A ClearSee-Based Clearing Protocol for 3D Visualization of <i>Arabidopsis thaliana</i> Embryos
Tissue clearing methods combined with confocal microscopy have been widely used for studying developmental biology. In plants, ClearSee is a reliable clearing method that is applicable to a wide range of tissues and is suitable for gene expression analysis using fluorescent reporters, but its applic...
| Main Authors: | , , , , , , |
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| Format: | Article |
| Language: | English |
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MDPI AG
2021-01-01
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| Series: | Plants |
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| Online Access: | https://www.mdpi.com/2223-7747/10/2/190 |
| _version_ | 1827599423686836224 |
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| author | Ayame Imoto Mizuki Yamada Takumi Sakamoto Airi Okuyama Takashi Ishida Shinichiro Sawa Mitsuhiro Aida |
| author_facet | Ayame Imoto Mizuki Yamada Takumi Sakamoto Airi Okuyama Takashi Ishida Shinichiro Sawa Mitsuhiro Aida |
| author_sort | Ayame Imoto |
| collection | DOAJ |
| description | Tissue clearing methods combined with confocal microscopy have been widely used for studying developmental biology. In plants, ClearSee is a reliable clearing method that is applicable to a wide range of tissues and is suitable for gene expression analysis using fluorescent reporters, but its application to the <i>Arabidopsis thaliana</i> embryo, a model system to study morphogenesis and pattern formation, has not been described in the original literature. Here, we describe a ClearSee-based clearing protocol which is suitable for obtaining 3D images of <i>Arabidopsis thaliana</i> embryos. The method consists of embryo dissection, fixation, washing, clearing, and cell wall staining and enables high-quality 3D imaging of embryo morphology and expression of fluorescent reporters with the cellular resolution. Our protocol provides a reliable method that is applicable to the analysis of morphogenesis and gene expression patterns in <i>Arabidopsis thaliana</i> embryos. |
| first_indexed | 2024-03-09T04:13:58Z |
| format | Article |
| id | doaj.art-52c3a48e76b94c3c877101a0b6aa5482 |
| institution | Directory Open Access Journal |
| issn | 2223-7747 |
| language | English |
| last_indexed | 2024-03-09T04:13:58Z |
| publishDate | 2021-01-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Plants |
| spelling | doaj.art-52c3a48e76b94c3c877101a0b6aa54822023-12-03T13:56:50ZengMDPI AGPlants2223-77472021-01-0110219010.3390/plants10020190A ClearSee-Based Clearing Protocol for 3D Visualization of <i>Arabidopsis thaliana</i> EmbryosAyame Imoto0Mizuki Yamada1Takumi Sakamoto2Airi Okuyama3Takashi Ishida4Shinichiro Sawa5Mitsuhiro Aida6Graduate School of Biological Sciences, Nara Institute of Science and Technology (NAIST), 8916-5 Takayama, Nara 630-0192, JapanInternational Research Organization for Advanced Science and Technology (IROAST), Kumamoto University, 2-39-1 Kurokami, Chuo-ku, Kumamoto 860-8555, JapanFaculty of Science, Kumamoto University, 2-39-1 Kurokami, Chuo-ku, Kumamoto 860-8555, JapanFaculty of Science, Kumamoto University, 2-39-1 Kurokami, Chuo-ku, Kumamoto 860-8555, JapanInternational Research Organization for Advanced Science and Technology (IROAST), Kumamoto University, 2-39-1 Kurokami, Chuo-ku, Kumamoto 860-8555, JapanGraduate School of Science and Technology, Kumamoto University, 2-39-1 Kurokami, Chuo-ku, Kumamoto 860-8555, JapanInternational Research Organization for Advanced Science and Technology (IROAST), Kumamoto University, 2-39-1 Kurokami, Chuo-ku, Kumamoto 860-8555, JapanTissue clearing methods combined with confocal microscopy have been widely used for studying developmental biology. In plants, ClearSee is a reliable clearing method that is applicable to a wide range of tissues and is suitable for gene expression analysis using fluorescent reporters, but its application to the <i>Arabidopsis thaliana</i> embryo, a model system to study morphogenesis and pattern formation, has not been described in the original literature. Here, we describe a ClearSee-based clearing protocol which is suitable for obtaining 3D images of <i>Arabidopsis thaliana</i> embryos. The method consists of embryo dissection, fixation, washing, clearing, and cell wall staining and enables high-quality 3D imaging of embryo morphology and expression of fluorescent reporters with the cellular resolution. Our protocol provides a reliable method that is applicable to the analysis of morphogenesis and gene expression patterns in <i>Arabidopsis thaliana</i> embryos.https://www.mdpi.com/2223-7747/10/2/190clearing3D imaging<i>Arabidopsis thaliana</i>embryoconfocal microscopycell wall staining |
| spellingShingle | Ayame Imoto Mizuki Yamada Takumi Sakamoto Airi Okuyama Takashi Ishida Shinichiro Sawa Mitsuhiro Aida A ClearSee-Based Clearing Protocol for 3D Visualization of <i>Arabidopsis thaliana</i> Embryos Plants clearing 3D imaging <i>Arabidopsis thaliana</i> embryo confocal microscopy cell wall staining |
| title | A ClearSee-Based Clearing Protocol for 3D Visualization of <i>Arabidopsis thaliana</i> Embryos |
| title_full | A ClearSee-Based Clearing Protocol for 3D Visualization of <i>Arabidopsis thaliana</i> Embryos |
| title_fullStr | A ClearSee-Based Clearing Protocol for 3D Visualization of <i>Arabidopsis thaliana</i> Embryos |
| title_full_unstemmed | A ClearSee-Based Clearing Protocol for 3D Visualization of <i>Arabidopsis thaliana</i> Embryos |
| title_short | A ClearSee-Based Clearing Protocol for 3D Visualization of <i>Arabidopsis thaliana</i> Embryos |
| title_sort | clearsee based clearing protocol for 3d visualization of i arabidopsis thaliana i embryos |
| topic | clearing 3D imaging <i>Arabidopsis thaliana</i> embryo confocal microscopy cell wall staining |
| url | https://www.mdpi.com/2223-7747/10/2/190 |
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