by Gulnara Fayzulina

At UTokyo

This past summer I have participated in University of Tokyo Research Internship Program (UTRIP). For six weeks, I got an opportunity to live in Japan and to do research in Dr. Kuroda’s Laboratory at the University of Tokyo. Dr. Kuroda’s Laboratory, part of the Biophysics and Biochemistry department in Graduate School of Sciences, works on research in the field of Systems Biology, which is an emerging field that incorporates an interdisciplinary approach to study biological systems holistically combining experimental data with mathematical modeling.

At a garden

The complexity that requires mathematical models and computer simulations to keep track of arises from the fact that communication from the surface of the cell down to the DNA in the nucleus is carried out by myriad of proteins, which form signal transduction pathways. The complex networks of signaling pathways regulate a number of cellular functions such as gene expression, enzyme activity, and ion channel-activity. Dr. Kuroda’s Laboratory works to understand how signal transduction pathways regulate cell-fate determination, synaptic plasticity, and insulin action, and how information is propagated by the pathways.

At a temple

In the first week and a half of the program, the professors gave us morning lectures, introducing us to their research. I found these lectures to be incredibly informative; as I learned about fields of science I didn’t know anything about and the current hot topics in science. From the lectures I learned about why earth quakes occur and the challenges to tsunami warning system, the history of green fluorescent protein (GFP), graphene, and much more. Meanwhile, in the laboratory for the first two weeks, each laboratory member talked to me individually, introducing his research to me. In addition, Dr. Kuroda’s Laboratory taught a week long introductory summer class to Systems Biology for third year undergraduate students. I attended the class and thanks to graduate students willing to translate for me, I was able to keep up and gained more experience with mathematical modeling.


In my research project I studied the activation mechanisms of extracellular signal-regulated kinase (ERK), a key protein in cell fate decision. Sustained ERK activation leads to cell differentiation, while transient ERK activation leads to cell proliferation. Extracellular stimulation by Endothelial Growth Factor (EGF) triggers transient ERK activation, because EGF stimuli activate EGF receptors, which in turn activate a fast ERK activation pathway, while activating a slow ERK inhibitory pathway. As part of my research I have created a simple mathematical model to simulate ERK activation by EGF. An experiment was first carried out using Western Blotting, and the model parameters were fit to the experimental data. Then using my model, I did various simulations to find out that a certain temporal pattern of EGF stimuli produced sustained ERK activation, which was quite counterintuitive, as it has been thought EGF only produces the transient ERK activation. To translate the simulation to practice, I stimulated cells every five minutes within an hour, and then lysed them at the time points for which I wanted to collect data. In my experiment, I observed twenty minute sustained ERK activation using EGF.
This summer, for the first time, I performed laboratory experiments. I learned how to handle cells and how to do Western Blotting, a popular method in biology used to detect protein presence in cells. At the end, I made a presentation on my research topic, and will be submitting a research report.

Boat ride

UTRIP is a great program. Not only did I learn more about science, but I learned more about Japan. UTRIP organized cultural activities for us, where we got a chance to practice calligraphy and Japanese flute, Shakuhachi. Even though, I wasn’t able to get my flute to produce much sound, it has been fun to try a new instrument. In addition, UTRIP sponsored a field trip to world heritage site Nikko and University of Tokyo Botanic Gardens. On the weekends, I got a chance to explore Tokyo and even take a trip to Hakone and Niigata. I was blown away by the beauty of the countryside in Japan. Also, I got to meet amazing new people who just like me by incredible chance came to Japan this summer through UTRIP. And talking in Japanese to the graduate students in my lab has helped improved my Japanese conversation skills and make friends.

With fellow UTRIP participant Olivia Waring

Ever since I studied abroad in Japan in high school, I enjoyed learning about Japan and its culture, and I hoped that one day I could go back. Coming back to a country where I have spent one year that has had a profound effect on me has led me to look back on my memories in Japan and then look forward to the new memories I will make. Seeing new places, meeting new people, learning new things has led my thoughts to new ideas, opening me up to new interests and new possibilities.
UTRIP has been really special experience to me, as it combined both my research interests and my interest in Japan, to make one unforgettable summer. Thank you Friends of UTokyo, Inc., as this wonderful experience would have never happened without you.