Advanced Platform Technology Development Unit Projects

Large‐Scale Research Projects

  1. JSPS Grant-in-Aid for Scientific Research (A) Water Oxidation on Semiconductor Photocatalysts: How Completed under Dilute Photon Flux(2020-2022)Onishi,H.
  2. NEDO Development of Common Basic Technology for Plant Productivity Control Establishment of a Domestic Technology Platform for Genome Editing(2016-2020)Nishida, K., Fujikura U., Mitsunobu, H., Katayama, K.
  3. JSPS Grant-in-Aid for Scientific Research on Innovative Areas Re-optimization of light-energy conversion system(2016-2020)Akimoto, S.
  4. JSPS Bilateral Open Partnership Joint Research Project(2016-2018)Onishi,H.
  5. MEXT Creation of Innnovation Center for Advanced Interdisciplinary Research Areas Program Innovative BioProduction Kobe (iBioK)(2008-2018)Kondo, A., Hasunuma, T., Nishida, K., Onishi, H., Tominaga, K., Maruyama, T., Akimoto, S., Ishii, J., Tsuge, K., Shimatani, Z.

Advanced Metrology Research Group

  1. Kosaka, T., Teduka, Y., Ogura, T., Zhou, Y., Hisatomi, T., Nishiyama, H., Domen, K., Takahashi, Y., Onishi, H. (2020) Transient Kinetics of O2 Evolution in Photocatalytic Water-Splitting Reaction. ACS Catalysis, 13159-13164.
  2. Sudrajat, H.; Fadlallah, M.; Tao, S.; Kitta, M.; Ichikuni, N.; Onishi, H. (2020) Dopant Site in Indium-Doped SrTiO3 Photocatalysts.Phys. Chem. Chem. Phys., 22, 19178-19187.
  3. Sudrajat, H.; Kitta, M.; Ito, R.; Nagai, S.; Yoshida, T.; Katoh, R.; Ohtani, B.; Ichikuni, N.; Onishi, H. (2020) Water Splitting Activity of La-Doped NaTaO3 Photocatalysts Sensitive to Spatial Distribution of Dopants. Journal of Physical Chemistry C , 124, 15285–15294.
  4. Fujiwara, T.; Sasahara, A.; Happo, N.; Kimura, K.; Hayashi, K.; Onishi, H. (2020) Single-Crystal Model of Highly Efficient Water-Splitting Photocatalysts: A KTaO3 Wafer Doped with Calcium Cations. Chemistry of Materials , 32, 1439–1447.
  5. Kitta, M.; Onishi, H. (2020) Preparation of the NaTaO3 Crystal from the KTaO3 Substrate Via Topotactic Alkaline Cation Substitution as Confirmed by Transmission Electron Microscopy. e-Journal of Surface Science and Nanotechnology , 18, 32–37.
  6. Teduka, Y.; Sasahara, A.; Onishi, H. (2020) Atomic Force Microscopy Imaging of Crystalline Sucrose in Alcohols. ACS Omega , 5, 2569–2574.
  7. Xue, S.; Sasahara, A.; Onishi, H. (2020) Atom-Scale Imaging of TiO2(110) Surface in Water by Frequency-Modulation Atomic Force Microscopy. The Journal of Chemical Physics, 152, 054703 (7 pages).
  8. Sudrajat, H.; Ichikuni, N.; Onishi, H. (2020) Visible Light Responsive La and Fe Co-Doped NaTaO3 Photocatalysts: Local Structure around Dopants. Chemical Physics, 531, 110648 (7 pages).
  9. Söngen, H.; Jaques, Y. M.; Zivanovic, L.; Seibert, S.; Bechstein, R.; Spijker, P.; Onishi, H.; Foster, A. S.; Kühnle, A. (2019)Hydration Layers at the Graphite–Water Interface: Attraction or Confinement? Physical Review B , 200, 205410.
  10. Moriguchi, S.; Tsujimoto, T.; Sasahara, A.; Kokawa, R.; Onishi, H. (2019) Nanometer-Scale Distribution of Lubricant Modifier on Iron Films: A Frequency-Modulation Atomic Force Microscopy Study Combined with Friction Test. ACS Omega, 4, 17593-17599.
  11. Sudrajat, H.; Kitta, M.; Ichikuni, N.; Onishi, H. (2019) Double Doping of NaTaO3 Photocatalysts with La and Mn for Strongly Enhanced Visible-Light Absorption. ACS Applied Energy Materials, 2, 7518-7526.
  12. Furukawa, S.; Amano, K.-i.; Ishihara, T.; Hashimoto, K.; Nishi, N.; Onishi, H.; Sakka, T.(2019)Enhancement of Stratification of Colloidal Particles near a Substrate Induced by Addition of Non-Adsorbing Polymers. Chemical Physics Letters, 734, 136705.
  13. Sudrajat, H.; Dhakal, D.; Kitta, M.; Sasaki, T.; Ozawa, A.; Babel, S.; Yoshida, T.; Ichikuni, N.; Onishi, H. (2019) Electron Population and Water Splitting Activity Controlled by Strontium Cations Doped in KTaO3 Photocatalysts. Journal of Physical Chemistry C , 123, 18387-18397.
  14. Mizutani, S.; Karimata, I.; An, L.; Sato, T.; Kobori, Y.; Onishi, H.; Tachikawa, T. (2019) Charge Carrier Dynamics in Sr-Doped NaTaO3 Photocatalysts Revealed by Deep Uv Single-Particle Microspectroscopy. Journal of Physical Chemistry C, 123, 12592-12598.
  15. Kitta, M.; Onishi, H. (2019) Preparation of Visible-Light Responsible Rutile-TiO2(110) Wafer with Well-Defined Surface by Chromium and Antimony Codoping. e-Journal of Surface Science and Nanotechnology, 17, 5-9.
  16. Sudrajat, H.; Zhou, Y.; Sasaki, T.; Ichikuni, N.; Onishi, H. (2019)The Atomic-Scale Structure of LaCrO3-NaTaO3 Solid Solution Photocatalysts with Enhanced Electron Population. Phys. Chem. Chem. Phys., 21, 5148-5157.
  17. Honda, H.; Sasahara, A.; Onishi, H. (2019) Cobalt Porphyrins on Mica: Atomic Force Microscope Imaging in Organic Solvents. Colloids and Surfaces A: Physicochemical and Engineering Aspects, 561, 194-200.
  18. Zhang, F., Wang, HW., Tominaga, K., Hayashi, M., Sasaki, T. (2019) Terahertz Fingerprints of Short-Range Correlations of Disordered Atoms in Diflunisal, J. Phys. Chem. A. 123(21), 4555-4564.
  19. Nagao, R., Yokono, M., Ueno, Y., Shen, J.-R., Akimoto, S. (2019) pH-Sensing machinery of excitation energy transfer in diatom PSI–FCPI complexes, J. Phys. Chem. Lett., 10, 3531–3535.
  20. Nagao, R., Kato, K., Suzuki, T., Ifuku, K., Uchiyama, I., Kashino, Y., Dohmae, N., Akimoto, S., Shen, J.-R., Miyazaki, N., Akita, F.(2019) Structural basis for energy harvesting and dissipation in a diatom PSII–FCPII supercomplex, Nature Plants, 5, 890–901.
  21. Ueno, Y., Nagao, R., Shen, J.-R., Akimoto, S.(2019) Spectral properties and excitation relaxation of novel fucoxanthin chlorophyll a/c-binding protein complexes, J. Phys. Chem. Lett., 10, 5148–5152.
  22. Araki, Y.; Sekine, T.; Chang, R.; Hayashi, T.; Onishi, H. (2018) Molecular-Scale Structures of Surface and Hydration of Bioinert Mixedcharged Self-Assembled Monolayers Investigated by the Frequency Modulation Atomic Force Microscopy. RSC Advances, 8, 24660-24664.
  23. An, L.; Sasaki, T.; Weidler, P.; Wöll, C.; Ichikuni, N.; Onishi, H. (2018) Local Environment of Strontium Cations Activating NaTaO3 Photocatalysts. ACS Catalysis, 8, 880-885.
  24. Okuda, M., Higashi, M., Ohta, K., Saito, S., Tominaga, K. (2018) Theoretical investigation on vibrational frequency fluctuations of SCN-derivatized vibrational probe molecule in water. Chemical Physics. 512. 82-87.
  25. Okuda, M., Ohta, K., Tominaga, K. (2018) Rotational Dynamics of Solutes with Multiple Single Bond Axes Studied by Infrared Pump–Probe Spectroscopy. J. Phys. Chem. A . 122(4), 946–954.
  26. Ueno, Y., Shimakawa, G., Miyake, S., Akimoto, C. (2018) Light-harvesting strategy during CO2-dependent photosynthesis in the green alga Chlamydomonas reinhardtii, J. Phys. Chem. Lett., 9, 1028–1033.
  27. Kosuge, K., Tokutsu, R., Kim, E., Akimoto, S., Yokono, M., Ueno, Y., Minagawa, J. (2018) LHCSR1-dependent fluorescence quenching is mediated by excitation energy transfer from LHCII to photosystem I in Chlamydomonas reinhardtii, Proc. Natl. Acad. Sci. USA,115, 3722–3727.

Genome Editing Research Group

  1. Sakata, RC., Ishiguro, S., Mori, H., Tanaka, M., Tatsuno, K., Ueda, H., Yamamoto, S., Seki, M., Masuyama, N., Nishida, K., Nishimasu, H., Arakawa, K., Kondo, A., Nureki, O., Tomita, M., Aburatani, H., Yachie, N. (2020) Base editors for simultaneous introduction of C-to-T and A-to-G mutations. Nature Biotechnology. Jul;38(7):865-869.
  2. Furuhata Y., Sakai A, Murakami T, Morikawa M, Nakamura C, Yoshizumi T, Fujikura U, Nishida K, Kato Y. (2019) A method using electroporation for the protein delivery of Cre recombinase into cultured Arabidopsis cells with an intact cell wall. Sci Rep. Feb 15;9(1):2163.
  3. Shimatani Z, Ariizumi T, Fujikura U, Kondo A, Ezura H, Nishida K. (2019) Targeted Base Editing with CRISPR-Deaminase in Tomato. Methods Mol Biol. 1917:297-307.
  4. Shimatani, Z., Fujikura, U., Ishii, H., Matsui, Y., Suzuki, M., Ueke, Y., Taoka, K., Terada, R., Nishida, K.*, Kondo, A.* (2018) Inheritance of co-edited genes by CRISPR-based targeted nucleotide substitutions in rice. Plant Physiology and Biochemistry, 131: 78-83
  5. Shimatani Z, Fujikura U, Ishii H, Terada R, Nishida K, Kondo A. (2018) Herbicide tolerance-assisted multiplex targeted nucleotide substitution in rice. Data Brief. 30;20:1325-1331.
  6. Tanaka S, Yoshioka S, Nishida K, Hosokawa H, Kakizuka A, Maegawa S. (2018) In vivo targeted single-nucleotide editing in zebrafish. Sci Rep. 30;8(1):11423.
  7. Arazoe T, Kondo A, Nishida K. (2018) Targeted Nucleotide Editing Technologies for Microbial Metabolic Engineering. Biotechnol J. 13(9)
  8. Banno, S., Nishida, K., Arazoe, T., Mitsunobu, H., Kondo, A. (2018) Deaminase-mediated multiplex genome editing in Escherichia coli. Nature Microbiology 3, 423-429

Genome Synthesis Research Group

  1. Yokomori, M., Tsuge, K., Shohda, K., Suyama, A. (2019) Improved measurement of absolute mRNA quantity without reversetranscription. Analytical Biochemistry, 579, 1-8
  2. Tamano, K., Cox 3rd, R. S., Tsuge, K., Miura, A., Itoh, A., Ishii, J., Tamura, T., Kondo, A., Machida, M. (2019) Heterologous production of free dihomo-ɤ-linolenic acid by Aspergillus oryzae and its extracellular release via surfactant supplementation. J. Biosci. Bioeng. 127, 452-457
  3. Chang, J. J., Anandharaj, M., Ho, C. Y., Tsuge, K., Tsai, T. Y., Ke, H. M., Lin, Y. J., Ha Tran, M. D., Li, W. H., Huang, C. C. (2018) Biomimetic strategy for constructing Clostridium thermocellum cellulosomal operons in Bacillus subtilis. Biotechnol. Biofuels. 11,157

Biofoundry Research Group

  1. Ito, Y., Terai, G., Ishigami, M., Hashiba, N., Nakamura, Y., Bamba, T., Kumokita, R., Hasunuma, T., Asai, K., Ishii, J.*, Kondo, A.* (2020) Exchange of endogenous and heterogeneous yeast terminators in Pichia pastoris to tune mRNA stability and gene expression. Nucleic Acids Research, in press
  2. Nitta, N., Iino, T., Isozaki, A., Yamagishi, M., Kitahama, Y., Sakuma, S., Suzuki, Y., Tezuka, H., Oikawa, M., Arai, F., Asai, T., Deng, D., Fukuzawa, H., Hase, M., Hasunuma, T., Hayakawa, T., Hiraki, K., Hiramatsu, K., Hoshino, Y., Inaba, M., Inoue, Y., Ito, T., Kajikawa, M., Karakawa, H., Kasai, Y., Kato, Y., Kobayashi, H., Lei, C., Matsusaka, S., Mikami, H., Nakagawa, A., Numata, K., Ota, T., Sekiya, T., Shiba, K., Shirasaki, Y., Suzuki, N., Tanaka, S., Ueno, S., Watarai, H., Yamano, T., Yazawa, M., Yonamine, Y., Di Carlo, D., Hosokawa, Y., Uemura, S., Sugimura, T., Ozeki, Y., Goda, K. (2020) Raman image-activated cell sorting. Nature Communications, 11, 3452
  3. Isozaki, A., Nakagawa, Y., Loo, MH., Shibata, Y., Tanaka, N., Setyaningrum, DL., Park, JW., Shirasaki, Y., Mikami, H., Huang, D., Tsoi, H., Riche, CT., Ota, T., Miwa, H., Kanda, Y., Ito, T., Yamada, K., Iwata, O., Suzuki, K., Ohnuki, S., Ohya, Y., Kato, Y., Hasunuma, T., Matsusaka, S., Yamagishi, M., Yazawa, M., Uemura, S., Nagasawa, K., Watarai, H., Di Carlo, D., Goda, K. (2020) Sequentially addressable dielectrophoretic array for high-throughput sorting of large-volume biological compartments. Science Advances, 6(22), eaba6712
  4. Watanabe, N., Murata, M., Ogawa, T., Vavricka, CJ., Kondo, A., Ogino, C., Araki, M. (2020) Exploration and evaluation of machine learning-based models for predicting enzymatic reactions. Journal of Chemical Information and Modeling, 60(3), 1833-1843
  5. Inokuma, K., Kurono, H., den Haan, R., van Zyl, W. H., Hasunuma, T., Kondo, A. (2020) Novel strategy for anchorage position control of GPI-attached proteins in the yeast cell wall using different GPI-anchoring domains. Metabolic Engineering, 57, 110-117
  6. Hillson, N., Caddick, M., Cai, Y., Carrasco, JA., Chang, MW., Curach, NC., Bell, DJ., Le Feuvre, R., Friedman, DC., Fu, X., Gold, ND., Herrgård, MJ., Holowko, MB., Johnson, JR., Johnson, RA., Keasling, JD., Kitney, RI., Kondo, A., Liu, C., Martin, VJJ., Menolascina, F., Ogino, C., Patron, NJ., Pavan, M., Poh, CL., Pretorius, IS., Rosser, SJ., Scrutton, NS., Storch, M., Tekotte, H., Travnik, E., Vickers, CE., Yew, WS., Yuan, Y., Zhao, H., Freemont, PS. (2019) Building a global alliance of biofoundries. Nature Communications, 10(1): 2040
  7. Vavricka, CJ., Yoshida, T., Kuriya, Y., Takahashi, S., Ogawa, T., Ono, F., Agari, K., Kiyota, H., Li, J., Ishii, J., Tsuge, K., Minami, H., Araki, M., Hasunuma, T., Kondo, A. (2019) Mechanism-based tuning of insect 3,4-dihydroxyphenylacetaldehyde synthase for synthetic bioproduction of benzylisoquinoline alkaloids. Nature Communications, 10, 2015
  8. Tominaga, D., Kawaguchi, H., Hori, Y., Hasunuma, T., Ogino, C., Aburatani, S. (2018) Mathematical model for small size time series data of bacterial secondary metabolic pathways, Bioinformatics and Biology Insights, 12: 1-7
  9. Bamba, T., Inokuma, K., Hasunuma, T., Kondo, A. (2018) Enhanced cell-surface display of a heterologous protein using SED1 anchoring system in SED1-disrupted Saccharomyces cerevisiae strain. Journal of Bioscience and Bioengineering, 125(3), 306-310
  10. Ito, Y., Watanabe, T., Aikawa, S., Nishi, T., Nishiyama, T., Nakamura, Y., Hasunuma, T., Okubo, Y., Ishii, J.*, Kondo, A.* (2018) Deletion of DNA ligase IV homolog confers higher gene targeting efficiency on homologous recombination in Komagataella phaffii. FEMS Yeast Research, 18(7)
  11. Eguchi, Y., Makanae, K., Hasunuma, T., Ishibashi, Y., Kito, K., Moriya, H. (2018) Estimating the protein burden limit of yeast cells by measuring expression limits of glycolytic proteins. eLife, 7: e34595
  12. Nakamura, Y., Nishi, T., Noguchi, R., Ito, Y., Watanabe, T., Nishiyama, T., Aikawa, S., Hasunuma, T., Ishii, J.*, Okubo, Y., Kondo, A.* (2018) A stable, autonomously replicating plasmid vector containing Pichia pastoris centromeric DNA. Applied and Environmental Microbiology, 84(15), e02882-17

Advanced Metabolomics Research Group

  1. Takenaka, M., Yoshida, T., Hori, Y., Bamba, T., Vavricka, CJ., Hattori, T., Hayakawa, Y., Hasunuma, T.*, Kondo, A. (2021) An ion-pair free LC-MS/MS method for quantitative metabolite profiling of microbial bioproduction systems, Talanta, 222, 121625
  2. Vavricka, CJ., Hasunuma, T., Kondo, A. (2020) Dynamic metabolomics for engineering biology: Accelerating learning cycles for bioproduction, Trends in Biotechnology, 38(1), 68-82
  3. Sakihama, Y., Hidese, R., Hasunuma, T.*, Kondo, A. * (2019) Increased flux in acetyl-CoA synthetic pathway and oxidative TCA cycle of Kluyveromyces marxianus under respiratory conditions, Scientific reports, in press
  4. Kato, Y., Fujihara, Y., Vavricka, CJ., Chang, JS., Hasunuma, T. *, Kondo, A. (2019) Light/dark cycling causes delayed lipid accumulation and increased photoperiod-based biomass yield by altering metabolic flux in oleaginous Chlamydomonas sp., Biotechnology for Biofuels, 12: 39


  1. Maruyama, T*., Restu, W. K. Intracellular self-assembly of supramolecular gelators to selectively kill cells of interest. Polymer J. 52, 883–889. 2020
  2. Onishi, H., Sodium Tantalate Photocatalysts Doped with Metal Cations: Why Are They Active for Water Splitting? ChemSusChem 12, 1825-1834. 2019
  3. Katayama K, Mitsunobu H, Nishida K. (2019) Mammalian synthetic biology by CRISPRs engineering and applications. Curr Opin Chem Biol. Oct;52:79-84.
  4. Yokono, M., Akimoto, S. Energy transfer and distribution in photosystem super/megacomplex of plants, Curr. Opin. Biotechnol., 54, 50–56. 2018.
  5. Arazoe, T., Kondo, A.*, Nishida, K.* (2018) Targeted nucleotide editing technologies for microbial metabolic engineering. Biotechnology Journal, 13(9), 1700596
  6. Nakamura, Y., Kondo, A., Ishii, J., Biosensing techniques in yeast: G-protein signaling and protein-protein interaction assays for monitoring ligand stimulation and oligomer formation of heterologous GPCRs. Peripheral Membrane Proteins, ISBN 978-1-78923-513-5, IntechOpen, Chapter 3, 25-48 (2018)
  7. Inokuma, K., Hasunuma, T., Kondo, A. Emerging Areas in Bioengineering:Whole cell biocatalysts using enzymes displayed on yeast cell surface. Chang HN (Ed) Wiley-VCH, 81-92 (2018)