Department of Biosciences and Informatics

Research Output 1987 2020

2020

Different strategies for tissue scaling in dwarf tailbud embryos revealed by single-cell analysis

Matsumura, K. D., Nakamura, M. J., Koizumi, W. C., Hotta, K. & Oka, K., 2020 Jan 1, (Accepted/In press) In : Developmental Biology.

Research output: Contribution to journalArticle

Single-Cell Analysis
Embryonic Structures
Cell Size
Cell Count
Chordata

Optical Dissection of Synaptic Plasticity for Early Adaptation in Caenorhabditis elegans

Ashida, K., Shidara, H., Hotta, K. & Oka, K., 2020 Jan 21, In : Neuroscience. 428, p. 112-121 10 p.

Research output: Contribution to journalArticle

Neuronal Plasticity
Caenorhabditis elegans
Dissection
Neurons
Interneurons
2019

A self-marker-like protein governs hemocyte allorecognition in Halocynthia roretzi

Ema, M., Okada, T., Takahashi, M., Uchiyama, M., Kubo, H., Moriyama, H., Miyakawa, H. & Matsumoto, M., 2019 Dec 16, In : Zoological Letters. 5, 1, 34.

Research output: Contribution to journalArticle

Open Access
Halocynthia roretzi
hemocytes
monophenol monooxygenase
proteins
Ascidiacea
8 Citations (Scopus)

Biodegradation of PET: Current Status and Application Aspects

Taniguchi, I., Yoshida, S., Hiraga, K., Miyamoto, K., Kimura, Y. & Oda, K., 2019 Jan 1, In : ACS Catalysis. p. 4089-4105 17 p.

Research output: Contribution to journalArticle

Biodegradation
Enzymes
Hydrolases
Degradation
Plastics

Brain-Machine Interface and Neuro-Rehabilitation

Ushiba, J., 2019 Jul 1, In : Brain and nerve = Shinkei kenkyu no shinpo. 71, 7, p. 793-804 12 p.

Research output: Contribution to journalArticle

Brain-Computer Interfaces
Rehabilitation
Robotics
Cybernetics
Brain

Cell-sized confinement controls generation and stability of a protein wave for spatiotemporal regulation in cells

Kohyama, S., Yoshinaga, N., Yanagisawa, M., Fujiwara, K. & Doi, N., 2019 Jul 1, In : eLife. 8, e44591.

Research output: Contribution to journalArticle

Open Access
Protein Stability
Confined Spaces
Proteins
Cell Division
Membrane Proteins

Chemistry and biology for the small molecules targeting characteristics of cancer cells

Imoto, M., 2019 Jan 1, In : Bioscience, Biotechnology and Biochemistry. 83, 1, p. 10-19 10 p.

Research output: Contribution to journalReview article

Cells
Molecules
Neoplasms
Biological Products
Screening

Chemoenzymatic Cascade Synthesis of Optically Pure Alkanoic Acids by Using Engineered Arylmalonate Decarboxylase Variants

Enoki, J., Mügge, C., Tischler, D., Miyamoto, K. & Kourist, R., 2019 Apr 1, In : Chemistry - A European Journal. 25, 19, p. 5071-5076 6 p.

Research output: Contribution to journalArticle

Open Access
Carboxylic acids
Acids
Enantiomers
Enantioselectivity
Reducing Agents

Comparison of Sexual Reproductive Behaviors in Two Species of Macrobiotidae (Tardigrada: Eutardigrada)

Sugiura, K., Minato, H., Suzuki, A. C., Arakawa, K., Kunieda, T. & Matsumoto, M., 2019 Jan 1, In : Zoological Science. 36, 2, p. 120-127 8 p.

Research output: Contribution to journalArticle

Tardigrada
sexual behavior
reproductive behavior
cloaca
ejaculation

Comparison of the transcriptomes of two tardigrades with different hatching coordination

Yoshida, Y., Sugiura, K., Tomita, M., Matsumoto, M. & Arakawa, K., 2019 Dec 9, In : BMC Developmental Biology. 19, 1, 24.

Research output: Contribution to journalArticle

Open Access
Molting
Transcriptome
Embryonic Development
Ecdysteroids
Juvenile Hormones

Deep learning for non-invasive determination of the differentiation status of human neuronal cells by using phase-contrast photomicrographs

Ooka, M., Tokuoka, Y., Nishimoto, S., Hiroi, N. F., Yamada, T. G. & Funahashi, A., 2019 Dec 1, In : Applied Sciences (Switzerland). 9, 24, 5503.

Research output: Contribution to journalArticle

Open Access
photomicrographs
stem cells
phase contrast
Stem cells
learning

Detection of influenza virus by agglutination using nanoparticles conjugated with a sialic acid-mimic peptide

Matsubara, T., Kubo, A. & Sato, T., 2019 Jan 1, (Accepted/In press) In : Polymer Journal.

Research output: Contribution to journalArticle

N-Acetylneuraminic Acid
Viruses
Peptides
Nanoparticles
Acids

Development of Rehabilitation System with Brain-Computer Interface for Subacute Stroke Patients

Hashimoto, Y., Kakui, T., Ushiba, J., Liu, M., Kamada, K. & Ota, T., 2019 Jan 16, Proceedings - 2018 IEEE International Conference on Systems, Man, and Cybernetics, SMC 2018. Institute of Electrical and Electronics Engineers Inc., p. 51-56 6 p. 8616013. (Proceedings - 2018 IEEE International Conference on Systems, Man, and Cybernetics, SMC 2018).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Brain-Computer Interfaces
Brain computer interface
Patient rehabilitation
Computer Systems
Rehabilitation
Open Access
Polyethylene Terephthalates
Surface-Active Agents
Mutagenesis
Recycling
Enzymes
1 Citation (Scopus)

Efficient generation of Knock-in/Knock-out marmoset embryo via CRISPR/Cas9 gene editing

Kumita, W., Sato, K., Suzuki, Y., Kurotaki, Y., Harada, T., Zhou, Y., Kishi, N., Sato, K., Aiba, A., Sakakibara, Y., Feng, G., Okano, H. & Sasaki, E., 2019 Dec 1, In : Scientific reports. 9, 1, 12719.

Research output: Contribution to journalArticle

Open Access
Clustered Regularly Interspaced Short Palindromic Repeats
Callithrix
Embryonic Structures
Gene Knockout Techniques
Primates
1 Citation (Scopus)

Enzyme kinetics of dUTPase from the planarian Dugesia ryukyuensis

Alam, M. S., Moriyama, H. & Matsumoto, M., 2019 Mar 22, In : BMC Research Notes. 12, 1, 163.

Research output: Contribution to journalArticle

Planarians
Pyrophosphatases
Enzyme kinetics
Deoxyuridine
Enzymes

Erratum to ‘Fast Electrophysiological Mapping of Rat Cortical Motor Representation on a Time Scale of Minutes during Skin Stimulation’ [Neuroscience 414C (2019) 245–254](S0306452219304828)(10.1016/j.neuroscience.2019.07.011)

Kosugi, A., Castagnola, E., Carli, S., Ricci, D., Fadiga, L., Taoka, M., Iriki, A. & Ushiba, J., 2019 Sep 15, In : Neuroscience. 416, 1 p.

Research output: Contribution to journalComment/debate

Neurosciences
Emotions
Skin

Fast Electrophysiological Mapping of Rat Cortical Motor Representation on a Time Scale of Minutes during Skin Stimulation

Kosugi, A., Castagnola, E., Carli, S., Ricci, D., Fadiga, L., Taoka, M., Iriki, A. & Ushiba, J., 2019 Aug 21, In : Neuroscience. 414, p. 245-254 10 p.

Research output: Contribution to journalArticle

Skin
Forelimb
Somatosensory Cortex
Wool
Wounds and Injuries

Guest Editorial for the 16th Asia Pacific Bioinformatics Conference

Yamanishi, Y., Sakakibara, Y. & Chen, Y. P. P., 2019 Jan 1, In : IEEE/ACM Transactions on Computational Biology and Bioinformatics. 16, 1, 8635414.

Research output: Contribution to journalEditorial

Bioinformatics
Computational Biology
1 Citation (Scopus)

Ktedonoketone and 2’-oxosattabacin, benzenoid metabolites from a thermophilic bacterium Thermosporothrix hazakensis in the phylum Chloroflexi

Igarashi, Y., Yamamoto, K., Ueno, C., Yamada, N., Saito, K., Takahashi, K., Enomoto, M., Kuwahara, S., Oikawa, T., Tashiro, E., Imoto, M., Xiaohanyao, Y., Zhou, T., Harunari, E. & Oku, N., 2019 Jan 1, In : Journal of Antibiotics.

Research output: Contribution to journalArticle

Chloroflexi
Adipocytes
Bacteria
Autophagy
Biological Products
1 Citation (Scopus)

Magnesium is a key player in neuronal maturation and neuropathology

Yamanaka, R., Shindo, Y. & Oka, K., 2019 Jul 2, In : International journal of molecular sciences. 20, 14, 3439.

Research output: Contribution to journalArticle

Open Access
Magnesium
magnesium
Homeostasis
homeostasis
RNA Stability
1 Citation (Scopus)
Caenorhabditis elegans
Dopamine
Food
Machine Learning
Learning

Near-Infrared Fluorescent Probes for Imaging of Intracellular Mg2+ and Application to Multi-Color Imaging of Mg2+, ATP, and Mitochondrial Membrane Potential

Murata, O., Shindo, Y., Ikeda, Y., Iwasawa, N., Citterio, D., Oka, K. & Hiruta, Y., 2019 Jan 1, (Accepted/In press) In : Analytical chemistry.

Research output: Contribution to journalArticle

Fluorescent Dyes
Adenosine Triphosphate
Rhodamines
Color
Infrared radiation

Neural properties of fundamental function encoding of sound selectivity in the female avian auditory cortex

Inda, M., Hotta, K. & Oka, K., 2019 Jan 1, (Accepted/In press) In : European Journal of Neuroscience.

Research output: Contribution to journalArticle

Auditory Cortex
Music
Acoustics
Finches
Equidae

Neurorehabilitation: Neural Plasticity and Functional Recovery 2018

Fujiwara, T., Ushiba, J. & Soekadar, S. R., 2019 Jan 1, In : Neural plasticity. 2019, 1 p.

Research output: Contribution to journalEditorial

Open Access
Neuronal Plasticity
Neurological Rehabilitation
Galactosidases
Fibroblasts
Diploidy
HeLa Cells
Mitosis

Poly-γ-glutamic acid production of Bacillus subtilis (natto) in the absence of DegQ: A gain-of-function mutation in yabJ gene

Hong, L. T. T., Hachiya, T., Hase, S., Shiwa, Y., Yoshikawa, H., Sakakibara, Y., Nguyen, S. L. T. & Kimura, K., 2019 Jan 1, In : Journal of Bioscience and Bioengineering.

Research output: Contribution to journalArticle

Bacilli
Bacillus subtilis
Glutamic Acid
Genes
Mutation

Predicting the future direction of cell movement with convolutional neural networks

Nishimoto, S., Tokuoka, Y., Yamada, T., Hiroi, N. F. & Funahashi, A., 2019 Jan 1, In : PloS one. 14, 9, e0221245.

Research output: Contribution to journalArticle

Open Access
cell movement
neural networks
Cell Movement
Cells
Neural networks
1 Citation (Scopus)

Preparation of optically pure flurbiprofen via an integrated chemo-enzymatic synthesis pathway

Enoki, J., Linhorst, M., Busch, F., Baraibar, Á. G., Miyamoto, K., Kourist, R. & Mügge, C., 2019 Apr 1, In : Molecular Catalysis. 467, p. 135-142 8 p.

Research output: Contribution to journalArticle

Flurbiprofen
routes
preparation
synthesis
Enzymes

Regulation of spatiotemporal patterning in artificial cells by a defined protein expression system

Yoshida, A., Kohyama, S., Fujiwara, K., Nishikawa, S. & Doi, N., 2019 Jan 1, In : Chemical Science. 10, 48, p. 11064-11072 9 p.

Research output: Contribution to journalArticle

Open Access
Cells
Proteins
Drug delivery
Genes
Robots
1 Citation (Scopus)
Toyocamycin
Unfolded Protein Response
Endoplasmic Reticulum Stress
Drug Discovery
Heat-Shock Proteins

Sensorimotor Connectivity after Motor Exercise with Neurofeedback in Post-Stroke Patients with Hemiplegia

Tsuchimoto, S., Shindo, K., Hotta, F., Hanakawa, T., Liu, M. & Ushiba, J., 2019 Sep 15, In : Neuroscience. 416, p. 109-125 17 p.

Research output: Contribution to journalArticle

Neurofeedback
Hemiplegia
Stroke
Exercise
Magnetic Resonance Imaging

Serotonin modulates behavior-related neural activity of RID interneuron in Caenorhabditis elegans

Mori, H., Ashida, K., Shidara, H., Nikai, T., Hotta, K. & Oka, K., 2019 Jan 1, In : PloS one. 14, 12, e0226044.

Research output: Contribution to journalArticle

Open Access
interneurons
Caenorhabditis elegans
Interneurons
serotonin
Serotonin

Stochastic thermodynamic limit on E. coli adaptation by information geometric approach

Ashida, K. & Oka, K., 2019 Jan 15, In : Biochemical and Biophysical Research Communications. 508, 3, p. 690-694 5 p.

Research output: Contribution to journalArticle

Thermodynamics
Escherichia coli
Costs and Cost Analysis
Biological systems
Noise
1 Citation (Scopus)

Synthesis of Various Glycopolymers Bearing Sialyllactose and the Effect of Their Molecular Mobility on Interaction with the Influenza Virus

Nagao, M., Matsubara, T., Hoshino, Y., Sato, T. & Miura, Y., 2019 Jul 8, In : Biomacromolecules. 20, 7, p. 2763-2769 7 p.

Research output: Contribution to journalArticle

Bearings (structural)
Viruses
Medical nanotechnology
Oligosaccharides
Hemagglutinins
1 Citation (Scopus)

The Input-Output Relationship of AIY Interneurons in Caenorhabditis elegans in Noisy Environment

Ashida, K., Hotta, K. & Oka, K., 2019 Sep 27, In : iScience. 19, p. 191-203 13 p.

Research output: Contribution to journalArticle

Open Access
Caenorhabditis elegans
Interneurons
Glutamic Acid
Neurosciences
Noise
3 Citations (Scopus)

Topological Design of Star Glycopolymers for Controlling the Interaction with the Influenza Virus

Nagao, M., Matsubara, T., Hoshino, Y., Sato, T. & Miura, Y., 2019 Apr 17, In : Bioconjugate Chemistry. 30, 4, p. 1192-1198 7 p.

Research output: Contribution to journalArticle

Orthomyxoviridae
Viruses
Sugars
Stars
Polymers

Two-stage regression of high-density scalp electroencephalograms visualizes force regulation signaling during muscle contraction

Hayashi, M., Tsuchimoto, S., Mizuguchi, N., Miyatake, M., Kasuga, S. & Ushiba, J., 2019 Aug 21, In : Journal of neural engineering. 16, 5, 1 p.

Research output: Contribution to journalArticle

Muscle Contraction
Electroencephalography
Scalp
Brain-Computer Interfaces
Muscle

XitoSBML: A Modeling Tool for Creating Spatial Systems Biology Markup Language Models From Microscopic Images

Ii, K., Mashimo, K., Ozeki, M., Yamada, T. G., Hiroi, N. & Funahashi, A., 2019 Oct 22, In : Frontiers in Genetics. 10, 1027.

Research output: Contribution to journalArticle

Open Access
Systems Biology
Language
Software
2018

14-3-3ϵa directs the pulsatile transport of basal factors toward the apical domain for lumen growth in tubulogenesis

Mizotani, Y., Suzuki, M., Hotta, K., Watanabe, H., Shiba, K., Inaba, K., Tashiro, E., Oka, K. & Imoto, M., 2018 Sep 18, In : Proceedings of the National Academy of Sciences of the United States of America. 115, 38, p. E8873-E8881

Research output: Contribution to journalArticle

Notochord
Growth
Larva
Myosin Type II
Pulsatile Flow
4 Citations (Scopus)

Acceleration of Enzymatic Degradation of Poly(ethylene terephthalate) by Surface Coating with Anionic Surfactants

Furukawa, M., Kawakami, N., Oda, K. & Miyamoto, K., 2018 Dec 11, In : ChemSusChem. 11, 23, p. 4018-4025 8 p.

Research output: Contribution to journalArticle

Hydrolases
Polyethylene Terephthalates
Anionic surfactants
Polyethylene terephthalates
ethylene
1 Citation (Scopus)

Accurate motor mapping in awake common marmosets using micro-electrocorticographical stimulation and stochastic threshold estimation

Kosugi, A., Takemi, M., Tia, B., Castagnola, E., Ansaldo, A., Sato, K., Awiszus, F., Seki, K., Ricci, D., Fadiga, L., Iriki, A. & Ushiba, J., 2018 Apr 6, In : Journal of Neural Engineering. 15, 3, 036019.

Research output: Contribution to journalArticle

Callithrix
Implanted Electrodes
Motor Evoked Potentials
Reproducibility of Results
Computer Simulation
2 Citations (Scopus)

A comprehensive comparison of sex-inducing activity in asexual worms of the planarian Dugesia ryukyuensis: The crucial sex-inducing substance appears to be present in yolk glands in Tricladida

Nakagawa, H., Sekii, K., Maezawa, T., Kitamura, M., Miyashita, S., Abukawa, M., Matsumoto, M. & Kobayashi, K., 2018 Jun 12, In : Zoological Letters. 4, 1, 14.

Research output: Contribution to journalArticle

Tricladida
Dugesia
gender
Polycladida
Platyhelminthes

Acquisition of a mental strategy to control a virtual tail via brain–computer interface

Fujisawa, A., Kasuga, S., Suzuki, T. & Ushiba, J., 2018 Jan 26, (Accepted/In press) In : Cognitive Neuroscience. p. 1-14 14 p.

Research output: Contribution to journalArticle

Tail
Buttocks
Haplorhini
Electroencephalography
Healthy Volunteers
1 Citation (Scopus)

A dual system using compartmentalized partnered replication for selection of arsenic-responsive transcriptional regulator

Aye, S. L., Fujiwara, K. & Doi, N., 2018 Nov 1, In : Journal of Biochemistry. 164, 5, p. 341-348 8 p.

Research output: Contribution to journalArticle

Arsenic
Synthetic Biology
Genetic Engineering
Networks (circuits)
Biosensing Techniques
2 Citations (Scopus)
RNA
Thermodynamics
Learning systems
Benchmarking
Computational Biology
5 Citations (Scopus)

Amyloid- fibrils assembled on ganglioside-enriched membranes contain both parallel -sheets and turns

Matsubara, T., Yasumori, H., Ito, K., Shimoaka, T., Hasegawa, T. & Sato, T., 2018 Jan 1, In : Journal of Biological Chemistry. 293, 36, p. 14146-14154 9 p.

Research output: Contribution to journalArticle

Gangliosides
Nanoclusters
Amyloid
Membranes
Alzheimer Disease
5 Citations (Scopus)

Artificial Cell Fermentation as a Platform for Highly Efficient Cascade Conversion

Fujiwara, K., Adachi, T. & Doi, N., 2018 Feb 16, In : ACS Synthetic Biology. 7, 2, p. 363-370 8 p.

Research output: Contribution to journalArticle

Artificial Cells
Fermentation
Enzymes
Stereoselectivity
Liposomes
1 Citation (Scopus)

A study on skill acquisition mechanism and development of skill transfer systems

Koike, H., Rekimoto, J., Ushiba, J., Furuya, S. & Ito, A., 2018 Jan 1, In : CEUR Workshop Proceedings. 2068

Research output: Contribution to journalConference article

Computer vision
Artificial intelligence
Robotics
23 Citations (Scopus)

A Transient Rise in Free Mg2+ Ions Released from ATP-Mg Hydrolysis Contributes to Mitotic Chromosome Condensation

Maeshima, K., Matsuda, T., Shindo, Y., Imamura, H., Tamura, S., Imai, R., Kawakami, S., Nagashima, R., Soga, T., Noji, H., Oka, K. & Nagai, T., 2018 Feb 5, In : Current Biology. 28, 3, p. 444-451.e6

Research output: Contribution to journalArticle

adenosine triphosphate
Chromosomes
Condensation
Hydrolysis
Adenosine Triphosphate