Microbial Systems Biology Group
Computing Applications and Research / Chemistry, Material, Life science Department
Lawrence Livermore National Laboratory
P.O.Box 808, L-452
Livermore, California, 94551
tamura2@llnl·gov or makio323@hotmail·com (please replace "·" with ".")
925-424-3845 (office), 312-498-3321 (cell)
Microbes are tiny creatures, but have made big impacts on the earth environment. Since the surface of this planet was covered by rocks, metals, salts, or other inorganic materials, microbes have produced various organic compounds and some microbes also exhaust oxygen though their energy producing processes. Oxygen is a very active molecule and actually a poison gas for many creatures. Once upon a time, ancient creatures faced to a very serious pollutant air problem of oxygen. Interestingly, some microbe also found a way to use the oxygen for producing energy. Our cells include the descendent of the savvy microbe, mitochondria. Now, we are facing many other environmental problems caused by our activities.
Let's microbes do something useful for us.
Technologies enable us to access a kernel of microbe, Genome, and it seems that we are encouraged to read hidden-wisdoms written there. It is hard to understand words of the DNA sequence, but that is what I am trying to do. Decoding the DNA sequence would give us ways to use microbes for solving many serious environmental problems.
I have a PhD in bioengineering and a MS in computer science, but the order is reversed.
I recently received the MS degree from the University of Illinois at Chicago (2006 July). Before going back to the UIC, I had worked on bioinformatics research about RNA structure at the Dr. Stephen R. Holbrook Lab, Computational and Theoretical Biology Group, Physical Biosciences Division, Lawrence Berkeley National Laboratory (LBL) as a postdoctoral fellow for three years. I received a doctoral degree in Bioengineering in March 2001 from the Tokyo Institute of Technology, Japan.
Our knowledge of the structure-function and structure-interaction relationships of biomolecules, such as light harvesting antenna, RNA, DNA or proteins, has been dramatically expanded. However, this information is rather specific for each case. A biomolecule is interacted with another one. These interacted biomolecules are also interacted with some other biomolecules and overall interactions form a complicated network. The comprehensive understanding of this interaction network in living organisms still remains very limited. In other words, we can take a machine apart into its components, but we do not know how to put the components back together. We need more experiments to accumulate the relevant knowledge, but at the same time, we need to understand the principle of this network in living organisms. With the idea that knowledge of mathematical and computer science could give me other hints to address this problem, I decided to enroll the computer science graduate program. I am very happy to say that learning the machine learning theories at the grad school was the fruitful and very exciting period.
My master project was for missing value estimation in matrix data supervised by Prof. Shmuel Friedland. It was very fun and exciting experience to work with the mathematical acrobat.
The first postdoctoral research at LBNL was a study of RNA structure and tertiary interactions. RNA is traditionally thought to act as transcription-mediator from DNA to protein, but RNA as transcription-controller have been also found recent years. However, even though these RNA structures had been determined rapidly with technological improvement, the understanding of structure-function relationships was limited. As a consequence of this, we developed a database of Structural Classification of RNA called SCOR under supervised by Prof Steven E Brenner and Dr. Stephen R. Holbrook.
My doctoral thesis research was a study of an artificial light harvesting antenna. Light harvesting antenna is very organized biomolecular complex. Each component is connected by weak interactions, but they can gather automatically under appropriate condition and then form the highly ordered complex. I used this self-assembly phenomena to synthesize artificial antennas, but their energy harvesting efficiency is far less than that in nature. I was even fascinated with well designed biomolecular structure and its interactions during the research.
I believe that a happiness is to find what we were given to give to others who need it, and then to practice it, and hope that Science is the way for me to get the happiness.