LiMe 京都大学医生物学研究所

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共同利⽤・共同研究拠点支援成果

☆ 医生物学研究所共同利用機器を利用した研究成果
iSAL共用研究機器を利用した研究成果

☆ Publications supported by Shared Research Facilities at LiMe
★ Publications supported by iSAL

T Iida, J Ando, M Yoshimura, A Makino, M Nakano, Y Kogo, H Shinoda, M Toyoda, T Noda, R Watanabe.

Portable wide-field femtoliter-chamber imaging system for point-of-care digital bioanalysis.

iScience. 27(9):110868. (2024)

doi: 10.1016/j.isci.2024.110868.

T Kuwata, Y Kaku, S Biswas, K Matsumoto, M Shimizu, Y Kawanami, R Uraki, K Okazaki, R Minami, Y Nagasaki, M Nagashima, I Yoshida, K Sadamasu, K Yoshimura, M Ito, M Kiso, S Yamayoshi, M Imai, T Ikeda, K Sato, M Toyoda, T Ueno, T Inoue, Y Tanaka, KT Kimura, T Hashiguchi, Y Sugita, T Noda, H Morioka, Y Kawaoka, S Matsushita.

Induction of IGHV3-53 public antibodies with broadly neutralising activity against SARS-CoV-2 including Omicron subvariants in a Delta breakthrough infection case.

EBioMedicine. 110:105439. (2024)

doi: 10.1016/j.ebiom.2024.105439.

A Hirabayashi , Y Muramoto, T Takenaga, Y Tsunoda, M Wakazaki, M Sato, Y Fujita-Fujiharu, N Nomura, K Yamauchi, C Onishi, M Nakano, K Toyooka, T Noda.

Coatomer complex I is required for the transport of SARS-CoV-2 progeny virions from the endoplasmic reticulum-Golgi intermediate compartment.

mBio. e0333124. (2024)

doi: 10.1128/mbio.03331-24.

K IIDA, M Ajiro, A Nakano-Kobayashi, Y Muramoto, T Takenaga, T Denawa, R Kurosawa, T Noda, M Hagiwara.

Switching of OAS1 splicing isoforms overcomes SNP-derived vulnerability to SARS-CoV-2 infection.

BMC biology. 23(1):60. (2025)

doi: 10.1186/s12915-025-02173-3.

Yoko Fujita-Fujiharu, Shangfan Hu, Ai Hirabayashi, Yuki Takamatsu, Yen Ni Ng, KazuyaHouri, YukikoMuramoto, Masahiro Nakano, Yukihiko Sugita, Takeshi Noda.

Structural basis for Ebola virus nucleocapsid assembly and function regulated by VP24.

Nature Communications. (2025) 16:2171

doi: 10.1038/s41467-025-57236-4

Y. Yamauchi, A. Hishida, T. Okada, A. Mochizuki, (2024)

Finding regulatory modules of chemical reaction systems.

Phys. Rev. Research 6, 023150.

doi: 10.1103/PhysRevResearch.6.023150

Hideshi Ooka, Marie E. Wintzer, Hirokazu Komatsu, Tomoharu Suda, Kiyohiro Adachi, Ailong Li, Shuang Kong, Daisuke Hashizume, Atsushi Mochizuki, Ryuhei Nakamura, (2024)

Microkinetic Model to Rationalize the Lifetime of Electrocatalysis: Trade-off between Activity and Stability.

Journal of Physical Chemistry Letters 15(40), 10079–10085.

doi: 10.1021/acs.jpclett.4c02162

Ryosuke Okino, Kazuaki Mukai, Shunpei Oguri, Masato Masuda, Satoshi Watanabe, Yosuke Yoneyama, Sumine Nagaosa, Takafumi Miyamoto, Atsushi Mochizuki, Shin-Ichiro Takahashi & Fumihiko Hakuno, (2024)

IGF-I concentration determines cell fate by converting signaling dynamics as a bifurcation parameter in L6 myoblasts.

Scientific Reports 14, 20699.

doi: 10.1038/s41598-024-71739-y

Shion Hosoda, Hisashi Iwata, Takuya Miura, Maiko Tanabe, Takashi Okada, Atsushi Mochizuki & Miwa Sato, (2024)

BayesianSSA: a Bayesian statistical model based on structural sensitivity analysis for predicting responses to enzyme perturbations in metabolic networks.

BMC Bioinformatics 25, 297.

doi: 10.1186/s12859-024-05921-4

Tsujino S, Deguchi S, Nomai T, Padilla-Blanco M, Plianchaisuk A, Wang L, Begum MM, Uriu K, Mizuma K, Nao N, Kojima I, Tsubo T, Li J, Matsumura Y, Nagao M, Oda Y, Tsuda M, Anraku Y, Kita S, Yajima H*, Sasaki-Tabata K, Guo Z, Hinay AA Jr, Yoshimatsu K, Yamamoto Y, Nagamoto T, Asakura H, Nagashima M, Sadamasu K, Yoshimura K, Nasser H, Jonathan M, Putri O, Kim Y, Chen L, Suzuki R, Tamura T, Maenaka K, Irie T, Matsuno K, Tanaka S, Ito J, Ikeda T, Takayama K, Zahradnik J, Hashiguchi T, Fukuhara T, Sato K; Genotype to Phenotype Japan (G2P‐Japan) Consortium. (2024)

Virological characteristics of the SARS-CoV-2 Omicron EG.5.1 variant.

Microbiol. Immunol. 68(9):305-330

doi: 10.1111/1348-0421.13165

Fukuhara H, Yumoto K, Sako M, Kajikawa M, Ose T, Kawamura M, Yoda M, Chen S, Ito Y, Takeda S, Mwaba M, Wang J, Hashiguchi T, Kamishikiryo J, Maita N, Kitatsuji C, Takeda M, Kuroki K, Maenaka K. (2024)

Glycan-shielded homodimer structure and dynamical features of the canine distemper virus hemagglutinin relevant for viral entry and efficient vaccination.

Elife 12:RP88929

doi: 10.7554/eLife.88929

Yajima H*, Nomai T, Okumura K, Maenaka K; Genotype to Phenotype Japan (G2P-Japan) Consortium; Ito J, Hashiguchi T, Sato K. (2024)

Molecular and structural insights into SARS-CoV-2 evolution: from BA.2 to XBB subvariants.

mBio. E0322023

doi: 10.1128/mbio.03220-23

☆★

Hisano Yajima, Yuki Anraku, Yu Kaku, Kanako Terakado Kimura, Arnon Plianchaisuk, Kaho Okumura, Yoshiko Nakada-Nakura, Yusuke Atarashi, Takuya Hemmi, Daisuke Kuroda, Yoshimasa Takahashi, Shunsuke Kita, Jiei Sasaki, Hiromi Sumita, The Genotype to Phenotype Japan (G2P-Japan) Consortium, Jumpei Ito, Katsumi Maenaka, Kei Sato & Takao Hashiguchi (2024).

Structural basis for receptor-binding domain mobility of the spike in SARS-CoV-2 BA.2.86 and JN.1.

Nature Communications, 15, 8574.

doi: 10.1038/s41467-024-52808-2

☆★

Sasaki J*, Sato A, Sasaki M, Okabe I, Kodama K, Otsuguro S, Yasuda K, Kojima H, Orba Y, Sawa H, Maenaka K, Yanagi Y, Hashiguchi T. (2024)

X-206 exhibits broad-spectrum anti-b-coronavirus activity, covering SARS-CoV-2 variants and drug-resistant isolates.

Antiviral research 232:106039

doi: 10.1016/j.antiviral.2024.106039

☆★

Gao Z, Sasaki J, Suzuki T, Suzuki T, Miwa Y, Sando S, *Hashiguchi T, *Morimoto J.

Discovery of potent measles virus fusion inhibitor peptides via structure-guided derivatization.

RSC Med Chem. 2025

doi: 10.1039/d4md01006j

Anraku Y*, Kita S, Onodera T, Sato A, Tadokoro T, Ito S*, Adachi Y, Kotaki R, Suzuki T, Sasaki J*, Shiwa-Sudo N, Iwata-Yoshikawa N, Nagata N, Kobayashi S*, Kazuki Y, Oshimura M, Nomura T, Sasaki M, Orba Y, Suzuki T, Sawa H, Hashiguchi T, Fukuhara H, Takahashi Y, Maenaka K. (2025)

Structural and virological identification of neutralizing antibody footprint provides insights into therapeutic antibody design against SARS-CoV-2 variants.

Communications Biology. 8, Article number: 483

doi: 10.1038/s42003-025-07827-0

Yusuke Sakamoto, Shota Fujii, Shin Takano, Jokichi Fukushima, Mitsuru Ando, Noriyuki Kodera, and Tomoki Nishimura (2024).

Manipulation of Macrophage Uptake by Controlling the Aspect Ratio of Graft Copolymer Micelles.

Nano Letters, 24, 19, 5838-5846.

doi: 10.1021/acs.nanolett.4c01054

Takashi Ohtsuki, Ikumi Sato, Ren Takashita, Shintaro Kodama, Kentaro Ikemura, Gabriel Opoku, Shogo Watanabe, Takayuki Furumatsu, Hiroshi Yamada, Mitsuru Ando, Kazunari Akiyoshi, Keiichiro Nishida and Satoshi Hirohata.

Distribution and Incorporation of Extracellular Vesicles into Chondrocytes and Synoviocytes.

Int. J. Mol. Sci. 2024, 25(22), 11942

doi: 10.3390/ijms252211942

Wenxuan Yang, Satoshi Abe, Mitsuru Ando and Yasuhiko Tabata.

Association with Cationized Gelatin Nanospheres Enhances Mitochondria Uptake and Membrane Potential.

Tissue Engineering Part A, Volume 31, Issue 15-16.

doi: 10.1089/ten.tea.2024.0265

Watanabe, A., Koyano, F., Imai, K., Hizukuri, Y., Ogiwara, S., Ito, T., Miyamoto, J., Shibuya, C., Kimura, M., Toriumi, K., Motono, C., Arai, M., Tanaka, K., Akiyama, Y., Yamano, K., and Matsuda, N.(2024)

The origin of esterase activity of Parkinson's disease causative factor DJ-1 implied by evolutionary trace analysis of its prokaryotic homolog HchA.

J. Biol. Chem. 300(7) 10747

doi: 10.1016/j.jbc.2024.107476