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FY2021-2025 Grant-in-Aid for Transformative Research Areas (A)
“Bottom-up creation of cell-free molecular systems: surpassing nature”

Research Achievements

Papers

  1. “A peptide nanocage constructed by self-assembly of oligoproline conjugates”
    Shogo Matsubara, Yui Okamoto, Masaru Yoshikawa, Shinya Tsukiji, Masahiro Higuchi
    Bioconj. Chem., 2022, 33, 10, 1785–1788.
    https://pubs.acs.org/doi/10.1021/acs.bioconjchem.2c00290

  2. “A methodology for creating thermostabilized mutants of G-protein coupled receptors by combining statistical thermodynamics and evolutionary molecular engineering”
    Kanna Sugaya, Satoshi Yasuda, Shingo Sato, Chen Sisi, Taisei Yamamoto, Daisuke Umeno, Tomoaki Matsuura, Tomohiko Hayashi, Satoshi Ogasawara, Masahiro Kinoshita, Takeshi Murata
    Protein Sci., 2022, 31, 9, e4404.
    https://onlinelibrary.wiley.com/doi/10.1002/pro.4404

  3. “A chemogenetic platform for controlling plasma membrane signaling and synthetic signal oscillation”
    Sachio Suzuki, Akinobu Nakamura, Yuka Hatano, Masaru Yoshikawa, Tatsuyuki Yoshii, Shunsuke Sawada, Kyoko Atsuta-Tsunoda, Kazuhiro Aoki, Shinya Tsukiji
    Cell Chem. Biol., 2022, 29, 9, 1446-1464.e10.
    https://www.cell.com/cell-chemical-biology/fulltext/S2451-9456(22)00237-9

  4. “Reisomerization of retinal represents a molecular switch mediating Na+ uptake and release by a bacterial sodium-pumping rhodopsin”
    Tomotsumi Fujisawa, Kouta Kinoue, Ryouhei Seike, Takashi Kikukawa, Masashi Unno
    J. Biol. Chem., 2022, 298, 9, 102366.
    https://www.sciencedirect.com/science/article/pii/S0021925822008092

  5. “Biomacromolecule-fueled transient volume phase transition of a hydrogel”
    Masahiko Nakamoto, Shiro Kitano, Michiya Matsusaki
    Angew. Chem. Int. Ed., 2022, 61, 33,e202205125.
    https://onlinelibrary.wiley.com/doi/10.1002/anie.202205125

  6. “Role of a bacterial glycolipid in Sec-independent membrane protein insertion”
    Kaoru Nomura, Shoko Mori, Kohki Fujikawa, Tsukiho Osawa, Shugo Tsuda, Kumiko Yoshizawa-Kumagaye, Shun Masuda, Hideki Nishio, Taku Yoshiya, Takao Yoda, Masafumi Shionyu, Tsuyoshi Shirai, Ken-ichi Nishiyama, Keiko Shimamoto
    Sci. Rep., 2022, 12, 12231.
    https://www.nature.com/articles/s41598-022-16304-1

  7. “Transfer RNA synthesis-coupled translation and DNA replication in a reconstituted transcription/translation system“
    Ryota Miyachi, Yoshihiro Shimizu, Norikazu Ichihashi
    ACS Synth. Biol., 2022, 11 , 8,2791-2799.
    https://pubs.acs.org/doi/10.1021/acssynbio.2c00163

  8. “One-step preparation of cell-free ATP regeneration module based on non-oxidative glycolysis using thermophilic enzymes“
    Gladwin Suryatin Alim, Kenji Okano, Kohsuke Honda
    ChemBioChem, 2022, 23, 16,e202200210.
    https://chemistry-europe.onlinelibrary.wiley.com/doi/10.1002/cbic.202200210

  9. “Pattern recognition of microRNA expression in body fluids using nanopore decoding at subfemtomolar concentrations”
    Nanami Takeuchi, Moe Hiratani, Ryuji Kawano
    JACS Au, 2022, 2, 9, 1829–1838.
    https://pubs.acs.org/doi/full/10.1021/jacsau.2c00117
    The graphic image was chosen for the Supplementary Cover of JACS Au
    Press Release:Successful Pattern Discrimination of Cancer Markers in Blood Using Nanopores! -Using Parallel Computing with DNA Computing Technology, Tokyo University of Agriculture and Technology
    Media coverage:Nihon Keizai Shimbun, EurekAlert!, Bioengineer.org, SCIENMAG, TECH+, GEN, ecancer, Jano.es, eBiotrade, List23, tetracyclined7k, AZoLifeSciences

  10. “A photoactivatable self-localizing ligand with improved photosensitivity for chemo-optogenetic control of protein localization in living cells”
    Tatsuyuki Yoshii, Choji Oki, Shinya Tsukiji
    Bioorg. Med. Chem. Lett., 2022, 72, 128865.
    https://www.sciencedirect.com/science/article/abs/pii/S0960894X22003419

  11. “A protocol to construct RNA-protein devices for photochemical translational regulation of synthetic mRNAs in mammalian cells”
    Hideyuki Nakanishi, Tatsuyuki Yoshii, Shinya Tsukiji, Hirohide Saito
    STAR Protoc., 2022, 101451.
    hhttps://star-protocols.cell.com/protocols/1714

  12. “One-step preparation of cell-free ATP regeneration module based on non-oxidative glycolysis using thermophilic enzymes”
    Gladwin Suryatin Alim, Kenji Okano, Kohsuke Honda
    ChemBioChem, 2022, e202200210.
    https://chemistry-europe.onlinelibrary.wiley.com/doi/10.1002/cbic.202200210

  13. “Fluorescent hydrogel based on self-assembling acridonylalanine-phenylalanine”
    Yuzuha Araki, Hiroki Shirakata, Tetsuya Nakagawa, Takashi Ubukata, Yasushi Yokoyama, Izuru Kawamura
    Chem. Lett., 2022, 51, 7, 687–689.
    https://www.frontiersin.org/articles/10.3389/fmats.2022.877755/full

  14. “Functionalized silicone elastomer via alkaline solution to coat phosphorylcholine-based copolymer containing organosilane to improve hemocompatibility for medical devices”
    Fang-Yu Chou, Shintaro Hara, Kazuto Uchida, Youichi Matsuo, Tsukuru Masuda, Ryo Yokoi, Toshiya Ono, Masaki Anraku, Takashi Isoyama, Madoka Takai
    Front. Mater., 2022, 9, 877755.
    https://www.frontiersin.org/articles/10.3389/fmats.2022.877755/full

  15. “Construction of a reduction-responsive DNA microsphere using a reduction-cleavable spacer based on a nitrobenzene scaffold”
    Sayuri L. Higashi, Ayaka Isogami, Junko Takahashi, Aya Shibata, Koichiro M. Hirosawa, Kenichi G.N. Suzuki, Shunsuke Sawada, Shinya Tsukiji, Kazunori Matsuura, Masato Ikeda
    Chem. Eur. J., 2022, 17, 10, e202200142.
    https://onlinelibrary.wiley.com/doi/full/10.1002/asia.202200142

  16. “Photoreaction pathways of bacteriorhodopsin and its D96N mutant as revealed by in-situ photoirradiation solid-state NMR”
    Arisu Shigeta, Yuto Otani, Ryota Miyasa, Yoshiteru Makino, Izuru Kawamura, Takashi Okitsu, Akimori Wada, Akira Naito
    Membranes, 2022, 12, 3, 279.
    https://www.mdpi.com/2077-0375/12/3/279

  17. “Silver-loaded carboxymethyl cellulose nonwoven sheet with controlled counterions for infected wound healing”
    Seiichi Ohta, Kento Mitsuhashi, Arvind K. Singh Chandel, Pan Qi, Noriko Nakamura, Akiko Nakamichi, Hiromi Yoshida, Gento Yamaguchi, Yuichi Hara, Ryo Sasaki, Masaya Fuke, Madoka Takai, Taichi Ito
    Carbohydr. Polym., 2022, 286, 119289.
    https://www.sciencedirect.com/science/article/abs/pii/S014486172200193X

  18. “Cell-free synthesis of human endothelin receptors and its application to ribosome display”
    Hiroki Nakai, Kinuka Isshiki, Masato Hattori, Hiromasa Maehira, Tatsumi Yamaguchi, Keiko Masuda, Yoshihiro Shimizu, Takayoshi Watanabe, Takahiro Hohsaka, Wataru Shihoya, Osamu Nureki, Yasuhiko Kato, Hajime Watanabe, and Tomoaki Matsuura
    Anal. Chem., 2022, 94, 9, 3831–3839.
    https://pubs.acs.org/doi/10.1021/acs.analchem.1c04714

  19. “Functional visualization of NK cell-mediated killing of metastatic single tumor cells”
    Hiroshi Ichise, Shoko Tsukamoto, Tsuyoshi Hirashima, Yoshinobu Konishi, Choji Oki, Shinya Tsukiji, Satoshi Iwano, Atsushi Miyawaki, Kenta Sumiyama, Kenta Terai, Michiyuki Matsuda
    eLife, 2022, 11, e76269.
    https://elifesciences.org/articles/76269

  20. Review “Recent progress and perspectives in applications of 2-methacryloyloxyethyl phosphorylcholine polymers in biodevices at small scales”
    Sasikarn Seetasang, Yan Xu
    J. Mater. Chem. B, 2022, 10, 14, 2323–2337.
    https://pubs.rsc.org/en/content/articlelanding/2022/tb/d1tb02675e

  21. Review “Condensate Formation by Metabolic Enzymes in Saccharomyces cerevisiae
    Natsuko Miura
    Microorganisms, 2022, 10, 2, 232.
    https://www.mdpi.com/2076-2607/10/2/232

  22. “A biomimetic anti-biofouling coating in nanofluidic channels”
    Sumire Fukuda, Yan Xu
    J. Mater. Chem. B, 2022, 10, 14, 2481–2489.
    Journal of Materials Chemistry B HOT Papersに選出されたhttps://pubs.rsc.org/en/content/articlelanding/2022/TB/D1TB02627E

  23. “Chimeric mutants of staphylococcal hemolysin, which actas both one-component and two-component hemolysin, created by grafting the stem domain”
    Nouran Ghanem, Natsuki Kanagami, Takashi Matsui, Kein Takeda, Jun Kaneko, Yasuyuki Shiraishi, Christian A. Choe, Tomomi Uchikubo-Kamo, Mikako Shirouzu, Tsubasa Hashimoto, Tomohisa Ogawa, Tomoaki Matsuura, Po-Ssu Huang, Takeshi Yokoyama, Yoshikazu Tanaka
    FEBS J., 2022, 289, 12, 3505–3520.
    https://febs.onlinelibrary.wiley.com/doi/full/10.1111/febs.16354

  24. Review “Design of biointerfaces composed of soft materials using controlled radical polymerization”
    Tsukuru Masuda, Madoka Takai
    J. Mater. Chem. B, 2022, 10, 10, 1473–1485.
    掲載号(2022年10巻10号)の表紙に採択https://pubs.rsc.org/en/content/articlelanding/2022/tb/d1tb02508b

  25. “Photoswitching of 5-phenylazopyrimidines in crystalline powders and thin films”
    Eliška Procházková, Juraj Filo, Lucie Mužíková Čechová, Martin Dračínský, Ivana Císařová, Zlatko Janeba, Izuru Kawamura, Akira Naito, Peter Nádaždy, Peter Šiffalovič, Marek Cigáň
    Dyes Pigm., 2022, 199, 110066.
    https://www.sciencedirect.com/science/article/pii/S0143720821009323

  26. “Cell adhesion and migration on thickness gradient bilayer polymer brush surfaces: effects of properties of polymeric materials of the underlayer”
    Zahra Afzali, Taishi Matsushita, Akinori Kogure, Tsukuru Masuda, Tomoyuki Azuma, Keiichiro Kushiro, Toshihiro Kasama, Ryo Miyake, Madoka Takai
    ACS Appl. Mater. Interfaces, 2022, 14, 2, 2605–2617.
    https://pubs.acs.org/doi/full/10.1021/acsami.1c21453

  27. Review “Recent advances in research on biointerfaces: From cell surfaces to artificial interfaces”
    Katsutoshi Hori, Shogo Yoshimoto, Tomoko Yoshino, Tamotsu Zako, Gen Hirao, Satoshi Fujita, Chikashi Nakamura, Ayana Yamagishi, Noriho Kamiya
    J. Biosci. Bioeng., 2022, 133, 3, 195–207.
    https://www.sciencedirect.com/science/article/pii/S1389172321003315

  28. “Two-dimensional imaging of a model pharmaceutical dosage tablet using a scanning vibrational circular dichroism system”
    Hisako Sato, Sumio Aisawa, Honoka Ida, Masaru Shimizu, Keisuke Watanabe, Jun Koshobu, Jun Yoshida, Izuru Kawamura
    Chem. Lett., 2022, 51, 2, 205–207.
    https://www.journal.csj.jp/doi/full/10.1246/cl.210635

  29. “Nanofluidics for sub-single cellular studies: Nascent progress, critical technologies, and future perspectives”
    Jinbin Yang, Yan Xu
    Chin. Chem. Lett., 2022, 33, 6, 2799–2806.
    https://www.sciencedirect.com/science/article/abs/pii/S1001841721007865

  30. “De novo design of a nanopore for single molecule detection that incorporates a β-hairpin peptide”
    Keisuke Shimizu, Batsaikhan Mijiddorj, Masataka Usami, Ikuro Mizoguchi, Shuhei Yoshida, Shiori Akayama, Yoshio Hamada, Akifumi Ohyama, Kenji Usui, Izuru Kawamura, Ryuji Kawano
    Nature Nanotechnol., 2022, 17, 67–75.
    https://www.nature.com/articles/s41565-021-01008-w

  31. “Identification of conditions for efficient cell-sized liposome preparation using commercially available reconstituted in vitro transcription-translation system”
    Atsuko Uyeda, Sabrina Galiñanes Reyes, Takashi Kanamori, Tomoaki Matsuura
    J. Biosci. Bioeng., 2022, 133, 2, 181–186.
    https://www.jstage.jst.go.jp/article/csf/46/2/46_21052/_article/-char/en

  32. “A Dual Promoter System to Monitor IFN-γ Signaling in vivo at Single-cell Resolution”
    Taisei Tanaka, Yoshinobu Konishi, Hiroshi Ichise, Shinya Tsukiji, Michiyuki Matsuda, Kenta Terai
    Cell Struct. Funct., 2022, 46, 2, 103–111.
    https://www.jstage.jst.go.jp/article/csf/46/2/46_21052/_article/-char/en

  33. “pH-responsive water-soluble polymer carriers for cell-selective metabolic sialylation labeling”
    Tingbi Zhao, Tsukuru Masuda, Madoka Takai
    Anal. Chem., 2021, 93, 46, 15420–15429.
    https://pubs.acs.org/doi/full/10.1021/acs.analchem.1c03261

  34. Viewpoint “Modularly built synthetic membraneless organelles enabling targeted protein sequestration and release”
    Shuhao Lin, Daiki Hirayama, Gembu Maryu, Kimiya Matsuda, Naoya Hino, Eriko Deguchi, Kazuhiro Masaru Yoshikawa, Shinya Tsukiji
    Biochemistry, 2021, 60, 44, 3273–3276.
    https://pubs.acs.org/doi/full/10.1021/acs.nanolett.1c02871

  35. “Redundant roles of EGFR ligands in the ERK activation waves during collective cell migration”
    Shuhao Lin, Daiki Hirayama, Gembu Maryu, Kimiya Matsuda, Naoya Hino, Eriko Deguchi, Kazuhiro Aoki, Ryo Iwamoto, Kenta Terai, Michiyuki Matsuda
    Life Sci. Alliance, 2021, 5, e202101206..
    https://pubs.acs.org/doi/full/10.1021/acs.nanolett.1c02871

  36. “Fabrication of nanoscale gas–liquid interfaces in hydrophilic/hydrophobic nanopatterned nanofluidic channels”
    Hiroto Kawagishi, Shuichi Kawamata, Yan Xu
    Nano Lett., 2021, 21, 24, 10555–10561.
    掲載号(2021年21巻24号)の表紙に採択
    https://pubs.acs.org/doi/full/10.1021/acs.nanolett.1c02871

Commercialized, patents

  1. 2022.07.14
    A01 Tsukiji group
    Reagent for inducing membrane localization of proteins「SLIPT-PM」on sale(Funakoshi)
    https://www.funakoshi.co.jp/contents/70609
    https://www.funakoshi.co.jp/contents/70604

Press Releases & Media Coverage

  1. Kasano group:JACS Aurelated

    Press Releases
    Successful Pattern Discrimination of Cancer Markers in Blood Using Nanopores! -Using Parallel Computing with DNA Computing Technology―, TUAT
    https://www.tuat.ac.jp/outline/disclosure/pressrelease/2022/20220627_01.html

    Media coverage
    Tokyo University of Agriculture and Technology succeeded in identifying patterns of cancer markers in blood using nanopores., Nikkei Net, 27 Jun 2022, 
    https://www.nikkei.com/article/DGXZRSP635247_X20C22A6000000/

    Detection of cancer biomarkers from blood samples using nanopore-based DNA computing technology, EurekAlert!, 27 Jun 2022
    https://www.eurekalert.org/news-releases/957090

    Detection of cancer biomarkers from blood samples using nanopore-based DNA computing technology, Bioengineer.org, 27 Jun 2022
    https://bioengineer.org/detection-of-cancer-biomarkers-from-blood-samples-using-nanopore-based-dna-computing-technology/

    Detection of cancer biomarkers from blood samples using nanopore-based DNA computing technology, ScienMag, 27 Jun 2022
    https://scienmag.com/detection-of-cancer-biomarkers-from-blood-samples-using-nanopore-based-dna-computing-technology/

    TUAT succeeded in identifying cholangiocarcinoma by DNA computing and nanopore measurement., TECH+, 28 Jun 2022
    https://news.mynavi.jp/techplus/article/20220628-2382598/

    Nanopore Technology Detects Cancer Biomarkers from Patients’ Blood, GEN, 28 Jun 2022
    https://www.genengnews.com/topics/translational-medicine/biomarkers/nanopore-technology-detects-cancer-biomarkers-from-patients-blood/

    Detection of cancer biomarkers from blood samples using nanopore-based DNA computing technology, ecancer, 28 Jun 2022
    https://ecancer.org/en/news/22000-detection-of-cancer-biomarkers-from-blood-samples-using-nanopore-based-dna-computing-technology

    Nuevo método para detectar biomarcadores de cáncer con muestras de sangre, Jano, 29 Jun 2022 
    https://www.jano.es/noticia-nuevo-metodo-detectar-biomarcadores-cancer-33440

    利用纳米孔DNA技术从血液样本中检测癌症生物标志物, ebiotrade, 29 Jun 2022
    https://www.ebiotrade.com/newsf/2022-6/20220628002541949.htm

    Cancer Biomarkers are detected from patients’ blood using nanopore technology, list23, 29 Jun 2022
    https://list23.com/936881-cancer-biomarkers-are-detected-from-patients-blood-using-nanopore-technology/

    Nanopore Technology Detects Cancer Biomarkers from Patients’ Blood, tetracyclined7k, 29 Jun 2022
    https://tetracyclined7k.com/nanopore-technology-detects-cancer-biomarkers-from-patients-blood/

    Researchers use nanopore-based DNA computing technology to detect cancer, AZO Life Sciences, 1 Jul 2022
    https://www.azolifesciences.com/news/20220701/Researchers-use-nanopore-based-DNA-computing-technology-to-detect-cancer.aspx

  2. Xu group:Nano Lettrelated

    Press Releases
    “Discovery of Material Concentration Effects at the Nanoscale – Fabrication and Effects of Ultra-Micro Gas-Liquid Interfaces Using Nanofluidic Devices”、Joint press release from Osaka Prefecture University and JST(Oct/14/2021)

    ▼Osaka Prefecture University website
    https://www.osakafu-u.ac.jp/press-release/pr20211014_3/

    ▼JST website
    https://www.jst.go.jp/pr/announce/20211014-3/index.html

    ▼Osaka Public University
    https://www.upc-osaka.ac.jp/new-univ/research/press_release/

    ▼Osaka Prefecture University Twitter
    https://twitter.com/OsakaPrefUniv/status/1448544485890166788

    ▼Osaka Prefecture University Facebook
    https://www.facebook.com/OsakaPrefectureUniv/posts/267661358698236

    ▼YouTube
    https://www.youtube.com/watch?v=ggQIXIDelgQ

    Media coverage
    Osaka Prefectural Univ. succeeds in fabricating nanoscale ultra-small gas-liquid interfaces with high precision and uniformity,Nikkan Kogyo Shimbun , Electric version、(Oct/15/2021)
    https://www.nikkan.co.jp/spaces/view/0061628

    First controllable nanoscale gas-liquid interface fabricated
    EurekAlert!
    https://www.eurekalert.org/news-releases/931973

    Asia Research News
    https://www.asiaresearchnews.com/content/first-controllable-nanoscale-gas-liquid-interface-fabricated

    Phys.orgPhys.org
    https://phys.org/news/2021-10-nanoscale-gas-liquid-interface-fabricated.html

    Nanowerk
    https://www.nanowerk.com/nanotechnology-news2/newsid=58952.php

    Chem Europe
    https://www.chemeurope.com/en/news/1173219/first-controllable-nanoscale-gas-liquid-interface-fabricated.html

    ScienMag
    https://scienmag.com/first-controllable-nanoscale-gas-liquid-interface-fabricated/

    True Viral News
    https://trueviralnews.com/52861-first-controllable-nanoscale-gas-liquid-interface-fabricated.html

    Mirage News
    https://www.miragenews.com/first-controllable-nanoscale-gas-liquid-655001/

    Nano LettersのOfficial Twitterにて紹介, (Nov/6/2021)
    https://mobile.twitter.com/NanoLetters/status/1456697932716154883

    The research results were published in Chinese Science Media Chemistry and Materials Chemistry., (Nov/22/2021)
    https://mp.weixin.qq.com/s/0aYt3dUtEerytmr3TKnm4A

    Research Results on Nanofluidic Devices for Fabrication of Nanoscale Ultramicro Gas-Liquid Interfaces Graced the Cover of Nano Letters (Volume 21, Issue 24, 2021), (Dec/22/2021)
    https://pubs.acs.org/pb-assets/images/_journalCovers/nalefd/nalefd_v021i024-3.jpg?0.4156400251492782

  3. Xu group:J Mater Chem Brelated

    “A biomimetic anti-biofouling coating in nanofluidic channels” was selected as HOT Paper of Journal of Materials Chemistry, (Jan/20/2022)
    https://pubs.rsc.org/en/content/articlelanding/2022/tb/d1tb02627e

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