Tsukada, Yuki



Faculty of Science and Technology, Department of Biosciences and Informatics (Yagami)


Senior Assistant Professor (Non-tenured)/Assistant Professor (Non-tenured)


Books 【 Display / hide

  • "個体行動の定量生物学" 定量生物学 小林 徹也 編

    塚田祐基, 化学同人, 2018

  • "細胞運動の定量生物学" 定量生物学 小林 徹也 編

    高木 拓明, 塚田 祐基, 化学同人, 2018

  • "ImageJではじめる生物画像解析"

    三浦 耕太, 塚田 祐基, 学研メディカル秀潤社, 2016

  • "Optogenetics in Caenorhabditis elegans" Optogenetics -Light-Sensing Proteins and Their Applications,

    Tsukada, Y, Mori, I, Springer, 2015

  • "Behavioral Analysis in Caenorhabditis elegans" Methods in Neuroethological Research

    Tsukada, Y, Mori, I, Springer, 2013

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Papers 【 Display / hide

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

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

    G3 12 (11), jkac248  2022


  • Composition for maintenance and/or improvement of memory/learning ability, and food, medicine and feed each containing said composition

    S Higurashi, N Kentaro, I Mori, S Nakano, Y Tsukada

    US Patent App. 17/628,744  2022


  • Optogenetics in Caenorhabditis elegans

    Y Tsukada, I Mori

    Optogenetics: Light-Sensing Proteins and Their Applications in Neuroscience …  2021


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

    Tzu‐Ting Huang, Hironori J. Matsuyama, Yuki Tsukada, Aakanksha Singhvi, Ru‐Ting Syu, Yun Lu, Shai Shaham, Ikue Mori, Chun‐Liang Pan

    Aging Cell (Wiley)  19 ( 5 )  2020.05

    Accepted,  ISSN  1474-9718

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

    Shunji Nakano, Muneki Ikeda, Yuki Tsukada, Xianfeng Fei, Takamasa Suzuki, Yusuke Niino, Rhea Ahluwalia, Ayana Sano, Rumi Kondo, Kunio Ihara, Atsushi Miyawaki, Koichi Hashimoto, Tetsuya Higashiyama, Ikue Mori

    Proceedings of the National Academy of Sciences of the United States of America 117 ( 3 ) 1638 - 1647 2020.01


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    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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Reviews, Commentaries, etc. 【 Display / hide

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

    Ichiro Aok, Makoto Shiota, Yuki Tsukada, Shunji Nakano, Ikue Mori

    PloS one (PLoS ONE)  17 ( 12 ) e0278343 2022.12

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    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.

  • Genetic screens identified dual roles of MAST kinase and CREB within a single thermosensory neuron in the regulation of C. elegans thermotaxis behavior.

    Shunji Nakano, Airi Nakayama, Hiroo Kuroyanagi, Riku Yamashiro, Yuki Tsukada, Ikue Mori

    G3 (Bethesda, Md.) (G3: Genes, Genomes, Genetics)  12 ( 11 )  2022.11

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    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 MAST 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 post-synaptic 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.

  • 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 2019.07

  • Uncoordinated centrosome cycle underlies the instability of nondiploid somatic cells in mammals

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

    J Cell Biol. (Rockefeller University Press)  217 ( 7 ) 2463 - 2483 2018.07

  • ImageJ定量階梯(第4回)簡単な画像処理とその応用(色符号化,マスク,鮮鋭化)

    塚田 祐基

    細胞工学 (学研メディカル秀潤社 ; 1982-)  33 ( 3 ) 337 - 342 2014

    ISSN  0287-3796

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Research Projects of Competitive Funds, etc. 【 Display / hide

  • Infophysics for animal navigation


    Japan Society for the Promotion of Science, Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area), Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area), Principal investigator

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  • 神経情報伝達におけるシナプス数と位置の役割


    日本学術振興会, Grants-in-Aid for Scientific Research, Grant-in-Aid for Scientific Research (C), Principal investigator

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    本研究では、神経回路に対して光を用いたマイクロ-ナノメートル単位の時空間操作を行い、その影響を神経活動と個体行動の計測として定量することで、神経回路の構造が回路全体の機能においてもつ役割の理解を進めることを目的とする。この目的達成のため、本年度は主に以下の項目について進捗があった。異所局在の解消、インテグラントの作成、蛍光3色イメージングの実現、パルスを用いた光毒性の軽減、AIY介在神 経細胞の応答ばらつき解消。まず異所局在の解消については、光遺伝学によるシナプスレベルの神経活動制御に対してminiSOGを用いた方法を進めているが、miniSOGを標的神経細胞へ発現させる際、シナプスへの局在と共に、細胞体のERらしき場所にも発現する問題があった。そのためER移行シグナルを付加させたタンパク質を新たに作成し、標的神経細胞のプロモーターと共に導入したところ、この異所局在が解消された。これにより光によるERへの不必要なダメージが低減されることが期待できる。これらのタンパク質を発現した線虫系統は、染色体外に導入遺伝子を保持するものであったため、ゲノムに挿入させたインテグラント系統の作成することで、遺伝子発現の安定化と系統のばらつき抑制を実現した。さらにこれまでGCaMPとRCaMPで神経活動を計測していた線虫系統に、633nmの長波長で励起される蛍光タンパクを導入し、シナプスをラベルした。この3色イメージングにより、シナプス位置を計測しながらレーザー手術を行うことが実現できた。また、連続光ではなくパルス光を使うことによる光毒性の低減、さらには実験操作の工夫により、ばらつきの多かったAIY介在神経細胞の応答を均一化することに成功した。

  • Principle of body malfunctioning through local cell division failure


    Japan Society for the Promotion of Science, Grants-in-Aid for Scientific Research Fund for the Promotion of Joint International Research (Fostering Joint International Research (B)), Fund for the Promotion of Joint International Research (Fostering Joint International Research (B)), Coinvestigator(s)

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  • Principle of chronic centrosome aberrations in whole-genome duplicated cells and its contribution to cellular heterogeneity


    日本学術振興会, Grants-in-Aid for Scientific Research, Uehara Ryota, Grant-in-Aid for Scientific Research (B), Coinvestigator(s)

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    In this study, we aimed to elucidate the principle and significance of centrosome hyperactivation associated with whole-genome duplication (WGD), a cellular abnormality common in 30% of cancers. We found that this phenomenon is caused by an increase in the accumulation of centrosomal proteins resulting from the doubling of the gene dosage of a centrosome scaffolding gene upon WGD. By developing a method to cancel this centrosome hyperactivation artificially, we found that this phenomenon does not play an adaptive role in the proliferation control of WGD cells. However, contrary to our initial expectation, we found that the centrosome hyperactivation made WGD cells more fragile in centrosomal structural homeostatic regulation, suggesting the feasibility of WGD cell-selective suppression through targeting their fragility.

  • 複数のカメラを用いた顕微鏡オートフォーカスアルゴリズムの開発


    公益財団法人堀科学芸術振興財団, 第2部研究助成, Principal investigator

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Courses Taught 【 Display / hide











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