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Loginov SV, Fermie J, Fokkema J, Agronskaia AV, De Heus C, Blab GA, Klumperman J, Gerritsen HC, Liv N. Correlative Organelle Microscopy: Fluorescence Guided Volume Electron Microscopy of Intracellular Processes. Front Cell Dev Biol 2022; 10:829545. [PMID: 35478966 PMCID: PMC9035751 DOI: 10.3389/fcell.2022.829545] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 03/04/2022] [Indexed: 01/19/2023] Open
Abstract
Intracellular processes depend on a strict spatial and temporal organization of proteins and organelles. Therefore, directly linking molecular to nanoscale ultrastructural information is crucial in understanding cellular physiology. Volume or three-dimensional (3D) correlative light and electron microscopy (volume-CLEM) holds unique potential to explore cellular physiology at high-resolution ultrastructural detail across cell volumes. However, the application of volume-CLEM is hampered by limitations in throughput and 3D correlation efficiency. In order to address these limitations, we describe a novel pipeline for volume-CLEM that provides high-precision (<100 nm) registration between 3D fluorescence microscopy (FM) and 3D electron microscopy (EM) datasets with significantly increased throughput. Using multi-modal fiducial nanoparticles that remain fluorescent in epoxy resins and a 3D confocal fluorescence microscope integrated into a Focused Ion Beam Scanning Electron Microscope (FIB.SEM), our approach uses FM to target extremely small volumes of even single organelles for imaging in volume EM and obviates the need for post-correlation of big 3D datasets. We extend our targeted volume-CLEM approach to include live-cell imaging, adding information on the motility of intracellular membranes selected for volume-CLEM. We demonstrate the power of our approach by targeted imaging of rare and transient contact sites between the endoplasmic reticulum (ER) and lysosomes within hours rather than days. Our data suggest that extensive ER-lysosome and mitochondria-lysosome interactions restrict lysosome motility, highlighting the unique capabilities of our integrated CLEM pipeline for linking molecular dynamic data to high-resolution ultrastructural detail in 3D.
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Affiliation(s)
- Sergey V. Loginov
- Molecular Biophysics, Debye Institute for Nanomaterials Science, Utrecht University, Utrecht, Netherlands
| | - Job Fermie
- Molecular Biophysics, Debye Institute for Nanomaterials Science, Utrecht University, Utrecht, Netherlands
- Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Jantina Fokkema
- Molecular Biophysics, Debye Institute for Nanomaterials Science, Utrecht University, Utrecht, Netherlands
| | - Alexandra V. Agronskaia
- Molecular Biophysics, Debye Institute for Nanomaterials Science, Utrecht University, Utrecht, Netherlands
| | - Cilia De Heus
- Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Gerhard A. Blab
- Molecular Biophysics, Debye Institute for Nanomaterials Science, Utrecht University, Utrecht, Netherlands
| | - Judith Klumperman
- Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Hans C. Gerritsen
- Molecular Biophysics, Debye Institute for Nanomaterials Science, Utrecht University, Utrecht, Netherlands
| | - Nalan Liv
- Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
- *Correspondence: Nalan Liv,
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VAN HEST J, AGRONSKAIA A, FOKKEMA J, MONTANARELLA F, GREGORIO PUIG A, DE MELLO DONEGA C, MEIJERINK A, BLAB G, GERRITSEN H. Towards robust and versatile single nanoparticle fiducial markers for correlative light and electron microscopy. J Microsc 2019; 274:13-22. [PMID: 30648740 PMCID: PMC6849797 DOI: 10.1111/jmi.12778] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 12/18/2018] [Accepted: 12/27/2018] [Indexed: 01/10/2023]
Abstract
Fiducial markers are used in correlated light and electron microscopy (CLEM) to enable accurate overlaying of fluorescence and electron microscopy images. Currently used fiducial markers, e.g. dye-labelled nanoparticles and quantum dots, suffer from irreversible quenching of the luminescence after electron beam exposure. This limits their use in CLEM, since samples have to be studied with light microscopy before the sample can be studied with electron microscopy. Robust fiducial markers, i.e. luminescent labels that can (partially) withstand electron bombardment, are interesting because of the recent development of integrated CLEM microscopes. In addition, nonintegrated CLEM setups may benefit from such fiducial markers. Such markers would allow switching back from EM to LM and are not available yet. Here, we investigate the robustness of various luminescent nanoparticles (NPs) that have good contrast in electron microscopy; 130 nm gold-core rhodamine B-labelled silica particles, 15 nm CdSe/CdS/ZnS core-shell-shell quantum dots (QDs) and 230 nm Y2 O3 :Eu3+ particles. Robustness is studied by measuring the luminescence of (single) NPs after various cycles of electron beam exposure. The gold-core rhodamine B-labelled silica NPs and QDs are quenched after a single exposure to 60 ke- nm-2 with an energy of 120 keV, while Y2 O3 :Eu3+ NPs are robust and still show luminescence after five doses of 60 ke- nm-2 . In addition, the luminescence intensity of Y2 O3 :Eu3+ NPs is investigated as function of electron dose for various electron fluxes. The luminescence intensity initially drops to a constant value well above the single particle detection limit. The intensity loss does not depend on the electron flux, but on the total electron dose. The results indicate that Y2 O3 :Eu3+ NPs are promising as robust fiducial marker in CLEM. LAY DESCRIPTION: Luminescent particles are used as fiducial markers in correlative light and electron microscopy (CLEM) to enable accurate overlaying of fluorescence and electron microscopy images. The currently used fiducial markers, e.g. dyes and quantum dots, loose their luminescence after exposure to the electron beam of the electron microscope. This limits their use in CLEM, since samples have to be studied with light microscopy before the sample can be studied with electron microscopy. Robust fiducial markers, i.e. luminescent labels that can withstand electron exposure, are interesting because of recent developments in integrated CLEM microscopes. Also nonintegrated CLEM setups may benefit from such fiducial markers. Such markers would allow for switching back to fluorescence imaging after the recording of electron microscopy imaging and are not available yet. Here, we investigate the robustness of various luminescent nanoparticles (NPs) that have good contrast in electron microscopy; dye-labelled silica particles, quantum dots and lanthanide-doped inorganic particles. Robustness is studied by measuring the luminescence of (single) NPs after various cycles of electron beam exposure. The dye-labelled silica NPs and QDs are quenched after a single exposure to 60 ke- nm-2 with an energy of 120 keV, while lanthanide-doped inorganic NPs are robust and still show luminescence after five doses of 60 ke- nm-2 . In addition, the luminescence intensity of lanthanide-doped inorganic NPs is investigated as function of electron dose for various electron fluxes. The luminescence intensity initially drops to a constant value well above the single particle detection limit. The intensity loss does not depend on the electron flux, but on the total electron dose. The results indicate that lanthanide-doped NPs are promising as robust fiducial marker in CLEM.
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Affiliation(s)
- J.J.H.A. VAN HEST
- Condensed Matter and Interfaces, Debye Institute for Nanomaterials ScienceUtrecht UniversityUtrechtThe Netherlands
- Molecular Biophysics, Debye Institute for Nanomaterials ScienceUtrecht UniversityUtrechtThe Netherlands
| | - A.V. AGRONSKAIA
- Molecular Biophysics, Debye Institute for Nanomaterials ScienceUtrecht UniversityUtrechtThe Netherlands
| | - J. FOKKEMA
- Molecular Biophysics, Debye Institute for Nanomaterials ScienceUtrecht UniversityUtrechtThe Netherlands
| | - F. MONTANARELLA
- Condensed Matter and Interfaces, Debye Institute for Nanomaterials ScienceUtrecht UniversityUtrechtThe Netherlands
- Soft Condensed Matter, Debye Institute for Nanomaterials ScienceUtrecht UniversityUtrechtThe Netherlands
| | - A. GREGORIO PUIG
- Condensed Matter and Interfaces, Debye Institute for Nanomaterials ScienceUtrecht UniversityUtrechtThe Netherlands
| | - C. DE MELLO DONEGA
- Condensed Matter and Interfaces, Debye Institute for Nanomaterials ScienceUtrecht UniversityUtrechtThe Netherlands
| | - A. MEIJERINK
- Condensed Matter and Interfaces, Debye Institute for Nanomaterials ScienceUtrecht UniversityUtrechtThe Netherlands
| | - G.A. BLAB
- Molecular Biophysics, Debye Institute for Nanomaterials ScienceUtrecht UniversityUtrechtThe Netherlands
| | - H.C. GERRITSEN
- Molecular Biophysics, Debye Institute for Nanomaterials ScienceUtrecht UniversityUtrechtThe Netherlands
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Quantitative morphometric analysis of adult teleost fish by X-ray computed tomography. Sci Rep 2018; 8:16531. [PMID: 30410001 PMCID: PMC6224569 DOI: 10.1038/s41598-018-34848-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 10/22/2018] [Indexed: 12/11/2022] Open
Abstract
Vertebrate models provide indispensable paradigms to study development and disease. Their analysis requires a quantitative morphometric study of the body, organs and tissues. This is often impeded by pigmentation and sample size. X-ray micro-computed tomography (micro-CT) allows high-resolution volumetric tissue analysis, largely independent of sample size and transparency to visual light. Importantly, micro-CT data are inherently quantitative. We report a complete pipeline of high-throughput 3D data acquisition and image analysis, including tissue preparation and contrast enhancement for micro-CT imaging down to cellular resolution, automated data processing and organ or tissue segmentation that is applicable to comparative 3D morphometrics of small vertebrates. Applied to medaka fish, we first create an annotated anatomical atlas of the entire body, including inner organs as a quantitative morphological description of an adult individual. This atlas serves as a reference model for comparative studies. Using isogenic medaka strains we show that comparative 3D morphometrics of individuals permits identification of quantitative strain-specific traits. Thus, our pipeline enables high resolution morphological analysis as a basis for genotype-phenotype association studies of complex genetic traits in vertebrates.
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ColorEM: analytical electron microscopy for element-guided identification and imaging of the building blocks of life. Histochem Cell Biol 2018; 150:509-520. [PMID: 30120552 PMCID: PMC6182685 DOI: 10.1007/s00418-018-1707-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/06/2018] [Indexed: 12/22/2022]
Abstract
Nanometer-scale identification of multiple targets is crucial to understand how biomolecules regulate life. Markers, or probes, of specific biomolecules help to visualize and to identify. Electron microscopy (EM), the highest resolution imaging modality, provides ultrastructural information where several subcellular structures can be readily identified. For precise tagging of (macro)molecules, electron-dense probes, distinguishable in gray-scale EM, are being used. However, practically these genetically-encoded or immune-targeted probes are limited to three targets. In correlated microscopy, fluorescent signals are overlaid on the EM image, but typically without the nanometer-scale resolution and limited to visualization of few targets. Recently, analytical methods have become more sensitive, which has led to a renewed interest to explore these for imaging of elements and molecules in cells and tissues in EM. Here, we present the current state of nanoscale imaging of cells and tissues using energy dispersive X-ray analysis (EDX), electron energy loss spectroscopy (EELS), cathodoluminescence (CL), and touch upon secondary ion mass spectroscopy at the nanoscale (NanoSIMS). ColorEM is the term encompassing these analytical techniques the results of which are then displayed as false-color at the EM scale. We highlight how ColorEM will become a strong analytical nano-imaging tool in life science microscopy.
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Garming MWH, Weppelman IGC, de Boer P, Martínez FP, Schirhagl R, Hoogenboom JP, Moerland RJ. Nanoparticle discrimination based on wavelength and lifetime-multiplexed cathodoluminescence microscopy. NANOSCALE 2017; 9:12727-12734. [PMID: 28829093 DOI: 10.1039/c7nr00927e] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Nanomaterials can be identified in high-resolution electron microscopy images using spectrally-selective cathodoluminescence. Capabilities for multiplex detection can however be limited, e.g., due to spectral overlap or availability of filters. Also, the available photon flux may be limited due to degradation under electron irradiation. Here, we demonstrate single-pass cathodoluminescence-lifetime based discrimination of different nanoparticles, using a pulsed electron beam. We also show that cathodoluminescence lifetime is a robust parameter even when the nanoparticle cathodoluminescence intensity decays over an order of magnitude. We create lifetime maps, where the lifetime of the cathodoluminescence emission is correlated with the emission intensity and secondary-electron images. The consistency of lifetime-based discrimination is verified by also correlating the emission wavelength and the lifetime of nanoparticles. Our results show how cathodoluminescence lifetime provides an additional channel of information in electron microscopy.
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Affiliation(s)
- Mathijs W H Garming
- Delft University of Technology, Lorentzweg 1, NL-2628CJ Delft, The Netherlands.
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Hemelaar SR, de Boer P, Chipaux M, Zuidema W, Hamoh T, Martinez FP, Nagl A, Hoogenboom JP, Giepmans BNG, Schirhagl R. Nanodiamonds as multi-purpose labels for microscopy. Sci Rep 2017; 7:720. [PMID: 28389652 PMCID: PMC5429637 DOI: 10.1038/s41598-017-00797-2] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Accepted: 03/13/2017] [Indexed: 11/09/2022] Open
Abstract
Nanodiamonds containing fluorescent nitrogen-vacancy centers are increasingly attracting interest for use as a probe in biological microscopy. This interest stems from (i) strong resistance to photobleaching allowing prolonged fluorescence observation times; (ii) the possibility to excite fluorescence using a focused electron beam (cathodoluminescence; CL) for high-resolution localization; and (iii) the potential use for nanoscale sensing. For all these schemes, the development of versatile molecular labeling using relatively small diamonds is essential. Here, we show the direct targeting of a biological molecule with nanodiamonds as small as 70 nm using a streptavidin conjugation and standard antibody labelling approach. We also show internalization of 40 nm sized nanodiamonds. The fluorescence from the nanodiamonds survives osmium-fixation and plastic embedding making them suited for correlative light and electron microscopy. We show that CL can be observed from epon-embedded nanodiamonds, while surface-exposed nanoparticles also stand out in secondary electron (SE) signal due to the exceptionally high diamond SE yield. Finally, we demonstrate the magnetic read-out using fluorescence from diamonds prior to embedding. Thus, our results firmly establish nanodiamonds containing nitrogen-vacancy centers as unique, versatile probes for combining and correlating different types of microscopy, from fluorescence imaging and magnetometry to ultrastructural investigation using electron microscopy.
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Affiliation(s)
- S R Hemelaar
- Groningen University, University Medical Center Groningen, Department of Biomedical Engineering, Antonius Deusinglaan 1, 9713, AW, Groningen, The Netherlands
| | - P de Boer
- Groningen University, University Medical Center Groningen, Department of Cell Biology, Antonius Deusinglaan 1, 9713, AW, Groningen, The Netherlands
| | - M Chipaux
- Groningen University, University Medical Center Groningen, Department of Biomedical Engineering, Antonius Deusinglaan 1, 9713, AW, Groningen, The Netherlands
| | - W Zuidema
- Delft University of Technology, Dept. Imaging Physics, Lorentzweg 1, 2628, CJ, Delft, The Netherlands
| | - T Hamoh
- Groningen University, University Medical Center Groningen, Department of Biomedical Engineering, Antonius Deusinglaan 1, 9713, AW, Groningen, The Netherlands
| | - F Perona Martinez
- Groningen University, University Medical Center Groningen, Department of Biomedical Engineering, Antonius Deusinglaan 1, 9713, AW, Groningen, The Netherlands
| | - A Nagl
- Groningen University, University Medical Center Groningen, Department of Biomedical Engineering, Antonius Deusinglaan 1, 9713, AW, Groningen, The Netherlands
| | - J P Hoogenboom
- Delft University of Technology, Dept. Imaging Physics, Lorentzweg 1, 2628, CJ, Delft, The Netherlands
| | - B N G Giepmans
- Groningen University, University Medical Center Groningen, Department of Cell Biology, Antonius Deusinglaan 1, 9713, AW, Groningen, The Netherlands
| | - R Schirhagl
- Groningen University, University Medical Center Groningen, Department of Biomedical Engineering, Antonius Deusinglaan 1, 9713, AW, Groningen, The Netherlands.
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Niioka H, Yamasaki J, Dung DTK, Miyake J. Enhancement of Near-infrared Luminescence of Y2O3:Ln, Yb (Ln = Tm, Ho, Er) by Li-ion Doping for Cellular Bioimaging. CHEM LETT 2016. [DOI: 10.1246/cl.160754] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Thi Kim Dung D, Fukushima S, Furukawa T, Niioka H, Sannomiya T, Kobayashi K, Yukawa H, Baba Y, Hashimoto M, Miyake J. Multispectral Emissions of Lanthanide-Doped Gadolinium Oxide Nanophosphors for Cathodoluminescence and Near-Infrared Upconversion/Downconversion Imaging. NANOMATERIALS (BASEL, SWITZERLAND) 2016; 6:E163. [PMID: 28335291 PMCID: PMC5224635 DOI: 10.3390/nano6090163] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Revised: 08/16/2016] [Accepted: 08/18/2016] [Indexed: 01/30/2023]
Abstract
Comprehensive imaging of a biological individual can be achieved by utilizing the variation in spatial resolution, the scale of cathodoluminescence (CL), and near-infrared (NIR), as favored by imaging probe Gd₂O₃ co-doped lanthanide nanophosphors (NPPs). A series of Gd₂O₃:Ln3+/Yb3+ (Ln3+: Tm3+, Ho3+, Er3+) NPPs with multispectral emission are prepared by the sol-gel method. The NPPs show a wide range of emissions spanning from the visible to the NIR region under 980 nm excitation. The dependence of the upconverting (UC)/downconverting (DC) emission intensity on the dopant ratio is investigated. The optimum ratios of dopants obtained for emissions in the NIR regions at 810 nm, 1200 nm, and 1530 nm are applied to produce nanoparticles by the homogeneous precipitation (HP) method. The nanoparticles produced from the HP method are used to investigate the dual NIR and CL imaging modalities. The results indicate the possibility of using Gd₂O₃ co-doped Ln3+/Yb3+ (Ln3+: Tm3+, Ho3+, Er3+) in correlation with NIR and CL imaging. The use of Gd₂O₃ promises an extension of the object dimension to the whole-body level by employing magnetic resonance imaging (MRI).
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Affiliation(s)
- Doan Thi Kim Dung
- Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan.
| | - Shoichiro Fukushima
- Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan.
| | - Taichi Furukawa
- Institute for NanoScience Design, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan.
| | - Hirohiko Niioka
- Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan.
| | - Takumi Sannomiya
- Department of Innovative and Engineered Materials, Tokyo Institute of Technology, 4259 Nagatsuta, Yokohama, Kanagawa 226-8503, Japan.
| | - Kaori Kobayashi
- Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan.
| | - Hiroshi Yukawa
- Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan.
- ImPACT Research Center for Advanced Nanobiodevices, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan.
| | - Yoshinobu Baba
- Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan.
- ImPACT Research Center for Advanced Nanobiodevices, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan.
- Health Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2217-14, Hayashi-cho, Takamatsu 761-0395, Japan.
| | - Mamoru Hashimoto
- Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan.
| | - Jun Miyake
- Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan.
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Nagayama K, Onuma T, Ueno R, Tamehiro K, Minoda H. Cathodoluminescence and Electron-Induced Fluorescence Enhancement of Enhanced Green Fluorescent Protein. J Phys Chem B 2016; 120:1169-74. [DOI: 10.1021/acs.jpcb.5b08138] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Kuniaki Nagayama
- National Institute for Physiological Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Japan
| | - Tsubasa Onuma
- Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo, Japan
| | - Ryosuke Ueno
- Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo, Japan
| | - Katsuyuki Tamehiro
- Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo, Japan
| | - Hiroki Minoda
- Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo, Japan
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