Laboratory for Synthetic Biology

By current progresses in molecular biology and genome science, huge information about biological systems, such like constituent biological molecules and molecular network structures, has been dramatically accumulated, and paradigm sift in biological research from reductionistic to synthetic approach has been undertaken in recent years. Even though the synthetic approach has been acknowledged as a central strategy of life science over the next few decades, basic technologies required in the synthetic approach, such like designing, controlling and manipulating biological molecules (DNAs, proteins and lipids) is remained to be established. The main tasks for laboratory for synthetic biology are to develop basic technologies for synthetic biology through close collaborative study within this center and to present pioneer studies in this new field.

Research Subjects

• Design of chemicals controlling proteins and proteins with novel functions based on the dynamics
• Design of molecular interactions in circadian clocks
• Development of high-throughput genome engineering system
• Gene synthesis for the design and construction of biological systems
• Design and measurement of protein network dynamics at a single-cell level

Publications

1. Jolley CC, Ode KL, Ueda HR.:
   "A design principle for a posttranslational biochemical oscillator "
   Cell Reports 2012 Oct 25;2(4):938-50 (2012)
2. Kasukawa T, Sugimoto M, Hida A, Minami Y, Mori M, Honma S, Honma K, Mishima K, Soga T, Ueda HR.:
   "Human blood metabolite timetable indicates internal body time "
   PNAS 109(37):15036-41 (2012)
3. Takeya Kasukawa, Koh-hei Masumoto, Itoshi Nikaido, Mamoru Nagano, Kenichiro D. Uno, Kaori Tsujino, Carina Hanashima, Yasufumi Shigeyoshi, Hiroki R. Ueda.:
   "Quantitative expression profile of distinct functional regions in the adult mouse brain "
   PLoS ONE 6(8), e23228 (2011)
4. Koyama, Y.M., Kobayashi, T.J., Ueda, H.R.:
   "Perturbation analyses of intermolecular interactions"
   Phys. Rev. E 84, 026704 (2011)
5. Ukai-Tadenuma, M., Yamada, R.G., Xu, H., Ripperger, J.A., Liu, A.C., Ueda, H.R.:
   "Delay in Feedback Repression by Cryptochrome 1 Is Required for Circadian Clock Function."
   Cell,144, 268-281 (2011)
6. Isojima, Y., Nakajima, M., Ukai, H., Fujishima, H., Yamada, R.G., Masumoto, K., Kiuchi, R., Ishida, M., Ukai-Tadenuma, M., Minami, Y., Kito, R., Nakao, K., Kishimoto, W., Yoo, S.H., Shimomura, K., Takao, T., Takano, A., Kojima, T., Nagai, K., Sakaki, Y.,, Takahashi JS, Ueda, HR.:
   "CKI ε/δ-dependent phosphorylation is a temperature-insensitive, period-determining process in the mammalian circadian clock."
   Proc. Natl. Acad. Sci. U.S.A. 106 (37), 15744-15749 (2009)
7. Koyama, Y.M., Kobayashi, T.J., Tomoda, S., Ueda, H.R.:
   "Perturbational formulation of principal component analysis in molecular dynamics simulation."
   Phys. Rev. E 78, 046702 (2008).
8. Ukai-Tadenuma, M., Kasukawa, T., Ueda, H.R.:
   "Proof-by-synthesis of the transcriptional logic of mammalian circadian clocks."
   Nat. Cell Biol. 10, 1154-1163 (2008)
9. Kumaki, Y., Ukai-Tadenuma, M., Uno, K.D., Nishio, J., Masumoto, K., Nagano, M., Komori, T., Shigeyoshi, Y., Hogenesch, J.B., Ueda, H.R.:
   "Analysis and synthesis of high-amplitude Cis-elements in the mammalian circadian clock."
   Proc. Natl. Acad. Sci. U.S.A. 105 (39), 14946-14951 (2008)
10. Ukai, H., Kobayashi, T.J., Nagano, M., Masumoto, K., Sujino, M., Kondo, T., Yagita, K., Shigeyoshi, Y., Ueda, H.R.:
    "Melanopsin-dependent photo-perturbation reveals desynchronization underlying the singularity of mammalian circadian clocks."
    Nat. Cell Biol. 9 (11), 1327-34 (2007)

Organization