Publications
 Link:Google Scholar Page
Corresponding authors of each publication are marked with asterisks (*).

2022

  1. Cytoplasmic delivery of siRNA using human-derived membrane penetration-enhancing peptide
    M Nakamura, K Fujiwara, N Doi*.
    J Nanobiotech in press

  2. Controlling the periodicity of a reaction-diffusion wave in artificial cells by a two-way energy supplier
    S Takada, N Yoshinaga, N Doi, K Fujiwara*.
    ACS Nano, in press

  3. Mode selection mechanism in traveling and standing waves revealed by Min wave reconstituted in artificial cells
    S Takada, N Yoshinaga*, N Doi, K Fujiwara*.
    Science Advances, 8, eabm8460, DOI:10.1126/sciadv.abm8460

  4. Characterization of the membrane penetration-enhancing peptide S19 derived from human syncytin-1 for the intracellular delivery of TAT-fused proteins
    M Suzuki, K Iwaki, M Kikuchi, K Fujiwara, N Doi*.
    Biochem Biophys Res Comm, 586:63-67, DOI:10.1016/j.bbrc.2021.11.065

    5. 総説

  5. Min波の人工細胞内再構成とそこから見えた細胞サイズ空間効果
    光山 隼史、義永 那津人、藤原 慶
    生物物理, 62(1):19-23

    6. Review

  6. Cell-Size Space Regulates the Behavior of Confined Polymers: From Nano- and Micromaterials Science to Biology
    M Yanagisawa*, C Watanabe, N Yoshinaga, K Fujiwara*.
    Langmuir, in press, DOI:10.1021/acs.langmuir.2c01397

    7. 2021

    1. Activation of a diluted E. coli cell-free transcription-translation system within liposomes by hypertonic concentration
      Y Matsui, T Akui, N Doi, K Fujiwara*.
      STAR protocols, 2(4):101003, doi:10.1016/j.xpro.2021.101003.

    2. Transcription-translation of Escherichia coli genome within artificial cells
      T Deyama, Y Matsui, Y Chadani, Y Sekine, N Doi, K Fujiwara*.
      Chemical Communications, 57, pp.10367-10370, DOI: 10.1039/d1cc04401j

    3. System concentration shift as a regulator of transcription-translation system within liposomes
      #T Akui, #K Fujiwara*, G Sato, M Takinoue, SM Nomura, N. Doi.
      (#: contributed equally to this work)
      iScience, 24(8), 102859, DOI:10.1016/j.isci.2021.102859

    4. Switching ON of transcription-translation system using GUV fusion by co-supplementation of calcium with long-chain polyethylene glycol
      Y Uwaguchi, K Fujiwara*, N Doi.
      ChemBioChem, 22, 2319-2324, DOI:10.1002/cbic.202100100

    5. A relationship between NTP and cell extract concentration for cell-free protein expression
      K Takahashi, G Sato, N Doi, K Fujiwara*
      Life, 11(3), 237, DOI:10.3390/life11030237

      6. 和文

    6. 大学の枠を越えたオンライン生体分子デザイン コン ペティションの 取り組み
      村田智、葛谷明紀、藤原 慶、平 順一、川又生吹、佐藤佑介、瀧ノ上正浩、野村 M. 慎一郎、角五 彰、堀 豊、安部桂太
      工学教育, 69 巻 4 号 pp. 4_31-4_39

      7. 翻訳

    7. Synthetic Biology 合成生物学 (ニュートンプレス)
      原著：Synthetic Biology: A Very Short Introduction (Jamie A. Davies)
      監訳: 藤原 慶、訳：徳永 美恵

      8. 著書

    8. これだけ！ 生化学 第2版 (秀和システム)
      著：生化学若い研究者の会 (執筆、編集を分担)、監修：稲垣賢二

      9. 2020

      1. Conformational equilibrium of MinE regulates allowable concentration ranges of a protein wave for cell division
        S Kohyama, K Fujiwara*, N Yoshinaga, N Doi
        Nanoscale, 12, 11960 - 11970, doi: 10.1039/D0NR00242A

      2. Self-Organization Assay for Min Proteins of Escherichia coli in Micro-droplets Covered with Lipids
        S Kohyama, K Fujiwara*, N Yoshinaga, N Doi
        bio-protocol, 10(6): e3561, doi: 10.21769/BioProtoc.3561

      3. Microfluidic screening system based on boron-doped diamond electrodes and dielectrophoretic sorting for directed evolution of NAD(P)-dependent oxidoreductases.
        H Goto, Y Kanai, A Yotusui, S Shimokihara, S Shitara, R Oyobiki, K Fujiwara, T Watanabe, Y Einaga, Y Matsumoto, N Miki, N Doi*
        Lab on a chip, 20(4):852-861, doi: 10.1039/C9LC01263J

        4. 2019

        1. Regulation of spatiotemporal patterning in artificial cells by a defined protein expression system
          #A Yoshida, #S Kohyama, #K Fujiwara*, S Nishikawa, N Doi
          (#: contributed equally to this work)
          Chemical Science, 10, pp. 11064-11072 (2019), doi: 10.1039/C9SC02441G

        2. Cell-sized confinement controls generation and stability of a protein wave for spatiotemporal regulation in cells
          S Kohyama, N Yoshinaga*, M Yanagisawa, K Fujiwara*, N Doi
          eLife, doi: 10.7554/eLife.44591

          3. 展望記事

        3. 酵素を内包した人工細胞が拓く新しい醸造業や医薬品の開発
          藤原 慶, MDB 技術予測レポート, 項目36, (2019)

          4. 2018

          1. A dual system using compartmentalized partnered replication for selection of arsenic-responsive transcriptional regulator
            SL Aye, K Fujiwara, N Doi*
            J. Biochem., 164(5), pp. 341-348, doi.org/10.1093/jb/mvy055

          2. Engineering of DNA polymerase I from Thermus thermophilus using compartmentalized self-replication
            SL Aye, K Fujiwara, A Ueki, N Doi*
            Biochem. Biophys. Res. Comm., 499(2), pp. 170-176

          3. Increasing elasticity through changes in the secondary structure of gelatin by gelation in a microsized lipid space
            A Sakai, #Y Murayama, #K Fujiwara,T Fujisawa, S Sasaki, S Kidoaki, M Yanagisawa*
            (#: contributed equally to this work)
            ACS Central Science, 4(4), pp.477-483

          4. Artificial cell fermentation as a platform for highly efficient cascade conversion
            K Fujiwara*, T Adachi, N Doi
            ACS Synthetic Biology, 7(2), pp 363-370 (2018), doi: 10.1021/acssynbio.7b00365

            5. Review

          5. Single micrometer-sized gels: Unique mechanics and characters for applications
            M Yanagisawa*, C Watanabe, K Fujiwara
            Gels, 4(2), 29, (2018); doi:10.3390/gels4020029

            6. 総説

          6. 細胞サイズ脂質膜小胞による”発酵”生産の可能性
            藤原 慶, バイオサイエンスとインダストリ−, 76(4) pp. 302-303 (2018)

            7. 2017

            1. Liposomal internal viscosity affects the fate of membrane deformation induced by hypertonic treatment
              #K Fujiwara*, #M Yanagisawa*
              (#: contributed equally to this work)
              Soft Matter, 13, pp. 9192-9198 (2017)

            2. Universal glass-forming behavior of in vitro and living cytoplasm
              #K Nishizawa, #K Fujiwara, M Ikenaga, N Nakajo, M Yanagisawa, and D Mizuno*
              (#: contributed equally to this work)
              Scientific Report, 7, Article number: 15143 (2017). doi:10.1038/s41598-017-14883-y

            3. In vitro transcription-translation using bacterial genome as a template to reconstitute intracellular profile
              #K Fujiwara*, #T Sawamura, T Niwa, T Deyama, SM Nomura, H Taguchi, N Doi
              (#: contributed equally to this work)
              Nucleic Acids Research, 45(19), pp. 11449-11458 (2017) DOI: 10.1093/nar/gkx776

            4. DNA cytoskeleton for stabilizing artificial cells.
              C Kurokawa, K Fujiwara, M Morita, I Kawamata, Y Kawagishi, A Sakai, Y Murayama, S M. Nomura, S Murata, M Takinoue*, M Yanagisawa*
              Proc. Natl. Acad. Sci. USA, 114(28), pp. 7228-7233 (2017), doi: 10.1073/pnas.1702208114

            5. Human-derived fusogenic peptides for the intracellular delivery of proteins.
              K Sudo, K Niikura, K Iwaki, S Kohyama, K Fujiwara, N Doi*
              J. Control. Release, 255(10), pp. 1-11 (2017), doi:10.1016/j.jconrel.2017.03.398

              6. 著書

            6. ペプチド医薬品のスクリーニング・安定化・製剤化技術
              技術情報協会, 「1-4. mRNAディスプレイ法によるペプチドのスクリーニング」
              須藤慧, 藤原 慶, 土居信英

            7. 人工細胞の創製とその応用
              CMC出版, 植田充美編,「3-4. 無細胞システムによる生命システムの理解」, 藤原 慶

              8. 2016

              1. In vitro selection of bispecific diabody fragments using covalent bicistronic DNA display.
                M Nakayama, S Komiya, K Fujiwara, K Horisawa, N Doi*
                Biochem. Biophys. Res. Comm., 478(16), pp. 606-611 (2016)

              2. Biochemical preparation of cell extract for cell-free protein synthesis without physical disruption.
                K Fujiwara*, N Doi
                PLOS ONE, 11(4): e0154614. (2016) doi:10.1371/journal.pone.0154614

              3. Identification of novel in vivo obligate GroEL/ES substrates based on data from a cell-free proteomics approach.
                T Niwa, K Fujiwara, H Taguchi*
                FEBS Lett., 590 (2), pp. 251-257 (2016)

                4. 翻訳

              4. 自然世界の高分子 (吉岡書店, 原題：Giant Molecules)
                原著：Alexander Y. Grosberg and Alexei R. Khokhlov、監訳: 田中 基彦、鴇田 正之
                訳: 田中 基彦、鴇田 正之、柳沢 実穂、坂上 貴洋、藤原 慶

                5. 著書

              5. DNA分子デザインのすべて〜BIOMOD虎の巻
                CBT学会eBOOK、分子ロボティクス研究会編(1章3,4,5,11の執筆担当：藤原 慶)

                6. 2015

                1. PURE mRNA display for in vitro selection of single-chain antibodies.
                  Y Nagumo, K Fujiwara, K Horisawa, H Yanagawa, N Doi*
                  J. Biochem., 159(5), pp. 519-526 (2015)

                2. Droplet-Shooting and Size-Filtration (DSSF) Method for Synthesis of Cell-Sized Liposomes with Controlled Lipid Compositions.
                  M Morita, H Onoe, M Yanagisawa, H Ito, M Ichikawa, K Fujiwara, H Saito, M Takinoue*
                  ChemBioChem, 16 (14), pp. 2029-2035 (2015), DOI: 10.1002/cbic.201500354

                3. Generation of monodisperse cell-sized microdroplets using a centrifuge-based axisymmetric co-flowing microfluidic device.
                  H Yamashita, M Morita, H Sugiura, K Fujiwara, H Onoe, M Takinoue*
                  J. Biosci. Bioeng., 119 (4), pp. 492-495 (2015), DOI: 10.1016/j.jbiosc.2014.09.018

                4. Peptide sequences converting polyglutamine into a prion in yeast.
                  W Odani, K Urata, M Okuda, S Okuma, H Koyama, CG Pack, K Fujiwara, T Nojima, M Kinjo, S Kawai-Noma, H Taguchi*
                  FEBS Lett., 282 (3), pp. 477-490 (2015)

                  5. 総説

                5. 高分子混雑効果を細胞モデル系から読み解く
                  柳澤 実穂, 藤原 慶
                  生物物理, 55(5) pp. 246-249 (2015)

                2014

                1. Multiple patterns of polymer gels in microspheres due to the interplay among phase separation, wetting, and gelation.
                  M Yanagisawa*, S Nigorikawa, T Sakaue, K Fujiwara, M Tokita.
                  Proc. Natl. Acad. Sci. USA, 111 (45), 15894-15899 (2014)

                2. Conversion of a Chaperonin GroEL-Independent Protein into an Obligate Substrate.
                  T Ishimoto, K Fujiwara, T Niwa, H Taguchi*.
                  J. Biol. Chem., 289: 32073-32080 (2014)

                3. Introducing Micrometer-Sized Artificial Objects into Live Cells: A Method for Cell-Giant Unilamellar Vesicle Electrofusion.
                  AC Saito, T Ogura, K Fujiwara, S Murata, SM Nomura*.
                  PLoS ONE, (9), e106853 (2014)

                4. Generation of Giant Unilamellar Liposomes Containing Biomacromolecules at Physiological Intracellular Concentrations using Hypertonic Conditions.
                  K Fujiwara*, M Yanagisawa*.
                  ACS Synthetic Biology, 3 (12), pp 870-874 (2014): 10.1021/sb4001917

                  5. Review

                5. Reconstitution of intracellular environments in vitro and in artificial cells.
                  K Fujiwara*, M Yanagisawa, SM Nomura.
                  BIOPHYSICS, 10 (0), pp. 43-48 (2014)

                  6. 和文

                6. DNAナノテクノロジーのためのアウトリーチツールの開発と評価.
                  吉澤 慧, 藤原 慶, 野村 M.慎一郎, 村田 智*
                  形の科学会誌, 2014, 29(2)： 表紙を飾りました

                  7. 紀要

                7. The rapid synthesis of cell-sized liposomes by centrifuge-based microfluidic device.
                  M Morita, H Onoe, M Yanagisawa, K Fujiwara, H Saito, M Takinoue.
                  18th International Conference on Miniaturized Systems for Chemistry and Life Sciences, MicroTAS 2014, pp. 336-338 (2014)

                  8. 著書

                8. これだけ！ 生化学 (秀和システム)
                  著：生化学若い研究者の会 (執筆、編集を分担)、監修：稲垣賢二

                2013

                1. A bacterial salt sensor created by multiplying phenotypes of GroE-depleted Escherichia coli.
                  K Fujiwara*, KB Aoi, SM Nomura*.
                  Analytical methods, 5 (21), 5918-5922 (2013)

                2. Cooperative working of bacterial chromosome replication proteins generated by a reconstituted protein expression system.
                  K Fujiwara*, T Katayama, SM Nomura.
                  Nucleic Acids Research, 41 (14): 7176-7183 (2013) doi:10.1093/nar/gkt489

                3. Condensation of an additive-free cell extract to mimic the conditions of live cells.
                  K Fujiwara*, SM Nomura*.
                  PLoS ONE 8(1): e54155 (2013) doi:10.1371/journal.pone.0054155

                4. Physicochemical analysis from real-time imaging of liposome tubulation reveals the characteristic of individual F-BAR domain proteins.
                  Y Takiguchi, T Itoh, K Tsujita, S Yamada, M Yanagisawa, K Fujiwara, M Ichikawa, A Yamamoto, K Takiguchi*.
                  Langmuir, Jan 8;29(1):328-36 (2013)

                  5. 紀要

                5. Molecular robotics approach for constructing artificial cell model
                  SM Nomura*, Y Sato, K Fujiwara.
                  12th European Conference on Artificial Life, ECAL, 488-491 (2013)

                6. Construction of remote-control supramolecular micro-crawler
                  D Komatsu, K Fujiwara, SM Nomura*.
                  12th European Conference on Artificial Life, ECAL, 208-209 (2013)

                  7. 総説

                7. 細胞内濃厚環境に近づいた無細胞発現系
                  藤原 慶, 野村 M. 慎一郎, 生物物理, 53(5), pp.262-263 (2013)

                8. 細胞抽出液の濃縮技術〜細胞再構築に向けた挑戦〜
                  野村 M. 慎一郎, 藤原 慶, 月刊バイオインダストリ, Vol. 30、No.8, p.59-65 (2013)

                2012

                1. Cell-Sized Confinement in Microspheres Accelerate the Reaction of Gene Expression.
                  A Kato, M Yanagisawa, YT Sato, K Fujiwara, K Yoshikawa*.
                  Scientific Report, 2, Article number: 283 (2012)

                2. Mechanism of overexpression of methionine synthase in chaperonin-depleted Escherichia coli.
                  K Fujiwara*, H Taguchi.
                  Microbiology, 158, 917-924 (2012)

                2003-2011

                1. A systematic survey of in vivo obligate chaperonin-dependent substrates.
                  K Fujiwara, Y Ishihama, K Nakahigashi, T Soga, H Taguchi*.
                  The EMBO Journal, Vol. 29, No.9, 1552-1564 (2010)

                2. Filamentous morphology in GroE-depleted Escherichia coli induced by impaired folding of FtsE.
                  K Fujiwara, H Taguchi*.
                  J. Bacteriol., Vol. 189, No. 16, 5860-5966 (2007)

                3. Involvement of the arginine repressor in lysine biosynthesis of Thermus thermophilus.
                  K Fujiwara, T Tsubouchi, T Kuzuyama, Nishiyama M*.
                  Microbiology, vol. 152, 3585-3594 (2006)

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