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
- Week 02: Language Learning & Trip to Mt. Fuji Lakes
- Week 03: Noticing Similarities, Noticing Differences
- Week 04: First Week at Research Lab
- Week 05: Critical Incident Analysis – Life in Japan
- Week 06: Preparation for Mid-Program Meeting
- Week 07: Overview of Mid-Program Meeting & Research Host Lab Visit
- Week 08: Research in Japan vs. Research in the U.S.
- Week 09: Reflections on Japanese Language Learning
- Week 10: Interview with a Japanese Researcher
- Week 11: Critical Incident Analysis – In the Lab
- Week 12: Final Week at Research Lab
- Week 13: Final Report
- Follow-on Project
- Tips for Future Participants
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.
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?
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?
- 10 Factors that Make Japan a Safe Country (Japan Today)
- Safety in Japan: Staying Alert in the World’s ‘Safest’ Country (Tofugu)
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.
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.
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.
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.
Week 03: Noticing Similarities, Noticing Differences
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.
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.
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?
- This is a pretty big question and I’d encourage you to consult Google-sensei about the pros and cons of Japanese investment in public transportation infrastructure. It’s a complex matter that ties in politics, the need for massive infrastructure to be rebuilt following WWII, and a huge influx of investment in infrastructure following the bursting of the economic bubble in Japan in the late 1990s and the Asian Financial Crisis in the 2000s. Here are a few articles to get you started:
- Why Tokyo’s Privately Owed Rail Systems Work So Well (Citylab)
- Japan’s Mission Impossible: To Spend $100 Billion in 15 Months (Reuters)
- What Japan can Teach America about Sustainable Transportation
- From the Shinkansen to the Maglev: Japan’s Railway – The Envy of Them All (GaijinPot)
- Why Japan Lead’s the World in High-Speed Trains (Economist)
- How the Shinkansen Bullet Train Made Tokyo Into the Monster it is Today (Guardian)
- How the Shinkansen Changed Japanese Cities (Museum of the City)
- Japan’s High-Spending Legacy (BBC News)
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!
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…
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
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?
- Since there are so many konbinis all competing with each other for limited market share, the goal is to have something new all the time to lure people into your store.
- People in Japan also tend to shop for groceries/food a few times in week (or even daily) since their kitchens/fridges are smaller. Since they can’t buy such large quantities of food, they may be more open to trying new flavors/items as they buy them in smaller packs.
- This also ties in with a more heightened focus on seasonal food items and flavors and regional specialties. Yes, there may be 300 different Kit-Kat varieties but you can only buy certain flavors at certain times of the year and in certain cities/regions. So shopping is always a bit of an adventure as you may have some new flavor or ingredient to try each month.
- In the U.S., we typically drive to the grocery store to do major grocery shopping once per week and stock up on the largest/most cost-effective sizes as and tend to have larger fridges, and pantries to store food in. Therefore, the focus tends to be on purchasing the same key brands that we know we will like since we don’t want to waste money on something new we may not like. This is actually why manufacturer’s in the U.S. entice customers to try new flavors/brands of food through coupons delivered via social media or the Sunday paper and market them heavily on TV as otherwise it might be hard to launch a new brand/favor.
- Convenience Stores in Japan: Surprisingly Convenient (Tofugu)
- A Comparison of the Three Major Convenience Stores in Japan (Matcha)
- Lawsons Geek: My Love Affair with Convenience Stores in Japan
- Top 5 Japanese Convenience Stores & Their Advantages
- Japan’s Seasonal Limited Editions are Full of Surprises
- The Sweet Flavors of Spring in Japan (GaijinPot)
- Flavors of Fall in Japan (Japan Crate)
- Seasonal Ingredients in Japan
- The 11 Japanese Seasons (Japan Talk)
- 10 Tips for Grocery Shopping in Japan (Healthy Tokyo)
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.
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.
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.
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.
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.
Week 06: Preparation for Mid-Program Meeting
It’s hard to believe that I’ve been in Japan for a full six weeks. I don’t even get to say that it’s less than halfway now! The first three weeks in Tokyo felt like they lasted a long time, with many different new activities and experiences every day. Now that I’ve settled into my research lab, time is going by much more quickly. During the week, I spend most of my time either at lab or doing chores like cooking and shopping, so the amount of time I have for exploring and seeing new things is limited. As for the weekend, I’ve been exploring lots of different areas around Kyoto, but it’s beginning to sink in that there’s no way I can visit everything I want to in the six weekends that are left. It’s been nice to take a break from the hectic pace I kept up in Tokyo, but from now on I want to be more strategic and make sure I don’t have any regrets at the end of another six weeks!
Overall, adapting to living in another country has been pretty smooth. I’m flexible food-wise, so buying mystery items at the supermarket and trying to figure out what they are after eating works just fine for me! I love being surprised by ingredients or combinations that seem completely strange. The other day I found a sandwich at a bakery that had spaghetti, tomato sauce, and fried tofu in it. Even though all those ingredients are perfectly acceptable in America, I can’t imagine that combination selling very well back home! (Like almost everything I’ve eaten in Japan, however, it was delicious.) I also like being in an environment where most things are in a foreign language. It’s like I moved up a difficulty level in an RPG. Doing everyday tasks like shopping and figuring out how to park my bike is more challenging, but also more rewarding. Just walking down the street is an opportunity to make a new discovery or learn a new character. The little engineer in me is secretly happy when I can’t find something I’m used to having in the US, because I have to get creative and find an alternative. There’s nothing I particularly miss from home, either, except perhaps cooler weather.
My biggest achievement so far has probably been how much progress I’ve made on reading Japanese. By studying kanji every day and paying attention to all of the signs and labels around me, I’ve gotten to the point where I can usually get the gist of what I see. I had a very proud moment when I realized I could read
a sign telling bicyclists to slow down – while I was going past on my bike! (I guess the sign had its intended effect on me, since I slowed down a bit to read it.) I guess in retrospect that doesn’t sound very impressive, but the sign had four kanji in it and I was really happy that I could recognize all of them quickly. I recently discovered that Kyoto University has an international student lounge with an impressive library of textbooks and Japanese study material available for checkout. I’m now working my way through Japanese graded readers and enjoying it immensely.
On the other hand, my biggest personal challenge has been finding ways to interact and speak with Japanese people. I knew this was going to be difficult for me, because I have a very hard time starting conversations. But I was hoping that a bit of determination would be enough to get out of my bubble and make some friends. So far, that hasn’t been the case. The two Japanese students in my lab work on different projects and don’t eat lunch here, so I’ve never gotten past saying hello. I managed to introduce myself to a couple of students at the Kyoto University cafeteria once, but after we exchanged majors and hometowns I was at a loss. My next attempt is posting my contact info on a language exchange board at Kyoto University, as well as contacting a couple of the people who had already posted, and trying to find a language partner that way. Hopefully I’ll have something more encouraging to report next week as a result.
On Saturday, I took a day trip to Osaka, which is very easy to reach from Kyoto – the train ride is actually cheaper than my commute to work for reasons I certainly can’t explain. I went to Osaka Castle, an impressive structure in the heart of the city that played an important role in Japanese history. On the inside was a history museum focusing on events related to the castle. I was expecting this to be fascinating, but I ended up getting lost in a sea of unfamiliar names and life summaries explained in stilted English. I did read a book on Japanese history before coming here, but I guess it didn’t go into enough detail to give me the necessary background to appreciate the museum. One part I did enjoy was a floor dedicated to the life of Toyotomi Hideyoshi, who built the castle. It illustrated his life story in a series of movies that seemed to have 2D actors projected into a real stage. There were lots of interesting special effects, and I would love to know how it all worked.
On Sunday, I went to Tenjin-san Flea Market, a monthly market that is one of the largest in the Kansai region with over a thousand stalls. After becoming used to seeing signs advertising kimono rentals for 3000 yen a day, I was shocked to find booth upon booth selling gorgeous used kimonos for only 1000 yen. Other popular items included old dishes and coins, as well as a good selection of festival food. That afternoon, I went to Fushimi-Inari shrine, a shrine dedicated to the goddess Inari and famous for having thousands of torii (red gates). I wasn’t prepared for the huge scale of this shrine. The torii extend all the way to the top of a 230m mountain, with periodic groups of small stone shrines along the way. The amount of effort it must take to transport all of that stone and wood up the mountain is staggering. It started raining about when I reached the top, saturating the green of the forest and the red of the gates into something almost unearthly.
Question of the Week
Fushimi-Inari left me wondering where shrines and temples get the money to maintain such beautiful structures. Fushimi-inari itself is no mystery – because of its fame businesses will pay large amounts to construct torii there – but what about smaller ones that are less well known?
- Primarily through donations and entrance fees and some temples and shrines are in economic crisis because of this. Here’s a Quora thread on this same question.
- Buddhist Temples in Japan are in Crisis
- Japanese Ministry Raises Prospect of Higher Admission Fees for Temples, Shrines
Research Project Update
This has been a slow week for research. For my project, now that I’ve identified the compounds that I need, I have to wait for them to arrive before I can start the experiment. Three compounds arrived on Thursday, but I won’t be able to start until I have at least five. I’m hoping to start the first experiment early next week. In the meantime, I’ve been preparing the cell culture chips, and now have four good ones ready for action. In addition, I started the differentiation procedure for day 0 cells with the help of my mentor on Thursday. Although I will most likely not use these cells in my own experiment (I am using a stock of frozen day-12 cells instead, in the interest of time), preparing them is good cell culture practice and if successful will help replenish the stock I’m depleting.
As for my mentor’s project, unfortunately there were a few more setbacks. The first was that Nicolas realized the stretching that the current chip allowed for (around 3% change in length) would not be enough to put significant amounts of strain on the cells. We decided to switch to an open culture chamber design that will allow for much more stretching. We were eager to get started, so I quickly made the necessary changes and got started, but unfortunately in the rush I didn’t check the measurements properly and had yet another useless mold on my hands. I’m now trying to get the fixed – and hopefully final – mold to produce some usable chips, but we won’t be able to start with culture until next week. To make things worse, I managed to crack the lid of the vacuum chamber we use for removing air bubbles from the PDMS before pouring into the mold. All of this was a little disheartening, but hopefully the end result will be a good experiment that will make up for all of the materials I’ve used!
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Week 07: Overview of Mid-Program Meeting & Research Host Lab Visit
It’s hard to believe that the Mid-Program Meeting has already come and gone. So much has happened over the last few days that I’m not even sure where to begin. Once again, I’ve been reminded of how privileged I am to be a part of this incredible program. It’s easy to get caught up in the day-to-day routine of going to lab, making food, and studying Japanese language and culture. But talking to all the other fellows again, especially the Japanese fellows, really brought home that being in a program like this is much more than just getting to do research in a foreign country. Because of the Nakatani Fellowship, I’ve been able to discuss my experiences with both American and Japanese students who are going through the same thing. Hearing about other fellows’ frustration with broken equipment and inability to make progress was therapeutic given how my own research has been going. And discussing things like cultural differences in classes and research with the Japanese students was also a little easier this time, since we were all a little more comfortable with each other.
My favorite part of the meeting were my two visits to Kamigamo Shrine. The first wasn’t an official part of the meeting at all, but I was invited to come because of my question in last week’s report about where shrines and temples get their income. Sarah, Ogawa-san, Kono-sensei, and I went to a mid-year festival held there, where your spiritual “dirt” is symbolically transferred to a special piece of paper and then floated down a river. The paper was 100 yen, and seeing as releasing them all took over ten minutes, I definitely got at least a partial answer to my question. We were there at the invitation of Horikawa-san, who works at the Nakatani Foundation and is a descendent of a family that has been caring for Kamigamo Shrine for over a thousand years. This is one of the things that has fascinated me the most about Japan – many people and places here have such strong roots. My favorite part of the event was the music played by the priests. There were several different kinds of flutes as well as chanting, but beyond that it’s difficult to describe. It was almost solemn and almost celebratory at the same time. All I can say for sure is that it left a large impression on me, and I’ll never entirely forget that sound.
The second visit was with all of the fellows, when we got a chance to tour the shrine during the daytime and see some of its buildings being restored. Because they are made entirely of wood, the shrine roofs need to be replaced about every twenty years. As it is a World Heritage Site, every detail of the restoration needs to preserve the original structure exactly, down to the type of wood used and what the nails are made of. I think it’s really interesting that, in a sense, it is the spirit of the building being preserved through generations rather than the building itself. Wood rots over time, but as long as there are people with the knowledge and will to rebuild, the “idea” of the building is immortal.
Another highlight of the meeting was getting to tour iCeMS, which is the institute my lab is part of. Although I’ve been here for several weeks, it was my first time getting to see other labs and learn about what they do. I’m very impressed with how multidisciplinary and interesting the research at iCeMS is. I know Kamei-sensei collaborates with a researcher in chemical engineering here on designing a way to control nitric oxide to examine its effects on intercellular communication. I think it’s very exciting to see all of these different fields being brought together in the same building, and apparently this is very rare in Japan. I’m very lucky to be working here!
Finally, we got a chance to experience some very traditional parts of Japanese culture: yukata wearing, tea ceremony, and ikebana (flower arranging). During the tea ceremony, it was interesting to see the very deliberate and graceful movements of the ceremony master as she prepared the ingredients and mixed the tea. I’ve read that every single movement has meaning, and that it takes many years of practice to perfect the performance. I can’t think of any parallels to this extreme attention to detail in American culture. As a results-oriented American, I can’t help but think that the tea would taste just as good without all of the ritual. But watching this, I did understand for the first time why the tea ceremony is considered an art form in Japan.
The biggest challenge from the meeting was that hanging out with the Japanese students again made me feel uncomfortably tall, an impression which was not helped by my inability to squeeze my feet into one-size-fits-all geta sandals. Singing at karaoke for the first time was also a little hard, but definitely worth it. I also enjoyed showing Kono-sensei and people from the Nakatani Foundation some of my lab equipment, such as the -150-degree freezer and 3D printed cell culture chips during the Host Lab Visit. Overall, I had a lot of fun during the meeting, and presenting about my research reminded me that I’m really interested in it, even if I sometimes get a little frustrated at the lack of results.
Mid-Program Meeting Research Introduction Presentation
As part of the Mid-Program Meeting, on Monday, July 3 our 12 U.S. Fellows gave a presentation at Kyoto University introducing their research project and future plans. Kaylene presented on the research she is doing in the Institute for Integrated Cell-Materials Sciences (iCeMS), Kamei Laboratory at Kyoto University entitled “Inducing Maturation of iPSC-derived Hepatocyte-like Cells for Higher Functionality“. Click here to download a PDF of her presentation.
Question of the Week
Japanese university students take many more classes at once than we do, but they only meet once or twice a week and don’t seem to require as much homework or outside reading per class as what I’m used to. What are the pros and cons of taking many different subjects at once versus focusing on only a few at a time?
- This is partially due to college being the ‘spring break of life’ in Japan. In comparison, in middle and high school in Japan many students attend regular school all day and then long hours of cram school at night. So, in a sense the amount/hours of the day you spend studying or in class might be flipped between the U.S. and Japan in terms of whether that is in high school or whether that is in college. You might want to read some of the articles on this topic under the Education in Japan section of our Life in Japan resources page.
- It may be even more helpful to reach out to a couple of the 2017 Japanese Fellows and ask if any of them might be willing to chat with you about this via LINE, email, or Skype. They probably could give you even better insight into what they believe the pros and cons are of how many classes they take at university in Japan – and will also likely be curious to know about how this compares with classes in the U.S. at the undergraduate level.
Research Project Update
On Monday, I finally had all of my compounds! We decided to thaw day-12 iPSCs on Wednesday. These cells were grown from day-0 iPSCs back around January by our lab technician, Terada-san. They were successfully differentiated into immature hepatocyte-like cells, and then frozen for future experiments. They’ve spent the last few months at a cool -150 degrees Celsius! This extreme temperature is necessary for complete preservation of the cells. I’m very lucky that we have these cells, as the experiment would take twice as long and have a much higher risk of failure if I had to start from scratch with day-0 cells.
Before thawing, I had to get everything else ready for culturing the cells. First up was coating a dish with serum for the cells to grow on right after being thawed. Then, I needed to prepare the microfluidics chamber, which I had made the week before. I used a plasma treatment on both the chamber and the plastic dish it rests on to make them stick together, then baked it in the oven overnight to complete the seal. (The plasma treatment oxidizes molecules on the surface of certain types of materials, making them reactive so that they easily form new molecular bonds.) Finally, I coated all 48 micro-chambers with serum, checking for leaks in the process. Although there were a couple, I only need around 36 chambers for the first experiment, so I should be in good shape.
The last step was to prepare stock solutions of my chemicals to add to the medium in each culture chamber. This turned out to be much more complicated than I imagined. Many of the compounds have limited solubility in water, so they need to be dissolved in a chemical called dimethyl sulfoxide (DMSO). However, DMSO itself can affect the cells’ differentiation, so I have to keep the total amount very low, and consistent between the different experimental conditions. Furthermore, some of the chemicals are applied in such high or low concentrations that DMSO can’t be used, and so I need to dissolve them in medium instead. Finally, I only received 5 mg of three of the compounds, so I have to be extremely careful not to spill or waste any of it, or I’m back to square one. I also had some issues using the highly precise analytical balance, which can measure to the nearest 0.1 mg but is extremely sensitive to being bumped. All of this ended up taking quite a while for what I thought was going to be some simple chemistry!
I thawed the cells on Wednesday as planned, and we decided to let them grow on the intermediate plate for 48 hours before transferring them to the microfluidics and starting the experiment on Friday. But when Thursday afternoon came around, I realized that I had completely forgotten Kamei-sensei had to go to a conference in Tokyo on Friday. He started trying to talk me through all of the things I would need to do, but it became clear that I wasn’t ready to try it on my own without any practice or supervision. So, we decided to put off the cell transfer until Monday, when I can come into lab after the mid-program activities. It was a little disappointing to be put off a few more days after all of that preparation, but at least I was kept busier this week and am making forward progress again after all of the waiting for my compounds to arrive.
The last task for the week was to start practicing immunocytochemistry on a hepatocyte cell line. These cells are cancerous hepatocytes that can replicate indefinitely in culture. They can’t be used for drug screening or other applications because they don’t represent healthy cells, but they still possess many hepatocyte traits and are useful for practice. With immunocytochemistry, I can determine whether certain proteins that are unique to hepatocytes can be detected, which is very useful for analyzing the results of my experiment. However, the hepatocytes I grew never seemed to thrive, and in the end, weren’t dense enough to run the immunocytochemistry procedure on. Fortunately, these cells are inexpensive and I won’t need to use the techniques on my iPSCs until the first experiment ends in two weeks, so I have plenty of time to start over and try again.
Week 08: Research in Japan vs. Research in the U.S.
I’ve been surprised at how similar my Japanese lab is to the two labs I’ve worked at in the U.S. As part of the orientation program, we learned a bit about how Japanese research labs can be different from ones in the U.S.: they tend to be larger, the principal investigator typically doesn’t do experimental work, and there are very few undergraduate students. There also tend to be long working hours, and a strict hierarchy is usually present from the PI on down. However, Kamei-sensei’s lab doesn’t match any of these stereotypes. Part of this is because it is a very new lab, so we don’t have postdocs or a larger number of students yet. (Right now, in addition to me and Kamei-sensei, there are two undergraduates, a lab tech, and a one visiting master’s student, my mentor Nicolas.) Everyone except the part-time undergraduates works a fairly steady 9 AM – 6 PM day, five days a week. Kamei-sensei still does experimental work and even shows me how to do procedures occasionally. Finally, I get a lot of direct interaction with Kamei-sensei, which is a great opportunity for me. Since no one in the lab has done my type of experiment before, he fields my questions on even minute details things like how to add compounds at high conecntrations without diluting the cell medium too much.
Both of the labs I’ve worked in in the U.S. also had just a few people, and I talked to the professor at least a couple times a week, so this is a comfortable environment for me. But from what I’ve heard from the other fellows, my experience isn’t at all typical. I think there are a few reasons for this. The first is that Kamei-sensei did research in the U.S. for seven years, and so has had the opportunity to observe both the American and Japanese ways of doing research and pick the aspects he likes best of both. Another is that Kamei-sensei’s lab got started very recently and hasn’t built up the large number of people that might lead to a more business-like environment. And finally, I think iCeMS itself is a very unique research institution. There are labs from many different fields of research in the same building, and researchers are encouraged to discuss their work and collaborate with others. It seems like multidisciplinarity is less common in Japan. For example, getting more than one major in college is almost unheard of. I think the iCeMS space, by bringing lots of people with different backgrounds together, encourages researchers to exchange ideas freely without getting too wrapped up in hierarchy or roles.
Of course, this is all coming from my perspective as an American, and one downside of my lab is that I haven’t gotten to experience the more “traditional” Japanese way of doing research. It would be nice to have the opportunity to do a better comparison, but from everything I’ve heard I think I’m glad to be working in a lab that follows the American model more closely.
One difference I have noticed about my lab is that very little is discussed at our weekly meetings, which tend to be short. Kamei-sensei gives a few announcements, and then Nicolas or Terada-san might bring up a brief point, and then we’re done. The undergraduate students hardly speak at all. I’m not sure if this is out of respect for the more senior members, or if it’s because they’re uncomfortable with English (which we’re all supposed to use). After a month here, I still have no idea what the undergraduates are working on, because we don’t discuss our projects at the meeting. Kamei-sensei sends us relevant journal articles to look at over email, but we never discuss them as a group. My U.S. labs had weekly journal meetings, which is something I really miss. Reading a paper every week and getting gaps that you missed or didn’t understand filled in is a great way to get acquainted with a new field.
As an example of how interactions in our lab usually work, last week I was checking the procedure for serum-coating a cell culture plate with Nicolas. He confirmed the steps with me, but I realized that he and Kamei-sensei had given me different temperatures for the plate to be stored at overnight. I went with what Kamei-sensei had told me, but a couple days later I asked Nicolas if the other temperature was written down in the official culture procedure write-up. It was, so I decided to go visit Kamei-sensei and ask him about it. He asked to see the procedure, and then went to double-check with our technician, Terada-san. Terada-san confirmed the different temperature, so after that I changed how I did the procedure. This whole experience ran contrary to my expectations about Japanese research. Kamei-sensei makes himself available for asking these types of questions, and wasn’t upset that I bothered him over something so trivial. And even though Terada-san is a technician, not a researcher, she is our expert on cell culture and had an important say in the final decision. Finally, catching the difference was possible because Nicolas kindly walks me through everything until I’m confident enough to do it on my own. Overall, I think we have a very positive dynamic.
Question of the Week
How uncommon are multidisciplinary research institutions like iCeMS in Japan and in the U.S.? Since it seems like they can be so beneficial, why don’t we see more of them?
- It depends a bit on the institution and funding mechanisms that are available to support these types of centers. At Rice, there is an interdisciplinary PhD program in Applied Physics through the Smalley-Curl Institute. While not its own stand-alone building like iCeMS, this center does bring together researchers and students working in a range of disciplines on quantum materials.
- You’ll likely find some sort of center/group like this at almost any university in the U.S. and it’s a good thing to look into when you are considering future graduate schools. What is the culture of interdisciplinary research on and across campus? Are there interdisciplinary research centers or even graduate degree programs you can join?
- The National Science Foundation also has special grant programs, such as the Engineering Research Centers and the Science & Technology Centers among others, that fund interdisciplinary and inter-institutional research centers around various themes. At Rice University, we are the headquarters for an NSF Engineering Research Center named “NEWT: Nanosystems Engineering Research Center for Nanotechnology Enabled Water Treatment Center”. These center grants are very large and are awarded to universities nationwide via a very competitive grant proposal process. Pittsburgh is currently in the running for a different large center grant for the Pittsburgh Supercomputing Center.
- Also, many new science and engineering buildings are being built to mirror the design of institutions like iCeMS where you have researchers from more than one department, center, or discipline working together in the same building and sharing common spaces. In this way, it is thought that there will be greater opportunity for informal and formal interdisciplinary engagement. (Though it’s also cheaper and makes better us of the limited land available rather than each department having its own stand-alone building).
Research Project Update
The frustrating theme of this week has been that the cells won’t grow. Even though it was the Mid-Program Meeting, I made arrangements to come into lab over the weekend and change the medium for my cells. However, they failed to grow well, and on Monday it became clear that they weren’t going to be viable to use in my experiment. Furthermore, there were huge chunks of something unidentified in the culture dish. After some investigative work, it turned out that some of the solutes in the medium I had been using had come out of solution while it was frozen for storage. Apparently, it was the lab’s first time using frozen medium, and I hadn’t even realized this was something I might need to worry about. The cells probably weren’t getting enough nutrients because the medium contents weren’t properly dissolved. I also found out that I needed to add two more proteins to the medium that are pretty important for happy hepatocytes.
With these mistakes corrected, we thawed more cells on Wednesday. This time, Kamei-sensei did the procedure to make sure that my inexperience didn’t damage them in some way. But when Friday rolled around, they still didn’t seem to be attaching and growing very well. We’re not sure why this is. Were the cells damaged somehow by being frozen? Were we transferring them to the dish at too-low concentrations for effective attachment and growth? Did something go wrong with them just before being frozen, and we only now see the effects? It’s difficult to say for sure, and this is a cause of great frustration for me. When I run a program, I’ve written for the first time, I expect there to be bugs that keep it from working. But those bugs always have a logical and identifiable cause, and getting the program to work correctly is just a matter of finding where what I want the computer to do differs from what I’ve actually told it to do. But I may never figure out why these cells aren’t growing properly, and I don’t know how to deal with that. If I had more time, I would be okay with letting things take their course and tweaking the procedure until I have a working experiment. But with only a month left, I don’t know what on earth I can present about when I haven’t even been able to start an experiment yet, much less get results.
As this was a short week due to the mid-program meeting, I don’t have much else to report. I made a wish at Tanabata for my cells to live, so maybe next week everything will finally start working!
Week 09: Reflections on Japanese Language Learning
I love learning Japanese. I’ve been fascinated by the writing system for a long time, but have always been daunted by the amount of time and effort it would take to learn. When I found out I was a finalist for this program, I finally had an excuse to devote time every day to learning kanji. The knowledge that I’d be grateful for everything I could pick up beforehand kept me going steadily up until my arrival in Japan. Ever since I’ve gotten here, however, learning new kanji and words hasn’t just been an abstract goal but something that I can immediately use in my everyday life. New words I learn seem to suddenly turn up everywhere. For example, after I learned the word for ‘caution,’ I realized that it was being used on train announcements for every stop.
Another huge motivating factor for me is the desire to read Japanese. I’ve been making a ton of progress here, and it’s very practical for reading signs like “this water isn’t safe to drink” or “one way except bicycles.” Being able to comfortably read books is still a ways off, but reading manga gets a little bit easier every week, and I’ve spent many evenings in the used bookstore chain Book Off hunting for good reading material. I will be lugging a small library back home with me in three weeks, and I have no regrets! Being in Japan and seeing all of the books, comics, and video games I want to experience firsthand has definitely strengthened my desire to achieve fluency.
Despite loving learning and reading Japanese, however, I haven’t spoken it very much while in Japan. First of all, Kamei-sensei prefers his students to use English, so lab meetings are held in that language. In addition, the only people in lab I regularly communicate with are Kamei-sensei and Nicolas. I wouldn’t want to waste Kamei-sensei’s time by trying to speak Japanese with him, and Nicolas doesn’t have much interest in trying to speak it beyond what’s needed to be polite. The one person in lab I do try to speak Japanese with is our technician, Terada-san. She doesn’t speak English very well, so whenever I need to talk with her I do my best in Japanese. One time, I needed to ask her about some medium I needed for cells to practice immunocytochemistry with. Kamei-sensei taught me how to say “immunocytochemistry” and “medium,” and then I went and made a list of other words I might need, like “experiment.” In the end, I was able to ask Terada-san what I wanted to and more or less understood her response! That was the most challenging experience I’ve had in Japanese, and also the most rewarding. I think Terada-san appreciated that I made the effort, too.
Outside of lab, my ability to speak to the people around me seems to vary a lot day by day. One of my best achievements was buying a discounted shinkansen ticket from a travel agency, which involved a half hour of conversation about timetables and cancellation policies entirely in Japanese. But on other days, I panic when asked something as simple as whether I want a bag for my groceries. I think I had slightly unrealistic expectations that living in Japan and being immersed in a foreign language would magically propel me to fluency in a month. Maybe if I had a year or two of Japanese under my belt before coming here I would be in better shape, but Japanese grammar is so different from English that I think it would be difficult to speak on the fly no matter what. I also sometimes have difficulty talking to strangers in English, so it’s no surprise that Japanese makes things even harder.
I’ve continued to study Japanese on my own since coming here, especially kanji. I know about 500 now! I use software called Wanikani, which is a little expensive but allows for very efficient memorization. I would highly recommend it for anyone who is serious about trying to read Japanese, but it isn’t very helpful for conversation. I also try to study grammar using my textbook from class, as well as web sites. This is a little harder to do on my own, since sometimes it can be difficult to memorize and use new grammar without the help of a teacher to give examples and answer questions.
On Saturday, I went to Himeji Castle, the most impressive of its kind in Japan. The 2.5-hour train ride from Kyoto was completely worth it: the castle was very beautiful, and a volunteer English tour guide took me under her wing and told me about all of the strategies for repelling enemy soldiers as we walked through. These are so varied and clever that I think it’s a shame the castle was never attacked! My favorite was a rock wall that was designed so that pulling any single stone would cause the entire structure to collapse over the path. Even the plants were chosen carefully – slippery reeds were planted all over the keep to impede an enemy’s progress.
On Sunday, a large group of us went to Kyoto’s Gion Matsuri in our yukata. Gion Matsuri is the second-largest festival in Japan, and it really showed. Street after street was completely packed with people. I’m very glad I went with other fellows, because if I were on my own I probably wouldn’t have lasted longer than fifteen minutes in that crowd! There was lots of delicious festival food to be had, and we talked about research and different places we’d visited while the sound of flutes and bells drifted down from the parade floats scattered about the city. As the evening went on, station entrances and were strategically blocked off and streets designated one-way to help manage the crowd. I think the logistics of managing an event like that must be fascinating. How do you ensure that as many people can enjoy the festivities as possible while not allowing the crowd to reach dangerous levels? In Japan, especially, I’m sure large cities must be very experienced with all this.
Question of the Week
How do Japanese people feel about tourism? Does it offend anyone when travelers visit shrines and temples as tourist destinations instead of viewing them as spiritual places? In general, are Japanese people happy to share their culture with foreigners, or do they get tired of people not following their customs? (Everyone in this program has been incredibly nice to me, but I wonder about people I see on the street!)
- In a city like Kyoto, where there are tons of tourists all the time (both domestic and foreign), I’m sure many locals who live there do tire of the crowds. It can be difficult to just go out and run your everyday errands and get around town with the streets, buses, and sidewalks are crowded with lots of tourists.
- But this is also why in all tourist cities/locations you’ll find areas that aren’t really heavily marketed to tourists that are quieter and more local in flavor, or that locals frequent in early morning or evening hours when tourists are less likely to be out. Locals may know that to beat the crowds its best to visit shrines/temples or other popular tourist spots when it’s raining or during the down season for tourists when they are less crowded. So, you just get a bit savvier about what you do and when if you want to avoid lots of crowded touristy places when you live in a city like Kyoto.
- You might also ask your labmates what they think of all the tourists in Kyoto and if there are ever times they get especially weary of the crowds or things that tourists do that particularly frustrate them.
- But there are stereotypes about foreigners, especially tourists, in Japan just like we have stereotypes about foreign tourists in the U.S. and some ‘types/groups’ of tourists may be more or less liked (stereotypically) than others. For more on this see the section on ‘What do People in Japan Think of Americans/Foreigners’ on our Life in Japan page.
Research Project Update
Another week has gone by where, unfortunately, we can’t seem to revive the frozen iPSCs successfully. This week I tried batches 4 and 5 with slight variations to the procedure, but without much improvement. I’ve been spending a lot of time thinking about what might be going wrong and discussing with Nicolas and Kamei-sensei. Since I don’t have any results or other developments to report, this week I’d like to go over all of the possible problems with trying to culture the cells, their likelihoods, and how I would try to fix each scenario.
Culture medium: I’ve been thawing small batches of one large preparation of medium created by Terada-san for iPSC-derived hepatocyte-like cells. If something were wrong with the entire batch, it would have affected every thawing attempt I’ve made. Alternatively, the original medium might have been fine, but the process of thawing it and re-dissolving the components might have damaged it. If this were the case, I’d want to try making fresh medium. I talked to Kamei-sensei about this possibility, but he says that freezing the medium is a routine procedure, and Terada-san has been using it for her cells without any problems. Since the medium components are probably expensive, it doesn’t make sense to make a large batch on a whim, so this is a dead end.
Low cell density: Perhaps there weren’t as many cells in the frozen vials as we thought, and we aren’t sowing them on the culture plate with enough density for success. I tested this with batch number 4, where I seeded one vial of cells to one culture plate instead of two. The cells looked very promising for one day or so, but started dying after the first medium change and failed to attach more or proliferate well. Given that the cells seemed okay at first but then failed to thrive, I think something else must be the root of the problem.
Substrate: I’ve been trying to culture the cells on serum-containing medium. This is regular medium which contains animal serum (blood with the blood cells removed, containing hormones and growth factors that are beneficial for animal cell growth). It’s necessary for the ‘3D’ part of my experiment, because cells grown on it in a microfluidic environment spontaneously form 3D tissue-like structures. However, it can also be somewhat unstable, and cells don’t attach to it as easily as Matrigel, the main alternative. Furthermore, there is batch-to-batch variation due to using a non-defined animal product as a major ingredient. In order to test the hypothesis that the serum medium might be the culprit, I cultured iPSC batch number 5 on Matrigel, a protein mixture that mimics the extracellular matrix of many tissues. However, batch 5 also failed to show much attachment or proliferation, so this also seems to be a dead end.
Growth factors added to medium: Whenever I thaw a new tube of medium, I have to add two growth factors, OSM (oncostatin M) and HGF (human growth factor). These need to be in appropriate concentrations and used relatively quickly since they are less stable than the other medium components. Although it is very possible that I made a mistake when adding these once, it’s hard to believe that I’ve messed it up for every single batch we’ve tried. I’ve double- and triple-checked my dilution calculations for how much to add, but I can’t see anything wrong with them. Another possibility is that the supply itself is bad in some way, but as Terada-san has been using it without problems, this seems unlikely.
My inexperience: Another possibility is that I’m somehow damaging the cells or taking too long while doing the thawing procedure. This has a strong chance of being the case, because I haven’t worked with live cells before and could easily be accidentally doing something that is fatal to the poor cells. However, for batch number 3 Kamei-sensei did the procedure himself while I observed so I could improve my technique. After this I made some small corrections to how I pipette, but neither Kamei-sensei’s batch nor my batches 4 and 5 were successful.
The frozen cells just aren’t viable: I’ve mostly eliminated all of the possible problems above, so this is the major one remaining. From what I can tell in the literature, freezing cells is a fairly routine process these days, but it still seems like it might be stressful or damaging to the cells. I’ll get a chance to test this next week, when Terada-san will finish culturing fresh iPSCs and be able to give me some day-12 cells without ever passing them through a freezer. These cells will go directly to the microfluidics, and will be my last chance to conduct my experiment before the end of the internship. Even though I know for a fact these cells are viable and have been growing well, putting them into the microfluidics still has some risks associated with it, so I’m very nervous. After all the difficulty I’ve had keeping cells alive for more than a couple days, keeping them alive for two weeks (with a bunch of weird chemicals added to boot!) seems like an insurmountable task. All I can do at this point is be very careful, ask lots of questions about the procedure, and hope for the best.
Week 10: Interview with Japanese Researcher
This week I talked to Dan Ohtan Wang-sensei and some of her lab members about their research and international experience. Wang-sensei is a PI at iCeMS who studies mechanisms of memory formation in the brain. She also happens to be married to Kamei-sensei! She did her undergraduate education and Master’s degree in Japan, and then got her PhD in the U.S. before returning to Japan and starting her current position.
Wang-sensei’s undergraduate degree is in bioengineering, which surprised me as it is a fairly new field. It was the newest department at her university when she went there, and she was attracted to it because it focused on more applied research than a traditional biology degree. Around that time, genetics research was really starting to take off (Dolly the cloned sheep was born in 1996), and she became very interested in how genetics work in the brain and decided to become a researcher. Her current research focuses on memory formation and how the brain reshapes itself in response to environmental cues. She says that if there were only one fascinating idea she could share with people outside her field, it’s that long-term memory is based on gene expression. In order for the brain to record new ideas and experiences, different proteins have to be expressed, and that happens because environmental cues change the way a neuron’s DNA is transcribed. It’s amazing to think that I have memories of our talk that are allowing me to write this report, and they only exist because some of my neurons changed their genetic expression.
Another topic we discussed was how research in Japan differs from that in other countries. Since Wang-sensei got her PhD in America, she is quite familiar with both the American and Japanese style research. She says that at UCLA, at least, she was impressed by how students took control of their research and brought significant projects to completion. Many of these students would take as much as 8 years to finish their PhD’s, but had very complete projects as a result. In Japan, on the other hand, most students finish their degrees in three years and feel pressure to wrap things up whether they have brought their project to a good conclusion or not. This system may mean that not as many ambitious projects are completed, but it does allow students to finish their education and get started with what they want to do next more quickly. In Wang-sensei’s experience, the overall level of research is pretty similar between the two countries, although America has many more labs and therefore more famous ones as well. One challenge with working in Japan as a female scientist is the low number of female PIs and professors, especially compared to the US. However, that is steadily improving with time.
Wang-sensei has a very international lab, with students from India and Egypt as well as Japan. Rohini, a graduate student from India, told me about her experience there as well. She said that while there are nationally funded labs in India with very hardworking researchers, there are definitely more barriers to doing research there. It can take a very long time to get reagents and other materials necessary for doing experiments, for example. Apart from the convenience of doing research in a more industrialized country, however, Rohini thinks that doing research internationally is very beneficial for anyone considering pursuing a career in academia. As she pointed out, the goal of a young researcher is to become a PI and have your own lab someday. If you can’t work with people from other countries as a student, how could you hope to do so when you have the responsibility of being a professor? Wang-sensei agreed, and added that as a graduate student you have great mobility, and can go anywhere you want. Both of them highly recommended doing graduate study in another country.
Wang-sensei also advised me not to worry too much about exactly what I study as a graduate student. It seems that most people do not end up making a career out of the exact same area of research that they did while obtaining their PhD. Although Wang-sensei’s PhD was in neuroscience, she didn’t start working on memory and neural plasticity until she became a postdoc at the University of California, Los Angeles. Although I didn’t go into the interview intending to talk about graduate study so much, I ended up having a lot of my concerns about it being addressed. A huge thank you to Wang-sensei and her students for welcoming me to their lab meeting and answering all my questions.
I’d also like to talk briefly about my trip to Koyasan on Saturday. Koyasan is a mountain a little over 100 km south of Kyoto. Koyasan is known as the place where the Kobo-Daishi, a Buddhist monk who is one of the most venerated religious figures in Japan, is said to have been in constant meditation for the past almost 1200 years. (Wikipedia will tell you that he died in 835, however.) The Kobo-Daishi, known as Kukai during his life, went to China to study Buddhism and founded the Shingon Buddhist sect in Japan. He also invented kana, the phonetic Japanese alphabet! Today, Koyasan is popular as a place of spiritual pilgrimage as well as a tourist destination. One of the things I love about Japan is that it’s perfectly acceptable to appreciate the historical and aesthetic value of places like this without any particular religious commitment, as long as you’re respectful.
Koyasan was absolutely beautiful. In front of Kobo-Daishi’s mausoleum, Torodo Hall contains more than 10,000 lanterns. Beyond this lies a cemetery that stretches for over a mile, where graves and statues from all over the last millennium rest in a forest of ancient cedar trees. (After Kobo-Daishi’s death / retreat to eternal meditation, everyone wanted to rest next to him.) Although these were the main attractions, I also visited two temples out of the several dozen on Koyasan. One, founded by Kukai, had the largest Zen rock garden in Japan as well as a beautiful series of screen door paintings depicting Kukai’s journey to China and return to Japan. An unexpected surprise, however, was my spontaneous visit to a small pagoda that had an almost cabinet of curiosities kind of vibe. Puppets, Buddha statues, and historical photographs were displayed on the walls, and it was the only temple I’ve been in where it was okay to take a picture of a priest chanting at the main altar. It also had a giant rosary that you could turn to get your fortune, and a pitch-black basement that you could walk around with the help of a handrail. Overall, my trip to Koyasan was one of my favorite days in Japan, despite the four-hour journey there and five-hour journey back (I was tired and got on the wrong train).
Question of the Week
Why do Japanese nutrition labels not provide as detailed information as their American counterparts? Does anyone actually read these labels, or are they mostly ignored like in America?
- What is required to be on nutrition labels us usually set by the federal government, in the U.S. through the Food and Drug Administration. This changes over time as regulations and how nutrition information is reported changes. Just Google nutrition labels 1970s and then 1980s and then 1990s and check out the differences in some of the images you find for U.S. labels.
- Here are some websites on food labels in Japan.
Research Project Update
This week, fresh iPSCs at day 14 cultured by Terada-san became available. I came into lab after the Gion Matsuri parade on Monday to finish preparing the microfluidics plates, and everything was ready to go. But of course, nothing goes quite according to plan in research… When Kamei-sensei had me bring out one of the plates so he could demonstrate the correct way to pipette into the tiny wells for introducing cells and fresh medium, it became clear that the PDMS polymer hadn’t adhered well to the plastic slide. Although I had been able to coat the wells with serum the day before without major leakage, it seemed that the introduction of liquid had worsened things overnight. Furthermore, pipetted liquid seemed more inclined to come back up the hole we pipetted into than travel into the culture well. This happened to me while introducing serum, but I thought it had more to do with my inexperience than the chip itself. In any case, Kamei-sensei concluded that the chip was unusable.
Things were looking grim, but Kamei-sensei had a secret weapon: a chip he designed back when he was a postdoc researcher at UCLA. This chip is much smaller, because it was made with the more precise soft lithography technique instead of 3D printing and therefore culture wells could be placed closer together. With this design, we could fit the chip onto a glass slide, which PDMS attaches to much better than plastic. We turned up the heat on the oven and made a chip using this mold as quickly as possible, finishing just in time to coat it with serum and leave overnight as required. With the new chip, pipetting became much easier, and I was encouraged to have something that seemed more reliable.
On Wednesday, we were ready to insert the cells. With Kamei-sensei watching to make sure everything went smoothly, and I successfully uprooted them from their old home and transferred them to the new chip.
The next day, I prepared the eight different media I would need. This was left until the last minute because of the fragility of proteins used in the culture medium. Since I had made stock solutions for all of my chemical compounds beforehand, it was just a matter of keeping careful track of how many microliters of each to pipette into which little tube. With that done, I made my first medium change on the cells and took pictures of every well. Although this was a little tedious with 54 wells to go through, I was very happy to be doing a real experiment. On Friday, Kamei-sensei agreed that the cells seemed to be doing well.
So, at the eleventh hour, I can finally say that the cells are alive! No matter what happens now, I have pictures showing how their shape and number changed while in the presence of my chemicals. That might not amount to publishable data, but it’s data all the same, and I’m thrilled to have it. Another, slightly less important batch of cells also pulled through – a second round of Hep G2 cells for immunocytochemistry practice did very well, and I started the fixing and staining process on Friday. This will give me practice with the experimental procedure as well as analyzing the results before I do the same for my one precious batch of iPSCs. This is especially good since time might be very tight between finishing my experiment and needing to incorporate data into my poster during the last week of the internship. Nicolas says he once got his final data less than 24 hours before the submission deadline for his thesis. While it makes for a good story, I hope things won’t be quite that tight for me!
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Week 11: Critical Incident Analysis – In the Lab
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Week 12: Final Week at Research Lab
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Week 13: Final Report
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Tips for Future Participants
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