Tsukada, Yuki

写真a

Affiliation

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

Position

Senior Assistant Professor (Non-tenured)/Assistant Professor (Non-tenured)
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Career 【 Display / hide 】

  • 2009.09
    -
    2023.03

    名古屋大学 理学(系)研究科(研究院), 助教

  • 2023.04
    -
    Present

    Keio University, Faculty of Science and Technology Department of Biosciences and Infomatics, Senior Assistant Professor

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Academic Background 【 Display / hide 】

  • 1998.04
    -
    2002.03

    International Christian University, 教養学部, 理学科

  • 2004.04
    -
    2008.12

    Nara Institute of Science and Technology, Graduate School of Information Science

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Research Areas 【 Display / hide 】

  • Life Science / Neuroscience-general

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Research Keywords 【 Display / hide 】

  • 包括脳ネットワーク

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Books 【 Display / hide 】

  • Optogenetics in Caenorhabditis elegans

    Y Tsukada, I Mori, Springer, 2021

    , Accepted

  • "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

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

    Tsukada, Y, Mori, I, Springer, 2013

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Papers 【 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

    　View Summary

    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

    Accepted

    　View Summary

    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.

  • 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

    Accepted

    　View Summary

    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.

  • 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

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Reviews, Commentaries, etc. 【 Display / hide 】

  • 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

  • Image Processing and Analysis in Java

    塚田 祐基

    細胞工学 (学研メディカル秀潤社 ; 1982-)  33 ( 7 ) 778 - 783 2014

    ISSN  0287-3796

  • Japanese studies on neural circuits and behavior of Caenorhabditis elegans

    Hiroyuki Sasakura, Yuki Tsukada, Shin Takagi, Ikue Mori

    FRONTIERS IN NEURAL CIRCUITS (FRONTIERS MEDIA SA)  7 ( 187 ) doi: 10.3389/fncir.2013.00187 2013.11

    ISSN  1662-5110

    　View Summary

    The nematode Caenorhabditis elegans is an ideal organism for studying neural plasticity and animal behaviors. A total of 302 neurons of a C. elegans hermaphrodite have been classified into 118 neuronal groups. This simple neural circuit provides a solid basis for understanding the mechanisms of the brains of higher animals, including humans. Recent studies that employ modern imaging and manipulation techniques enable researchers to study the dynamic properties of nervous systems with great precision. Behavioral and molecular genetic analyses of this tiny animal have contributed greatly to the advancement of neural circuit research. Here, we will review the recent studies on the neural circuits of C. elegans that have been conducted in Japan. Several laboratories have established unique and clever methods to study the underlying neuronal substrates of behavioral regulation in C. elegans. The technological advances applied to studies of C. elegans have allowed new approaches for the studies of complex neural systems. Through reviewing the studies on the neuronal circuits of C. elegans in Japan, we will analyze and discuss the directions of neural circuit studies.

  • システム神経科学スプリングスクール2013開催報告

    中江 健, 本田 直樹, 浦久保 秀俊, 山尾 将隆, 塚田 祐基, 石井 信

    日本神経回路学会誌 = The Brain & neural networks (日本神経回路学会)  20 ( 2 ) 84 - 87 2013.06

    ISSN  1340-766X

  • Feedback regulation of microscopes by image processing

    Yuki Tsukada, Koichi Hashimoto

    Development Growth and Differentiation 55 ( 4 ) 550 - 562 2013.05

    ISSN  0012-1592

    　View Summary

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

  • Infophysics for animal navigation

    2022.04
    -
    2024.03

    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

    　View Summary

    線虫は温度勾配上に置かれると、それまでに餌を得ていた温度へ向かって探索しながら移動する（温度走性）。このときトラッキングシステムで温度勾配上を探索している個体の行動を計測すると同時に、蛍光画像で非侵襲に特定の神経活動を計測する。
    計測には申請者が開発したトラッキング顕微鏡システムを用い、行動中の線虫を自動的に顕微鏡視野内に捕捉し、神経活動と行動の同時計測を行う。これらのデータを情報量と神経活動の情報伝達に注目して定量的に解析する。また探索行動戦略について数理モデルを構築し、シミュレーション解析を行う。さらにシミュレーション予測に基づいて光遺伝学を用いた検証実験を行う。

  • Elucidating a role of the number and location of synapse for information transmission

    2020.04
    -
    2023.03

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

    　View Summary

    We succeeded in creating a transgenic C. elegans that carries fluorescent labels on synapses and specific neurons with three different fluorescent proteins. We used it to perform laser surgery experiments for cutting an axon along with a specific synaptic position. The effect on neurotransmission was evaluated for each synapse group by performing calcium imaging on these nematodes. We also succeeded in inducing synapse-specific expression of miniSOG, which suppresses synaptic function locally in response to light, and confirmed that light illumination suppresses neurotransmission. Along with the laser surgery experiments, we discovered axonal regeneration in head ganglion neurons and elucidated some of the molecular and cellular mechanisms involved in this process.

  • Principle of body malfunctioning through local cell division failure

    2019.10
    -
    2024.03

    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)

    　View Summary

    本研究では、生体内で起こる少数細胞の分裂制御エラーが、個体発生や機能に及ぼす影響を定量的に明らかにして、細胞分裂異常に起因する病態形成のメカニズムを理解することを目的としている。2020年度は、前年度に作成に成功した光応答性CenpE阻害剤をゼブラフィッシュ初期胚に導入し、同化合物を用いた生体局所分裂障害の導入の実現性を明らかにすることを主な目標とした。化合物が水溶性に比較的乏しいため、投薬条件の特定に、当初予定以上に多くの検証を要した。しかし、最終的に最適処理条件を見出すことに成功し、受精直後からの投薬によって、受精後３時間程度の発生胚から再現性よく、照射光波長依存的に細胞分裂期の染色体運動をon/off制御することに成功した（固定胚を用いた蛍光抗体法および、蛍光ヒストン安定発現系統を用いた生細胞観察により確認した）。さらに、異なる光照射条件下で、同化合物処理胚の発生、生存性を追跡したところ、CenpE活性を阻害する光照射条件下（可視光照射）では、受精後１０時間前後で重篤な発生障害をともなってすべての胚が死滅するのに対し、CenpE活性阻害を解除する照射条件下（UV光照射）においては、すべての胚が、無処理コントロールと差異なく正常な発生を行うことができることを見出した。このことから、同化合物を用いた分裂阻害が、CenpE阻害条件では生体機能を阻害するのに十分に高効率な分裂阻害能をもつ一方で、阻害解除条件では優れた低侵襲性を保っていることが明らかになった。一方で、より多様な細胞分裂の空間制御を実現するために、光学異性化特性の異なる数種の分裂期モータータンパク質の光応答性阻害剤の作成に着手し、そのうちの一部について、培養細胞モデルにおいて、高い時空間分解能で細胞分裂進行をon/off制御できることを見出した。

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

    2019.04
    -
    2022.03

    Japan Society for the Promotion of Science, Grants-in-Aid for Scientific Research, Uehara Ryota, Grant-in-Aid for Scientific Research (B), Coinvestigator(s)

    　View Summary

    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

    2017.04
    -
    2018.03

    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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Intellectual Property Rights, etc. 【 Display / hide 】

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

    Date announced： US Patent App. 17/628,744   

    Patent, Joint

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Courses Taught 【 Display / hide 】

  • TOPICS IN BIOSCIENCES AND INFORMATICS 2

    2024

  • SEMINAR IN BIOSCIENCES AND INFORMATICS

    2024

  • LABORATORY IN SCIENCE

    2024

  • INTRODUCTION TO BIOLOGY TODAY

    2024

  • CELL BIOLOGY 3

    2024

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