Tetsuro Toyoda

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Toyoda, Tetsuro

Tetsuro Toyoda was born in Tokyo, Japan, in 1968. He graduated from the Faculty of Pharmaceutical Sciences at the University of Tokyo in 1992, and obtained his PhD in 1997 from the same university. He started as a researcher at the Institute of Medical Molecular Design in 1997, and joined RIKEN as team leader in the Genomic Sciences Center in 2001. He became director of the RIKEN Bioinformatics and Systems Engineering Division when it was established in 2008.

His expertise is in bioinformatics and computer-aided rational design of biomolecules, including rational database-supported drug design based on protein structural information and rational genome design in synthetic biology for biomass engineering. He promotes Japan’s database integration projects as a member of several national database committees.

Thu July 11 | 2:00 - 4:00 | Parallel Session

Biological engineering problems require innovative DNA designs. Once a DNA design problem has been defined, crowd innovation can be harnessed to explore solutions. We proposed the problem of formaldehyde detoxification in Arabidopsis thaliana, based on known enzymatic pathways from other organisms. In GenoCon, the first international rational genomic design contest, contestants designed DNA to introduce these pathways by codon optimization and addition of various cellular localization tags. As a competition, GenoCon presents challenges for rational design of DNA sequences to enhance plant physiology, using public data, followed by outsourcing experimental synthesis and biological assays. Participants designed DNA sequences on our system: a web-based platform for sharing life science data along with a scripting interface for DNA design. Outsourcees of experiments synthesize the designed DNA sequences, transform the DNA into Arabidopsis thaliana, and assay the function: in this case growth tolerance to formaldehyde. We quantitatively analyze the growth in the presence of formaldehyde; this analytical process deeply depends on the expertise of the physiology of interest and requires collaboration among physiological specialists and informaticians. GenoCon also educates young scientists as genome design specialists, and as a web bioinformatics activity, no time consuming and expensive experiments are needed to participate. This first GenoCon challenge had 66 entries including eight high school students. The designs used three different synthetic pathways and varied the cellular location of each enzyme with protein localization tags directing to the chloroplasts, the mitochondria, and the endoplasmic reticulum. Five designs including two high school students were selected as finalists. We assayed the performance of the designs, and found several that displayed dramatic formaldehyde tolerance at intermediate formaldehyde levels.