Article
Plant Sciences
Beata Siemiatkowska, Matteo Chiara, Bhaskara G. Badiger, Matteo Riboni, Francesca D'Avila, Daniele Braga, Mohamed Abd Allah Salem, Damiano Martignago, Sara Colanero, Massimo Galbiati, Patrick Giavalisco, Chiara Tonelli, Thomas E. Juenger, Lucio Conti
Summary: Transcriptional reprogramming prior to morphological and physiological acclimation is crucial in drought stress responses, with the phytohormone abscisic acid (ABA) being the key signal regulating gene expression. GIGANTEA (GI) is identified as a key regulator of ABA-regulated transcriptional and physiological responses, controlling oscillations in ABA signals through DNA binding or function of different classes of transcription factors (TFs). GI plays a role in establishing a phase of reduced ABA sensitivity and related physiological responses by interacting with TFs at target regions.
PLANT AND CELL PHYSIOLOGY
(2022)
Article
Plant Sciences
Daniel A. Careno, Soledad Perez Santangelo, Richard C. Macknight, Marcelo J. Yanovsky
Summary: Circadian rhythms are regulated by a set of clock genes, and this study identified LSM1 and XRN4 as factors involved in mRNA decay pathway that affects clock function in plants.
PLANT AND CELL PHYSIOLOGY
(2022)
Article
Multidisciplinary Sciences
Fuyuki Asano, Staci J. Kim, Tomoyuki Fujiyama, Chika Miyoshi, Noriko Hotta-Hirashima, Nodoka Asama, Kanako Iwasaki, Miyo Kakizaki, Seiya Mizuno, Michihiro Mieda, Fumihiro Sugiyama, Satoru Takahashi, Shoi Shi, Arisa Hirano, Hiromasa Funato, Masashi Yanagisawa
Summary: Deficiency of SIK3 in GABAergic neurons or NMS-producing neurons delays the arousal peak phase, while a gain-of-function mutant allele of Sik3 in GABAergic neurons advances the activity onset. Furthermore, HDAC4 deficiency shortens the circadian cycle.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Biology
Yian Xu, Masoud Asadi-Zeydabadi, Randall Tagg, Orrin Shindell
Summary: Study reveals that the circadian dynamical system of Arabidopsis plants exhibits characteristics similar to a Hopf bifurcation, with models showing supercritical Hopf bifurcation and deriving the Stuart-Landau amplitude equation through weakly nonlinear analysis. The research indicates differences in the models in terms of proximity to bifurcation, pre- and post-bifurcation states, and the kinetic parameters leading to bifurcation.
JOURNAL OF MATHEMATICAL BIOLOGY
(2021)
Article
Biology
Ruby Kim, Thomas P. Witelski
Summary: This paper investigates the dynamics of dopamine in the circadian timekeeping system and explores the disruptions in the daily rhythmicity of dopamine caused by decoupling and quasiperiodic behaviors. The imbalance of dopamine is often associated with disrupted circadian rhythms, and this model provides new insights into the link between the circadian clock and dopamine, which can be used to study the impact of circadian rhythms on the dopaminergic system and develop therapeutic strategies.
MATHEMATICAL BIOSCIENCES
(2022)
Article
Plant Sciences
Selin Buelbuel, Yasuhito Sakuraba, Mastoureh Sedaghatmehr, Mutsumi Watanabe, Rainer Hoefgen, Salma Balazadeh, Bernd Mueller-Roeber
Summary: BBX14 is a negative regulator of nitrogen starvation-induced leaf senescence and is directly regulated by PIF4 and MYB44. It directly regulates the transcription of EIN3, which is involved in nitrogen signaling and leaf senescence.
Review
Nutrition & Dietetics
Aleix Ribas-Latre, Kristin Eckel-Mahan
Summary: White adipose tissue is a metabolic organ that can retract and expand based on energy needs. It is made up of mature adipocytes and cells from the stromal vascular cell fraction. The circadian clock in adipose tissue plays a crucial role in maintaining the health and function of fat.
Review
Plant Sciences
Luis Cervela-Cardona, Benjamin Alary, Paloma Mas
Summary: A fundamental principle shared by all organisms is the conversion of nutrients into energy, requiring precise spatiotemporal programming. Cellular metabolism can adapt to external time, relying on the circadian clock. The circadian clock plays a prevalent role in controlling the timing of mitochondrial activity and cellular energy in Arabidopsis thaliana, with evidence showing metabolic signals can feedback to the clock.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Ophthalmology
Shumet T. Gegnaw, Cristina Sandu, Jorge Mendoza, Arthur A. Bergen, Marie-Paule Felder-Schmittbuhl
Summary: The retinal circadian system, consisting of clocks in different retinal cell types, regulates rhythmic processes in the retina. Studies on mice with rod-specific knockout of Bmal1 show that the circadian clock in rods plays a crucial role in regulating visual processing in a cell autonomous manner. This study suggests that the clock in rods influences visual function by modulating retinal responses to light stimuli.
EXPERIMENTAL EYE RESEARCH
(2021)
Article
Plant Sciences
Marta Francisco, Daniel J. Kliebenstein, Victor M. Rodriguez, Pilar Soengas, Rosaura Abilleira, Maria E. Cartea
Summary: In this study, the researchers identified and characterized NAD-DEPENDENT MALIC ENZYME 1 (NAD-ME1) as a key gene regulating plant metabolism and circadian clock outputs. They found that NAD-ME1 plays a crucial role in coordinating both primary and secondary metabolism in plants, as well as plant immunity phytochemicals.
Article
Plant Sciences
Takahiro N. Uehara, Takashi Nonoyama, Kyomi Taki, Keiko Kuwata, Ayato Sato, Kazuhiro J. Fujimoto, Tsuyoshi Hirota, Hiromi Matsuo, Akari E. Maeda, Azusa Ono, Tomoaki T. Takahara, Hiroki Tsutsui, Takamasa Suzuki, Takeshi Yanai, Steve A. Kay, Kenichiro Itami, Toshinori Kinoshita, Junichiro Yamaguchi, Norihito Nakamichi
Summary: This study demonstrates the necessity of CDKC;2 in maintaining the circadian period in Arabidopsis. Through chemical biology and genetic approaches, it was found that CDKC;2 maintains transcriptional activity by phosphorylating the C-terminal domain of RNA polymerase II, affecting clock gene expression and period length.
PLANT AND CELL PHYSIOLOGY
(2022)
Article
Plant Sciences
Takahiro N. Uehara, Saori Takao, Hiromi Matsuo, Ami N. Saito, Eisuke Ota, Azusa Ono, Kenichiro Itami, Toshinori Kinoshita, Takafumi Yamashino, Junichiro Yamaguchi, Norihito Nakamichi
Summary: A novel synthetic small molecule called TU-892 has been found to affect the amount of PRR7 protein, leading to lengthening of the circadian clock period in plants. The study showed that TU-892 treatment upregulates the expression of CCA1 gene and reduces the amount of PRR7 protein. This novel clock modulator provides new tools and avenues for studying the circadian clock in plants.
PLANT AND CELL PHYSIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Aleksandra Eckstein, Joanna Grzyb, Pawel Hermanowicz, Piotr Zglobicki, Justyna Labuz, Wojciech Strzalka, Dariusz Dziga, Agnieszka Katarzyna Banas
Summary: The study investigates the role of blue light photoreceptors in plant leaf senescence, finding that the symptoms of senescence were less pronounced in mutants with phototropin mutations, indicating delayed senescence in these plants. This suggests different mechanisms of phototropin involvement in regulating senescence-related processes.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Plant Sciences
Luis Cervela-Cardona, Takuya Yoshida, Youjun Zhang, Masaaki Okada, Alisdair Fernie, Paloma Mas
Summary: The Arabidopsis clock component TOC1 plays a crucial role in the diurnal regulation of metabolism by repressing the expression of the TCA-related gene FUMARASE 2 at night. This regulation affects the accumulation of fumarate and contributes to the molecular and physiological energy-deprivation phenotypes of TOC1 over-expressing plants.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Plant Sciences
Jessica A. S. Barros, Joao Henrique F. Cavalcanti, Karla G. Pimentel, David B. Medeiros, Jose C. F. Silva, Jorge A. Condori-Apfata, Taly Lapidot-Cohen, Yariv Brotman, Adriano Nunes-Nesi, Alisdair R. Fernie, Tamar Avin-Wittenberg, Wagner L. Araujo
Summary: This study investigated the metabolic adjustments in plants under carbon starvation and the role of the transcription factor WRKY45. The results showed that overexpression of WRKY45 leads to early senescence and altered amino acid metabolism, and is associated with dysregulation of mitochondrial signaling and activation of alternative respiration.
PLANT CELL AND ENVIRONMENT
(2022)
Article
Multidisciplinary Sciences
Naohiro Kawamoto, Hiroshi Ito, Isao T. Tokuda, Hideo Iwasaki
NATURE COMMUNICATIONS
(2020)
Article
Computer Science, Hardware & Architecture
Kazuyoshi Ishimura, Ryota Inden, Naoto Komeno, Isao T. Tokuda
Summary: This study investigates the entrainment property of a Pierce oscillator circuit under sinusoidal external forcing, revealing an asymmetric shape in the entrainment region in a 2D parameter space. The asymmetric shape is attributed to the reactance of the Pierce circuit and the authors propose that driving a slow oscillator circuit with a fast circuit is more advantageous for efficient synchronization. The research provides insights for optimal network configuration of coupled crystal oscillators for applications in distributed digital clocks and wireless communication systems.
JOURNAL OF CIRCUITS SYSTEMS AND COMPUTERS
(2021)
Article
Acoustics
Takuma Matsumoto, Mayuka Kanaya, Kazuyoshi Ishimura, Isao T. Tokuda
Summary: Ventricular folds located above the vocal folds can vibrate under certain conditions, affecting voice quality. Research shows that vocal and ventricular folds can co-oscillate at the same frequency with an out-of-phase relation, which is crucial for sustaining vocal vibrations.
JOURNAL OF THE ACOUSTICAL SOCIETY OF AMERICA
(2021)
Article
Multidisciplinary Sciences
Kosaku Masuda, Isao T. Tokuda, Norihito Nakamichi, Hirokazu Fukuda
Summary: Circadian clocks enable organisms to synchronize physiological processes with diurnal variations, with the phase response curve being a key tool to understand clock entrainment. This study demonstrates that fundamental properties of the curve can be recovered from the singularity response, which can be easily measured by applying a single stimulus to a desynchronized cellular network. The method is simple, accurate, and applicable to other coupled oscillator systems, offering potential to study circadian clock entrainment in plants and other species in a cost-effective manner.
NATURE COMMUNICATIONS
(2021)
Article
Robotics
Longchuan Li, Shugen Ma, Isao Tokuda, Fumihiko Asano, Makoto Nokata, Yang Tian, Liang Du
Summary: This study introduces a modified snake-like robot model with additional oscillation elements to generate efficient and stable rectilinear gait, and theoretical analysis is based on dynamic morphological computation. The resonance curves of the linear oscillator are used to elucidate locomotion performance and estimate optimal parameters for locomotion control.
IEEE ROBOTICS AND AUTOMATION LETTERS
(2021)
Article
Acoustics
Annemie Van Hirtum, Anne Bouvet, Isao Tokuda, Xavier Pelorson
Summary: The study found that angular asymmetry affects the decay of vocal fold vibration modes, with a stiff epithelium-like surface layer increasing the mode decay. Spatial mode patterns near the glottal aperture reflect the mode order and the imposed angular asymmetry reduces the spatial mode extent near the tilted vocal fold edge.
JOURNAL OF SOUND AND VIBRATION
(2022)
Article
Acoustics
Takuto Honda, Mayuka Kanaya, Isao T. Tokuda, Anne Bouvet, Annemie Van Hirtum, Xavier Pelorson
Summary: This study examined the quasi-steady approximation of glottal flow by measuring intraglottal pressure distributions in a scaled-up static vocal fold model under time-varying flow conditions. The results showed that the pressure profiles and air-jet separation point were indistinguishable between time-varying and steady flow conditions with matching subglottal pressure. Therefore, it suggests that time-varying glottal flow can be approximated as a series of steady flow states with a matching subglottal pressure in the range of normal vocalization frequencies.
JOURNAL OF THE ACOUSTICAL SOCIETY OF AMERICA
(2022)
Article
Biochemistry & Molecular Biology
Mark Greenwood, Isao T. Tokuda, James C. W. Locke
Summary: Individual plant cells possess a circadian clock that times internal processes to the day-night cycle. This clock is regulated by a genetic network and is sensitive to light. The cells communicate their timing through local or long-distance sharing of clock components, allowing for spatial coordination. Local coupling minimizes timing errors caused by noisy light-dark cycles and maintains different clock phases in different plant regions.
MOLECULAR SYSTEMS BIOLOGY
(2022)
Article
Multidisciplinary Sciences
Takeshi Nishimura, Isao T. Tokuda, Shigehiro Miyachi, Jacob C. Dunn, Christian T. Herbst, Kazuyoshi Ishimura, Akihisa Kaneko, Yuki Kinoshita, Hiroki Koda, Jaap P. P. Saers, Hirohiko Imai, Tetsuya Matsuda, Ole Naesbye Larsen, Uwe Jurgens, Hideki Hirabayashi, Shozo Kojima, W. Tecumseh Fitch
Summary: Human speech production follows the same acoustic principles as vocal production in other animals but has distinctive features due to simplifications in laryngeal anatomy. The loss of vocal membranes allows human speech to avoid spontaneous nonlinear phenomena and acoustic chaos found in other primate vocalizations, leading to stable and harmonic-rich phonation.
Article
Multidisciplinary Sciences
Florian Grziwotz, Chun -Wei Chang, Vasilis Dakos, Egbert H. van Nes, Markus Schwarzlaender, Oliver Kamps, Martin Hessler, Isao T. Tokuda, Arndt Telschow, Chih-hao Hsieh
Summary: Critical transitions occur in various real-world systems and forecasting their occurrence is of great interest. This study introduces a powerful early warning signal called dynamical eigenvalue (DEV) that estimates the dominant eigenvalue of a system using bifurcation theory. The efficacy of the DEV approach is demonstrated in model systems with known bifurcation types and tested on various critical transitions in real-world systems.
Article
Biology
Rintaro Miyazaki, Tomoki Yoshitani, Mayuka Kanaya, Shigehiro Miyachi, Akihisa Kaneko, Yuki Kinoshita, Kanta Nakamura, Takeshi Nishimura, Isao T. Tokuda
Summary: We conducted ex vivo and in vivo experiments to study the role of the ventricular folds in sound production in macaques. Our results show that the ventricular folds co-oscillate with the vocal folds and significantly lower the fundamental frequency. A mathematical model suggests that this is due to the low oscillation frequency of the ventricular folds entraining the vocal folds. The findings suggest that macaques may use the ventricular folds more frequently than humans in vocalization.
JOURNAL OF EXPERIMENTAL BIOLOGY
(2023)
Article
Multidisciplinary Sciences
Alan Zigler, Stephanie Straw, Isao Tokuda, Ellen Bronson, Tobias Riede
Summary: The Panamanian golden frog, a critically endangered species, only survives and reproduces in human care. Their vocal behavior and patterns were studied to better understand their behavior and improve breeding efforts. The results showed individual and population specificity in male advertisement calls, as well as circadian and circannual periodicity in vocal activities. The findings have important implications for improving breeding success and care of the Panamanian golden frog.
Article
Physics, Fluids & Plasmas
Kota Shiozawa, Taisuke Uemura, Isao T. Tokuda
Summary: A method is proposed to detect the dynamical instability of complex time series by studying the evolution of the partitioned entropy of an initially localized region of the attractor. The growth rate of the partitioned entropy is found to correspond to the first Lyapunov exponent. A criterion is introduced to distinguish chaos from limit cycles or tori to avoid spurious detection. Numerical experiments and analysis of experimental data demonstrate the effectiveness and robustness of the method.
Article
Acoustics
Mayuka Kanaya, Takuma Matsumoto, Taisuke Uemura, Rei Kawabata, Takeshi Nishimura, Isao T. Tokuda
Summary: The vocal membrane, an extended part of the vocal fold, has been observed in various species and is predicted to enhance efficiency of vocalizations by lowering the phonation threshold pressure. A synthetic model of the vocal membrane was developed and experiments showed that it indeed lowered the phonation threshold pressure and resulted in chaotic oscillations.
JASA EXPRESS LETTERS
(2022)
Article
Mathematics, Interdisciplinary Applications
Kota Shiozawa, Takaya Miyano, Isao T. Tokuda
Summary: This paper introduces a modified version of the Kuramoto model as a new method for data synchronization, which can solve clustering problems by setting the natural frequencies of the oscillators. The proposed method outperforms existing data-clustering algorithms in handling datasets with non-convex shaped clusters, as demonstrated through three case studies.
IEICE NONLINEAR THEORY AND ITS APPLICATIONS
(2022)