研究者詳細 - 塚田　祐基

論文 - 塚田　祐基

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cGMP dynamics that underlies thermosensation in temperature-sensing neuron regulates thermotaxis behavior in C. elegans

I Aok, M Shiota, Y Tsukada, S Nakano, I Mori

PLOS ONE （PLoS ONE） 17 （ 12 ） e0278343 2022年12月

Living organisms including bacteria, plants and animals sense ambient temperature so that they can avoid noxious temperature or adapt to new environmental temperature. A nematode C. elegans can sense innocuous temperature, and navigate themselves towards memorize past cultivation temperature (Tc) of their preference. For this thermotaxis, AFD thermosensory neuron is pivotal, which stereotypically responds to warming by increasing intracellular Ca2+ level in a manner dependent on the remembered past Tc. We aimed to reveal how AFD encodes the information of temperature into neural activities. cGMP synthesis in AFD is crucial for thermosensation in AFD and thermotaxis behavior. Here we characterized the dynamic change of cGMP level in AFD by imaging animals expressing a fluorescence resonance energy transfer (FRET)-based cGMP probe specifically in AFD and found that cGMP dynamically responded to both warming and cooling in a manner dependent on past Tc. Moreover, we characterized mutant animals that lack guanylyl cyclases (GCYs) or phosphodiesterases (PDEs), which synthesize and hydrolyze cGMP, respectively, and uncovered how GCYs and PDEs contribute to cGMP and Ca2+ dynamics in AFD and to thermotaxis behavior.

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Genetic screens identified dual roles of microtubule-associated serine threonine kinase and CREB within a single thermosensory neuron in the regulation of Caenorhabditis elegans thermotaxis behavior

S Nakano, A Nakayama, H Kuroyanagi, R Yamashiro, Y Tsukada, I Mori

G3 Genes|Genomes|Genetics （G3: Genes, Genomes, Genetics） 12 （ 11 ） 2022年11月

査読有り

Animals integrate sensory stimuli presented at the past and present, assess the changes in their surroundings and navigate themselves toward preferred environment. Identifying the neural mechanisms of such sensory integration is pivotal to understand how the nervous system generates perception and behavior. Previous studies on thermotaxis behavior of Caenorhabditis elegans suggested that a single thermosensory neuron AFD plays an important role in integrating the past and present temperature information and is essential for the neural computation that drives the animal toward the preferred temperature region. However, the molecular mechanisms by which AFD executes this neural function remained elusive. Here we report multiple forward genetic screens to identify genes required for thermotaxis. We reveal that kin-4, which encodes the C. elegans homolog of microtubule-associated serine threonine kinase, plays dual roles in thermotaxis and can promote both cryophilic and thermophilic drives. We also uncover that a thermophilic defect of mutants for mec-2, which encodes a C. elegans homolog of stomatin, can be suppressed by a loss-of-function mutation in the gene crh-1, encoding a C. elegans homolog CREB transcription factor. Expression of crh-1 in AFD restored the crh-1-dependent suppression of the mec-2 thermotaxis phenotype, indicating that crh-1 can function in AFD to regulate thermotaxis. Calcium imaging analysis from freely moving animals suggest that mec-2 and crh-1 regulate the neuronal activity of the AIY interneuron, a postsynaptic partner of the AFD neuron. Our results suggest that a stomatin family protein can control the dynamics of neural circuitry through the CREB-dependent transcriptional regulation within a sensory neuron.

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Age‐dependent changes in response property and morphology of a thermosensory neuron and thermotaxis behavior in Caenorhabditis elegans

TT Huang, HJ Matsuyama, Y Tsukada, A Singhvi, RT Syu, Y Lu, ...

Aging cell 19 (5), e13146 （Wiley） 19 （ 5 ） 2020年05月

査読有り, ISSN 1474-9718

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Presynaptic MAST kinase controls opposing postsynaptic responses to convey stimulus valence in Caenorhabditis elegans

S Nakano, M Ikeda, Y Tsukada, X Fei, T Suzuki, Y Niino, R Ahluwalia, ...

Proceedings of the National Academy of Sciences 117 (3), 1638-1647 117 （ 3 ） 1638 - 1647 2020年01月

査読有り

Presynaptic plasticity is known to modulate the strength of synaptic transmission. However, it remains unknown whether regulation in presynaptic neurons can evoke excitatory and inhibitory postsynaptic responses. We report here that the Caenorhabditis elegans homologs of MAST kinase, Stomatin, and Diacylglycerol kinase act in a thermosensory neuron to elicit in its postsynaptic neuron an excitatory or inhibitory response that correlates with the valence of thermal stimuli. By monitoring neural activity of the valence-coding interneuron in freely behaving animals, we show that the alteration between excitatory and inhibitory responses of the interneuron is mediated by controlling the balance of two opposing signals released from the presynaptic neuron. These alternative transmissions further generate opposing behavioral outputs necessary for the navigation on thermal gradients. Our findings suggest that valence-encoding interneuronal activity is determined by a presynaptic mechanism whereby MAST kinase, Stomatin, and Diacylglycerol kinase influence presynaptic outputs.

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A behavior-based drug screening system using a Caenorhabditis elegans model of motor neuron disease

Ikenaka K, Tsukada Y, Giles AC, Arai T, Nakadera Y, Nakano S, Kawai K, Mochizuki H, Katsuno M, Sobue G, Mori I

Scientific Reports 9 （ 1 ） 10104 2019年07月

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Uncoordinated centrosome cycle underlies the instability of non-diploid somatic cells in mammals

Kan Yaguchi and Takahiro Yamamoto and Ryo Matsui and Yuki Tsukada and Atsuko Shibanuma and Keiko Kamimura and Toshiaki Koda and Ryota Uehara

Journal of Cell Biology （Rockefeller University Press） 217 （ 7 ） 2463 - 2483 2018年07月

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Identification of animal behavioral strategies by inverse reinforcement learning

S Yamaguchi, H Naoki, M Ikeda, Y Tsukada, S Nakano, I Mori, S Ishii

PLoS computational biology 14 (5), e1006122 （Public Library of Science） 14 （ 5 ） e1006122. 2018年05月

査読有り, ISSN 1553-7358

Animals are able to reach a desired state in an environment by controlling various behavioral patterns. Identification of the behavioral strategy used for this control is important for understanding animals’ decision-making and is fundamental to dissect information processing done by the nervous system. However, methods for quantifying such behavioral strategies have not been fully established. In this study, we developed an inverse reinforcement-learning (IRL) framework to identify an animal’s behavioral strategy from behavioral time-series data. We applied this framework to C. elegans thermotactic behavior
after cultivation at a constant temperature with or without food, fed worms prefer, while starved worms avoid the cultivation temperature on a thermal gradient. Our IRL approach revealed that the fed worms used both the absolute temperature and its temporal derivative and that their behavior involved two strategies: directed migration (DM) and isothermal migration (IM). With DM, worms efficiently reached specific temperatures, which explains their thermotactic behavior when fed. With IM, worms moved along a constant temperature, which reflects isothermal tracking, well-observed in previous studies. In contrast to fed animals, starved worms escaped the cultivation temperature using only the absolute, but not the temporal derivative of temperature. We also investigated the neural basis underlying these strategies, by applying our method to thermosensory neuron-deficient worms. Thus, our IRL-based approach is useful in identifying animal strategies from behavioral time-series data and could be applied to a wide range of behavioral studies, including decision-making, in other organisms.

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Thermotactic behavioral strategy of C. elegans identified using inverse reinforcement learning

Yamaguchi, S, Naoki, H, Ikeda, M, Tsukada, Y, Nakano, S, Mori, I, Ishii, S

PLoS Computational Biology 2018年

査読有り

温度受容神経細胞のシステム同定と温度環境の再構築

塚田祐基, 森郁恵

自動制御連合講演会講演論文集（自動制御連合講演会） 60 999 - 1000 2017年

査読有り

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Reconstruction of spatial thermal gradient encoded in thermosensory neuron AFD in Caenorhabditis elegans

Y Tsukada, M Yamao, H Naoki, T Shimowada, N Ohnishi, A Kuhara, ...

Journal of Neuroscience 36 (9), 2571-2581 （SOC NEUROSCIENCE） 36 （ 9 ） 2571 - 2581 2016年03月

査読有り, ISSN 0270-6474

During navigation, animals process temporal sequences of sensory inputs to evaluate the surrounding environment. Thermotaxis of Caenorhabditis elegans is a favorable sensory behavior to elucidate how navigating animals process sensory signals from the environment. Sensation and storage of temperature information by a bilaterally symmetric pair of thermosensory neurons, AFD, is essential for the animals to migrate toward the memorized temperature on a thermal gradient. However, the encoding mechanisms of the spatial environment with the temporal AFD activity during navigation remain to be elucidated. Here, we show how the AFD neuron encodes sequences of sensory inputs to perceive spatial thermal environment. We used simultaneous calcium imaging and tracking system for a freely moving animal and characterized the response property of AFD to the thermal stimulus during thermotaxis. We show that AFD neurons respond to shallow temperature increases with intermittent calcium pulses and detect temperature differences with a critical time window of 20 s, which is similar to the timescale of behavioral elements of C. elegans, such as turning. Convolution of a thermal stimulus and the identified response property successfully reconstructs AFD activity. Conversely, deconvolution of the identified response kernel and AFD activity reconstructs the shallow thermal gradient with migration trajectory, indicating that AFD activity and the migration trajectory are sufficient as the encoded signals for thermal environment. Our study demonstrates bidirectional transformation between environmental thermal information and encoded neural activity.

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Aurora B and Kif2A control microtubule length for assembly of a functional central spindle during anaphase

R Uehara, Y Tsukada, T Kamasaki, I Poser, K Yoda, DW Gerlich, ...

Journal of Cell Biology 202 (4), 623-636 202 （ 4 ） 623 - 36 2013年08月

査読有り

The central spindle is built during anaphase by coupling antiparallel microtubules (MTs) at a central overlap zone, which provides a signaling scaffold for the regulation of cytokinesis. The mechanisms underlying central spindle morphogenesis are still poorly understood. In this paper, we show that the MT depolymerase Kif2A controls the length and alignment of central spindle MTs through depolymerization at their minus ends. The distribution of Kif2A was limited to the distal ends of the central spindle through Aurora B-dependent phosphorylation and exclusion from the spindle midzone. Overactivation or inhibition of Kif2A affected interchromosomal MT length and disorganized the central spindle, resulting in uncoordinated cell division. Experimental data and model simulations suggest that the steady-state length of the central spindle and its symmetric position between segregating chromosomes are predominantly determined by the Aurora B activity gradient. On the basis of these results, we propose a robust self-organization mechanism for central spindle formation.

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Feedback regulation of microscopes by image processing

Y Tsukada, K Hashimoto

Development, growth & differentiation 55 (4), 550-562 55 （ 4 ） 550 - 562 2013年05月

査読有り, ISSN 0012-1592

Computational microscope systems are becoming a major part of imaging biological phenomena, and the development of such systems requires the design of automated regulation of microscopes. An important aspect of automated regulation is feedback regulation, which is the focus of this review. As modern microscope systems become more complex, often with many independent components that must work together, computer control is inevitable since the exact orchestration of parameters and timings for these multiple components is critical to acquire proper images. A number of techniques have been developed for biological imaging to accomplish this. Here, we summarize the basics of computational microscopy for the purpose of building automatically regulated microscopes focus on feedback regulation by image processing. These techniques allow high throughput data acquisition while monitoring both short- and long-term dynamic phenomena, which cannot be achieved without an automated system. Development, Growth &amp
Differentiation © 2013 Japanese Society of Developmental Biologists.

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Central spindle formation through the regulation of microtubule depolymerization during cytokinesis

R Uehara, Y Tsukada, G Goshima

MOLECULAR BIOLOGY OF THE CELL 23 2012年

査読有り

Monitoring neuronal activities during thermotaxis of C. elegans

Y Tsukada

Neuroscience Research, e185 2010年

査読有り

Sprouty4, an FGF Inhibitor, Displays Cyclic Gene Expression under the Control of the Notch Segmentation Clock in the Mouse PSM

S Hayashi, T Shimoda, M Nakajima, Y Tsukada, Y Sakumura, JK Dale, ...

PLoS One 4 (5), e5603 （PUBLIC LIBRARY SCIENCE） 4 （ 5 ） e5603 2009年05月

査読有り, ISSN 1932-6203

Background: During vertebrate embryogenesis, somites are generated at regular intervals, the temporal and spatial periodicity of which is governed by a gradient of fibroblast growth factor (FGF) and/or Wnt signaling activity in the presomitic mesoderm (PSM) in conjunction with oscillations of gene expression of components of the Notch, Wnt and FGF signaling pathways.
Principal Findings: Here, we show that the expression of Sprouty4, which encodes an FGF inhibitor, oscillates in 2-h cycles in the mouse PSM in synchrony with other oscillating genes from the Notch signaling pathway, such as lunatic fringe. Sprouty4 does not oscillate in Hes7-null mutant mouse embryos, and Hes7 can inhibit FGF-induced transcriptional activity of the Sprouty4 promoter.
Conclusions: Thus, periodic expression of Sprouty4 is controlled by the Notch segmentation clock and may work as a mediator that links the temporal periodicity of clock gene oscillations with the spatial periodicity of boundary formation which is regulated by the gradient of FGF/Wnt activity.

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On the synchrony of morphological and molecular signaling events in cell migration

J. Dauwels, Y. Tsukada, Y. Sakumura, S. Ishii, K. Aoki, T. Nakamura, M. Matsuda, F. Vialatte, A. Cichocki

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) 5506 LNCS （ PART 1 ） 469 - 477 2009年

査読有り

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Quantification of local morphodynamics and local GTPase activity by edge evolution tracking

Y Tsukada, K Aoki, T Nakamura, Y Sakumura, M Matsuda, S Ishii

PLoS computational biology 4 (11), e1000223 （PUBLIC LIBRARY SCIENCE） 4 （ 11 ） e1000223 2008年11月

査読有り, ISSN 1553-734X

Advances in time-lapse fluorescence microscopy have enabled us to directly observe dynamic cellular phenomena. Although the techniques themselves have promoted the understanding of dynamic cellular functions, the vast number of images acquired has generated a need for automated processing tools to extract statistical information. A problem underlying the analysis of time-lapse cell images is the lack of rigorous methods to extract morphodynamic properties. Here, we propose an algorithm called edge evolution tracking (EET) to quantify the relationship between local morphological changes and local fluorescence intensities around a cell edge using time-lapse microscopy images. This algorithm enables us to trace the local edge extension and contraction by defining subdivided edges and their corresponding positions in successive frames. Thus, this algorithm enables the investigation of cross-correlations between local morphological changes and local intensity of fluorescent signals by considering the time shifts. By applying EET to fluorescence resonance energy transfer images of the Rho-family GTPases Rac1, Cdc42, and RhoA, we examined the cross-correlation between the local area difference and GTPase activity. The calculated correlations changed with time-shifts as expected, but surprisingly, the peak of the correlation coefficients appeared with a 6-8 min time shift of morphological changes and preceded the Rac1 or Cdc42 activities. Our method enables the quantification of the dynamics of local morphological change and local protein activity and statistical investigation of the relationship between them by considering time shifts in the relationship. Thus, this algorithm extends the value of time-lapse imaging data to better understand dynamics of cellular function.

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Quantitative analyses for the systems of Rho-family small GTPases and regulation of cellular morphodynamics

Y Tsukada

奈良先端科学技術大学院大学 2008年

査読有り

A molecular model for axon guidance based on cross talk between Rho GTPases

Y Sakumura, Y Tsukada, N Yamamoto, S Ishii

BIOPHYSICAL JOURNAL （BIOPHYSICAL SOCIETY） 89 （ 2 ） 812 - 822 2005年08月

査読有り, ISSN 0006-3495

To systematically understand the molecular events that underlie biological phenomena, we must develop methods to integrate an enormous amount of genomic and proteomic data. The integration of molecular data should go beyond the construction of biochemical cascades among molecules to include tying the biochemical phenomena to physical events. For the behavior and guidance of growth cones, it remains largely unclear how biochemical events in the cytoplasm are linked to the morphological changes of the growth cone. We take a computational approach to simulate the biochemical signaling cascade involving members of the Rho family of GTPases and examine their potential roles in growth-cone motility and axon guidance. Based on the interactions between Cdc42, Rac, and RhoA, we show that the activation of a Cdc42-specific GEF resulted in switching responses between oscillatory and convergent activities for all three GTPases. We propose that the switching responses of these GTPases are the molecular basis for the decision mechanism that determines the direction of the growth-cone expansion, providing a spatiotemporal integration mechanism that allows the growth cone to detect small gradients of external guidance cues. These results suggest a potential role for the cross talk between Rho GTPases in governing growth-cone movement and axon guidance and underscore the link between chemodynamic reactions and cellular behaviors.

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論文 - 塚田　祐基