE, RPE65 enzymatically converts retinyl esters into 11-cis retinal. CRALBP is an 11-cis-retinal binding protein expressed in human RPE and Muller glia. Loss-of-function mutations in either protein results in autosomal recessive forms of blindness. Modeling these human conditions using RPE65 or CRALBP murine knockout models have enhanced our understanding of their biochemical function, associated disease pathogenesis and development of therapeutics. However, rod-dominated murine retinae provide a challenge to assess cone function. The cone-rich zebrafish model is amenable to cost-effective maintenance of a variety of strains. Interestingly, gene duplication in zebrafish resulted in three Rpe65 and two Cralbp isoforms with differential temporal and spatial expression patterns. Functional investigations of zebrafish Rpe65 and Cralbp were restricted to gene knockdown with morpholino oligonucleotides. However, transient silencing, off-target effects and discrepancies between knockdown and knockout models, highlight a need for more comprehensive alternatives for functional genomics. CRISPR/Cas9 in zebrafish has emerged as a formidable technology enabling targeted gene knockout, knock-in, activation, or silencing to single base-pair resolution. Effective, targeted gene editing by CRISPR/Cas9 in zebrafish enables unprecedented opportunities to create genetic research models. This review will discuss existing knowledge gaps regarding RPE65 and CRALBP. We explore the benefits of CRISPR/Cas9 to establish innovative zebrafish models to enhance knowledge of the visual cycle.
Collapse
Affiliation(s)
- Rebecca Ward
- UCD School of Biomolecular & Biomedical Science, UCD Conway Institute, University College Dublin, Dublin, Ireland
| | - Husvinee Sundaramurthi
- UCD School of Biomolecular & Biomedical Science, UCD Conway Institute, University College Dublin, Dublin, Ireland
- UCD School of Medicine, University College Dublin, Dublin, Ireland
- Systems Biology Ireland, University College Dublin, Dublin, Ireland
| | | | - Breandán N. Kennedy
- UCD School of Biomolecular & Biomedical Science, UCD Conway Institute, University College Dublin, Dublin, Ireland
- *Correspondence: Breandán N. Kennedy
| |
Collapse
|
25
|
Lambing C, Heckmann S. Tackling Plant Meiosis: From Model Research to Crop Improvement. FRONTIERS IN PLANT SCIENCE 2018; 9:829. [PMID: 29971082 PMCID: PMC6018109 DOI: 10.3389/fpls.2018.00829] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 05/28/2018] [Indexed: 05/04/2023]
Abstract
Genetic engineering and traditional plant breeding, which harnesses the natural genetic variation that arises during meiosis, will have key roles to improve crop varieties and thus deliver Food Security in the future. Meiosis, a specialized cell division producing haploid gametes to maintain somatic diploidy following their fusion, assures genetic variation by regulated genetic exchange through homologous recombination. However, meiotic recombination events are restricted in their total number and their distribution along chromosomes limiting allelic variations in breeding programs. Thus, modifying the number and distribution of meiotic recombination events has great potential to improve and accelerate plant breeding. In recent years much progress has been made in understanding meiotic progression and recombination in plants. Many genes and factors involved in these processes have been identified primarily in Arabidopsis thaliana but also more recently in crops such as Brassica, rice, barley, maize, or wheat. These advances put researchers in the position to translate acquired knowledge to various crops likely improving and accelerating breeding programs. However, although fundamental aspects of meiotic progression and recombination are conserved between species, differences in genome size and organization (due to repetitive DNA content and ploidy level) exist, particularly among plants, that likely account for differences in meiotic progression and recombination patterns found between species. Thus, tools and approaches are needed to better understand differences and similarities in meiotic progression and recombination among plants, to study fundamental aspects of meiosis in a variety of plants including crops and non-model species, and to transfer knowledge into crop species. In this article, we provide an overview of tools and approaches available to study plant meiosis, highlight new techniques, give examples of areas of future research and review distinct aspects of meiosis in non-model species.
Collapse
Affiliation(s)
- Christophe Lambing
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
- *Correspondence: Christophe Lambing, Stefan Heckmann,
| | - Stefan Heckmann
- Independent Research Group Meiosis, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
- *Correspondence: Christophe Lambing, Stefan Heckmann,
| |
Collapse
|