Publications
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Corresponding authors of each publication are marked with asterisks (*).

2024

  1. STALL-seq: mRNA-display selection of bacterial and eukaryotic translational arrest sequences from large random-sequence libraries
    T Hamano, Y Nagumo, T Umehara, K Hirono, K Fujiwara, H Taguchi, Y Chadani, N Doi*
    J. Biol. Chem. in press

  2. Cell-free protein expression by a reconstituted transcription-translation system energized by sugar catabolism
    G Sato, S Miyazawa, N Doi, K Fujiwara*
    Molecules 29(13), 2956, DOI: 10.3390/molecules29132956

  3. Metabolic tug-of-war between glycolysis and translation revealed by a biochemical reconstitution
    G Sato, S Kinoshita, TG Yamada, S Arai, T Kitaguchi, A Funahashi, N Doi, K Fujiwara*
    ACS Synthetic Biology 13(5), 1572-1581, DOI: 10.1021/acssynbio.4c00209

    4. Review

  4. Artificial cell system as a tool for investigating pattern formation mechanisms of intracellular reaction-diffusion waves
    S Takada*, K Fujiwara.
    Biophysics and Physicobiology in press

    5. 2023

    1. Multimolecular Competition Effect as a Modulator of Protein Localization and Biochemical Networks in Cell-size Space
      S Nishikawa, G Sato, S Takada, S Kohyama, G Honda, M Yanagisawa, Y Hori, N Doi, N Yoshinaga, K Fujiwara*
      Advanced Science 11(6), 2308030. DOI:10.1002/advs.202308030

    2. Phase-Separated Giant Liposomes for Stable Elevation of α-Hemolysin Concentration in Lipid Membranes
      M Kobayashi,H Noguchi, G Sato, C Watanabe, K Fujiwara*, M Yanagisawa*
      Langmuir 39, 32, pp.11481-11489, DOI:10.1021/acs.langmuir.3c02019

      3. 総説

    3. 生命の折り合い：単純と複雑の調和
      藤原 慶、栁澤実穂
      現代化学, 2024年1月号, pp. 26-28 (2023)

    4. 酵素をひたすら混ぜる研究
      藤原 慶
      生物工学会誌, 101(12) pp. 639 (2023)

      5. 2022

      1. Cytoplasmic delivery of siRNA using human-derived membrane penetration-enhancing peptide
        M Nakamura, K Fujiwara, N Doi*.
        J Nanobiotech 20, 458, DOI;10.1186/s12951-022-01667-4

      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, 16(10), 16853-16861, DOI:10.1021/acsnano.2c06756

      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, 38(39), 11811?11827, 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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