Coordinating Group
- Head
- Michio Suzuki (Graduate School of Agricultural and Life Sciences, The University of Tokyo) Life Science
- Taiga Okumura (Faculty of Education and Integrated Sciences, Waseda University) Materials Science
- Takashi Toyofuku (Research Institute for Marine Resources and Environment, JAMSTEC) Ecological Science
- Kozue Nishida (School of Environment and Society, Institute of Science Tokyo) Environmental Science
Life Science Group
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LeaderMichio Suzuki
Graduate School of Agricultural and Life Sciences
The University of Tokyo
Professor
We aim to elucidate the molecular mechanisms of organic–inorganic interactions in molluscan calcification and to identify the specific stages of the biological process where protons are released.
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Takeshi Takeuchi
Japan Pearl Promotion Society
Chief Researcher
We perform single-cell RNA sequencing on the mantle tissue of bivalves to identify genes that function specifically in shell-forming cells. We also analyze the spatiotemporal expression patterns of these genes and conduct functional analyses using gene knockdown techniques.
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Akira Iguchi
Integrated Research Center of Nature Positive Technology, National Institute of Advanced Industrial Science and Technology (AIST), Team Leader
There are various genes involved in coral calcification. However, differences in life cycle stages and day-night cycles may affect the nature of calcification, and even similar genes can show different expression patterns. In this project, we aim to explore the diverse ways in which corals carry out calcification through genetic analysis.
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Kei Sato
Institute of Liberal Arts and Science
Kanazawa University
Lecturer
Our main research focus is on molluscan shells. We study the branching patterns of morphological traits and investigate the environmental factors and genetic mechanisms that control these traits. Through this, we aim to answer the question: why has molluscan diversity emerged? In this project, we focus on elucidating the genetic mechanisms underlying the calcification process in mollusks.
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Yugo Kato
Graduate School of Agricultural and Life Sciences
The University of Tokyo
Assistant Professor
We are developing a system to culture calcifying organisms in a sealed container isolated from the environment, enabling the measurement of material balances in both aqueous and gaseous phases. Within the system, mollusks and unicellular organisms that perform calcification are cultured, with monitoring and sampling measurements conducted.
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Akio Sohma
Graduate School of Engineering
Osaka Metropolitan University
Professor
Based on experimental results from living organisms, we will develop a new mathematical model of material cycling in calcifying organisms and investigate whether calcification contributes to carbon sequestration.
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Mariko Iijima
Integrated Research Center of Nature Positive Technology, National Institute of Advanced Industrial Science and Technology (AIST), Resercher
Coral calcification responds sensitively to environmental changes at both global and local scales. At the local scale, the effects of nutrient loading have long been debated, and I have particularly focused on phosphorus-induced inhibition of coral calcification. In this project, we aim to further explore the relationship between coral calcification and phosphorus.
Materials Science Group
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LeaderTaiga Okumura
Faculty of Education and Integrated Sciences
Waseda University
Associate Professor
We investigate the structure and formation mechanisms of substances present in the Earth's surface layer at the nanoscale, aiming to understand macroscopic phenomena from a bottom-up perspective. In this project, we aim to clarify how biominerals differ from purely inorganic minerals and to decompose biomineralization into its fundamental processes.
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Tomoya Yamazaki
Institute of Low Temperature Science
Hokkaido University
Associate Professor
I am interested in crystallization and work on visualizing and understanding the process using microscopy. Specifically, I focus on observing crystallization from solution using environmental (liquid cell) transmission electron microscopy. In this project, I aim to capture the moment of carbonate formation with transmission electron microscopy and, based on these observations, investigate the formation process of carbonates with particular attention to the role of organic molecules.
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Jun Kawano
Faculty of Science
Hokkaido University
Associate Professor
I conduct research on the mechanisms of mineral and crystal growth and structural changes. In this project, we theoretically evaluate the interactions between crystals and organic molecules through computer simulations, and image local changes in pH and ion concentrations during the inorganic formation and dissolution of carbonate minerals. By comparing these results with those from the Ecological Science group, we aim to clarify the role of biological processes in biomineral formation.
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Yuki Araki
College of Science and Engineering
Kanazawa University
Assistant Professor
Specializing in interface science and crystal growth, I conduct in situ observations of various natural minerals and material surfaces using high-resolution atomic force microscopy (AFM). In this project, we aim to visualize the effects of organic substances on the growth dynamics of biominerals during the initial stages of crystal formation.
Ecological Science Group
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LeaderTakashi Toyofuku
Super-cutting-edge Grand and Advanced Research (SUGAR) Program, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Senior Research Scientist
I oversee the group’s coordination and am responsible for lab cultivation and observation of calcifying organisms such as corals and foraminifera. Through real-time imaging techniques, including pH and calcium microscopy, I advance the visualization and analysis of shell formation processes while managing the group.
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Ko Yasumoto
Kitasato University School of Marine Biosciences
Associate Professor
I am responsible for pH imaging of corals and box experiments. I have proposed a calcification mechanism involving biogenic polyamines, and I cultivate juvenile corals to observe their growth. Using confocal laser scanning microscopy, I visualize pH elevation associated with calcification. Through these studies, I aim to elucidate the role of calcification in the global carbon cycle.
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Motai Satoko
Faculty of Science
Yamagata University
Assistant Professor
I aim to elucidate the calcification process based on microscopic observation of biominerals (hard tissues). My research mainly focuses on the skeletal structures of reef-building corals, including both natural specimens and those obtained from laboratory experiments. In this project, I will work on developing and optimizing observational methods to better understand the relationship between living organisms and their hard tissues.
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Sentoku Asuka
Faculty of Science
The University of the Ryukyus
Assistant Professor
Through rearing experiments with corals and brachiopods, we aim to clarify how these organisms carry out calcification, from macroscopic to microscopic scales, by measuring skeletal growth and observing fine structures. By employing techniques to visualize shell and skeletal formation processes in vivo, we conduct multifaceted analyses of the relationship between soft tissues and hard tissues, advancing comparative studies of diverse calcification strategies.
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Yukiko Nagai
Super-cutting-edge Grand and Advanced Research (SUGAR) Program, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Research Associate
We conduct research on the formation of shells and the ecology of foraminifera, which are single-celled organisms, by cultivating them in laboratory settings. In our study of shell formation, we have established methods for the simultaneous microstructural observation of the cells at the calcification sites and the resulting hard tissues. These structures are examined at multiple scales. In this project, we aim to elucidate the diverse calcification strategies of various organisms through the cultivation and observation of foraminifera and other calcifying organisms, as well as through simultaneous microstructural observation of calcification-related cells and hard tissues, and pH and calcium imaging.
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Koichi Watanabe
Faculty of Human Development and Culture
Fukushima University
Professor
Building on the foundation of STEAM (Science, Technology, Engineering, Arts, and Mathematics), we aim to advance research that not only identifies and analyzes the morphology of biominerals, but also generates innovative approaches by combining the mindsets of scientists and engineers with those of artists and designers.
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Takenori Sasaki
The University Museum
The University of Tokyo
Associate Professor
We conduct nanoscale observations and comparative analyses of the microstructures of molluscan biominerals. By employing X-ray diffraction and Raman spectroscopy, we analyze their functions and adaptive significance through macroscopic morphological analyses and 3D reconstructions. We also utilize MXCT (Micro X-ray Computed Tomography) for three-dimensional modeling, expanding morphological studies of mollusks and other organisms.
Environmental Science Group
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LeaderKozue Nishida
School of Environment and Society Department of Transdisciplinary Science and Engineering, Institute of Science Tokyo
Associate Professor
I serve as the coordinator of the Environmental Science Group, working under the theme “Deciphering Material Cycling in Carbonate Formation through Skeletal Analyses.” My expertise lies in isotope geoscience and paleontology. Using stable isotope analyses of carbonates—including clumped isotopes, carbon isotopes, and oxygen isotopes—I aim to elucidate the carbon budget and calcification mechanisms in carbonate-forming organisms.
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Kentaro Tanaka
Faculty of Science and Engineering
Tokyo City University
Associate Professor
My specialty is geochemistry. Focusing on biogenic carbonates, I analyze trace element concentrations and isotope ratios to develop methods that elucidate the dynamics of elements related to biomineralization.
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Hisashi Asanuma
Faculty of Integrated Human Studies
Kyoto University
Lecturer
By utilizing mass spectrometry techniques, I strive to measure spatial and chemical speciation information of elements involved in biomineralization. I aim to provide fundamental data that integrates chemistry, ecology, and environmental science.
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Kaoru Kubota
Research Institute for Marine Geodynamics, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Resercher
My specialty is paleoenvironmental reconstruction using trace elements and isotopes of biogenic calcium carbonate. In particular, I have focused on boron isotope analysis in my research. I use this proxy as a tool to clarify the carbonate system of calcifying fluids and aim to reveal the actual biomineralization processes in various model organisms.
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Tomoko Ariga
National Institute of Advanced Industrial Science and Technology, National Metrology Institute of Japan
Senior Research Scientist
I work on advancing isotope ratio analysis and elemental quantification using inductively coupled plasma mass spectrometry (ICP-MS). In this project, by detecting stable isotope ratios of Sr and Ca in mollusk shells and in vitro synthesized calcium carbonate crystals mimicking biological systems, I aim to elucidate the biomineralization control mechanisms mediated by organic matrices.