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Hickman KA, Hariharan S, De Melo J, Ylanko J, Lustig LC, Penn LZ, Andrews DW. Image-Based Analysis of Protein Stability. Cytometry A 2020; 97:363-377. [PMID: 31774248 PMCID: PMC7187295 DOI: 10.1002/cyto.a.23928] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Revised: 10/28/2019] [Accepted: 10/29/2019] [Indexed: 12/14/2022]
Abstract
Short half-life proteins regulate many essential processes, including cell cycle, transcription, and apoptosis. However, few well-characterized protein-turnover pathways have been identified because traditional methods to measure protein half-life are time and labor intensive. To overcome this barrier, we developed a protein stability probe and high-content screening pipeline for novel regulators of short half-life proteins using automated image analysis. Our pilot probe consists of the short half-life protein c-MYC (MYC) fused to Venus fluorescent protein (MYC-Venus). This probe enables protein half-life to be scored as a function of fluorescence intensity and distribution. Rapid turnover prevents maximal fluorescence of the probe due to the relatively longer maturation time of the fluorescent protein. Cells expressing the MYC-Venus probe were analyzed using a pipeline in which automated confocal microscopy and image analyses were used to score MYC-Venus stability by two strategies: assaying the percentage of cells with Venus fluorescence above background, and phenotypic comparative analysis. To evaluate this high-content screening pipeline and our probe, a kinase inhibitor library was screened by confocal microscopy to identify known and novel kinases that regulate MYC stability. Compounds identified were shown to increase the half-life of both MYC-Venus and endogenous MYC, validating the probe and pipeline. Fusion of another short half-life protein, myeloid cell leukemia 1 (MCL1), with Venus also demonstrated an increase in percent Venus-positive cells after treatment with inhibitors known to stabilize MCL1. Together, the results validate the use of our automated microscopy and image analysis pipeline of stability probe-expressing cells to rapidly and quantitatively identify regulators of short half-life proteins. © 2019 The Authors. Cytometry Part A published by Wiley Periodicals, Inc. on behalf of International Society for Advancement of Cytometry.
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Affiliation(s)
- K. Ashley Hickman
- Sunnybrook Research InstituteTorontoON M4N 3M5Canada
- Princess Margaret Cancer CenterTorontoON M5G 1L7Canada
- Faculty of Medicine, Department of Medical BiophysicsUniversity of TorontoTorontoON M5G 1L7Canada
| | - Santosh Hariharan
- Sunnybrook Research InstituteTorontoON M4N 3M5Canada
- Faculty of Medicine, Department of Medical BiophysicsUniversity of TorontoTorontoON M5G 1L7Canada
| | - Jason De Melo
- Princess Margaret Cancer CenterTorontoON M5G 1L7Canada
| | - Jarkko Ylanko
- Sunnybrook Research InstituteTorontoON M4N 3M5Canada
| | - Lindsay C. Lustig
- Princess Margaret Cancer CenterTorontoON M5G 1L7Canada
- Faculty of Medicine, Department of Medical BiophysicsUniversity of TorontoTorontoON M5G 1L7Canada
| | - Linda Z. Penn
- Princess Margaret Cancer CenterTorontoON M5G 1L7Canada
- Faculty of Medicine, Department of Medical BiophysicsUniversity of TorontoTorontoON M5G 1L7Canada
| | - David W. Andrews
- Sunnybrook Research InstituteTorontoON M4N 3M5Canada
- Faculty of Medicine, Department of Medical BiophysicsUniversity of TorontoTorontoON M5G 1L7Canada
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Watabe T, Terai K, Sumiyama K, Matsuda M. Booster, a Red-Shifted Genetically Encoded Förster Resonance Energy Transfer (FRET) Biosensor Compatible with Cyan Fluorescent Protein/Yellow Fluorescent Protein-Based FRET Biosensors and Blue Light-Responsive Optogenetic Tools. ACS Sens 2020; 5:719-730. [PMID: 32101394 DOI: 10.1021/acssensors.9b01941] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Genetically encoded Förster resonance energy transfer (FRET)-based biosensors have been developed for the visualization of signaling molecule activities. Currently, most of them are comprised of cyan and yellow fluorescent proteins (CFP and YFP), precluding the use of multiple FRET biosensors within a single cell. Moreover, the FRET biosensors based on CFP and YFP are incompatible with the optogenetic tools that operate at blue light. To overcome these problems, here, we have developed FRET biosensors with red-shifted excitation and emission wavelengths. We chose mKOκ and mKate2 as the favorable donor and acceptor pair by calculating the Förster distance. By optimizing the order of fluorescent proteins and modulatory domains of the FRET biosensors, we developed a FRET biosensor backbone named "Booster". The performance of the protein kinase A (PKA) biosensor based on the Booster backbone (Booster-PKA) was comparable to that of AKAR3EV, a previously developed FRET biosensor comprising CFP and YFP. For the proof of concept, we first showed simultaneous monitoring of activities of two protein kinases with Booster-PKA and ERK FRET biosensors based on CFP and YFP. Second, we showed monitoring of PKA activation by Beggiatoa photoactivated adenylyl cyclase, an optogenetic generator of cyclic AMP. Finally, we presented PKA activity in living tissues of transgenic mice expressing Booster-PKA. Collectively, the results demonstrate the effectiveness and versatility of Booster biosensors as an imaging tool in vitro and in vivo.
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Affiliation(s)
- Tetsuya Watabe
- Department of Pathology and Biology of Diseases, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
| | - Kenta Terai
- Research Center for Dynamic Living Systems, Graduate School of Biostudies, Kyoto University, Kyoto 606-8501, Japan
| | - Kenta Sumiyama
- Laboratory for Mouse Genetic Engineering, RIKEN Center for Biosystems Dynamics Research, Osaka 565-0874, Japan
| | - Michiyuki Matsuda
- Department of Pathology and Biology of Diseases, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
- Research Center for Dynamic Living Systems, Graduate School of Biostudies, Kyoto University, Kyoto 606-8501, Japan
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Luginbuehl LH, El‐Sharnouby S, Wang N, Hibberd JM. Fluorescent reporters for functional analysis in rice leaves. PLANT DIRECT 2020; 4:e00188. [PMID: 32072132 PMCID: PMC7011658 DOI: 10.1002/pld3.188] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 08/19/2019] [Accepted: 11/07/2019] [Indexed: 05/22/2023]
Abstract
Fluorescent reporters have facilitated non-invasive imaging in multiple plant species and thus allowed the analysis of processes ranging from gene expression and protein localization to cellular patterning. However, in rice, a globally important crop and model species, there are relatively few reports of fluorescent proteins being used in leaves. Fluorescence imaging is particularly difficult in the rice leaf blade, likely due to a high degree of light scattering in this tissue. To address this, we investigated approaches to improve deep imaging in mature rice leaf blades. We found that ClearSee treatment, which has previously been used to visualize fluorescent reporters in whole tissues of plants, led to improved imaging in rice. Removing epidermal and subtending mesophyll cell layers was faster than ClearSee and also reduced light scattering such that imaging of fluorescent proteins in deeper leaf layers was possible. To expand the range of fluorescent proteins suitable for imaging in rice, we screened twelve whose spectral profiles spanned most of the visible spectrum. This identified five proteins (mTurquoise2, mNeonGreen, mClover3, mKOκ, and tdTomato) that are robustly expressed and detectable in mesophyll cells of stably transformed plants. Using microparticle bombardment, we show that mTurquoise2 and mNeonGreen can be used for simultaneous multicolor imaging of different subcellular compartments. Overall, we conclude that mTurquoise2, mNeonGreen, mClover3, mKOκ, and tdTomato are suitable for high-resolution live imaging of rice leaves, both after transient and stable transformation. Along with the rapid microparticle bombardment method, which allows transient transformation of major cell types in the leaf blade, these fluorescent reporters should greatly facilitate the analysis of gene expression and cell biology in rice.
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Affiliation(s)
| | | | - Na Wang
- Department of Plant SciencesUniversity of CambridgeCambridgeUK
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54
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Sapar ML, Ji H, Wang B, Poe AR, Dubey K, Ren X, Ni JQ, Han C. Phosphatidylserine Externalization Results from and Causes Neurite Degeneration in Drosophila. Cell Rep 2020; 24:2273-2286. [PMID: 30157423 PMCID: PMC6174084 DOI: 10.1016/j.celrep.2018.07.095] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 05/25/2018] [Accepted: 07/27/2018] [Indexed: 01/20/2023] Open
Abstract
Phagocytic clearance of degenerating dendrites or axons is critical for maintaining tissue homeostasis and preventing neuroinflammation. Externalized phosphatidylserine (PS) has been postulated to be an ‘‘eat-me’’ signal allowing recognition of degenerating neurites by phagocytes. Here we show that in Drosophila, PS is dynamically exposed on degenerating dendrites during developmental pruning and after physical injury, but PS exposure is suppressed when dendrite degeneration is genetically blocked. Ectopic PS exposure via phospholipid flippase knockout and scramblase overexpression induced PS exposure preferentially at distal dendrites and caused distinct modes of neurite loss that differ in larval sensory dendrites and in adult olfactory axons. Surprisingly, extracellular lactadherin that lacks the integrin-interaction domain induced phagocyte-dependent degeneration of PS-exposing dendrites, revealing an unidentified bridging function that potentiates phagocytes. Our findings establish a direct causal relationship between PS exposure and neurite degeneration in vivo. Using in vivo phosphatidylserine (PS) sensors, Sapar et al. reveal dynamic patterns of PS exposure on degenerating dendrites in Drosophila. Flippase knockout and scramblase overexpression lead to ectopic PS exposure on distal dendrites and context-dependent neurite degeneration. Lactadherin potentiates phagocytes to destruct PS-exposing dendrites, independent of its integrin-interaction domain.
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Affiliation(s)
- Maria L Sapar
- Weill Institute for Cell and Molecular Biology, Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Hui Ji
- Weill Institute for Cell and Molecular Biology, Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Bei Wang
- Weill Institute for Cell and Molecular Biology, Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Amy R Poe
- Weill Institute for Cell and Molecular Biology, Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Kush Dubey
- Weill Institute for Cell and Molecular Biology, Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Xingjie Ren
- Gene Regulatory Lab, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Jian-Quan Ni
- Gene Regulatory Lab, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Chun Han
- Weill Institute for Cell and Molecular Biology, Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA.
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55
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Matlashov ME, Shcherbakova DM, Alvelid J, Baloban M, Pennacchietti F, Shemetov AA, Testa I, Verkhusha VV. A set of monomeric near-infrared fluorescent proteins for multicolor imaging across scales. Nat Commun 2020; 11:239. [PMID: 31932632 PMCID: PMC6957686 DOI: 10.1038/s41467-019-13897-6] [Citation(s) in RCA: 92] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2019] [Accepted: 12/03/2019] [Indexed: 11/09/2022] Open
Abstract
Bright monomeric near-infrared (NIR) fluorescent proteins (FPs) are in high demand as protein tags for multicolor microscopy and in vivo imaging. Here we apply rational design to engineer a complete set of monomeric NIR FPs, which are the brightest genetically encoded NIR probes. We demonstrate that the enhanced miRFP series of NIR FPs, which combine high effective brightness in mammalian cells and monomeric state, perform well in both nanometer-scale imaging with diffraction unlimited stimulated emission depletion (STED) microscopy and centimeter-scale imaging in mice. In STED we achieve ~40 nm resolution in live cells. In living mice we detect ~105 fluorescent cells in deep tissues. Using spectrally distinct monomeric NIR FP variants, we perform two-color live-cell STED microscopy and two-color imaging in vivo. Having emission peaks from 670 nm to 720 nm, the next generation of miRFPs should become versatile NIR probes for multiplexed imaging across spatial scales in different modalities.
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Affiliation(s)
- Mikhail E Matlashov
- Department of Anatomy and Structural Biology and Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, New York, 10461, USA
| | - Daria M Shcherbakova
- Department of Anatomy and Structural Biology and Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, New York, 10461, USA
| | - Jonatan Alvelid
- Department of Applied Physics and Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Mikhail Baloban
- Department of Anatomy and Structural Biology and Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, New York, 10461, USA
| | - Francesca Pennacchietti
- Department of Applied Physics and Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Anton A Shemetov
- Department of Anatomy and Structural Biology and Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, New York, 10461, USA
| | - Ilaria Testa
- Department of Applied Physics and Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Vladislav V Verkhusha
- Department of Anatomy and Structural Biology and Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, New York, 10461, USA. .,Medicum, Faculty of Medicine, University of Helsinki, 00029, Helsinki, Finland.
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56
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Jin X, Hapsari ND, Lee S, Jo K. DNA binding fluorescent proteins as single-molecule probes. Analyst 2020; 145:4079-4095. [DOI: 10.1039/d0an00218f] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
DNA binding fluorescent proteins are useful probes for a broad range of biological applications.
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Affiliation(s)
- Xuelin Jin
- Department of Chemistry and Interdisciplinary Program of Integrated Biotechnology
- Sogang University
- Seoul
- Republic of Korea
| | - Natalia Diyah Hapsari
- Department of Chemistry and Interdisciplinary Program of Integrated Biotechnology
- Sogang University
- Seoul
- Republic of Korea
- Chemistry Education Program
| | - Seonghyun Lee
- Department of Chemistry and Interdisciplinary Program of Integrated Biotechnology
- Sogang University
- Seoul
- Republic of Korea
| | - Kyubong Jo
- Department of Chemistry and Interdisciplinary Program of Integrated Biotechnology
- Sogang University
- Seoul
- Republic of Korea
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57
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Xu Y, Deng M, Zhang S, Yang J, Peng L, Chu J, Zou P. Imaging Neuronal Activity with Fast and Sensitive Red-Shifted Electrochromic FRET Indicators. ACS Chem Neurosci 2019; 10:4768-4775. [PMID: 31725259 DOI: 10.1021/acschemneuro.9b00501] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Genetically encoded voltage indicators (GEVIs) allow optical recording of neuronal activities with high spatial resolution. While most existing GEVIs emit in the green range, red-shifted GEVIs are highly sought after because they would enable simultaneous stimulation and recording of neuronal activities when paired with optogenetic actuators, or two-color imaging of signaling and neuronal activities when used along with GFP-based indicators. In this study, we present several improved red-shifted GEVIs based on the electrochromic Förster resonance energy transfer (eFRET) between orange/red fluorescent proteins/dyes and rhodopsin mutants. Through structure-guided mutagenesis and cell-based sensitivity screening, we identified a mutant rhodopsin with a single mutation that exhibited more than 2-fold improvement in voltage sensitivity. Notably, this mutation has been independently discovered by Pieribone et al. ( Pieribone, V. A. et al. Nat Methods 2018 , 15 ( 12 ), 1108 - 1116 ). In cultured rat hippocampal neurons, our sensors faithfully reported action potential waveforms and subthreshold activities. We also demonstrated that this mutation could enhance the sensitivity of hybrid indicators, thus providing insights for future development.
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Affiliation(s)
- Yongxian Xu
- School of Life Sciences, Tsinghua University, Beijing 100084, China
- College of Chemistry and Molecular Engineering, Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, PKU-IDG/McGovern Institute for Brain Research, Beijing 100871, China
- Peking-Tsinghua Center for Life Sciences, Beijing, China
| | - Mengying Deng
- Laboratory for Biomedical Optics and Molecular Imaging, CAS Key Laboratory of Health Informatics, Shenzhen Institute of Synthetic Biology, Shenzhen-Hong Kong Institute of Brain Science, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Shu Zhang
- Laboratory for Biomedical Optics and Molecular Imaging, CAS Key Laboratory of Health Informatics, Shenzhen Institute of Synthetic Biology, Shenzhen-Hong Kong Institute of Brain Science, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Junqi Yang
- Peking-Tsinghua-NIBS Joint Graduate Program, Peking University, Beijing 100871, China
| | - Luxin Peng
- College of Chemistry and Molecular Engineering, Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, PKU-IDG/McGovern Institute for Brain Research, Beijing 100871, China
| | - Jun Chu
- Laboratory for Biomedical Optics and Molecular Imaging, CAS Key Laboratory of Health Informatics, Shenzhen Institute of Synthetic Biology, Shenzhen-Hong Kong Institute of Brain Science, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Peng Zou
- College of Chemistry and Molecular Engineering, Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, PKU-IDG/McGovern Institute for Brain Research, Beijing 100871, China
- Peking-Tsinghua Center for Life Sciences, Beijing, China
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58
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Kiełbus M, Czapiński J, Kałafut J, Woś J, Stepulak A, Rivero-Müller A. Genetically Engineered Lung Cancer Cells for Analyzing Epithelial-Mesenchymal Transition. Cells 2019; 8:E1644. [PMID: 31847480 PMCID: PMC6953058 DOI: 10.3390/cells8121644] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 12/06/2019] [Accepted: 12/09/2019] [Indexed: 12/13/2022] Open
Abstract
Cell plasticity, defined as the ability to undergo phenotypical transformation in a reversible manner, is a physiological process that also exerts important roles in disease progression. Two forms of cellular plasticity are epithelial-mesenchymal transition (EMT) and its inverse process, mesenchymal-epithelial transition (MET). These processes have been correlated to the poor outcome of different types of neoplasias as well as drug resistance development. Since EMT/MET are transitional processes, we generated and validated a reporter cell line. Specifically, a far-red fluorescent protein was knocked-in in-frame with the mesenchymal gene marker VIMENTIN (VIM) in H2170 lung cancer cells. The vimentin reporter cells (VRCs) are a reliable model for studying EMT and MET showing cellular plasticity upon a series of stimulations. These cells are a robust platform to dissect the molecular mechanisms of these processes, and for drug discovery in vitro and in vivo in the future.
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Affiliation(s)
- Michał Kiełbus
- Department of Biochemistry and Molecular Biology, Medical University of Lublin, 20-093 Lublin, Poland; (M.K.); (J.C.); (J.K.); (A.S.)
| | - Jakub Czapiński
- Department of Biochemistry and Molecular Biology, Medical University of Lublin, 20-093 Lublin, Poland; (M.K.); (J.C.); (J.K.); (A.S.)
- Postgraduate School of Molecular Medicine, 02-091 Warsaw, Poland
| | - Joanna Kałafut
- Department of Biochemistry and Molecular Biology, Medical University of Lublin, 20-093 Lublin, Poland; (M.K.); (J.C.); (J.K.); (A.S.)
| | - Justyna Woś
- Department of Clinical Immunology, Medical University of Lublin, 20-093 Lublin, Poland;
| | - Andrzej Stepulak
- Department of Biochemistry and Molecular Biology, Medical University of Lublin, 20-093 Lublin, Poland; (M.K.); (J.C.); (J.K.); (A.S.)
| | - Adolfo Rivero-Müller
- Department of Biochemistry and Molecular Biology, Medical University of Lublin, 20-093 Lublin, Poland; (M.K.); (J.C.); (J.K.); (A.S.)
- Faculty of Natural Sciences and Technology, Åbo Akademi University, 20500 Turku, Finland
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59
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Calamera G, Li D, Ulsund AH, Kim JJ, Neely OC, Moltzau LR, Bjørnerem M, Paterson D, Kim C, Levy FO, Andressen KW. FRET-based cyclic GMP biosensors measure low cGMP concentrations in cardiomyocytes and neurons. Commun Biol 2019; 2:394. [PMID: 31701023 PMCID: PMC6820734 DOI: 10.1038/s42003-019-0641-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 10/02/2019] [Indexed: 01/13/2023] Open
Abstract
Several FRET (fluorescence resonance energy transfer)-based biosensors for intracellular detection of cyclic nucleotides have been designed in the past decade. However, few such biosensors are available for cGMP, and even fewer that detect low nanomolar cGMP concentrations. Our aim was to develop a FRET-based cGMP biosensor with high affinity for cGMP as a tool for intracellular signaling studies. We used the carboxyl-terminal cyclic nucleotide binding domain of Plasmodium falciparum cGMP-dependent protein kinase (PKG) flanked by different FRET pairs to generate two cGMP biosensors (Yellow PfPKG and Red PfPKG). Here, we report that these cGMP biosensors display high affinity for cGMP (EC50 of 23 ± 3 nM) and detect cGMP produced through soluble guanylyl cyclase and guanylyl cyclase A in stellate ganglion neurons and guanylyl cyclase B in cardiomyocytes. These biosensors are therefore optimal tools for real-time measurements of low concentrations of cGMP in living cells.
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Affiliation(s)
- Gaia Calamera
- Department of Pharmacology, Institute of Clinical Medicine, University of Oslo and Oslo University Hospital, Oslo, Norway
- Center for Heart Failure Research, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Dan Li
- Department of Physiology, Anatomy and Genetics, Oxford University, Oxford, UK
| | - Andrea Hembre Ulsund
- Department of Pharmacology, Institute of Clinical Medicine, University of Oslo and Oslo University Hospital, Oslo, Norway
- Center for Heart Failure Research, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Jeong Joo Kim
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX USA
| | - Oliver C. Neely
- Department of Physiology, Anatomy and Genetics, Oxford University, Oxford, UK
| | - Lise Román Moltzau
- Department of Pharmacology, Institute of Clinical Medicine, University of Oslo and Oslo University Hospital, Oslo, Norway
- Center for Heart Failure Research, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Marianne Bjørnerem
- Department of Pharmacology, Institute of Clinical Medicine, University of Oslo and Oslo University Hospital, Oslo, Norway
- Center for Heart Failure Research, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - David Paterson
- Department of Physiology, Anatomy and Genetics, Oxford University, Oxford, UK
| | - Choel Kim
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX USA
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX USA
| | - Finn Olav Levy
- Department of Pharmacology, Institute of Clinical Medicine, University of Oslo and Oslo University Hospital, Oslo, Norway
- Center for Heart Failure Research, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Kjetil Wessel Andressen
- Department of Pharmacology, Institute of Clinical Medicine, University of Oslo and Oslo University Hospital, Oslo, Norway
- Center for Heart Failure Research, University of Oslo and Oslo University Hospital, Oslo, Norway
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60
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Paulikat M, Mata RA, Gelabert R. A high-throughput computational approach to UV-Vis spectra in protein mutants. Phys Chem Chem Phys 2019; 21:20678-20692. [PMID: 31508628 DOI: 10.1039/c9cp03908b] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
In this work we present a high-throughput approach to the computation of absorption UV-Vis spectra tailored to mutagenesis studies. The scheme makes use of a single molecular dynamics trajectory of a reference (non-mutated) species. The shifts in absorption energy caused by a residue mutation are evaluated by building an effective potential of the environment and computing a correction term based on perturbation theory. The sampling is only performed in the phase space of the initial protein. We analyze the robustness of the method by comparing different approximations for the effective potential, the sampling of mutant residue geometries and observing the impact in the prediction of both bathocromic and hypsochromic shifts. As a test subject, we consider a red fluorescent protein variant with potential biotechnological applications.
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Affiliation(s)
- Mirko Paulikat
- Institute of Physical Chemistry, University of Goettingen, Tammannstraße 6, D-37077 Göttingen, Germany.
| | - Ricardo A Mata
- Institute of Physical Chemistry, University of Goettingen, Tammannstraße 6, D-37077 Göttingen, Germany.
| | - Ricard Gelabert
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain.
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61
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Two-Color Spatial Cumulant Analysis Detects Heteromeric Interactions between Membrane Proteins. Biophys J 2019; 117:1764-1777. [PMID: 31606123 DOI: 10.1016/j.bpj.2019.09.028] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Revised: 08/19/2019] [Accepted: 09/19/2019] [Indexed: 11/19/2022] Open
Abstract
Fluorescence fluctuation spectroscopy can be used to measure the aggregation of fluorescently labeled molecules and is typically performed using time series data. Spatial intensity distribution analysis and fluorescence moment image analysis are established tools for measuring molecular brightnesses from single-color images collected with laser scanning microscopes. We have extended these tools for analysis of two-color images to resolve heteromeric interactions between molecules labeled with spectrally distinct chromophores. We call these new methods two-color spatial intensity distribution analysis and two-color spatial cumulant analysis (2c-SpCA). To implement these techniques on a hyperspectral imaging system, we developed a spectral shift filtering technique to remove artifacts due to intrinsic cross talk between detector bins. We determined that 2c-SpCA provides better resolution from samples containing multiple fluorescent species; hence, this technique was carried forward to study images of living cells. We used fluorescent heterodimers labeled with enhanced green fluorescent protein and mApple to quantify the effects of resonance energy transfer and incomplete maturation of mApple on brightness measurements. We show that 2c-SpCA can detect the interaction between two components of trimeric G-protein complexes. Thus, 2c-SpCA presents a robust and computationally expedient means of measuring heteromeric interactions in cellular environments.
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62
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Li S, Prasanna X, Salo VT, Vattulainen I, Ikonen E. An efficient auxin-inducible degron system with low basal degradation in human cells. Nat Methods 2019. [PMID: 31451765 DOI: 10.1038/s41592-019–0512-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/09/2023]
Abstract
Auxin-inducible degron technology allows rapid and controlled protein depletion. However, basal degradation without auxin and inefficient auxin-inducible depletion have limited its utility. We have identified a potent auxin-inducible degron system composed of auxin receptor F-box protein AtAFB2 and short degron miniIAA7. The system showed minimal basal degradation and enabled rapid auxin-inducible depletion of endogenous human transmembrane, cytoplasmic and nuclear proteins in 1 h with robust functional phenotypes.
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Affiliation(s)
- Shiqian Li
- Department of Anatomy and Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Minerva Foundation Institute for Medical Research, Helsinki, Finland
| | - Xavier Prasanna
- Department of Physics, University of Helsinki, Helsinki, Finland
| | - Veijo T Salo
- Department of Anatomy and Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Minerva Foundation Institute for Medical Research, Helsinki, Finland
| | - Ilpo Vattulainen
- Department of Physics, University of Helsinki, Helsinki, Finland
- Computational Physics Laboratory, Tampere University, Tampere, Finland
| | - Elina Ikonen
- Department of Anatomy and Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland.
- Minerva Foundation Institute for Medical Research, Helsinki, Finland.
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63
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An efficient auxin-inducible degron system with low basal degradation in human cells. Nat Methods 2019; 16:866-869. [DOI: 10.1038/s41592-019-0512-x] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 07/08/2019] [Indexed: 01/20/2023]
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64
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Nance J, Frøkjær-Jensen C. The Caenorhabditis elegans Transgenic Toolbox. Genetics 2019; 212:959-990. [PMID: 31405997 PMCID: PMC6707460 DOI: 10.1534/genetics.119.301506] [Citation(s) in RCA: 86] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 06/01/2019] [Indexed: 12/30/2022] Open
Abstract
The power of any genetic model organism is derived, in part, from the ease with which gene expression can be manipulated. The short generation time and invariant developmental lineage have made Caenorhabditis elegans very useful for understanding, e.g., developmental programs, basic cell biology, neurobiology, and aging. Over the last decade, the C. elegans transgenic toolbox has expanded considerably, with the addition of a variety of methods to control expression and modify genes with unprecedented resolution. Here, we provide a comprehensive overview of transgenic methods in C. elegans, with an emphasis on recent advances in transposon-mediated transgenesis, CRISPR/Cas9 gene editing, conditional gene and protein inactivation, and bipartite systems for temporal and spatial control of expression.
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Affiliation(s)
- Jeremy Nance
- Helen L. and Martin S. Kimmel Center for Biology and Medicine, Skirball Institute of Biomolecular Medicine, Department of Cell Biology, New York University School of Medicine, New York 10016
| | - Christian Frøkjær-Jensen
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Science and Engineering Division (BESE), KAUST Environmental Epigenetics Program (KEEP), Thuwal 23955-6900, Saudi Arabia
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65
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Crawford M, Leclerc V, Barr K, Dagnino L. Essential Role for Integrin-Linked Kinase in Melanoblast Colonization of the Skin. J Invest Dermatol 2019; 140:425-434.e10. [PMID: 31330146 DOI: 10.1016/j.jid.2019.07.681] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 06/21/2019] [Accepted: 07/02/2019] [Indexed: 01/16/2023]
Abstract
Melanocytes are pigment-producing cells found in the skin and other tissues. Alterations in the melanocyte lineage give rise to a plethora of human diseases, from neurocristopathies and pigmentation disorders to melanoma. During embryogenesis, neural crest cell subsets give rise to two waves of melanoblasts, which migrate dorsolaterally, hone to the skin, and differentiate into melanocytes. However, the mechanisms that govern colonization of the skin by the first wave of melanoblasts are poorly understood. Here we report that targeted inactivation of the integrin-linked kinase gene in first wave melanoblasts causes defects in the ability of these cells to form long pseudopods, to migrate, and to proliferate in vivo. As a result, integrin-linked kinase-deficient melanoblasts fail to populate normally the developing epidermis and hair follicles. We also show that defects in motility and dendricity occur upon integrin-linked kinase gene inactivation in mature melanocytes, causing abnormalities in cell responses to the extracellular matrix substrates collagen I and laminin 332. Significantly, the ability to form long protrusions in mutant cells in response to collagen is restored in the presence of constitutively active Rac1, suggesting that an integrin-linked kinase-Rac1 nexus is likely implicated in melanocytic cell establishment, dendricity, and functions in the skin.
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Affiliation(s)
- Melissa Crawford
- Department of Physiology and Pharmacology, Children's Health Research Institute, Lawson Health Research Institute, London, Ontario, Canada
| | - Valerie Leclerc
- Department of Physiology and Pharmacology, Children's Health Research Institute, Lawson Health Research Institute, London, Ontario, Canada
| | - Kevin Barr
- Department of Physiology and Pharmacology, Children's Health Research Institute, Lawson Health Research Institute, London, Ontario, Canada
| | - Lina Dagnino
- Department of Physiology and Pharmacology, Children's Health Research Institute, Lawson Health Research Institute, London, Ontario, Canada; Department of Oncology, University of Western Ontario, London, Ontario, Canada.
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66
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Li Z, Li J, Liu S, Wang H, Xie Z, Wang Y, Chen Z. Green Fluorescent Protein Nanovessel Serves as a Nucleolus Targeting Material and Molecule Carrier in Living Cells. ACTA ACUST UNITED AC 2019; 3:e1900047. [PMID: 32648676 DOI: 10.1002/adbi.201900047] [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: 03/01/2019] [Revised: 05/15/2019] [Indexed: 11/09/2022]
Abstract
The nucleolus is responsible for RNA transcription, processing, and ribosome assembly, the dysfunction of which is associated with a number of diseases. In this report, a new member of fluorescent protein nanovessels (FPNs), constructed using thioflavin-T (ThT) and bovine serum albumin (BSA) as building blocks, is described. As a popular amyloid specific dye, ThT is nonfluorescent by itself, while its fluorescence can be lighted up upon interacting with amyloid proteins. Herein, ThT is coassembled with the BSA scaffold at high temperature to form T(hT)-FPNs. These green fluorescence emissive bio-abiotic hybrid materials can serve as a novel probe for real-time nucleolus imaging of living cells. Besides, T-FPNs show potential in delivering insoluble and/or impenetrable drugs into living cells, suggesting another role as a molecule carrier.
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Affiliation(s)
- Zhenhua Li
- State Key Laboratory of Supramolecular Structure and Materials, Institute of Theoretical Chemistry, College of Chemistry, and International Joint Research Laboratory of Nano-Micro Architecture Chemistry, Jilin University, 2699 Qianjin Street, Changchun, 130012, P. R. China
| | - Jia Li
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing, 100875, P. R. China
| | - Shi Liu
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, P. R. China
| | - Haojie Wang
- State Key Laboratory of Supramolecular Structure and Materials, Institute of Theoretical Chemistry, College of Chemistry, and International Joint Research Laboratory of Nano-Micro Architecture Chemistry, Jilin University, 2699 Qianjin Street, Changchun, 130012, P. R. China
| | - Zhigang Xie
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, P. R. China
| | - Youjun Wang
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing, 100875, P. R. China
| | - Zhijun Chen
- State Key Laboratory of Supramolecular Structure and Materials, Institute of Theoretical Chemistry, College of Chemistry, and International Joint Research Laboratory of Nano-Micro Architecture Chemistry, Jilin University, 2699 Qianjin Street, Changchun, 130012, P. R. China
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67
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The role of the genome in experience-dependent plasticity: Extending the analogy of the genomic action potential. Proc Natl Acad Sci U S A 2019; 117:23252-23260. [PMID: 31127037 DOI: 10.1073/pnas.1820837116] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Our past experiences shape our current and future behavior. These experiences must leave some enduring imprint on our brains, altering neural circuits that mediate behavior and contributing to our individual differences. As a framework for understanding how experiences might produce lasting changes in neural circuits, Clayton [D. F. Clayton, Neurobiol. Learn. Mem. 74, 185-216 (2000)] introduced the concept of the genomic action potential (gAP)-a structured genomic response in the brain to acute experience. Similar to the familiar electrophysiological action potential (eAP), the gAP also provides a means for integrating afferent patterns of activity but on a slower timescale and with longer-lasting effects. We revisit this concept in light of contemporary work on experience-dependent modification of neural circuits. We review the "Immediate Early Gene" (IEG) response, the starting point for understanding the gAP. We discuss evidence for its involvement in the encoding of experience to long-term memory across time and biological levels of organization ranging from individual cells to cell ensembles and whole organisms. We explore distinctions between memory encoding and homeostatic functions and consider the potential for perpetuation of the imprint of experience through epigenetic mechanisms. We describe a specific example of a gAP in humans linked to individual differences in the response to stress. Finally, we identify key objectives and new tools for continuing research in this area.
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68
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An orange calcium-modulated bioluminescent indicator for non-invasive activity imaging. Nat Chem Biol 2019; 15:433-436. [PMID: 30936501 PMCID: PMC6563924 DOI: 10.1038/s41589-019-0256-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Accepted: 02/26/2019] [Indexed: 12/20/2022]
Abstract
Fluorescent indicators are widely used to visualize calcium dynamics downstream of membrane depolarization or G protein-coupled receptor activation, but are poorly suited for non-invasive imaging in mammals. Here, we report a bright calcium-modulated bioluminescent indicator named Orange CaMBI. Orange CaMBI reports calcium dynamics in single cells and, in the context of a transgenic mouse, reveals calcium oscillations in whole organs in an entirely noninvasive manner.
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69
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St-Georges-Robillard A, Masse M, Cahuzac M, Strupler M, Patra B, Orimoto AM, Kendall-Dupont J, Péant B, Mes-Masson AM, Leblond F, Gervais T. Fluorescence hyperspectral imaging for live monitoring of multiple spheroids in microfluidic chips. Analyst 2019; 143:3829-3840. [PMID: 29999046 DOI: 10.1039/c8an00536b] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Tumor spheroids represent a realistic 3D in vitro cancer model because they provide a missing link between monolayer cell culture and live tissues. While microfluidic chips can easily form and assay thousands of spheroids simultaneously, few commercial instruments are available to analyze this massive amount of data. Available techniques to measure spheroid response to external stimuli, such as confocal imaging and flow cytometry, are either not appropriate for 3D cultures, or destructive. We designed a wide-field hyperspectral imaging system to analyze multiple spheroids trapped in a microfluidic chip in a single acquisition. The system and its fluorescence quantification algorithm were assessed using liquid phantoms mimicking spheroid optical properties. Spectral unmixing was tested on three overlapping spectral entities. Hyperspectral images of co-culture spheroids expressing two fluorophores were compared with confocal microscopy and spheroid growth was measured over time. The system can spectrally analyze multiple fluorescent markers simultaneously and allows multiple time-points assays, providing a fast and versatile solution for analyzing lab on a chip devices.
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Affiliation(s)
- Amélie St-Georges-Robillard
- Department of Engineering Physics, Polytechnique Montréal, C.P. 6079, Succ. Centre-ville, Montreal, Qc H3C 3A7, Canada.
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70
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Thomas BJ, Wight IE, Chou WYY, Moreno M, Dawson Z, Homayouni A, Huang H, Kim H, Jia H, Buland JR, Wambach JA, Cole FS, Pak SC, Silverman GA, Luke CJ. CemOrange2 fusions facilitate multifluorophore subcellular imaging in C. elegans. PLoS One 2019; 14:e0214257. [PMID: 30913273 PMCID: PMC6435234 DOI: 10.1371/journal.pone.0214257] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 03/08/2019] [Indexed: 11/18/2022] Open
Abstract
Due to its ease of genetic manipulation and transparency, Caenorhabditis elegans (C. elegans) has become a preferred model system to study gene function by microscopy. The use of Aequorea victoria green fluorescent protein (GFP) fused to proteins or targeting sequences of interest, further expanded upon the utility of C. elegans by labeling subcellular structures, which enables following their disposition during development or in the presence of genetic mutations. Fluorescent proteins with excitation and emission spectra different from that of GFP accelerated the use of multifluorophore imaging in real time. We have expanded the repertoire of fluorescent proteins for use in C. elegans by developing a codon-optimized version of Orange2 (CemOrange2). Proteins or targeting motifs fused to CemOrange2 were distinguishable from the more common fluorophores used in the nematode; such as GFP, YFP, and mKate2. We generated a panel of CemOrange2 fusion constructs, and confirmed they were targeted to their correct subcellular addresses by colocalization with independent markers. To demonstrate the potential usefulness of this new panel of fluorescent protein markers, we showed that CemOrange2 fusion proteins could be used to: 1) monitor biological pathways, 2) multiplex with other fluorescent proteins to determine colocalization and 3) gain phenotypic knowledge of a human ABCA3 orthologue, ABT-4, trafficking variant in the C. elegans model organism.
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Affiliation(s)
- Brian J. Thomas
- Department of Pediatrics, Washington University School of Medicine and St. Louis Children’s Hospital, St. Louis, MO, United States of America
| | - Ira E. Wight
- Department of Pediatrics, Washington University School of Medicine and St. Louis Children’s Hospital, St. Louis, MO, United States of America
| | - Wendy Y. Y. Chou
- Department of Pediatrics, Washington University School of Medicine and St. Louis Children’s Hospital, St. Louis, MO, United States of America
| | - Marco Moreno
- Department of Pediatrics, Washington University School of Medicine and St. Louis Children’s Hospital, St. Louis, MO, United States of America
| | - Zachary Dawson
- Department of Pediatrics, Washington University School of Medicine and St. Louis Children’s Hospital, St. Louis, MO, United States of America
| | - Arielle Homayouni
- Division of Biology and Biomedical Sciences, Washington University in St. Louis, St. Louis, MO, United States of America
| | - Huiyan Huang
- Department of Pediatrics, Washington University School of Medicine and St. Louis Children’s Hospital, St. Louis, MO, United States of America
| | - Hyori Kim
- Department of Pediatrics, Washington University School of Medicine and St. Louis Children’s Hospital, St. Louis, MO, United States of America
| | - Hanna Jia
- Department of Pediatrics, Washington University School of Medicine and St. Louis Children’s Hospital, St. Louis, MO, United States of America
| | - Justin R. Buland
- Department of Pediatrics, Washington University School of Medicine and St. Louis Children’s Hospital, St. Louis, MO, United States of America
| | - Jennifer A. Wambach
- Department of Pediatrics, Washington University School of Medicine and St. Louis Children’s Hospital, St. Louis, MO, United States of America
| | - F. Sessions Cole
- Department of Pediatrics, Washington University School of Medicine and St. Louis Children’s Hospital, St. Louis, MO, United States of America
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO, United States of America
| | - Stephen C. Pak
- Department of Pediatrics, Washington University School of Medicine and St. Louis Children’s Hospital, St. Louis, MO, United States of America
| | - Gary A. Silverman
- Department of Pediatrics, Washington University School of Medicine and St. Louis Children’s Hospital, St. Louis, MO, United States of America
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO, United States of America
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, United States of America
| | - Cliff J. Luke
- Department of Pediatrics, Washington University School of Medicine and St. Louis Children’s Hospital, St. Louis, MO, United States of America
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71
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Filonov GS, Song W, Jaffrey SR. Spectral Tuning by a Single Nucleotide Controls the Fluorescence Properties of a Fluorogenic Aptamer. Biochemistry 2019; 58:1560-1564. [PMID: 30838859 DOI: 10.1021/acs.biochem.9b00048] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Fluorogenic aptamers are genetically encoded RNA aptamers that bind and induce the fluorescence of otherwise nonfluorescent small molecule dyes. These RNA-fluorophore complexes can be highly fluorescent and useful for RNA visualization and genetically encoded biosensors. Notably, different RNA aptamers can bind the same fluorophore, resulting in complexes that exhibit spectrally distinct fluorescence properties. The basis for spectral tuning of small molecule fluorophores has not yet been studied. Here we explore the mechanism of spectral tuning in three highly related RNA aptamers, Broccoli, Orange Broccoli, and Red Broccoli, each of which binds the DFHO (3,5-difluoro-4-hydroxybenzylidene imidazolinone-2-oxime) fluorophore and generates distinct spectral emissions. We show that DFHO fluorescence spectral tuning is controlled by interaction of the oxime moiety of the fluorophore and one specific nucleotide that is different in each RNA aptamer. Our finding presents, for the first time, a mechanism by which RNA can control the properties of a bound small molecule fluorophore. More broadly, our finding can guide further development of fluorogenic aptamers with novel spectral properties.
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Affiliation(s)
- Grigory S Filonov
- Department of Pharmacology, Weill Medical College , Cornell University , New York , New York 10065 , United States
| | - Wenjiao Song
- Department of Pharmacology, Weill Medical College , Cornell University , New York , New York 10065 , United States
| | - Samie R Jaffrey
- Department of Pharmacology, Weill Medical College , Cornell University , New York , New York 10065 , United States
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72
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Cook ZT, Brockway NL, Tobias ZJC, Pajarla J, Boardman IS, Ippolito H, Nkombo Nkoula S, Weissman TA. Combining near-infrared fluorescence with Brainbow to visualize expression of specific genes within a multicolor context. Mol Biol Cell 2019; 30:491-505. [PMID: 30586321 PMCID: PMC6594444 DOI: 10.1091/mbc.e18-06-0340] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 12/13/2018] [Accepted: 12/18/2018] [Indexed: 12/18/2022] Open
Abstract
Fluorescent proteins are a powerful experimental tool, allowing the visualization of gene expression and cellular behaviors in a variety of systems. Multicolor combinations of fluorescent proteins, such as Brainbow, have expanded the range of possible research questions and are useful for distinguishing and tracking cells. The addition of a separately driven color, however, would allow researchers to report expression of a manipulated gene within the multicolor context to investigate mechanistic effects. A far-red or near-infrared protein could be particularly suitable in this context, as these can be distinguished spectrally from Brainbow. We investigated five far-red/near-infrared proteins in zebrafish: TagRFP657, mCardinal, miRFP670, iRFP670, and mIFP. Our results show that both mCardinal and iRFP670 are useful fluorescent proteins for zebrafish expression. We also introduce a new transgenic zebrafish line that expresses Brainbow under the control of the neuroD promoter. We demonstrate that mCardinal can be used to track the expression of a manipulated bone morphogenetic protein receptor within the Brainbow context. The overlay of near-infrared fluorescence onto a Brainbow background defines a clear strategy for future research questions that aim to manipulate or track the effects of specific genes within a population of cells that are delineated using multicolor approaches.
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Affiliation(s)
- Zoe T. Cook
- Biology Department, Lewis and Clark College, Portland, OR 97219
| | | | | | - Joy Pajarla
- Biology Department, Lewis and Clark College, Portland, OR 97219
| | | | - Helen Ippolito
- Biology Department, Lewis and Clark College, Portland, OR 97219
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73
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Zhou K, Ding Y, Vuletic I, Tian Y, Li J, Liu J, Huang Y, Sun H, Li C, Ren Q, Lu Y. In vivo long-term investigation of tumor bearing mKate2 by an in-house fluorescence molecular imaging system. Biomed Eng Online 2018; 17:187. [PMID: 30594200 PMCID: PMC6310933 DOI: 10.1186/s12938-018-0615-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 12/05/2018] [Indexed: 11/10/2022] Open
Abstract
Background Optical imaging is one of the most common, low-cost imaging tools used for investigating the tumor biological behavior in vivo. This study explores the feasibility and sensitivity of a near infrared fluorescent protein mKate2 for a long-term non-invasive tumor imaging in BALB/c nude mice, by using a low-power optical imaging system. Methods In this study, breast cancer cell line MDA-MB-435s expressing mKate2 and MDA-MB-231 expressing a dual reporter gene firefly luciferase (fLuc)-GFP were used as cell models. Tumor cells were implanted in different animal body compartments including subcutaneous, abdominal and deep tissue area and closely monitored in real-time. A simple and low-power optical imaging system was set up to image both fluorescence and bioluminescence in live animals. Results The presence of malignant tissue was further confirmed by histopathological assay. Considering its lower exposure time and no need of substrate injection, mKate2 is considered a superior choice for subcutaneous imaging compared with fLuc. On the contrary, fLuc has shown to be a better option when monitoring the tumor in a diffusive area such as abdominal cavity. Furthermore, both reporter genes have shown good stability and sensitivity for deep tissue imaging, i.e. tumor within the liver. In addition, fLuc has shown to be an excellent method for detecting tumor cells in the lung. Conclusions The combination of mKate2 and fLuc offers a superior choice for long-term non-invasive real-time investigation of tumor biological behavior in vivo.
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Affiliation(s)
- Kedi Zhou
- Department of Biomedical Engineering, College of Engineering, Peking University, No. 5 Yiheyuan Road, Beijing, 100871, China
| | - Yichen Ding
- Department of Biomedical Engineering, College of Engineering, Peking University, No. 5 Yiheyuan Road, Beijing, 100871, China
| | - Ivan Vuletic
- Department of Biomedical Engineering, College of Engineering, Peking University, No. 5 Yiheyuan Road, Beijing, 100871, China
| | - Yonglu Tian
- Laboratory Animal Centre, Peking University, No. 5 Yiheyuan Road, Beijing, 100871, China
| | - Jun Li
- Laboratory Animal Centre, Peking University, No. 5 Yiheyuan Road, Beijing, 100871, China
| | - Jinghao Liu
- Laboratory Animal Centre, Peking University, No. 5 Yiheyuan Road, Beijing, 100871, China
| | - Yixing Huang
- Department of Biomedical Engineering, College of Engineering, Peking University, No. 5 Yiheyuan Road, Beijing, 100871, China
| | - Hongfang Sun
- Department of Biomedical Engineering, College of Engineering, Peking University, No. 5 Yiheyuan Road, Beijing, 100871, China.
| | - Changhui Li
- Department of Biomedical Engineering, College of Engineering, Peking University, No. 5 Yiheyuan Road, Beijing, 100871, China
| | - Qiushi Ren
- Department of Biomedical Engineering, College of Engineering, Peking University, No. 5 Yiheyuan Road, Beijing, 100871, China
| | - Yanye Lu
- Department of Biomedical Engineering, College of Engineering, Peking University, No. 5 Yiheyuan Road, Beijing, 100871, China.
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74
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Watkins DS, True JD, Mosley AL, Baucum AJ. Proteomic Analysis of the Spinophilin Interactome in Rodent Striatum Following Psychostimulant Sensitization. Proteomes 2018; 6:proteomes6040053. [PMID: 30562941 PMCID: PMC6313900 DOI: 10.3390/proteomes6040053] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Revised: 12/10/2018] [Accepted: 12/13/2018] [Indexed: 12/13/2022] Open
Abstract
Glutamatergic projections from the cortex and dopaminergic projections from the substantia nigra or ventral tegmental area synapse on dendritic spines of specific GABAergic medium spiny neurons (MSNs) in the striatum. Direct pathway MSNs (dMSNs) are positively coupled to protein kinase A (PKA) signaling and activation of these neurons enhance specific motor programs whereas indirect pathway MSNs (iMSNs) are negatively coupled to PKA and inhibit competing motor programs. An imbalance in the activity of these two programs is observed following increased dopamine signaling associated with exposure to psychostimulant drugs of abuse. Alterations in MSN signaling are mediated by changes in MSN protein post-translational modifications, including phosphorylation. Whereas direct changes in specific kinases, such as PKA, regulate different effects observed in the two MSN populations, alterations in the specific activity of serine/threonine phosphatases, such as protein phosphatase 1 (PP1) are less well known. This lack of knowledge is due, in part, to unknown, cell-specific changes in PP1 targeting proteins. Spinophilin is the major PP1-targeting protein in striatal postsynaptic densities. Using proteomics and immunoblotting approaches along with a novel transgenic mouse expressing hemagglutainin (HA)-tagged spinophilin in dMSNs and iMSNs, we have uncovered cell-specific regulation of the spinophilin interactome following a sensitizing regimen of amphetamine. These data suggest regulation of spinophilin interactions in specific MSN cell types and may give novel insight into putative cell-specific, phosphatase-dependent signaling pathways associated with psychostimulants.
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Affiliation(s)
- Darryl S Watkins
- Stark Neurosciences Research Institute, Indiana University School of Medicine Medical Neuroscience Graduate Program, Indianapolis, IN 46278, USA.
| | - Jason D True
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46278, USA.
- Department of Biology, Ball State University, Muncie, IN 47306, USA.
| | - Amber L Mosley
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46278, USA.
| | - Anthony J Baucum
- Department of Biology, Indiana University-Purdue University Indianapolis, Indianapolis, IN 46202, USA.
- Stark Neurosciences Research Institute Indianapolis, Indianapolis, IN 46202, USA.
- Department of Pharmacology and Toxicology, Indiana University School of Medicine, Indianapolis, IN 46202, USA.
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75
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Schlechter RO, Jun H, Bernach M, Oso S, Boyd E, Muñoz-Lintz DA, Dobson RCJ, Remus DM, Remus-Emsermann MNP. Chromatic Bacteria - A Broad Host-Range Plasmid and Chromosomal Insertion Toolbox for Fluorescent Protein Expression in Bacteria. Front Microbiol 2018; 9:3052. [PMID: 30631309 PMCID: PMC6315172 DOI: 10.3389/fmicb.2018.03052] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 11/27/2018] [Indexed: 12/26/2022] Open
Abstract
Differential fluorescent labeling of bacteria has become instrumental for many aspects of microbiological research, such as the study of biofilm formation, bacterial individuality, evolution, and bacterial behavior in complex environments. We designed a variety of plasmids, each bearing one of eight unique, constitutively expressed fluorescent protein genes in conjunction with one of four different antibiotic resistance combinations. The fluorophores mTagBFP2, mTurquoise2, sGFP2, mClover3, sYFP2, mOrange2, mScarlet-I, and mCardinal, encoding for blue, cyan, green, green-yellow, yellow, orange, red, and far-red fluorescent proteins, respectively, were combined with selectable markers conferring tetracycline, gentamicin, kanamycin, and/or chloramphenicol resistance. These constructs were cloned into three different plasmid backbones: a broad host-range plasmid, a Tn5 transposon delivery plasmid, and a Tn7 transposon delivery plasmid. The utility of the plasmids and transposons was tested in bacteria from the phyla Actinobacteria, Proteobacteria, and Bacteroidetes. We were able to tag representatives from the phylum Proteobacteria at least via our Tn5 transposon delivery system. The present study enables labeling bacteria with a set of plasmids available to the community. One potential application of fluorescently-tagged bacterial species is the study of bacteria-bacteria, bacteria-host, and bacteria-environment interactions.
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Affiliation(s)
- Rudolf O. Schlechter
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
- Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand
| | - Hyunwoo Jun
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Michał Bernach
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
- Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand
| | - Simisola Oso
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Erica Boyd
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Dian A. Muñoz-Lintz
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Renwick C. J. Dobson
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
- Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand
- Bio21 Molecular Science and Biotechnology Institute, Department of Biochemistry and Molecular Biology, The University of Melbourne, Parkville, VIC, Australia
| | - Daniela M. Remus
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
- Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand
- Protein Science & Engineering, Callaghan Innovation, School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Mitja N. P. Remus-Emsermann
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
- Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand
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76
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Sawyer EM, Joshi PR, Jorgensen V, Yunus J, Berchowitz LE, Ünal E. Developmental regulation of an organelle tether coordinates mitochondrial remodeling in meiosis. J Cell Biol 2018; 218:559-579. [PMID: 30538140 PMCID: PMC6363441 DOI: 10.1083/jcb.201807097] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Revised: 10/26/2018] [Accepted: 11/21/2018] [Indexed: 12/25/2022] Open
Abstract
Cellular differentiation involves remodeling cellular architecture to transform one cell type to another. By investigating mitochondrial dynamics during meiotic differentiation in budding yeast, we sought to understand how organelle morphogenesis is developmentally controlled in a system where regulators of differentiation and organelle architecture are known, but the interface between them remains unexplored. We analyzed the regulation of mitochondrial detachment from the cell cortex, a known meiotic alteration to mitochondrial morphology. We found that mitochondrial detachment is enabled by the programmed destruction of the mitochondria-endoplasmic reticulum-cortex anchor (MECA), an organelle tether that bridges mitochondria and the plasma membrane. MECA regulation is governed by a meiotic transcription factor, Ndt80, which promotes the activation of a conserved kinase, Ime2. We further present evidence for Ime2-dependent phosphorylation and degradation of MECA in a temporally controlled manner. Our study defines a key mechanism that coordinates mitochondrial morphogenesis with the landmark events of meiosis and demonstrates that cells can developmentally regulate tethering to induce organelle remodeling.
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Affiliation(s)
- Eric M Sawyer
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA
| | - Pallavi R Joshi
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA
| | - Victoria Jorgensen
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA
| | - Julius Yunus
- Department of Genetics and Development, Columbia University Medical Center, New York, NY
| | - Luke E Berchowitz
- Department of Genetics and Development, Columbia University Medical Center, New York, NY
| | - Elçin Ünal
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA
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77
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Canty L, Hariharan S, Liu Q, Haney SA, Andrews DW. Peak emission wavelength and fluorescence lifetime are coupled in far-red, GFP-like fluorescent proteins. PLoS One 2018; 13:e0208075. [PMID: 30485364 PMCID: PMC6261627 DOI: 10.1371/journal.pone.0208075] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 11/12/2018] [Indexed: 11/25/2022] Open
Abstract
The discovery and use of fluorescent proteins revolutionized cell biology by allowing the visualization of proteins in living cells. Advances in fluorescent proteins, primarily through genetic engineering, have enabled more advanced analyses, including Förster resonance energy transfer (FRET) and fluorescence lifetime imaging microscopy (FLIM) and the development of genetically encoded fluorescent biosensors. These fluorescence protein-based sensors are highly effective in cells grown in monolayer cultures. However, it is often desirable to use more complex models including tissue explants, organoids, xenografts, and whole animals. These types of samples have poor light penetration owing to high scattering and absorption of light by tissue. Far-red light with a wavelength between 650-900nm is less prone to scatter, and absorption by tissues and can thus penetrate more deeply. Unfortunately, there are few fluorescent proteins in this region of the spectrum, and they have sub-optimal fluorescent properties including low brightness and short fluorescence lifetimes. Understanding the relationships between the amino-acid sequences of far-red fluorescence proteins and their photophysical properties including peak emission wavelengths and fluorescence lifetimes would be useful in the design of new fluorescence proteins for this region of the spectrum. We used both site-directed mutagenesis and gene-shuffling between mScarlet and mCardinal fluorescence proteins to create new variants and assess their properties systematically. We discovered that for far-red, GFP-like proteins the emission maxima and fluorescence lifetime have a strong inverse correlation.
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Affiliation(s)
- Laura Canty
- Department of Biological Sciences, Sunnybrook Research Institute, Toronto, Ontario, Canada
| | - Santosh Hariharan
- Department of Biological Sciences, Sunnybrook Research Institute, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Qian Liu
- Department of Biological Sciences, Sunnybrook Research Institute, Toronto, Ontario, Canada
| | - Steven A. Haney
- Department of Oncology and Translational Research, Eli Lilly and Company, Indianapolis, Indiana, United States of America
| | - David W. Andrews
- Department of Biological Sciences, Sunnybrook Research Institute, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
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78
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Holzapfel HY, Stern AD, Bouhaddou M, Anglin CM, Putur D, Comer S, Birtwistle MR. Fluorescence Multiplexing with Spectral Imaging and Combinatorics. ACS COMBINATORIAL SCIENCE 2018; 20:653-659. [PMID: 30339749 PMCID: PMC9827428 DOI: 10.1021/acscombsci.8b00101] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Ultraviolet-to-infrared fluorescence is a versatile and accessible assay modality but is notoriously hard to multiplex due to overlap of wide emission spectra. We present an approach for fluorescence called multiplexing using spectral imaging and combinatorics (MuSIC). MuSIC consists of creating new independent probes from covalently linked combinations of individual fluorophores, leveraging the wide palette of currently available probes with the mathematical power of combinatorics. Probe levels in a mixture can be inferred from spectral emission scanning data. Theory and simulations suggest MuSIC can increase fluorescence multiplexing ∼4-5 fold using currently available dyes and measurement tools. Experimental proof-of-principle demonstrates robust demultiplexing of nine solution-based probes using ∼25% of the available excitation wavelength window (380-480 nm), consistent with theory. The increasing prevalence of white lasers, angle filter-based wavelength scanning, and large, sensitive multianode photomultiplier tubes make acquisition of such MuSIC-compatible data sets increasingly attainable.
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Affiliation(s)
- Hadassa Y. Holzapfel
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA,Medical School for International Health, Faculty of Health Sciences, Ben-Gurion University of the Negev, Be’er Sheva, 84105, Israel
| | - Alan D. Stern
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Mehdi Bouhaddou
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Caitlin M. Anglin
- Department of Chemical and Biomolecular Engineering, Clemson University, Clemson, SC 29634, USA
| | - Danielle Putur
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Sarah Comer
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Marc R. Birtwistle
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA,Department of Chemical and Biomolecular Engineering, Clemson University, Clemson, SC 29634, USA,To whom correspondence should be addressed
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79
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Kamper M, Ta H, Jensen NA, Hell SW, Jakobs S. Near-infrared STED nanoscopy with an engineered bacterial phytochrome. Nat Commun 2018; 9:4762. [PMID: 30420676 PMCID: PMC6232180 DOI: 10.1038/s41467-018-07246-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2018] [Accepted: 10/17/2018] [Indexed: 01/18/2023] Open
Abstract
The near infrared (NIR) optical window between the cutoff for hemoglobin absorption at 650 nm and the onset of increased water absorption at 900 nm is an attractive, yet largely unexplored, spectral regime for diffraction-unlimited super-resolution fluorescence microscopy (nanoscopy). We developed the NIR fluorescent protein SNIFP, a bright and photostable bacteriophytochrome, and demonstrate its use as a fusion tag in live-cell microscopy and STED nanoscopy. We further demonstrate dual color red-confocal/NIR-STED imaging by co-expressing SNIFP with a conventional red fluorescent protein.
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Affiliation(s)
- Maria Kamper
- Department of NanoBiophotonics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Haisen Ta
- Department of NanoBiophotonics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Nickels A Jensen
- Department of NanoBiophotonics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Stefan W Hell
- Department of NanoBiophotonics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Stefan Jakobs
- Department of NanoBiophotonics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany. .,Department of Neurology, University Medical Center Göttingen, Göttingen, Germany.
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80
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Willadsen M, Chaise M, Yarovoy I, Zhang AQ, Parashurama N. Engineering molecular imaging strategies for regenerative medicine. Bioeng Transl Med 2018; 3:232-255. [PMID: 30377663 PMCID: PMC6195904 DOI: 10.1002/btm2.10114] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 08/30/2018] [Accepted: 09/01/2018] [Indexed: 12/15/2022] Open
Abstract
The reshaping of the world's aging population has created an urgent need for therapies for chronic diseases. Regenerative medicine offers a ray of hope, and its complex solutions include material, cellular, or tissue systems. We review basics of regenerative medicine/stem cells and describe how the field of molecular imaging, which is based on quantitative, noninvasive, imaging of biological events in living subjects, can be applied to regenerative medicine in order to interrogate tissues in innovative, informative, and personalized ways. We consider aspects of regenerative medicine for which molecular imaging will benefit. Next, genetic and nanoparticle-based cell imaging strategies are discussed in detail, with modalities like magnetic resonance imaging, optical imaging (near infra-red, bioluminescence), raman microscopy, and photoacoustic microscopy), ultrasound, computed tomography, single-photon computed tomography, and positron emission tomography. We conclude with a discussion of "next generation" molecular imaging strategies, including imaging host tissues prior to cell/tissue transplantation.
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Affiliation(s)
- Matthew Willadsen
- Department of Chemical and Biological Engineering University at Buffalo, State University of New York, Furnas Hall Buffalo New York 14228
| | - Marc Chaise
- Jacobs School of Medicine and Biomedical Sciences University at Buffalo State University of New York 955 Main St., Buffalo, New York 14203
| | - Iven Yarovoy
- Department of Chemical and Biological Engineering University at Buffalo, State University of New York, Furnas Hall Buffalo New York 14228
| | - An Qi Zhang
- Department of Chemical and Biological Engineering University at Buffalo, State University of New York, Furnas Hall Buffalo New York 14228
| | - Natesh Parashurama
- Department of Chemical and Biological Engineering University at Buffalo, State University of New York, Furnas Hall Buffalo New York 14228.,Department of Biomedical Engineering University at Buffalo, State University of New York, Bonner Hall Buffalo New York 14228.,Clinical and Translation Research Center (CTRC) University at Buffalo, State University of New York 875 Ellicott St., Buffalo, New York 14203
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81
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Manna P, Hung ST, Mukherjee S, Friis P, Simpson DM, Lo MN, Palmer AE, Jimenez R. Directed evolution of excited state lifetime and brightness in FusionRed using a microfluidic sorter. Integr Biol (Camb) 2018; 10:516-526. [PMID: 30094420 PMCID: PMC6141309 DOI: 10.1039/c8ib00103k] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Green fluorescent proteins (GFP) and their blue, cyan and red counterparts offer unprecedented advantages as biological markers owing to their genetic encodability and straightforward expression in different organisms. Although significant advancements have been made towards engineering the key photo-physical properties of red fluorescent proteins (RFPs), they continue to perform sub-optimally relative to GFP variants. Advanced engineering strategies are needed for further evolution of RFPs in the pursuit of improving their photo-physics. In this report, a microfluidic sorter that discriminates members of a cell-based library based on their excited state lifetime and fluorescence intensity is used for the directed evolution of the photo-physical properties of FusionRed. In-flow measurements of the fluorescence lifetime are performed in a frequency-domain approach with sub-millisecond sampling times. Promising clones are sorted by optical force trapping with an infrared laser. Using this microfluidic sorter, mutants are generated with longer lifetimes than their precursor, FusionRed. This improvement in the excited state lifetime of the mutants leads to an increase in their fluorescence quantum yield up to 1.8-fold. In the course of evolution, we also identified one key mutation (L177M), which generated a mutant (FusionRed-M) that displayed ∼2-fold higher brightness than its precursor upon expression in mammalian (HeLa) cells. Photo-physical and mutational analyses of clones isolated at the different stages of mutagenesis reveal the photo-physical evolution towards higher in vivo brightness.
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Affiliation(s)
- Premashis Manna
- JILA, NIST and University of Colorado, Boulder, Colorado 80309, USA.
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82
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Syga Ł, Spakman D, Punter CM, Poolman B. Method for immobilization of living and synthetic cells for high-resolution imaging and single-particle tracking. Sci Rep 2018; 8:13789. [PMID: 30213985 PMCID: PMC6137044 DOI: 10.1038/s41598-018-32166-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 08/16/2018] [Indexed: 12/15/2022] Open
Abstract
Super-resolution imaging and single-particle tracking require cells to be immobile as any movement reduces the resolution of the measurements. Here, we present a method based on APTES-glutaraldehyde coating of glass surfaces to immobilize cells without compromising their growth. Our method of immobilization is compatible with Saccharomyces cerevisiae, Escherichia coli, and synthetic cells (here, giant-unilamellar vesicles). The method introduces minimal background fluorescence and is suitable for imaging of single particles at high resolution. With S. cerevisiae we benchmarked the method against the commonly used concanavalin A approach. We show by total internal reflection fluorescence microscopy that modifying surfaces with ConA introduces artifacts close to the glass surface, which are not present when immobilizing with the APTES-glutaraldehyde method. We demonstrate validity of the method by measuring the diffusion of membrane proteins in yeast with single-particle tracking and of lipids in giant-unilamellar vesicles with fluorescence recovery after photobleaching. Importantly, the physical properties and shape of the fragile GUVs are not affected upon binding to APTES-glutaraldehyde coated glass. The APTES-glutaraldehyde is a generic method of immobilization that should work with any cell or synthetic system that has primary amines on the surface.
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Affiliation(s)
- Łukasz Syga
- Department of Biochemistry University of Groningen Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Dian Spakman
- Department of Biochemistry University of Groningen Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Christiaan M Punter
- Department of Biochemistry University of Groningen Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Bert Poolman
- Department of Biochemistry University of Groningen Nijenborgh 4, 9747 AG, Groningen, The Netherlands.
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83
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Ricard C, Arroyo ED, He CX, Portera-Cailliau C, Lepousez G, Canepari M, Fiole D. Two-photon probes for in vivo multicolor microscopy of the structure and signals of brain cells. Brain Struct Funct 2018; 223:3011-3043. [PMID: 29748872 PMCID: PMC6119111 DOI: 10.1007/s00429-018-1678-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Accepted: 05/03/2018] [Indexed: 02/07/2023]
Abstract
Imaging the brain of living laboratory animals at a microscopic scale can be achieved by two-photon microscopy thanks to the high penetrability and low phototoxicity of the excitation wavelengths used. However, knowledge of the two-photon spectral properties of the myriad fluorescent probes is generally scarce and, for many, non-existent. In addition, the use of different measurement units in published reports further hinders the design of a comprehensive imaging experiment. In this review, we compile and homogenize the two-photon spectral properties of 280 fluorescent probes. We provide practical data, including the wavelengths for optimal two-photon excitation, the peak values of two-photon action cross section or molecular brightness, and the emission ranges. Beyond the spectroscopic description of these fluorophores, we discuss their binding to biological targets. This specificity allows in vivo imaging of cells, their processes, and even organelles and other subcellular structures in the brain. In addition to probes that monitor endogenous cell metabolism, studies of healthy and diseased brain benefit from the specific binding of certain probes to pathology-specific features, ranging from amyloid-β plaques to the autofluorescence of certain antibiotics. A special focus is placed on functional in vivo imaging using two-photon probes that sense specific ions or membrane potential, and that may be combined with optogenetic actuators. Being closely linked to their use, we examine the different routes of intravital delivery of these fluorescent probes according to the target. Finally, we discuss different approaches, strategies, and prerequisites for two-photon multicolor experiments in the brains of living laboratory animals.
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Affiliation(s)
- Clément Ricard
- Brain Physiology Laboratory, CNRS UMR 8118, 75006, Paris, France
- Faculté de Sciences Fondamentales et Biomédicales, Université Paris Descartes, PRES Sorbonne Paris Cité, 75006, Paris, France
- Fédération de Recherche en Neurosciences FR 3636, Paris, 75006, France
| | - Erica D Arroyo
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, USA
| | - Cynthia X He
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, USA
| | - Carlos Portera-Cailliau
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, USA
- Department of Neurobiology, David Geffen School of Medicine, University of California, Los Angeles, USA
| | - Gabriel Lepousez
- Unité Perception et Mémoire, Département de Neuroscience, Institut Pasteur, 25 rue du Docteur Roux, 75724, Paris Cedex 15, France
| | - Marco Canepari
- Laboratory for Interdisciplinary Physics, UMR 5588 CNRS and Université Grenoble Alpes, 38402, Saint Martin d'Hères, France
- Laboratories of Excellence, Ion Channel Science and Therapeutics, Grenoble, France
- Institut National de la Santé et Recherche Médicale (INSERM), Grenoble, France
| | - Daniel Fiole
- Unité Biothérapies anti-Infectieuses et Immunité, Département des Maladies Infectieuses, Institut de Recherche Biomédicale des Armées, BP 73, 91223, Brétigny-sur-Orge cedex, France.
- Human Histopathology and Animal Models, Infection and Epidemiology Department, Institut Pasteur, 28 rue du docteur Roux, 75725, Paris Cedex 15, France.
- ESRF-The European Synchrotron, 38043, Grenoble cedex, France.
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84
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Argüello-Miranda O, Liu Y, Wood NE, Kositangool P, Doncic A. Integration of Multiple Metabolic Signals Determines Cell Fate Prior to Commitment. Mol Cell 2018; 71:733-744.e11. [PMID: 30174289 DOI: 10.1016/j.molcel.2018.07.041] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Revised: 06/13/2018] [Accepted: 07/27/2018] [Indexed: 11/18/2022]
Abstract
Cell-fate decisions are central to the survival and development of both uni- and multicellular organisms. It remains unclear when and to what degree cells can decide on future fates prior to commitment. This uncertainty stems from experimental and theoretical limitations in measuring and integrating multiple signals at the single-cell level during a decision process. Here, we combine six-color live-cell imaging with the Bayesian method of statistical evidence to study the meiosis/quiescence decision in budding yeast. Integration of multiple upstream metabolic signals predicts individual cell fates with high probability well before commitment. Cells "decide" their fates before birth, well before the activation of pathways characteristic of downstream cell fates. This decision, which remains stable through several cell cycles, occurs when multiple metabolic parameters simultaneously cross cell-fate-specific thresholds. Taken together, our results show that cells can decide their future fates long before commitment mechanisms are activated.
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Affiliation(s)
- Orlando Argüello-Miranda
- Department of Cell Biology, UT Southwestern Medical Center, 6000 Harry Hines Boulevard, Dallas, TX 75390, USA.
| | - Yanjie Liu
- Department of Cell Biology, UT Southwestern Medical Center, 6000 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - N Ezgi Wood
- Department of Cell Biology, UT Southwestern Medical Center, 6000 Harry Hines Boulevard, Dallas, TX 75390, USA.
| | - Piya Kositangool
- Department of Cell Biology, UT Southwestern Medical Center, 6000 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Andreas Doncic
- Department of Cell Biology, UT Southwestern Medical Center, 6000 Harry Hines Boulevard, Dallas, TX 75390, USA; Green Center for Systems Biology, UT Southwestern Medical Center, 6001 Forest Park Road, Dallas, TX 75390, USA
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85
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Hirakawa M, Nagakubo D, Kanzler B, Avilov S, Krauth B, Happe C, Swann JB, Nusser A, Boehm T. Fundamental parameters of the developing thymic epithelium in the mouse. Sci Rep 2018; 8:11095. [PMID: 30038304 PMCID: PMC6056470 DOI: 10.1038/s41598-018-29460-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 07/09/2018] [Indexed: 01/09/2023] Open
Abstract
The numbers of thymic epithelial cells (TECs) and thymocytes steadily increase during embryogenesis. To examine this dynamic, we generated several TEC-specific transgenic mouse lines, which express fluorescent proteins in the nucleus, the cytosol and in the membranes under the control of the Foxn1 promoter. These tools enabled us to determine TEC numbers in tissue sections by confocal fluorescent microscopy, and in the intact organ by light-sheet microscopy. Compared to histological procedures, flow cytometric analysis of thymic cellularity is shown to underestimate the numbers of TECs by one order of magnitude; using enzymatic digestion of thymic tissue, the loss of cortical TECs (cTECs) is several fold greater than that of medullary TECs (mTECs), although different cTEC subsets appear to be still present in the final preparation. Novel reporter lines driven by Psmb11 and Prss16 promoters revealed the trajectory of differentiation of cTEC-like cells, and, owing to the additional facility of conditional cell ablation, allowed us to follow the recovery of such cells after their depletion during embryogenesis. Multiparametric histological analyses indicate that the new transgenic reporter lines not only reveal the unique morphologies of different TEC subsets, but are also conducive to the analysis of the complex cellular interactions in the thymus.
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Affiliation(s)
- Mayumi Hirakawa
- Department of Developmental Immunology, Max Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, 79108, Freiburg, Germany
| | - Daisuke Nagakubo
- Department of Developmental Immunology, Max Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, 79108, Freiburg, Germany.,Division of Health and Hygienic Sciences, Faculty of Pharmaceutical Sciences, Himeji Dokkyo University, 7-2-1 Kamiohno, Himeji, Hyogo, 670-8524, Japan
| | - Benoît Kanzler
- Transgenic Mouse Core Facility, Max Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, 79108, Freiburg, Germany
| | - Sergiy Avilov
- Imaging Facility, Max Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, 79108, Freiburg, Germany
| | - Brigitte Krauth
- Department of Developmental Immunology, Max Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, 79108, Freiburg, Germany
| | - Christiane Happe
- Department of Developmental Immunology, Max Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, 79108, Freiburg, Germany
| | - Jeremy B Swann
- Department of Developmental Immunology, Max Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, 79108, Freiburg, Germany
| | - Anja Nusser
- Department of Developmental Immunology, Max Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, 79108, Freiburg, Germany
| | - Thomas Boehm
- Department of Developmental Immunology, Max Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, 79108, Freiburg, Germany.
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86
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Dunsing V, Luckner M, Zühlke B, Petazzi RA, Herrmann A, Chiantia S. Optimal fluorescent protein tags for quantifying protein oligomerization in living cells. Sci Rep 2018; 8:10634. [PMID: 30006597 PMCID: PMC6045628 DOI: 10.1038/s41598-018-28858-0] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 07/02/2018] [Indexed: 11/30/2022] Open
Abstract
Fluorescence fluctuation spectroscopy has become a popular toolbox for non-disruptive analysis of molecular interactions in living cells. The quantification of protein oligomerization in the native cellular environment is highly relevant for a detailed understanding of complex biological processes. An important parameter in this context is the molecular brightness, which serves as a direct measure of oligomerization and can be easily extracted from temporal or spatial fluorescence fluctuations. However, fluorescent proteins (FPs) typically used in such studies suffer from complex photophysical transitions and limited maturation, inducing non-fluorescent states. Here, we show how these processes strongly affect molecular brightness measurements. We perform a systematic characterization of non-fluorescent states for commonly used FPs and provide a simple guideline for accurate, unbiased oligomerization measurements in living cells. Further, we focus on novel red FPs and demonstrate that mCherry2, an mCherry variant, possesses superior properties with regards to precise quantification of oligomerization.
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Affiliation(s)
- Valentin Dunsing
- Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476, Potsdam, Germany
| | - Madlen Luckner
- Institute for Biology, IRI Life Sciences, Humboldt-Universität zu Berlin, Invalidenstraße 42, 10115, Berlin, Germany
| | - Boris Zühlke
- Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476, Potsdam, Germany
| | - Roberto A Petazzi
- Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476, Potsdam, Germany
| | - Andreas Herrmann
- Institute for Biology, IRI Life Sciences, Humboldt-Universität zu Berlin, Invalidenstraße 42, 10115, Berlin, Germany
| | - Salvatore Chiantia
- Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476, Potsdam, Germany.
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87
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Morphometric analysis and neuroanatomical mapping of the zebrafish brain. Methods 2018; 150:49-62. [PMID: 29936090 DOI: 10.1016/j.ymeth.2018.06.008] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 06/14/2018] [Indexed: 12/21/2022] Open
Abstract
Large-scale genomic studies have recently identified genetic variants causative for major neurodevelopmental disorders, such as intellectual disability and autism. However, determining how underlying developmental processes are affected by these mutations remains a significant challenge in the field. Zebrafish is an established model system in developmental neurogenetics that may be useful in uncovering the mechanisms of these mutations. Here we describe the use of voxel-intensity, deformation field, and volume-based morphometric techniques for the systematic and unbiased analysis of gene knock-down and environmental exposure-induced phenotypes in zebrafish. We first present a computational method for brain segmentation based on transgene expression patterns to create a comprehensive neuroanatomical map. This map allowed us to disclose statistically significant changes in brain microstructure and composition in neurodevelopmental models. We demonstrate the effectiveness of morphometric techniques in measuring changes in the relative size of neuroanatomical subdivisions in atoh7 morphant larvae and in identifying phenotypes in larvae treated with valproic acid, a chemical demonstrated to increase the risk of autism in humans. These tools enable rigorous evaluation of the effects of gene mutations and environmental exposures on neural development, providing an entry point for cellular and molecular analysis of basic developmental processes as well as neurodevelopmental and neurodegenerative disorders.
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88
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Sanchez C, Berthier C, Allard B, Perrot J, Bouvard C, Tsutsui H, Okamura Y, Jacquemond V. Tracking the sarcoplasmic reticulum membrane voltage in muscle with a FRET biosensor. J Gen Physiol 2018; 150:1163-1177. [PMID: 29899059 PMCID: PMC6080890 DOI: 10.1085/jgp.201812035] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 05/16/2018] [Indexed: 11/20/2022] Open
Abstract
The sarcoplasmic reticulum membrane contains ion channels, but it is unknown whether it experiences voltage changes during cellular activity. By expressing voltage-sensitive fluorescence biosensors in this membrane, Sanchez et al. suggest that it remains electrically silent during muscle activation. Ion channel activity in the plasma membrane of living cells generates voltage changes that are critical for numerous biological functions. The membrane of the endoplasmic/sarcoplasmic reticulum (ER/SR) is also endowed with ion channels, but whether changes in its voltage occur during cellular activity has remained ambiguous. This issue is critical for cell functions that depend on a Ca2+ flux across the reticulum membrane. This is the case for contraction of striated muscle, which is triggered by opening of ryanodine receptor Ca2+ release channels in the SR membrane in response to depolarization of the transverse invaginations of the plasma membrane (the t-tubules). Here, we use targeted expression of voltage-sensitive fluorescence resonance energy transfer (FRET) probes of the Mermaid family in differentiated muscle fibers to determine whether changes in SR membrane voltage occur during depolarization–contraction coupling. In the absence of an SR targeting sequence, FRET signals from probes present in the t-tubule membrane allow calibration of the voltage sensitivity and amplitude of the response to voltage-clamp pulses. Successful SR targeting of the probes was achieved using an N-terminal domain of triadin, which completely eliminates voltage-clamp–activated FRET signals from the t-tubule membrane of transfected fibers. In fibers expressing SR-targeted Mermaid probes, activation of SR Ca2+ release in the presence of intracellular ethyleneglycol-bis(β-amino-ethyl ether)-N,N,N′,N′-tetra acetic acid (EGTA) results in an accompanying FRET signal. We find that this signal results from pH sensitivity of the probe, which detects cytosolic acidification because of the release of protons upon Ca2+ binding to EGTA. When EGTA is substituted with either 1,2-bis(o-aminophenoxy)ethane-N,N,N′,N′-tetraacetic acid or the contraction blocker N-benzyl-p-toluene sulfonamide, we find no indication of a substantial change in the FRET response caused by a voltage change. These results suggest that the ryanodine receptor–mediated SR Ca2+ efflux is well balanced by concomitant counterion currents across the SR membrane.
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Affiliation(s)
- Colline Sanchez
- Université Claude Bernard Lyon 1, Institut NeuroMyoGène, Villeurbanne, France
| | - Christine Berthier
- Université Claude Bernard Lyon 1, Institut NeuroMyoGène, Villeurbanne, France
| | - Bruno Allard
- Université Claude Bernard Lyon 1, Institut NeuroMyoGène, Villeurbanne, France
| | - Jimmy Perrot
- Université Claude Bernard Lyon 1, Institut NeuroMyoGène, Villeurbanne, France
| | - Clément Bouvard
- Université Claude Bernard Lyon 1, Institut NeuroMyoGène, Villeurbanne, France
| | - Hidekazu Tsutsui
- Laboratory of Integrative Physiology, Graduate School of Medicine, Osaka University, Osaka, Japan.,Bioscience and Bioengineering, Japan Advanced Institute of Science and Technology, Nomi, Ishikawa, Japan
| | - Yasushi Okamura
- Laboratory of Integrative Physiology, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Vincent Jacquemond
- Université Claude Bernard Lyon 1, Institut NeuroMyoGène, Villeurbanne, France
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89
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Wiklander OPB, Bostancioglu RB, Welsh JA, Zickler AM, Murke F, Corso G, Felldin U, Hagey DW, Evertsson B, Liang XM, Gustafsson MO, Mohammad DK, Wiek C, Hanenberg H, Bremer M, Gupta D, Björnstedt M, Giebel B, Nordin JZ, Jones JC, El Andaloussi S, Görgens A. Systematic Methodological Evaluation of a Multiplex Bead-Based Flow Cytometry Assay for Detection of Extracellular Vesicle Surface Signatures. Front Immunol 2018; 9:1326. [PMID: 29951064 PMCID: PMC6008374 DOI: 10.3389/fimmu.2018.01326] [Citation(s) in RCA: 140] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 05/28/2018] [Indexed: 01/07/2023] Open
Abstract
Extracellular vesicles (EVs) can be harvested from cell culture supernatants and from all body fluids. EVs can be conceptually classified based on their size and biogenesis as exosomes and microvesicles. Nowadays, it is however commonly accepted in the field that there is a much higher degree of heterogeneity within these two subgroups than previously thought. For instance, the surface marker profile of EVs is likely dependent on the cell source, the cell’s activation status, and multiple other parameters. Within recent years, several new methods and assays to study EV heterogeneity in terms of surface markers have been described; most of them are being based on flow cytometry. Unfortunately, such methods generally require dedicated instrumentation, are time-consuming and demand extensive operator expertise for sample preparation, acquisition, and data analysis. In this study, we have systematically evaluated and explored the use of a multiplex bead-based flow cytometric assay which is compatible with most standard flow cytometers and facilitates a robust semi-quantitative detection of 37 different potential EV surface markers in one sample simultaneously. First, assay variability, sample stability over time, and dynamic range were assessed together with the limitations of this assay in terms of EV input quantity required for detection of differently abundant surface markers. Next, the potential effects of EV origin, sample preparation, and quality of the EV sample on the assay were evaluated. The findings indicate that this multiplex bead-based assay is generally suitable to detect, quantify, and compare EV surface signatures in various sample types, including unprocessed cell culture supernatants, cell culture-derived EVs isolated by different methods, and biological fluids. Furthermore, the use and limitations of this assay to assess heterogeneities in EV surface signatures was explored by combining different sets of detection antibodies in EV samples derived from different cell lines and subsets of rare cells. Taken together, this validated multiplex bead-based flow cytometric assay allows robust, sensitive, and reproducible detection of EV surface marker expression in various sample types in a semi-quantitative way and will be highly valuable for many researchers in the EV field in different experimental contexts.
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Affiliation(s)
- Oscar P B Wiklander
- Clinical Research Center, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden.,Evox Therapeutics Limited, Oxford, United Kingdom
| | - R Beklem Bostancioglu
- Clinical Research Center, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Joshua A Welsh
- Molecular Immunogenetics and Vaccine Research Section, Vaccine Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
| | - Antje M Zickler
- Clinical Research Center, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden.,Division of Pathology F56, Department of Laboratory Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Florian Murke
- Institute for Transfusion Medicine, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Giulia Corso
- Clinical Research Center, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Ulrika Felldin
- Clinical Research Center, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Daniel W Hagey
- Clinical Research Center, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Björn Evertsson
- Department of Clinical Neuroscience, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Xiu-Ming Liang
- Clinical Research Center, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Manuela O Gustafsson
- Clinical Research Center, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Dara K Mohammad
- Clinical Research Center, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Biology, College of Science, Salahaddin University-Erbil, Erbil, Iraq
| | - Constanze Wiek
- Department of Otorhinolaryngology & Head/Neck Surgery, University Hospital Düsseldorf, Heinrich Heine University of Düsseldorf, Düsseldorf, Germany
| | - Helmut Hanenberg
- Department of Otorhinolaryngology & Head/Neck Surgery, University Hospital Düsseldorf, Heinrich Heine University of Düsseldorf, Düsseldorf, Germany.,Department of Pediatrics III, University Children's Hospital of Essen, University Duisburg-Essen, Essen, Germany
| | - Michel Bremer
- Institute for Transfusion Medicine, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Dhanu Gupta
- Clinical Research Center, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Mikael Björnstedt
- Division of Pathology F56, Department of Laboratory Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Bernd Giebel
- Institute for Transfusion Medicine, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Joel Z Nordin
- Clinical Research Center, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden.,Evox Therapeutics Limited, Oxford, United Kingdom
| | - Jennifer C Jones
- Molecular Immunogenetics and Vaccine Research Section, Vaccine Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
| | - Samir El Andaloussi
- Clinical Research Center, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden.,Evox Therapeutics Limited, Oxford, United Kingdom.,Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
| | - André Görgens
- Clinical Research Center, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden.,Evox Therapeutics Limited, Oxford, United Kingdom.,Institute for Transfusion Medicine, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
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90
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Kong Y, Cirillo JD. Fluorescence Imaging of Mycobacterial Infection in Live Mice Using Fluorescent Protein-Expressing Strains. Methods Mol Biol 2018; 1790:75-85. [PMID: 29858784 DOI: 10.1007/978-1-4939-7860-1_6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
Abstract
Fluorescence imaging has been applied to various areas of biological research, including studies of physiological, neurological, oncological, cell biological, molecular, developmental, immunological, and infectious processes. In this chapter, we describe methods of fluorescent imaging applied to examination of subcutaneous and pulmonary mycobacterial infections in an animal model. Since slow growth of Mycobacterium tuberculosis (Mtb) hinders development of new diagnostics, therapeutics, and vaccines for tuberculosis (TB), we developed fluorescent protein (FP) expressing mycobacterial strains for in vivo imaging, which can be used to track bacterial location and to quantitate bacterial load directly in living animals. After comparison of imaging data using strains expressing different fluorescent proteins, we found that strains expressing L5-tdTomato display the greatest fluorescence. Here, we describe detailed protocols for tdTomato-labeled M. bovis BCG imaging in real time for subcutaneous and pulmonary infections in living mice. These procedures allow rapid and accurate determination of bacterial numbers in live mice.
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Affiliation(s)
- Ying Kong
- Department of Microbiology, Immunology, and Biochemistry, University of Tennessee Health Science Center, Memphis, TN, USA.
| | - Jeffrey D Cirillo
- Department of Microbial Pathogenesis and Immunology, Texas A & M University Health Science Center, Bryan, TX, USA
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91
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Wan G, Fields BD, Spracklin G, Shukla A, Phillips CM, Kennedy S. Spatiotemporal regulation of liquid-like condensates in epigenetic inheritance. Nature 2018; 557:679-683. [PMID: 29769721 PMCID: PMC6479227 DOI: 10.1038/s41586-018-0132-0] [Citation(s) in RCA: 115] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 04/10/2018] [Indexed: 11/09/2022]
Abstract
Non-membrane bound organelles such as nucleoli, processing bodies, cajal bodies, and germ granules form via spontaneous self-assembly of specific proteins and RNAs. How these biomolecular condensates form and interact are poorly understood. Here we identify two proteins, ZNFX-1 and WAGO-4, that localize to C. elegans germ granules (P granules) in early germline blastomeres. Later in germline development, ZNFX-1/WAGO-4 separate from P granules to define an independent liquid-like condensate that we term the Z granule. In adult germ cells, Z granules assemble into ordered tri-condensate assemblages with P granules and Mutator foci, which we term the PZM granule. Finally, we show that one biological function of ZNFX-1 and WAGO-4 is to interact with silencing RNAs in the C. elegans germline to direct transgenerational epigenetic inheritance (TEI). We speculate that the temporal and spatial ordering of liquid droplet organelles may help cells organize and coordinate the complex RNA processing pathways underlying gene regulatory systems, such as RNA-directed TEI.
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Affiliation(s)
- Gang Wan
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Brandon D Fields
- Department of Genetics, Harvard Medical School, Boston, MA, USA.,Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI, USA
| | - George Spracklin
- Department of Genetics, Harvard Medical School, Boston, MA, USA.,Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI, USA
| | - Aditi Shukla
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Carolyn M Phillips
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Scott Kennedy
- Department of Genetics, Harvard Medical School, Boston, MA, USA.
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92
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Szczesny RJ, Kowalska K, Klosowska-Kosicka K, Chlebowski A, Owczarek EP, Warkocki Z, Kulinski TM, Adamska D, Affek K, Jedroszkowiak A, Kotrys AV, Tomecki R, Krawczyk PS, Borowski LS, Dziembowski A. Versatile approach for functional analysis of human proteins and efficient stable cell line generation using FLP-mediated recombination system. PLoS One 2018; 13:e0194887. [PMID: 29590189 PMCID: PMC5874048 DOI: 10.1371/journal.pone.0194887] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Accepted: 03/12/2018] [Indexed: 12/21/2022] Open
Abstract
Deciphering a function of a given protein requires investigating various biological aspects. Usually, the protein of interest is expressed with a fusion tag that aids or allows subsequent analyses. Additionally, downregulation or inactivation of the studied gene enables functional studies. Development of the CRISPR/Cas9 methodology opened many possibilities but in many cases it is restricted to non-essential genes. Recombinase-dependent gene integration methods, like the Flp-In system, are very good alternatives. The system is widely used in different research areas, which calls for the existence of compatible vectors and efficient protocols that ensure straightforward DNA cloning and generation of stable cell lines. We have created and validated a robust series of 52 vectors for streamlined generation of stable mammalian cell lines using the FLP recombinase-based methodology. Using the sequence-independent DNA cloning method all constructs for a given coding-sequence can be made with just three universal PCR primers. Our collection allows tetracycline-inducible expression of proteins with various tags suitable for protein localization, FRET, bimolecular fluorescence complementation (BiFC), protein dynamics studies (FRAP), co-immunoprecipitation, the RNA tethering assay and cell sorting. Some of the vectors contain a bidirectional promoter for concomitant expression of miRNA and mRNA, so that a gene can be silenced and its product replaced by a mutated miRNA-insensitive version. Our toolkit and protocols have allowed us to create more than 500 constructs with ease. We demonstrate the efficacy of our vectors by creating stable cell lines with various tagged proteins (numatrin, fibrillarin, coilin, centrin, THOC5, PCNA). We have analysed transgene expression over time to provide a guideline for future experiments and compared the effectiveness of commonly used inducers for tetracycline-responsive promoters. As proof of concept we examined the role of the exoribonuclease XRN2 in transcription termination by RNAseq.
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Affiliation(s)
- Roman J. Szczesny
- Laboratory of RNA Biology and Functional Genomics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, Poland
- * E-mail: (RJS); (AD)
| | - Katarzyna Kowalska
- Laboratory of RNA Biology and Functional Genomics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Kamila Klosowska-Kosicka
- Laboratory of RNA Biology and Functional Genomics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Aleksander Chlebowski
- Laboratory of RNA Biology and Functional Genomics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Ewelina P. Owczarek
- Laboratory of RNA Biology and Functional Genomics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Zbigniew Warkocki
- Laboratory of RNA Biology and Functional Genomics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Tomasz M. Kulinski
- Laboratory of RNA Biology and Functional Genomics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Dorota Adamska
- Laboratory of RNA Biology and Functional Genomics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Kamila Affek
- Laboratory of RNA Biology and Functional Genomics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Agata Jedroszkowiak
- Laboratory of RNA Biology and Functional Genomics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Anna V. Kotrys
- Laboratory of RNA Biology and Functional Genomics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Rafal Tomecki
- Laboratory of RNA Biology and Functional Genomics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Pawel S. Krawczyk
- Laboratory of RNA Biology and Functional Genomics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Lukasz S. Borowski
- Laboratory of RNA Biology and Functional Genomics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Andrzej Dziembowski
- Laboratory of RNA Biology and Functional Genomics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, Poland
- * E-mail: (RJS); (AD)
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93
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Ganier O, Schnerch D, Oertle P, Lim RY, Plodinec M, Nigg EA. Structural centrosome aberrations promote non-cell-autonomous invasiveness. EMBO J 2018; 37:embj.201798576. [PMID: 29567643 PMCID: PMC5920242 DOI: 10.15252/embj.201798576] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Revised: 02/14/2018] [Accepted: 02/27/2018] [Indexed: 12/12/2022] Open
Abstract
Centrosomes are the main microtubule‐organizing centers of animal cells. Although centrosome aberrations are common in tumors, their consequences remain subject to debate. Here, we studied the impact of structural centrosome aberrations, induced by deregulated expression of ninein‐like protein (NLP), on epithelial spheres grown in Matrigel matrices. We demonstrate that NLP‐induced structural centrosome aberrations trigger the escape (“budding”) of living cells from epithelia. Remarkably, all cells disseminating into the matrix were undergoing mitosis. This invasive behavior reflects a novel mechanism that depends on the acquisition of two distinct properties. First, NLP‐induced centrosome aberrations trigger a re‐organization of the cytoskeleton, which stabilizes microtubules and weakens E‐cadherin junctions during mitosis. Second, atomic force microscopy reveals that cells harboring these centrosome aberrations display increased stiffness. As a consequence, mitotic cells are pushed out of mosaic epithelia, particularly if they lack centrosome aberrations. We conclude that centrosome aberrations can trigger cell dissemination through a novel, non‐cell‐autonomous mechanism, raising the prospect that centrosome aberrations contribute to the dissemination of metastatic cells harboring normal centrosomes.
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Affiliation(s)
| | | | - Philipp Oertle
- Biozentrum, University of Basel, Basel, Switzerland.,Swiss Nanoscience Institute, University of Basel, Basel, Switzerland
| | - Roderick Yh Lim
- Biozentrum, University of Basel, Basel, Switzerland.,Swiss Nanoscience Institute, University of Basel, Basel, Switzerland
| | - Marija Plodinec
- Biozentrum, University of Basel, Basel, Switzerland.,Swiss Nanoscience Institute, University of Basel, Basel, Switzerland
| | - Erich A Nigg
- Biozentrum, University of Basel, Basel, Switzerland
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94
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Suphatrakul A, Duangchinda T, Jupatanakul N, Prasittisa K, Onnome S, Pengon J, Siridechadilok B. Multi-color fluorescent reporter dengue viruses with improved stability for analysis of a multi-virus infection. PLoS One 2018; 13:e0194399. [PMID: 29547653 PMCID: PMC5856417 DOI: 10.1371/journal.pone.0194399] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Accepted: 03/03/2018] [Indexed: 01/08/2023] Open
Abstract
Reporter virus is a versatile tool to visualize and to analyze virus infections. However, for flaviviruses, it is difficult to maintain the inserted reporter genes on the viral genome, limiting its use in several studies that require homogeneous virus particles and several rounds of virus replication. Here, we showed that flanking inserted GFP genes on both sides with ribosome-skipping 2A sequences improved the stability and the consistency of their fluorescent signals for dengue-virus-serotype 2 (DENV2) reporter viruses. The reporter viruses can infect known susceptible mammalian cell lines and primary CD14+ human monocytes. This design can accommodate several fluorescent protein genes, enabling the generation of multi-color DENV2-16681 reporter viruses with comparable replication capabilities, as demonstrated by their abilities to maintain their fluorescent intensities during co-infections and to exclude superinfections regardless of the fluorescent tags. The reported design of multi-color DENV2 should be useful for high-throughput analyses, single-cell analysis, and characterizations of interference and superinfection in animal models.
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Affiliation(s)
- Amporn Suphatrakul
- National Center for Genetic Engineering and Biotechnology, Klong Luang, Pathumthani, Thailand
| | - Thaneeya Duangchinda
- National Center for Genetic Engineering and Biotechnology, Klong Luang, Pathumthani, Thailand
| | - Natapong Jupatanakul
- National Center for Genetic Engineering and Biotechnology, Klong Luang, Pathumthani, Thailand
| | - Kanjanawadee Prasittisa
- National Center for Genetic Engineering and Biotechnology, Klong Luang, Pathumthani, Thailand
| | - Suppachoke Onnome
- National Center for Genetic Engineering and Biotechnology, Klong Luang, Pathumthani, Thailand
| | - Jutharat Pengon
- National Center for Genetic Engineering and Biotechnology, Klong Luang, Pathumthani, Thailand
| | - Bunpote Siridechadilok
- National Center for Genetic Engineering and Biotechnology, Klong Luang, Pathumthani, Thailand
- * E-mail:
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95
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Sapoznik E, Niu G, Zhou Y, Prim PM, Criswell TL, Soker S. A real-time monitoring platform of myogenesis regulators using double fluorescent labeling. PLoS One 2018; 13:e0192654. [PMID: 29444187 PMCID: PMC5812636 DOI: 10.1371/journal.pone.0192654] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 01/26/2018] [Indexed: 11/18/2022] Open
Abstract
Real-time, quantitative measurement of muscle progenitor cell (myoblast) differentiation is an important tool for skeletal muscle research and identification of drugs that support skeletal muscle regeneration. While most quantitative tools rely on sacrificial approach, we developed a double fluorescent tagging approach, which allows for dynamic monitoring of myoblast differentiation through assessment of fusion index and nuclei count. Fluorescent tagging of both the cell cytoplasm and nucleus enables monitoring of cell fusion and the formation of new myotube fibers, similar to immunostaining results. This labeling approach allowed monitoring the effects of Myf5 overexpression, TNFα, and Wnt agonist on myoblast differentiation. It also enabled testing the effects of surface coating on the fusion levels of scaffold-seeded myoblasts. The double fluorescent labeling of myoblasts is a promising technique to visualize even minor changes in myogenesis of myoblasts in order to support applications such as tissue engineering and drug screening.
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Affiliation(s)
- Etai Sapoznik
- Wake Forest Institute for Regenerative Medicine, Winston Salem, North Carolina, United States of America
| | - Guoguang Niu
- Wake Forest Institute for Regenerative Medicine, Winston Salem, North Carolina, United States of America
| | - Yu Zhou
- Wake Forest Institute for Regenerative Medicine, Winston Salem, North Carolina, United States of America
| | - Peter M. Prim
- Wake Forest Institute for Regenerative Medicine, Winston Salem, North Carolina, United States of America
| | - Tracy L. Criswell
- Wake Forest Institute for Regenerative Medicine, Winston Salem, North Carolina, United States of America
| | - Shay Soker
- Wake Forest Institute for Regenerative Medicine, Winston Salem, North Carolina, United States of America
- * E-mail:
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96
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Ahmad R, Destgeer G, Afzal M, Park J, Ahmed H, Jung JH, Park K, Yoon TS, Sung HJ. Acoustic Wave-Driven Functionalized Particles for Aptamer-Based Target Biomolecule Separation. Anal Chem 2017; 89:13313-13319. [PMID: 29148722 DOI: 10.1021/acs.analchem.7b03474] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
We developed a hybrid microfluidic device that utilized acoustic waves to drive functionalized microparticles inside a continuous flow microchannel and to separate particle-conjugated target proteins from a complex fluid. The acoustofluidic device is composed of an interdigitated transducer that produces high-frequency surface acoustic waves (SAW) and a polydimethylsiloxane (PDMS) microfluidic channel. The SAW interacted with the sample fluid inside the microchannel and deflected particles from their original streamlines to achieve separation. Streptavidin-functionalized polystyrene (PS) microparticles were used to capture aptamer (single-stranded DNA) labeled at one end with a biotin molecule. The free end of the customized aptamer15 (apt15), which was attached to the microparticles via streptavidin-biotin linkage to form the PS-apt15 conjugate, was used to capture the model target protein, thrombin (th), by binding at exosite I to form the PS-apt15-th complex. We demonstrated that the PS-apt15 conjugate selectively captured thrombin molecules in a complex fluid. After the PS-apt15-th complex was formed, the sample fluid was pumped through a PDMS microchannel along with two buffer sheath flows that hydrodynamically focused the sample flow prior to SAW exposure for PS-apt15-th separation from the non-target proteins. We successfully separated thrombin from mCardinal2 and human serum using the proposed acoustofluidic device.
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Affiliation(s)
- Raheel Ahmad
- Department of Mechanical Engineering, KAIST , 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Korea
| | - Ghulam Destgeer
- Department of Mechanical Engineering, KAIST , 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Korea
| | - Muhammad Afzal
- Department of Proteome Structural Biology, KRIBB School of Bioscience, Korea University of Science and Technology , 125 Gwahak-ro Yuseong-gu, Daejeon 34141, Korea
| | - Jinsoo Park
- Department of Mechanical Engineering, KAIST , 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Korea
| | - Husnain Ahmed
- Department of Mechanical Engineering, KAIST , 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Korea
| | - Jin Ho Jung
- Department of Mechanical Engineering, KAIST , 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Korea
| | - Kwangseok Park
- Department of Mechanical Engineering, KAIST , 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Korea
| | - Tae-Sung Yoon
- Department of Proteome Structural Biology, KRIBB School of Bioscience, Korea University of Science and Technology , 125 Gwahak-ro Yuseong-gu, Daejeon 34141, Korea
| | - Hyung Jin Sung
- Department of Mechanical Engineering, KAIST , 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Korea
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97
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Site Specific Modification of Adeno-Associated Virus Enables Both Fluorescent Imaging of Viral Particles and Characterization of the Capsid Interactome. Sci Rep 2017; 7:14766. [PMID: 29116194 PMCID: PMC5676692 DOI: 10.1038/s41598-017-15255-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 10/24/2017] [Indexed: 01/10/2023] Open
Abstract
Adeno-associated viruses (AAVs) are attractive gene therapy vectors due to their low toxicity, high stability, and rare integration into the host genome. Expressing ligands on the viral capsid can re-target AAVs to new cell types, but limited sites have been identified on the capsid that tolerate a peptide insertion. Here, we incorporated a site-specific tetracysteine sequence into the AAV serotype 9 (AAV9) capsid, to permit labelling of viral particles with either a fluorescent dye or biotin. We demonstrate that fluorescently labelled particles are detectable in vitro, and explore the utility of the method in vivo in mice with time-lapse imaging. We exploit the biotinylated viral particles to generate two distinct AAV interactomes, and identify several functional classes of proteins that are highly represented: actin/cytoskeletal protein binding, RNA binding, RNA splicing/processing, chromatin modifying, intracellular trafficking and RNA transport proteins. To examine the biological relevance of the capsid interactome, we modulated the expression of two proteins from the interactomes prior to AAV transduction. Blocking integrin αVβ6 receptor function reduced AAV9 transduction, while reducing histone deacetylase 4 (HDAC4) expression enhanced AAV transduction. Our method demonstrates a strategy for inserting motifs into the AAV capsid without compromising viral titer or infectivity.
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98
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Upadhya R, Lam WC, Maybruck BT, Donlin MJ, Chang AL, Kayode S, Ormerod KL, Fraser JA, Doering TL, Lodge JK. A fluorogenic C. neoformans reporter strain with a robust expression of m-cherry expressed from a safe haven site in the genome. Fungal Genet Biol 2017; 108:13-25. [PMID: 28870457 PMCID: PMC5681388 DOI: 10.1016/j.fgb.2017.08.008] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Revised: 08/30/2017] [Accepted: 08/31/2017] [Indexed: 12/25/2022]
Abstract
C. neoformans is an encapsulated fungal pathogen with defined asexual and sexual life cycles. Due to the availability of genetic and molecular tools for its manipulation, it has become a model organism for studies of fungal pathogens, even though it lacks a reliable system for maintaining DNA fragments as extrachromosomal plasmids. To compensate for this deficiency, we identified a genomic gene-free intergenic region where heterologous DNA could be inserted by homologous recombination without adverse effects on the phenotype of the recipient strain. Since such a site in the C. neoformans genome at a different location has been named previously as "safe haven", we named this locus second safe haven site (SH2). Insertion of DNA into this site in the genome of the KN99 congenic strain pair caused minimal change in the growth of the engineered strain under a variety of in vitro and in vivo conditions. We exploited this 'safe' locus to create a genetically stable highly fluorescent strain expressing mCherry protein (KN99mCH); this strain closely resembled its wild-type parent (KN99α) in growth under a variety of in vitro stress conditions and in the expression of virulence traits. The efficiency of phagocytosis and the proliferation of KN99mCH inside human monocyte-derived macrophages were comparable to those of KN99α, and the engineered strain showed the expected organ dissemination after inoculation, although there was a slight reduction in virulence. The mCherry fluorescence allowed us to measure specific association of cryptococci with leukocytes in the lungs and mediastinal lymph nodes of infected animals and, for the first-time, to assess their live/dead status in vivo. These results highlight the utility of KN99mCH for elucidation of host-pathogen interactions in vivo. Finally, we generated drug-resistant KN99 strains of both mating types that are marked at the SH2 locus with a specific drug resistant gene cassette; these strains will facilitate the generation of mutant strains by mating.
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Affiliation(s)
- Rajendra Upadhya
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Woei C Lam
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Brian T Maybruck
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Maureen J Donlin
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO, USA
| | - Andrew L Chang
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Sarah Kayode
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Kate L Ormerod
- Australian Infectious Diseases Research Centre and School of Chemistry& Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - James A Fraser
- Australian Infectious Diseases Research Centre and School of Chemistry& Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Tamara L Doering
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Jennifer K Lodge
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA.
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99
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Dunsing V, Mayer M, Liebsch F, Multhaup G, Chiantia S. Direct evidence of amyloid precursor-like protein 1 trans interactions in cell-cell adhesion platforms investigated via fluorescence fluctuation spectroscopy. Mol Biol Cell 2017; 28:3609-3620. [PMID: 29021345 PMCID: PMC5706989 DOI: 10.1091/mbc.e17-07-0459] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Revised: 09/13/2017] [Accepted: 10/04/2017] [Indexed: 01/25/2023] Open
Abstract
The amyloid precursor–like protein 1 (APLP1) plays a role in synaptic adhesion and synaptogenesis. In this work, we use quantitative fluorescence microscopy to demonstrate the existence of APLP1–APLP1 trans interaction across cell–cell junctions and propose a model explaining the molecular mechanism driving APLP1 multimerization. The amyloid precursor–like protein 1 (APLP1) is a type I transmembrane protein that plays a role in synaptic adhesion and synaptogenesis. Past investigations indicated that APLP1 is involved in the formation of protein–protein complexes that bridge the junctions between neighboring cells. Nevertheless, APLP1–APLP1 trans interactions have never been directly observed in higher eukaryotic cells. Here, we investigated APLP1 interactions and dynamics directly in living human embryonic kidney cells using fluorescence fluctuation spectroscopy techniques, namely cross-correlation scanning fluorescence correlation spectroscopy and number and brightness analysis. Our results show that APLP1 forms homotypic trans complexes at cell–cell contacts. In the presence of zinc ions, the protein forms macroscopic clusters, exhibiting an even higher degree of trans binding and strongly reduced dynamics. Further evidence from giant plasma membrane vesicles suggests that the presence of an intact cortical cytoskeleton is required for zinc-induced cis multimerization. Subsequently, large adhesion platforms bridging interacting cells are formed through APLP1–APLP1 trans interactions. Taken together, our results provide direct evidence that APLP1 functions as a neuronal zinc-dependent adhesion protein and allow a more detailed understanding of the molecular mechanisms driving the formation of APLP1 adhesion platforms.
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Affiliation(s)
- Valentin Dunsing
- Institute of Biochemistry and Biology, University of Potsdam, 14476 Potsdam, Germany
| | - Magnus Mayer
- Institute of Chemistry and Biochemistry, Free University of Berlin, 14195 Berlin, Germany
| | - Filip Liebsch
- Department of Pharmacology and Therapeutics/Integrated Program in Neuroscience, McGill University, Montreal, QC H3G 1Y63, Canada
| | - Gerhard Multhaup
- Department of Pharmacology and Therapeutics/Integrated Program in Neuroscience, McGill University, Montreal, QC H3G 1Y63, Canada
| | - Salvatore Chiantia
- Institute of Biochemistry and Biology, University of Potsdam, 14476 Potsdam, Germany
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100
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Wegner W, Ilgen P, Gregor C, van Dort J, Mott AC, Steffens H, Willig KI. In vivo mouse and live cell STED microscopy of neuronal actin plasticity using far-red emitting fluorescent proteins. Sci Rep 2017; 7:11781. [PMID: 28924236 PMCID: PMC5603588 DOI: 10.1038/s41598-017-11827-4] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Accepted: 08/30/2017] [Indexed: 12/30/2022] Open
Abstract
The study of proteins in dendritic processes within the living brain is mainly hampered by the diffraction limit of light. STED microscopy is so far the only far-field light microscopy technique to overcome the diffraction limit and resolve dendritic spine plasticity at superresolution (nanoscopy) in the living mouse. After having tested several far-red fluorescent proteins in cell culture we report here STED microscopy of the far-red fluorescent protein mNeptune2, which showed best results for our application to superresolve actin filaments at a resolution of ~80 nm, and to observe morphological changes of actin in the cortex of a living mouse. We illustrate in vivo far-red neuronal actin imaging in the living mouse brain with superresolution for time periods of up to one hour. Actin was visualized by fusing mNeptune2 to the actin labels Lifeact or Actin-Chromobody. We evaluated the concentration dependent influence of both actin labels on the appearance of dendritic spines; spine number was significantly reduced at high expression levels whereas spine morphology was normal at low expression.
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Affiliation(s)
- Waja Wegner
- Optical Nanoscopy in Neuroscience, Center for Nanoscale Microscopy and Molecular Physiology of the Brain, University Medical Center Göttingen, Göttingen, Germany
- Collaborative Research Center 889, University of Göttingen, Göttingen, Germany
- Max Planck Institute of Experimental Medicine, Göttingen, Germany
| | - Peter Ilgen
- Optical Nanoscopy in Neuroscience, Center for Nanoscale Microscopy and Molecular Physiology of the Brain, University Medical Center Göttingen, Göttingen, Germany
- Collaborative Research Center 889, University of Göttingen, Göttingen, Germany
- Max Planck Institute of Experimental Medicine, Göttingen, Germany
| | - Carola Gregor
- Department of NanoBiophotonics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Joris van Dort
- Optical Nanoscopy in Neuroscience, Center for Nanoscale Microscopy and Molecular Physiology of the Brain, University Medical Center Göttingen, Göttingen, Germany
- Max Planck Institute of Experimental Medicine, Göttingen, Germany
| | - Alexander C Mott
- Optical Nanoscopy in Neuroscience, Center for Nanoscale Microscopy and Molecular Physiology of the Brain, University Medical Center Göttingen, Göttingen, Germany
- Max Planck Institute of Experimental Medicine, Göttingen, Germany
| | - Heinz Steffens
- Optical Nanoscopy in Neuroscience, Center for Nanoscale Microscopy and Molecular Physiology of the Brain, University Medical Center Göttingen, Göttingen, Germany
- Collaborative Research Center 889, University of Göttingen, Göttingen, Germany
- Max Planck Institute of Experimental Medicine, Göttingen, Germany
- Department of NanoBiophotonics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Katrin I Willig
- Optical Nanoscopy in Neuroscience, Center for Nanoscale Microscopy and Molecular Physiology of the Brain, University Medical Center Göttingen, Göttingen, Germany.
- Collaborative Research Center 889, University of Göttingen, Göttingen, Germany.
- Max Planck Institute of Experimental Medicine, Göttingen, Germany.
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