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Research interests:
Bioimaging; Learning and Memory; Neuroethology; Auditory Processing; Anatomy, Development and Evolution

Ongoing research projects:

[Worm Group]
- In vivo calcium imaging of AIY interneuron related to early adaptation in C. elegans

- In vivo cGMP imaging of AWC sensory neuron related to olfactory sensing in C. elegans

[Bird Group]
- In vivo pH imaging of auditory stimulation-induced neural activity in female zebra finch
- Neuronal cytoarchitecture of hippocampal formation in female zebra finch

[Cell Group]
- Mitochondrial Magnesium Imaging Using Newly Developed Fluorescent Probe
- Subcellular analysis of paxillin contribution to bradykinin-induced neurite retraction with a photoinactivatable paxillin

[Ascidian Group]
- Evolution and Development of Chordate
- Quantitative analysis of ascidian tailbud stage embryo at single cell level by constructing 3D Virtual Embryo
- Analysis of network structure of projections extending from peripheral neurons in tunic of ascidian larva


Lab Members:

Proffesor, Kotaro OKA, E-mail: oka (at) bio.keio.ac.jp
Assistant Professor, Kohji HOTTA, E-mail: khotta (at) bio.keio.ac.jp
Secretary, Itoka KAMIGASAKO

Toshinobu SIMOI
Takeshi FUKAWA

PhD course

Master's course
Taichi IMAI
Masahiro INDA
Hiromochi MURAOKA
Mitsuru IIZUMI
Shunsei INOUE
Haruka MORI

Shota UENO
Taiki KATO
Tubasa SEO



  1. Taichi Akahoshi, Kohji Hotta, Kotaro Oka
    Characterization of calcium transients during early embryogenesis in ascidians Ciona robusta (Ciona intestinalis type A) and Ciona savignyi
    Dev Biol., 2017 Sep.
  2. Shinobu Hirai, Kohji Hotta, Yoshihiro Kubo, Atsuo Nishino, Shigeo Okabe, Yasushi Okamura, Haruo Okado
    AMPA glutamate receptors are required for sensory-organ formation and morphogenesis in the basal chordate
    Proc Natl Acad Sci U S A., 2017 Mar.
  3. Hisashi Shidara, Kohji Hotta, Kotaro Oka
    Compartmentalized cGMP responses of olfactory sensory neurons in Caenorhabditis elegans.
    J Nuerosci., 2017 May.


  1. Ryo Tanamotoa, Yutaka Shindoa, Mariko Niwanoa, Yoshinori Matsumotob, Norihisa Mikic, Kohji Hottaa, Kotaro Oka
    Qualitative and quantitative estimation of comprehensive synaptic connectivity in short- and long-term cultured rat hippocampal neurons with new analytical methods inspired by Scatchard and Hill plots
    Biochem Biophys Res Commun., 2016 Feb.
  2. Yuichi Tanimoto, Takumi Hiraiwa, Yuichiro Nakai, Yutaka Shindo, Kotaro Oka, Noriko Hiroi, Akira Funahashi Detection of Temperature Difference in Neuronal Cells
    Sci Rep., 2016 Mar.
  3. Yutaka Shindo, Ryu Yamanaka, Koji Suzuki, Kohji Hotta, Kotaro Oka
    Altered expression of Mg2+ transport proteins during Parkinson's disease-like dopaminergic cell degeneration in PC12 cells.
    Biochim Biophys Acta., 2016 May.
  4. Yutaka Shindo, Hirokazu Komatsu, Kohji Hotta, Katsuhiko Ariga, Kotaro Oka
    An Artificial Reaction Promoter Modulates Mitochondrial Functions via Chemically Promoting Protein Acetylation
    Sci Rep., 2016 Jul.
  5. Ryu Yamanaka, Sho Tabata, Yutaka Shindo, Kohji Hotta, Koji Suzuki, Tomoyoshi Soga, Kotaro Oka
    Mitochondrial Mg(2+) homeostasis decides cellular energy metabolism and vulnerability to stress.
    Sci Rep., 2016 Jul.


  1. Yuji Mizotani, Shun Itoh, Kohji Hotta, Etsu Tashiro, Kotaro Oka, Masaya Imoto
    Evaluation of drug toxicity profiles based on the phenotypes of ascidian Ciona intestinalis
    Biochem Biophys Res Commun., 2015 Aug.
  2. Mariko Ogawa, Hisashi Shidara, Kotaro Oka, Masaru Kurosawa, Nobuyuki Nukina, Yoshiaki Furukawa
    Cysteine residues in Cu,Zn-superoxide dismutase are essential to toxicity in Caenorhabditis elegans model of amyotrophic lateral sclerosis
    Biochem Biophys Res Commun. 2015 Aug.
  3. Ryo Tanamoto, Yutaka Shindo, Norihisa Miki, Yoshinori Matsumoto, Kohji Hotta, Kotaro Oka Electrical stimulation of cultured neurons using a simply patterned indium-tin-oxide (ITO) glass electrode
    J Neurosci Methods., 2015 Sep.
  4. Hiroto Ogawa and Kotaro Oka Direction-Specific Adaptation in Neuronal and Behavioral Responses of an Insect Mechanosensory System
    J Neurosci. 2015 Aug.
  5. Yutaka Shindo, Ryu Yamanaka, Koji Suzuki, Kohji Hotta, Kotaro Oka, Intracellular magnesium level determines cell viability in the MPP+ model of Parkinson's disease
    Biochim Biophys Acta. 2015 Aug.
  6. Rika Suzuki, Kohji Hotta, Kotaro Oka Spatiotemporal quantification of subcellular ATP levels in a single HeLa cell during changes in morphology
    Sci Rep. 2015 Nov.
  7. Ryu Yamanaka, Yutaka Shindo, Takamasa Karube, Kohji Hotta, Koji Suzuki, Kotaro Oka Neural depolarization triggers Mg(2+) influx in rat hippocampal neurons
    Neuroscience. 2015 Dec.


  1. Takatoshi D Yokoyama, Kohji Hotta, Kotaro Oka
    Comprehensive Morphological Analysis of Individual Peripheral Neuron Dendritic Arbors in Ascidian Larvae using the Photoconvertible Protein Kaede
    Dev Dyn., 2014 Oct.
  2. Hirabayashi A, Shindo Y, Oka K, Takahashi D, Toshima K.
    Photodegradation of amyloid β and reduction of its cytotoxicity to PC12 cells using porphyrin derivatives.
    Chem Commun (Camb). 2014 Jul 11.
  3. Iwasaki M, Poulsen TM, Oka K, Hessler NA.
    Sexually dimorphic activation of dopaminergic areas depends on affiliation during courtship and pair formation.
    Front Behav Neurosci. 2014 Jun 11;8:210.
  4. Lucia Manni, Fabio Gasparini, Kohji Hotta, Katherine J. Ishizuka, Lorenzo Ricci, Stefano Tiozzo, Ayelet Voskoboynik, Delphine Dauga
    Ontology for the asexual development and anatomy of the colonial chordate Botryllus schlosseri.
    PLOSONE, 2014 May 1;9(5):e96434.
  5. Komatus H, Shindo Y, Oka K, Hill JP, Ariga K.
    Ubiquinone-Rhodol (UQ-Rh) for Fluorescence Imaging of NAD(P)H through Intracellular Activation.
    Angew Chem Int Ed Engl. 2014 Apr 7;53(15):3993-5.
  6. Shimoi T, Mizutani K, Kojima D, Kitamura Y, Hotta K, Ogawa H, Oka K.
    Identification of oscillatory firing neurons associated with locomotion in the earthworm through synapse imaging.
    Neuroscience. 2014 Mar 19;268C:149-158
  7. Fujii, Tomohiko; Shindo, Yutaka; Hotta, Kohji; Citterio, Daniel; Nishiyama, Shigeru; Suzuki, Koji; Oka, Kotaro
    Design and Synthesis of a FlAsH type Mg2+ Fluorescent Probe for Specific Protein Labeling
    J. Am. Chem. Soc, 2014, Feb 12;136(6):2374-81.
  8. Lucia Manni, Fabio Gasparini , Kohji Hotta, Katherine J. Ishizuka, Lorenzo Ricci, Stefano Tiozzo, Ayelet Voskoboynik, Delphine Dauga Ontology for the asexual development and anatomy of the colonial chordate Botryllus schlosseri
    PLoS One. 2014 May.


  1. Mai Iwasaki, Thomas M. Poulsen,Kotaro Oka, Neal A. Hessler
    Singing-Related Activity in Anterior Forebrain of Male Zebra Finches Reflects Courtship Motivation for Target Females
    PLOS ONE, 2013, Nov 29;8(11):e81725.
  2. Takahiko Kobayashi, Fumiaki Nagase, Kohji Hotta, Kotaro Oka
    Crosstalk between Second Messengers Predicts the Motility of the Growth Cone
    Scientific Reports, 2013, Nov 1;3:3118.
  3. Mitsuru J Nakamura, Kohji Hotta, Kotaro Oka
    Raman spectroscopic imaging of the whole Ciona intestinalis embryo during development
    PLOS ONE, 2013 Aug 20;8(8):e71739. 
  4. Ryu Yamanaka, Yutaka Shindo, Kohji Hotta, Koji Suzuki, Kotaro Oka
    NO/cGMP/PKG Signaling Pathway Induces Magnesium Release Mediated by mitoKATP Channel Opening in Rat Hippocampal Neurons
    FEBS Lett. 2013 Jul 4. pii: S0014-5793(13)00507-3.
  5. Kobayashi J, Shidara H, Morisawa Y, Kawakami M, Tanahashi Y, Hotta K, Oka K.
    A method for selective ablation of neurons in C. elegans using the phototoxic fluorescent protein, KillerRed.
    Neurosci Lett. 2013 Jun 4. pii: S0304-3940(13)00500-4.
  6. Komatsu H, Shindo Y, Kawashima SA, Yamatsugu K, Oka K, Kanai M.
    Intracellular Activation of Acetyl-CoA by Artificial Reaction Promoter and Its Fluorescent Detection
    Chem. Commun., 2013, 49 (28), 2876 - 2878
  7. Hisashi Shidara, Junya Kobayashi, Ryo Tanamoto, Kohji Hotta, Kotaro Oka
    Odorant-induced membrane potential depolarization of AIY interneuron in Caenorhabditis elegans
    Neuroscience letters, 2013 Apr 29;541:199-203.


  1. Mitsuru J Nakamura, Jun Terai, Reiko Okubo, Kohji Hotta, Kotaro Oka
    Three-Dimensional Anatomy of the Ciona intestinalis Tailbud Embryo at Single-cell Resolution
    Developmental Biology, 372(2):274-84, 2012 Supporting Page


  2. Horita H, Kobayashi M, Liu WC, Oka K, Jarvis ED, Wada K.
    Specialized Motor-Driven dusp1 Expression in the Song Systems of Multiple Lineages of Vocal Learning Birds
    PLoS One,7(8):e42173, Online Journal, 2012
  3. Hiroi N, Klann M, Iba K, Heras Ciechomski PD, Yamashita S, Tabira A, Okuhara T, Kubojima T, Okada Y, Oka K, Mange R, Unger M, Funahashi A, Koeppl H
    From microscopy data to in silico environments for in vivo-oriented simulations
    EURASIP J Bioinform Syst Biol., 2012(1):7, Online Journal, 2012


  1. Matsui A., Umezawa K, Shindo Y., Fujii T., Citterio D., Oka K., Suzuki K.
    A Near-Infrared Fluorescent Calcium Probe: a New Tool for Intracellular Multicolor Ca2+ Imaging
    Chem. Commun. (Camb), 2011, Oct 7;47(37):10407-9.
  2. Yutaka Shindo, Tomohiko Fujii, Hirokazu Komatsu, Daniel Citterio, Kohji Hotta, Koji Suzuki, Kotaro Oka: Newly Developed Mg2+?Selective Fluorescent Probe Enables Visualization of Mg2+ Dynamics in Mitochondria
    PLoS One. 2011; Accepted
  3. Kawada T, Ogasawara M, Sekiguchi T, Aoyama M, Hotta K, Oka K, Satake H. Peptidomic Analysis of the Central Nervous System of the Protochordate, Ciona intestinalis: Homologs and Prototypes of Vertebrate Peptides and Novel Peptides. Endocrinology. 2011 Apr 5. [Epub ahead of print] PubMed PMID: 21467196.
  4. Mamiko Suzuki, Tetsuya Kimura, Hiroto Ogawa, Kohji Hotta, Kotaro Oka: Chromatophore Activity during Natural Pattern Expression by the Squid Sepioteuthis lessoniana: Contributions of Miniature Oscillation
    PLoS One. 2011; Published online 2011 April 1.


  1. Endo T, Ueno K, Yonezawa K, Mineta K, Hotta K, Satou Y, Yamada L, Ogasawara M, Takahashi H, Nakajima A, et al.: CIPRO 2.5: Ciona intestinalis protein database, a unique integrated repository of large-scale omics data, bioinformatic analyses and curated annotation, with user rating and reviewing functionality. Nucleic Acids Res 2010.
  2. Shindo Y, Fujimoto A, Hotta K, Suzuki K, Oka K: Glutamate-induced calcium increase mediates magnesium release from mitochondria in rat hippocampal neurons.J Neurosci Res 2010, 88:3125-3132.
  3. Terakubo HQ, Nakajima Y, Sasakura Y, Horie T, Konno A, Takahashi H, Inaba K, Hotta K, Oka K: Network structure of projections extending from peripheral neurons in the tunic of ascidian larva. Dev Dyn 2010, 239:2278-2287.
  4. Tassy O, Dauga D, Daian F, Sobral D, Robin F, Khoueiry P, Salgado D, Fox V, Caillol D, Schiappa R, Laporte B, Rios A, Luxardi G, Kusakabe T, Joly JS, Darras S, Christiaen L, Contensin M, Auger H, Lamy C, Hudson C, Rothbächer U, Gilchrist MJ, Makabe KW, Hotta K, Fujiwara S, Satoh N, Satou Y, Lemaire P : The ANISEED database: digital representation, formalization, and elucidation of a chordate developmental program. Genome Res 2010, 20:1459-1468.
  5. Takahashi H, Hotta K, Takagi C, Ueno N, Satoh N, Shoguchi E: Regulation of notochord-specific expression of Ci-Bra downstream genes in Ciona intestinalis embryos.Zoolog Sci 2010, 27:110-118.
  6. Niino Y, Hotta K, Oka K: Blue fluorescent cGMP sensor for multiparameter fluorescence imaging.PLoS One 2010, 5:e9164.
  7. Okazaki S, Kanoh S, Tsukada M, Oka K: Neural substrate of sound duration discrimination during an auditory sequence in the guinea pig primary auditory cortex. Hear Res 2010, 259:107-116.
  8. Konno A, Kaizu M, Hotta K, Horie T, Sasakura Y, Ikeo K, Inaba K: Distribution and structural diversity of cilia in tadpole larvae of the ascidian Ciona intestinalis. Dev Biol 2010, 337:42-62.


  1. Yamada S, Hotta K, Yamamoto TS, Ueno N, Satoh N, Takahashi H: Interaction of notochord-derived fibrinogen-like protein with Notch regulates the patterning of the central nervous system of Ciona intestinalis embryos.Dev Biol 2009, 328:1-12.
  2. Suzuki M, Kimura T, Ogawa H, Hotta K, Oka K: FMRFamide elicits chromatophore expansion and retraction depending on its type and development in the squid, Sepioteuthis lessoniana. Invert Neurosci 2009, 9:185-193.
  3. Yanashima R, Kitagawa N, Matsubara Y, Weatheritt R, Oka K, Kikuchi S, Tomita M, Ishizaki S: Network Features and Pathway Analyses of a Signal Transduction Cascade. Front Neuroinformatics 2009, 3:13.
  4. Niino Y, Hotta K, Oka K: Simultaneous live cell imaging using dual FRET sensors with a single excitation light.PLoS One 2009, 4:e6036.
  5. Morita K, Saito Y, Sato K, Oka K, Hotta K, Sakakibara Y: Genome-wide searching with base-pairing kernel functions for noncoding RNAs: computational and expression analysis of snoRNA families in Caenorhabditis elegans. Nucleic Acids Res 2009, 37:999-1009.
  6. Hasegawa Y, Honda A, Umezawa K, Niino Y, Oka K, Chiba T, Aiso S, Tanimoto A, Citterio D, Suzuki K:Cell-based in vivo dual imaging probes using genetically expressed tags and chemical contrast agents. Chem Commun (Camb) 2009:4040-4042.


  1. Ogawa H, Cummins GI, Jacobs GA, Oka K: Dendritic design implements algorithm for synaptic extraction of sensory information. J Neurosci 2008, 28:4592-4603.
  2. Matsubara Y, Kikuchi S, Sugimoto M, Oka K, Tomita M: Algebraic method for the analysis of signaling crosstalk. Artif Life 2008, 14:81-94.
  3. Aonuma H, Kitamura Y, Niwa K, Ogawa H, Oka K: Nitric oxide-cyclic guanosine monophosphate signaling in the local circuit of the cricket abdominal nervous system. Neuroscience 2008, 157:749-761. 
  4. Satou Y, Mineta K, Ogasawara M, Sasakura Y, Shoguchi E, Ueno K, Yamada L, Matsumoto J, Wasserscheid J, Dewar K, et al.: Improved genome assembly and evidence-based global gene model set for the chordate Ciona intestinalis: new insight into intron and operon populations.Genome Biol 2008, 9:R152.
  5. Hotta K, Takahashi H, Satoh N, Gojobori T: Brachyury-downstream gene sets in a chordate, Ciona intestinalis: integrating notochord specification, morphogenesis and chordate evolution.Evol Dev 2008, 10:37-51.
  6. Homma K, Niino Y, Hotta K, Oka K: Ca(2+) influx through P2X receptors induces actin cytoskeleton reorganization by the formation of cofilin rods in neurites. Mol Cell Neurosci 2008, 37:261-270.
  7. Aoyama M, Kawada T, Fujie M, Hotta K, Sakai T, Sekiguchi T, Oka K, Satoh N, Satake H: A novel biological role of tachykinins as an up-regulator of oocyte growth: identification of an evolutionary origin of tachykininergic functions in the ovary of the ascidian, Ciona intestinalis.Endocrinology 2008, 149:4346-4356.


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