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Sindeeva OA, Demina PA, Kozyreva ZV, Muslimov AR, Gusliakova OI, Laushkina VO, Mordovina EA, Tsyupka D, Epifanovskaya OS, Sapach AY, Goryacheva IY, Sukhorukov GB. Labeling and Tracking of Individual Human Mesenchymal Stromal Cells Using Photoconvertible Fluorescent Microcapsules. Int J Mol Sci 2023; 24:13665. [PMID: 37686471 PMCID: PMC10488098 DOI: 10.3390/ijms241713665] [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: 07/23/2023] [Revised: 08/28/2023] [Accepted: 08/31/2023] [Indexed: 09/10/2023] Open
Abstract
The behavior and migration of human mesenchymal stromal cells (hMSCs) are focal points of research in the biomedical field. One of the major aspects is potential therapy using hMCS, but at present, the safety of their use is still controversial owing to limited data on changes that occur with hMSCs in the long term. Fluorescent photoconvertible proteins are intensively used today as "gold standard" to mark the individual cells and study single-cell interactions, migration processes, and the formation of pure lines. A crucial disadvantage of this method is the need for genetic modification of the primary culture, which casts doubt on the possibility of exploring the resulting clones in personalized medicine. Here we present a new approach for labeling and tracking hMSCs without genetic modification based on the application of cell-internalizable photoconvertible polyelectrolyte microcapsules (size: 2.6 ± 0.5 μm). These capsules were loaded with rhodamine B, and after thermal treatment, exhibited fluorescent photoconversion properties. Photoconvertible capsules demonstrated low cytotoxicity, did not affect the immunophenotype of the hMSCs, and maintained a high level of fluorescent signal for at least seven days. The developed approach was tested for cell tracking for four days and made it possible to trace the destiny of daughter cells without the need for additional labeling.
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Affiliation(s)
- Olga A. Sindeeva
- Vladimir Zelman Center for Neurobiology and Brain Rehabilitation, Skolkovo Institute of Science and Technology, Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, 121205 Moscow, Russia; (Z.V.K.); (O.I.G.); (A.Y.S.); (I.Y.G.)
| | - Polina A. Demina
- Science Medical Center, Saratov State University, 83 Astrakhanskaya Str., 410012 Saratov, Russia; (P.A.D.); (E.A.M.); (D.T.)
| | - Zhanna V. Kozyreva
- Vladimir Zelman Center for Neurobiology and Brain Rehabilitation, Skolkovo Institute of Science and Technology, Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, 121205 Moscow, Russia; (Z.V.K.); (O.I.G.); (A.Y.S.); (I.Y.G.)
| | - Albert R. Muslimov
- Scientific Center for Translational Medicine, Sirius University of Science and Technology, 1 Olympic Ave., 354340 Sirius, Russia;
- Laboratory of Nano and Microencapsulation of Biologically Active Substances, Peter the Great St. Petersburg Polytechnic University, Polytechnicheskaya 29, 195251 St. Petersburg, Russia
- RM Gorbacheva Research Institute, Pavlov University, L’va Tolstogo 6-8, 197022 St. Petersburg, Russia; (V.O.L.); (O.S.E.)
| | - Olga I. Gusliakova
- Vladimir Zelman Center for Neurobiology and Brain Rehabilitation, Skolkovo Institute of Science and Technology, Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, 121205 Moscow, Russia; (Z.V.K.); (O.I.G.); (A.Y.S.); (I.Y.G.)
- Science Medical Center, Saratov State University, 83 Astrakhanskaya Str., 410012 Saratov, Russia; (P.A.D.); (E.A.M.); (D.T.)
| | - Valeriia O. Laushkina
- RM Gorbacheva Research Institute, Pavlov University, L’va Tolstogo 6-8, 197022 St. Petersburg, Russia; (V.O.L.); (O.S.E.)
| | - Ekaterina A. Mordovina
- Science Medical Center, Saratov State University, 83 Astrakhanskaya Str., 410012 Saratov, Russia; (P.A.D.); (E.A.M.); (D.T.)
| | - Daria Tsyupka
- Science Medical Center, Saratov State University, 83 Astrakhanskaya Str., 410012 Saratov, Russia; (P.A.D.); (E.A.M.); (D.T.)
| | - Olga S. Epifanovskaya
- RM Gorbacheva Research Institute, Pavlov University, L’va Tolstogo 6-8, 197022 St. Petersburg, Russia; (V.O.L.); (O.S.E.)
| | - Anastasiia Yu. Sapach
- Vladimir Zelman Center for Neurobiology and Brain Rehabilitation, Skolkovo Institute of Science and Technology, Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, 121205 Moscow, Russia; (Z.V.K.); (O.I.G.); (A.Y.S.); (I.Y.G.)
| | - Irina Yu. Goryacheva
- Vladimir Zelman Center for Neurobiology and Brain Rehabilitation, Skolkovo Institute of Science and Technology, Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, 121205 Moscow, Russia; (Z.V.K.); (O.I.G.); (A.Y.S.); (I.Y.G.)
- Science Medical Center, Saratov State University, 83 Astrakhanskaya Str., 410012 Saratov, Russia; (P.A.D.); (E.A.M.); (D.T.)
| | - Gleb B. Sukhorukov
- Vladimir Zelman Center for Neurobiology and Brain Rehabilitation, Skolkovo Institute of Science and Technology, Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, 121205 Moscow, Russia; (Z.V.K.); (O.I.G.); (A.Y.S.); (I.Y.G.)
- School of Engineering and Materials Science, Queen Mary University of London, Mile End Road, London E1 4NS, UK
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Demina PA, Sindeeva OA, Abramova AM, Saveleva MS, Sukhorukov GB, Goryacheva IY. Fluorescent polymer markers photoconvertible with a 532 nm laser for individual cell labeling. JOURNAL OF BIOPHOTONICS 2023; 16:e202200379. [PMID: 36726223 DOI: 10.1002/jbio.202200379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 01/25/2023] [Accepted: 01/31/2023] [Indexed: 06/07/2023]
Abstract
Fluorescent photoconvertible materials and molecules have been successfully exploited as bioimaging markers and cell trackers. Recently, the novel fluorescent photoconvertible polymer markers have been developed that allow the long-term tracking of individual labeled cells. However, it is still necessary to study the functionality of this type of fluorescent labels for various operating conditions, in particular for commonly used discrete wavelength lasers. In this article, the photoconversion of fluorescent polymer labels with both pulsed and continuous-wave lasers with 532 nm-irradiation wavelength, and under different laser power densities were studied. The photoconversion process was described and its possible mechanism was proposed. The peculiarities of fluorescent polymer capsules performance as an aqueous suspension and as a single capsule were described. We performed the successful nondestructivity marker photoconversion inside RAW 264.7 monocyte/macrophage cells under continuous-wave laser with 532 nm-irradiation wavelength, showing prospects of these fluorescent markers for long-term live cell labeling.
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Affiliation(s)
- P A Demina
- Science Medical Center, Saratov State University, Saratov, Russia
| | - O A Sindeeva
- A.V. Zelmann Center for Neurobiology and Brain Rehabilitation, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - A M Abramova
- Science Medical Center, Saratov State University, Saratov, Russia
| | - M S Saveleva
- Science Medical Center, Saratov State University, Saratov, Russia
| | - G B Sukhorukov
- A.V. Zelmann Center for Neurobiology and Brain Rehabilitation, Skolkovo Institute of Science and Technology, Moscow, Russia
- School of Engineering and Materials Science, Queen Mary University of London, London, UK
| | - I Y Goryacheva
- Science Medical Center, Saratov State University, Saratov, Russia
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3
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Lycas MD, Ejdrup AL, Sørensen AT, Haahr NO, Jørgensen SH, Guthrie DA, Støier JF, Werner C, Newman AH, Sauer M, Herborg F, Gether U. Nanoscopic dopamine transporter distribution and conformation are inversely regulated by excitatory drive and D2 autoreceptor activity. Cell Rep 2022; 40:111431. [PMID: 36170827 PMCID: PMC9617621 DOI: 10.1016/j.celrep.2022.111431] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 07/22/2022] [Accepted: 09/08/2022] [Indexed: 11/30/2022] Open
Abstract
The nanoscopic organization and regulation of individual molecular components in presynaptic varicosities of neurons releasing modulatory volume neurotransmitters like dopamine (DA) remain largely elusive. Here we show, by application of several super-resolution microscopy techniques to cultured neurons and mouse striatal slices, that the DA transporter (DAT), a key protein in varicosities of dopaminergic neurons, exists in the membrane in dynamic equilibrium between an inward-facing nanodomain-localized and outward-facing unclustered configuration. The balance between these configurations is inversely regulated by excitatory drive and DA D2 autoreceptor activation in a manner dependent on Ca2+ influx via N-type voltage-gated Ca2+ channels. The DAT nanodomains contain tens of transporters molecules and overlap with nanodomains of PIP2 (phosphatidylinositol-4,5-bisphosphate) but show little overlap with D2 autoreceptor, syntaxin-1, and clathrin nanodomains. The data reveal a mechanism for rapid alterations of nanoscopic DAT distribution and show a striking link of this to the conformational state of the transporter.
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Affiliation(s)
- Matthew D Lycas
- Molecular Neuropharmacology and Genetics Laboratory, Department of Neuroscience, Faculty of Health and Medical Sciences, University of Copenhagen, Maersk Tower 7.5, 2200 Copenhagen, Denmark
| | - Aske L Ejdrup
- Molecular Neuropharmacology and Genetics Laboratory, Department of Neuroscience, Faculty of Health and Medical Sciences, University of Copenhagen, Maersk Tower 7.5, 2200 Copenhagen, Denmark
| | - Andreas T Sørensen
- Molecular Neuropharmacology and Genetics Laboratory, Department of Neuroscience, Faculty of Health and Medical Sciences, University of Copenhagen, Maersk Tower 7.5, 2200 Copenhagen, Denmark
| | - Nicolai O Haahr
- Molecular Neuropharmacology and Genetics Laboratory, Department of Neuroscience, Faculty of Health and Medical Sciences, University of Copenhagen, Maersk Tower 7.5, 2200 Copenhagen, Denmark
| | - Søren H Jørgensen
- Molecular Neuropharmacology and Genetics Laboratory, Department of Neuroscience, Faculty of Health and Medical Sciences, University of Copenhagen, Maersk Tower 7.5, 2200 Copenhagen, Denmark
| | - Daryl A Guthrie
- Medicinal Chemistry Section, Molecular Targets and Medications Discovery Branch, National Institute on Drug Abuse-Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Jonatan F Støier
- Molecular Neuropharmacology and Genetics Laboratory, Department of Neuroscience, Faculty of Health and Medical Sciences, University of Copenhagen, Maersk Tower 7.5, 2200 Copenhagen, Denmark
| | - Christian Werner
- Department of Biotechnology and Biophysics, Biocenter, Julius-Maximilians-Universität Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Amy Hauck Newman
- Medicinal Chemistry Section, Molecular Targets and Medications Discovery Branch, National Institute on Drug Abuse-Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Markus Sauer
- Department of Biotechnology and Biophysics, Biocenter, Julius-Maximilians-Universität Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Freja Herborg
- Molecular Neuropharmacology and Genetics Laboratory, Department of Neuroscience, Faculty of Health and Medical Sciences, University of Copenhagen, Maersk Tower 7.5, 2200 Copenhagen, Denmark
| | - Ulrik Gether
- Molecular Neuropharmacology and Genetics Laboratory, Department of Neuroscience, Faculty of Health and Medical Sciences, University of Copenhagen, Maersk Tower 7.5, 2200 Copenhagen, Denmark.
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Zhang M, Seitz C, Chang G, Iqbal F, Lin H, Liu J. A guide for single-particle chromatin tracking in live cell nuclei. Cell Biol Int 2022; 46:683-700. [PMID: 35032142 PMCID: PMC9035067 DOI: 10.1002/cbin.11762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 12/29/2021] [Accepted: 01/08/2022] [Indexed: 11/09/2022]
Abstract
The emergence of labeling strategies and live cell imaging methods enables the imaging of chromatin in living cells at single digit nanometer resolution as well as milliseconds temporal resolution. These technical breakthroughs revolutionize our understanding of chromatin structure, dynamics and functions. Single molecule tracking algorithms are usually preferred to quantify the movement of these intranucleus elements to interpret the spatiotemporal evolution of the chromatin. In this review, we will first summarize the fluorescent labeling strategy of chromatin in live cells which will be followed by a sys-tematic comparison of live cell imaging instrumentation. With the proper microscope, we will discuss the image analysis pipelines to extract the biophysical properties of the chromatin. Finally, we expect to give practical suggestions to broad biologists on how to select methods and link to the model properly according to different investigation pur-poses. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Mengdi Zhang
- Department of Physics, Indiana University-Purdue University Indianapolis, Indianapolis, IN, USA
| | - Clayton Seitz
- Department of Physics, Indiana University-Purdue University Indianapolis, Indianapolis, IN, USA
| | - Garrick Chang
- Department of Physics, Indiana University-Purdue University Indianapolis, Indianapolis, IN, USA
| | - Fadil Iqbal
- Department of Physics, Indiana University-Purdue University Indianapolis, Indianapolis, IN, USA
| | - Hua Lin
- Department of Physics, Indiana University-Purdue University Indianapolis, Indianapolis, IN, USA
| | - Jing Liu
- Department of Physics, Indiana University-Purdue University Indianapolis, Indianapolis, IN, USA.,Indiana University Melvin and Bren Simon Comprehensive Cancer Center, Indianapolis, IN, USA.,Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN, USA
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Demina PA, Sindeeva OA, Abramova AM, Prikhozhdenko ES, Verkhovskii RA, Lengert EV, Sapelkin AV, Goryacheva IY, Sukhorukov GB. Fluorescent Convertible Capsule Coding Systems for Individual Cell Labeling and Tracking. ACS APPLIED MATERIALS & INTERFACES 2021; 13:19701-19709. [PMID: 33900738 DOI: 10.1021/acsami.1c02767] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
In modern biomedical science and developmental biology, there is significant interest in optical tagging to study individual cell behavior and migration in large cellular populations. However, there is currently no tagging system that can be used for labeling individual cells on demand in situ with subsequent discrimination in between and long-term tracking of individual cells. In this article, we demonstrate such a system based on photoconversion of the fluorescent dye rhodamine B co-confined with carbon nanodots in the volume of micron-sized polyelectrolyte capsules. We show that this new fluorescent convertible capsule coding system is robust and is actively uptaken by cell lines while demonstrating low toxicity. Using a variety of cellular lines, we demonstrate how this tagging system can be used for code-like marking and long-term tracking of multiple individual cells in large cellular populations.
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Affiliation(s)
- Polina A Demina
- Saratov State University, 83 Astrakhanskaya Street, Saratov 410012, Russia
| | - Olga A Sindeeva
- Saratov State University, 83 Astrakhanskaya Street, Saratov 410012, Russia
- Skolkovo Institute of Science and Technology, Moscow 121205, Russia
| | - Anna M Abramova
- Saratov State University, 83 Astrakhanskaya Street, Saratov 410012, Russia
| | | | | | | | - Andrei V Sapelkin
- Saratov State University, 83 Astrakhanskaya Street, Saratov 410012, Russia
- Queen Mary University of London, Mile End Road, London E1 4NS, U.K
| | | | - Gleb B Sukhorukov
- Skolkovo Institute of Science and Technology, Moscow 121205, Russia
- Queen Mary University of London, Mile End Road, London E1 4NS, U.K
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A two-tier junctional mechanism drives simultaneous tissue folding and extension. Dev Cell 2021; 56:1469-1483.e5. [PMID: 33891900 DOI: 10.1016/j.devcel.2021.04.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 02/18/2021] [Accepted: 03/31/2021] [Indexed: 11/20/2022]
Abstract
During embryo development, tissues often undergo multiple concomitant changes in shape. It is unclear which signaling pathways and cellular mechanisms are responsible for multiple simultaneous tissue shape transformations. We focus on the process of concomitant tissue folding and extension that is key during gastrulation and neurulation. We use the Drosophila embryo as model system and focus on the process of mesoderm invagination. Here, we show that the prospective mesoderm simultaneously folds and extends. We report that mesoderm cells, under the control of anterior-posterior and dorsal-ventral gene patterning synergy, establish two sets of adherens junctions at different apical-basal positions with specialized functions: while apical junctions drive apical constriction initiating tissue bending, lateral junctions concomitantly drive polarized cell intercalation, resulting in tissue convergence-extension. Thus, epithelial cells devise multiple specialized junctional sets that drive composite morphogenetic processes under the synergistic control of apparently orthogonal signaling sources.
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Moser B, Hochreiter B, Basílio J, Gleitsmann V, Panhuber A, Pardo-Garcia A, Hoesel B, Salzmann M, Resch U, Noreen M, Schmid JA. The inflammatory kinase IKKα phosphorylates and stabilizes c-Myc and enhances its activity. Mol Cancer 2021; 20:16. [PMID: 33461590 PMCID: PMC7812655 DOI: 10.1186/s12943-021-01308-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 01/04/2021] [Indexed: 02/06/2023] Open
Abstract
Background The IκB kinase (IKK) complex, comprising the two enzymes IKKα and IKKβ, is the main activator of the inflammatory transcription factor NF-κB, which is constitutively active in many cancers. While several connections between NF-κB signaling and the oncogene c-Myc have been shown, functional links between the signaling molecules are still poorly studied. Methods Molecular interactions were shown by co-immunoprecipitation and FRET microscopy. Phosphorylation of c-Myc was shown by kinases assays and its activity by improved reporter gene systems. CRISPR/Cas9-mediated gene knockout and chemical inhibition were used to block IKK activity. The turnover of c-Myc variants was determined by degradation in presence of cycloheximide and by optical pulse-chase experiments.. Immunofluorescence of mouse prostate tissue and bioinformatics of human datasets were applied to correlate IKKα- and c-Myc levels. Cell proliferation was assessed by EdU incorporation and apoptosis by flow cytometry. Results We show that IKKα and IKKβ bind to c-Myc and phosphorylate it at serines 67/71 within a sequence that is highly conserved. Knockout of IKKα decreased c-Myc-activity and increased its T58-phosphorylation, the target site for GSK3β, triggering polyubiquitination and degradation. c-Myc-mutants mimicking IKK-mediated S67/S71-phosphorylation exhibited slower turnover, higher cell proliferation and lower apoptosis, while the opposite was observed for non-phosphorylatable A67/A71-mutants. A significant positive correlation of c-Myc and IKKα levels was noticed in the prostate epithelium of mice and in a variety of human cancers. Conclusions Our data imply that IKKα phosphorylates c-Myc on serines-67/71, thereby stabilizing it, leading to increased transcriptional activity, higher proliferation and decreased apoptosis. Supplementary Information The online version contains supplementary material available at 10.1186/s12943-021-01308-8.
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Affiliation(s)
- Bernhard Moser
- Institute of Vascular Biology and Thrombosis Research, Center for Physiology and Pharmacology, Medical University of Vienna, Schwarzspanierstraße 17, 1090, Vienna, Austria
| | - Bernhard Hochreiter
- Institute of Vascular Biology and Thrombosis Research, Center for Physiology and Pharmacology, Medical University of Vienna, Schwarzspanierstraße 17, 1090, Vienna, Austria
| | - José Basílio
- Institute of Vascular Biology and Thrombosis Research, Center for Physiology and Pharmacology, Medical University of Vienna, Schwarzspanierstraße 17, 1090, Vienna, Austria
| | - Viola Gleitsmann
- Institute of Vascular Biology and Thrombosis Research, Center for Physiology and Pharmacology, Medical University of Vienna, Schwarzspanierstraße 17, 1090, Vienna, Austria
| | - Anja Panhuber
- Institute of Vascular Biology and Thrombosis Research, Center for Physiology and Pharmacology, Medical University of Vienna, Schwarzspanierstraße 17, 1090, Vienna, Austria
| | - Alan Pardo-Garcia
- Institute of Vascular Biology and Thrombosis Research, Center for Physiology and Pharmacology, Medical University of Vienna, Schwarzspanierstraße 17, 1090, Vienna, Austria
| | - Bastian Hoesel
- Institute of Vascular Biology and Thrombosis Research, Center for Physiology and Pharmacology, Medical University of Vienna, Schwarzspanierstraße 17, 1090, Vienna, Austria
| | - Manuel Salzmann
- Institute of Vascular Biology and Thrombosis Research, Center for Physiology and Pharmacology, Medical University of Vienna, Schwarzspanierstraße 17, 1090, Vienna, Austria
| | - Ulrike Resch
- Institute of Vascular Biology and Thrombosis Research, Center for Physiology and Pharmacology, Medical University of Vienna, Schwarzspanierstraße 17, 1090, Vienna, Austria
| | - Mamoona Noreen
- Institute of Vascular Biology and Thrombosis Research, Center for Physiology and Pharmacology, Medical University of Vienna, Schwarzspanierstraße 17, 1090, Vienna, Austria
| | - Johannes A Schmid
- Institute of Vascular Biology and Thrombosis Research, Center for Physiology and Pharmacology, Medical University of Vienna, Schwarzspanierstraße 17, 1090, Vienna, Austria.
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Frolova AY, Pakhomov AA, Martynov VI. Physicochemical Properties of Photoconvertible Fluorescent Protein from Montastraea cavernosa. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2021. [DOI: 10.1134/s1068162021010052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Marathe P, H S MS, Nair D, Bhattacharyya D. mEosBrite Are Bright Variants of mEos3.2 Developed by Semirational Protein Engineering. J Fluoresc 2020; 30:703-715. [PMID: 32385659 DOI: 10.1007/s10895-020-02537-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 04/13/2020] [Indexed: 10/24/2022]
Abstract
mEos3.2 is a photoconvertible fluorescence protein with comparatively low brightness, which limits its application in live Super resolution microscopy. To address this issue, we have used semi-rational protein engineering to develop mEosBrite, a new class of improved brightness variants. The improvement in the brightness was confirmed by expression in E.coli as well as mammalian cell lines. Furthermore, biophysical characterization suggests that all the three mEosBrite variant proteins display higher quantum yield, truly monomeric form, less cytotoxicity and lower protein aggregation as compared to the wild type mEos3.2 protein. Most importantly, because of their high photoconversion efficiency mEosBrite variants could be an excellent tool for single-molecule and intensity fluctuation based super-resolution microscopy.
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Affiliation(s)
- Pravin Marathe
- Department of Cell and Tumor Biology, Advanced Centre for Treatment Research & Education in Cancer (ACTREC), Tata Memorial Centre, Sector 22, Kharghar, Navi Mumbai, MH, 410210, India.,Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, MH, 400085, India
| | - Mahadeva Swamy H S
- Centre For Neuroscience, Indian Institute of Science, Bangalore, 560012, India
| | - Deepak Nair
- Centre For Neuroscience, Indian Institute of Science, Bangalore, 560012, India
| | - Dibyendu Bhattacharyya
- Department of Cell and Tumor Biology, Advanced Centre for Treatment Research & Education in Cancer (ACTREC), Tata Memorial Centre, Sector 22, Kharghar, Navi Mumbai, MH, 410210, India. .,Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, MH, 400085, India.
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Single-molecule localization to study cytoskeletal structures, membrane complexes, and mechanosensors. Biophys Rev 2019; 11:745-756. [PMID: 31529362 DOI: 10.1007/s12551-019-00595-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 09/03/2019] [Indexed: 12/21/2022] Open
Abstract
In the last decades, a promising breakthrough in fluorescence imaging was represented by the advent of super-resolution microscopy (SRM). Super-resolution techniques recently became a popular method to study sub-cellular structures, providing a successful approach to observe cytoskeletal and focal adhesion proteins. Among the SR techniques, single-molecule localization microscopy plays a significant role due to its ability to unveil structures and molecular organizations in biological systems. Furthermore, since they provide information at the molecular level, these techniques are increasingly being used to study the stoichiometry and interaction between several membrane channel proteins and their accessory subunits. The aim of this review is to describe the single-molecule localization-based techniques and their applications relevant to cytoskeletal structures and membrane complexes in order to provide as future prospective an overall picture of their correlation with the mechanosensor channel expression and activity.
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11
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Mei Y, Wang Y, Hu T, Yang X, Lozano-Duran R, Sunter G, Zhou X. Nucleocytoplasmic Shuttling of Geminivirus C4 Protein Mediated by Phosphorylation and Myristoylation Is Critical for Viral Pathogenicity. MOLECULAR PLANT 2018; 11:1466-1481. [PMID: 30523782 DOI: 10.1016/j.molp.2018.10.004] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Revised: 10/17/2018] [Accepted: 10/17/2018] [Indexed: 05/13/2023]
Abstract
Many geminivirus C4 proteins induce severe developmental abnormalities in plants. We previously demonstrated that Tomato leaf curl Yunnan virus (TLCYnV) C4 induces plant developmental abnormalities at least partically by decreasing the accumulation of NbSKη, an ortholog of Arabidopsis BIN2 kinase involved in the brassinosteroid signaling pathway, in the nucleus through directing it to the plasma membrane. However, the molecular mechanism by which the membrane-associated C4 modifies the localization of NbSKη in the host cell remains unclear. Here, we show that TLCYnV C4 is a nucleocytoplasmic shuttle protein, and that C4 shuttling is accompanied by nuclear export of NbSKη. TLCYnV C4 is phosphorylated by NbSKη in the nucleus, which promotes myristoylation of the viral protein. Myristoylation of phosphorylated C4 favors its interaction with exportin-α (XPO I), which in turn facilitates nuclear export of the C4/NbSKη complex. Supporting this model, chemical inhibition of N-myristoyltransferases or exportin-α enhanced nuclear retention of C4, and mutations of the putative phosphorylation or myristoylation sites in C4 resulted in increased nuclear retention of C4 and thus decreased severity of C4-induced developmental abnormalities. The impact of C4 on development is also lessened when a nuclear localization signal or a nuclear export signal is added to its C-terminus, restricting it to a specific cellular niche and therefore impairing nucleocytoplasmic shuttling. Taken together, our results suggest that nucleocytoplasmic shuttling of TLCYnV C4, enabled by phosphorylation by NbSKη, myristoylation, and interaction with exportin-α, is critical for its function as a pathogenicity factor.
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Affiliation(s)
- Yuzhen Mei
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Yaqin Wang
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Tao Hu
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Xiuling Yang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Rosa Lozano-Duran
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 201602, China
| | - Garry Sunter
- Department of Biology, University of Texas at San Antonio, San Antonio, TX 78249, USA
| | - Xueping Zhou
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, Zhejiang 310058, China; State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
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12
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Bayarmagnai B, Perrin L, Esmaeili Pourfarhangi K, Gligorijevic B. Intravital Imaging of Tumor Cell Motility in the Tumor Microenvironment Context. Methods Mol Biol 2018; 1749:175-193. [PMID: 29525998 PMCID: PMC5996994 DOI: 10.1007/978-1-4939-7701-7_14] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Cancer cell motility and invasion are key features of metastatic tumors. Both are highly linked to tumor microenvironmental parameters, such as collagen architecture or macrophage density. However, due to the genetic, epigenetic and microenvironmental heterogeneities, only a small portion of tumor cells in the primary tumor are motile and furthermore, only a small portion of those will metastasize. This creates a challenge in predicting metastatic fate of single cells based on the phenotype they exhibit in the primary tumor. To overcome this challenge, tumor cell subpopulations need to be monitored at several timescales, mapping their phenotype in primary tumor as well as their potential homing to the secondary tumor site. Additionally, to address the spatial heterogeneity of the tumor microenvironment and how it relates to tumor cell phenotypes, large numbers of images need to be obtained from the same tumor. Finally, as the microenvironment complexity results in nonlinear relationships between tumor cell phenotype and its surroundings, advanced statistical models are required to interpret the imaging data. Toward improving our understanding of the relationship between cancer cell motility, the tumor microenvironment context and successful metastasis, we have developed several intravital approaches for continuous and longitudinal imaging, as well as data classification via support vector machine (SVM) algorithm. We also describe methods that extend the capabilities of intravital imaging by postsacrificial microscopy of the lung as well as correlative immunofluorescence in the primary tumor.
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Affiliation(s)
| | - Louisiane Perrin
- Department of Bioengineering, Temple University, Philadelphia, PA, USA
| | | | - Bojana Gligorijevic
- Department of Bioengineering, Temple University, Philadelphia, PA, USA.
- Cancer Biology Program, Fox Chase Cancer Center, Philadelphia, PA, USA.
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13
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Pakhomov AA, Martynov VI, Orsa AN, Bondarenko AA, Chertkova RV, Lukyanov KA, Petrenko AG, Deyev IE. Fluorescent protein Dendra2 as a ratiometric genetically encoded pH-sensor. Biochem Biophys Res Commun 2017; 493:1518-1521. [PMID: 28986251 DOI: 10.1016/j.bbrc.2017.09.170] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 09/30/2017] [Indexed: 10/18/2022]
Abstract
Fluorescent protein Dendra2 is a monomeric GFP-like protein that belongs to the group of Kaede-like photoconvertible fluorescent proteins with irreversible photoconversion from a green- to red-emitting state when exposed to violet-blue light. In an acidic environment, photoconverted Dendra2 turns green due to protonation of the phenolic group of the chromophore with pKa of about 7.5. Thus, photoconverted form of Dendra2 can be potentially used as a ratiometric pH-sensor in the physiological pH range. However, incomplete photoconversion makes ratiometric measurements irreproducible when using standard filter sets. Here, we describe the method to detect fluorescence of only photoconverted Dendra2 form, but not nonconverted green Dendra2. We show that the 350 nm excitation light induces solely the fluorescence of photoconverted protein. By measuring the red to green fluorescence ratio, we determined intracellular pH in live CHO and HEK 293 cells. Thus, Dendra2 can be used as a novel ratiometric genetically encoded pH sensor with emission maxima in the green-red spectral region, which is suitable for application in live cells.
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Affiliation(s)
- Alexey A Pakhomov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia.
| | - Vladimir I Martynov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
| | - Alexander N Orsa
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
| | - Alena A Bondarenko
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
| | - Rita V Chertkova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
| | - Konstantin A Lukyanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
| | - Alexander G Petrenko
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
| | - Igor E Deyev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
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14
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Shashkova S, Leake MC. Single-molecule fluorescence microscopy review: shedding new light on old problems. Biosci Rep 2017; 37:BSR20170031. [PMID: 28694303 PMCID: PMC5520217 DOI: 10.1042/bsr20170031] [Citation(s) in RCA: 147] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Revised: 07/08/2017] [Accepted: 07/10/2017] [Indexed: 12/19/2022] Open
Abstract
Fluorescence microscopy is an invaluable tool in the biosciences, a genuine workhorse technique offering exceptional contrast in conjunction with high specificity of labelling with relatively minimal perturbation to biological samples compared with many competing biophysical techniques. Improvements in detector and dye technologies coupled to advances in image analysis methods have fuelled recent development towards single-molecule fluorescence microscopy, which can utilize light microscopy tools to enable the faithful detection and analysis of single fluorescent molecules used as reporter tags in biological samples. For example, the discovery of GFP, initiating the so-called 'green revolution', has pushed experimental tools in the biosciences to a completely new level of functional imaging of living samples, culminating in single fluorescent protein molecule detection. Today, fluorescence microscopy is an indispensable tool in single-molecule investigations, providing a high signal-to-noise ratio for visualization while still retaining the key features in the physiological context of native biological systems. In this review, we discuss some of the recent discoveries in the life sciences which have been enabled using single-molecule fluorescence microscopy, paying particular attention to the so-called 'super-resolution' fluorescence microscopy techniques in live cells, which are at the cutting-edge of these methods. In particular, how these tools can reveal new insights into long-standing puzzles in biology: old problems, which have been impossible to tackle using other more traditional tools until the emergence of new single-molecule fluorescence microscopy techniques.
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Affiliation(s)
- Sviatlana Shashkova
- Department of Physics, Biological Physical Sciences Institute (BPSI), University of York, York YO10 5DD, U.K
- Department of Biology, Biological Physical Sciences Institute (BPSI), University of York, York YO10 5DD, U.K
| | - Mark C Leake
- Department of Physics, Biological Physical Sciences Institute (BPSI), University of York, York YO10 5DD, U.K.
- Department of Biology, Biological Physical Sciences Institute (BPSI), University of York, York YO10 5DD, U.K
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15
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Stout RF, Spray DC. Cysteine residues in the cytoplasmic carboxy terminus of connexins dictate gap junction plaque stability. Mol Biol Cell 2017; 28:2757-2764. [PMID: 28835376 PMCID: PMC5638580 DOI: 10.1091/mbc.e17-03-0206] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Revised: 07/21/2017] [Accepted: 08/14/2017] [Indexed: 01/01/2023] Open
Abstract
Cysteine residues within the cytoplasmic carboxyl-terminus of gap junction–forming proteins are required to stabilize gap junction plaque organization. The stability of gap junction plaque organization can be modified. Gap junction stability may provide a stable supramolecular platform for modulation of gap junction functions. Gap junctions are cellular contact sites composed of clustered connexin transmembrane proteins that act in dual capacities as channels for direct intercellular exchange of small molecules and as structural adhesion complexes known as gap junction nexuses. Depending on the connexin isoform, the cluster of channels (the gap junction plaque) can be stably or fluidly arranged. Here we used confocal microscopy and mutational analysis to identify the residues within the connexin proteins that determine gap junction plaque stability. We found that stability is altered by changing redox balance using a reducing agent—indicating gap junction nexus stability is modifiable. Stability of the arrangement of connexins is thought to regulate intercellular communication by establishing an ordered supramolecular platform. By identifying the residues that establish plaque stability, these studies lay the groundwork for exploration of mechanisms by which gap junction nexus stability modulates intercellular communication.
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Affiliation(s)
- Randy F Stout
- Department of Biomedical Sciences, New York Institute of Technology College of Osteopathic Medicine, Old Westbury, NY 11568-8000 .,Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY 10461
| | - David C Spray
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY 10461
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16
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Xu Z, Rui YN, Balzeau J, Menezes MR, Niu A, Hagan JP, Kim DH. Highly efficient one-step scarless protein tagging by type IIS restriction endonuclease-mediated precision cloning. Biochem Biophys Res Commun 2017; 490:8-16. [PMID: 28576485 DOI: 10.1016/j.bbrc.2017.05.153] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Accepted: 05/26/2017] [Indexed: 12/22/2022]
Abstract
Protein tagging with a wide variety of epitopes and/or fusion partners is used routinely to dissect protein function molecularly. Frequently, the required DNA subcloning is inefficient, especially in cases where multiple constructs are desired for a given protein with unique tags. Additionally, the generated clones have unwanted junction sequences introduced. To add versatile tags into the extracellular domain of the transmembrane protein THSD1, we developed a protein tagging technique that utilizes non-classical type IIS restriction enzymes that recognize non-palindromic DNA sequences and cleave outside of their recognition sites. Our results demonstrate that this method is highly efficient and can precisely fuse any tag into any position of a protein in a scarless manner. Moreover, this method is cost-efficient and adaptable because it uses commercially available type IIS restriction enzymes and is compatible with the traditional cloning system used by many labs. Therefore, precision tagging technology will benefit a number of researchers by providing an alternate method to integrate an array of tags into protein expression constructs.
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Affiliation(s)
- Zhen Xu
- Department of Neurosurgery, The University of Texas Health Science Center at Houston, TX, United States.
| | - Yan-Ning Rui
- Department of Neurosurgery, The University of Texas Health Science Center at Houston, TX, United States
| | - Julien Balzeau
- Department of Neurosurgery, The University of Texas Health Science Center at Houston, TX, United States
| | - Miriam R Menezes
- Department of Neurosurgery, The University of Texas Health Science Center at Houston, TX, United States
| | - Airu Niu
- Department of Neurosurgery, The University of Texas Health Science Center at Houston, TX, United States
| | - John P Hagan
- Department of Neurosurgery, The University of Texas Health Science Center at Houston, TX, United States
| | - Dong H Kim
- Department of Neurosurgery, The University of Texas Health Science Center at Houston, TX, United States.
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17
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Fenix AM, Taneja N, Buttler CA, Lewis J, Van Engelenburg SB, Ohi R, Burnette DT. Expansion and concatenation of non-muscle myosin IIA filaments drive cellular contractile system formation during interphase and mitosis. Mol Biol Cell 2016; 27:mbc.E15-10-0725. [PMID: 26960797 PMCID: PMC4850034 DOI: 10.1091/mbc.e15-10-0725] [Citation(s) in RCA: 84] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Revised: 02/25/2016] [Accepted: 03/01/2016] [Indexed: 11/19/2022] Open
Abstract
Cell movement and cytokinesis are facilitated by contractile forces generated by the molecular motor, non-muscle myosin II (NMII). NMII molecules form a filament (NMII-F) through interactions of their C-terminal rod domains, positioning groups of N-terminal motor domains on opposite sides. The NMII motors then bind and pull actin filaments toward the NMII-F, thus driving contraction. Inside of crawling cells, NMIIA-Fs form large macromolecular ensembles (i.e., NMIIA-F stacks) but how this occurs is unknown. Here we show NMIIA-F stacks are formed through two non-mutually exclusive mechanisms: expansion and concatenation. During expansion, NMIIA molecules within the NMIIA-F spread out concurrent with addition of new NMIIA molecules. Concatenation occurs when multiple NMIIA-F/NMIIA-F stacks move together and align. We found NMIIA-F stack formation was regulated by both motor-activity and the availability of surrounding actin filaments. Furthermore, our data showed expansion and concatenation also formed the contractile ring in dividing cells. Thus, interphase and mitotic cells share similar mechanisms for creating large contractile units, and these are likely to underlie how other myosin II-based contractile systems are assembled.
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Affiliation(s)
- Aidan M Fenix
- Vanderbilt University School of Medicine, Nashville, TN 37232
| | - Nilay Taneja
- Vanderbilt University School of Medicine, Nashville, TN 37232
| | | | - John Lewis
- Vanderbilt University School of Medicine, Nashville, TN 37232 Kalamazoo College, Kalamazoo, MI 49008
| | | | - Ryoma Ohi
- Vanderbilt University School of Medicine, Nashville, TN 37232
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18
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Ai M, Mills H, Kanai M, Lai J, Deng J, Schreiter E, Looger L, Neubert T, Suh G. Green-to-Red Photoconversion of GCaMP. PLoS One 2015; 10:e0138127. [PMID: 26382605 PMCID: PMC4575167 DOI: 10.1371/journal.pone.0138127] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Accepted: 08/25/2015] [Indexed: 11/18/2022] Open
Abstract
Genetically encoded calcium indicators (GECIs) permit imaging intracellular calcium transients. Among GECIs, the GFP-based GCaMPs are the most widely used because of their high sensitivity and rapid response to changes in intracellular calcium concentrations. Here we report that the fluorescence of GCaMPs--including GCaMP3, GCaMP5 and GCaMP6--can be converted from green to red following exposure to blue-green light (450-500 nm). This photoconversion occurs in both insect and mammalian cells and is enhanced in a low oxygen environment. The red fluorescent GCaMPs retained calcium responsiveness, albeit with reduced sensitivity. We identified several amino acid residues in GCaMP important for photoconversion and generated a GCaMP variant with increased photoconversion efficiency in cell culture. This light-induced spectral shift allows the ready labeling of specific, targeted sets of GCaMP-expressing cells for functional imaging in the red channel. Together, these findings indicate the potential for greater utility of existing GCaMP reagents, including transgenic animals.
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Affiliation(s)
- Minrong Ai
- Department of Cell Biology, Skirball Institute of Biomolecular Medicine, New York University, School of Medicine, New York, New York, United States of America
- * E-mail: (MA); (GS)
| | - Holly Mills
- Department of Cell Biology, Skirball Institute of Biomolecular Medicine, New York University, School of Medicine, New York, New York, United States of America
| | - Makoto Kanai
- Department of Cell Biology, Skirball Institute of Biomolecular Medicine, New York University, School of Medicine, New York, New York, United States of America
| | - Jason Lai
- Department of Cell Biology, Skirball Institute of Biomolecular Medicine, New York University, School of Medicine, New York, New York, United States of America
| | - Jingjing Deng
- Department of Biochemistry and Molecular Pharmacology, Skirball Institute of Biomolecular Medicine, New York University, School of Medicine, New York, New York, United States of America
| | - Eric Schreiter
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, United States of America
| | - Loren Looger
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, United States of America
| | - Thomas Neubert
- Department of Biochemistry and Molecular Pharmacology, Skirball Institute of Biomolecular Medicine, New York University, School of Medicine, New York, New York, United States of America
| | - Greg Suh
- Department of Cell Biology, Skirball Institute of Biomolecular Medicine, New York University, School of Medicine, New York, New York, United States of America
- * E-mail: (MA); (GS)
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19
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de Boer P, Hoogenboom JP, Giepmans BNG. Correlated light and electron microscopy: ultrastructure lights up! Nat Methods 2015; 12:503-13. [PMID: 26020503 DOI: 10.1038/nmeth.3400] [Citation(s) in RCA: 303] [Impact Index Per Article: 33.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2014] [Accepted: 04/15/2015] [Indexed: 12/15/2022]
Abstract
Microscopy has gone hand in hand with the study of living systems since van Leeuwenhoek observed living microorganisms and cells in 1674 using his light microscope. A spectrum of dyes and probes now enable the localization of molecules of interest within living cells by fluorescence microscopy. With electron microscopy (EM), cellular ultrastructure has been revealed. Bridging these two modalities, correlated light microscopy and EM (CLEM) opens new avenues. Studies of protein dynamics with fluorescent proteins (FPs), which leave the investigator 'in the dark' concerning cellular context, can be followed by EM examination. Rare events can be preselected at the light microscopy level before EM analysis. Ongoing development-including of dedicated probes, integrated microscopes, large-scale and three-dimensional EM and super-resolution fluorescence microscopy-now paves the way for broad CLEM implementation in biology.
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Affiliation(s)
- Pascal de Boer
- Department of Cell Biology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Jacob P Hoogenboom
- Faculty of Applied Sciences, Delft University of Technology, Delft, the Netherlands
| | - Ben N G Giepmans
- Department of Cell Biology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
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20
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Stout RF, Snapp EL, Spray DC. Connexin Type and Fluorescent Protein Fusion Tag Determine Structural Stability of Gap Junction Plaques. J Biol Chem 2015; 290:23497-514. [PMID: 26265468 DOI: 10.1074/jbc.m115.659979] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2015] [Indexed: 12/22/2022] Open
Abstract
Gap junctions (GJs) are made up of plaques of laterally clustered intercellular channels and the membranes in which the channels are embedded. Arrangement of channels within a plaque determines subcellular distribution of connexin binding partners and sites of intercellular signaling. Here, we report the discovery that some connexin types form plaque structures with strikingly different degrees of fluidity in the arrangement of the GJ channel subcomponents of the GJ plaque. We uncovered this property of GJs by applying fluorescence recovery after photobleaching to GJs formed from connexins fused with fluorescent protein tags. We found that connexin 26 (Cx26) and Cx30 GJs readily diffuse within the plaque structures, whereas Cx43 GJs remain persistently immobile for more than 2 min after bleaching. The cytoplasmic C terminus of Cx43 was required for stability of Cx43 plaque arrangement. We provide evidence that these qualitative differences in GJ arrangement stability reflect endogenous characteristics, with the caveat that the sizes of the GJs examined were necessarily large for these measurements. We also uncovered an unrecognized effect of non-monomerized fluorescent protein on the dynamically arranged GJs and the organization of plaques composed of multiple connexin types. Together, these findings redefine our understanding of the GJ plaque structure and should be considered in future studies using fluorescent protein tags to probe dynamics of highly ordered protein complexes.
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Affiliation(s)
- Randy F Stout
- From the Dominick P. Purpura Department of Neuroscience and
| | - Erik Lee Snapp
- the Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, New York 10461
| | - David C Spray
- From the Dominick P. Purpura Department of Neuroscience and
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21
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Green to red photoconversion of GFP for protein tracking in vivo. Sci Rep 2015; 5:11771. [PMID: 26148899 PMCID: PMC4493561 DOI: 10.1038/srep11771] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Accepted: 04/27/2015] [Indexed: 12/22/2022] Open
Abstract
A variety of fluorescent proteins have been identified that undergo shifts in spectral emission properties over time or once they are irradiated by ultraviolet or blue light. Such proteins are finding application in following the dynamics of particular proteins or labelled organelles within the cell. However, before genes encoding these fluorescent proteins were available, many proteins have already been labelled with GFP in transgenic cells; a number of model organisms feature collections of GFP-tagged lines and organisms. Here we describe a fast, localized and non-invasive method for GFP photoconversion from green to red. We demonstrate its use in transgenic plant, Drosophila and mammalian cells in vivo. While genes encoding fluorescent proteins specifically designed for photoconversion will usually be advantageous when creating new transgenic lines, our method for photoconversion of GFP allows the use of existing GFP-tagged transgenic lines for studies of dynamic processes in living cells.
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22
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Caires HR, Gomez-Lazaro M, Oliveira CM, Gomes D, Mateus DD, Oliveira C, Barrias CC, Barbosa MA, Almeida CR. Finding and tracing human MSC in 3D microenvironments with the photoconvertible protein Dendra2. Sci Rep 2015; 5:10079. [PMID: 25974085 PMCID: PMC4431349 DOI: 10.1038/srep10079] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2014] [Accepted: 03/27/2015] [Indexed: 11/20/2022] Open
Abstract
Mesenchymal Stem/Stromal Cells (MSC) are a promising cell type for cell-based therapies - from tissue regeneration to treatment of autoimmune diseases - due to their capacity to migrate to damaged tissues, to differentiate in different lineages and to their immunomodulatory and paracrine properties. Here, a simple and reliable imaging technique was developed to study MSC dynamical behavior in natural and bioengineered 3D matrices. Human MSC were transfected to express a fluorescent photoswitchable protein, Dendra2, which was used to highlight and follow the same group of cells for more than seven days, even if removed from the microscope to the incubator. This strategy provided reliable tracking in 3D microenvironments with different properties, including the hydrogels Matrigel and alginate as well as chitosan porous scaffolds. Comparison of cells mobility within matrices with tuned physicochemical properties revealed that MSC embedded in Matrigel migrated 64% more with 5.2 mg protein/mL than with 9.6 mg/mL and that MSC embedded in RGD-alginate migrated 51% faster with 1% polymer concentration than in 2% RGD-alginate. This platform thus provides a straightforward approach to characterize MSC dynamics in 3D and has applications in the field of stem cell biology and for the development of biomaterials for tissue regeneration.
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Affiliation(s)
- Hugo R Caires
- 1] Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Portugal [2] INEB - Instituto de Engenharia Biomédica, Universidade do Porto, Rua do Campo Alegre, 823, 4150-180 Porto, Portugal [3] ICBAS - Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Rua Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal
| | - Maria Gomez-Lazaro
- 1] Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Portugal [2] INEB - Instituto de Engenharia Biomédica, Universidade do Porto, Rua do Campo Alegre, 823, 4150-180 Porto, Portugal [3] b.IMAGE - Bioimaging Center for Biomaterials and Regenerative Therapies, INEB, Universidade do Porto, Rua do Campo Alegre 823, 4150-180 Porto, Portugal
| | - Carla M Oliveira
- 1] Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Portugal [2] INEB - Instituto de Engenharia Biomédica, Universidade do Porto, Rua do Campo Alegre, 823, 4150-180 Porto, Portugal [3] ISPUP - Instituto de Saúde Pública da Universidade do Porto, Rua das Taipas, 135, 4050-600 Porto, Portugal
| | - David Gomes
- 1] Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Portugal [2] INEB - Instituto de Engenharia Biomédica, Universidade do Porto, Rua do Campo Alegre, 823, 4150-180 Porto, Portugal
| | - Denisa D Mateus
- 1] Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Portugal [2] IPATIMUP - Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Rua Dr. Roberto Frias s/n, 4200-465 Porto, Portugal
| | - Carla Oliveira
- 1] Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Portugal [2] IPATIMUP - Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Rua Dr. Roberto Frias s/n, 4200-465 Porto, Portugal [3] Medical Faculty of the University of Porto, Alameda Hernani Monteiro, 4200-319 Porto, Portugal
| | - Cristina C Barrias
- 1] Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Portugal [2] INEB - Instituto de Engenharia Biomédica, Universidade do Porto, Rua do Campo Alegre, 823, 4150-180 Porto, Portugal
| | - Mário A Barbosa
- 1] Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Portugal [2] INEB - Instituto de Engenharia Biomédica, Universidade do Porto, Rua do Campo Alegre, 823, 4150-180 Porto, Portugal [3] ICBAS - Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Rua Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal
| | - Catarina R Almeida
- 1] Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Portugal [2] INEB - Instituto de Engenharia Biomédica, Universidade do Porto, Rua do Campo Alegre, 823, 4150-180 Porto, Portugal
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23
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Zhu X, Zhang L, Kao YT, Xu F, Min W. A tunable fluorescent timer method for imaging spatial-temporal protein dynamics using light-driven photoconvertible protein. JOURNAL OF BIOPHOTONICS 2015; 8:226-232. [PMID: 24488612 DOI: 10.1002/jbio.201300174] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2013] [Revised: 12/10/2013] [Accepted: 01/07/2014] [Indexed: 06/03/2023]
Abstract
Cellular function is largely determined by protein behaviors occurring in both space and time. While regular fluorescent proteins can only report spatial locations of the target inside cells, fluorescent timers have emerged as an invaluable tool for revealing coupled spatial-temporal protein dynamics. Existing fluorescent timers are all based on chemical maturation. Herein we propose a light-driven timer concept that could report relative protein ages at specific sub-cellular locations, by weakly but chronically illuminating photoconvertible fluorescent proteins inside cells. This new method exploits light, instead of oxygen, as the driving force. Therefore its timing speed is optically tunable by adjusting the photoconverting laser intensity. We characterized this light-driven timer method both in vitro and in vivo and applied it to image spatiotemporal distributions of several proteins with different lifetimes. This novel timer method thus offers a flexible "ruler" for studying temporal hierarchy of spatially ordered processes with exquisite spatial-temporal resolution.
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Affiliation(s)
- Xinxin Zhu
- Department of Chemistry, Columbia University, New York, NY 10027, USA
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24
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Amen T, Kaganovich D. Dynamic droplets: the role of cytoplasmic inclusions in stress, function, and disease. Cell Mol Life Sci 2015; 72:401-415. [PMID: 25283146 PMCID: PMC11113435 DOI: 10.1007/s00018-014-1740-y] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Revised: 09/16/2014] [Accepted: 09/22/2014] [Indexed: 12/12/2022]
Abstract
Neurodegenerative diseases and other proteinopathies constitute a class of several dozen illnesses etiologically linked to pathological protein misfolding and aggregation. Because of this strong association with disease pathology, cell death, and aging, accumulation of proteins in aggregates or aggregation-associated structures (inclusions) has come to be regarded by many as a deleterious process, to be avoided if possible. Recent work has led us to see inclusion structures and disordered aggregate-like protein mixtures (which we call dynamic droplets) in a new light: not necessarily as a result of a pathological breakdown of cellular order, but as an elaborate cellular architecture regulating function and stress response. In this review, we discuss what is currently known about the role of inclusion structures in cellular homeostasis, stress response, toxicity, and disease. We will focus on possible mechanisms of aggregate toxicity, in contrast to the homeostatic function of several inclusion structures.
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Affiliation(s)
- Triana Amen
- Department of Cell and Developmental Biology, Alexander Silberman Institute of Life Sciences, Hebrew University of Jerusalem, Jerusalem, 91904, Israel
- Alexander Grass Center for Bioengineering, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Daniel Kaganovich
- Department of Cell and Developmental Biology, Alexander Silberman Institute of Life Sciences, Hebrew University of Jerusalem, Jerusalem, 91904, Israel.
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Galanzha EI, Nedosekin DA, Sarimollaoglu M, Orza AI, Biris AS, Verkhusha VV, Zharov VP. Photoacoustic and photothermal cytometry using photoswitchable proteins and nanoparticles with ultrasharp resonances. JOURNAL OF BIOPHOTONICS 2015; 8:81-93. [PMID: 24259123 DOI: 10.1002/jbio.201300140] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Revised: 10/18/2013] [Accepted: 10/18/2013] [Indexed: 05/29/2023]
Abstract
Photoswitchable fluorescent proteins (PSFPs) with controllable spectral shifts in emission in response to light have led to breakthroughs in cell biology. Conventional photoswitching, however, is not applicable to weakly fluorescent proteins. As an alternative, photothermal (PT) and photoacoustic (PA) spectroscopy have demonstrated a tremendous potential for studying absorbing nonfluorescent proteins and nanoparticles. However, little progress has been made in the development of switchable PT and PA probes with controllable spectral shifts in absorption. Here, we introduce the concept of photothermally switchable nanoparticles (PTSNs). To prove the concept, we demonstrated fast, reversible magnetic-PT switching of conventional and gold-coated magnetic nanoparticle clusters in cancer cells in vitro and PT switching of nonlinear ultrasharp plasmonic resonances in gold nanorods molecularly targeted to circulating cells in vivo. We showed that genetically encoded PSFPs with relatively slow switching can serve as triple-modal fluorescent, PT, and PA probes under static conditions, while PTSNs with ultrafast switching may provide higher PA sensitivity in the near-infrared window of tissue transparency under dynamic flow conditions. Application of nonlinear phenomena for super-resolution spectral PT and PA cytometry, microscopy, and spectral burning beyond the diffraction and spectral limits are also proposed.
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Affiliation(s)
- Ekaterina I Galanzha
- Arkansas Nanomedicine Center, University of Arkansas for Medical Sciences, 4301 West Markham Street, Slot #543, Little Rock, Arkansas, 72205, USA
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Owens GC, Edelman DB. Photoconvertible fluorescent protein-based live imaging of mitochondrial fusion. Methods Mol Biol 2015; 1313:237-46. [PMID: 25947670 DOI: 10.1007/978-1-4939-2703-6_18] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Mitochondria are highly dynamic organelles that undergo fusion and fission on a relatively fast time scale. Here, a straightforward method is described for capturing mitochondrial fusion events in real time using a photoconvertible fluorescent protein and a far-field fluorescence microscope equipped with appropriate image acquisition and analysis software. The Kaede photoconvertible fluorescent protein is tagged with a mitochondrial targeting sequence and delivered to primary neurons by lentiviral transduction, which ensures efficient low copy number transgene insertion, as well as stable transgene expression.
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Affiliation(s)
- Geoffrey C Owens
- Department of Neurosurgery, David Geffen School of Medicine at the University of California, Los Angeles, 300 Stein Plaza, Ste. 562, Los Angeles, CA, 90095, USA,
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27
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Fluorescence-Based Methods for the Study of Protein Localization, Interaction, and Dynamics in Filamentous Fungi. Fungal Biol 2015. [DOI: 10.1007/978-3-319-22437-4_2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Meckes B, Ambrosi C, Barnard H, Arce FT, Sosinsky GE, Lal R. Atomic force microscopy shows connexin26 hemichannel clustering in purified membrane fragments. Biochemistry 2014; 53:7407-14. [PMID: 25365227 PMCID: PMC4255643 DOI: 10.1021/bi501265p] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
![]()
Connexin
proteins form hexameric assemblies known as hemichannels.
When docked to form gap junction (GJ) channels, hemichannels play
a critical role in cell–cell communication and cellular homeostasis,
but often are functional entities on their own in unapposed cell membranes.
Defects in the Connexin26 (Cx26) gene are the major cause of hereditary
deafness arising from dysfunctional hemichannels in the cochlea. Structural
studies of Cx26 hemichannels properly trafficked and inserted in plasma
membranes, including their clustering that forms a plaque-like feature
in whole gap junctions, are limited. We used atomic force microscopy
(AFM) to study the surface topography of Cx26 hemichannels using two
different membrane preparations. Rat Cx26 containing appended carboxy
terminal V5 and hexahistidine tags were expressed in baculovirus/Sf9
cell systems. The expressed Cx26 proteins form hemichannels in situ
in Sf9 cells that were then purified either as (1) Sf9 membrane fragments
containing Cx26 hemichannels or (2) solubilized hemichannels. The
latter were subsequently reconstituted in liposomes. AFM images of
purified membrane fragments showed clusters of protein macromolecular
structures in the membrane that at higher magnification corresponded
to Cx26 hemichannels. Hemichannels reconstituted into DOPC bilayers
displayed two populations of channel heights likely resulting from
differences in orientations of inserted hemichannels. Hemichannels
in the protein rich portions of purified membranes also showed a reduced
channel height above the bilayer compared to membranes with reconstituted
hemichannels perhaps due to reduced AFM probe access to the lipid
bilayer. These preparations of purified membranes enriched for connexin
hemichannels that have been properly trafficked and inserted in membranes
provide a platform for high-resolution AFM imaging of the structure,
interconnexon interactions, and cooperativity of properly trafficked
and inserted noncrystalline connexin hemichannels.
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Affiliation(s)
- Brian Meckes
- Department of Bioengineering, ‡National Center for Microscopy and Imaging Research, §Department of Aerospace and Mechanical Engineering, ∥Department of Neurosciences, and ⊥Materials Science Program, University of California San Diego , 9500 Gillman Drive, La Jolla, California 92093, United States
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Mellott AJ, Shinogle HE, Moore DS, Detamore MS. Fluorescent Photo-conversion: A second chance to label unique cells. Cell Mol Bioeng 2014; 8:187-196. [PMID: 25914756 DOI: 10.1007/s12195-014-0365-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Not all cells behave uniformly after treatment in tissue engineering studies. In fact, some treated cells display no signs of treatment or show unique characteristics not consistent with other treated cells. What if the "unique" cells could be isolated from a treated population, and further studied? Photo-convertible reporter proteins, such as Dendra2, allow for the ability to selectively identify unique cells with a secondary label within a primary labeled treated population. In the current study, select cells were identified and labeled through photo-conversion of Dendra2-transfected human Wharton's Jelly cells (hWJCs) for the first time. Robust photo-conversion of green-to-red fluorescence was achieved consistently in arbitrarily selected cells, allowing for precise cell identification of select hWJCs. The current study demonstrates a method that offers investigators the opportunity to selectively label and identify unique cells within a treated population for further study or isolation from the treatment population. Photo-convertible reporter proteins, such as Dendra2, offer the ability over non-photo-convertible reporter proteins, such as green fluorescent protein, to analyze unique individual cells within a treated population, which allows investigators to gain more meaningful information on how a treatment affects all cells within a target population.
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Affiliation(s)
- Adam J Mellott
- Bioengineering Graduate Program, University of Kansas, Lawrence, Kansas 66045
| | - Heather E Shinogle
- Microscopy and Analytical Imaging Laboratory, University of Kansas, Lawrence, Kansas 66045
| | - David S Moore
- Microscopy and Analytical Imaging Laboratory, University of Kansas, Lawrence, Kansas 66045
| | - Michael S Detamore
- Bioengineering Graduate Program, University of Kansas, Lawrence, Kansas 66045 ; Department of Chemical and Petroleum Engineering, University of Kansas, Lawrence, Kansas 66045
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Woods E, Courtney J, Scholz D, Hall WW, Gautier VW. Tracking protein dynamics with photoconvertible Dendra2 on spinning disk confocal systems. J Microsc 2014; 256:197-207. [PMID: 25186063 DOI: 10.1111/jmi.12172] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2014] [Accepted: 07/31/2014] [Indexed: 01/25/2023]
Abstract
Understanding the dynamic properties of cellular proteins in live cells and in real time is essential to delineate their function. In this context, we introduce the Fluorescence Recovery After Photobleaching-Photoactivation unit (Andor) combined with the Nikon Eclipse Ti E Spinning Disk (Andor) confocal microscope as an advantageous and robust platform to exploit the properties of the Dendra2 photoconvertible fluorescent protein (Evrogen) and analyse protein subcellular trafficking in living cells. A major advantage of the spinning disk confocal is the rapid acquisition speed, enabling high temporal resolution of cellular processes. Furthermore, photoconversion and imaging are less invasive on the spinning disk confocal as the cell exposition to illumination power is reduced, thereby minimizing photobleaching and increasing cell viability. We have tested this commercially available platform using experimental settings adapted to track the migration of fast trafficking proteins such as UBC9, Fibrillarin and have successfully characterized their differential motion between subnuclear structures. We describe here step-by-step procedures, with emphasis on cellular imaging parameters, to successfully perform the dynamic imaging and photoconversion of Dendra2-fused proteins at high spatial and temporal resolutions necessary to characterize the trafficking pathways of proteins.
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Affiliation(s)
- Elena Woods
- Centre for Research in Infectious Diseases, School of Medicine and Biomedical Science, University College Dublin (UCD), Dublin, Ireland
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31
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Photo-convertible tagging for localization and dynamic analyses of low-expression proteins in filamentous fungi. Fungal Genet Biol 2014; 70:33-41. [DOI: 10.1016/j.fgb.2014.06.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Revised: 06/16/2014] [Accepted: 06/17/2014] [Indexed: 11/23/2022]
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Abstract
Unlike most cells, protozoa in the phylum Apicomplexa divide by a distinctive process in which multiple daughters are assembled within the mother (schizogony or endodyogeny), using scaffolding known as the inner membrane complex (IMC). The IMC underlies the plasma membrane during interphase, but new daughters develop in the cytoplasm, as cytoskeletal filaments associate with flattened membrane cisternae (alveolae), which elongate rapidly to encapsulate subcellular organelles. Newly assembled daughters acquire their plasma membrane as they emerge from the mother, leaving behind vestiges of the maternal cell. Although the maternal plasma membrane remains intact throughout this process, the maternal IMC disappears – is it degraded, or recycled to form the daughter IMC? Exploiting fluorescently tagged IMC markers, we have used live-cell imaging, fluorescence recovery after photobleaching (FRAP) and mEos2 photoactivation to monitor the dynamics of IMC biogenesis and turnover during the replication of Toxoplasma gondii tachyzoites. These studies reveal that the formation of the T. gondii IMC involves two distinct steps – de novo assembly during daughter IMC elongation within the mother cell, followed by recycling of maternal IMC membranes after the emergence of daughters from the mother cell.
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Affiliation(s)
- Dinkorma T Ouologuem
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA Malaria Research & Training Centre, Department of Epidemiology of Parasitic Diseases, Bamako, BP 1805, Mali
| | - David S Roos
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
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33
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Combining RNAi and in vivo confocal microscopy analysis of the photoconvertible fluorescent protein Dendra2 to study a DNA repair protein. Biotechniques 2014; 55:198-203. [PMID: 24107251 DOI: 10.2144/000114088] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2013] [Accepted: 09/07/2013] [Indexed: 11/23/2022] Open
Abstract
Clinical approaches for tumor treatment often rely on combination therapy where a DNA damaging agent is used in combination with a DNA repair protein inhibitor. For this reason, great efforts have been made during the last decade to identify inhibitors of DNA repair proteins or, alternatively, small molecules that specifically alter protein stability or trafficking. Unfortunately, when studying these drug candidates, classical biochemical approaches are prone to artifacts. The apurinic/apyrimidinic endonuclease (APE1) protein is an essential component of the base excision repair (BER) pathway that is responsible for repairing DNA damage caused by oxidative and alkylating agents. In this work, we combined conditional gene expression knockdown of APE1 protein by RNA interference (RNAi) technology with re-expression of an ectopic recombinant form of APE1 fused with the photoconvertible fluorescent protein (PCFP) Dendra2. Dendra2 did not alter the subcellular localization or endonuclease activity of APE1. We calculated APE1 half-life and compared these results with the classical biochemical approach, which is based on cycloheximide (CHX) treatment. In conclusion, we combined RNAi and in vivo confocal microscopy to study a DNA repair protein demonstrating the feasibility and the advantage of this approach for the study of the cellular dynamic of a DNA repair protein.
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34
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Récamier V, Izeddin I, Bosanac L, Dahan M, Proux F, Darzacq X. Single cell correlation fractal dimension of chromatin: a framework to interpret 3D single molecule super-resolution. Nucleus 2014; 5:75-84. [PMID: 24637833 PMCID: PMC4028358 DOI: 10.4161/nucl.28227] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Chromatin is a major nuclear component, and it is an active matter of debate to understand its different levels of spatial organization, as well as its implication in gene regulation. Measurements of nuclear chromatin compaction were recently used to understand how DNA is folded inside the nucleus and to detect cellular dysfunctions such as cancer. Super-resolution imaging opens new possibilities to measure chromatin organization in situ. Here, we performed a direct measure of chromatin compaction at the single cell level. We used histone H2B, one of the 4 core histone proteins forming the nucleosome, as a chromatin density marker. Using photoactivation localization microscopy (PALM) and adaptive optics, we measured the three-dimensional distribution of H2B with nanometric resolution. We computed the distribution of distances between every two points of the chromatin structure, namely the Ripley K(r) distribution. We found that the K(r) distribution of H2B followed a power law, leading to a precise measurement of the correlation fractal dimension of chromatin of 2.7. Moreover, using photoactivable GFP fused to H2B, we observed dynamic evolution of chromatin sub-regions compaction. As a result, the correlation fractal dimension of chromatin reported here can be interpreted as a dynamically maintained non-equilibrium state.
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Affiliation(s)
- Vincent Récamier
- Functional Imaging of Transcription; Ecole Normale Supérieur; Institut de Biologie de l'ENS (IBENS); Inserm U1024; CNRS UMR 8197; Paris, France; Paris Descartes University; Paris, France
| | - Ignacio Izeddin
- Functional Imaging of Transcription; Ecole Normale Supérieur; Institut de Biologie de l'ENS (IBENS); Inserm U1024; CNRS UMR 8197; Paris, France
| | - Lana Bosanac
- Functional Imaging of Transcription; Ecole Normale Supérieur; Institut de Biologie de l'ENS (IBENS); Inserm U1024; CNRS UMR 8197; Paris, France; Molecular and Cellular Biology Department; University of California; Berkeley, CA USA
| | - Maxime Dahan
- Laboratoire Physico-Chimie Curie; Institut Curie; CNRS UMR168; Université Pierre et Marie Curie-Paris; Paris, France
| | - Florence Proux
- Functional Imaging of Transcription; Ecole Normale Supérieur; Institut de Biologie de l'ENS (IBENS); Inserm U1024; CNRS UMR 8197; Paris, France
| | - Xavier Darzacq
- Functional Imaging of Transcription; Ecole Normale Supérieur; Institut de Biologie de l'ENS (IBENS); Inserm U1024; CNRS UMR 8197; Paris, France
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35
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Adam V. Phototransformable fluorescent proteins: which one for which application? Histochem Cell Biol 2014; 142:19-41. [PMID: 24522394 DOI: 10.1007/s00418-014-1190-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/24/2014] [Indexed: 01/10/2023]
Abstract
In these last two decades , fluorescent proteins (FPs) have become highly valued imaging tools for cell biology, owing to their compatibility with living samples, their low levels of invasiveness and the possibility to specifically fuse them to a variety of proteins of interest. Remarkably, the recent development of phototransformable fluorescent proteins (PTFPs) has made it possible to conceive optical imaging experiments that were unimaginable only a few years ago. For example, it is nowadays possible to monitor intra- or intercellular trafficking, to optically individualize single cells in tissues or to observe single molecules in live cells. The tagging specificity brought by these genetically encoded highlighters leads to constant progress in the engineering of increasingly powerful, versatile and non-cytotoxic FPs. This review is focused on the recent developments of PTFPs and highlights their contribution to studies within cells, tissues and even living organisms. The aspects of single-molecule localization microscopy, intracellular tracking of photoactivated molecules, applications of PTFPs in biotechnology/optobiology and complementarities between PTFPs and other microscopy techniques are particularly discussed.
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Affiliation(s)
- Virgile Adam
- Institut de Biologie Structurale (IBS), Univ. Grenoble Alpes, F-38000, Grenoble, France,
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36
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Cross TA, Murray DT, Watts A. Helical membrane protein conformations and their environment. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2013; 42:731-55. [PMID: 23996195 PMCID: PMC3818118 DOI: 10.1007/s00249-013-0925-x] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Revised: 07/25/2013] [Accepted: 08/12/2013] [Indexed: 02/02/2023]
Abstract
Evidence that membrane proteins respond conformationally and functionally to their environment is growing. Structural models, by necessity, have been characterized in preparations where the protein has been removed from its native environment. Different structural methods have used various membrane mimetics that have recently included lipid bilayers as a more native-like environment. Structural tools applied to lipid bilayer-embedded integral proteins are informing us about important generic characteristics of how membrane proteins respond to the lipid environment as compared with their response to other nonlipid environments. Here, we review the current status of the field, with specific reference to observations of some well-studied α-helical membrane proteins, as a starting point to aid the development of possible generic principles for model refinement.
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Affiliation(s)
- Timothy A. Cross
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306, USA
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, FL 32310, USA
| | - Dylan T. Murray
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, FL 32310, USA
| | - Anthony Watts
- Biomembrane structure Unit, Biochemistry Department, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
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37
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Tiwari DK, Nagai T. Smart fluorescent proteins: Innovation for barrier-free superresolution imaging in living cells. Dev Growth Differ 2013; 55:491-507. [DOI: 10.1111/dgd.12064] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2013] [Revised: 03/06/2013] [Accepted: 03/22/2013] [Indexed: 01/08/2023]
Affiliation(s)
- Dhermendra K. Tiwari
- The Institute of Scientific and Industrial Research; Osaka University; Mihogaoka 8-1; Ibaraki; Osaka; 567-0047; Japan
| | - Takeharu Nagai
- The Institute of Scientific and Industrial Research; Osaka University; Mihogaoka 8-1; Ibaraki; Osaka; 567-0047; Japan
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38
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Jásik J, Boggetti B, Baluška F, Volkmann D, Gensch T, Rutten T, Altmann T, Schmelzer E. PIN2 turnover in Arabidopsis root epidermal cells explored by the photoconvertible protein Dendra2. PLoS One 2013; 8:e61403. [PMID: 23637828 PMCID: PMC3630207 DOI: 10.1371/journal.pone.0061403] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Accepted: 03/10/2013] [Indexed: 11/18/2022] Open
Abstract
The steady state level of integral membrane proteins is dependent on a strictly controlled delivery and removal. Here we show that Dendra2, a green-to-red photoconvertible fluorescent protein, is a suitable tool to study protein turnover in plants. We characterized the fluorescence properties of Dendra2 expressed either as a free protein or as a tag in Arabidopsis thaliana roots and optimized photoconversion settings to study protein turnover. Dendra2 was fused to the PIN2 protein, an auxin transporter in the root tip, and by time-lapse imaging and assessment of red and green signal intensities in the membrane after photoconversion we quantified directly and simultaneously the rate of PIN2 delivery of the newly synthesized protein into the plasma membrane as well as the disappearance of the protein from the plasma membrane due to degradation. Additionally we have verified several factors which are expected to affect PIN2 protein turnover and therefore potentially regulate root growth.
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Affiliation(s)
- Ján Jásik
- Max Planck Institute for Plant Breeding Research, Köln, Germany.
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39
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Fron E, Van der Auweraer M, Moeyaert B, Michiels J, Mizuno H, Hofkens J, Adam V. Revealing the excited-state dynamics of the fluorescent protein Dendra2. J Phys Chem B 2013; 117:2300-13. [PMID: 23356883 DOI: 10.1021/jp309219m] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Green-to-red photoconversion is a reaction that occurs in a limited number of fluorescent proteins and that is currently mechanistically debated. In this contribution, we report on our investigation of the photoconvertible fluorescent protein Dendra2 by employing a combination of pump-probe, up-conversion and single photon timing spectroscopic techniques. Our findings indicate that upon excitation of the neutral green state an excited state proton transfer proceeds with a time constant of 3.4 ps between the neutral green and the anionic green states. In concentrated solution we detected resonance energy transfer (25 ps time constant) between green and red monomers. The time-resolved emission spectra suggest also the formation of a super-red species, first observed for DsRed (a red fluorescent protein from the corallimorph species Discosoma) and consistent with peculiar structural details present in both proteins.
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Affiliation(s)
- Eduard Fron
- Division of Molecular Imaging and Photonics, Department of Chemistry, Katholieke Universiteit Leuven, Celestijnenlaan 200F, 3001 Heverlee, Belgium
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40
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Lombardo VA, Sporbert A, Abdelilah-Seyfried S. Cell tracking using photoconvertible proteins during zebrafish development. J Vis Exp 2012:4350. [PMID: 23052298 DOI: 10.3791/4350] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Embryogenesis is a dynamic process that is best studied by using techniques that allow the documentation of developmental changes in vivo. The use of genetically-encoded fluorescent proteins has proven a valuable strategy for elucidating dynamic morphogenetic processes as they occur in the intact organism. During the past decade, the development of photoactivatable and photoconvertible fluorescent proteins has opened the possibility to investigate the fate of discrete subpopulations of tagged proteins. Unlike photoactivatable proteins, photoconvertible fluorescent proteins (PCFPs) are readily tracked and imaged in their native emission state prior to photoconversion, making it easier to identify and select regions by optical inspection. PCFPs, such as Kaede, KikGR, Dendra and EosFP, can be shifted from green to red upon exposure to UV or blue light due to a His-Tyr-Gly tripeptide sequence which forms a green chromophore that can be photoconverted to a red one by a light-catalyzed β-elimination and subsequent extension of a π-conjugated system. PCFPs and their monomeric variants are useful tools for tracking cells and studying protein dynamics, respectively. During recent years, PCFPs have been expressed in different animal model, such as zebrafish, chicken and mouse for cell fate tracking. Here we report a protocol for cell-specific photoconversion of PCFPs in the living zebrafish embryo and further tracking of photoconverted proteins at later developmental stages. This methodology allows studying, in a tissue-specific manner, cell biological events underlying morphogenesis in the zebrafish animal model.
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Abstract
Reconstructing the lineage of cells is central to understanding development and is now also an important issue in stem cell research. Technological advances in genetically engineered permanent cell labeling, together with a multiplicity of fluorescent markers and sophisticated imaging, open new possibilities for prospective and retrospective clonal analysis.
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Affiliation(s)
- Margaret E Buckingham
- Molecular Genetics of Development Unit, CNRS URA 2578, Department of Developmental Biology, Institut Pasteur, Paris, France.
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42
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Modern fluorescent proteins and imaging technologies to study gene expression, nuclear localization, and dynamics. Curr Opin Cell Biol 2011; 23:310-7. [PMID: 21242078 DOI: 10.1016/j.ceb.2010.12.004] [Citation(s) in RCA: 117] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2010] [Revised: 12/09/2010] [Accepted: 12/15/2010] [Indexed: 01/03/2023]
Abstract
Recent developments in reagent design can address problems in single cells that were not previously approachable. We have attempted to foresee what will become possible, and the sorts of biological problems that become tractable with these novel reagents. We have focused on the novel fluorescent proteins that allow convenient multiplexing, and provide for a time-dependent analysis of events in single cells. Methods for fluorescently labeling specific molecules, including endogenously expressed proteins and mRNA have progressed and are now commonly used in a variety of organisms. Finally, sensitive microscopic methods have become more routine practice. This article emphasizes that the time is right to coordinate these approaches for a new initiative on single cell imaging of biological molecules.
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