Fujiwara, Kei



Faculty of Science and Technology, Department of Biosciences and Informatics (Yagami)


Assistant Professor/Senior Assistant Professor

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Profile 【 Display / hide

  • Disrupted cells won't go back into its living states. We are trying to clarify why this process is irreversible and developing a method to reconstruct living cells from biomolecules mixtures using artificial cells engineering.

Career 【 Display / hide

  • 2009.04

    The university of Tokyo, Graduate School of Frontier Sciences, Department of Medical Genome Sciences, JSPS research associate

  • 2010.04

    Kyoto university, Institute for Integrated Cell-Material Sciences, Research Associate

  • 2011.04

    Tohoku University, Department of Bioengineering and Robotics, JSPS research associate

Academic Background 【 Display / hide

  • 2004.04

    The University of Tokyo, Graduate School of Agricultural and Life Sciences, Department of Applied Biological Chemistry

    Graduate School, Completed, Master's course

  • 2006.04

    The University of Tokyo, Graduate School of Frontier Sciences, Department of Medical Genome Sciences

    Graduate School, Completed, Doctoral course

Academic Degrees 【 Display / hide

  • 博士(生命科学), The University of Tokyo, Coursework, 2009.03



Research Areas 【 Display / hide

  • System genome science

  • Molecular biology

  • Biophysics

Research Keywords 【 Display / hide

  • Artificial-Cell engineering

  • Synthetic Biology

  • Bacteriology

  • Cell-free Life Sciences


Books 【 Display / hide

  • ペプチド医薬品のスクリーニング・安定化・製剤化技術

    SUDO Kei, FUJIWARA Kei, DOI Nobuhide, 技術情報協会, 2017.12

    Scope: 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

  • 人工細胞の創製とその応用

    FUJIWARA Kei, CMC出版, 2017.01

    Scope: 「3-4. 無細胞システムによる生命システムの理解」の執筆

  • DNA分子デザインのすべて ~BIOMOD虎の巻

    FUJIWARA Kei, CBT学会eBOOK, 2016.04

    Scope: p. 15-20, p. 33-34の執筆を担当

     View Summary


  • 「自然世界の高分子」

    TANAKA Motohiko, TOKITA masayuki, YANAGISAWA Miho, SAKAUE Takahiro, FUJIWARA Kei, 吉岡書店, 2016.03

    Scope: 9章から11章の翻訳を担当

     View Summary

    「Giant molecules」Alexander Y. Grosberg and Alexei R. Khokhlovの邦訳版(翻訳)

  • これだけ!生化学

    生化学若い研究者の会, 秀和システム, 2014.12

    Scope: 編集、2章分担執筆

Papers 【 Display / hide

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

    Seaim Lwin Aye, Kei Fujiwara, Nobuhide Doi

    The Journal of Biochemistry    mvy055 2018.06

    Research paper (scientific journal), Joint Work, Accepted

     View Summary

    Engineering and design of genetic circuit in living cell is critical in accessing the beneficial application of synthetic biology. Directed evolution can avoid the complicated rational design of such circuit by screening or selecting functional circuit from non-functional one. Here, we proposed a positive–negative selection system for selecting a transcription factor that activates gene expression in response to arsenic in solution. First, we developed a whole cell biosensor for sensing arsenite in liquid using a regulator (ArsR) and a reporter (GFP), and evaluated its performance. Second, we developed a positive selection system for active ArsR using compartmentalized partnered replication that uses thermostable DNA polymerase as the reporter of activity. Third, we developed a negative selection system using sucrose-induced suicide gene SacB as the reporter for exclusion of inactive ArsR variants.

  • Engineering of DNA polymerase I from Thermus thermophilus using compartmentalized self-replication

    Aye Seaim Lwin, Fujiwara Kei, Ueki Asuka, Doi Nobuhide

    Biochemical and Biophysical Research Communications 499 ( 2 ) 170 - 176 2018.05

    Research paper (scientific journal), Joint Work, Accepted,  ISSN  0006-291X

     View Summary

    <p>Although compartmentalized self-replication (CSR) and compartmentalized partnered replication (CPR) are powerful tools for directed evolution of proteins and gene circuits, limitations remain in the emulsion PCR process with the wild-type Taq DNA polymerase used so far, including long run times, low amounts of product, and false negative results due to inhibitors. In this study, we developed a high-efficiency mutant of DNA polymerase I from Thermus thermophilus HB27 (Tth pol) suited for CSR and CPR. We modified the wild-type Tth pol by (i) deletion of the N-terminal 5′ to 3′ exonuclease domain, (ii) fusion with the DNA-binding protein Sso7d, (iii) introduction of four known effective point mutations from other DNA polymerase mutants, and (iv) codon optimization to reduce the GC content. Consequently, we obtained a mutant that provides higher product yields than the conventional Taq pol without decreased fidelity. Next, we performed four rounds of CSR selection with a randomly mutated library of this modified Tth pol and obtained mutants that provide higher product yields in fewer cycles of emulsion PCR than the parent Tth pol as well as the conventional Taq pol.</p>

  • Increasing Elasticity through Changes in the Secondary Structure of Gelatin by Gelation in a Microsized Lipid Space

    Sakai Atsushi, Murayama Yoshihiro, Fujiwara Kei, Fujisawa Takahiro, Sasaki Saori, Kidoaki Satoru, Yanagisawa Miho

    ACS Central Science 4 ( 4 ) 477 - 483 2018.04

    Research paper (scientific journal), Joint Work, Accepted,  ISSN  2374-7943

     View Summary

    <p>Even though microgels are used in a wide variety of applications, determining their mechanical properties has been elusive because of the difficulties in analysis. In this study, we investigated the surface elasticity of a spherical microgel of gelatin prepared inside a lipid droplet by using micropipet aspiration. We found that gelation inside a microdroplet covered with lipid membranes increased Young's modulus E toward a plateau value E∗ along with a decrease in gel size. In the case of 5.0 wt % gelatin gelled inside a microsized lipid space, the E∗ for small microgels with R ≤ 50 μm was 10-fold higher (35-39 kPa) than that for the bulk gel (∼3 kPa). Structural analysis using circular dichroism spectroscopy and a fluorescence indicator for ordered beta sheets demonstrated that the smaller microgels contained more beta sheets in the structure than the bulk gel. Our finding indicates that the confinement size of gelling polymers becomes a factor in the variation of elasticity of protein-based microgels via secondary structure changes.</p>

  • Single Micrometer-Sized Gels: Unique Mechanics and Characters for Applications.

    Yanagisawa Miho, Watanabe Chiho, Fujiwara Kei

    Gels (MDPI)  4 ( 2 ) 29 2018.03

    Research paper (scientific journal), Joint Work, Accepted

     View Summary

    Microgels—small gels of submicron to micron size—are widely used in food, cosmetics and biomedical applications because of their biocompatibility and/or fast response to external environments. However, the properties of “single” microgels have not been characterized due to limitations in preparation technologies and measurement methods for single microgels with sizes in the multi-micrometer range. The synthesis of multiple shapes of single microgels and their characterization are important for further functionalization and application of gel-based materials. In this review, we explain the recent advancements in microgel fabrication and characterization methods for single microgels. The first topic discussed includes the self-assembly methods for single microgel fabrication using physical phenomena such as phase separation, interfacial wetting and buckling instability. The second topic deals with methods for analyzing the mechanics of single microgels and the differences between their mechanical characteristics and those of bulk gels. The recent progress in the fabrication and characterization of single microgels will bring important insights to the design and functionalization of gel-based materials.

  • Artificial Cell Fermentation as a Platform for Highly Efficient Cascade Conversion

    Fujiwara Kei, Adachi Takuma, Doi Nobuhide

    ACS Synthetic Biology 7 ( 2 ) 363 - 370 2018.02

    Research paper (scientific journal), Joint Work, Accepted,  ISSN  2161-5063

     View Summary

    <p>Because of its high specificity and stereoselectivity, cascade reactions using enzymes have been attracting attention as a platform for chemical synthesis. However, the sensitivity of enzymes outside their optimum conditions and their rapid decrease of activity upon dilution are drawbacks of the system. In this study, we developed a system for cascade enzymatic conversion in bacteria-shaped liposomes formed by hypertonic treatment, and demonstrated that the system can overcome the drawbacks of the enzymatic cascade reactions in bulk. This system produced final products at a level equivalent to the maximum concentration of the bulk system (0.10 M, e.g., 4.6 g/L), and worked even under conditions where enzymes normally lose their function. Under diluted conditions, the conversion rate of the artificial cell system was remarkably higher than that in the bulk system. Our results indicate that artificial cells can behave as a platform to perform fermentative production like microorganisms.</p>

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Papers, etc., Registered in KOARA 【 Display / hide

Reviews, Commentaries, etc. 【 Display / hide

  • Artificial cell fermentation as a next platform for biosynthesis


    バイオサイエンスとインダストリー ((一財)バイオインダストリー協会)  76 ( 4 ) 302 - 303 2018.07

    Introduction and explanation (commerce magazine), Single Work

  • DNA ナノテクノロジー コラム ”BIOMODへ参加しよう!”

    FUJIWARA Kei, Tadakuma Hisashi

    現代化学 (東京化学同人)   ( 11 ) 36 - 37 2016.10

    Introduction and explanation (commerce magazine), Joint Work

  • Microdroplets as a Model System for the Study of Macromolecular Crowding in Cells


    生物物理 (日本生物物理学会)  55 ( 5 ) 246 - 249 2015.09

    Introduction and explanation (scientific journal), Joint Work

  • Reconstitution of intracellular environments in vitro and in artificial cells

    FUJIWARA Kei, Yanagisawa Miho, Nomura M. Shin-ichiro

    BIOPHYSICS (The Biophysics Society of Japan)  10   43 - 48 2014.08

    Introduction and explanation (scientific journal), Joint Work

Presentations 【 Display / hide

  • 細胞を創る:細胞分裂面決定機構の人工細胞内再構成


    第91回 日本生化学会大会 (京都国際会館) , 2018.09, Oral Presentation(guest/special)

  • 細胞サイズの微小液滴表面におけるMinタンパク質波の特異的な振る舞い


    第69回コロイドおよび界面化学討論会 (筑波大学) , 2018.09, Oral Presentation(guest/special)

  • 細胞を壊し、細胞を創る:創ることによる生命の理解


    第58回生物物理若手の会 夏の学校 (ぎふ長良川温泉パーク) , 2018.08, Oral Presentation(guest/special)

  • A localization wave of proteins reconstituted in artificial cells with crowding environments


    第55回生物物理学会年会 (熊本大学) , 2017.09, Oral Presentation(guest/special)

  • Behavior and characters of Min protein localization wave in cell-sized space


    アクティブマターの概念で繋ぐ生命機能の階層性 (グリーンピア大沼) , 2017.09, Oral Presentation(guest/special)

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Research Projects of Competitive Funds, etc. 【 Display / hide

  • Elucidation of physics underlying spatiotemporal pattern formation in cell size spaces


    MEXT,JSPS, Grant-in-Aid for Scientific Research, 藤原 慶, Grant-in-Aid for Scientific Research (B), Principal Investigator

  • Understanding cell-sized space effects of multi-molecular crowding on biomolecular systems


    MEXT,JSPS, Grant-in-Aid for Scientific Research, 藤原 慶, Grant-in-Aid for Scientific Research on Innovative Areas, Principal Investigator

  • 分子夾雑が引き起こす生命システム動態転移の構成的な理解


    日本学術振興会, Grant-in-Aid for Scientific Research, 藤原慶, Research grant, Principal Investigator

  • 冥王代における高分子濃度シナリオの検証


    Grant-in-Aid for Scientific Research, 藤原慶, Research grant, Principal Investigator

  • 細胞スケール閉鎖空間内における反応拡散波の物理


    Grant-in-Aid for Scientific Research, Research grant, Principal Investigator

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Courses Taught 【 Display / hide











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Courses Previously Taught 【 Display / hide

  • 微生物学

    慶應義塾大学, 2018