生物の飛翔や遊泳、集団運動等を生物流体力学や非線形数理の手法により解析することで生命活動の秘密に迫り、また生物運動の素晴らしい機能を抽出して数理科学的な意味を探り、応用に貢献することを目指しています。

We study bio-fluid mechanics and related problems such as flight and swimming of animals, collective behaviors of microorganisms, and transportation inside body, by using mathematical analysis. Our aim is to extract essential behavior of biological activity, movements and functions in terms of mathematics for future applications.

keywords：fluid mechanics, biofluid, swimming, flight, collective behavior, mathematical structure

1. Optimal external forces of the lock-in phenomena for flow past an inclined plate in uniform flow, PRE 109, 045102（2024）
2. Emergence of a Euglena bioconvection spot controlled by non-uniform light, Front. Ecol. Evol. 11:1132956（2023）
3. Active lift inversion process of heaving wing in uniform flow by temporal change of wing kinematics, Phys Rev E, 99: 043110（2019）

MALDIというイオン化法は、「質量情報」と「位置情報」を同時に取得できるが、これをマトリックスを用いないMALDI法と組み合わせることにより、「マイクロ天然物化学」とでも呼ぶべき新しい天然物化学の展開を始めている。

The ionization method called MALDI can acquire “mass information” and “position information” at the same time, but by combining this with the MALDI method that does not use a matrix, we would like to start the development of “micro natural product chemistry.”

keywords：MALDI, mass information, position information

1. Mass spectrometric characterization of histone H3 Isolated from in-Vitro reconstituted and acetylated nucleosome core particle/Mass
   Spectrometry/2020
2. 3-Hydroxy-4-nitrobenzoic Acid as a MALDI Matrix for In-Source Decay/ Analytical Chemistry / 2016
3. Alkylated Trihydroxyacetophenone as a MALDI Matrix for Hydrophobic Peptides/ Analytical Chemistry/ 2013

最先端のゲノム科学の手法を使って、キンギョやメダカなど観賞魚の表現型多様性をテーマに、脊椎動物の進化や形態多様性の仕組み、ヒトの遺伝病との関連や脳神経科学の研究をすすめています。

We focus on the phenotypic diversity of ornamental teleost fish such as goldfish and medaka. We study the evolution and the mechanism of morphological diversity of vertebrates, the relationship with human genetic diseases and neuroscience by genomics.

keywords：genome science, human disease model, whole genome duplication, single cell RNA-seq, teleost fish

1. Single-cell transcriptomics of the goldfish retina reveals genetic divergence in the asymmetrically evolved subgenomes after allotetraploid-ization. Communications Biology 5, 1404（2022）
2. The genetic basis of morphological diversity in domesticated goldfish. Current Biology 30, 2260-2274（2020）
3. De Novo assembly of the goldfish（Carassius auratus）genome and the evolution of genes after whole genome duplication. Science Ad-vances, 5, eaav0547（2019）

環境応答を担う因子や代謝機能、それらの制御機構の解明を通じて植物の成長生存戦略を理解し、ストレス耐性や過酷環境への適応ポテンシャルの増大、藻類バイオ燃料創成等の植物機能開発と高度化研究を展開している。

My research interests lie in plant science, primarily elucidating molecular mechanisms of how plants re-spond to and survive in changing environments. Applied research is also conducted to exploit the capabili-ties of plants, including microalgae, for better performance under stress and towards the practical produc-tion of useful substances such as biofuels.

keywords：plant molecular physiology, plant hormone, plant metabolite, stress response, stress tolerance, biotechnology

1. Dynamics of the leaf endoplasmic reticulum modulate ß-glucosidase-mediated stress-activated ABA production from its glucosyl ester, J Exp Bot, 71: 2058-2071（2020）
2. Allantoin, a stress-related purine metabolite, can activate jasmonate signaling in a MYC2-regulated and abscisic acid-dependent manner, J Exp Bot, 67: 2519-2532（2016）
3. The purine metabolite allantoin enhances abiotic stress tolerance through synergistic activation of abscisic acid metabolism, Plant Cell Environ, 37: 1022-1036（2014）

ヒト・タンパク質の50％を占める安定な立体構造をとらない領域がもつ構造・機能を、物理計測、細胞生物学的解析、計算器シミュレーションを駆使して研究しています。新たなタンパク質構造科学の構築を目指します。

My research focus is on the structure and function relations of intrinsically disordered proteins（IDPs）that constitute about 50% of human proteins with combinatorial use of theoretical and experimental approach-es including NMR, molecular dynamics simulation, biochemistry, and cell biology. Students with a physics diploma are very welcome.

keywords：biophysics, structural biology, protein, IDP

1. Ultrasensitive Change in Nucleosome Binding by Multiple Phosphorylations to the Intrinsically Disordered Region of the Histone Chaperone FACT/J.Mol.Biol./2020
2. Non-RVD mutations that enhance the dynamics of the TAL repeat array along the superhelical axis improve TALEN genome editing efficacy/Sci. Rep./2016
3. Allosteric breakage of the hydrogen bond within the dual-histidine motif in the active site of human Pin1 PPIase/Biochemistry/2015

自然界や生体系では、リズムやパターンを形成する現象をよく見かける。このような時空間発展現象は、非平衡下における非線形現象又は自己組織化とよばれる。私の研究は、非生物のモデル実験系を構築し、自己組織化の機構解明を研究目的とする。具体的には、特徴的な運動様相を示す自己駆動体や化学振動反応を用いた実験を行う。

Rhythm and pattern observed in living organisms and nature are called “self-organization”. Artificial exper-imental systems are developed to physicochemically elucidate the mechanism of self-organziation. Char-acteristic features of motion, such as collective motion and synchronized sailing, and oscillatory motion of self-propelled objects and chemical oscillation are examined.

keywords：self-organization, oscillation, pattern formation, synchronization

1. Evolution of self-propelled objects – From the viewpoint of nonlinear science, Chem. A Euro. J., 2018.
2. Oscillatory Motion of an Organic Droplet Reflecting a Reaction, J. Phys. Chem. Lett., 2023. Scheme
3. Phospholipid Molecular Layer that Enhances Distinction of Odors Based on Artificial Sniffing, ACS Sensors, 2023.

数理モデルと実データ解析から生命や社会の発生・進化・共存の理を探究。細胞-多細胞-器官-個体の多階層にわたる動植物・微生物の振舞い（分子ネットワーク、形、動き）など複雑なシステムを理解し予測。

Theoretical study（mathematical modeling and data analysis）of evolving multi-level dynamics（gene ex-pression, shape, and behaviors）in plants, animals, and microbes.

keywords：theoretical biology, complex systems, biophysics, evolution, diversity, multi-scales

1. Geodesic theory of long association fibers arrangement in the human fetal cortex. Cerebral Cortex 33: 9778-86（2023）
2. Patterned proliferation orients tissue-wide stress to control root vascular symmetry in Arabidopsis. Current Biology 33: 886-898.e8（2023）
3. A design principle for floral organ number and arrangement in flowers with bilateral symmetry. Development 147: 20200204（2020）

データ駆動型ゲノム育種（デジタル育種）に向けて、バイオDXと呼ばれるバイオインフォマティクスを駆使した遺伝子機能解析を中心に、ゲノム編集に必須のデータ解析基盤技術を開発している。

Toward data-driven genome breeding （digital breeding）, we are developing data analysis infrastructure technology essential for genome editing, focusing on gene function analysis using bioinformatics called BioDX.

keywords：BioDX, bioinformatics, genome editing, transcriptome analysis, functional annotation, public database, open source software, hypoxia, oxidative stress, meta-analysis

1. A highly contiguous genome assembly of red perilla（Perilla frutescens） domesticated in Japan. DNA Research, 30:dsac044（2023）
2. Systematic functional annotation workflow for insects. Insects, 13:586（2022）
3. Exploratory meta-analysis of hypoxic transcriptomes using a precise transcript reference sequence set. Life Science Alliance, 6: e202201518
   （2023）

様々な生物で利用可能なゲノム編集技術の開発と産業利用を目指した研究を進めています。

We are developing genome editing technologies that can be used in various organisms and trying their use in various fields.

keywords：genome editing, developmental biology

1. Biased genome editing using the local accumulation of DSB repair molecules system, NATURE COMMUNICATIONS, 9:3270（2018）
2. Single-Molecule Nanoscopy Elucidates RNA Polymerase II Transcription at Single Genes in Live Cells, CELL, 78:491-506.e28（2019）
3. Zinc-finger nuclease-mediated targeted insertion of reporter genes for quantitative imaging of gene expression in sea urchin embryos,PNAS, 109:10915-20（2012）

動的かつ複雑な生命現象の背後に潜む規則性やメカニズムを理解するために、数理モデリングと機械学習を組み合わせることで、生命現象を司る支配方程式をデータ駆動的に解読する研究を展開している。

To understand the mechanisms behind dynamic and complex biological phenomena, we are combining mathematical modeling and machine learning for decoding the governing rules or equations that govern biological systems.

keywords：data-driven biology, mathematical modeling, machine learning

1. Decoding reward–curiosity coflict in decision-making from irrational behaviors. Nature Computational Science 3, 418–432（2023）
2. Stem cell homeostasis regulated by hierarchy and neutral competition. Communication Biology 5, 1268（2022）
3. Model-based prediction of spatial gene expression via generative linear mapping. Nature Communications 12: 3731（2021）

ゲノム動態による遺伝子制御機序とその発生過程との関係、細胞内高次分子構造体および多細胞生物の形態の形成機序と機能、等に関する数理と実験による研究。ネコ・ヒトの基礎医科学への応用。

We progress theory-experimant hybrid studies for i）structural dynamics of biomolecular populations, ii）genome dynamics and gene regulation, iii）development and morphogenesis of multi-cellular organisms.

keywords：mathematical model, biological, medical, and veterinary data analysis, experiment for molecular and develop-mental biology

1. Partial exogastrulation due to apical-basal polarity of F-actin distribution disruption in sea urchin embryo by omeprazole. Genes to Cells27: 392-408（2022）
2. Mathematical model of structural changes in nuclear speckle. Biophys. and Physicobiol. 20: e200020（2023）
3. Possibilities of skin coat color-dependent risks and risk factors of squamous cell carcinoma and deafness of domestic cats inferred via RNA-seq data. Genes to Cells 28: 893-905（2023）

これまでの研究・教育の総仕上げ的に、「制御工学と数理科学の交差点で」というキャッチフレーズの下、MBPC (モデル予測制御、Model Based Predictive Control) の研究を行っている。特に、工学部の制御工学科や数理工学科などで学ぶ様々な知恵が役立つ制御理論は面白い対象であると思う。また、最近は、産学協同に携わっており、MEMSなどのナノテク技術と関連したモノつくりの電気・通信工学の方々と協働している。

As a final step in my research and education, I am currently conducting research on MBPC (Model Based Predictive Control) under the catchphrase "At the intersection of control engineering and mathematical science." Recently, I have also been involved in industry-academia collaboration, working with electrical and communication engineers involved in the manufacturing of products related to nanotechnology such as MEMS.

keywords： MBPC,  At the intersection of control engineering and mathematical science,   industry-academia collaboration

1. A mathematically scientific study of cyanobacteria’s circadian rhythm based on induced memory by hysteresis structure of covalent modification as self-feedforward auto-control system、American J. Engineering research,, Volume-13 ^~Issue-6 ^~ (June-2024)
2. “Standard model of a binary digit of memory with multiple covalent modifications in a cell”, J. of pure and applied math., 2（1）, p1 – 11（2018）
3. “A mathematical study of the one dimensional Keller and Rubinow model for Liesegang bands”, J. Stat Phys（2009）Vol.135: 107–132

蛋白質や核酸などの生体高分子のX線結晶構造解析による分子構造の解明に取り組んできた。それら蛋白質の由来はヒト、黄色ブドウ球菌、植物、海藻など多様で、さらに立体構造からみた分子進化にも興味を持っている。

Structure and function analysis of protein by X-ray crystallography. Target proteins are DNA-repair enzyme;toxin proteins from staphylococcus aureus, lectin from algae; proteins relating to cancer and Parkinson’s disease; proteins from plant, glucokinase, and so on. Molecular evolution of protein is also analyzed from X-ray structure of artificial proteins.

keywords：protein, crystallography, structural biology, chemistry, physics, data science, synchrotron radiation, pharmacy

1. Three-dimensional structure of ribonuclease H from E. coli./Nature 347, 306–309/1990
2. X-ray structure of T4 endonuclease V: An exision repair enzyme specific for a pyrimidine dimer./Science 256, 523-526/1992
3. Structure-function relationship of assimilatory nitrite reductases from the leaf and root of tobacco based on high resolution structures./Prot.Sci. 21, 383-395/2012

動的で複雑な生命現象を対象として、数理生物・生物物理学の観点から理論的研究を行う。数理モデル解析や大規模数値計算、機械学習解析を通して様々な生物種に共通する普遍的な性質の理解を目指す。

The aim of our research group is to understand dynamic and complex biological phenomena from the per-spective of biophysics and mathematical biology, and to elucidate the underlying mechanisms universal to various biological species through mathematical modeling, machine learning analysis, and large scale numerical computation.

keywords：biophysics, mathematical biology

1. Three-dimensional morphodynamic simulations of macropinocytic cups. iScience 24（10）1-22（2021）
2. A deep learning approach for morphological feature extraction based on variational auto-encoder: an application to mandible shape. NPJ Syst. Biol. Appl. 9（1）, 30. 1-12（2023）
3. Theoretical analysis of discreteness-induced transition in autocatalytic reaction dynamics. Phys. Rev. E. 91, 022707 1-7（2015）

ウニの発生をモデルとして分子生物学的手法およびゲノム編集により、形態形成の分子メカニズムの解明、発生過程における遺伝子・クロマチン・染色体の動態の解明、インスレーターの作用機構の解明を目指す。

Using sea urchin development as a model, I aim to elucidate the molecular mechanisms for transcriptional regulation of morphogenetic genes, nuclear dynamics of gene, chromatin and chromosome during devel-opment, and insulator activity with molecular biology techniques and genome editing.

keywords：sea urchin development, transcription, nuclear dynamics

1. Establishment of knockout adult sea urchins by using a CRISPR-Cas9 system. Dev Growth Differ 61:378-388.（2019）
2. Dynamic changes in the interchromosomal interaction of early histone gene loci during development of sea urchin. J Cell Sci 130:4097-4107.（2017）
3. Cilia play a role in breaking left–right symmetry of the sea urchin embryo. Genes Cells 21:568-578.（2016）

地球温暖化ガスであるCO₂の削減や世界的な食糧危機対策に寄与すると考えられる光合成の活性上昇機構に注目している。複数の光合成タンパク質酸化抑制機構を明らかにし、光合成活性上昇植物の育種に成功した。

We are studying the mechanisms to increase photosynthesis activity, which may contribute to the reduc-tion of CO₂ as greenhouse gas, and countermeasures against the global food crisis. We have revealed sev-eral mechanisms of inhibition of photosynthetic protein oxidation and have succeeded in breeding plants with increased photosynthetic activity.

keywords：photosynthesis, Rubisco, redox, oxidative stress

1. Overexpression of BUNDLE SHEATH DEFECTIVE 2 improves the efficiency of photosynthesis and growth in Arabidopsis.（2020）Plant J.102: 129-137.
2. Arabidopsis BSD2 reveals a novel redox regulation of Rubisco physiology in vivo.（2020）Plant Signal. Behav. 15
3. Overexpression of the protein disulfide isomerase AtCYO1 in chloroplasts slows dark- induced senescence in Arabidopsis.（2018）BMC Plant Biology 18: 1-9.

２０万ガウスの超伝導磁石〜数百ガウスの永久磁石の磁場と、一方で、超伝導磁石が造り出す地上の重力制御環境場のそれぞれが、光化学反応や最近では麹菌の生体反応に及ぼす効果や影響を研究しています。

Research fields consist of（1）effect of steady high magnetic fields up to 200,000 gauss and（2）effect of magnetically regulated gravitational fields, especially microgravity and hypergravity, on photochemical re -actions and biological phenomena of Aspergillus oryzae.

keywords：magneto-science, magnetic field, magnetically regulated gravitational field, microgravity, hypergravity,photochemical reation, aspergillus oryzae

1. Effect of High Magnetic Fields on the Reverse Electron Transfer Process in an α-Cyclodextrin Inclusion Complex of Phenothiazine-Viologen Chain-Linked Compound / Chem. Phys. Lett., 259, 361-367 / 1996.
2. Effect of Horizontal Strong Static Magnetic Field on Swimming Behavior of Paramecium caudatum / Mol. Phys., 104, 1659-1666 / 2006.
3. Effect of Hypergravity Created by Strong Magnetic Force on Orientation of Porphyrin Nanorods / J. Magn. Magn. Mater., 310, 2859-2861 / 2007.

深海微生物の細胞内温度や圧力は外部の環境と同じであるため、深海微生物が産生する酵素は同じ条件下で機能している。深海微生物由来酵素は、水との相互作用の制御により高圧力に適応していることを明らかにした。

Since the internal and external hydrostatic pressures of deep-sea microorganisms are the same, their enzymes must work under high hydrostatic pressure and have some kind of pressure-adaptation mecha-nisms. Elucidation of such pressure-adaptation mechanisms of deep-sea enzymes can contribute to basic bioscience and industrial applications.

keywords：deep sea enzyme, high pressure, hydration, molecular adaptation, partial molar volume.

1. Functional, structural, and thermodynamic characteristics of enzymes from deep-sea microorganisms. Microbial Catalysts Volume 1: 325-343（2019）.
2. Stability, flexibility, and function of dihydrofolate reductases from Escherichia coli and deep-sea bacteria. Current Research in Microbiology:1-36（2018）.
3. Similar structural stabilities of 3-isopropylmalate dehydrogenases from the obligatory piezophilic bacterium Shewanella benthica strain DB21MT-2 and its atmospheric congener S. oneidensis strain MR-1. Biocim. Biophys. Acta 1866: 680-691（2018）.

生物は常に大気に曝され体内に取り込んで生きています。大気中に含まれているさまざまな物質は何かしら生物に影響を及ぼしています。私は大気中の微量成分である窒素酸化物（NOx、主に一酸化窒素NOと二酸化窒素NO₂）に対する植物の応答を分子生理学手法を用いて研究しています。NOxは植物の成長促進作用を有しており生産量を約２倍に増加します。この作用機構の解明と作用を利用した生産量増加について研究しています。

Nitrogen dioxide is a trace component of the atmosphere, and is used to be known as a pollutant. I have found that nitrogen dioxide is a positive regulator for plants to nearly double their organ size and shoot bio-mass. I have been studying the molecular mechanism of how nitrogen dioxide acts on plants.

keywords：nitrogen dioxide, nitrogen oxide, plant, Arabidopsis, environment

1. Dual selective nitration in Arabidopsis: Almost exclusive nitration of PsbO and PsbP, and highly susceptible nitration of four non-PSII pro-teins, including peroxiredoxin II E/Electrophoresis/2015
2. Nitrogen dioxide regulates organ growth by controlling cell proliferation and enlargement in Arabidopsis/New Phytol/2014
3. Atmospheric nitrogen dioxide gas is a plant-vitalization signal to increase plant size and the contents of cell constituents/New Phytol/2005

多細胞動物の形態の多様性と保存性を理解するために、発生過程における形態形成とその調節機構を種間で比較解析してきた。多細胞体制の構築に不可欠な細胞外基質の分子環境、機能と進化に関する研究を行っている。

To understand the morphological diversity and conservation of multicellular animals, I have been studying the regulatory mechanisms for morphogenesis during development using sea urchin, medaka and mouse.
I am currently investigating the molecular environment, function and evolution of novel extracellular matrix,which is indispensable for constructing multicellular systems.

keywords：morphogenesis, development, extracellular matrix, cell differentiation

1. Cell-surface arylsulfatase A and B on sinusoidal endothelial cells, hepatocytes, and Kupffer cells in mammalian livers. Med Mol Morphol42:63-69.（2009）
2. Sea urchin arylsulfatase, an extracellular matrix component, is involved in gastrulation during embryogenesis. Dev Genes Evol 219:281-288.（2009）
3. Distributions of H⁺,K⁺-ATPase and Cl^-,HCO3^（-）-ATPase in micromere-derived cells of sea urchin embryos. Differentiation 35:190-196.（1987）

数理モデリングとデータ解析を駆使して、生命現象の理解を目指しています。最近では特に分子・細胞内小器官や細胞の形・動きと機能の連関や細胞内の情報伝達に注目しています。

We aim to understand biological phenomena by using mathematical modeling and data analysis. Recently,we are focusing on the relationship among structure, movement and function of molecules, subcellular or-ganelles and cells.

keywords：mathematical modeling, statistics, biophysics, systems biology, bioinformatics

1. Logical design of oral glucose ingestion pattern minimizing blood glucose in humans/npj Syst. Biol. Appl. 5:31/2019
2. Robustness against additional noise in cellular information transmission/Phys. Rev. E 100:042403/2019
3. Small-Volume Effect Enables Robust, Sensitive, and Efficient Information Transfer in the Spine/Biophys. J. 112:813/2017

超分子化学や非線形科学の視座から人工的に生物様システムを創製し、「生命の起源」や「生命とは何か」という問いに対する普遍的な解を探究しています。さらに、再現した生命の特性を産業技術に応用することにも挑戦しています。

Construct artificial life-like systems from the aspects of supramolecular chemistry and nonlinear science to approach universal answers to “Origins of Life” and “What is Life?”. Also try to apply characteristic features of life to industry.

keywords：supramolecular chemistry, nonlinear science, life-like systems, protocells, artificial cells, origins of life

1. Proliferating Coacervate Droplets as the Missing link between Chemistry and Biology in the Origins of Life. Nature Commun 12(1): 5487 (2021)
2. Evolution of Proliferative Model Protocells Highly Responsive to the Environment. Life 12(10):1635 (2022)
3. Oscillatory Motion of an Organic Droplet Reflecting a Reaction Scheme. J Phys Chem Lett 14: 14546-14551 (2023)

生物が生物“らしい”振る舞いをするには、細胞中で「どのような分子が、いつ、どこで、どのように」機能を発揮するかが制御されている必要があります。細胞内分子の局所的振る舞いに興味を持って研究しています。

My research interest is in the mechanisms of cell-polarization, and how they contribute to biologicalevents, including human disease.

keywords：cell polarity, biomolecular condensates, local translation, bio-imaging

1. “The RNA-binding protein Fus directs translation of localized mRNAs in APC-RNP granules.” eLife, 2019
2. “FUS inclusions disrupt RNA localization by sequestering kinesin-1 and inhibiting microtubule detyrosination.” J. C. Biol., 2017.
3. “Translation regulation of protrusion-localized RNAs involves silencing and clustering after trasnport..” J. C. Biol., 2013.

動的な時空間パターンを自律的に形成する化学反応を用いて、複雑な生命現象を無生物系で模倣・再現し、生物らしい挙動の発現に必要な共通要素の探索およびその理解を目指す研究を進めています。

To understand the mechanisms of complex biological phenomena, we construct nonliving experimental systems using a unique chemical reaction that spontaneously forms dynamic spatio-temporal patterns and search for important factors in biological phenomena.

keywords：nonlinear phenomena, oscillating chemical reaction, belousov-zhabotinsky reaction, pattern formation,self-propelled motion

1. Distinguishing the Dynamic Fingerprints of Two-and Three-Dimensional Chemical Waves in Microbeads., J. Phys. Chem. A 122: 1967-1971（2018）
2. Switching between Two Oscillatory States Depending on the Electrical Potential., J. Phys. Chem. B 125: 3638-3643（2021）
3. Traveling waves propagating through coupled microbeads in the Belousov-Zhabotinsky reaction., Phys. Chem. Chem. Phys. 23: 24175-24179（2021）

生物の形態（昆虫の翅）や自然環境に注目し、流体力学を中心とした数理科学的な観点から解析します。そして、生物が複雑な環境を苦にすることなく、自由自在に行動できる秘密を解明することを目指しています。

We study the relationship between flow and the structure of insect wings using mathematical analysis to understand how organisms fly through complex environments.

keywords：fluid mechanics, biofluid, insect flight, vortex dynamics, mathematical structure

1. Dynamic Lift Enhancement Mechanism of Dragonfly Wing Model by Vortex-Corrugation Interaction, PRFluids, 8, 123101（2023）.
2. Aerodynamic Performance of Dragonfly Wing Model That Starts Impulsively: How Vortex Motion Works, JFST, 18, 1, JFST0013（2023）.
3. Dead-Water Region around Two-Dimensional Sand-Dune Models, JPSJ, 89, 063901（2020）.