2017 Kaylene Stocking

Kaylene Caswell Stocking
Home University: University of Pittsburgh
Field of Study: Computer Engineering and Bioengineering
Current Status: Sophomore
Expected Graduation Date: Spring 2019
Host Lab in Japan: Kyoto University – Institute for Integrated Cell-Materials Sciences (iCeMS), Kamei Laboratory

Why Nakatani RIES?

This program combines two things that are very important to me – research and understanding other cultures. I have very deep reserves of curiosity about nearly everything, from how computers work to why neurons allow us to think to the history of music. Normally I’m torn between all of the things I want to learn about, but Nakatani RIES gives me the fantastic opportunity to both conduct research in a new field and learn about the inner workings of a culture very different from my own. Furthermore, I will have the opportunity to learn how to collaborate with international research teams, which I think is critical for the advancement of science and engineering in the modern age. In my career in science I want to be able to reach out to others doing similar work, even if they’re from other countries and cultures. I also think living independently abroad in a very different culture will be an incredible experience that will cause me to grow as an individual.

The opportunity to complete a research project in Japan is especially amazing to me because I’ve been fascinated with Japanese culture for a long time. The movies of Hayao Miyazaki and books like Miyuki Miyabe’s Brave Story left a huge impression on me as a child, and as I grew older I became more interested in the country and culture that produced them. To me, Japan seems like a place where ancient tradition is incorporated into modern innovation instead of conflicting with it. I’m very excited to see both ancient temples and huge, high-tech cities. I will get to see Japan with my own eyes, not just as a tourist but as someone who lives and works there (if only for a short time!).

Goals for the Summer

  • Complete a research project that allows me to apply the knowledge and skills I have gained so far to generate something new, as well as deepen my understanding of a new area of research
  • Learn how to live independently in a culture very different from my own
  • Be able to communicate in Japanese and actively seek to converse with others
  • Visit many different Japanese cultural sites, both ancient and modern, to deepen my appreciation of Japanese art and culture
  • Try as many different kinds of food as possible!

Excerpts from Kaylene’s Weekly Reports

Week 01: Arrival in Japan

Traveling from Narita Airport to Tokyo, the first thing that struck me was how green and peaceful everything was. There were trees and rice paddies surrounding the airport, and traffic was fairly light. As we got closer to Tokyo, high-rise apartment buildings began to appear, and finally the city proper was spread out before us. There’s no doubt it’s huge and busy and impressive here, but that first impression of peaceful green fields hasn’t entirely disappeared. It’s not so much a specific trait as it is a collection of little things: people wait for the light to change to cross the street even when no cars are nearby. No one litters. Shopkeepers leave their wares out on the street in perfect confidence that no one would even consider taking something without paying. Tiny produce stores run out of houses are everywhere, with attractively packaged tomatoes and oranges in neat rows. Bright white vending machines with rows of colorful drinks are on every street corner. Shopkeepers are genuinely friendly and seem to take pride in being polite and good at their jobs. And little shrines with bright red flags can be found even on busy streets.

Imperial Palace Gardens path: A small slice of what Tokyo looked like hundreds of years ago. ~ Kaylene Stocking

One of the things that fascinated me most about Japanese culture before I came here was how despite being packed into dense cities, Japanese people seem to feel an intense connection to nature. (There are countless examples of this, but you don’t need to look any further than a Miyazaki movie.) Now that I’m here, I think I understand a bit better. Tokyo is filled with plants. It puts even my home city of Seattle, where trees grow like weeds, to shame. In residential areas, each tiny apartment has at least a couple of flowering vines, and in all but the densest commercial districts, trees line the streets. Parks sport lush miniature forests with huge old trees. Despite all of the pavement and skyscrapers, it’s easy to tell that Tokyo used to be a forest, and would happily return if left to its own devices.

Something else that has surprised me is how little English is spoken here. In a country where everyone is required to take English for several years, I assumed many would be eager to get some practice with the local foreigner. (I certainly do this to any French speakers unlucky enough to come across my path in the states.) Furthermore, English words are everywhere in Japan, which prefers borrowing words to making up new ones for any new item. But contrary to my expectations, I’ve only been spoken to in English a couple of times in the past week. Even then, it was only by shopkeepers hoping to attract tourist money. In a way I’m happy about this, because it means I have to try to fake it with my very rough Japanese. But I’m very confused as to why Japanese people invest so much time in learning a language that most don’t seem to have any desire to use. Do many people here resent spending so much time on English? Do they make any attempt to use it after they graduate from school?

The view from my hotel room: Even next to skyscrapers, the forest peeks through. ~ Kaylene Stocking

Speaking of language learning, I can already tell that my Japanese speaking ability has improved a lot over the last week. Before this program, I had never taken a formal Japanese class and had never tried to speak Japanese. In classes here we are encouraged to say everything we can in Japanese, and I’m steadily getting to the point where I can communicate what I want to, albeit slowly and with lots of grammatical mistakes. My knowledge of kanji is also improving from context and food labels, and I’ve gotten a lot faster at reading kana. However, I’m not as pleased with my progress in listening. Even after being immersed in Japanese for a week and 17.5 hours of class, I still have no idea what people around me on the street are saying. A week isn’t a very long time, but I guess I hoped that immersion would speed things up a little more. My goal for the next week is to start talking more to shopkeepers and other people I interact with, so that I can continue to get as much practice as possible.

The Intro to Japanese Culture and Society seminars and outings have been interesting, but as I read about Japan quite a bit (read: obsessively) before coming here, most of the information hasn’t been new. The presentations by Ogawa-san and Gibbs-sensei were the most helpful. Gibbs-sensei gave some very good advice for fitting in here, including watching NHK on TV (very correct, standard Japanese) and finding a speaking partner of your own age group and gender so you speak appropriately. I’m not happy about the large difference in speaking styles between genders, but for now I just want to fit in and speak as well as possible. As for activities, I enjoyed going to the Edo-Tokyo Museum. My favorite part was the Edo-era bookstore and a display on how Ukiyo-e prints were made. Sumo wrestling was also fun to watch, even though I had no idea what was going on or who to root for.

Overall, I’ve had an incredible time in Japan over the past week. I still can’t believe how fortunate I am to be given this opportunity, and I want to make every moment of it count. One week is already over, but it was packed with new sights and experiences and I don’t have any regrets. Here’s hoping for another amazing week!

Research Project Update
There have been lots of interesting research-related activities during the first week in Japan. The site visit to Tokyo University’s extremely sophisticated labs was very cool, but unfortunately I had a difficult time understanding what the often soft-spoken professors were saying over the loud hum of the machines. Nishikawa-sensei gave a lecture on Friday about “Life science as a major agenda for the 21st century.” He examined the development of life science from an information science perspective, which was new to me and quite interesting. He finished his talk by discussing and comparing the emergence of life on Earth and the emergence of language in humans. I’ve never thought to draw this parallel before and I thought the comparison was interesting. Although I’ve read about the emergence of life, the emergence of language was new to me, and Nishikawa-sensei’s explanation of why it’s such a difficult topic to study was fascinating.

Question of the Week
I’ve noticed that Japanese people don’t seem to worry about theft at all, with many stores displaying products out front with no one watching over. Why is there such a culture of trust here, and why aren’t people tempted to steal? Is this changing at all as the number of foreign people in Tokyo increases?

Research Project Introduction & Article Overview
During the pre-departure orientation at Rice, we went over a lot of general safety training and some general guidelines for working in a Japanese lab. Surprisingly, my favorite part of this turned out to be one of the safety training sessions. I was the only one taking the biohazard training, and the guy who led it was clearly passionate about biology. We ended up geeking out about cool microorganisms as we went through the various guidelines. It reminded me of why I became interested in biology in the first place all the way back in junior high school. (On the off chance you’re reading this, thanks Mr. Davis!) Oddly enough, that safety training more than anything else has gotten me excited about the research I’m going to start in just two weeks.

As for the research itself, I don’t know much about what my project will be yet. However, after reading a few of Kamei-sensei’s papers I have a general idea of what topics he is pursuing. Kamei-sensei is part of Kyoto University’s Integrated Cell-Material Sciences Institute (ICEMS), which is a large institute with many professors that focuses on research uniting biomolecular and materials science research. Kamei-sensei’s research focuses on the best artificial environment for culturing stem cells, which fits in perfectly. Ultimately, he wants to create a “Body on a Chip,” which would allow researchers to recreate physiological conditions inside the human body on a tiny chip reminiscent of a circuit board. This would be valuable both in basic biological research and in drug trials, where initial screening could be done accurately without the use of animals. Ultimately, a system like this might be used to predict the response of an individual to a particular treatment. I’m very interested in this kind of research because I want to provide faster, safer, and more humane alternatives to animal testing in drug development. The first lab I worked in approached the problem from a computer simulation perspective, so I am excited to work on it again with a different approach.

In the next few paragraphs I am going to do my best to review a recent paper for which Kamei-sensei is a corresponding author. Its title is “Nano-on-micro fibrous extracellular matrices for scalable expansion of human ES/iPS cells.” This paper describes an artificial extracellular matrix for culturing human stem cells that enables the cells to be easily manipulated. Manipulating the cells is important so that they can be easily retrieved and used after culturing, an important step for clinical use of stem cells in therapy or drug testing. Furthermore, the newly developed matrix more closely mimics the ECM found in the human body, resulting in more realistic interactions between the cells and matrix.

Although the paper does not describe how the authors came up with the proposed artificial matrix, it does go into detail about how the matrix is made in the lab. It consists of nano-fiber and micro-fiber layers, which combine desirable properties of each to create a substance that is both stable and promotes cell adhesion. Cells were cultured on this matrix for seven days, and then a variety of experiments were done to determine how effective the matrix was. These included immunocytochemistry, reverse transcription, flow cytometry, embryoid body formation, and teratoma formation.

An experiment using fluorescent molecules showed that they easily diffused throughout the culture, meaning that the newly developed culture successfully allows easy manipulation of cells through diffusible agents such as hormones. Cells adhered to the matrix more strongly than an existing standard cell culture method, and the growth rate was similar. Furthermore, it was demonstrated that the method could be scaled up to culture a large number of cells in a space-efficient manner. At the end of the seven-day culture period, a large majority of the cells (>95%) were confirmed to be pluripotent as desired. When compared to the standard method, the new matrix produced a slightly smaller number of cells in the same volume of culture, but the percentage of dead cells was significantly lower, indicating a higher quality and more useful culture.

The paper concludes that the new culture matrix allows for large-scale culturing of high-quality hPSCs. It also notes that the method should be versatile and might be useful for culturing differentiated cell types as well. Overall, this paper represents an important step forward in stem cell culture methods. Although the matrix system describe in it is only an initial step, it already promises to be more effective than the standard method used. Further refinement in future research could allow for more significant improvements. Since the entire field of stem cell research could stand to benefit from better cell culture methods, this line of study could have a large impact.

Citation
dx.doi.org/10.1016/j.biomaterials.2017.01.039.

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Week 02: Language Learning and Trip to Mt. Fuji Lakes

It feels like it was just a couple days ago that I wrote my last report! I’ve gotten to have a lot of new experiences over the past week, but now that I’ve settled in, time seems to be going by much more quickly. Unfortunately, this extends to my language classes – I’d be hard pressed to say exactly how I’ve improved since last time. Meeting the Japanese Nakatani fellows (more on this later) has been wonderful, but it’s a little sad that I can only really communicate with them in English. It feels unfair to ask them to speak to me in my native language, especially since we’re in Japan. So, my new language goal is to talk to everyone in Japanese when we all meet again at the Mid-Program Meeting in five weeks. The largest barrier right now is listening, so I’m going to start making a greater effort to watch TV and listen to the radio in Japanese when I have free time. I know I can’t expect fluency in twelve weeks, but I want to make the most of my time here!

There have been some positive experiences with Japanese too, however. On Friday, my language teacher gave us two children’s books to read: the true story of Hachi the loyal dog, and a famous Japanese folk story called Momotarou. I really enjoyed the latter and was surprised at how well I could understand it. Being able to read Japanese is my ultimate goal, so this was really exciting! I’m going to try and track down some more books at a similar level so I can continue to improve. Another cool moment came during our trip to an aquarium on Sunday. Last Monday we went to the Earth Science Museum in Yokohama and learned about the research submarine called the Shinkai 6500. The name didn’t mean anything to me at the time, but at the aquarium I realized that shinkai meant deep ocean – “shin” is 深 -deep and “kai” Is 海 – sea. On paper, it doesn’t sound like much, but at the time I was thrilled to have made a new connection. And finally, we went to the AJALT offices on Tuesday and I was able to have a 40-minute conversation with a new teacher-in-training. She had to speak slowly and repeat things for me, but we almost never resorted to English words.

This week has been especially amazing for learning about Japanese culture. On Wednesday, we had a taiko drumming class in a soundproofed studio in Shibuya. Although the rhythms were simple, the power of the drums resonated throughout the room to make a sound much greater than the sum of its parts. After the class, the instructor gave a short performance on one of the larger, upright drums. He was an incredible musician, but what struck me most was the way he moved before playing a single note. It was as if the drum was a living thing and he needed to ask permission before he could use it.

Detail of a kimono at the Tokyo National Museum: Are kimono and other aspects of traditional Japanese culture fading away? ~ Kaylene Stocking

On Friday, I went to the Tokyo National Museum, a huge museum that has art pieces from throughout the history of Japan. I was impressed all over again with just how far back Japan’s memory goes. I can’t stop thinking about the fascinating balance this country strikes between tradition and innovation. Kento-san, who came to give us a talk about the history of kimono, said that many Japanese people don’t know their own culture very well, and that there is a strong divide between the old and the new. I was surprised to hear this, because my image of Japan is still of beautiful old shrines and parks tucked between skyscrapers. But now that I think about it, almost everyone at the museum was much older than me. I’d like to learn more about Japanese culture and how it is evolving with new generations during my time here.

Of course, the biggest experience with Japanese culture came this weekend, during the trip to Fuji-san and surrounding areas. The twelve Japanese Nakatani fellows were with us, and there were plenty of opportunities to talk with them about all kinds of subjects. Miki-san said that the biggest shock for her on the weekend trip was that so many of the other fellows are women (both US and Japanese fellows are split evenly between genders). Her university classes are only about 25% female. From there we discussed standards for women and how they are changing, and why so few women go into science. The Japanese fellows said that a large reason many women stop working once they marry is that child support is not very good in Japan, so it’s very difficult to raise children while working. I think this might also affect the subjects women choose to study in university: if you know you’re going to have to drop out of the workforce after a few years, why bother investing so much time and effort in a difficult degree? Another major problem is that the pay gap between men and women is very large in Japan. The Japanese fellows told me that this is changing, but that it’s very slow and difficult. Miki-san wants to raise children in a different country where it is possible to have a family but still maintain a good work-life balance.

Another cultural difference fascinated me during our stay at a hotel with an onsen (hot spring). Although Japanese people tend to dress much more conservatively than the Americans, they are much more comfortable than us being naked around their own gender. When I told the Japanese fellows I was nervous about going to the onsen, they thought I was afraid of the hot water! Although I enjoyed being in the onsen, I think the stress of being in the locker room before and after canceled out the relaxing effect of the water. The first time is probably the hardest though, so I would go again if I get a chance.

I could go on and on about the different things I saw and experienced over the weekend, but I’ll try to wrap up with just a few. Going up to the 5th station of Fuji-san, I was struck by all of the other people there just to take a few photos and buy some themed souvenirs from the shops. Climbing season hasn’t even started yet, so no one was actually hiking the mountain. Of course, we were doing the exact same thing. I’m grateful to the Nakatani Foundation for giving us a chance to see Japan’s most famous mountain up close, but I’m not used to driving to a place just to look around for an hour, and it was a confusing experience. The visits to lakes fed by Fuji-san streams and to a very impressive Shinto shrine, Kitaguchi Hongu Fuji Sengen, were more my style. And I can’t finish without expressing my appreciation for all of the incredible food we got to try: an udon set meal, two large buffets, and a grill-your-own seafood restaurant. I was in heaven!

Overall, it was an amazing weekend, with plenty of good company, new experiences, and great food. As I try to make the most of my last week in Tokyo, I know I’ll continue to reflect on everything I learned.

Question of the Week
Is it true that the younger generations aren’t very interested in traditional Japanese culture? If so, will they become more interested as they become older, or does this mark a major shift in Japan?

  • I’ll first ask a question back. Are young people in America are very interested in our ‘traditional’ cultures?  It is a little harder since the U.S is a very heterogeneous nation, but in terms various cultural heritages, do you see young people really embracing the traditions of say their familial/cultural heritage?  What about the historical or cultural sites and museums in and around your hometown or state? Do most college-age students often seek out opportunities to visit these places on your own? Or were these places typically students only visited as part of a school trip/group? I think when asking this question, it’s important to first turn the lens back on your own society and consider if ‘traditional’ culture, arts, or religion are typically very important among young people in your home country too.  It is an interesting question to reflect on in terms of what culture, particularly traditional culture, might mean.
  • I’d also continue to encourage you to ask questions about this topic with the Japanese friends you may make in your labs or among the Japanese Fellows. What do they like to do for fun on the weekends? Where would they like to travel to in Japan and why? Do they enjoy visiting places like Kyoto where there are many temples and shrines? Why or why not? What are the traditions that they hold dear within their families and/or Japanese society as a whole?  For example, do they go to a temple or shrine for good luck before exams?
  • Finally,  try to see if you can look beyond the tip of the iceberg in terms of traditional culture in Japan (things you can see/feel/experience like museums, temples, and shrines) to ask if you can see aspects of traditional that are uniquely reflective of Japanese culture or society in modern society or norms. For example, think back to the lecture on kimono and the cultural meaning of when and what pattern of kimono you might wear.  This is an aspect of traditional culture that carries over into society today.
  • You may also want to read some of the articles on our Life in Japan page under the Traditional vs. Modern, Religion in Japan, or Youth Culture sections for more on this question/topic.

Research Project Update
Prof. Kono gave us some material properties questions to consider in relation to our projects. The material I will be working with is substrates for cell cultures. Various materials can be used, and indeed my project might involve modifying or developing new ones. Typical experimental setups involve attaching extracellular matrix molecules to a clear hard (e.g. glass) or flexible (e.g. PDMS, poly-dimethylsiloxan) and then culturing cells on the result. In all cases this is definitely a 3D system in a quantum-mechanical sense, and an insulator since no metals are involved. Properties that we might be interested in studying include stresses on the cells inside the culture and gradients of interesting molecules. From a basic science perspective, this material is interesting in that it can provide insight into properties inside the human body and how they affect cell development and function. From a more practical standpoint, getting to the point where we can engineer an environment that provides easy access to and manipulation of cells while closely mimicking their natural habitat would result in many possible applications. These include drug testing and personalized medicine.

Supercomputer at Earth Science Museum: JAMSTEC director describes the supercomputers used to model earthquakes and perform other important research.

I’d like to spend the rest of this section discussing the science and engineering seminars from the past week. My favorite was the visit to Yokohama’s Earth Science Museum (JAMSTEC), where we learned about Japan’s extensive earthquake warning system. Every evening in Tokyo you can hear a song play from loudspeakers all over the city. This song lets children know it’s time to head home for dinner, but it’s also a test of the speakers, which instantly emit sirens if a disaster such as an earthquake occurs. A large network of sensors off the coast of Japan, called DONET, monitors vibrations along the plate boundary. These sensors are monitored constantly by the Japanese government, which issues a warning if an earthquake is about to occur. This gives people in most parts of Japan an extra twelve seconds to prepare, which is small but incredibly important. Train operators can brake, and people everywhere have time to turn off their stoves, open doors, and get away from windows or other hazards before the earthquake starts. Wakayama prefecture has a special system because it is so close to the epicenter of many earthquakes: supercomputers monitor the DONET system and run constant simulations on what the data means. If an earthquake seems possible, a warning is automatically issued just for that prefecture. The rest of Japan doesn’t use this system because the extra few seconds is not worth the potential for false signals. In more rural areas where loudspeakers aren’t as prevalent, there are elaborate systems emergency systems where people communicate with each other to spread the news as quickly as possible. Of course, modern cell phones issue alarms as well. Overall, it’s an incredible system that gave me an increased appreciation for human ingenuity in response to difficult problems.

This week we started the official lectures on science and engineering. There has been a large focus on materials and quantum effects, which are completely new topics for me. I’ve never taken a modern physics course, so these talks have been very interesting but also quite confusing at times. On the one hand I am very curious about these topics and want to learn more, but on the other they seem pretty far from anything I might be able to apply in practice. I’m torn between doing more background reading so I can better understand the physics and focusing on topics more closely related to my own research project. And Tokyo is always lurking behind my back, tempting me with unexplored neighborhoods, shops, and temples. If only I didn’t need to sleep!

Prof. Kono gave two lectures on nanomaterials and quantum mechanics, while Itoh-sensei from Keio University talked about quantum computing and Kawata-sensei from Osaka University talked about how nanotechnology can unite photonics and biology. Dr. Kono’s lectures were very interesting, especially the first one, because they introduced many new concepts and gave me an overview of nano-related research topics. In particular, I was fascinated by quantum dots and characteristic dimensionality, which is when materials are so small that they actually trap electrons and limit their movement to less than three dimensions. This produces a variety of interesting effects, including inducing the same material to be different colors by changing the size of its particles.

As a computer engineering major I was looking forward to Itoh-sensei’s talk on quantum computing, but unfortunately, I had a difficult time following much of the material he discussed. I definitely want to go back and read more about this topic later so I can have a better understanding of the physics behind it. My main takeaway from this talk was that storing and maintaining information in the spin state of electrons is difficult but feasible, and that this technology is no longer a pipe dream but something we can expect to see on the market within a couple of decades. Kawata-sensei’s talk covered not just the research done in his lab but also some of his thoughts on the future of his fields. He thinks that in the 21st century, it will be impractical to study biology or chemistry or physics. Instead, we will study “transdisciplinary” fields like nanotechnology, photonics, and complex systems. I think this would be a positive development. Even after two years of university and lots of reading on my own, I feel like there are huge gaps in my basic knowledge of how things related to my research work.

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Week 03: Noticing Similarities, Noticing Differences

Shinjuku Arcade: Nothing beats taking a break from all the serious stuff by playing taiko drums along to anime theme songs! ~ Kaylene Stocking

Both in Seattle and Pittsburgh, public buses were my primary mode of transportation. Therefore, I was no stranger to public transportation when I came to Tokyo. Although there are a lot of differences between the Tokyo subway and the bus systems that I’m used to, I think a lot of it has more to do with the mode of transportation than the country. Japanese subways and trains are famous for being exactly on time, but with a bus system it’s simply not possible to force traffic to comply and keep buses on time. Transfers in a subway system are easy because you can stay within the same station, while with a bus system hunting for the next stop can be difficult. With a convenient and comprehensive subway system, it’s no surprise that the trains are frequent and the train cars are crowded in Tokyo. A good subway system is a much more effective replacement for owning a car than a bus system, even if you happen to live somewhere where the buses are relatively okay.

Goshinchou: My goshuinchou (red seal book) features stamps from the two temples I felt the strongest connection with in Tokyo: Senso-ji (where Sanja Matsuri was held) and Zojo-ji (a place I stumbled upon on my very first day in Japan).

There are other differences that are more cultural, however. In the US, public transportation often has a stigma attached to it. People who can afford to own cars usually don’t take it, even when it’s reasonably convenient. In Tokyo, only fairly wealthy people seem to own cars, and people from all walks of life take the train. This is definitely at least partly a practical difference. Space is at a premium in Tokyo, and owning a garage and paying for parking are out of reach for most people. I’ve never understood why many people I know in the US don’t even consider taking the bus, however. I wonder if it has something to do with the strong value we place on individuality and efficiency in the US: taking a car allows you to go straight from point A to point B, without making any concessions for others. I’d be curious to know if Americans who go abroad to countries with good public transportation and get used to it use it more when they get back.

Owl café: This is Kabuki-chan. I will never forget her. ~ Kaylene Stocking

There are also differences in acceptable behavior on public transportation between the US and Japan. On the bus systems I’m used to, eating and drinking is technically against the rules, but most people do it anyways. In Japan, no one ever eats, and drinking is also very uncommon. I’ve learned that this is out of consideration for others: bothering them with the smell or sound of you eating is taboo. Similarly, talking is rare on Japanese trains, and when it happens it’s very quiet. This is a very nice change of pace for me – I’m used to trying to read on the bus and being forced to listen to someone’s phone conversation instead. Japanese people typically use their phones or sleep on the train, although I’ve noticed many books as well. I think that’s great, as I hardly ever see adults reading books in the US!  Some of the other fellows have been surprised that Japanese people can sleep on the train without missing their stop, but I did this on a near-daily basis during my senior year of high school and only missed my stop once. It’s just a matter of habit!

In summary, I think the use of public transportation in Tokyo is a good example of several core Japanese values. Respect for others comes into the quietness and lack of eating on trains. Furthermore, the fact that so many people use it shows the greater emphasis that Japanese people place on society rather than the individual (although this also has to do with the practical costs of car ownership here). Finally, respect for the elderly is evident in that there are priority seats that others actually respect.

Overview of Week Three of Orientation Program in Tokyo 
This week, we had several cultural talks. Dr. Baker spoke of his experience working at a Japanese research center for multiple years. He also mentioned that there is a scholarship for going to graduate school in Japan, which is something I might want to look into. Ishioka-sensei spoke about the gender disparity in higher education in Japan, but how being a scientist has been a very fulfilling and freeing career for her. Futaba-sensei gave us some advice about how to experience Japan beyond the tourist surface. Saeki-sensei talked about how women are portrayed in Japanese media and how this has changed over the last few decades. She showed several examples of working and independent women getting more representation, but unfortunately this is limited to media where the target audience is only women. Thus, while Japanese are getting more comfortable with the idea of working independence, men seem to be less on board. Finally, the most practical talk was Ozaki-sensei’s discussion of survival Japanese to use in our labs. In addition to having a better idea of what polite expressions to use when, I also now know how to gracefully leave a party. For me, that last one is pretty important!

Learning about the plastic food models that restaurants put in their windows was also a highlight of this week. They can be really incredible works of art sometimes, and they look so realistic I want to eat them even up close! Because of the trip to make plastic food, I was thinking a lot about the differences between Japanese and American restaurants. My theory is that these differences stem from the way people find out about new restaurants in each country. In the US, people drive between places and don’t have enough time to take a good look at places to eat along the way. When we want to go out to eat, we’ll generally read reviews online or ask for recommendations from friends beforehand. Then, we drive directly to where we want to go. In Japan, people walk a lot more and have more time to look at individual storefronts. Restaurants can afford to be very small and have no online presence as long as something about how they look attracts enough customers who walk by. Plastic food plays a huge role in this. I also love that Japanese restaurants often display their prices outside where it’s easy to decide whether a certain place fits my budget. I think this, too, is a consequence of people walking so much and trying new restaurants based on their outside appearance.

Question of the Week
What political and societal factors have allowed Japan to build such impressive public transportation infrastructure, while even in highly populated US cities it continues to struggle?

Research Project Update
Many of the seminars this week combined science and cultural aspects, so most of the talks I mentioned in the cultural section also have science components. Dr. Baker spoke about the protein data bank and his work in developing better tools for viewing and searching for proteins. I really enjoyed this talk because my first internship had to do with protein structure, and I’ve used the protein data bank several times for school and research. Ishioka-sensei talked about her research in ultrafast spectroscopy at the Japanese National Institute for Materials Science. She devoted a large portion of her talk to the most promising experimental solar cell type, the lead-halide perovskite solar cell. Although this cell is cheap and easy to manufacture and boasts high efficiency, it degrades quickly under sunlight, which is a huge problem! Ishioka-sensei studies this cell type in the hopes of understanding why it’s so efficient and maybe even passing that efficiency on to a more robust material. Futaba-sensei talked about carbon nanotubes. We had already covered the basics of these in previous talks, but Futaba-sensei spoke about his discovery of a much faster way to grow aligned tubes into a useable material. This was really interesting and gave me more determination to try lots of different things and think outside the box in my own research this summer.

Professor Stanton gave two lectures on semiconductors, nanostructures, and femtosecond laser spectroscopy. These talks were very interesting, and after hearing the basics of semiconductors and quantum mechanics a few times in previous lectures, I felt like I was finally starting to develop some intuition for how all of this fits together.

As I go into my research project, I’m still not sure exactly what I’ll be working on, but I’m interested in learning more about the factors that influence cell differentiation. Chemical effects have been thoroughly explored by this point, but other influences such as mechanical stimuli are still relatively new and poorly understood. If I have one question at this point, it’s how researchers in biology are able to decide what to tackle next when there is such an incredible number of possible chemical and physical factors that influence cell behavior. I hate trial and error, so I can’t help but wonder if there’s a more efficient way to predict and understand what’s going on and why. With such a short time in my host lab, I don’t want to waste weeks on experiments that might be unlikely to produce interesting results. Hopefully as I learn from my mentors and become better versed in this area of research I’ll have a better idea of what to do next!

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Week 04: First Week at Research Lab

Joining the Kamei Lab at Kyoto University has been a surprisingly smooth process. Labs at iCeMS (the Institute for Integrated Cell-Material Sciences) seem very similar to labs I’ve spent time with in the US. Each Principal Investigator is a professor interested in a certain research topic, with a small group of post-docs, graduate students, and undergrads working under them on various projects. Working hours are around 9-6, and many people left closer to 5 on Friday. Also, English is the primary language for all lab activities. Kamei-sensei strongly encourages his lab members to speak English because it’s so critical for a career as a researcher. While all this has made for an amazingly easy transition for me, I’m a little disappointed that my international research experience feels a lot like the research I do back home. From what other fellows have said, our lab environments vary widely in hours, how close-knit the members are, and how much English is spoken. I think it’s very interesting that there’s so much variety. Perhaps because research is so international, professors feel more comfortable running their labs the way they want to rather than following strict Japanese norms.

On my first day at the lab, Kamei-sensei gave me a quick tour of the facilities and equipment, and told me I should focus on helping the one graduate student in our lab with his project. This was news to the graduate student – Nicolas, a biomaterials student from France – but he quickly started introducing me to his research. Nicolas is an excellent mentor and very willing to teach me new techniques. However, he came to Japan because he was really interested in iCeMS, not because he was interested in Japan. He speaks English fluently, so it’s very easy for us to communicate. But I also feel like this isolates us from the other two (Japanese) students in the lab to a certain extent. I really want to get to know them, but I have no idea how to approach them, and I think all three of us are embarrassed about our skills in the others’ language. Now that I’m settled into my lab and have gotten through the process of moving, my goal for next week is to interact more with Japanese people, starting with the ones in my lab!

My housing is a building for international students run by Kyoto University. It’s pretty rundown, but everyone seems friendly and the staff is very nice and helpful. However, none of the residents speak Japanese, so I’m not getting much practice either at home or at work. My housing is rather close to Kyoto University, but unfortunately transit in Kyoto is a lot more expensive than it was in Tokyo. Taking the subway and a bus to work would cost 900 yen a day! So, after my third day of work I went and bought a bike. I love the freedom it gives me to explore anywhere I want without having to worry about last trains or expensive transfers. Parking at Kyoto University and my housing is free, and there are bike parking lots all over Kyoto. I’m not the only one who has concluded that cycling is the best way to get around here – over half of iCeMS employees commute by bicycle! It makes me really happy to see all the bikes parked outside of supermarkets and konbinis. People of all ages and genders ride bikes here, and they seem totally at home on them. When it was raining one day, I saw many people carrying an umbrella with one hand while riding! I’m nowhere near that coordinated now, but if I ride every day maybe I’ll be able to do it too by the end of the summer…

Looking at Kyoto from the top of Daimonji-yama ~ Kaylene Stocking

On Saturday, I went to a Buddhist temple called Bishamon-do and hiked from there to the top of Daimonji-yama. The name translates to “great letter mountain,” and every year in mid-August a giant bonfire is lit on it in the shape of the kanji 大 (dai, great) as part of Daimonji Gozan Okuriburi. There are five of these fires on five different mountains surrounding Kyoto, and the origins of the tradition are obscure but probably ancient. Daimonji-yama was covered with beautiful cedar forests, and there was an amazing view of downtown Kyoto from the top. The temple was also impressive, with several ornate altars and the residence of Emperor Gosai (1638-85) on its premises. On Sunday, I went with a group of US fellows to Arashiyama, a more traditional district of Kyoto

Tame wild monkeys in Arashiyama. ~ Kaylene Stocking

that reminded me a lot of Asakusa in Tokyo. The main attractions were a monkey park and bamboo forest. The monkeys are technically wild but so used to being fed by humans that they will come very close to you. If I had to choose between monkeys and owls there would be no contest, but this was definitely a wonderful experience. I also got a delicious set lunch and ice cream with four different tea flavors! I feel so lucky to be living in a city that not only has lots to see and do but is also surrounded by beautiful forests and mountains. For me, it’s the best of both worlds.

Research Project Update
Kamei-sensei’s lab is focused on creating something called a body-on-a-chip. The basic premise is that if we can culture cells from various vital organs – heart, liver, lungs, etc. – we can create a versatile model of the human body for important applications like drug testing and understanding rare diseases. In order to get all of these cell types, we want to take induced pluripotent stem cells (iPSCs) and get them to differentiate into the various cell types that we need. iPSCs are ordinary cells (like skin) that have been “induced” to become stem cells. Right now, we can take iPSCs and cause them to differentiate into a wide range of cell types, but their functionality is not close enough to the real thing to serve as a good model. My project has to do with producing better hepatocyte (liver) cells from iPSCs. In human development, a number of factors probably work together to cause hepatocyte differentiation, including chemical signals and the structure of the surroundings. We can make educated guesses about what they might be, but the only way to tell for sure is to experiment and see what works.

My graduate student mentor is working on testing different mechanical stimuli by designing a culture environment that will allow us to “stretch” cells by different amounts. We know that in a developing fetus the liver and vascular system are closely connected, so it makes sense that there would be pressure on the developing liver cells. I’m assisting my mentor with that project, while also performing my own experiments on chemical factors. While many promising chemical factors have already been identified, most have only been tested with 2D cultures, where cells are cultured on a flat surface. I will be testing the effects of these factors on cells in a 3D culture environment to see if this improves their differentiation. Ideally, one or even both of these projects will result in cells that more closely resemble mature hepatocytes than has previously been reported.

For the mechanical stimulus project, we need to design a culture environment that allows cells to be stretched by different amounts. This has been my focus over the past week. We use a technique called soft lithography to make unique culture “chips” that meet an experimental need. First, a mold of the desired chip is designed in CAD software and printed with a very high-resolution 3D printer. The mold is then used to shape a polymer called PDMS, which has some very useful properties. First, it’s highly flexible, which more closely mimics human tissue than traditional glass or plastic culture substrates. Second, it’s extremely clear, which allows us to observe the cells and do image analysis without disrupting the culture. For the stretching stimuli, we use two chips: one contains the cell culture chambers, and the other gas chambers. We put a very thin membrane between them. When air is pumped into the gas chambers, the membrane expands into the culture chambers and stretches the cells. My first week was spent refining the chip design, but we should start culturing the first batch of cells this week.

As for my project, we already have a suitable 3D culture environment, so my first task is to identify promising compounds in literature. Once I have some good candidates, I will be able to start culturing cells with them. The experimental side of this project is fairly straightforward, but in order to analyze my results I’ll need to learn a variety of techniques. This will probably include things like fluorescence microscopy and RNA assays. I’ve never done this kind of research before, so I’ll have to receive training in how to culture and analyze cells.

Here is a rough timeline of my project, to the best of my knowledge:

  • Week 1: Assist mentor and learn more about the research topic.
  • Week 2: Identify promising compounds for 3D culture experiment and purchase them. Start learning about cell culturing techniques.
  • Week 3-4: 3D culture experiment round 1
  • Week 5-6: 3D culture experiment round 2 (to test robustness of results from round 1)
  • Week 7-8: 3D culture experiment round 3, using results from previous two rounds to refine combinations of chemicals used
  • Week 9: Finish analyzing results and prepare for poster presentation.

Throughout this time period I will also continue to work on the mechanical stimulus project, but I’m less sure of the exact timeline for it.

Question of the Week
There are so many different kinds of snacks in Konbinis and 100-yen stores! For example, in the US we only have a couple of Kit-Kat flavors, but Japan has seen over 300. Why does variety do so much better in Japan than it does in America?

Assessment of Orientation Program and Language Classes
Overall, I thought the orientation program was very interesting and worthwhile. I appreciated the variety in speakers and topics, and some of the seminars were really fascinating. My favorites were seeing supercomputers and learning about Japan’s earthquake warning system in Yokohama and learning about new physics concepts like quantum dots. I also enjoyed the culture presentations, especially the one about the history of kimonos. Finally, Nozaki-sensei’s presentation on basic Japanese etiquette has been very helpful for getting around on my own in Kyoto! On the other hand, I was slightly disappointed that the presentations didn’t go much into Japanese history. I’ve been reading on my own, but it would be nice to have more context for all of the amazing things I’ve seen here.

As I learned more about Japanese culture during the orientation, I had a strange feeling of dislocation. In some respects, my values are much more Japanese than American, especially when it comes to respect for others, privacy, and forming few but long-lasting friendships. But in other ways, I don’t fit in at all. I value being straightforward when speaking, and the rigid divisions between genders here bothers me. I find myself thinking a lot about what it means to “belong” to a culture, and why I have the values that I do. This is definitely something I’ll continue to mull over for the rest of my time here.

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Week 05: Critical Incident Analysis – Life in Japan

This week, I was asked to describe an instance of “cross-cultural communication” I’ve experienced in Japan. Essentially, this means a situation where another person and I were communicating from different cultural perspectives, which resulted in some sort of misunderstanding or confusion. I can think of one occasion that stands out as fitting the bill, although it’s now been a while since it occurred.

During the afternoon sessions of our first week in Tokyo, we took a field trip to Tokyo University (Tōdai) to tour some of the laboratories there. After seeing all of the lab equipment, we had a chance to meet with some student researchers from the university. Shivani and I ended up talking to one person in particular quite a bit. After a while, it became clear that all three of us were interested in origami. The Japanese student mentioned that Tōdai was going to have its annual school festival that weekend, and that the origami club would have a display. Shivani and I really wanted to go, and the Japanese student offered to meet us at the festival to show us around. I was excited! I was only in Japan for one week, and I already had an offer to spend time with a Japanese student and see a traditional school festival. I’d heard a lot about these (they’re very common in Japanese comics) but never expected to have the chance to see one myself.

That Saturday, I went to Tōdai at the time we agreed on. The festival was in full swing, and as I waited outside the famous red gate that is the university’s main entrance, I could hear music being performed while a club advertised their crepe booth at the top of their lungs. The Japanese student was pretty late, however. When he finally got there with a friend of his, the four of us went out to explore. We saw the origami exhibition as well as displays by the photography and Lego clubs, and ate fried ice cream and takoyaki. The food was delicious and the displays were really neat! Eventually, we made our way to the main stage, where a girl idol group was performing a J-pop dance number. Our Japanese hosts seemed more into this than the previous activities, but Shivani and I didn’t enjoy it that much. I have a hard time with loud noise and ended up plugging my ears. We walked around the festival a little more after this, but things became increasingly awkward and eventually Shivani and I left to go see other parts of Tokyo.

Afterwards, I realized I had no idea whether the Japanese students wanted to be there with us or were even enjoying themselves at all. The second Japanese student didn’t speak much English and might have felt a little left out, while I wanted to try speaking in Japanese but was embarrassed about my abilities. I think the Japanese students liked the J-pop performance, and I felt really bad for plugging my ears because it might have looked like I thought the music was awful. I tried to explain, but in retrospect I might not have done enough, especially with the language barrier and noise making communication more difficult.

My best guess is that the Japanese students were being polite by offering to show us the festival but genuinely didn’t mind hanging out a little, at least at first. But after a while they might have gotten tired of English, and I think I might have offended them at the concert. If I had another chance I would have tried to be more sensitive to what they were interested in, and maybe tried to speak a little more in Japanese to show that I was trying to meet them in the middle.  But it’s hard to know whether this would have helped, especially if they never wanted to be there in the first place.

Phoenix Hall, a temple built almost 1000 years ago. ~ Kaylene Stocking

I’m conflicted about what to take away from this experience. On the one hand, I really want to be as social as my personality allows while in Japan, and talk to Japanese people as much as possible. But on the other hand, I don’t want to impose on others, especially when I can’t even tell if I’m bothering them. Should I have declined the invitation? Should I have tried harder to find common ground? Maybe I was completely imagining how awkward it was, and by never following up I missed out on making a good friend! I still have no idea. I have a hard time dealing with these kinds of situations even back home, so knowing the right thing to do in Japan seems like a long stretch.

 

Fresh hōji-cha (roasted green tea) coming out of a roaster on a street in Uji. ~ Kaylene Stocking

Before I wrap up this section, I’d also like to talk briefly about this past weekend. On Saturday, Emily and I went to Uji, a city near Kyoto famous for its tea. There’s a temple there called Byōdō-in, which features an incredible building known as Phoenix Hall. It was built in 1053 and has survived all the way into the present day, albeit with significant restoration work. It is featured on the Japanese 10-yen coin. It’s incredible to think of a single building being that old, let alone one so beautiful and impressive! 1000 years is such a long time on a human scale. I have a hard time imagining buildings like the Space Needle or Tokyo Tower still being around in 3017. For that matter, I have a hard time imagining whether humans will even live on earth by then.

 

Ramen: probably the most satisfying comfort food ever created. ~ Kaylene Stocking

On a lighter note, Emily and I had incredible matcha parfaits in Uji: green tea ice cream, mochi, and red beans combined into a perfect dessert. To top it off, on Sunday I ate one of the best meals of my life: a bowl of Sapporo-style miso ramen and amazing dumplings at Kyoto Station’s ramen street. Even though I’m not even halfway through the summer yet, I already feel phantom pangs at the thought of having to leave all this food behind in seven weeks. What am I going to live off of without onigiri, bento, and cheap delicious noodles? Pittsburgh is a Japanese food desert! I might have to learn how to cook this stuff myself if I want to make it through the next school year…


Question of the Week

I’ve noticed that bookstores, especially ones for used books, are very common in Japan. I also see many people reading in public, especially on the train or in parks. Why is reading so popular here, when it has been practically replaced by smartphones in America? What kinds of books do people usually read?

  • Japan has historically had very high literacy rates and this can be traced back to Tokugawa period (1600 – 1867) as, after unifying the country, education became increasingly important to develop the government bureaucrats needed to run the government and for the common people; who could now focus on education as opposed to struggling through an endless series of clashes between various warring clans.  By the end of the Tokugawa period, literacy was estimated at 40%.  During the Meiji period, formal public schools at the primary, middle, and university level was established and both girls and boys were required to attend primary school.  This led to even higher rates of literacy among both genders. These historically high literacy rates enabled Japan to develop a robust publishing industry that in turn led to a rise in the numbers of people in Japan who read for pleasure, at all level of society. For more on this topic see Popular Literacy in Early Modern Japan.
  • Japanese bookstores have a wide array of titles among all genres, including many translations of foreign books into Japanese.  If you go to a new bookstore, you will often see displays with covers of books you may recognize as being popular best-sellers in the U.S. – but they are in Japanese. Business and self-help books are often translated into Japanese along with popular fiction.
  • As you note, people in Japan tend to prefer paper books to e-readers and often will read small, paperbacks during their daily subway commutes.  For privacy, most people use paper book covers over their books so that others on the train won’t know what they are reading. When you buy a book in Japan at a bookstore you can even ask them to put a paper cover on the book for you or buy special plastic covers that you can slip on and off books as needed.  Therefore, it’s hard to tell what people are reading unless you watch what they buy at the bookstore before the cover gets put on.
  • One big reason e-readers are not popular is that there aren’t a lot of e-books in Japanese available.  Until Japanese publishers start investing in publishing Japanese books in e-reader form you probably won’t see many people reading digital books.  The plethora of used book stores in Japan also means that buying an inexpensive, used paperback to read on the train is likely cheaper than an e-book would be. E-books are becoming more popular though and you can now find some Japanese content through Amazon.jp, Rakuten, and other outlets. There have also been a number of e-book sellers/providers in Japan that have shut down unexpectedly so it may be that Japanese consumers are a bit shy about committing to a certain e-book platform as they worry it may be discontinued (like the Nook from Barnes and Noble).
  • Why Japanese Readers Don’t Like E-books (Fortune)
  • Well-bitten Consumers Shy of Japan’s Disappearing E-books (Japan Times)
  • Why e-readers succeeded as a disruptive technology in the U.S., but not in Japan (LSE)
  • Printed Books Aren’t Dying Yet, but Japanese Manga is Boosting Ebook Sales (Inquisitor)
  •  Kondansha International’s Bilingual Book Series (Tofugu) 
  • There is a Japanese Word for People Who Buy Too Many Books to Read (Huff Post)
  • Japan Times Articles on Books 

Research Project Update
This has been an interesting week in the lab! The good news is that my literature search for promising chemical compounds for inducing hepatocyte differentiation and maturation was a success. I was able to identify five compounds from four different papers that haven’t been tested with a 3D microfluidic culture environment yet. Kamei-sensei also encouraged me to look for a “wild card” candidate, something that hasn’t been considered for hepatocyte differentiation at all yet. I was a bit apprehensive about this because I had no idea where to start looking, but I stumbled on something really interesting! While investigating genes that are known to be involved in hepatocyte differentiation, I found a reference to a chemical factor that upregulates one of these genes. The compound comes from a plant that has been used in natural aides for diabetes for a long time because it promotes insulin release. It has already been tested on mature hepatocytes because of this property, so I know that it’s not toxic to them and have a good idea of what amount to use. But there isn’t any record of using it to induce hepatocyte maturation! If it turns out to have a good effect, I would make a small but completely original discovery, and that’s really exciting to me. Of course, that’s a huge if…

In addition, I’m continuing to learn new laboratory procedures that I’ll need throughout the summer. My mentor, Nicolas, has been showing me the basics of culturing and maintaining cells, as well as using various pieces of equipment. I’ve also been getting thorough training on sterilization procedures, since a very small number of opportunistic bacteria is enough to ruin several weeks of experimentation in biology. Kamei-sensei also showed me how to make culture medium. Although I won’t be able to use any of this until the chemical compounds I need have been shipped, it’s good to build up slowly so that I won’t have to learn everything at once. Doing the literature search for the compounds has also been a good learning experience, and really helped me gain a better understanding of my research topic.

On the other hand, it has been a rough week for my mentor’s project. I designed a new chip for use in his project last week, and 3D-printed the mold for it on Monday. We decided to set a target of Wednesday for thawing frozen day-12 hepatoblasts, and then moving them to two of the new chips on Friday. This gave me several days to produce the chips, which seemed reasonable – I can do one a day if I let it bake in an oven overnight. The first two chips made from a new mold are unusable because the PDMS polymer sticks to the chip and is too difficult to extract without breaking. Even so, I should have had just enough time – but unfortunately things didn’t go to plan.

The new chip design is taller and features smaller tubes for regulating air pressure, making these features on the mold very fragile. While trying to take out the first chip from the new mold, I broke one of these tubes off. We tweaked the design slightly to make the mold more durable and printed again the next day, and I rushed back to the lab after my welcome party to get the chip in the oven overnight. But when I came back the next morning, I had the hardest time I’ve ever had trying to remove the PDMS, and ended up breaking two tubes in the process. I realized later that this was because I hadn’t been mixing the PDMS enough before pouring into the mold, and that it wasn’t fully hardening as a result. On Friday, I finally removed the crucial first PDMS layer without breaking anything, but I still didn’t have any functional chips and there isn’t a way to pause the cells from doing their thing once we’ve thawed them.

I was feeling pretty bad about this, but as it turned out the week was a comedy of errors. First of all, my mentor hadn’t realized that the thawed cells would be unusable if we waited too long – he probably wouldn’t have bet on me finishing with the chip in time otherwise. And secondly, we found out on Friday that our lab’s technician made a mistake with labeling, and the cells we thawed on Wednesday weren’t even the right kind of cell! So, there were a total of three different errors from three different people, any one of which would have been enough to ruin the whole experiment. As Nicolas summed it up, it’s better to have three mistakes at once than one a week for three weeks in a row, so we should probably be grateful we got it all out of the way early on! Hopefully next week we can build on our mistakes and get going for real.

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Week 06: Preparation for Mid-Program Meeting

Coming this summer!

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Week 07: Overview of Mid-Program Meeting & Research Host Lab Visit

Coming this summer!
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Week 08: Research in Japan vs. Research in the U.S.

Coming this summer!

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Week 09: Reflections on Japanese Language Learning

Coming this summer!

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Week 10: Interview with Japanese Researcher

Coming this summer!

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Week 11: Critical Incident Analysis – In the Lab

Coming this summer!

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Week 12: Final Week at Research Lab

Coming this summer!

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Week 13: Final Report

Coming this summer!

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Follow-on Project

Coming this summer!

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Tips for Future Participants

Coming this summer!

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