Faculty Profiles - SHIMIZU, Takashi

Papers - SHIMIZU, Takashi

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The zebrafish cerebellar neural circuits are involved in orienting behavior Reviewed

S Hosaka, M Hosokawa, M Hibi, T Shimizu

Vol. 11 ( 10 ) 2024.10

Foxp- and Skor-family proteins control differentiation of Purkinje cells from Ptf1a and Neurogenin1-expressing progenitors in zebrafish.

Itoh T, Uehara M, Yura S, Wang JC, Fujii Y, Nakanishi A, Shimizu T, Hibi M

Development (Cambridge, England) 2024.3

A gene regulatory network combining Pax3/7, Sox10 and Mitf generates diverse pigment cell types in medaka and zebrafish

Miyadai, M; Takada, H; Shiraishi, A; Kimura, T; Watakabe, I; Kobayashi, H; Nagao, Y; Naruse, K; Higashijima, SI; Shimizu, T; Kelsh, RN; Hibi, M; Hashimoto, H

DEVELOPMENT Vol. 150 ( 19 ) 2023.10

Optogenetic manipulation of neuronal and cardiomyocyte functions in zebrafish using microbial rhodopsins and adenylyl cyclases. Reviewed

Hagio H, Koyama W, Hosaka S, Song AD, Narantsatsral J, Matsuda K, Shimizu T, Hososhima S, Tsunoda SP, Kandori H, Hibi M.

Elife Vol. 12 ( e83975 ) 2023.8

Optogenetic manipulation of Gq- and Gi/o-coupled receptor signaling in neurons and heart muscle cells. Invited Reviewed

Hagio H, Koyama W, Hosaka S, Song AD, Narantsatsral J, Matsuda K, Sugihara T, Shimizu T, Koyanagi M, Terakita A, Hibi M.

Elife Vol. 12 ( e83974 ) 2023.8

Cfdp1 controls the cell cycle and neural differentiation in the zebrafish cerebellum and retina Reviewed

Vol. 250 ( 11 ) page： 1618 - 1633 2021.11

Involvement of cerebellar neural circuits in active avoidance conditioning in zebrafish Reviewed

Wataru Koyama, Ryo Hosomi, Koji Matsuda, Koichi Kawakami, Masahiko Hibi, Takashi Shimizu

eNeuro Vol. 8 ( 3 ) page： 507 - 520 2021

Gsx2 is required for specification of neurons in the inferior olivary nuclei from Ptf1a-expressing neural progenitors in zebrafish. Reviewed International journal

Tsubasa Itoh, Miki Takeuchi, Marina Sakagami, Kazuhide Asakawa, Kenta Sumiyama, Koichi Kawakami, Takashi Shimizu, Masahiko Hibi

Development (Cambridge, England) Vol. 147 ( 19 ) 2020.10

Language：English Publishing type：Research paper (scientific journal)

Neurons in the inferior olivary nuclei (IO neurons) send climbing fibers to Purkinje cells to elicit functions of the cerebellum. IO neurons and Purkinje cells are derived from neural progenitors expressing the proneural gene ptf1a In this study, we found that the homeobox gene gsx2 was co-expressed with ptf1a in IO progenitors in zebrafish. Both gsx2 and ptf1a zebrafish mutants showed a strong reduction or loss of IO neurons. The expression of ptf1a was not affected in gsx2 mutants, and vice versa. In IO progenitors, the ptf1a mutation increased apoptosis whereas the gsx2 mutation did not, suggesting that ptf1a and gsx2 are regulated independently of each other and have distinct roles. The fibroblast growth factors (Fgf) 3 and 8a, and retinoic acid signals negatively and positively, respectively, regulated gsx2 expression and thereby the development of IO neurons. mafba and Hox genes are at least partly involved in the Fgf- and retinoic acid-dependent regulation of IO neuronal development. Our results indicate that gsx2 mediates the rostro-caudal positional signals to specify the identity of IO neurons from ptf1a-expressing neural progenitors.

DOI： 10.1242/dev.190603

Web of Science

PubMed

Role of Reelin in cell positioning in the cerebellum and the cerebellum-like structure in zebrafish. Reviewed

Nimura T, Itoh T, Hagio H, Hayashi T, Di Donato V, Takeuchi M, Itoh T, Inoguchi F, Sato Y, Yamamoto N, Katsuyama Y, Del Bene F, Shimizu T, Hibi M

Developmental biology Vol. 455 ( 2 ) page： 393 - 408 2019.11

Tracing of Afferent Connections in the Zebrafish Cerebellum Using Recombinant Rabies Virus

Dohaku Ryuji, Yamaguchi Masahiro, Yamamoto Naoyuki, Shimizu Takashi, Osakada Fumitaka, Hibi Masahiko

FRONTIERS IN NEURAL CIRCUITS Vol. 13 2019.4

Roles of maternal wnt8a transcripts in axis formation in zebrafish. Reviewed

Hino H, Nakanishi A, Seki R, Aoki T, Yamaha E, Kawahara A, Shimizu T, Hibi M

Devlopmental Biology Vol. 434 ( 1 ) page： 96-107 2018.2

Roles of maternal wnt8a transcripts in axis formation in zebrafish. International journal

Hino H, Nakanishi A, Seki R, Aoki T, Yamaha E, Kawahara A, Shimizu T, Hibi M

Devlopmental Biology Vol. 434 ( 1 ) page： 96 - 107 2018.2

Language：English Publishing type：Research paper (scientific journal)

In early zebrafish development, the program for dorsal axis formation begins soon after fertilization. Previous studies suggested that dorsal determinants (DDs) localize to the vegetal pole, and are transported to the dorsal blastomeres in a microtubule-dependent manner. The DDs activate the canonical Wnt pathway and induce dorsal-specific genes that are required for dorsal axis formation. Among wnt-family genes, only the wnt8a mRNA is reported to localize to the vegetal pole in oocytes and to induce the dorsal axis, suggesting that Wnt8a is a candidate DD. Here, to reveal the roles of maternal wnt8a, we generated wnt8a mutants by transcription activator-like effector nucleases (TALENs), and established zygotic, maternal, and maternal zygotic wnt8a mutants by germ-line replacement. Zebrafish wnt8a has two open reading frames (ORF1 and ORF2) that are tandemly located in the genome. Although the zygotic ORF1 or ORF2 wnt8a mutants showed little or no axis-formation defects, the ORF1/2 compound mutants showed antero-dorsalized phenotypes, indicating that ORF1 and ORF2 have redundant roles in ventrolateral and posterior tissue formation. Unexpectedly, the maternal wnt8a ORF1/2 mutants showed no axis-formation defects. The maternal-zygotic wnt8a ORF1/2 mutants showed more severe antero-dorsalized phenotypes than the zygotic mutants. These results indicated that maternal wnt8a is dispensable for the initial dorsal determination, but cooperates with zygotic wnt8a for ventrolateral and posterior tissue formation. Finally, we re-examined the maternal wnt genes and found that Wnt6a is an alternative candidate DD.

DOI： 10.1016/j.ydbio.2017.11.016

Web of Science

PubMed

Axis Formation and Its Evolution in Ray-Finned Fish

Hibi Masahiko, Takeuchi Masaki, Hashimoto Hisashi, Shimizu Takashi

REPRODUCTIVE AND DEVELOPMENTAL STRATEGIES: THE CONTINUITY OF LIFE page： 709-+ 2018

Granule cells control recovery from classical conditioned fear responses in the zebrafish cerebellum

Koji Matsuda, Masayuki Yoshida, Koichi Kawakami, Masahiko Hibi, Takashi Shimizu

SCIENTIFIC REPORTS Vol. 7 ( 1 ) page： 11865 2017.9

Language：English Publishing type：Research paper (scientific journal) Publisher：NATURE PUBLISHING GROUP

Although previous studies show that the cerebellum is involved in classical fear conditioning, it is not clear which components in the cerebellum control it or how. We addressed this issue using a delayed fear-conditioning paradigm with late-stage zebrafish larvae, with the light extinguishment as the conditioned stimulus (CS) and an electric shock as the unconditioned stimulus (US). The US induced bradycardia in the restrained larvae. After paired-associate conditioning with the CS and US, a substantial population of the larvae displayed CS-evoked bradycardia responses. To investigate the roles of the zebrafish cerebellum in classical fear conditioning, we expressed botulinum toxin or the Ca2+ indicator GCaMP7a in cerebellar neurons. The botulinum-toxin-dependent inhibition of granule-cell transmissions in the corpus cerebelli (CCe, the medial lobe) did not suppress the CS-evoked bradycardia response, but rather prolonged the response. We identified cerebellar neurons with elevated CS-evoked activity after the conditioning. The CS-evoked activity of these neurons was progressively upregulated during the conditioning and was downregulated with repetition of the unpaired CS. Some of these neurons were activated immediately upon the CS presentation, whereas others were activated after a delay. Our findings indicate that granule cells control the recovery from conditioned fear responses in zebrafish.

DOI： 10.1038/s41598-017-10794-0

Web of Science

PubMed

Granule cells control recovery from classical conditioned fear responses in the zebrafish cerebellum. Reviewed

Matsuda K, Yoshida M, Kawakami K, Hibi M, Shimizu T.

Scientific reports Vol. 7 ( 1 ) 2017.9

Medaka and zebrafish contactin1 mutants as a model for understanding neural circuits for motor coordination. Reviewed

Takeuchi M, Inoue C, Goshima A, Nagao Y, Shimizu K, Miyamoto H, Shimizu T, Hashimoto H, Yonemura S, Kawahara A, Hirata Y, Yoshida M, Hibi M1

Genes to Cells Vol. 22 ( 8 ) page： 723-741 2017.8

Medaka and zebrafish contactin1 mutants as a model for understanding neural circuits for motor coordination

Takeuchi Miki, Inoue Chikako, Goshima Akiko, Nagao Yusuke, Shimizu Koichi, Miyamoto Hiroki, Shimizu Takashi, Hashimoto Hisashi, Yonemura Shigenobu, Kawahara Atsuo, Hirata Yutaka, Yoshida Masayuki, Hibi Masahiko

GENES TO CELLS Vol. 22 ( 8 ) page： 723-741 2017.8

Gene expression profiling of granule cells and Purkinje cells in the zebrafish cerebellum. International journal

Miki Takeuchi, Shingo Yamaguchi, Yoshimasa Sakakibara, Takuto Hayashi, Koji Matsuda, Yuichiro Hara, Chiharu Tanegashima, Takashi Shimizu, Shigehiro Kuraku, Masahiko Hibi

The Journal of comparative neurology Vol. 525 ( 7 ) page： 1558 - 1585 2017.5

Language：English Publishing type：Research paper (scientific journal)

The structure of the neural circuitry of the cerebellum, which functions in some types of motor learning and coordination, is generally conserved among vertebrates. However, some cerebellar features are species specific. It is not clear which genes are involved in forming these conserved and species-specific structures and functions. This study uses zebrafish transgenic larvae expressing fluorescent proteins in granule cells, Purkinje cells, or other cerebellar neurons and glial cells to isolate each type of cerebellar cells by fluorescence-activated cell sorting and to profile their gene expressions by RNA sequencing and in situ hybridization. We identify genes that are upregulated in granule cells or Purkinje cells, including many genes that are also expressed in mammalian cerebella. Comparison of the transcriptomes in granule cells and Purkinje cells in zebrafish larvae reveals that more developmental genes are expressed in granule cells, whereas more neuronal-function genes are expressed in Purkinje cells. We show that some genes that are upregulated in granule cells or Purkinje cells are also expressed in the cerebellum-like structures. Our data provide a platform for understanding the development and function of the cerebellar neural circuits in zebrafish and the evolution of cerebellar circuits in vertebrates. J. Comp. Neurol. 525:1558-1585, 2017. © 2016 Wiley Periodicals, Inc.

DOI： 10.1002/cne.24114

Web of Science

PubMed

Evolutionary mechanisms that generate morphology and neural-circuit diversity of the cerebellum

Hibi Masahiko, Matsuda Koji, Takeuchi Miki, Shimizu Takashi, Murakami Yasunori

DEVELOPMENT GROWTH & DIFFERENTIATION Vol. 59 ( 4 ) page： 228-243 2017.5

Gene expression profiling of granule cells and Purkinje cells in the zebrafish cerebellum. Reviewed

Takeuchi M., Yamaguchi S., Sakakibara M., Hayashi T., Matsuda K., Hara Y., Tanegashima C., Shimizu T., Kuraku S., Hibi M.

J Comp Neurol. 2016.9

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Papers - SHIMIZU, Takashi