Updated on 2025/09/30

写真a

 
HAMADA Mayuko
 
Organization
Faculty of Environmental, Life, Natural Science and Technology Professor
Position
Professor
External link

Degree

  • 博士(理学) ( お茶の水女子大学 )

Research Interests

  • 共生

  • 環境ゲノム

  • 生体防御

  • 比較ゲノム

  • 進化

Research Areas

  • Life Science / Evolutionary biology

  • Life Science / Genome biology

  • Life Science / Developmental biology

Education

  • Ochanomizu University   人間文化研究科(博士後期課程)   人間環境科学専攻

    2000.4 - 2003.3

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  • Ochanomizu University   人間文化研究科(博士前期課程)   ライフサイエンス専攻

    1998.4 - 2000.3

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  • Ochanomizu University   理学部   生物学科

    1994.4 - 1998.3

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Research History

  • Okayama University   環境生命自然科学学域/臨海実験所   Professor

    2025.2

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  • Okayama University   Ushimado Marine Institute   Associate Professor

    2020.12

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  • Okayama University   Ushimado Marine Institute   Assistant Professor

    2016.4

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  • Kiel University   Zoological Institute   Visiting Researcher

    2012.2 - 2013.10

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  • Okinawa Institute of Science and Technology Graduate University   マリンゲノミクスユニット   Researcher

    2008.4 - 2016.4

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  • Kyoto University   理学研究科 動物学教室   Researcher

    2003.4 - 2008.3

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Papers

  • Animal–chlorophyte photosymbioses: evolutionary origins and ecological diversity Reviewed

    Isabel Jiah-Yih Liao, Tosuke Sakagami, Thomas D. Lewin, Xavier Bailly, Mayuko Hamada, Yi-Jyun Luo

    Biology Letters   21 ( 7 )   2025.7

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    Authorship:Corresponding author   Publishing type:Research paper (scientific journal)   Publisher:The Royal Society  

    Photosynthetic symbiosis occurs across diverse animal lineages, including Porifera, Cnidaria, Xenacoelomorpha and Mollusca. These associations between animal hosts and photosynthetic algae often involve the exchange of essential macronutrients, supporting adaptation to a wide range of aquatic environments. A small yet taxonomically widespread subset of animals host photosymbionts from the core chlorophytes, a phylogenetically expansive clade of green algae. These rare instances of ‘plant-like’ animals have arisen independently across distantly related lineages, resulting in striking ecological and physiological diversity. Although such associations provide valuable insights into the evolution of symbiosis and adaptation to novel ecological niches, animal–chlorophyte photosymbioses remain relatively understudied. Here, we present an overview of photosymbioses between animals and chlorophytes, highlighting their independent evolutionary origins, ecological diversity and emerging genomic resources. Focusing on Porifera, Cnidaria and Xenacoelomorpha, we review shared and lineage-specific adaptations underlying these associations. We also contrast them with dinoflagellate-based systems to demonstrate their distinct ecological and cellular features. Our work sets the stage for elucidating the molecular mechanisms underlying these associations, enhancing our understanding of how interspecies interactions drive adaptation to unique ecological niches through animal–chlorophyte symbiosis.

    DOI: 10.1098/rsbl.2025.0250

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    Other Link: https://royalsocietypublishing.org/doi/full-xml/10.1098/rsbl.2025.0250

  • Tunicate-specific protein Epi-1 is essential for conferring hydrophilicity to the larval tunic in the ascidian Ciona Reviewed

    Kazu Kuroiwa, Kaoru Mita-Yoshida, Mayuko Hamada, Akiko Hozumi, Atsuo S. Nishino, Yasunori Sasakura

    Developmental Biology   520   41 - 52   2025.4

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    Publishing type:Research paper (scientific journal)   Publisher:Elsevier BV  

    DOI: 10.1016/j.ydbio.2025.01.002

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  • Environmental DNA Reveals the Impact of Submarine Groundwater Discharge on the Spatial Variability of Coastal Fish Diversity Reviewed

    Nguyen Hong Nhat, Mitsuyo Saito, Shin-ichi Onodera, Mayuko Hamada, Fujio Hyodo, Hideaki Nagare

    Biology   13 ( 8 )   609 - 609   2024.8

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    Publishing type:Research paper (scientific journal)   Publisher:MDPI AG  

    Submarine groundwater discharge (SGD) has recently been recognized as an influential factor in coastal ecosystems; however, little research has been conducted on its effects on coastal fish diversity. To investigate the relationship between SGD and fish diversity, we conducted a survey at the coastal island scale using the environmental DNA (eDNA) method. Our findings indicate that fish species richness and functional richness peak at stations with high SGD. Environmental variables, such as salinity, dissolved inorganic nitrogen (DIN) concentration, and SGD, significantly influence fish diversity. Carnivore fish richness was negatively correlated with salinity, while planktivore fish richness was positively correlated. Additionally, SGD and DIN concentrations were found to be crucial in shaping omnivorous and pelagic communities, respectively. This study highlights the role of SGD in enhancing nutrient conditions favorable for diverse fish communities and demonstrates the effectiveness of eDNA metabarcoding for rapid marine biodiversity assessment. These findings provide valuable insights for coastal ecosystem monitoring and management.

    DOI: 10.3390/biology13080609

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  • The Evolution and Characterization of the RNA Interference Pathways in Lophotrochozoa Reviewed

    Alessandro Formaggioni, Gianmarco Cavalli, Mayuko Hamada, Tatsuya Sakamoto, Federico Plazzi, Marco Passamonti

    Genome Biology and Evolution   16 ( 5 )   2024.5

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    Publishing type:Research paper (scientific journal)   Publisher:Oxford University Press (OUP)  

    Abstract

    In animals, three main RNA interference mechanisms have been described so far, which respectively maturate three types of small noncoding RNAs (sncRNAs): miRNAs, piRNAs, and endo-siRNAs. The diversification of these mechanisms is deeply linked with the evolution of the Argonaute gene superfamily since each type of sncRNA is typically loaded by a specific Argonaute homolog. Moreover, other protein families play pivotal roles in the maturation of sncRNAs, like the DICER ribonuclease family, whose DICER1 and DICER2 paralogs maturate respectively miRNAs and endo-siRNAs. Within Metazoa, the distribution of these families has been only studied in major groups, and there are very few data for clades like Lophotrochozoa. Thus, we here inferred the evolutionary history of the animal Argonaute and DICER families including 43 lophotrochozoan species. Phylogenetic analyses along with newly sequenced sncRNA libraries suggested that in all Trochozoa, the proteins related to the endo-siRNA pathway have been lost, a part of them in some phyla (i.e. Nemertea, Bryozoa, Entoprocta), while all of them in all the others. On the contrary, early diverging phyla, Platyhelminthes and Syndermata, showed a complete endo-siRNA pathway. On the other hand, miRNAs were revealed the most conserved and ubiquitous mechanism of the metazoan RNA interference machinery, confirming their pivotal role in animal cell regulation.

    DOI: 10.1093/gbe/evae098

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    Other Link: https://academic.oup.com/gbe/article-pdf/16/5/evae098/58028616/evae098.pdf

  • Evaluation of the Effects of Environmental Factors on Seasonal Variations in Fish Diversity on a Coastal Island in Western Japan Reviewed

    Nguyen Hong Nhat, Mitsuyo Saito, Mayuko Hamada, Shin-ichi Onodera

    Environments   11 ( 3 )   60 - 60   2024.3

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    Publishing type:Research paper (scientific journal)   Publisher:MDPI AG  

    Coastal habitats are crucial for supporting ecological processes and serve as vital ecosystems for diverse fish species, providing essential functions such as feeding, nursery provision, and reproductive habitats. Fish communities are ecologically important components of coastal ecosystems and are affected by multiple environmental factors. Despite their importance, determining the effects of environmental factors on seasonal variations in fish species diversity and community dynamics remains a challenge. The advent of environmental DNA (eDNA) technology, an environmentally conscious approach, has resulted in considerable advancements in recent years and has been progressively adopted for marine fish population monitoring. Here, we used environmental DNA metabarcoding to study seasonal variations in fish community structure on a coastal island, and we assessed the effects of environmental factors in structuring these communities. Our findings revealed a rich diversity of 72 fish species across 40 families and 23 orders in the seawater surrounding an island of the Seto Inland Sea (SIS), Western Japan. Notably, the composition of fish communities varied significantly between seasons, with seawater temperature, salinity, and dissolved inorganic phosphorus (DIP) concentration identified as important factors correlated with fish communities’ structures. In conclusion, our study provides useful information of fish diversity, and we suggest that eDNA is a valuable technique for monitoring fish diversity in coastal areas. These findings are crucial for ecological studies and the environmental monitoring of oceanic coastal environments.

    DOI: 10.3390/environments11030060

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  • Structure of putative epidermal sensory receptors in an acoel flatworm, Praesagittifera naikaiensis Reviewed

    Tosuke Sakagami, Kaho Watanabe, Mayuko Hamada, Tatsuya Sakamoto, Toshimitsu Hatabu, Motonori Ando

    Cell and Tissue Research   395 ( 3 )   299 - 311   2024.2

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    Publishing type:Research paper (scientific journal)   Publisher:Springer Science and Business Media LLC  

    Abstract

    Acoel flatworms possess epidermal sensory-receptor cells on their body surfaces and exhibit behavioral repertoires such as geotaxis and phototaxis. Acoel epidermal sensory receptors should be mechanical and/or chemical receptors; however, the mechanisms of their sensory reception have not been elucidated. We examined the three-dimensional relationship between epidermal sensory receptors and their innervation in an acoel flatworm, Praesagittifera naikaiensis. The distribution of the sensory receptors was different between the ventral and dorsal sides of worms. The nervous system was mainly composed of a peripheral nerve net, an anterior brain, and three pairs of longitudinal nerve cords. The nerve net was located closer to the body surface than the brain and the nerve cords. The sensory receptors have neural connections with the nerve net in the entire body of worms. We identified five homologs of polycystic kidney disease (PKD): PKD1-1, PKD1-2, PKD1-3, PKD1-4, and, PKD2, from the P. naikaiensis genome. All of these PKD genes were implied to be expressed in the epidermal sensory receptors of P. naikaiensis. PKD1-1 and PKD2 were dispersed across the entire body of worms. PKD1-2, PKD1-3, and PKD1-4 were expressed in the anterior region of worms. PKD1-4 was also expressed around the mouth opening. Our results indicated that P. naikaiensis possessed several types of epidermal sensory receptors to convert various environmental stimuli into electrical signals via the PKD channels and transmit the signals to afferent nerve and/or effector cells.

    DOI: 10.1007/s00441-024-03865-y

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    Other Link: https://link.springer.com/article/10.1007/s00441-024-03865-y/fulltext.html

  • Model systems for discovering evolutionary singularity of bilaterian physiological regulation: lessons from studies on simple/primitive flatworms Reviewed

    Shunsuke Mori, Aoshi Kobayashi, Hirotaka Sakamoto, Mayuko Hamada, Tatsuya Sakamoto, Ryo Nakamura

    Biophysics and Physicobiology   2024

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    Publishing type:Research paper (scientific journal)   Publisher:Biophysical Society of Japan  

    DOI: 10.2142/biophysico.bppb-v21.s012

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  • Fbxl4 Regulates the Photic Entrainment of Circadian Locomotor Rhythms in the Cricket Gryllus bimaculatus Reviewed

    Kazuki Takeuchi, Mirai Matsuka, Tsugumichi Shinohara, Mayuko Hamada, Yasuaki Tomiyama, Kenji Tomioka

    Zoological Science   40 ( 1 )   2023.1

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    Publishing type:Research paper (scientific journal)   Publisher:Zoological Society of Japan  

    DOI: 10.2108/zs220047

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  • Quantitative PCR method to detect an extremely endangered bitterling fish (Rhodeus atremius suigensis) using environmental DNA Reviewed

    Kanoko Otsuki, Mayuko Hamada, Noriyuki Koizumi, Tatsuya Sakamoto, Kazuyoshi Nakata

    Landscape and Ecological Engineering   2022.11

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    Authorship:Lead author   Publishing type:Research paper (scientific journal)   Publisher:Springer Science and Business Media LLC  

    DOI: 10.1007/s11355-022-00531-9

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    Other Link: https://link.springer.com/article/10.1007/s11355-022-00531-9/fulltext.html

  • De novo transcriptome analysis of the centrohelid Raphidocystis contractilis to identify genes involved in microtubule-based motility. Reviewed International journal

    Risa Ikeda, Tosuke Sakagami, Mayuko Hamada, Tatsuya Sakamoto, Toshimitsu Hatabu, Noboru Saito, Motonori Ando

    The Journal of eukaryotic microbiology   70 ( 2 )   e12955   2022.11

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

    The centrohelid heliozoan Raphidocystis contractilis has many radiating axopodia, each containing axopodial microtubules. The axopodia show rapid contraction at nearly a video rate (30 frames per second) in response to mechanical stimuli. The axopodial contraction is accompanied by cytoskeletal microtubule depolymerization, but the molecular mechanism of this phenomenon has not been elucidated. In this study, we performed de novo transcriptome sequencing of R. contractilis to identify genes involved in microtubule dynamics such as the rapid axopodial contraction. The transcriptome sequencing generated 7.15-Gbp clean reads in total, which were assembled as 31,771 unigenes. Using the obtained gene sets, we identified several microtubule-severing proteins which might be involved in the rapid axopodial contraction, and kinesin-like genes that occur gene duplication. On the other hand, some genes for microtubule motor proteins involved in the formation and motility of flagella were not found in R. contractilis, suggesting that the gene repertoire of R. contractilis reflected the morphological features of non-flagellated protists. Our transcriptome analysis provides basic information for the analysis of the molecular mechanism underlying microtubule dynamics in R. contractilis.

    DOI: 10.1111/jeu.12955

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  • How green algae have created a symbiotic relationship with Hydra

    BSJ-Review   13   13 - 30   2022.5

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

    DOI: 10.24480/bsj-review.13a3.00221

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  • d-Serine controls epidermal vesicle release via NMDA receptor, allowing tissue migration during the metamorphosis of the chordate Ciona. Reviewed International journal

    Gabriel Krasovec, Akiko Hozumi, Tomoyuki Yoshida, Takayuki Obita, Mayuko Hamada, Akira Shiraishi, Honoo Satake, Takeo Horie, Hisashi Mori, Yasunori Sasakura

    Science advances   8 ( 10 )   eabn3264   2022.3

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

    d-Serine, a free amino acid synthesized by serine racemase, is a coagonist of N-methyl-d-aspartate-type glutamate receptor (NMDAR). d-Serine in the mammalian central nervous system modulates glutamatergic transmission. Functions of d-serine in mammalian peripheral tissues such as skin have also been described. However, d-serine's functions in nonmammals are unclear. Here, we characterized d-serine-dependent vesicle release from the epidermis during metamorphosis of the tunicate Ciona. d-Serine leads to the formation of a pocket that facilitates the arrival of migrating tissue during tail regression. NMDAR is the receptor of d-serine in the formation of the epidermal pocket. The epidermal pocket is formed by the release of epidermal vesicles' content mediated by d-serine/NMDAR. This mechanism is similar to observations of keratinocyte vesicle exocytosis in mammalian skin. Our findings provide a better understanding of the maintenance of epidermal homeostasis in animals and contribute to further evolutionary perspectives of d-amino acid function among metazoans.

    DOI: 10.1126/sciadv.abn3264

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  • Vasopressin-oxytocin–type signaling is ancient and has a conserved water homeostasis role in euryhaline marine planarians Reviewed

    Aoshi Kobayashi, Mayuko Hamada, Masa-aki Yoshida, Yasuhisa Kobayashi, Naoaki Tsutsui, Toshio Sekiguchi, Yuta Matsukawa, Sho Maejima, Joseph J. Gingell, Shoko Sekiguchi, Ayumu Hamamoto, Debbie L. Hay, John F. Morris, Tatsuya Sakamoto, Hirotaka Sakamoto

    Science Advances   8 ( 9 )   2022.3

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    Publishing type:Research paper (scientific journal)   Publisher:American Association for the Advancement of Science (AAAS)  

    Vasopressin/oxytocin (VP/OT)–related peptides are essential for mammalian antidiuresis, sociosexual behavior, and reproduction. However, the evolutionary origin of this peptide system is still uncertain. Here, we identify orthologous genes to those for VP/OT in Platyhelminthes, intertidal planarians that have a simple bilaterian body structure but lack a coelom and body-fluid circulatory system. We report a comprehensive characterization of the neuropeptide derived from this VP/OT-type gene, identifying its functional receptor, and name it the “platytocin” system. Our experiments with these euryhaline planarians, living where environmental salinities fluctuate due to evaporation and rainfall, suggest that platytocin functions as an “antidiuretic hormone” and also organizes diverse actions including reproduction and chemosensory-associated behavior. We propose that bilaterians acquired physiological adaptations to amphibious lives by such regulation of the body fluids. This neuropeptide-secreting system clearly became indispensable for life even without the development of a vascular circulatory system or relevant synapses.

    DOI: 10.1126/sciadv.abk0331

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  • Observing Phylum-Level Metazoan Diversity by Environmental DNA Analysis at the Ushimado Area in the Seto Inland Sea Reviewed

    Takeshi Kawashima, Masa-aki Yoshida, Hideyuki Miyazawa, Hiroaki Nakano, Natumi Nakano, Tatsuya Sakamoto, Mayuko Hamada

    Zoological Science   39 ( 1 )   157 - 165   2022.1

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    Authorship:Corresponding author   Language:English   Publishing type:Research paper (scientific journal)   Publisher:Zoological Society of Japan  

    The dynamics of microscopic marine plankton in coastal areas is a fundamental theme in marine biodiversity research, but studies have been limited because the only available methodology was collection of plankton using plankton-nets and microscopic observation. In recent years, environmental DNA (eDNA) analysis has exhibited potential for conducting comprehensive surveys of marine plankton diversity in water at fixed points and depths in the ocean. However, few studies have examined how eDNA analysis reflects the actual distribution and dynamics of organisms in the field, and further investigation is needed to determine whether it can detect distinct differences in plankton density in the field. To address this, we analyzed eDNA in seawater samples collected at 1 km intervals at three depths over a linear distance of approximately 3.0 km in the Seto Inland Sea. The survey area included a location with a high density of Acoela (Praesagittifera naikaiensis). However, the eDNA signal for this was little to none, and its presence would not have been noticed if we did not have this information beforehand. Meanwhile, eDNA analysis enabled us to confirm the presence of a species of Placozoa that was previously undiscovered in the area. In summary, our results suggest that the number of sequence reads generated from eDNA samples in our project was not sufficient to predict the density of a particular species. However, eDNA can be useful for detecting organisms that have been overlooked using other methods.

    DOI: 10.2108/zs210073

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  • The gastrin-releasing peptide/bombesin system revisited by a reverse-evolutionary study considering Xenopus Reviewed International journal

    Asuka Hirooka, Mayuko Hamada, Daiki Fujiyama, Keiko Takanami, Yasuhisa Kobayashi, Takumi Oti, Yukitoshi Katayama, Tatsuya Sakamoto, Hirotaka Sakamoto

    Scientific Reports   11 ( 1 )   13315 - 13315   2021.6

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    Authorship:Lead author   Language:English   Publishing type:Research paper (scientific journal)   Publisher:Springer Science and Business Media LLC  

    <title>Abstract</title>Bombesin is a putative antibacterial peptide isolated from the skin of the frog, <italic>Bombina bombina</italic>. Two related (bombesin-like) peptides, gastrin-releasing peptide (GRP) and neuromedin B (NMB) have been found in mammals. The history of GRP/bombesin discovery has caused little attention to be paid to the evolutionary relationship of GRP/bombesin and their receptors in vertebrates. We have classified the peptides and their receptors from the phylogenetic viewpoint using a newly established genetic database and bioinformatics. Here we show, by using a clawed frog (<italic>Xenopus tropicalis</italic>), that GRP is not a mammalian counterpart of bombesin and also that, whereas the GRP system is widely conserved among vertebrates, the NMB/bombesin system has diversified in certain lineages, in particular in frog species. To understand the derivation of GRP system in the ancestor of mammals, we have focused on the GRP system in <italic>Xenopus</italic>. Gene expression analyses combined with immunohistochemistry and Western blotting experiments demonstrated that GRP peptides and their receptors are distributed in the brain and stomach of <italic>Xenopus</italic>. We conclude that GRP peptides and their receptors have evolved from ancestral (GRP-like peptide) homologues to play multiple roles in both the gut and the brain as one of the <italic>‘gut-brain peptide’</italic> systems.

    DOI: 10.1038/s41598-021-92528-x

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    Other Link: http://www.nature.com/articles/s41598-021-92528-x

  • A Reference Genome from the Symbiotic Hydrozoan, Hydra viridissima Reviewed

    Mayuko Hamada, Noriyuki Satoh, Konstantin Khalturin

    G3; Genes|Genomes|Genetics   10 ( 11 )   3883 - 3895   2020.11

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    Authorship:Lead author, Corresponding author   Publishing type:Research paper (scientific journal)   Publisher:Oxford University Press (OUP)  

    Various <italic>Hydra</italic> species have been employed as model organisms since the 18th century. Introduction of transgenic and knock-down technologies made them ideal experimental systems for studying cellular and molecular mechanisms involved in regeneration, body-axis formation, senescence, symbiosis, and holobiosis. In order to provide an important reference for genetic studies, the <italic>Hydra magnipapillata</italic> genome (species name has been changed to <italic>H. vulgaris</italic>) was sequenced a decade ago (Chapman <italic>et al.</italic>, 2010) and the updated genome assembly, Hydra 2.0, was made available by the National Human Genome Research Institute in 2017. While <italic>H. vulgaris</italic> belongs to the non-symbiotic brown hydra lineage, the green hydra, <italic>Hydra viridissima</italic>, harbors algal symbionts and belongs to an early diverging clade that separated from the common ancestor of brown and green hydra lineages at least 100 million years ago (Schwentner and Bosch 2015; Khalturin <italic>et al.</italic>, 2019). While interspecific interactions between <italic>H. viridissima</italic> and endosymbiotic unicellular green algae of the genus <italic>Chlorella</italic> have been a subject of interest for decades, genomic information about green hydras was nonexistent. Here we report a draft 280-Mbp genome assembly for <italic>Hydra viridissima</italic> strain A99, with a scaffold N50 of 1.1 Mbp. The <italic>H. viridissima</italic> genome contains an estimated 21,476 protein-coding genes. Comparative analysis of Pfam domains and orthologous proteins highlights characteristic features of <italic>H. viridissima</italic>, such as diversification of innate immunity genes that are important for host-symbiont interactions. Thus, the <italic>H. viridissima</italic> assembly provides an important hydrozoan genome reference that will facilitate symbiosis research and better comparisons of metazoan genome architectures.

    DOI: 10.1534/g3.120.401411

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  • GABA-Induced GnRH Release Triggers Chordate Metamorphosis Reviewed International journal

    Akiko Hozumi, Shohei Matsunobu, Kaoru Mita, Nicholas Treen, Takaho Sugihara, Takeo Horie, Tetsushi Sakuma, Takashi Yamamoto, Akira Shiraishi, Mayuko Hamada, Noriyuki Satoh, Keisuke Sakurai, Honoo Satake, Yasunori Sasakura

    Current Biology   30 ( 8 )   1555 - 1561.e4   2020.4

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    Language:English   Publishing type:Research paper (scientific journal)   Publisher:Elsevier BV  

    Metamorphosis, a widespread life history strategy in metazoans, allows dispersal and use of different ecological niches through a dramatic body change from a larval stage [1, 2]. Despite its conservation and importance, the molecular mechanisms underlying its initiation and progression have been characterized in only a few animal models. In this study, through pharmacological and gene functional analyses, we identified neurotransmitters responsible for metamorphosis of the ascidian Ciona. Ciona metamorphosis converts swimming tadpole larvae into vase-like, sessile adults. Here, we show that the neurotransmitter GABA is a key regulator of metamorphosis. We found that gonadotropin-releasing hormone (GnRH) is a downstream neuropeptide of GABA. Although GABA is generally thought of as an inhibitory neurotransmitter, we found that it positively regulates secretion of GnRH through the metabotropic GABA receptor during Ciona metamorphosis. GnRH is necessary for reproductive maturation in vertebrates, and GABA is an important excitatory regulator of GnRH in the hypothalamus during puberty [3, 4]. Our findings reveal another role of the GABA-GnRH axis in the regulation of post-embryonic development in chordates.

    DOI: 10.1016/j.cub.2020.02.003

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  • A Nearly Complete Genome of Ciona intestinalis Type A (C. robusta) Reveals the Contribution of Inversion to Chromosomal Evolution in the Genus Ciona. Reviewed International journal

    Yutaka Satou, Ryohei Nakamura, Deli Yu, Reiko Yoshida, Mayuko Hamada, Manabu Fujie, Kanako Hisata, Hiroyuki Takeda, Noriyuki Satoh

    Genome biology and evolution   11 ( 11 )   3144 - 3157   2019.11

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

    Since its initial publication in 2002, the genome of Ciona intestinalis type A (Ciona robusta), the first genome sequence of an invertebrate chordate, has provided a valuable resource for a wide range of biological studies, including developmental biology, evolutionary biology, and neuroscience. The genome assembly was updated in 2008, and it included 68% of the sequence information in 14 pairs of chromosomes. However, a more contiguous genome is required for analyses of higher order genomic structure and of chromosomal evolution. Here, we provide a new genome assembly for an inbred line of this animal, constructed with short and long sequencing reads and Hi-C data. In this latest assembly, over 95% of the 123 Mb of sequence data was included in the chromosomes. Short sequencing reads predicted a genome size of 114-120 Mb; therefore, it is likely that the current assembly contains almost the entire genome, although this estimate of genome size was smaller than previous estimates. Remapping of the Hi-C data onto the new assembly revealed a large inversion in the genome of the inbred line. Moreover, a comparison of this genome assembly with that of Ciona savignyi, a different species in the same genus, revealed many chromosomal inversions between these two Ciona species, suggesting that such inversions have occurred frequently and have contributed to chromosomal evolution of Ciona species. Thus, the present assembly greatly improves an essential resource for genome-wide studies of ascidians.

    DOI: 10.1093/gbe/evz228

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  • Medusozoan genomes inform the evolution of the jellyfish body plan. Reviewed International journal

    Konstantin Khalturin, Chuya Shinzato, Maria Khalturina, Mayuko Hamada, Manabu Fujie, Ryo Koyanagi, Miyuki Kanda, Hiroki Goto, Friederike Anton-Erxleben, Masaya Toyokawa, Sho Toshino, Noriyuki Satoh

    Nature ecology & evolution   3 ( 5 )   811 - 822   2019.5

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

    Cnidarians are astonishingly diverse in body form and lifestyle, including the presence of a jellyfish stage in medusozoans and its absence in anthozoans. Here, we sequence the genomes of Aurelia aurita (a scyphozoan) and Morbakka virulenta (a cubozoan) to understand the molecular mechanisms responsible for the origin of the jellyfish body plan. We show that the magnitude of genetic differences between the two jellyfish types is equivalent, on average, to the level of genetic differences between humans and sea urchins in the bilaterian lineage. About one-third of Aurelia genes with jellyfish-specific expression have no matches in the genomes of the coral and sea anemone, indicating that the polyp-to-jellyfish transition requires a combination of conserved and novel, medusozoa-specific genes. While no genomic region is specifically associated with the ability to produce a jellyfish stage, the arrangement of genes involved in the development of a nematocyte-a phylum-specific cell type-is highly structured and conserved in cnidarian genomes; thus, it represents a phylotypic gene cluster.

    DOI: 10.1038/s41559-019-0853-y

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  • Metabolic co-dependence drives the evolutionarily ancient Hydra-Chlorella symbiosis. Reviewed International journal

    Mayuko Hamada, Katja Schröder, Jay Bathia, Ulrich Kürn, Sebastian Fraune, Mariia Khalturina, Konstantin Khalturin, Chuya Shinzato, Nori Satoh, Thomas Cg Bosch

    eLife   7   2018.5

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    Authorship:Lead author   Language:English   Publishing type:Research paper (scientific journal)  

    Many multicellular organisms rely on symbiotic associations for support of metabolic activity, protection, or energy. Understanding the mechanisms involved in controlling such interactions remains a major challenge. In an unbiased approach we identified key players that control the symbiosis between Hydra viridissima and its photosynthetic symbiont Chlorella sp. A99. We discovered significant up-regulation of Hydra genes encoding a phosphate transporter and glutamine synthetase suggesting regulated nutrition supply between host and symbionts. Interestingly, supplementing the medium with glutamine temporarily supports in vitro growth of the otherwise obligate symbiotic Chlorella, indicating loss of autonomy and dependence on the host. Genome sequencing of Chlorella sp. A99 revealed a large number of amino acid transporters and a degenerated nitrate assimilation pathway, presumably as consequence of the adaptation to the host environment. Our observations portray ancient symbiotic interactions as a codependent partnership in which exchange of nutrients appears to be the primary driving force.

    DOI: 10.7554/eLife.35122

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  • Evolution of the chordate regeneration blastema: Differential gene expression and conserved role of notch signaling during siphon regeneration in the ascidian Ciona Reviewed

    Mayuko Hamada, Spela Goricki, Mardi S. Byerly, Noriyuki Satoh, William R. Jeffery

    DEVELOPMENTAL BIOLOGY   405 ( 2 )   304 - 315   2015.9

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    DOI: 10.1016/j.ydbio.2015.07.017

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  • Hox10-regulated endodermal cell migration is essential for development of the ascidian intestine Reviewed

    Narudo Kawai, Yosuke Ogura, Tetsuro Ikuta, Hidetoshi Saiga, Mayuko Hamada, Tetsushi Sakuma, Takashi Yamamoto, Nori Satoh, Yasunori Sasakura

    DEVELOPMENTAL BIOLOGY   403 ( 1 )   43 - 56   2015.7

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    DOI: 10.1016/j.ydbio.2015.03.018

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  • How do environmental factors influence life cycles and development? An experimental framework for early-diverging metazoans Reviewed

    Thomas C. G. Bosch, Maja Adamska, Rene Augustin, Tomislav Domazet-Loso, Sylvain Foret, Sebastian Fraune, Noriko Funayama, Juris Grasis, Mayuko Hamada, Masayuki Hatta, Bert Hobmayer, Kotoe Kawai, Alexander Klimovich, Michael Manuel, Chuya Shinzato, Uli Technau, Seungshic Yum, David J. Miller

    BIOESSAYS   36 ( 12 )   1185 - 1194   2014.12

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    DOI: 10.1002/bies.201400065

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  • Transposon-mediated targeted and specific knockdown of maternally expressed transcripts in the ascidian Ciona intestinalis Reviewed

    Takako Iitsuka, Kaoru Mita, Akiko Hozumi, Mayuko Hamada, Nori Satoh, Yasunori Sasakura

    SCIENTIFIC REPORTS   4 ( 4 )   5050   2014.5

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    DOI: 10.1038/srep05050

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  • Draft assembly of the symbiodinium minutum nuclear genome reveals dinoflagellate gene structure Reviewed

    Eiichi Shoguchi, Chuya Shinzato, Takeshi Kawashima, Fuki Gyoja, Sutada Mungpakdee, Ryo Koyanagi, Takeshi Takeuchi, Kanako Hisata, Makiko Tanaka, Mayuki Fujiwara, Mayuko Hamada, Azadeh Seidi, Manabu Fujie, Takeshi Usami, Hiroki Goto, Shinichi Yamasaki, Nana Arakaki, Yutaka Suzuki, Sumio Sugano, Atsushi Toyoda, Yoko Kuroki, Asao Fujiyama, Mónica Medina, Mary Alice Coffroth, Debashish Bhattacharya, Nori Satoh

    Current Biology   23 ( 15 )   1399 - 1408   2013.8

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    DOI: 10.1016/j.cub.2013.05.062

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  • A methodical microarray design enables surveying of expression of a broader range of genes in Ciona intestinalis Reviewed

    Hiromi Matsumae, Mayuko Hamada, Manabu Fujie, Yoshihito Niimura, Hiroshi Tanaka, Takeshi Kawashima

    GENE   519 ( 1 )   82 - 90   2013.4

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    DOI: 10.1016/j.gene.2013.01.042

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  • The Complex NOD-Like Receptor Repertoire of the Coral Acropora digitifera Includes Novel Domain Combinations Reviewed

    Mayuko Hamada, Eiichi Shoguchi, Chuya Shinzato, Takeshi Kawashima, David J. Miller, Nori Satoh

    MOLECULAR BIOLOGY AND EVOLUTION   30 ( 1 )   167 - 176   2013.1

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    DOI: 10.1093/molbev/mss213

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  • Differential gene regulation by V-IV and V-V ions in the branchial sac, intestine, and blood cells of a vanadium-rich ascidian, Ciona intestinalis Reviewed

    Satoshi Kume, Tatsuya Ueki, Hiroki Matsuoka, Mayuko Hamada, Nori Satoh, Hitoshi Michibata

    BIOMETALS   25 ( 5 )   1037 - 1050   2012.10

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    DOI: 10.1007/s10534-012-9569-z

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  • The Repertoire of Chemical Defense Genes in the Coral Acropora digitifera Genome Reviewed

    Chuya Shinzato, Mayuko Hamada, Eiichi Shoguchi, Takeshi Kawashima, Nori Satoh

    ZOOLOGICAL SCIENCE   29 ( 8 )   510 - 517   2012.8

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    DOI: 10.2108/zsj.29.510

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  • No chromosomal clustering of housekeeping genes in the marine chordate Ciona intestinalis Reviewed

    Eiichi Shoguchi, Manabu Fujie, Mayuko Hamada

    MARINE GENOMICS   4 ( 3 )   151 - 157   2011.9

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    DOI: 10.1016/j.margen.2011.01.002

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  • Direct examination of chromosomal clustering of organ-specific genes in the chordate Ciona intestinalis Reviewed

    Eiichi Shoguchi, Mayuko Hamada, Manabu Fujie, Nori Satoh

    Genesis   49 ( 8 )   662 - 672   2011.8

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    DOI: 10.1002/dvg.20730

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  • Using the Acropora digitifera genome to understand coral responses to environmental change Reviewed

    Chuya Shinzato, Eiichi Shoguchi, Takeshi Kawashima, Mayuko Hamada, Kanako Hisata, Makiko Tanaka, Manabu Fujie, Mayuki Fujiwara, Ryo Koyanagi, Tetsuro Ikuta, Asao Fujiyama, David J. Miller, Nori Satoh

    NATURE   476 ( 7360 )   320 - U82   2011.8

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    DOI: 10.1038/nature10249

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  • Expression of neuropeptide- and hormone-encoding genes in the Ciona intestinalis larval brain Reviewed

    Mayuko Hamada, Naoki Shimozono, Naoyuki Ohta, Yutaka Satou, Takeo Horie, Tsuyoshi Kawada, Honoo Satake, Yasunori Sasakura, Nori Satoh

    DEVELOPMENTAL BIOLOGY   352 ( 2 )   202 - 214   2011.4

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    DOI: 10.1016/j.ydbio.2011.01.006

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  • Differential Regional Expression of Genes in the Developing Brain of Ciona intestinalis Embryos Reviewed

    Naoki Shimozono, Naoyuki Ohta, Nori Satoh, Mayuko Hamada

    ZOOLOGICAL SCIENCE   27 ( 2 )   103 - 109   2010.2

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    DOI: 10.2108/zsj.27.103

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  • Early zygotic expression of transcription factors and signal molecules in fully dissociated embryonic cells of Ciona intestinalis: A microarray analysis Reviewed

    Takeshi Noda, Mayuko Hamada, Makoto Hamaguchi, Manabu Fujie, Nori Satoh

    DEVELOPMENT GROWTH & DIFFERENTIATION   51 ( 7 )   639 - 655   2009.9

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    DOI: 10.1111/j.1440-169X.2009.01124.x

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  • M-Ras evolved independently of R-Ras and its neural function is conserved between mammalian and ascidian, which lacks classical Ras. Reviewed International journal

    Etsuko Keduka, Ai Kaiho, Mayuko Hamada, Haruko Watanabe-Takano, Kazunori Takano, Michio Ogasawara, Yutaka Satou, Nori Satoh, Takeshi Endo

    Gene   429 ( 1-2 )   49 - 58   2009.1

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    The Ras family small GTPases play a variety of essential roles in eukaryotes. Among them, classical Ras (H-Ras, K-Ras, and N-Ras) and its orthologues are conserved from yeast to human. In ascidians, which phylogenetically exist between invertebrates and vertebrates, the fibroblast growth factor (FGF)-Ras-MAP kinase signaling is required for the induction of neural system, notochord, and mesenchyme. Analyses of DNA databases revealed that no gene encoding classical Ras is present in the ascidians, Ciona intestinalis and Halocynthia roretzi, despite the presence of classical Ras-orthologous genes in nematode, fly, amphioxus, and fish. By contrast, both the ascidians contain single genes orthologous to Mras, Rras, Ral, Rap1, and Rap2. A single Mras orthologue exists from nematode to mammalian. Thus, Mras evolved in metazoans independently of other Ras family genes such as Rras. Whole-mount in situ hybridization showed that C. intestinalis Mras orthologue (Ci-Mras) was expressed in the neural complex of the ascidian juveniles after metamorphosis. Knockdown of Ci-Mras with morpholino antisense oligonucleotides in the embryos and larvae resulted in undeveloped tails and neuronal pigment cells, abrogation of the notochord marker brachyury expression, and perturbation of the neural marker Otx expression, as has been shown in the experiments of the FGF-Ras-MAP kinase signaling inhibition. Mammalian Ras and M-Ras mediate nerve growth factor-induced neuronal differentiation in rat PC12 cells by activating the ERK/MAP kinase pathway transiently and sustainedly, respectively. Activated Ci-M-Ras bound to target proteins of mammalian M-Ras and Ras. Exogenous expression of an activated Ci-M-Ras in PC12 cells caused ERK activation and induced neuritogenesis via the ERK pathway as do mammalian M-Ras and Ras. These results suggest that the ascidian M-Ras orthologue compensates for lacked classical Ras and plays essential roles in neurogenesis in the ascidian.

    DOI: 10.1016/j.gene.2008.10.001

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  • Novel genes involved in canonical Wnt/beta-catenin signaling pathway in early Ciona intestinalis embryos Reviewed

    Shuichi Wada, Mayuko Hamada, Kenji Kobayashi, Nori Satoh

    DEVELOPMENT GROWTH & DIFFERENTIATION   50 ( 4 )   215 - 227   2008.5

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    DOI: 10.1111/j.1440-169x.2008.01012.x

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  • 動物ゲノム解読の10年がもたらした新しい進化観

    川島武士, 濱田麻友子, 新里宙也, 佐藤矩行, 将口栄一

    科学   78   1070 - 1079   2008

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  • Novel genes involved in Ciona intestinalis embryogenesis: Characterization of gene knockdown embryos Reviewed

    Mayuko Hamada, Shuichi Wada, Kenji Kobayashi, Nori Satoh

    DEVELOPMENTAL DYNAMICS   236 ( 7 )   1820 - 1831   2007.7

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    DOI: 10.1002/dvdy.21181

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  • A genomewide analysis of genes for the heat shock protein 70 chaperone system in the ascidian Ciona intestinalis Reviewed

    Shuichi Wada, Mayuko Hamada, Nori Satoh

    Cell Stress and Chaperones   11 ( 1 )   23 - 33   2006.3

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    DOI: 10.1379/CSC-137R.1

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  • Ci-Rga, a gene encoding an MtN3/saliva family transmembrane protein, is essential for tissue differentiation during embryogenesis of the ascidian Ciona intestinalis Reviewed

    M Hamada, S Wada, K Kobayashi, N Satoh

    DIFFERENTIATION   73 ( 7 )   364 - 376   2005.9

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    DOI: 10.1111/j.1432-0436.2005.00037.x

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  • Signals from primary mesenchyme cells regulate endoderm differentiation in the sea urchin embryo Reviewed

    M Hamada, M Kiyomoto

    DEVELOPMENT GROWTH & DIFFERENTIATION   45 ( 4 )   339 - 350   2003.8

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    DOI: 10.1046/j.1440-169X.2003.00702.x

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Books

  • Generality and diversity of photosymbionts: Algal symbiotic systems in green hydra and coral

    ( Role: Sole author)

    2023.5 

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  • 扁形動物ヒラムシから紐解くGnRHの祖先型機能

    森俊輔, 酒井丈実, 濱田麻友子, 坂本竜哉, 坂本浩隆

    日本比較内分泌学会大会及びシンポジウムプログラム・講演要旨   45th   2021

  • 脊索動物ホヤにおいてHox10は消化管形成に必要な内胚葉索の細胞移動を制御する。

    河合成道, 小椋陽介, 吉田麗子, 濱田麻友子, 生田哲朗, 佐藤矩行, 西駕秀俊, 笹倉靖徳

    生化学   2010

  • Transcriptome analysis of drosophila kept in the longterm darkness using microarrays

    Mayuko Hamada, Shuji Shigenob, Satoru Kobayashi, Hiroshi Kubota, Michio Imafuku, Nori Satoh

    ZOOLOGICAL SCIENCE   23 ( 12 )   1221 - 1222   2006.12

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Research Projects

  • Generality and diversity of photosymbiosis across the animal kingdom: comparative genome analysis of symbiosis in Xenacoelomorpha.

    Grant number:24K09559  2024.04 - 2027.03

    Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research  Grant-in-Aid for Scientific Research (C)

    濱田 麻友子

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    Grant amount:\4550000 ( Direct expense: \3500000 、 Indirect expense:\1050000 )

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  • Revealing symbiotic mechanisms from useful metabolites of microorganisms in corals

    Grant number:23H02132  2023.04 - 2026.03

    Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research  Grant-in-Aid for Scientific Research (B)

    將口 栄一, 濱田 麻友子, 久保田 高明, 竹内 猛

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    Grant amount:\18720000 ( Direct expense: \14400000 、 Indirect expense:\4320000 )

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  • Understanding of the symbiotic mechanism based on the technological development for utilization of metabolic products of coral symbiotic microorganisms

    Grant number:23K26825  2023.04 - 2026.03

    Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research  Grant-in-Aid for Scientific Research (B)

    將口 栄一, 濱田 麻友子, 久保田 高明, 竹内 猛

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  • 左右相称動物の普遍的ホルモンペプチドの祖先的機能:珍無腸動物カルシトニンの研究

    Grant number:23K05844  2023.04 - 2026.03

    日本学術振興会  科学研究費助成事業  基盤研究(C)

    関口 俊男, 坂本 竜哉, 濱田 麻友子

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    Grant amount:\4680000 ( Direct expense: \3600000 、 Indirect expense:\1080000 )

    本研究の目的は、原始的な左右相称動物と考えられている珍無腸動物を用いカルシトニン(CT)の祖先的機能や、前口・後口動物の分岐に伴うCT機能の進化機構を提唱することにある。CTは哺乳類の骨代謝を司るホルモンである。我々は、CTが無脊椎動物にも存在することを示してきた。その後のゲノム解析等から、CT遺伝子が左右相称動物(前口・後口動物)に広く存在することが知られている。それらの機能を見渡すと、概日リズムの調整がCTの共通の作用である可能性が見出された。そこで、本研究では、原始的な左右相称動物とされる珍無腸動物ナイカイムチョウウズムシを用い、この仮説を検証し、前口・後口動物を跨ぐペプチド遺伝子スーパーファミリーの機能進化解明のモデルとする。
    令和5年度は、ナイカイムチョウウズムシのCT(Pn-CT)及びCT受容体(Pn-CTR)全長配列の決定を行った。Pn-CTは36アミノ酸残基であった。様々な動物のCTに存在する2つのCys 残基が保存されており、ジスルフィド結合による環状構造を持つと考えられる。さらにCTに特徴的なPro残基とアミド化シグナルが保存されていた。さらにPn-CTRの分子系統解析により、Pn-CTRが左右相称動物のCTRやCTR様受容体(CLR)と相同性であることを確認した。さらに Whole mount in situ hybridization 解析により、ナイカイムチョウウズムシのPn-CT及びPn-CTRの発現局在を検討した結果、Pn-CTとPn-CTR mRNAが共に頭部に局在していることが明らかとなった。その発現パターンから、Pn-CTとPn-CTR mRNAは、ニューロンに発現していると予想される。特にPn-CTの局在は、GABAニューロンのマーカー遺伝子の局在と類似していた。これらの解析によって、珍無腸動物CT機能解析の基盤を整えることができた。

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  • “ステロイドホルモン系”の原始左右相称動物での黎明は、共生藻がもたらしたか?

    Grant number:22K19312  2022.06 - 2024.03

    日本学術振興会  科学研究費助成事業 挑戦的研究(萌芽)  挑戦的研究(萌芽)

    坂本 竜哉, 永田 晋治, 濱田 麻友子, 坂本 浩隆

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  • 広塩性の扁形動物を原点に探る淡水進出における体液調節能獲得の動物界を跨ぐ新概念

    Grant number:21H02520  2021.04 - 2025.03

    日本学術振興会  科学研究費助成事業 基盤研究(B)  基盤研究(B)

    坂本 竜哉, 片山 侑駿, 坂本 浩隆, 関口 俊男, 濱田 麻友子, 前嶋 翔

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    Grant amount:\17290000 ( Direct expense: \13300000 、 Indirect expense:\3990000 )

    国際研究グループで、新しい水・塩分環境への進出をもたらした動物界を貫く体液調節機構と提唱する抗利尿ホルモン(バソプレシン)系―腎臓の原型を、原始左右相称動物の扁形動物ヒラムシ(海産プラナリアの仲間)を用いて解明している。
    まず、ヒラムシの、水陸両生、50~150%海水への順応―体液調節できること等を見出した。そして、脊椎動物の水・塩分環境適応の“要”でもある「バソプレシン/オキシトシン」の同族ペプチドをヒラムシから発見した。この神経ペプチドは、脊椎動物と無脊椎動物において広く存在することから、左右相称動物に普遍的な神経ペプチドとして、その共通祖先においてすでに存在していたと考えられるが、その進化起源は明らかになってなかった。今回、左右相称動物の共通祖先に近いとされるシンプルな体制を持つ、原始左右相称動物である扁形動物門(Platyhelminthes)から、その同族ペプチドを特定することに成功し、この祖先型ホルモンをプラチトシン(platytocin)系と名付けた。このホルモンは脳神経節の2対のニューロンのみで産生され、脱水で誘導された。さらに、プラチトシン系は扁形動物でも哺乳類と同様に抗利尿ホルモンとして機能していることを見出した。従って、『抗利尿ホルモン系による“腎臓” i.e., 体液の調節』の起源が、新しい水・塩分環境への進出をはじめた扁形動物まで遡れる。また、これまで不明であった神経シナプス系からの内分泌系/液性調節の誕生:神経内分泌の進化起源の解明も期待される。

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  • 広塩性の扁形動物を原点に探る淡水進出における体液調節能獲得の動物界を跨ぐ新概念

    Grant number:23K21320  2021.04 - 2025.03

    日本学術振興会  科学研究費助成事業  基盤研究(B)

    坂本 竜哉, 坂本 浩隆, 関口 俊男, 濱田 麻友子, 中村 遼, 田中 祥貴, 片山 侑駿, 前嶋 翔

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    当初計画は順調に進み、研究目的は達成されつつあるが、その過程で、ヒラムシのGnRHの神経回路等、進化的に保存され普遍的な神経ペプチド群に関する新発見もしている。これら普遍的なペプチド系分子は、前に分岐した散在神経系の動物には見出せない。また我々は、原始的な後口動物の珍無腸動物ムチョウウズムシのシンプルな中枢神経系でも、祖先型GnRHを発見している。その中枢神経系でのTRP群の発現も見出している(Sakagami, Hamada, Sakamoto T ら Cell Tissue Res 2023等)。
    以上の興味深い成果から、解析対象にムチョウウズムシも加え、数百の細胞からなる中枢神経系の原型に、1細胞/空間トランスクリプトーム/コネクトーム解析を駆使すれば、構成細胞の浸透圧センサーのような固有特性や神経ネットワークなど細胞・分子基盤を包括的に解明できる。マウス、ショウジョウバエでの知見とも包括的に比較でき、原始左右相称動物に共通な“シン原始脳”の神経ネットワークが、前口・後口動物で、いかに保存/分化されたかに迫れる。そこで、空間トランスクリプトームも始めた。また、原始海産無脊椎動物の神経系の本技術等に優れる分担者の中村(Hayakawa, Nakamura ら Nature Ecol Evol 2022 他等)を、当実験所に採用した。非モデル生物でも1細胞トランスクリプトーム、遺伝子編集による機能解析が急速に行われている。実際、中村は前左右相称動物の有櫛動物や刺胞動物で成果を挙げている(Nakamura ら Nature Commun リバイズ中等)。研究の舵を切り、このビッグチャンスを掴みたい。

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  • Transition process of seagrass-seaweed meadows driven by water and material transport from watersheds: Toward quantification and utilization of the ecosystem services

    Grant number:21H03650  2021.04 - 2024.03

    Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research (B)  Grant-in-Aid for Scientific Research (B)

    齋藤 光代, 小野寺 真一, 作野 裕司, 濱田 麻友子, 兵藤 不二夫

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    Grant amount:\17290000 ( Direct expense: \13300000 、 Indirect expense:\3990000 )

    本研究では,多様な生態系サービス機能を有する沿岸藻場の分布や藻場生態系の多様性変遷過程について,特に流域の水・物質輸送の影響に着目し明らかにすることを目的とし,初年度であるR3年度は以下のとおり実施した.
    (1)河川水・地下水流出にともなう物質輸送量評価:1)流域水・物質輸送評価:①沿岸域に藻場が分布する瀬戸内海の島嶼(広島県生口島)を対象に,島内の流域において河川流量および地下水位のモニタリングを実施した.②対象流域に水・物質輸送モデル(Soil & Water Assessment Tool: SWAT)を適用・構築する準備を行った.2)SGD物質輸送評価:①対象流域沿岸の藻場分布域において,海底湧水(SGD)のトレーサーとなる塩分,水温,ラドン濃度,および栄養塩濃度の海水中の空間分布を確認するとともに,潮間帯にSGD観測用ピエゾメーターを設置し,同様に塩分,水温,ラドンおよび栄養塩濃度のモニタリングを実施した.
    (2)藻場と構成種の空間分布・時間変化の把握:①ドローンを用いて対象流域沿岸の藻場の空撮を実施し,取得した画像データの解析から藻場とその構成種の空間分布を明らかにした.②現地での踏査調査(海草・海藻類の分布密度,種類,固体サイズなどの測定)を実施し,それらに基づき①の結果の検証を行った.
    (3)藻場生態系の食物連鎖構造および栄養塩循環の解明:1)食物連鎖構造解析:①対象流域の藻場分布域において河川水・地下水および海水,堆積物試料,藻場を構成する海草・海藻類のサンプリングを実施し,窒素・炭素安定同位体比を測定した.2)栄養塩循環評価:①藻場分布域でのクロロフィルaと濁度の測定,および水試料の採取と栄養塩分析を行った.
    (4)藻場生態系の生物多様性評価:①対象流域の藻場分布域において海水および堆積物試料を採取し,環境DNAの分析を行った.

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  • ヒドラ属の生存戦略の差を生み出した種分化メカニズムの解明

    Grant number:21K06289  2021.04 - 2024.03

    日本学術振興会  科学研究費助成事業 基盤研究(C)  基盤研究(C)

    濱田 麻友子

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    Grant amount:\4160000 ( Direct expense: \3200000 、 Indirect expense:\960000 )

    本研究では近縁種間で異なる栄養獲得戦略を取るヒドラを用いて、種分化の分子メカニズムの解明を目指している。ヒドラ属には、細胞内共生クロレラと栄養面で相利共生の関係にあるグリーンヒドラと、非共生性で捕食によって栄養を獲得する比較的大型のブラウンヒドラが存在している。興味深いことに、グリーンヒドラとブラウンヒドラの分岐の直後にブラウンヒドラ系統ではレトロトランスポゾンの大規模な挿入によるゲノムサイズの増加が起こっており、このことがヒドラ属の生存戦略の違いを生み出した原因の一つになっているかもしれない。また、トランスポゾンの活性はエピジェネティクスによる制御を受けており、グリーンヒドラとブラウンヒドラでその制御に差がある可能性がある。そこで本研究ではヒドラ属におけるトランスポゾンの遺伝子発現調節メカニズムへの関与とエピジェネティクス制御に焦点を当て、種分化の分子メカニズムを解明することを目的とする。
    まず、これまでのショートリードアセンブルでは難しかったリピート領域を正確にシーケンスするため、グリーンヒドラHydra viridissima A99およびブラウンヒドラHydra vulgaris AEPから高分子ゲノムDNAを抽出し、Oxford Nanopore社のMiNIONを用いたロングリードシーケンスを行った。また、グリーンヒドラに関しては共生クロレラからの作用を明らかにするため、これまでに取得したChlorella sp. A99系統のゲノム・遺伝子配列を利用し、遺伝子構成を遊泳性のクロレラのものと比較することで、その特徴を探った。

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  • Chordate steroid receptor is ancient in the acoel

    Grant number:20K21429  2020.07 - 2022.03

    Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research Grant-in-Aid for Challenging Research (Exploratory)  Grant-in-Aid for Challenging Research (Exploratory)

    Sakamoto Tatsuya

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    Grant amount:\6500000 ( Direct expense: \5000000 、 Indirect expense:\1500000 )

    We isolated and characterized the steroid hormone receptors (SRs) of the acoel Praesagittifera naikaiensis, which belongs to a clade (Xenacoelomorpha) that could be a sister group to other animals with bilateral symmetry (Bilateria) or could belong within deuterostomes, closely related to a group that includes sea stars (Ambulacraria). The P. naikaiensis genome contains two SRs: PnEER, an ortholog of the vertebrate estrogen-related receptors, and PnSR, an ortholog of the vertebrate receptors for androgens, progestins, and corticosteroids. PnSR does not activate transcription in response to conventional steroid hormones of vertebrate. These genes are expressed in the statocyst and gonad specifically, suggesting an ancient role in behaviours affected by environmental stimuli and germ cell development.

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  • Revealing the symbiotic mechanisms from useful metabolites of dinoflagellates in corals

    Grant number:20K05798  2020.04 - 2023.03

    Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research (C)  Grant-in-Aid for Scientific Research (C)

    將口 栄一, 濱田 麻友子

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    Grant amount:\4290000 ( Direct expense: \3300000 、 Indirect expense:\990000 )

    白化に耐性があると考えられる渦鞭毛藻Durusdinium trenchiiのゲノム概要配列を報告してきた(Shoguchi et al., 2021)。比較ゲノム解析により、D. trenchiiのゲノムにはUV吸収物質として知られているマイコスポリン様アミノ酸(MAA)の生合成遺伝子クラスターがコードされていることを明らかにした。しかしながらD. trenchiiがどのような種類のMAAを生合成しているのかについての詳細は分かっていない。D. trenchiiの二次代謝産物の解析を試みた。シャコガイを主な宿主としていると考えられる渦鞭毛藻Symbiodinium tridacnidorumのMAA生合成遺伝子クラスターと比較することにより、その領域が高度に保存されていることを明らかにした。そのゲノム領域だけが、「その2種の各々は約1億6000万年前の共通祖先から分岐したと考えられる別々のグループに属する」というこれまでの報告とは一致していないようであった。その結果に基づいて、「最近起こった、サンゴ共生渦鞭毛藻間における水平伝播の可能性」についての仮説を報告した(Shoguchi, 2022)。高度に保存されたゲノム領域の配列を比較解析することにより、渦鞭毛藻類間の遺伝子水平伝播のメカニズムについて推察した。比較を行うために、白化しやすいサンゴに共生している渦鞭毛藻とバクテリアの単離とそれらが生合成した二次代謝産物の解析のための準備を進めた。共生渦鞭毛藻培養中に共在する4種のバクテリアのゲノムを解析した。またその二次代謝産物の同定を試みた。

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  • Comparative genomics of metabolic strategies and speciation in genus Hydra.

    Grant number:18K06364  2018.04 - 2021.03

    Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research (C)  Grant-in-Aid for Scientific Research (C)

    Hamada Mayuko

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    Grant amount:\4420000 ( Direct expense: \3400000 、 Indirect expense:\1020000 )

    To elucidate the mechanisms of adaptation and speciation in animal evolution, we performed comparative genome analyses among cnidarians and between closely related species using hydras, which have different nutritional acquisition strategies depending on the species. The genus Hydra includes green hydras, which established mutualistic relationship with the symbiotic Chlorella, and brown hydras, which are predatory and have relatively large body. Their genomes are thought to reflect different survival strategies. In this study, we show differences in the distribution of RNA transposons in the genome of green hydra compared to that of brown hydra, an increase in the number of genes and domain complexity of innate immunity genes, and a gradual loss of genes related to body plan such as homeobox genes, and clarify the phylogenetic evolution and speciation from a genomic perspective.

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  • Interactions and genome evolution in animal-algae-microbe symbiotic system in green hydra

    Grant number:15K07173  2015.04 - 2019.03

    Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research (C)  Grant-in-Aid for Scientific Research (C)

    Hamada Mayuko, Bosch Thomas CG

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    Grant amount:\4940000 ( Direct expense: \3800000 、 Indirect expense:\1140000 )

    To understand the interspecies interactions and evolution of animal-algal symbiosis and the involvement of microbes such as bacteria in the symbiotic system, we analyzed genome/ transcriptome of the Cnidarian green hydra and the Chlorella symbionts. The result suggested, in the common ancestor of Chlorella, duplication of amino acid transporter genes and acquisition by horizontal transfer of chitin metabolic gene occurred, which may have contributed to frequent occurrence of symbiosis in Chlorella family. In addition, acquisition of genes for synthesis of specific secondary metabolites by horizontal transfer from bacteria and large-scale duplication of pattern recognition receptor genes were found in green hydra genome, suggesting unique defense mechanisms.

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  • Analysis of molecular interaction and genome evolution in the symbiotic system of green hydra and Chlorella

    Grant number:25840132  2013.04 - 2016.03

    Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research Grant-in-Aid for Young Scientists (B)  Grant-in-Aid for Young Scientists (B)

    Hamada Mayuko, BOSCH C. G. Thomas

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    Grant amount:\4550000 ( Direct expense: \3500000 、 Indirect expense:\1050000 )

    To understand common principles of animal-algal symbiosis and their links to evolution at the molecular- and the genome-level, we focused on the mechanisms of interactions between Hydra and Chlorella and the specific features in their genome. We identified candidate genes upregulated only when the specific symbiosis has been established. They included genes involved in nitrogen assimilation and phosphate transport. In addition, the expression of these genes showed clear correlation with photosynthesis of Chlorella. We also performed genome sequencing of the symbiotic Chlorella to understand the genome evolution in the dependent relation. As a result, we found that some genes necessary for nitrate assimilation in plants and their cluster structure have been lost. This indicates that symbiotic Chlorella is dependent on the nitrogen source provided from Hydra and that the nitrate assimilation pathway in symbiotic Chlorella is degenerated.

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  • Study of mechanism of metamorphosis by transcriptome analysis of the mutants of Ciona intestinalis

    Grant number:19770193  2007 - 2008

    Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research Grant-in-Aid for Young Scientists (B)  Grant-in-Aid for Young Scientists (B)

    HAMADA Mayuko

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    Grant amount:\3620000 ( Direct expense: \3200000 、 Indirect expense:\420000 )

    本研究ではカタユウレイボヤの変態過程の一部に異常が見られる変異体sj1, sj2, sj4 (trf : tail regression failure)において、どのような遺伝子発現の変化が見られるかをマイクロアレイを用いて解析した。その結果、体軸回転が進行するsj1では間充織で発現する遺伝子の増加が見られた。また、尾部吸収が起こらず、成体組織が成長するtrfでは神経系で発現する遺伝子の減少が示唆された。また、これらの変異体間において発現差が見られた遺伝子は、変異体ごとに異なっており、変態過程が独立の過程から起こることが遺伝子レベルでも示唆される結果となった。

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