Publications

• Original articles
• Reviews 　
• Conference papers
• Books , Magazines, etc. 
• Others

Original articles

1. Sugii, S., Hagino, K., Mizuuchi, R., Ichihashi, N.*
   Cell-Free Expression of RuBisCO for ATP Production in the Synthetic Cells.
   Synthetic Biology, 8 (1), ysad016. (2023)
2. Ueda, K., Mizuuchi, R.*, Ichihashi, N.*
   Emergence of linkage between cooperative RNA replicators encoding replication and metabolic enzymes through experimental evolution.
   PLOS Genetics, 19 (8), e1010471. (2023)
3. Mizuuchi, R.*, Ichihashi, N.
   Minimal RNA self-reproduction discovered from a random pool of oligomers.
   Chemical Science, 14, 7656–7664. (2023)
   #プレスリリース,  Featured: #月刊化学 解説, #現代化学 FLASH, #Newton FOCUS
4. Maeda, Y., Mizuuchi, R., Shigenobu, S., Shibai, A., Kotani, H., Furusawa, C, Ichihashi N.
   Experimental evidence for the correlation between RNA structural fluctuations and the frequency of beneficial mutations.
   RNA, 28 (12), 1659–1667. (2022)
5. Kamiura, R., Mizuuchi, R., Ichihashi N.
   Plausible pathway for a host-parasite molecular replication network to increase its complexity through Darwinian evolution.
   PLOS Computational Biology, 18 (12), e1010709. (2022)
   #プレスリリース
6. Yukawa, K., Mizuuchi, R., Ichihashi, N.
   Relaxed substrate specificity in Qβ replicase through long-term in vitro evolution.
   Life, 21 (1), 32. (2022)
7. Mizuuchi, R.*, Furubayashi, T., Ichihashi N.*
   Evolutionary transition from a single RNA replicator to a multiple replicator network.
   Nature Communications, 13, 1460. (2022)
   #プレスリリース, #Press release, Featured: #Top 25 Life and Biological Sciences Articles of 2022 in Nature Communications, #DISPATCH of Current Biology, #Quanta Magazine, #SYFY WIRE, #日経サイエンス, #日本経済新聞, #東京新聞, among other >50 media outlets.
8. Reyes, S., G., Kuruma, Y., Fujimi, M., Yamazaki, M., Eto, S., Nishikawa, S., Tamaki, S., Kobayashi, A., Mizuuchi, R., Rothschild, L., Ditzler, M., Fujishima, K.
   PURE mRNA display and cDNA display provide rapid detection of core epitope motif via high-throughput sequencing.
   Biotechnology and Bioengineering, 118 (4), 1736–1749. (2021)
   #プレスリリース、#Press release
9. Mizuuchi, R.*, Ichihashi, N.
   Translation-coupled RNA replication and parasitic replicators in membrane-free compartments.
   Chemical Communications, 56, 13453–13456. (2020)
10. Furubayashi, T., Ueda, K., Bansho, Y., Motooka, D., Nakamura, S., Mizuuchi, R., Ichihashi, N.
    Emergence and diversification of a host-parasite RNA ecosystem through Darwinian evolution.
    eLife, 9, e56038. (2020)
    #プレスリリース
11. Sakatani, Y., Mizuuchi, R., Ichihashi, N.
    In vitro evolution of phi29 DNA polymerases through compartmentalized gene expression and rolling-circle replication.
    Protein Engineering Design and Selection, 32 (11), 481–487. (2020)
12. Mizuuchi, R., Usui, K., Ichihashi, N.
    Structural transition of replicable RNAs during in vitro evolution with Qβ replicase.
    RNA, 26, 83–89. (2020)
13. Ueda, K., Mizuuchi, R., Matsuda, F., Ichihashi, N.
    A fusion method to develop an expanded artificial genomic RNA replicable by Qβ replicase.
    ChemBioChem, 20, 2331–2335. (2019)
14. Mizuuchi, R.*, Blokhuis, A., Vincent, L., Nghe, P., Lehman. N., and Baum, D.
    Mineral surfaces select for longer RNA molecules.
    Chemical Communications, 55, 2090–2093. (2019)
    Featured: #Chemistry World, Royal Society of Chemistry
15. Mizuuchi, R.*, Lehman, N.
    Limited Sequence Diversity Within a Population Supports Prebiotic RNA Reproduction.
    Life, 9 (1), 20. (2019)
16. Smail, B.A., Clifton,B.E., Mizuuchi, R.*, Lehman, N.
    Spontaneous advent of genetic diversity in RNA populations through multiple recombination mechanisms.
    RNA, 25, 453–464. (2019)
17. Mizuuchi, R., Ichihashi, N.
    Sustainable replication and coevolution of cooperative RNAs in an artificial cell-like system.
    Nature Ecology & Evolution, 2, 1654–1660. (2018)
    #academist Journal, #Behind the Paper, Featured: #News & Views of Nature Ecology & Evolution, #Ars Technica
18. Mizuuchi, R., Kawase, H., Shin, H., Iwai, D., Kondo, S.
    Simple rules for construction of a geometric nest structure by pufferfish.
    Scientific Reports, 8, 12366. (2018)
    #プレスリリース, Featured: #Science writer Willy van Strien’s blog, #南海日日新聞
19. Kawase, H., Mizuuchi, R., Shin, H., Kitajima, Y., Hosoda, K., Shimizu, M., Iwai, D., Kondo, S.
    Discovery of an earliest-stage “mystery circle” and development of the structure constructed by pufferfish, Torquigener albomaculosus (Pisces: Tetraodontidae).
    Fishes, 2 (3), 14. (2017)
20. Mizuuchi, R., Ichihashi, N., Yomo, T.
    Adaptation and diversification of an RNA replication system under initiation- or termination-impaired translational conditions.
    ChemBioChem, 17 (13), 1229–1232. (2016)
21. Mizuuchi, R., Ichihashi, N., Usui, K., Kazuta, Y., Yomo, T.
    Adaptive Evolution of an Artificial RNA Genome to a Reduced Ribosome Environment.
    ACS Synthetic Biology, 4 (3), 292–298. (2015)
    

Reviews

1. Jia, T. Z.*, Mizuuchi, R.*
   How biophysics shapes the origins of life: a 21st IUPAB/62nd BSJ joint congress symposium overview.
   Biophysical Reviews, in press. (2024)
2. Mizuuchi, R.*
   Constraint on an RNA World on Montmorillonite Clay.
   Biophysical Journal, 123 (4), 421–423. (2024)
3. Yukawa, K., Mizuuchi, R., Ichihashi, N.
   How prebiotic complexity increases through Darwinian evolution.
   Current Opinion in Systems Biology, 34, 100456. (2023)
4. 水内良*
   原始生命を模した分子複製システムの進化と改良
   Viva Origino, 49 (3), 10. (2021)
5. Mizuuchi, R.*, Ichihashi, N.*
   Primitive compartmentalization for the sustainable replication of genetic molecules.
   Life, 11 (3), 191. (2021)

Conference papers

1. 川瀬裕司、水内良、進寛史、北嶋友喜、細田耕、清水正宏、岩井大輔、近藤滋
   アマミホシゾラフグがつくる「ミステリーサークル」の謎を解く
   計測自動制御学会システム・情報部門学術講演会講演論文集、ROMBUNNO.GS03–5. (2017)
2. Mizuuchi, R., Ichihashi, N., Usui, K., Yomo, T.
   Evolution and Adaptation of the RNA Coupled with an Artificial Life-Like Self-Replication System to a Severe Translational Environment
   Proceeding of International Astrobiology Workshop 2013, 1006. (2013)

Books, Magazines, etc.

1. 市橋伯一、水内良「RNA ワールド仮説と生命の起源」RNAの科学、金井 昭夫 (編)、朝倉書店、p241–249、2024年7月
2. 水内良「進化を予測するのは想像以上に難しい」実験医学 2024年3月号、p560–561
3. 水内良「生命の起源の謎を解く 自己複製する最小のRNAとは？」月刊 化学 2023年12月号、p44–47
4. 水内良「研究最前線」分子サイバネティクス ニュースレター Vol.6 2022年6月
5. 水内良「生命の起源 – 原始的な複製体はいかに複雑化しうるのか？」academist Journal, 2018年10月
6. Ryo Mizuuchi. “Survive and evolve, dynamics of cooperative RNA replicators in a compartment” Behind the Paper of Nature Ecology & Evolution, August 2018

Others

1. 水内良「研究奨励賞受賞記 生命の起源に魅せられて」日本進化学会ニュースVol.24 No.1, 2023年3月
2. 水内良「第22回大会 ポスター発表賞 最優秀賞 受賞記」日本進化学会ニュースVol.21 No.3, 2020年12月