Professor Yasushi Okada’s lab at the University of Tokyo

by Hunter Liu

This summer, through the University of Tokyo Research Internship Program, I interned for six weeks in Professor Yasushi Okada’s lab at the University of Tokyo. Under the supervision of my mentor, Assistant Professor Takanobu Katoh, I investigated the localization patterns of a specific protein, polycistin-2 (Pkd2), within the primary cilia of various cell types and how those patterns change upon the addition of a specific morphogen.

Pkd2 was originally discovered as one of the genes that cause autosomal dominant polycystic kidney disease (ADPKD), but researchers are still uncovering its functions today. In the primary cilium, a non-motile appendage protruding from certain cell types that are not actively dividing, the Pkd2 protein combines with other proteins to form a sensor that detects fluid flow across the cell. This sensor affects many important processes within humans and other vertebrates, ranging from calcium homeostasis within cells to the breaking of left-right symmetry within mammalian embryos.

Determining where Pkd2 localizes within the cilium is crucial to understanding its mechanism of action. However, until a few years ago, without nanometer-level optical resolution, studying Pkd2’s localization patterns was nearly impossible. Now, with super-resolution microscopy, we can finally observe these patterns.

I spent the first several weeks optimizing cell culture conditions for microscopy observation, trying to find the optimal conditions for growing and observing cilia. While superficially straightforward, this task proved to be nontrivial. I eventually discovered that cilia grew on the cell lines I was using only after several days at full confluency, aided by a specific cell coating. While experimenting with various cell culture conditions, I also optimized the immunostaining procedure and practiced sample observation via the confocal microscope.

Once I had developed a reasonable workflow, I began observing samples via a stimulated emission-depletion (STED) microscope that would provide resolution down to 40 nanometers. I completed several experimental runs, scanned my samples, and analyzed the raw data to determine whether Pkd2 localized to a specific side of the cilium.

Unfortunately, it was difficult to obtain any statistically rigorous conclusions regarding Pkd2 localization patterns due to software issues with the STED microscope, but my results will inform my mentor’s future work in this area. Additionally, my mentor provided a healthy balance of independence and guidance, enabling me to grow in my ability and confidence to conduct research experiments independently.

I had an amazing experience within my lab, but I learned at least as much outside of it. This was my first time coming to Japan, and initially it wasn’t easy despite having taken some Japanese language courses. Finding specific toiletries and ordering from a menu with unfamiliar dishes were some of the interesting challenges I tackled.

However, as I acclimated to Japanese culture, I grew to appreciate it. I felt Tokyo’s pulse at the Shibuya Crossing, tried a few delicious restaurants at Shinjuku, visited nine-story shops in Akihabara and Ginza, and tasted some of the freshest seafood I’ve ever had at the Tsukiji fish market. I was also fortunate enough to travel via the shinkansen to Kyoto for a weekend and attend the Gion Matsuri.

These attractions are what Tokyo, and Japan in general, are known for. They paint Tokyo and Japan in terms not entirely inaccurate: a bustling land with flashy culture, ultramodern technology, and unimaginable convenience. But Tokyo and Japan are far more than that. Every day I took a new route going to and from my lab, and as a result I chanced upon delicious hole- in-the-wall restaurants and a historic well. While exploring the massive and tranquil Shinjuku Gyōen, a park ranger and I exchanged our surprise at seeing a group of rhinoceros beetles in broad daylight. In Kyoto, because my friend and I decided impromptu to trek down the backside of a mountain instead of returning to the attraction we went there for, we experienced a beautiful sunset overlooking Kyoto. I cherished these small moments because they were a glimpse into the less obvious parts of Japan and Japanese culture; those that are understated, insulated from the hustle and bustle, and/or dependent upon heavier effort.

Above all else, the true highlight of my time in Japan was the amazing people I got to meet. My research mentors tolerated my broken Japanese and strove to comprehensively answer my questions despite the language barrier. The owner of one restaurant in Kyoto offered us her delicious tea for free, and even tried to gift us her umbrellas. My friends in my lab and program exposed me to perspectives from around the world.

I am glad that I participated in the UTRIP program and grateful to the Okada lab, UTRIP, and FUTI for making all this possible. My six weeks in Japan changed the way I look at the world, and I’ll treasure the pictures and memories I made in Japan for the rest of my life.