Kyushu University Academic Staff Educational and Research Activities Database
List of Papers
Hiroshi Ito Last modified date:2020.10.29

Associate Professor / Section on Modeling and Optimization / Department of Human Science / Faculty of Design

1. Naohiro Kawamoto, Hiroshi Ito, Isao T. Tokuda, Hideo Iwasaki, Damped circadian oscillation in the absence of KaiA in Synechococcus, Nature communications, 10.1038/s41467-020-16087-x, 11, 1, 2020.12, Proteins KaiA, KaiB and KaiC constitute a biochemical circadian oscillator in the cyanobacterium Synechococcus elongatus. It has been reported kaiA inactivation completely abolishes circadian oscillations. However, we show here that kaiBC promoter activity exhibits a damped, low-amplitude oscillation with a period of approximately 24 h in kaiA-inactivated strains. The damped rhythm resonates with external cycles with a period of 24–26 h, indicating that its natural frequency is similar to that of the circadian clock. Double-mutation experiments reveal that kaiC, kaiB, and sasA (encoding a KaiC-binding histidine kinase) are all required for the damped oscillation. Further analysis suggests that the kaiA-less damped transcriptional rhythm requires KaiB-KaiC complex formation and the transcription-translation feedback loop, but not the KaiC phosphorylation cycle. Our results provide insights into mechanisms that could potentially underlie the diurnal/circadian behaviors observed in other bacterial species that possess kaiB and kaiC homologues but lack a kaiA homologue..
2. Takuma Sugi, Hiroshi Ito, Masaki Nishimura, Ken H. Nagai, C. elegans collectively forms dynamical networks, Nature communications, 10.1038/s41467-019-08537-y, 10, 1, 2019.01, Understanding physical rules underlying collective motions requires perturbation of controllable parameters in self-propelled particles. However, controlling parameters in animals is generally not easy, which makes collective behaviours of animals elusive. Here, we report an experimental system in which a conventional model animal, Caenorhabditis elegans, collectively forms dynamical networks of bundle-shaped aggregates. We investigate the dependence of our experimental system on various extrinsic parameters (material of substrate, ambient humidity and density of worms). Taking advantage of well-established C. elegans genetics, we also control intrinsic parameters (genetically determined motility) by mutations and by forced neural activation via optogenetics. Furthermore, we develop a minimal agent-based model that reproduces the dynamical network formation and its dependence on the parameters, suggesting that the key factors are alignment of worms after collision and smooth turning. Our findings imply that the concepts of active matter physics may help us to understand biological functions of animal groups..
3. Nao Nakatsuji, Hisayasu Ihara, Takeharu Senoo, Hiroshi Ito, Visualizing similarity of appearance by arrangement of cards, Frontiers in Psychology, 10.3389/fpsyg.2016.00698, 7, MAY, 2016.01, This study proposes a novel method to extract the configuration of the psychological space by directly measuring subjects' similarity rating without computational work. Although multidimensional scaling (MDS) is well-known as a conventional method for extracting the psychological space, the method requires many pairwise evaluations. The times taken for evaluations increase in proportion to the square of the number of objects in MDS. The proposed method asks subjects to arrange cards on a poster sheet according to the degree of similarity of the objects. To compare the performance of the proposed method with the conventional one, we developed similarity maps of typefaces through the proposed method and through non-metric MDS. We calculated the trace correlation coefficient among all combinations of the configuration for both methods to evaluate the degree of similarity in the obtained configurations. The threshold value of trace correlation coefficient for statistically discriminating similar configuration was decided based on random data. The ratio of the trace correlation coefficient exceeding the threshold value was 62.0% so that the configurations of the typefaces obtained by the proposed method closely resembled those obtained by non-metric MDS. The required duration for the proposed method was approximately one third of the non-metric MDS's duration. In addition, all distances between objects in all the data for both methods were calculated. The frequency for the short distance in the proposed method was lower than that of the non-metric MDS so that a relatively small difference was likely to be emphasized among objects in the configuration by the proposed method. The card arrangement method we here propose, thus serves as a easier and time-saving tool to obtain psychological structures in the fields related to similarity of appearance..
4. Murayama Y, Kori H, Oshima C, Kondo T, Iwasaki H, Ito H, Low temperature nullifies the circadian clock in cyanobacteria through Hopf bifurcation, Proceedings of National Academy of Sciences, 114, 5641-5646, 2017.05, Cold temperatures lead to nullification of circadian rhythms in many organisms. Two typical scenarios explain the disappearance of rhythmicity: the first is oscillation death, which is the transition from self-sustained oscillation to damped oscillation that occurs at a critical temperature. The second scenario is oscillation arrest, in which oscillation terminates at a certain phase. In the field of nonlinear dynamics, these mechanisms are called the Hopf bifurcation and the saddle-node on an invariant circle bifurcation, respectively. Although these mechanisms lead to distinct dynamical properties near the critical temperature, it is unclear to which scenario the circadian clock belongs. Here we reduced the temperature to dampen the reconstituted circadian rhythm of phosphorylation of the recombinant cyanobacterial clock protein KaiC. The data led us to conclude that Hopf bifurcation occurred at ∼19 °C. Below this critical temperature, the self-sustained rhythms of KaiC phosphorylation transformed to damped oscillations, which are predicted by the Hopf bifurcation theory. Moreover, we detected resonant oscillations below the critical temperature when temperature was periodically varied, which was reproduced by numerical simulations. Our findings suggest that the transition to a damped oscillation through Hopf bifurcation contributes to maintaining the circadian rhythm of cyanobacteria through resonance at cold temperatures..
5. Shingo Gibo, Hiroshi Ito, Discrete and ultradiscrete models for biological rhythms comprising a simple negative feedback loop, Journal of Theoretical Biology, 2015.05.
6. Masaki Ogawa, Hiroshi Ito, Takeharu Seno, Vection Is Unaffected by Circadian Rhythms, Psychology, 6, 4, 440-446, 2015.03.
7. Goda K, Ito H, Kondo T, Oyama T, Fluorescence correlation spectroscopy to monitor Kai protein–based circadian oscillations in real time, Journal of Biological Chemistry, 10.1074/jbc.M111.265777, 287, 3241-3248, 2012.01.
8. Hosokawa N, Hatakeyama T, Kojima T, Kikuchi Y, Ito H, Iwasaki H., Circadian transcriptional regulation by the posttranslational oscillator without de novo clock gene expression in Synechococcus, Proceedings of National Academy of Sciences, 10.1073/pnas.1019612108, 108, 15396-15401, 2011.09.
9. Nakajima M*, Ito H*, Kondo T.(*Equally contributed), In vitro regulation of circadian phosphorylation rhythm of cyanobacterial clock protein KaiC by KaiA and KaiB, FEBS Letters, 10.1016/j.febslet.2010.01.016, 584, 898-902, 2010.01.
10. Ito H*, Mutsuda M, Murayama Y, Tomita J, Hosokawa N, Terauchi K, Sugita C, Sugita M, Kondo T, Iwasaki H*. (*Equally contributed), Cyanobacterial daily life with Kai-based circadian and diurnal genome-wide transcriptional control in Synechococcus elongatus., Proceedings of National Academy of Sciences , 10.1073/pnas.0902587106, 106 (2009), 14168-14173, 2011.07.
11. Nakajima M, Imai K, Ito H, Nishiwaki T, Murayama Y, Iwasaki H, Oyama T, Kondo T, Reconstitution of circadian oscillation of cyanobacterial KaiC phosphorylation in vitro., Science, 308, 414-5, 2005.04.
12. Ito H, Kageyama H, Mutsuda M, Nakajima M, Oyama T, Kondo T., Autonomous synchronization of the circadian KaiC phosphorylation rhythm, Nature Structural and Molecular Biology, 10.1038/nsmb1312, 14, 1084-1088, 2007.11.
13. Yoshida T*, Murayama Y*, Ito H*, Kageyama H, Kondo T. (*Equally contributed), Non-parametric entrainment of the in vitro circadian phosphorylation rhythm of cyanobacterial KaiC by temperature cycle
, Proceedings of National Academy of Sciences, 10.1073/pnas.0806741106, 106, 1648-1653, 2009.01.