Article
Chemistry, Multidisciplinary
Dusan Kolarski, Simon Miller, Tsuyoshi Oshima, Yoshiko Nagai, Yugo Aoki, Piermichele Kobauri, Ashutosh Srivastava, Akiko Sugiyama, Kazuma Amaike, Ayato Sato, Florence Tama, Wiktor Szymanski, Ben L. Feringa, Kenichiro Itami, Tsuyoshi Hirota
Summary: CRY1 and CRY2 proteins are essential components of the circadian clock. Developing CRY1-selective compounds that can be manipulated through light-dependent mechanisms allows for a better understanding of the specific functions of CRY1 and CRY2. By utilizing benzophenone derivatives to interact with the photo lyase region of CRY1, researchers were able to activate CRY1 without affecting CRY2, demonstrating a potential for spatiotemporal regulation of CRY1 activity for health and disease research.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2021)
Article
Genetics & Heredity
Yaling Wu, Haijiao Zhao, Eric Erquan Zhang, Na Liu
Summary: PCBP1 is a novel clock modifier that negatively regulates the activation of the clock by enhancing the association of CRY1 with the CLOCK/BMAL1 complex.
FRONTIERS IN GENETICS
(2021)
Article
Multidisciplinary Sciences
Serena Riccitelli, Fabio Boi, Davide Lonardoni, Lidia Giantomasi, Olga Barca-Mayo, Davide De Pietri Tonelli, Silvia Bisti, Stefano Di Marco, Luca Berdondini
Summary: Clock genes in glial cells play an important role in regulating visual information processing in the retina, affecting retinal physiology and the activity of retinal ganglion cells in a circadian manner.
SCIENTIFIC REPORTS
(2022)
Article
Neurosciences
Fabrics Bertile, Marine Plumel, Pauline Maes, Aurelie Hirschler, Etienne Challet
Summary: The study identified day-night variations in the cerebellar proteome of mice fed during daytime or nighttime, showing changes in proteins related to heat-shock proteins, enzymes, and neuronal activity in daytime food-restricted mice. Additionally, a significant feeding x time-of-day interaction was found for changes in the intensity of 20 spots.
FRONTIERS IN MOLECULAR NEUROSCIENCE
(2021)
Review
Cell Biology
Jonathan S. Yi, Nicolas M. Diaz, Shane D'Souza, Ethan D. Buhr
Summary: Most organisms have self-sustained circadian clocks that can be synchronized by environmental stimuli or oscillate indefinitely. In mammals, this is true at the molecular level for most cell types, with a core set of clock genes forming a transcriptional/translational feedback loop (TTFL) with a 24-hour period. The TTFL mechanism varies slightly in different cell types, but all involve similar core clock genes. The clock has unique outputs in different tissues, as cells convert the TTFL timing signals into orchestrated transcriptional oscillations of clock-controlled genes and cellular processes.
SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY
(2022)
Article
Multidisciplinary Sciences
Xuemei Cao, Yanyan Yang, Christopher P. Selby, Zhenxing Liu, Aziz Sancar
Summary: The mammalian circadian clock is regulated by a transcription-translation feedback loop involving CLOCK-BMAL1 activators and CRY-PER repressors. Previous studies have shown that CRY and CRY-PER inhibit CLOCK-BMAL1 in different mechanisms. This study reveals the involvement of CRY-PER in displacing CLOCK-BMAL1 by recruiting CK1 delta, leading to the dissociation of CLOCK-BMAL1 from the E-box.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Endocrinology & Metabolism
Jeanne F. Duffy, Wei Wang, Joseph M. Ronda, Charles A. Czeisler
Summary: Aging is associated with changes in sleep, and improving sleep can have important consequences for the health and quality of life of older adults. Melatonin, especially at higher doses, may be a viable option for sleep aid in older adults, as it can increase sleep efficiency during both the day and night.
JOURNAL OF PINEAL RESEARCH
(2022)
Article
Multidisciplinary Sciences
Altar Sorkac, Yiannis A. Savva, Doruk Savas, Mustafa Talay, Gilad Barnea
Summary: Through experiments involving neuronal inhibition and selective neuronal activation, researchers revealed a four-order circuit for light avoidance in Drosophila larvae, helping to understand the relationship between neural circuits and behavior in fruit flies.
NATURE COMMUNICATIONS
(2022)
Letter
Plant Sciences
James Ronald, Anthony J. Wilkinson, Seth J. Davis
Summary: The sub-nuclear localization of EARLY FLOWERING3 gene responds to changes in ambient temperature.
Article
Biochemistry & Molecular Biology
German Murcia, Cristina Nieto, Romina Sellaro, Salome Prat, Jorge J. Casal
Summary: Hypocotyl growth in Arabidopsis thaliana during the night is not only influenced by the current temperature, but also by preceding daytime temperatures, indicating a short-term memory of previous conditions. Transcriptional regulator ELF3 and factors PIF4 and HY5 play crucial roles in this temperature-dependent growth response.
Article
Plant Sciences
Ulf Lagercrantz, Anja Billhardt, Sabine N. Rousku, Martina Leso, Salim Hossain Reza, D. Magnus Eklund
Summary: Previous studies on the evolution of plant circadian clocks have often focused on genes and models defined in Arabidopsis, but this study took a more unbiased approach by looking at clock genes in liverwort Marchantia polymorpha. The results showed that a homologue to the transcriptional co-repressor Arabidopsis DE-ETIOLATED1 plays an important role in clock gene expression and rhythms, particularly in the liverwort's circadian clock.
Review
Biochemistry & Molecular Biology
Amnon Brzezinski, Seema Rai, Adyasha Purohit, Seithikurippu R. Pandi-Perumal
Summary: Circadian rhythms play a crucial role in controlling reproductive function, with melatonin regulating the reproductive responses of animals to environmental light conditions. Clock genes and circadian rhythms are associated with optimal reproductive performance through the synchronization of endogenous molecular clocks in various tissues throughout the body.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Review
Endocrinology & Metabolism
Si-Ke He, Jia-Hao Wang, Tao Li, Shan Yin, Jian-Wei Cui, Yun-Fei Xiao, Yin Tang, Jia Wang, Yun-Jin Bai
Summary: This article reviews the relationship between circadian rhythm disturbance and kidney stone disease (KSD), summarizing the risk factors and treatment methods. The results indicate that KSD is associated with systemic disorders such as metabolic syndrome, inflammatory bowel disease, and microbiome dysbiosis, and some chronotherapies have been proven effective.
FRONTIERS IN ENDOCRINOLOGY
(2023)
Article
Multidisciplinary Sciences
Yasuhiro Umemura, Nobuya Koike, Yoshiki Tsuchiya, Hitomi Watanabe, Gen Kondoh, Ryoichiro Kageyama, Kazuhiro Yagita
Summary: Circadian clocks are suppressed during early embryonic stages and pluripotent stem cells in mammals, but gradually emerge during ontogenesis. The expression of CLOCK/BMAL1 affects the oscillation of the segmentation clock, which controls somitogenesis in the early developmental stage.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Endocrinology & Metabolism
Haoran Xin, Rongfeng Huang, Meiyu Zhou, Jianghui Chen, Jianxin Zhang, Tingting Zhou, Shushen Ji, Xiao Liu, He Tian, Sin Man Lam, Xinyu Bao, Lihua Li, Shifei Tong, Fang Deng, Guanghou Shui, Zhihui Zhang, Catherine C. L. Wong, Min-Dian Li
Summary: Meal timing, specifically day/sleep time-restricted feeding, enhances running endurance and regulates muscle diurnal rhythms in mice. The circadian clock and a mitochondrial oxidative metabolism-centric network play key roles in mediating the effects of meal timing on physical endurance. Knockdown of the myocyte lipid droplet protein perilipin-5 in muscle tissues mimics the effects of day/sleep time-restricted feeding.
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
Genetics & Heredity
Jacob Bradford, Timothy Chappell, Dimitri Perrin
Summary: The design of CRISPR-Cas9 guide RNAs is a complex and computationally demanding task. In this study, the authors propose a new method called Crackling, which combines multiple scoring approaches and incorporates Inverted Signature Slice Lists (ISSL) to enhance the efficiency and accuracy of guide RNA design. The results show that Crackling outperforms other popular tools in terms of guide selection and off-target scoring speed.
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)