先端プラットフォーム技術開発部門プロジェクト

代表的な大型プロジェクト

  1. JST産学イノベーション加速事業【先端計測分析技術・機器開発】「大気中・液中で動作する原子分解能顕微鏡」(2005-2010年度)(研究担当者:大西洋 教授)
  2. JSPS国際共同研究加速基金(国際共同研究強化(B))「人工光合成の学理:タンタル酸ナトリウム光触媒をプラットフォームとする多国間協働」(2018-2022年度)(研究代表者:大西洋 教授)
  3. JSPS基盤研究(A)「タンタル酸ナトリウム光触媒のダイナミズム:世界最高収率を実現するしくみの解明」(2015-2019年度)(研究代表者:大西洋 教授)
  4. JSPS基盤研究(B)「界面液体のFM-AFM計測:固液界面における構造接続のメカニズム解明」(2011-2015年度)(研究代表者:大西洋 教授)
  5. JSPS二国間共同研究事業「固液界面エピタキシャル接合の分子論的理解:ピコ力学計測と分子動力学計算の恊働」(2016-2018年度)(研究代表者:大西洋 教授)
  6. 文部科学省特定領域研究「高次系分子科学」計画研究「走査プローブ顕微鏡を用いた分子系高次機能の研究」(2008-2012年度)(研究代表者:大西洋 教授)
  7. JST 研究成果展開事業 産学共創基礎基盤研究プログラム 「凝縮相テラヘルツ分子科学の深化」(2011-2015年度)(研究担当者:富永圭介 教授)
  8. JST-CREST「海洋性藻類からのバイオエタノール生産技術の開発」(2010-2015)(研究担当者:秋本誠志 准教授)
  9. JSPS 科研費 新学術領域研究「光エネルギー変換システムの再最適化」(2016-2020)(研究担当者:秋本誠志 准教授)
  10. 文部科学省 バイオプロダクション次世代農工連携拠点(2008-2018年度)(研究担当者:近藤昭彦 教授)
  11. 文部科学省 地域イノベーション・エコシステム形成プログラム「バイオ経済を加速する革新技術: ゲノム編集・合成技術の事業化」 (2017-2021年度)(研究担当者:近藤昭彦 教授,西田敬二 教授,柘植謙爾 特命准教授,佐々木建吾 特命准教授)
  12. AMED 次世代治療・診断実現のための創薬基盤技術開発事業「国際基準に適合した次世代抗体医薬等の製造技術のうち高生産宿主構築の効率化基盤技術開発に係るもの」 (2014-2017年度) (研究担当者:近藤昭彦 教授)
  13. NEDO 植物等の生物を用いた高機能品生産技術の開発「高生産性微生物創製に資する情報解析システムの開発」(2016-2020年度)(研究担当者:近藤昭彦 教授,蓮沼誠久 教授)

先端計測研究グループ

  1. Honda, H.; Sasahara, A.; Onishi, H., Cobalt Porphyrins on Mica: Atomic Force Microscope Imaging in Organic Solvents. Colloids and Surfaces A: Physicochemical and Engineering Aspects 2019, 561, 194-200.
  2. Araki, Y.; Sekine, T.; Chang, R.; Hayashi, T.; Onishi, H., Molecular-Scale Structures of Surface and Hydration of Bioinert Mixedcharged Self-Assembled Monolayers Investigated by the Frequency Modulation Atomic Force Microscopy. RSC Advances 2018, 8, 24660-24664.
  3. An, L.; Sasaki, T.; Weidler, P.; Wöll, C.; Ichikuni, N.; Onishi, H., Local Environment of Strontium Cations Activating Natao3 Photocatalysts. ACS Catalysis 2018, 8, 880-885.
  4. Hirayama, T.; Kawamura, R.; Fujino, K.; Matsuoka, T.; Komiya, H.; Onishi, H., Cross-Sectional Imaging of Boundary Lubrication Layer Formed by Fatty Acid by Means of Frequency-Modulation Atomic Force Microscopy. Langmuir 2017, 33, 10492–10500.
  5. Minato, T.; Araki, Y.; Umeda, K.; Yamanaka, T.; Okazaki, K.-i.; Onishi, H.; Abe, T.; Ogumi, Z., Interface Structure between Tetraglyme and Graphite. Journal of Chemical Physics 2017, 147, 124701 (6 pages).
  6. Araki, Y.; Satoh, H.; Okumura, M.; Onishi, H., Localization of Cesium on Montmorillonite Surface Investigated by Frequency Modulation Atomic Force Microscopy. Surface Science 2017, 665, 32-36.
  7. Kawasaki, S.; Holmström, E.; Takahashi, R.; Spijker, P.; Foster, A.; Onishi, H.; Lippmaa, M., Intrinsic Superhydrophilicity of Titania-Terminated Surfaces. Journal of Physical Chemistry C 2017, 121, 2268-2275.
  8. Amano, K.-i.; Kobayashi, K.; Miyazawa, K.; Liang, Y.; Hashimoto, K.; Fukami, K.; Nishi, N.; Sakka, T.; Onishi, H.; Fukuma, T., Transform Theory for Obtaining Number Density Distribution of Solvent Molecules or Colloidal Particles on a Substrate: A Theory for Atomic Force Microscopy. Physical Chemistry Chemical Physics 2016, 18, 15534-15544.
  9. Uchida, K.; Mita, K.; Matsuoka, O.; Isaki, T.; Kimura, K.; Onishi, H., The Structure of Uniaxially Stretched Isotactic Polypropylene Films: Imaging with Frequency-Modulation Atomic Force Microscopy. Polymer 2016, 82, 349-355.
  10. Amano, K.-i.; Tanaka, E.; Kobayashi, K.; Onishi, H.; Nishi, N.; Sakka, T., Force Measurement Reveals Structure of a Confined Liquid: Observation of the Impenetrable Space. Surface Science 2015, 641, 242-246.
  11. Kitta, M.; Kohyama, M.; Onishi, H., True Atomic-Scale Imaging of a Spinel Li4ti5o12(111) Surface in Aqueous Solution by Frequency-Modulation Aatomic Force Microscopy. Applied Physics Letters 2014, 105, 111606 (3 pages).
  12. Hotta, Y.; Motoyanagi, J.; Suiko, S.; Onishi, H.; Iozaki, D.; Arakawa, R.; Tsuda, A., Physical Operation of Hydrodynamic Orientation of an Azobenzene Supramolecular Assembly with Light and Sound. ChemComm 2014, 50, 5615-5618.
  13. Hiasa, T.; Onishi, H., Mercaptohexanol Assembled on Gold: Fm-Afm Imaging in Water. Colloids and Surfaces A: Physicochemical and Engineering Aspects 2014, 441, 149-154.
  14. Spijker, P.; Hiasa, T.; Musso, T.; Nishioka, R.; Onishi, H.; Foster, A., Understanding the Interface of Liquids with an Organic Crystal Surface from Atomistic Simulations and Afm Experiments. Journal of Physical Chemistry C 2014, 118, 2058-2066.
  15. Amano, K.-i.; Suzuki, K.; Fukuma, T.; Takahashi, O.; Onishi, H., The Relationship between Local Liquid Density and Force Applied on a Tip of Atomic Force Microscope: A Theoretical Analysis for Simple Liquids. Journal of Chemical Physics 2013, 139, 224710 (7 pages).
  16. Imada, H.; Kimura, K.; Onishi, H., Water and 2-Propanol Structured on Calcite (104) Probed by Frequency-Modulation Atomic Force Microscopy. Langmuir 2013, 29, 10744-10751.
  17. Feng Zhang ; Houng-Wei Wang ; Keisuke Tominaga ; Michitoshi Hayashi ; Tetsuo Sasaki, Terahertz Fingerprints of Short-Range Correlations of Disordered Atoms in Diflunisal, J. Phys. Chem. A 2019. 123(21), 4555-4564.
  18. Masaki Okuda, Masahiro Higashi, Kaoru Ohta, Shinji Saito, Keisuke Tominaga. Theoretical investigation on vibrational frequency fluctuations of SCN-derivatized vibrational probe molecule in water. Chemical Physics. 2018. 512. 82-87.
  19. Masaki Okuda, Kaoru Ohta, Keisuke Tominaga. Rotational Dynamics of Solutes with Multiple Single Bond Axes Studied by Infrared Pump–Probe Spectroscopy. J. Phys. Chem. A 2018. 122(4), 946–954.
  20. K. Nishimori, S. Kitahata, T. Nishino, T. Maruyama, Controlling surface-segregation of a polymer to display carboxy groups on an outermost surface using perfluoroacyl group. Langmuir 2018, 34, 6396–6404.
  21. Shiota, S. Yamamoto, A. Shimomura, A. Ojida, T. Nishino, T. Maruyama, Quantification of amino groups on solid surfaces using cleavable fluorescent compounds. Langmuir 2015, 31, 8824-8829.
  22. A. Shimomura, T. Nishino, T. Maruyama, Display of amino groups on substrate surfaces by simple dip-coating of methacrylatebased polymers and its application to DNA immobilization. Langmuir 2013, 29, 932–938.
  23. M. Iwai, M. Yokono, M. Kono, K. Noguchi, S. Akimoto, A. Nakano, Light-harvesting complex Lhcb9 confers a green alga-type photosystem I supercomplex to the moss Physcomitrella patens, Nature Plants, 1, 14008 (2015).
  24. M. Yokono, A. Takabayashi, S. Akimoto, A. Tanaka, A megacomplex composed of both photosystem reaction centres in higher plants, Nature communications, 6, 6675 (2015).
  25. Y. Ueno, S. Aikawa, A. Kondo, S. Akimoto, Energy transfer in cyanobacteria and red algae: confirmation of spillover in intact megacomplexes of phycobilisome and photosystems, J. Phys. Chem. Lett., 7, 3567–3571 (2016).
  26. E. Kim, S. Akimoto, R. Tokutsu, M. Yokono, J. Minagawa, Fluorescence lifetime analyses reveal how the high light-responsive protein LHCSR3 transforms PSII light-harvesting complexes into an energy-dissipative state, J. Biol. Chem., 292, 18951–18960 (2017).
  27. Y. Ueno, G. Shimakawa, C. Miyake, S. Akimoto, Light-harvesting strategy during CO2-dependent photosynthesis in the green alga Chlamydomonas reinhardtii, J. Phys. Chem. Lett., 9, 1028–1033 (2018).
  28. K. Kosuge, R. Tokutsu, E. Kim, S. Akimoto, M. Yokono, Y. Ueno, J. Minagawa, 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 (2018).
  29. R. Nagao, M. Yokono, Y. Ueno, J.-R. Shen, S. Akimoto, pH-Sensing machinery of excitation energy transfer in diatom PSI–FCP1 complexes, J. Phys. Chem. Lett., 10, 3531–3535 (2019).
  30. R. Nagao, K. Kato, T. Suzuki, K. Ifuku, I. Uchiyama, Y. Kashino, N. Dohmae, S. Akimoto, Structure basis for energy harvesting and dissipation in a diatom PSI–FCP1 supercomplexes, J.-R. Shen, N. Miyazaki, F. Akita Nature Plants, 5, 890–901(2019).
  31. Y. Ueno, R. Nagao, J.-R. Shen, S. Akimoto, Spectral properties and excitation relaxation of novel fucoxanthin chlorophyll a/c-binding protein complexes, J. Phys. Chem. Lett., 10, 5148–5152 (2019).

ゲノム編集研究グループ

  1. Nishida K, Arazoe T, Yachie N, Banno S, Kakimoto M, Tabata M, Mochizuki M, Miyabe A, Araki M, Hara KY, Shimatani Z, Kondo A. (2016) Targeted nucleotide editing using hybrid prokaryotic and vertebrate adaptive immune systems. Science. Sep 16;353(6305). pii: aaf8729. doi: 10.1126/science.aaf8729.
  2. Shimatani Z, Kashojiya S, Takayama M, Terada R, Arazoe T, Ishii H, Teramura H, Yamamoto T, Komatsu H, Miura K, Ezura H, Nishida K*, Ariizumi T, Kondo A. (2017) Targeted base editing in rice and tomato using a CRISPR-Cas9 cytidine deaminase fusion. Nat Biotechnol. May;35(5):441-443. doi: 10.1038/nbt.3833.
  3. Banno S, Nishida K*, Arazoe T, Mitsunobu H, Kondo A. (2018) Deaminase-mediated multiplex genome editing in Escherichia coli. Nat Microbiol. Feb 5. doi: 10.1038/s41564-017-0102-6.

ゲノム合成研究グループ

  1. 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
  2. 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
  3. Chin, W. C., Lin, K. H., Liu, C. C., Tsuge, K., Huang, C. C. (2017) Improved n-butanol production via co-expression of membrane-targeted tilapia metallothionein and the clostridial metabolic pathway in Escherichia coli. BMC Biotechnol., 17, 36
  4. Han, C-H., Tsuge, K., Iba, H. (2016) Optimization of artificial operon construction by consultation algorithms utilizing LCS. 2016 IEEE Congress on Evolutionary Computation, 4273-4280
  5. Tsuge, K., Sato, Y., Kobayashi, Y., Gondo, M., Hasebe, M., Togashi, T.,Tomita, M., Itaya, M. (2015) Method of preparing an equimolar DNA mixture for one-step DNA assembly of over 50 fragments, Scientific Reports, 5, 10655
  6. Itaya, M., Fujita, K., Kuroki, A., Tsuge, K. (2008) Bottom-up genome assembly using the Bacillus subtilis genome vector, Nature Methods, 5, 41-43
  7. Itaya, M., Tsuge, K., Koizumi, M., Fujita, K. (2005) Combining two genomes in one Cell: Stable cloning of the cyanobacterium PCC6803 genome in the Bacillus subtilis 168 genome, Proceeding of the National Academy of Sciences, USA, 102, 15971-15976
  8. Tsuge, K., Matsui, K., Itaya, M. (2003) One step assembly of multiple DNA fragments with a designed order and orientation in Bacillus subtilis plasmid, Nucleic Acids Research, 31, e133

バイオファウンドリー研究グループ

  1. Hasunuma, T., Matsuda, M., Kato, Y., Vavricka, CJ., Kondo, A. (2018) Temperature enhanced succinate production concurrent with increased central metabolism turnover in the cyanobacterium Synechocystis sp. PCC 6803, Metabolic Engineering, 48, 109-120
  2. 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
  3. Noda, S., Shirai, T., Mori, Y., Oyama, S., Kondo, A. (2017) Engineering a synthetic pathway for maleate in Escherichia coli, Nature Communications, 8(1): 1153
  4. Hsu, H., Araki, M., Mochizuki, M., Hori, Y., Murata, M., Kahar, P., Yoshida, T., Hasunuma, T., Kondo, A. (2017) A systematic approach to time-series metabolite profiling and RNA-seq analysis of Chinese hamster ovary cell culture, Scientific Reports, 7:43518
  5. Shirai, T., Osanai, T., Kondo, A. (2016) Designing intracellular metabolism for production of target compounds by introducing a heterogenous metabolic reaction based on a Synechosystis sp. 6803 genome-scale model, Microbial Cell Factories, 15(1): 13
  6. Araki, M., Cox III, RS., Makiguchi, H., Ogawa, T., Taniguchi, T., Miyaoku, K., Nakatsui M., Hara, KY., Kondo, A. (2015) M-path : A compass for navigating potential metabolic pathways, Bioinformatics, 31(6), 905-911
  7. Tsuge, K., Sato, Y., Kobayashi, Y., Gondo, M., Hasebe, M., Togashi, T., Tomita, M., Itaya, M. (2015) Method of preparing an equimolar DNA mixture for one-step DNA assembly of over 50 fragments, Scientific Reports, 5, 10655

先端メタボロミクス研究グループ

  1. Sakihama, Y., Hidese, R., Hasunuma, T.*, Kondo, A. * Increased flux in acetyl-CoA synthetic pathway and oxidative TCA cycle of Kluyveromyces marxianus under respiratory conditions, Scientific reports, in press
  2. Kato, Y., Fujihara, Y., Vavricka, CJ., Chang, JS., Hasunuma, T. *, Kondo, A. Light/dark cycling causes delayed lipid accumulation and increased photoperiod-based biomass yield by altering metabolic flux in oleaginous Chlamydomonas sp., Biotechnology for Biofuels, in press
  3. Ho, SH., Nakanishi, A., Kato, Y., Yamasaki, H., Chang, JS., Misawa, N., Hirose, Y., Minagawa, J., Hasunuma, T. *, Kondo, A. (2017) Dynamic metabolic profiling together with transcription analysis reveals salinity-induced starch-to-lipid biosynthesis in alga Chlamydomonas sp. JSC4, Scientific Reports, 4;7: 45471
  4. Hsu, H., Araki, M., Mochizuki, M., Hori, Y., Murata, M., Kahar, P., Yoshida, T., Hasunuma, T., Kondo, A. (2017) A systematic approach to time-series metabolite profiling and RNA-seq analysis of Chinese hamster ovary cell culture, Scientific Reports, 7:43518
  5. Kono, T., Mehrotra, S., Endo, C., Kizu, N., Matsuda, M., Kimura, H., Mizohata, E., Inoue, T., Hasunuma, T., Yokota, A., Matsumura, H., Ashida, H. (2017) A RuBisCO-mediated carbon metabolic pathway in methanogenic archaea., Nature Communications, 8: 14007
  6. Ohtani, M., Morisaki, K., Sawada, Y., Sano, R., Uy, L. T. A., Yamamoto, A., Kurata, T., Nakano, Y., Suzuki, S., Matsuda, M., Hasunuma, T., Hirai, M., Demura, T. (2016) Primary metabolism during biosynthesis of secondary wall polymers of protoxylem vessel elements., Plant Physiology,172(3), 1612-1624
  7. Ueno, M., Sae-Tang, P., Kusama, Y., Hihara, Y., Matsuda, M., Hasunuma, T., Nishiyama, Y. (2016) Moderate heat stress stimulates repair of photosystem II during photoinhibition in Synechocystis sp. PCC 6803., Plant and Cell Physiology, 57(11), 2417-2426
  8. Sumiya, N., Kawase, Y., Hayakawa, J., Matsuda, M., Nakamura, M., Era, A., Tanaka, K., Kondo, A., Hasunuma, T., Imamura, S., Miyagishima, S. (2015) Expression of cyanobacterial acyl-ACP reductase elevates the triacylglycerol level in the red alga Cyanidioschyzon merolae., Plant and Cell Physiology, 56(10), 1962-1980
  9. Hasunuma, T. *, Kikuyama, F., Matsuda, M., Aikawa, S., Izumi, Y., Kondo, A. (2013) Dynamic metabolic profiling of cyanobacterial glycogen biosynthesis under conditions of nitrate depletion., Journal of Experimental Botany, 64(10), 2943-2954
  10. Hasunuma, T., Sanda, T., Yamada, R., Yoshimura, K., Ishii, J., Kondo, A. (2011) Metabolic pathway engineering based on metabolomics confers acetic and formic acid tolerance to a recombinant xylose-fermenting strain of Saccharomyces cerevisiae., Microbial Cell Factories, 10(1): 2
  11. Hasunuma, T., Harada, K., Miyazawa, S., Kondo, A., Fukusaki, E., Miyake, C. (2010) Metabolic turnover analysis by a combination of in vivo 13C-labelling from 13CO2 and metabolic profiling with CE-MS/MS reveals rate-limiting steps of the C3 photosynthetic pathway in Nicotiana tabacum leaves., Journal of Experimental Botany, 61(4), 1041-1051

総説

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  9. S. Akimoto, M. Yokono, How light-harvesting and energy-transfer processes are modified under different light conditions: studies by time-resolved fluorescence spectroscopy, H.J.M. Hou, M.M. Najafpour, G.F. Moore, S.I. Allakhverdiev (eds.), "Photosynthesis: Structures, mechanisms, and applications", Springer, pp. 169–184 (2017).
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  19. Itaya, M., Kaneko, S., Tsuge, K. Chapter 4 Efficient and accurate production of de novo designed large-size gene clusters by a novel Bacillus subtilis-based system. In Microbial Production, Anazawa, H., and Shimizu, S. eds. Springer (2014)
  20. Itaya, M., Tsuge, K. Construction and manipulation of giant DNA by use of a genome vector. Methods in Enzymol., 498, 427-448 (2011).
  21. Tsuge, K., Itaya, M. Chapter 5: Gene Cluster or Operon Design by Ordered Gene Assembly in Bacillus subtilis (OGAB) Method. In Bioengineering: Principles, Methodologies and Applications, Nova Science Publishers, 153-168 (2010).
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