Article
Biochemical Research Methods
Hendrik A. Messal, Jorge Almagro, May Zaw Thin, Antonio Tedeschi, Alessandro Ciccarelli, Laura Blackie, Kurt I. Anderson, Irene Miguel-Aliaga, Jacco van Rheenen, Axel Behrens
Summary: The FLASH technique is a quick and customizable method for molecular phenotyping of intact tissue volumes. It enables detection of a multitude of antigens in whole mouse organs and embryos, human biopsies, organoids, and Drosophila. FLASH allows for epithelial marker retrieval and immunolabeling, and preserves sample architecture for subsequent histopathological analysis.
Article
Multidisciplinary Sciences
G. Allan Johnson, Yuqi Tian, David G. Ashbrook, Gary P. Cofer, James J. Cook, James C. Gee, Adam Hall, Kathryn Hornburg, Catherine C. Kaczorowski, Yi Qi, Fang-Cheng Yeh, Nian Wang, Leonard E. White, Robert W. Williams
Summary: We have developed workflows to align 3D magnetic resonance histology (MRH) of the mouse brain with light sheet microscopy (LSM) and 3D delineations of the same specimen. The result is a high-dimensional integrated volume with registration (HiDiver) with alignment precision better than 50 μm. HiDiver is being used in quantitative studies of the impact of gene variants and aging on mouse brain cytoarchitecture and connectomics.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Developmental Biology
Alba Vieites-Prado, Nicolas Renier
Summary: Tissue clearing technology enhances the transparency of late developmental stages and enables deep imaging in fixed organisms. Successful implementation of these techniques requires a good understanding of sample processing, imaging, and the possibilities offered by image analysis.
Article
Cell Biology
Simona Machacova, Helena Chmelova, Anna Vavrova, Zbynek Kozmik, Iryna Kozmikova
Summary: Cephalochordates serve as representatives of the most basally divergent group of the chordate phylum, offering crucial insights into vertebrate evolution. In evolutionary developmental research, the combination of light sheet microscopy and tissue clearing methods allows for visualization of anatomical structures and individual cells of amphioxus in 3D space.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Cell Biology
Xiaojun Wang, Hanqing Xiong, Yurong Liu, Tao Yang, Anan Li, Fei Huang, Fangfang Yin, Lei Su, Ling Liu, Ning Li, Longhui Li, Shenghua Cheng, Xiaoxiang Liu, Xiaohua Lv, Xiuli Liu, Jun Chu, Tonghui Xu, Fuqiang Xu, Hui Gong, Qingming Luo, Jing Yuan, Shaoqun Zeng
Summary: CSFT technique utilizing chemical switching of fluorescent proteins enables high-resolution imaging of brain structures for studying neuron connections and cellular compositions. It also allows quantitative acquisition at the single-neuron level.
Review
Medicine, Research & Experimental
Xiaohan Liang, Haiming Luo
Summary: Tissue optical clearing technology has rapidly developed in the past decade, allowing observation at single-cell resolution and the ultimate goal of making intact primate and human brains optically transparent. By combining optical clearance with large-volume tissue labeling technology, it is possible to preserve anatomical structure and visualize multiple molecular information from intact samples in situ.
Article
Neurosciences
Henriette Rusch, Malte Brammerloh, Jens Stieler, Mandy Sonntag, Siawoosh Mohammadi, Nikolaus Weiskopf, Thomas Arendt, Evgeniya Kirilina, Markus Morawski
Summary: The accessibility of new wide-scale multimodal imaging techniques has led to the emergence of numerous tissue clearing techniques. This study compares seven different tissue clearing approaches for aged human brain tissue blocks (>5 mm) to identify the most practical and efficient method. The results show that combining the CLARITY or iDISCO techniques with specific imaging setups is the best approach for clearing aged human brain tissue and generating 3D microscopic images.
Article
Polymer Science
Alexander Richardson, Sandra Fok, Victoria Lee, Kerry-Anne Rye, Nick Di Girolamo, Blake J. Cochran
Summary: Advances in tissue clearing and light sheet fluorescence microscopy have improved our understanding of tissue morphology and disease pathology without the need for histological sectioning. This study addresses the challenges of sample handling and preservation during staining and imaging protocols by synthesizing hydrogels with a high-water content and refractive index matching typical clearing solutions. The hydrogels proved to be stable and allowed for successful imaging of cleared mouse tissues and embryos.
Article
Biochemistry & Molecular Biology
Akos Diosdi, Dominik Hirling, Maria Kovacs, Timea Toth, Maria Harmati, Krisztian Koos, Krisztina Buzas, Filippo Piccinini, Peter Horvath
Summary: 3D multicellular spheroids are used as in vitro models to better represent the in vivo tumor environment, but current microscopy technologies face difficulties visualizing individual cells in deeper layers due to limited light penetration and scattering. Various optical clearing methods have been proposed, but a lack of a gold standard metric remains an open issue. A guideline for 3D light microscopy imaging is introduced, including a validation experiment, comparison of quality metrics, and a large dataset for testing, aiming to find a promising quality metric applicable for comparing optical clearing protocols.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2021)
Article
Cell Biology
Etsuo A. Susaki, Minoru Takasato
Summary: Organoids, developed from stem cells, exhibit a miniaturized 3D structure and part of the functions of original organs, replacing real organs for various research purposes. Recent tissue clearing and 3D imaging techniques allow for comprehensive analysis and examination of organoids, enhancing their utility in basic biology and clinical applications such as organoid production and drug screening.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Biochemical Research Methods
Ruiyao Cai, Zeynep Ilgin Kolabas, Chenchen Pan, Hongcheng Mai, Shan Zhao, Doris Kaltenecker, Fabian F. Voigt, Muge Molbay, Tzu-lun Ohn, Cecile Vincke, Mihail I. Todorov, Fritjof Helmchen, Jo A. Van Ginderachter, Ali Ertuerk
Summary: A nanobody-based immunolabeling and clearing method is reported, which renders a whole mouse transparent in 3 weeks and enhances the signal of fluorescent proteins. This method allows the analysis of fluorescent signal in intact rodents at cellular resolution and enables the study of whole-body phenomena and connectivity.
Article
Medicine, Research & Experimental
Dominik Schneidereit, Anita Broellochs, Paul Ritter, Lucas Kreiss, Zeinab Mokhtari, Andreas Beilhack, Gerhard Kroenke, Jochen A. Ackermann, Maria Faas, Anika Grueneboom, Sebastian Schuermann, Oliver Friedrich
Summary: Structural remodeling or damage in tissues is often unevenly distributed depending on the location and extent of damaging stimuli. By optimizing different clearing protocols, aqueous solution-based protocols using 2,2'-thiodiethanol (TDE) were found to be advantageous in preserving muscle morphology. Applying TDE clearing allows for the assessment of muscle fiber integrity in 3D and quantification of muscle necrosis.
Article
Physiology
Ali M. Elagoz, Ruth Styfhals, Sofia Maccuro, Luca Masin, Lieve Moons, Eve Seuntjens
Summary: Gene expression analysis is crucial for understanding the function of key factors during embryonic development, and combining immunohistochemistry with tissue clearing technologies allows for more comprehensive observation of gene expression. Three-dimensional reconstruction reveals additional spatial organization that may not be discovered using traditional two-dimensional methods.
FRONTIERS IN PHYSIOLOGY
(2022)
Review
Neurosciences
Hannah C. Bennett, Yongsoo Kim
Summary: This article highlights advances in high-resolution 3D mapping methods for studying the cerebrovascular network and neurovascular unit (NVU) in the mouse brain. The use of block-face imaging and light sheet fluorescent microscopy has enabled researchers to examine the anatomical arrangement of the cerebrovascular network and gain biological insights. These imaging techniques have the potential to advance our understanding of brain disorders and overall brain health.
Article
Multidisciplinary Sciences
Jiongfang Xie, Ruili Feng, Yanlu Chen, Liang Gao
Summary: This study provides a comprehensive 3D view of five descending tracts from the midbrain, hindbrain, and cerebellum to the mouse spinal cord. Notable features of these tracts and their axonal morphologies were identified, and monosynaptic connections between the tracts and spinal motor neurons were investigated using a novel tissue expansion method. This study contributes to a better understanding of the projection patterns and anatomical features of descending tracts in the mouse spinal cord.
SCIENTIFIC REPORTS
(2023)
Article
Multidisciplinary Sciences
Hiroto Q. Yamaguchi, Koji L. Ode, Hiroki R. Ueda
Summary: By modeling reversible phosphorylation dynamics, it was found that a reaction system composed of a set of kinases and phosphatases and two substrates with two modification sites can exhibit chaos behavior, suggesting the existence of a design principle for autonomous chaos generation.
Editorial Material
Biochemistry & Molecular Biology
Rikuhiro G. Yamada, Hiroki R. Ueda
Summary: Intestinal organoids possess species-specific circadian clocks similar to their respective in vivo context, making them promising platforms for studying circadian medicine.
Article
Biology
Yoichi Minami, Yufei Yuan, Hiroki R. Ueda
Summary: Animal models are crucial for biological experiments, but increasing the throughput of such experiments has been a challenge. Traditional high-throughput methods faced barriers, while new genetics techniques have the potential to enhance efficiency and speed up gene identification.
JOURNAL OF BIOLOGICAL RHYTHMS
(2022)
Article
Multidisciplinary Sciences
Koji L. Ode, Shoi Shi, Machiko Katori, Kentaro Mitsui, Shin Takanashi, Ryo Oguchi, Daisuke Aoki, Hiroki R. Ueda
Summary: An algorithm named ACCEL was developed to classify sleep and wake episodes using raw accelerometer data, achieving high sensitivity and specificity in sleep-wake classification. The algorithm also successfully recorded periodic activities consistent with pulse waves.
Article
Biochemistry & Molecular Biology
Haruka Chino, Akinori Yamasaki, Koji L. Ode, Hiroki R. Ueda, Nobuo N. Noda, Noboru Mizushima
Summary: This study reveals the critical role of LIR phosphorylation in the interaction, localization, and initiation of autophagy of the ER-phagy receptor TEX264 with ATG8. Structural analysis shows that phosphorylation increases binding affinity by generating multiple hydrogen bonds with ATG8, which cannot be mimicked by acidic residues. This finding highlights the importance of LIR phosphorylation in LIR-ATG8 interactions.
Article
Biochemical Research Methods
Adam K. Glaser, Kevin W. Bishop, Lindsey A. Barner, Etsuo A. Susaki, Shimpei I. Kubota, Gan Gao, Robert B. Serafin, Pooja Balaram, Emily Turschak, Philip R. Nicovich, Hoyin Lai, Luciano A. G. Lucas, Yating Yi, Eva K. Nichols, Hongyi Huang, Nicholas P. Reder, Jasmine J. Wilson, Ramya Sivakumar, Elya Shamskhou, Caleb R. Stoltzfus, Xing Wei, Andrew K. Hempton, Marko Pende, Prayag Murawala, Hans-Ulrich Dodt, Takato Imaizumi, Jay Shendure, Brian J. Beliveau, Michael Y. Gerner, Li Xin, Hu Zhao, Lawrence D. True, R. Clay Reid, Jayaram Chandrashekar, Hiroki R. Ueda, Karel Svoboda, Jonathan T. C. Liu
Summary: This article introduces a flexible hybrid light-sheet microscope system that can meet the requirements of different imaging applications, including resolution, sample size, and transparent sample holder material. Experimental results demonstrate that the system can efficiently image sparse axons and perform high-throughput automated imaging of multiple specimens.
Article
Multidisciplinary Sciences
Machiko Katori, Shoi Shi, Koji L. Ode, Yasuhiro Tomita, Hiroki R. Ueda
Summary: By analyzing a large-scale dataset of human sleep phenotypes, we identified 16 sleep phenotypes, including social jet lag, chronotypes (morning/night person), and seven different insomnia-like phenotypes. These analyses contribute to the advancement of research on genetic and environmental factors underlying human sleep patterns, and offer potential for the development of digital biomarkers for psychiatric disorders.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Multidisciplinary Sciences
Tetsuya Yamada, Shoi Shi, Hiroki R. Ueda
Summary: Neural oscillations are regulated by molecular mechanisms and network connectivity of neurons. Recent research has found that slowly inactivating potassium channels play a crucial role in the firing pattern of spindle oscillations, while leak sodium and potassium channels competitively regulate the base value and time constant of spindle oscillations.
Article
Gastroenterology & Hepatology
Satoshi Nojima, Shoichi Ishida, Kei Terayama, Katsuhiko Matsumoto, Takahiro Matsui, Shinichiro Tahara, Kenji Ohshima, Hiroki Kiyokawa, Kansuke Kido, Koto Ukon, Shota Y. Yoshida, Tomoki T. Mitani, Yuichiro Doki, Tsunekazu Mizushima, Yasushi Okuno, Etsuo A. Susaki, Hiroki R. Ueda, Eiichi Morii
Summary: This study developed a novel fluorescence staining method and a three-dimensional imaging system based on it, which enabled clear and detailed imaging of the three-dimensional architecture of crypts in human colorectal mucosa. The imaging method also identified abnormal changes in crypts and the distribution of neutrophils in inflammatory bowel diseases. Quantitative analysis of crypts based on three-dimensional morphologic changes allowed for differential diagnosis of ulcerative colitis, Crohn's disease, and non-inflammatory bowel disease, surpassing the capabilities of pathologists. Additionally, a deep learning-based system using the three-dimensional imaging could accurately distinguish these diseases.
CELLULAR AND MOLECULAR GASTROENTEROLOGY AND HEPATOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Jun-ichi Sakamaki, Koji L. Ode, Yoshitaka Kurikawa, Hiroki R. Ueda, Hayashi Yamamoto, Noboru Mizushima
Summary: This study reveals that ubiquitin family proteins can conjugate to phospholipids, not only ATG8. This conjugation mainly occurs in endosomes and vacuoles and increases during starvation. In vitro experiments also demonstrate that liposomes containing ubiquitin-phospholipid can recruit specific protein components.
Article
Multidisciplinary Sciences
Kei Takahashi, Ko Abe, Shimpei Kubota, Noriaki Fukatsu, Yasuyuki Morishita, Yasuhiro Yoshimatsu, Satoshi Hirakawa, Yoshiaki Kubota, Tetsuro Watabe, Shogo Ehata, Hiroki R. Ueda, Teppei Shimamura, Kohei Miyazono
Summary: Understanding blood and lymphatic vasculature networks is currently limited by imaging and quantification limitations. This study presents the use of CUBIC for generating 3D images and extracting geometric features to evaluate the structural difference of vasculatures. The results demonstrate the utility of CUBIC as an analysis modality for vascular structures.
NATURE COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Daisuke Tone, Koji L. Ode, Qianhui Zhang, Hiroshi Fujishima, Rikuhiro G. Yamada, Yoshiki Nagashima, Katsuhiko Matsumoto, Zhiqing Wen, Shota Y. Yoshida, Tomoki T. Mitani, Yuki Arisato, Rei-ichiro Ohno, Maki Ukai-Tadenuma, Junko Yoshida Garcon, Mari Kaneko, Shoi Shi, Hideki Ukai, Kazunari Miyamichi, Takashi Okada, Kenta Sumiyama, Hiroshi Kiyonari, Hiroki R. Ueda
Summary: This study reveals the important role of CaMKII beta kinase in sleep regulation. Activation or inhibition of this kinase can increase or decrease the duration of sleep in mice. Furthermore, the phosphorylation states of CaMKII beta differently control sleep induction and maintenance processes.
Article
Cell Biology
Shunsuke Ishii, Haruka Chino, Koji L. Ode, Yoshitaka Kurikawa, Hiroki R. Ueda, Akira Matsuura, Noboru Mizushima, Eisuke Itakura
Summary: The endoplasmic reticulum (ER) is a crucial cellular compartment for protein-related processes. ER-phagy is a mechanism that removes abnormal proteins to maintain cellular homeostasis. The identification of CCPG1 as an ER-phagy receptor sheds light on the recognition of ER luminal proteins by the ER-phagy machinery.
MOLECULAR BIOLOGY OF THE CELL
(2023)
Review
Neurosciences
Yuyang Wang, Yoichi Minami, Koji L. Ode, Hiroki R. Ueda
Summary: Sleep is a conserved phenotype shared by most animals. Prolonged wakefulness leads to increased sleep need or pressure. Recent studies have found that Ca2+ signaling may play a role in sleep regulation. Significant changes in sleep phenotype have been observed through calcium-related channels, receptors, and pumps. Mathematical modeling suggests that these molecules contribute to a Ca2+-dependent hyperpolarization mechanism, which may trigger and maintain sleep through the activation of CaMKII.
FRONTIERS IN SYSTEMS NEUROSCIENCE
(2022)
Review
Neurosciences
Brian Dean, Geor Bakker, Hiroki R. Ueda, Andrew B. Tobin, Alastair Brown, Richard A. A. Kanaan
Summary: Pre-clinical models, postmortem and neuroimaging studies all suggest that muscarinic receptors are involved in the molecular pathology of schizophrenia. Clinical trials have shown that activating central muscarinic M1 and M4 receptors can reduce the severity of symptoms. This review discusses the growing evidence for the critical roles of muscarinic M1 and M4 receptors in CNS functions and their implication in schizophrenia.
FRONTIERS IN CELLULAR NEUROSCIENCE
(2023)
