FUTI Report

Chung-an Max Wu

Group Photo

Group Photo


This summer, I participated in the University of Tokyo Summer Internship Program (UTSIP). For 4 weeks, I had the opportunity to live in Japan and conduct research in the lab of Prof. Takuya Ueda, in the Department of Medical Genome Sciences.
Prof. Ueda’s lab specializes in the emerging field of synthetic biology, which aims to build de novo biochemically active systems – the ultimate goal being an artificial cellular life form. There are two broad approaches toward this goal, genetic and biochemical. The genetic approach relies on inserting user-defined genetic elements into an “empty” membrane-enclosed structure and allowing this artificial “cell” to build itself up. On the other hand, the biochemical approach aims to synthesize all protein components necessary for cellular life from scratch and then combine them together to form an artificial cell. In 2001, Prof. Ueda’s lab reported the first successful in vitro re-constitution of the entire protein translation machinery of Escherichia coli; this yields biochemical extract that takes user-defined DNA as its input and produces the desired protein product as its output. With this system, termed PURE (protein synthesis using recombinant elements), one can theoretically produce any protein of interest, a major step toward the goal of making an artificial cell. During my stay, I utilized the PURE system to try and engineer an artificial bioreactor that can respond to environmental stimulus.
With lab in Nasu

With lab in Nasu


Cells can control protein production is through inducible systems, where some soluble factor of external or internal origin stimulates or inhibits protein synthesis. One such system that has found common use in molecular biology is the LacI/IPTG on-off switch. Synthesis of a protein under the control of the LacO operator sequence is normally inhibited by the protein LacI; however, in the presence of the soluble compound IPTG, LacI inhibition is lifted and protein synthesis proceeds. If this entire system is placed in a biochemically controlled environment, such as the interior of a liposome, this yields an artificial bioreactor where a protein of interest can be switched on or off by presence or absence of IPTG in its surrounding environment.
Our first challenge was to determine if IPTG could pass spontaneously through the membranes of liposomes. We observed that although IPTG could cross membranes spontaneously, protein productivity in such a system was extremely low, necessitating the use of some channel protein to promote IPTG entry into liposomes. We investigated the use of alpha-hemolysin, a bacterial toxin that forms non-specific pores in membranes, and LacY, a protein that selectively transports IPTG across membranes. LacY expression did not increase IPTG permeability, most likely due to LacY protein misfolding within the liposomes and being unable to localize to the membrane. Alpha-hemolysin also did not increase IPTG permeability, but we observed localization to liposome membranes, both by radiolabeling and fluorescent confocal microscopy. Ultimately, the goal of this project would be to generate liposomes capable of quorum sensing, where the protein under inducible control also acts as the expression-inducing molecule itself. This is seen in nature when populations of cells change their gene expression based on local cell density.
With lab members

With lab members


In addition to bench research, UTSIP professors also gave lectures introducing their research. Topics varied as widely as evolutionary biology and materials science, and it was a great opportunity to see how vast the scope of research being conducted at UT Kashiwa is; it was clear that the Graduate School of Frontier Sciences lived up to its name. UTSIP also organized several trips for all the summer interns, such as to see the Toshogu mausoleum in Nikko or to watch kabuki in the Tokyo National Theatre. Through both cultural and academic experiences provided by UTSIP, my stay in Japan was extremely fulfilling. It was also very enjoyable getting to know the members of my lab. They were all very welcoming and eager to both learn about other cultures and teach me about their own. One of my major goals in coming to Japan had been to work on my conversational abilities, and I was definitely able to improve by spending time with lab members both in and out of school. Living in Japan has given me an appreciation for different cultures and helped me make many new friends.
Thank you UTSIP and FUTI for this immersive and incredible opportunity.

This summer, I participated in the University of Tokyo Summer Internship Program (UTSIP). For 4 weeks, I had the opportunity to live in Japan and conduct research in the lab of Prof. Takuya Ueda, in the Department of Medical Genome Sciences.

Prof. Ueda’s lab specializes in the emerging field of synthetic biology, which aims to build de novo biochemically active systems – the ultimate goal being an artificial cellular life form. There are two broad approaches toward this goal, genetic and biochemical. The genetic approach relies on inserting user-defined genetic elements into an “empty” membrane-enclosed structure and allowing this artificial “cell” to build itself up. On the other hand, the biochemical approach aims to synthesize all protein components necessary for cellular life from scratch and then combine them together to form an artificial cell. In 2001, Prof. Ueda’s lab reported the first successful in vitro re-constitution of the entire protein translation machinery of Escherichia coli; this yields biochemical extract that takes user-defined DNA as its input and produces the desired protein product as its output. With this system, termed PURE (protein synthesis using recombinant elements), one can theoretically produce any protein of interest, a major step toward the goal of making an artificial cell. During my stay, I utilized the PURE system to try and engineer an artificial bioreactor that can respond to environmental stimulus.

Cells can control protein production is through inducible systems, where some soluble factor of external or internal origin stimulates or inhibits protein synthesis. One such system that has found common use in molecular biology is the LacI/IPTG on-off switch. Synthesis of a protein under the control of the LacO operator sequence is normally inhibited by the protein LacI; however, in the presence of the soluble compound IPTG, LacI inhibition is lifted and protein synthesis proceeds. If this entire system is placed in a biochemically controlled environment, such as the interior of a liposome, this yields an artificial bioreactor where a protein of interest can be switched on or off by presence or absence of IPTG in its surrounding environment.

Our first challenge was to determine if IPTG could pass spontaneously through the membranes of liposomes. We observed that although IPTG could cross membranes spontaneously, protein productivity in such a system was extremely low, necessitating the use of some channel protein to promote IPTG entry into liposomes. We investigated the use of alpha-hemolysin, a bacterial toxin that forms non-specific pores in membranes, and LacY, a protein that selectively transports IPTG across membranes. LacY expression did not increase IPTG permeability, most likely due to LacY protein misfolding within the liposomes and being unable to localize to the membrane. Alpha-hemolysin also did not increase IPTG permeability, but we observed localization to liposome membranes, both by radiolabeling and fluorescent confocal microscopy. Ultimately, the goal of this project would be to generate liposomes capable of quorum sensing, where the protein under inducible control also acts as the expression-inducing molecule itself. This is seen in nature when populations of cells change their gene expression based on local cell density.

In addition to bench research, UTSIP professors also gave lectures introducing their research. Topics varied as widely as evolutionary biology and materials science, and it was a great opportunity to see how vast the scope of research being conducted at UT Kashiwa is; it was clear that the Graduate School of Frontier Sciences lived up to its name. UTSIP also organized several trips for all the summer interns, such as to see the Toshogu mausoleum in Nikko or to watch kabuki in the Tokyo National Theatre. Through both cultural and academic experiences provided by UTSIP, my stay in Japan was extremely fulfilling. It was also very enjoyable getting to know the members of my lab. They were all very welcoming and eager to both learn about other cultures and teach me about their own. One of my major goals in coming to Japan had been to work on my conversational abilities, and I was definitely able to improve by spending time with lab members both in and out of school. Living in Japan has given me an appreciation for different cultures and helped me make many new friends.

Thank you UTSIP and FUTI for this immersive and incredible opportunity.

With lab in Nasu

Group photo

With lab members