業績

原著論文

市橋グループ

  1. Aita, T., Ichihashi, N., Yomo, T. Inference of fitness values and putative appearance time points for evolvable self-replicating molecules from time series of occurrence frequencies in an evolution reactor. J Theoretical Biol, 401, 38-42 (2016)
  2. Sunami, T., Ichihashi, N., Nishikawa, T., Kazuta, Y., Yomo, T. Effect of Liposome Size on Internal RNA Replication Coupled with Replicase Translation. ChemBioChem, 17, 1282-1289 (2016)
  3. 3. Mizuuchi, R., Ichihashi, N.*, Yomo, T. (*corresponding) Adaptation and diversification of an RNA replication system under initiation- or termination-impaired translational conditions. ChemBioChem, 17, 1229-1232 (2016)
  4. Bansho, Y., Furubayashi, T., Ichihashi, N.*, Yomo, T.* (*co-corresponding).(2016) Host-parasite oscillation dynamics and evolution in a compartmentalized RNA replication system. PNAS,113(5),4045?4050.
  5. Furubayashi T, Nakano T, Eckford A, Okaie Y, Yomo T.(2016) Packet Fragmentation and Reassembly in Molecular Communication. IEEE Transactions on NanoBioscience ,(99),1-5.
  6. Taro Furubayashi, Tadashi Nakano, Andrew Eckford, Norikazu Ichihashi, Tetsuya Yomo.(2015) Packet Replication and Noise in Reliable End-to-end Molecular Communication. 9th EAI International Conference on Bio-inspired Information and Communications Technologies,1-2.
  7. Taro Furubayashi, Tadashi Nakano, Andrew Eckford, Tetsuya Yomo.(2015) Reliable End-to-end Molecular Communication with Packet Replication and Retransmission. 2015 IEEE Global Communications Conference (GLOBECOM),1-6.
  8. Tomita K, Ichihashi N, Yomo T.(2015) Replication of partial double-stranded RNAs by Qβ replicase. Biochem Biophys Res Commun,467(2),293-296.
  9. Yoshiyama T, Motohashi C, Ichihashi N, Ichii T, Yomo T.(2015) Maintenance of a translation-coupled RNA replication in dynamic micro-sized compartments under continuous stirring and flow. Chemical Engineering Journa,283(14015),896-902.
  10. Ichihashi N, Aita T, Motooka D, Nakamura S, Yomo T.(2015) Periodic pattern of genetic and fitness diversity during evolution of an artificial cell-like system. Molecular Biology and Evolution,32(12),3205-3214.
  11. Takako Awai, Norikazu Ichihashi,Tetsuya Yomo.(2015) Activities of 20 aminoacyl-tRNA synthetases expressed in a reconstituted translation system in Escherichia coli. Biochemistry and Biophysics Reports,3,140-143.
  12. Usui, K.*, Ichihashi, N.*, Yomo, T. (*equally contributed) (2015) A design principle for a single-stranded RNA genome that replicates with less double-strand formation. Nucleic Acids Research,43(16),8033-8043.
  13. Sakatani Y, Ichihashi N, Kazuta Y, Yomo T.(2015) A transcription and translation-coupled DNA replication system using rolling-circle replication. Scientific Reports,5,(10404),10.1038/srep10404,1-9.
  14. Kotaro Nishiyama, Norikazu Ichihashi, Yasuaki Kazuta, Tetsuya Yomo.(2015) Development of a reporter peptide that catalytically produces a fluorescent signal through α-complementation. Protein Science,24,(5),599-603.
  15. Ichihashi N, Kobori S, Yomo T.(2015) Simple identification of two causes of noise in an aptazyme system by monitoring cell-free transcription. Methods in Enzymology,550,93-107.
  16. Uno K, Sunami T, Ichihashi N, Kazuta Y, Matsuura T, Yomo T.(2014) The Evolutionary Enhancement of Genotype-Phenotype Linkages in the Presence of Multiple Copies of Genetic Material. Chembiochem,15(15),2281?2288.
  17. Ryo Mizuuchi,Norikazu Ichihashi,Kimihito Usui,Yasuaki Kazuta,and Tetsuya Yomo.(2014) Adaptive Evolution of an Artificial RNA Genome to a Reduced Ribosome . ACS Synthetic Biology,4(3),292-298.
  18. Yasuaki Kazuta,Tomoaki Matsuura,Norikazu Ichihashi,Tetsuya Yomo.(2014) Synthesis of milligram quantities of proteins using a reconstituted in vitro protein synthesis system. Journal of Bioscience and Bioengineering,118(5),554?557.
  19. Kimihito Usui, Norikazu Ichihashi, Yasuaki Kazuta, Tomoaki Matsuura, Tetsuya Yomo.(2014) Effects of ribosomes on the kinetics of Qb replication. FEBS Letters.,588(1),117-123.
  20. Takuyo Aita, Norikazu Ichihashia, Tetsuya Yomo. (2013) Probabilistic model based error correction in a set of various mutant sequences analyzed by next-generation sequencing. Computational Biology and Chemistry.,2013(47),221-230.
  21. Norikazu Ichihashi, Kimihito Usui, Yasuaki Kazuta, Takeshi Sunami, Tomoaki Matsuura, Tetsuya Yomo. (2013) Darwinian evolution in a translation-coupled RNA replication system within a cell-like compartment. Nature Communications.,4(2494),1-7.
  22. Kimihito Usui, Norikazu Ichihashi, Yasuaki Kazuta, Tomoaki Matsuura, Tetsuya Yomo.(2013) Kinetic model of double-stranded RNA formation during long RNA replication by Qβ replicase. FEBS Letters.,2013(587),2565-2571.
  23. Shungo Kobori, Norikazu Ichihashi, Yasuaki Kazuta, Tetsuya Yomo.(2013) A controllable gene expression system in liposomes that includes a positive feedback loop. Mol. BioSyst.,9(6),1282-1285.
  24. Kotaro Nishiyama, Norikazu Ichihashi, Tomoaki Matsuura, Yasuaki Kazuta, Tetsuya Yomo.(2012) α-Complementation in an artificial genome replication system in liposomes. Chembiochem. ,2012(13),2701-2706.
  25. Takehiro Nishikawa, Takeshi Sunami, TomoakiMatsuura, Tetsuya Yomo.(2012) Directed Evolution of Proteins through In Vitro Protein Synthesis in Liposomes. Journal of Nucleic Acids.,2012,1-11.
  26. Tomoaki Matsuura, Kazufumi Hosoda, Yasuaki Kazuta, Norikazu Ichihashi, Hiroaki Suzuki, Tetsuya Yomo.(2012) Effects of Compartment Size on the Kinetics of Intracompartmental Multimeric Protein Synthesis. ACS Synth. Biol.,2012(1),1431-1437.
  27. Shungo Kobori, Norikazu Ichihashi, Yasuaki Kazuta, Tomoaki Matsuura, Tetsuya Yomo.(2012) Kinetic analysis of aptazyme-regulated gene expression in a cell-free translation system:modeling of ligand-dependent and -independent expression. RNA.,18(8),1458-1465.
  28. Yohsuke Bansho, Norikazu Ichihashi, Yasuaki Kazuta, Tomoaki Matsuura, Hiroaki Suzuki, Tetsuya Yomo.(2012) Importance of parasite RNA species repression for prolonged translation-coupled RNA self-replication. Chemistry and Biology.,19(4),478-487.
  29. Takehiro Nishikawa, Takeshi Sunami, Tomoaki Matsuura, Norikazu Ichihashi, Tetsuya Yomo.(2012) Construction of Gene Screening System Using Giant Unilamellar Liposomes and Fluorescence Activated Cell Sorter. analytical chemistry 2012.,84,5017-5024.
  30. Tomoaki Matsuura, Kazufumi Hosoda, Norikazu Ichihashi, Yasuaki Kazuta, Tetsuya Yomo.(2011) Kinetic Analysis of -Galactosidase and -Glucuronidase Tetramerization Coupled with Protein Translation. Journal of Biological Chemistry.,286(25),22028-22034.
  31. Norikazu Ichihashi, Tomoaki Matsuura, Kazufumi Hosoda and Tetsuya Yomo.(2010) Identification of two forms of Qβ replicase with different thermal stabilities but identical RNA replication activity. The Journal of Biological Chemistry.,285(48), 37210-37217.
  32. Hiroya Urabe, Norikazu Ichihashi, Tomoaki Matsuura, Kazufumi Hosoda, Yasuaki Kazuta, Hiroshi Kita, Tetsuya Yomo.(2010) Compartmentalization in a water-in-oil emulsion repressed the spontaneous amplification of RNA by Qbeta replicase. Biochemistry, 49(9), 1809-1813.
  33. Kurokawa, K., Mizumura, H., Takaki, T., Ishii, Y., Ichihashi, N., Bok Luel Lee, Sekimizu, K. Rapid Exchange of Bound ADP on the Staphylococcus aureus Replication Initiation protein DnaA. Journal of Biological Chemistry, 284, 34201-10, (2009)
  34. Ichihashi, N., Matsuura, T., Kita, H., Hosoda, K., Sunami, T., Tsukada, K., and Yomo, T. (2008) Importance of translation-replication balance for efficient replication by the self-encoded replicase ChemBioChem, 9 (18),3023-3028.
  35. Kita, H., Matsuura, T., Sunami, T., Hosoda, K., Ichihashi, N., Tsukada, K., Urabe, I., and Yomo T. (2008) Replication of genetic information with self-encoded replicase in liposomes. ChemBioChem, 9 (15),2403-2410.
  36. Hosoda, K., Matsuura, T., Kita, H., Ichihashi, N., Tsukada, K., Urabe, I., and Yomo, T. (2008) A novel sequence-specific RNA quantification method using nicking endonuclease,dual-labeled fluorescent DNA probe, and conformation-interchangeable oligo-DNA. RNA,14,584-592.
    Supplementaly Information
  37. Hosoda, K., Matsuura, T., Kita, H., Ichihashi, N., Tsukada, K.,and Yomo, T. (2007) Kinetic analysis of the entire RNA amplification process by Qβreplicase.J. Biol. Chem., 282 (21),15516-15527.
  38. Murai, N., Kurokawa, K., Ichihashi, N., Matsuo, M., Sekimizu, K. Isolation of a temperature-sensitive dnaA mutant of Staphylococcus aureus. FEMS microbiology letters, 254, 19-26, (2006)
  39. Oku, Y., Kurokawa, K., Ichihashi, N., Sekimizu, K. Characterization of the Staphylococcus aureus mprF gene, involved in lysinylation of phosphatidylglycerol Microbiology 150, 45-51, (2004)
  40. Ichihashi, N., Kurokawa, K., Matsuo, M., Kaito, C., Sekimizu, K. Inhibitory effects of basic or neutral phospholipid on acidic phospholipid-mediated dissociation of adenine nucleotide bound to DnaA protein, the initiator of chromosomal DNA replication. Journal of Biological Chemistry, 278, 28778-28786, (2003)

角南グループ

  1. Sunami, T., Ichihashi, N., Nishikawa, T., Kazuta, Y., Yomo, T. Effect of Liposome Size on Internal RNA Replication Coupled with Replicase Translation. ChemBioChem, 17, 1282-1289 (2016)
  2. Gakushi Tsuji, Satoshi Fujii, Takeshi Sunami, Tetsuya Yomo.(2016) Sustainable proliferation of liposomes compatible with inner RNA replication. Proceedings of the National Academy of Sciences of the United States of America,113(3),590-595.
  3. Uno K, Sunami T, Ichihashi N, Kazuta Y, Matsuura T, Yomo T.(2014) The Evolutionary Enhancement of Genotype-Phenotype Linkages in the Presence of Multiple Copies of Genetic Material. Chembiochem,15(15),2281?2288.
  4. Satoshi fujii, Tomoaki Matsuura, Takeshi Sunami, Takehiro Nishikawa, Yasuaki Kazuta, Tetsuya Yomo..(2014) Liposome display for in vitro selection and evolution of membrane proteins. Nature protocols,9(7),1578-1591.
  5. Nishimura K, Matsuura T, Sunami T, Fujii S, Nishimura K, Suzuki H & Yomo T.(2014) Identification of giant unilamellar vesicles with permeability to small charged molecules. RSC Advances,4,35224-35232.
  6. Satoshi Fujii, Tomoaki Matsuura, Takeshi Sunami, Yasuaki Kazuta, Tetsuya Yomo.(2013) In vitro evolution of hemolysin using a liposome display. PNAS.,110(42),16796-16801.
  7. Takehiro Nishikawa, Takeshi Sunami, TomoakiMatsuura, Tetsuya Yomo.(2012) Directed Evolution of Proteins through In Vitro Protein Synthesis in Liposomes. Journal of Nucleic Acids.,2012,1-11.
  8. Nishimura Koji, Matsuura Tomoaki, Nishimura Kazuya, Sunami Takeshi, Suzuki Hiroaki, Yomo Tetsuya.(2012) Cell-free protein synthesis inside giant unilamellar vesicles analyzed by flow cytometry. Langmuir,2012(28),8426-8432.
  9. Takehiro Nishikawa, Takeshi Sunami, Tomoaki Matsuura, Norikazu Ichihashi, Tetsuya Yomo.(2012) Construction of Gene Screening System Using Giant Unilamellar Liposomes and Fluorescence Activated Cell Sorter. analytical chemistry 2012.,84,5017-5024.
  10. Filippo Caschera, Takeshi Sunami, Tomoaki Matsuura, Hiroaki Suzuki, Martin M. Hanczyc, and Tetsuya Yomo.(2011) Programmed Vesicle Fusion Triggers Gene Expression. Langmuir.,27(21),13082-13090.
  11. Takeshi Sunami, Filippo Caschera, Yuuki Morita, Taro Toyota, Kazuya Nishimura,Tomoaki Matsuura, Hiroaki Suzuki, Martin M. Hanczyc, and Tetsuya Yomo (2010) Detection of Association and Fusion of Giant Vesicles Using a Fluorescence-Activated Cell Sorter. Langmuir., 26(19),15098-15103.
  12. Takeshi Sunami, Kazufumi Hosoda, Hiroaki Suzuki, Tomoaki Matsuura, Tetsuya Yomo. (2010) Cellular compartment model for exploring the effect of the lipidic membrane on the kinetics of encapsulated biochemical reactions. Langmuir, 26(11), 8544-8551.
  13. Nishimura, K., Hosoi, T., Sunami, T., Toyota, T., Fujinami, M., Oguma, K., Matsuura, T., Suzuki, H., and Yomo, T. (2009) Population analysis of structural properties of giant liposomes by flow cytometry. Langmuir, 25(18), 10439-10443.
  14. Hosoda, K., Sunami, T., Kazuta, Y., Matsuura,T., Suzuki, H., and Yomo, T. (2008) Quantitative study of the structure of multilamellar giant liposomes as a container of protein synthesis reaction. Langmuir, 24 (23),13540-13548.
  15. Ichihashi, N., Matsuura, T., Kita, H., Hosoda, K., Sunami, T., Tsukada, K., and Yomo, T. (2008) Importance of translation-replication balance for efficient replication by the self-encoded replicase ChemBioChem, 9 (18),3023-3028.
  16. Kita, H., Matsuura, T., Sunami, T., Hosoda, K., Ichihashi, N., Tsukada, K., Urabe, I., and Yomo T. (2008) Replication of genetic information with self-encoded replicase in liposomes. ChemBioChem, 9 (15),2403-2410.
  17. Sunami, T., Sato, K., Matsuura, T., Tsukada, K., Urabe, I. and Yomo,T. (2006) Femtoliter compartment in liposomes for in vitro selection of proteins. Anal. Biochem., 357,128-136.

津留グループ

  1. Rebecca Baumstark, Sonja H?nzelmann, Saburo Tsuru, Yolanda Schaerli, Mirko Francesconi, Francesco M. Mancuso, Robert Castelo & Mark Isalan.(2015) The propagation of perturbations in rewired bacterial gene networks. Nature Communications,6,10105.
  2. Tsuru S, Ishizawa Y, Shibai A, Takahashi Y, Motooka D, Nakamura S, Yomo T.(2015) Genomic confirmation of nutrient-dependent mutability of mutators in Escherichia coli. Genes to Cells,20(12),972-981.
  3. Ying BW, Honda T, Tsuru S, Seno S, Matsuda H, Kazuta Y, Yomo T.(2015) Evolutionary Consequence of a Trade-Off between Growth and Maintenance along with Ribosomal Damages. PLOS ONE,10(8),e0135639.
  4. Kishimoto T, Ying BW, Tsuru S, Iijima L, Suzuki S, Hashimoto T, Oyake A, Kobayashi H, Someya Y, Narisawa D, Yomo T.(2015) Molecular Clock of Neutral Mutations in a Fitness-Increasing Evolutionary Process. Journal of Theoretical Biology,11(7),e1005392.
  5. Yoshie Murakami,Yuki Matsumoto, Saburo Tsuru, Bei-Wen Ying,Tetsuya Yomo.(2014) Global coordination in adaptation to gene rewiring. Nucleic Acids Research,42(2),1304-1316.
  6. Yoshida Mari, Tsuru Saburo, Hirata Naoko, Seno Shigeto,Matsuda Hideo, Ying Bei-Wen, Yomo Tetsuya.(2014) Directed evolution of cell size in Escherichia coli. BMC Evolutionary Biology,14(257).
  7. Ishizawa Y, Ying BW, Tsuru S, Yomo T.(2014) Nutrient-dependent growth defects and mutability of mutators in Escherichia coli. Genes Cells.,20(1),68-76.
  8. Nishimura K, Tsuru S, Suzuki H, Yomo T.(2014) Stochasticity in gene expression in a cell-sized compartment. ACS Synth. Biol.,4(5),566-576.
  9. Atsushi Shibai, Saburo Tsuru, Bei-Wen Ying, Daisuke Motooka, Kazuyoshi Gotoh, Shota Nakamura and Tetsuya Yomo.(2014) Mutation accumulation in bacteria exposed to UV radiation. Artificial Life 14 ,88,11459-114688.
  10. Yuya Akeno, Bei-Wen Ying, Saburo Tsuru, Tetsuya Yomo.(2014) A reduced genome decreases the host carrying capacity for foreign DNA. Microbial Cell Factories 2014,13(49),1-9.
  11. Bei-Wen Ying, Saburo Tsuru, Shigeto Seno, Hideo Matsudab, Tetsuya Yomo.(2014) Gene expression scaled by distance to the genome replication site. Mol. BioSyst.,10,(3),375-379.
  12. Yuki Matsumoto, Yoshie Murakami, Saburo Tsuru, Bei-Wen Ying, Tetsuya Yomo.(2013) Growth rate-coordinated transcriptome reorganization in bacteria. BMC Genomics 2013.,14(808),1-10.
  13. YukiMatsumoto, Yoichiro Ito, Saburo Tsuru, Bei-Wen Ying, Tetsuya Yomo.(2011) Bacterial Cells Carrying Synthetic Dual-Function Operon Survived Starvation. Journal of Biomedicine and Biotechnology.,2011,1-10.
  14. Yoshihiro Shimizu, Saburo Tsuru, Yoichiro Ito, Bei-Wen Ying, Tetsuya Yomo.(2011) Stochastic Switching Induced Adaptation in a Starved Escherichia coli Population. PLoS ONE.,6(9),e23953.
  15. Saburo Tsuru, Nao Yasuda, Yoshie Murakami, Junya Ushioda, Akiko Kashiwagi, Shingo Suzuki, Kotaro Mori, Bei-Wen Ying, Tetsuya Yomo.(2011) Adaption by stochastic switching of a monostable genetic circuit in Escherichia coil. Molecular Systems Biology.,7(493),1-10.
  16. Tsuru, S., Ichinose, J., Kashiwagi, A., Ying, B-W., Kaneko, K., and Yomo, T. (2009) Noisy cell growth rate leads to fluctuating protein concentration in bacteria. Physical Biology, 6(3),036015.
  17. Kashiwagi, A., Sakurai, T., Tsuru, S., Ying, B-W., Mori, K., and Yomo, T. (2009) Construction of Escherichia coli gene expression level perturbation collection. Metabolic Engineering,11(1),56-63.