Home University: The University of Tokyo
Field of Study: Bioinformatics and Systems Biology
Status: B3 Expected Graduation: March 2019
Research Host Lab: Prof. Junghae Suh, Department of Bioengineering
Why Nakatani RIES?
The two main reasons why I applied to the Nakatani RIES program is that I believe it will help me think about my career as a research scientist and that it would broaden my horizons. In Japan, many people believe the research environment in the US is quite different from that of Japan, and that experiencing research there would be a big plus for one’s career. Experiencing this for myself through this program would help me decide whether I should study abroad in the future for graduate or post graduate studies. I am also curious about the careers of female researchers and the challenges they may face. The number of female researchers in Japan is still limited and I cannot help but anticipate my future in such environment. In the US, there is much research done in computational biology, which I’m majoring in, and I wish to experience such atmosphere where it is so appreciated as well.
I also wish to broaden my horizons by learning about the various research done at Rice University, including research in areas that I am not yet familiar with; meeting people from different backgrounds and communicating with them; experiencing things new to me including food and culture. I believe this program is an invaluable opportunity for undergraduate students to experience research in the US. It will support students who love science, refuel their passion for it, and encourage them to pursue their dreams.
- Practice to explain things logistically using English in an easily understandable way.
- Learn about the career path for researchers in the US.
- Experience various cultures and communicate with many people with different values.
Excerpts from Nina’s Weekly Reports
- Week 01: Arrival in the U.S.
- Week 02: First Week in My Research Lab at Rice
- Week 03: Interview with a U.S. Researcher
- Week 04: Reflections on English Language & Life in the U.S.
- Week 05: Research in the U.S. vs. Research in Japan
- Week 06: Final Week at Rice & Research Poster Presentation
- Week 07: Visit to Washington, DC & New York City
- Final Report & Tips for Future Participants
Week 01: Arrival in the U.S.
As a part of the opening ceremony in Tokyo, we attended a lecture by Dr. Nishikawa on the importance of life science in the 21st century, and Prof. Ida on PhD careers. Although they were both very interesting, I particularly appreciated the one by Dr. Nishikawa as his topics was directly related to my current major. I was lucky enough to talk to him over lunch, and asked him advice about pursuing a career in research related to immunology. This is not only what my interest is in but is also what Dr. Nishikawa specialised in early in his career. Surprisingly, he told me that he would advise me not to go into that particular field, but to pursue other interesting areas such as the brain, as there isn’t much left to study. He also stressed that I should keep my mind open for topics seemingly unrelated to my specialty, as I might happen across a research topic that inspires me to pursue, or to collaborate with others. I was enticed by immunology since the first time I learned about it in high school, and hearing not exactly encouraging things about it from a well-known researcher of that field made me really think and doubt my passion for it. During this program, I will be doing research about viruses. Virology is closely related, or is even a part of immunology in the sense that viruses meddle with, and elegantly circumvents the host immune system. Through studying about viruses and doing research, I intend to rethink about my interests in immunology, and keep my eyes open for new fields of study to broaden my perspectives as Dr. Nishikawa advised and this is obviously a helpful thing.
What surprised me about Houston is its humidity. For some reason, I assumed Houston would be hot but without humidity, like in a desert. My friends at home even texted me on the night of my arrival asking me whether I had seen any cowboys yet. As it turns out, Texas doesn’t even have a desert. On the contrary, the area in Houston where we are staying is greener than any other city I have been to in Japan; the park I saw from my window turned out to be a residential area. And of course, Houstonians being super friendly is hard to miss. When I went to Sydney, Australia couple of years ago, I was surprised that complete strangers walking down the street would smile at me when passing by. But Houstonians are even friendlier. They don’t just smile, but really beam at me. They also never fail to voice a greeting, asking me how I am. This is especially a surprise to me as those who live in Tokyo are a quiet, shy and conservative bunch. While I am here in Houston, seemingly the friendliest city in the country, I would try and be as friendly as the others so as not to be rude. As they say; when in Rome, do as the Romans do.
On Wednesday, our first full day in the US, we had orientations and a very helpful but hot campus tour. The next day we attended general and bio-safety lab training, and later on Prof. Kono and Sarah gave us a
lecture on research in the US and intercultural communication respectively. Prof. Kono insisting that it would be better for us to go to the US as a full-time student as earliest possible was interesting, because normally I hear people saying that there are many paths possible and each has a full set of its own advantages and disadvantages.
On Saturday, I went to Minute Maid Park to watch the Astros vs Athletics game with some other Nakatani fellows. As a fan of baseball, I was very excited. Compared to the games in Japan, I felt that this one had a speedy feeling to it, which may be due to the pitchers throwing faster balls, or how swiftly the teams switch places after each inning. To our delight, the Astros won the game by 3-2. It was an great experience but would have been perfect if Nori Aoki, who I am a fan of, was still with the Astros (He was traded to Toronto Blue Jays at the end of last month).
One afternoon, I went to Chinatown using the local bus system. It took about an hour to get there but it seemed to cost us only $1.25 which was amazing compared to Uber. Me and my friend imagined Chinatown to be something similar to the one in Yokohama, Japan, with many small family-owned stores lined up on both sides of a street. The Chinatown in Houston turned out to be more like Rice Village, with a several dozen stores surrounding a parking lot and one huge Chinese grocery store. The grocery store had many Chinese products, and surprisingly, I felt more at home and relaxed than I felt at H-mart, the Korean store. This may be because I have been to China but not to Korea. This was especially interesting for me because before I started learning Chinese and went to China, I never felt a particular liking for Chinese culture including its cuisine. After this program, I may even feel nostalgia for American food. After we left the grocery store, we asked whether there was a place for sightseeing, like a temple, and it turned out there wasn’t any. We then searched on google map and learned that there indeed was a temple but was a 20-minute ride from where we were. We rode the bus and walked for a very hot 10 minutes under the blazing sun and finally got to the temple! The lesson I learned from this experience is that things are not always what you expect to be, and that culture may be acquired.
Preparing for Research in the U.S.
Before arriving at Rice, I contacted my mentor who recommended some papers for me to read. For future participants, I would advise them that the sooner they start reading the papers the better, and that they should start by reading literature reviews to help them grasp a general understanding of the topic.
Question of the Week
Why are the bathroom doors so small? It seems quite easy to peek from above the door. As the ones in Japan covers more area from top to bottom, the ones here do not feel private enough to me.
- Yes, this is a common complaint that many foreigners have about bathrooms in the U.S. If you Google Public Bathroom Doors in the U.S. you’ll find many funny comments about this same problem.
- America, Why Are There Huge Gaps at the Bottom of your Bathroom Doors? (Buzzfeed)
- 7 Answers to Why Public Restroom Doors have Gaps
- Video: Why Japan’s Public Bathrooms Put America to Shame
- 12 Awesome Features of Japanese Bathrooms you Won’t Find in the West (Japan Today)
- Why Japanese Toilets are Failing in the U.S. (Tofugu)
- Also, tubs in the U.S. are typically much shallower and longer than in Japan where deep-soaking tubs are standard. In the U.S., where ‘time is money’ most people prefer to take showers which are faster (typically in the morning) rather than take a long hot bath at night. In many hotel rooms in the U.S., there won’t even be a tub, just a shower.
Week 02: First Week in My Research Lab at Rice
There are five undergraduate students in my host lab, who are all in the same year as I am, and are all very friendly. On my first day, two of the undergraduates, Kiara and Joanna, were in lab, and they showed me around and talked me through the completed/ongoing projects of the lab. This was very helpful because although I had read about many of the projects prior to my arrival from the papers my mentor recommended, I did not feel like I understood the concepts introduced in full as there were many field specific terms used. My host lab is at the BRC, BioScience Research Collaborative, which is located between Rice University’s main campus and the Texas Medical Center. It may be due to its collaboration promoting nature, or just unique to my floor, but on the walls of the hallway connecting the student’s office and the lab, there are posters about prior research done by the labs on that floor. Kiara and Joanna used those posters to explain the projects to me, which made it considerably easier for me to grasp the concepts. I experienced for myself just how much a figure is helpful to an outsider, and made a mental note to put nice pictures or figures on my own poster so that my audience would hopefully, like me, have an easier time understanding my project when I present it in the final week. The other lab members were all very friendly and welcoming as well. Interestingly, it may be because Prof. Suh is a female as well, but more than half of the lab members are women. I believe one would be hard pressed to find such a lab in Japan.
My mentor, Nikki, is a fourth-year PhD candidate and has a very sharp minded but is also a kind and friendly person. She seems to have a lot of experience with undergraduates, and has a realistic view of what I can and should learn during my short stay, which I very much appreciate. It is also hard to miss how organized and efficient she is with her lab work. This is currently my top priority of things to learn while I am here, as biology-related lab work tends to be tedious and time consuming. This is one of the things I anticipated when considering a career in this field. As far as I have observed, proficient use of technology and careful planning seems to be a part of her secret.
Explaining something in a scientific context is something I need to practice and learn. This is partly because I have hardly ever studied science, especially math, in English. For example, when you are mixing substances in chemistry, you would probably say something like “mix a and b in a ratio of 3:1”. This is a sentence you would not learn at an English class. However, it is possible to come across such phrase in a book or paper and thus learn it. Interestingly, the part I had the most trouble with was reading “3:1” as “three to one”. I obviously understand what the symbols mean, but did not know how to read them aloud and felt for a split second like a seven-year-old. Luckily, my mentor talks me through what she is doing when we are in the lab, so I watch and listen, both for the science and the language.
At the end of the week, I have come to conclude that my conversational English is sufficient to manage life and keep away from eminent danger in an English-speaking country, but rather I sometimes do not know what I should say regardless of the language. Suppose a graduate student was talking to me about something non-work-related. In Japan, I would just kindly agree with them or even flatter them a little because they are older, and such respect is expected of me. Here, undergraduates in the same circumstance may give the elders their advice or if they are agreeing, they will do so very enthusiastically using frank words. For now, I still feel awkward not knowing how to react or comment on people’s words but as Sarah said, I believe I would have to “feel my way” by observing and experimenting.
This week we also had a seminar on how to design and develop a poster and lab safety training. Because the lecturer spoke to us in an engaging way and did not just read off her notes, the lab safety training was surprisingly enjoyable compared to those in Japan. It was also helpful to have the poster presentation session before we started with our projects because then we would know what our goal is.
Besides research, one evening we went to the Houston Museum of Natural Science. They had an extensive taxidermy display, which I enjoyed. I was also excited to see the exhibition centering the ecology of Texas’s gulf coast. As I am fascinated with ecology, I spent a lot of time here studying the exhibits. Overall, this opportunity made me remember once again what made me enthralled with science in the first place; my love and curiosity towards mother nature and its mysterious beauty.
I also went to the Cheesecake Factory, which was recommended by past Japanese fellows. I love cheese and sweets, and felt a swarm of pure happiness for the first few bites; but the cakes were in American size and were just too much for even me. But still, the cakes were great, and I highly recommend anyone who likes cheesecakes to try it out at least once.
Research Project Update
My mentor is examining whether a model called Protein Frustratometer that calculates the local energetic stability of a given protein conformation, may be applied to proteins consisting viral capsids in AAV, Adeno Associated Viruses. This is done by first identifying amino acids of the capsid protein with an unique energetic trait, and then replacing them with a neutral amino acid and examining the effect. I would probably help confirming the model’s credibility for one or two amino acids predicted to have be energetically neutral, as a control experiment. This means that if the viruses I modified had different characteristics compared to the unmodified ones, the whole credibility of my mentor’s project would become questionable. But that was just me being dramatic, and I believe the results would turn out okay.
The project would require bioengineering techniques such as designing plasmids (calculating what kind of mutation to introduce to change the amino acid), transfection (amplifying plasmids, which are circular DNAs) and transduction (introducing the viruses into the cell). We will also need to quantify the DNAs by using techniques such as qPCR. I have experienced these before, but not with mammalian cells which I hear is considerably more complicated to work with. Moreover, at school we were given a book with methods used for decades in the course, and we were to just follow them. But the method used in my mentor’s research is what she thought of, and it is interesting to think over, and sometimes ask, all the reasons and logic behind her choosing each procedure.
For now, I am more focused on reading papers and understanding the theory the project is based on. The Frustratometer uses an unique concept called “frustration” which is originally a term used in condensed matter physics, and is probably the model’s namesake. A protein region which is minimally frustrated would presumably comprise a stable folding core, whereas a highly frustrate region would be involved in binding with other proteins. Further, the Frustratometer’s calculation is based on a model called AWSEM, which, according to my understanding, predicts the tertiary structure of a given protein based on its amino acid sequence and environment. It is relevantly easy to vaguely grasp the concept of frustration and AWSEM, but it is considerably difficult to understand it enough to explain it to another person, which I would have to do at my poster presentation. Moreover, since I am a natural science student and not an engineer, I tend to be inclined to understand the theory as much as possible before considering its application, or just using them in general. And because this time, the concepts are those of biophysics, which I have circumvented in the past, there is a lot for me to learn. On the bright side, this is a better opportunity than any for me to get to know about the field, as I have an excellent mentor to help me when I am in need.
Question of the Week
This weekend, we unfortunately experienced hurricane/tropical storm Harvey and saw on TV the numerous floods it caused around Houston and Harris county. In Japan, especially in a developed city like Tokyo, we have drains every several feet along each road no matter how narrow it may be. These drains are connected to huge underground tunnels and vast space which are designed to store the excess water until we can safely drain them through our conventional drainage systems. As a result, although flooding of rivers is sometimes a problem, but other areas are mostly safe. Conversely, I have noticed that such road drainages are not prevalent here, and have also heard tell that Houston and Rice are both prone to flooding. As Houston is close to the Gulf of Mexico and evidently experiences many storms, I cannot help but wonder why they have not yet implemented an effective solution for flooding. I understand that the development seen in this city recently is remarkably rapid, and installing such extensive drainage system would be challenging, but I feel that the safety of people’s lives should come first.
(Note: My question is what kind of measures Houston has taken towards flooding)
- This is a very big question and I hope that the talk we had by the William Fulton of the Kinder Institute during his webinar this week helped to address this a bit.
- In summary, investing in this type of infrastructure in Houston would be very, very expensive because the water table is so high so the pressure on these types of tunnels would be immense. Houston is also geographically very flat and some parts of the region are even technically at sea-level or below. This makes it very hard for water to drain away from the city because gravity cannot help as much as it could in cities that are not as flat.
- Houston, as a fast-growing city, also developed and grew so large, so quickly that it has been difficult for the infrastructure to keep up with the current development and population. Also, Houston is a very un-regulated city when it comes to building and doesn’t have a lot of ‘zoning’. This is a pro-business policy as it allows entrepreneur’s to build housing developments, shopping centers, and office buildings almost anywhere but the downside is that then the city can’t plan as well for where it needs to invest most in infrastructure updates and development. This pro-business and pro-development policy has led Houston to have a booming economy – even during economic downturns in the rest of the U.S. – with relatively inexpensive housing costs. So even more people want to move to Houston – and build more homes and offices – and pave over yet more land that could serve as a sponge for some of this water.
- However, it is not true to say that Houston doesn’t have any infrastructure to address flooding. In Houston, most neighborhoods streets are built slightly lower than the houses. This may not seem like a big difference but, because the geography of Houston is so flat, a little bit of elevation makes a huge difference and keeps many homes from flooding even though the streets may be flooded. Also, the street drains do empty out in the bayous (they look like rivers) which then empty out in the Gulf of Mexico and during most storms they work quite well. Furthermore, a number of highways flooded such as Hwy 59 or 288, during Harvey but this is again, what they are supposed to do. These highways have been designed to be overflow reservoirs for when the bayous are at capacity. Rain water from the neighborhood streets can drain into the highways and be held there until, eventually, the bayous go down and then the flooding on the highways will drain off into the now more empty bayous and drain out into the Gulf of Mexico. So, those dramatic images of highways and bayous being flooded that were shown on TV were actually examples of the infrascructure in place to help hold rainwater away from neighborhoods; but the existing structures were overwhelmed by this storm. Due to the extreme nature of Tropical Storm Harvey, a number of other reservoirs designed to hold flood waters in the Houston area were at capacity and in danger of bursting so there were also controlled releases of waters from these reservoirs that, unfortunately, did flood a number of neighborhoods in West Houston but this was necessary to present a massive catastrophe if the reservoir/dam had broken.
- However, Harvey was a once in 500 years or even once in 1,000 year storm and the very worst rain/flooding event to have ever occurred in the entire history of the U.S. So, this was a unique situation.
- However, Harvey was a wake-up call for infrastructure in Houston and it is believed that in the years ahead Houston will make improvements to help prevent some of the worst flooding issues we faced during this storm. After every natural disaster towns, states, and countries make new investments in infrastructure that seek to present another occurrence. For example, after Hurricane Ike which occurred in 2008 in Houston many parts of the city lost power for 5, 10, or 15 days. After that hurricane, a lot of money was invested in upgrades to the power stations and energy infrastructure and those investments paid off as most parts of Houston did not lose power during Tropical Storm Harvey. Also, Rice University made a lot of investment in drainage infrastructure after Hurricane Ike in 2008 and that has also paid off since the university itself did not flood at all during this storm.
- Some events are truly unprecedented, such as the 3/11 Earthquake and Tsunami in Japan. No matter how well prepared you think you are, sometimes it is still not enough and you must learn and improve from that event; though it does not take away from the destruction and heartache these disasters cause in the moment.
- Harvey is a 1,000 Year Flood Event on an Unprecedented Scale (Washington Post)
- NASA Video Shows Harvey’s 1,000 Year Flood Event (Houston Chronicle)
- Why Hurricane Harvey Flooded Houston (Business Insider)
- A Storm Forces Houston, the Limitless City to Consider Its Limits (NY Times)
- 3 Reasons Houston Was a Sitting Duck for Harvey Flooding (NPR)
- Texas GOP Leaders Pursuing High-Dollar Flood Infrastructure Projects (The Texan Tribune)
- Did Houston Flood Because of a Lack of Zoning? (Forbes)
- Don’t Blame Lax Zoning for Harvey’s Destruction (Slate)
- The Monumental Task of Restoring Houston after Harvey (Wired)
- How Houston Can Become Stronger After Harvey (Huff Post)
- Houston’s Flooding is a Design Problem (Atlantic)
- Map of Houston’s Flood Control Infrastructures Shows Areas in Need of Repair (Houston Chronicle)
- Dissecting Houston’s Massive Infrastructure (Houston Chronicle)
- Kinder Institute
Week 03: Interview with a U.S. Researcher
Coming this summer!
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Week 04: Reflections on English Language & Life in the U.S.
Coming this summer!
Week 05: Research in the U.S. vs. Research in Japan
Coming this summer!
Week 06: Final Week at Rice & Research Poster Presentation
Coming this summer!
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Week 07: Visit to Washington D.C. and New York City
Coming this summer!
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Final Report & Tips for Future Participants
Coming this summer!