[:en]2018 Mayu Shibata[:]

[:en]Mayu Shibata
Hometown in Japan: Tokyo
University in Japan: Ochanomizu University
Major & School Year: Biology, B2
Host Advisor: Prof. José Onuchic, Dept. of Physics and Astronomy
Host Lab: Center for Theoretical Biological Physics 
Research Poster (PDF): “Homo Dimer Structure Prediction of Bacterial Signaling Protein Utilizing Structural and Sequence Information”

Why TOMODACHI STEM @ Rice University?
I applied to TOMODACHI STEM program because I believed each discovery and real-life experience at Rice University would introduce me to new ideas and would motivate me to keep working hard toward my academic goal of pursuing the mystery of life.

My aim during this program is to absorb as many things as possible: from professional knowledge, the scientific way of thinking and practical English to how researchers with different backgrounds communicate with each other. However, among them, there are two things I am most eager to learn: the way top-class research is carried out and the way people in the U.S. accept and value various cultures. I believe these are great benefits of TOMODACHI STEM program, which provides precious opportunities for undergraduate students in STEM area to experience the research environment at Rice University and understand other cultures firsthand. Learning about these things and integrating them with what I have already learned will motivate me throughout my undergraduate days to improve both my academic capability and my personality to challenge the mystery of life in the future.

Goals

  • Do output (writing, speaking, discussion) as much as input
  • Interact a lot with whom I meet
  • Learn how to develop scientific thinking

Excerpts from Eria’s Weekly Reports

Week 01: Arrival in the U.S.

Rice University campus ~ Mayu Shibata

One of the most interesting things I noticed in the first week in Houston was that people don’t press the “close-the-door button” on the elevator. It was a surprise to me because I am used to pressing it and people doing so in order to save our time. However, people here don’t seem to care when the elevator door will close, which made me puzzled at first. However, going to lab for a week, I come to understand the reason why they are not in a rush on the elevator.

The thing is they clearly separate the time they use for work and for private things, which is the opposite for typical Japanese people, including me. I am a work-is-my-hobby kind of person and often in a rush to use my time efficiently. In my definition, efficiency is to use as much time as possible to work without stressing myself. As can be imagined, my weekend is often spent studying or working on my research project in Japan. Of course, I spent a whole day simply to relax, but only once in a while. However, the definition of efficiency in the U.S. seems to be different. People try to finish their work as quickly as possible so that they can have more time to spare on private things, such as spending time with their family, doing what they like for fun and exercising.

Day by day, I have come to be aware of this difference in efficiency more and more keenly through my everyday experiences and observations. The more I am aware of the cultural difference, more I appreciate the orientation program seminar on intercultural differences which outlined the U.S. core values and those of Japanese people. In this first week, I have already bumped up with numerous cultural differences, and the class helped me understand and overcome them.

Roller Skating at Discovery Park ~ Mayu Shibata

Trying to learn efficiency in the U.S. definition, I joined many events and did a lot of activities this weekend. On Saturday, the first day off in Houston, my friends and I set out for roller-skating at Discovery Green, ate Tex-Mex food, and listened to an orchestra performance at Rice University. On the next day, we visited NASA and had Vietnamese Pho.

 

Initial Reflections on U.S. vs. Japanese Culture

My office at Rice University ~ Mayu Shibata

It was during my first meeting at my host laboratory that I bumped up against both some of the U.S. core values and those of Japan at the same time. During my first meeting with my professor and the mentors, they started to outline the theme of the research project I would be working on as soon as I finished introducing my name. Here, I encountered the core U.S. value of efficiency, and the typical Japanese core values I had, ningen kankei, in another word, human relationship. I was initially surprised at this situation since, in Japan, it would be more usual for me to tell them couple more things about myself in addition to my name, such as my university, major and motivation at the laboratory before we get into discussion. Then, I started to feel uncomfortable at the thought that only the project mattered to them. I didn’t mean that I wanted to attract their attention or be liked by them at the first place and of course I understand that they are very, very busy, but for a moment I felt that they were not expecting to have good relation with me.

In Japanese culture, it is usual to take time to get to know people, especially when people meet for the first time to show that they are interested in them, as building a good ningen kankei (or relationship) is essential in life and work. Although I felt a bit of a sense of discomfort at this point, I focused on the discussion and kept talking about the project. Then, after the meeting, the professor and mentors asked me where I was from, and other things about my background. This cleared up my discomfort. I realized that they began discussion right away because they were trying to accomplish the goal of the meeting which was to decide and describe the theme of the project, and that being efficient didn’t mean they were not trying to build a good relationship with me even if they acted different from the typical Japanese building-good-ningen-kankei norm. This experience taught me that I unconsciously shared this Japanese core value and was ignorant about it.

Question of the Week
Since I saw a lot of people in workout clothing, I wonder how often people in the U.S. workout and which activity is the most popular in Houston.

Preparing for Research in the U.S.
During my first meeting at the host lab, the professor and two mentors gave me a brief introduction about my research project. One of my mentors is a postdoctoral research associate and the other, a graduate student. They both are organized, dedicated and open-minded researchers and are also encouraging, patient and caring mentors. Under their instruction, my first week at lab was spent to understand the overview of the project, especially the background and methods. The theme of my research is to infer protein-protein homodimer interaction using direct coupling analysis, a statistical method, and structure-based modeling, a computational simulation. Looking back after a week in the lab, I am grateful that I read some additional reading materials which I thought would help me understand the papers given by the professor because they made it easier for me to get an overview of the project.

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Week 02: First Week at Research Host Lab

My typical weekday goes as follows: I go to the lab in the morning, have a meeting in the afternoon with my mentors, and review what I learned at night by myself. In the morning, I either study the theoretical background with one of my mentors or do what I can to advance my research. During the meeting, my mentors and I work on the project together and at night I summarize what we did during the meeting.

Chicks at rodeo ~ Mayu Shibata

During weekends or when I have time, I try to explore Houston to learn more about the local culture. This week, all the participants and I went to the Houston Rodeo, an annual festival in Houston. Before going to the rodeo, I regarded it as a traditional fun event. However, it was more than that. There were several booths next to the rodeo stadium in the Agventure, such as giving-birth booth, petting zoo for animals and booths where we could watch baby chicks hatch. Going around these exhibits, I came to think that the festival rodeo is not held just to have fun and enjoy Texan tradition, but also to remind people of the importance of life and provide an opportunity for agricultural education. This was the biggest finding about Texan culture this week.

Another thing I learned this week is that you don’t need to feel bad for asking questions even when asking the same thing for multiple times. English in everyday context is quite different from our school English almost in every way. The grammar, vocabulary, speed and accents differ from person to person. This real-life English confuses me a lot, even when I listen carefully. During the first week, I asked the person whom I talk with to repeat what he/she said when I didn’t get it only one time because I thought asking the same thing for several times is rude. However, this idea turned out to be wrong. People here don’t mind repeating the same thing if you are trying to understand what they are saying. There was an example of this. I was having a conversation with the shuttle driver and I asked to repeat what he had said twice. I felt really bad for doing it and apologized for taking trouble and thanked him for his patience. Then he said, “No problem!” with a big laugh. I appreciated his kindness and realized that I don’t need to hesitate to ask something if I didn’t understand. This lesson helped me to have more interaction with others in both academic and everyday situations and I have been trying to do the same thing to others in gratitude for the people who were nice to me.

Research Project Update

Me at laboratory writing a script ~ Mayu Shibata

The goal of my research project is to understand how homo dimer proteins interact with each other utilizing computational methods.

Most bacteria have a signal transduction system called two-component signaling which converts physical and chemical stimuli into cytoplasmic signals. This system employs two types of proteins: histidine kinase and response regulator. When the receptor detects the stimulus, the information is first transferred to histidine kinase and then conveyed to response regulator. Once it receives the information, it forms homo dimer and work as a transcriptional factor, which contributes to regulate gene expression of the organism. This research focuses on the interaction of two response regulators, because understanding the mechanism behind the behavior of these proteins will provide better insights of bacterial gene expression and ultimately be useful in drug designing.

In order to infer the structure of homo dimer response regulators, two computational methods, direct coupling analysis (DCA) and structure-based modeling (SBM) were conducted. DCA extracts coevolving residue pairs in the protein sequence alignments. These pairs can be interpreted as pairs that are close in the stereoscopic structures within one protein or with other proteins that share the same sequence. The knowledge of the coevolving residue pairs will then be integrated into SBM, one way of defining the potential in molecular dynamics simulation, which is a computational method to simulate the conformational/motional change over time.

One of the main interests of this research project is to know if the proteins dimerize in sys position or trans position. Prior research elucidated that one family of response regulator takes trans position when forming homo dimer, however conformational preference of other families is still unknown. Therefore, finding out about these preferences will be one of the interesting results that can be gained from this research.

This week was spent on reproducing the results of prior research. I have done DCA and SBM of monomer and learned theoretical background of SBM. Integration of DCA and SBM will be done, and if the results are consistent with the previous work, I will move on to another family of the protein next week.

Question of the Week
Was Museum District built on purpose or somehow museums happened to be located around the area?

You could read about the history of each museum and see when they were founded. My guess is that Hermann Park and the Museum of Fine Arts Houston were founded first and then other museums were slowly established around the same area.

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Week 03: Interview With a Female Researchers

 

I interviewed a second year PhD student who is going to be graduate from Rice University this March. He is pursuing his PhD course under Systems, Synthetic, and Physical Biology (SSPB) program and is going to be one of the first alumni of the program. His current research involves modeling of interplay between glycolysis and oxidative phosphorylation in cancer.

He obtained his bachelor’s degree in systems biology in China. Although his major was systems biology, he studied other scientific areas as well due to the requirement of the curriculum. There he cultivated the scientific background to take up the challenge of doing interdisciplinary research in the field of SSPB. When he was a senior  undergraduate (B4), he began to think of applying for universities in the U.S. because he was seeking opportunities to try something new. He says that at that time, he was looking for a life that was beyond his imagination and a life that would excite him.

He is now convinced that his decision brought him more good than his expectations at that time. He learned academic skills – problem-solving skills, presentation skills and English-language skills – as well as living skills such as cooking skills and driving skills through doing his PhD program in the U.S. Thanks to his mentor during his PhD, he was allowed to take his time to foster these abilities. Among the acquired skills, he put the most emphasis on problem-solving skills. He learned how to identify the problem, come up with multiple potential solutions, and analyze the results he gets. Overall, he reflects that learning experience in the U.S. affected his life in a positive way in respect of both academic and everyday-life respects.

He will be working as a postdoctoral fellow at the same laboratory after graduation for a short term. He said that his long-term goal was to continue research but he also said that he was open to other options as well. His adventurous spirit and actions led him to where he is right now and his story is colored by so many events that this report can only include just a small fraction of them. I am sure that his story will have more colors in the future and am grateful for his willingness to share his own career story.

Reflections on Interviews

The Glamour and Romance of Oscar de la Renta ~ Mayu Shibata

Listening to the career path of students/researchers was far more interesting and inspiring than I had ever expected. This interview enabled me to see the interviewees’ current careers in their context of their life, which enlightened me with various ideas about planning my own career path and making decisions. I am grateful to those who kindly accepted my interview request and this program which offered an opportunity to do an interview because otherwise, I would never have known that conducting informational interviews could broaden my own understanding of career paths this much. Now, I am eager to continue interviewing other students/researchers both in the U.S. and in Japan.

This week, some of my friends and I also went to the Museum of Fine Arts, Houston to see the special exhibit, The Glamour and Romance of Oscar de la Renta. There were various kinds of dresses, such as party dress worn by Taylor Swift and wedding dress worn by Amal Clooney. The class of his dresses overwhelmed me and it was the first time for me to be amazed by the beauty of fashion.

Research Project Update

The most surprising thing this week (you happened to meet 2 doughnuts on the elevator. After 30 min one took off, and another 30 min later “and there were none…”) ~ Mayu Shibata

We continued working on reproducing the results of the prior research. This week’s focus was on the integration of molecular simulation and structural constraints gained from sequence information. Although I did get a result, it didn’t match the structure presented in the previous work. Therefore, we went through all our methods to check if anything was wrong. Nothing was obviously wrong, so we tried the same simulation under several different schemes.

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Week 04: Research in the U.S. vs. Research in Japan

At the final poster presentation. ~ Mayu Shibata

The last week in Houston was all about preparing for the poster session. I did the final analysis of the dimeric structures, created the poster, and practiced giving a short overview of my research project. Although I was very nervous at presenting the poster and answering questions before the session, it was a pleasure for me to have conversations with people who were curious about my project and to gain new ideas about my project through discussions with various audience members. If I could go back to before the presentation, I would ask my mentors to listen to my overview of the project and give me some advice for it. Other participants and I did peer feedbacks many times and it helped a lot, but I also needed feedbacks from my mentors because they would be able to point out if my explanation was missing some important part of the project. In future poster presentation, I would like to ask someone who knows my research well to check my overview as well as people from different disciplines.

Although it was not a long-term research experience, I came to notice that equality and respect are valued in terms of academic research in the U.S. Of course, those are valued in Japan as well, but in my opinion, researchers in the U.S. seem to put a strong emphasis on them. I strongly felt this when my mentors had different opinions about what they thought about the results of the simulation. One said we can continue the simulation and the other said the opposite. I felt uncomfortable with this situation because I had an experience where the situation became awkward for a moment. However, what they did cleared my anxiety up. They talked about their opinions with each other in an organized way. They first outlined the conclusion and then gave concrete reasons to make their claims more clear. At the same time, they listened and carefully considered each other’s thinking with an open-minded attitude. In the end, we came to an agreement that we should try the next step of the simulation and see if it works. It was the idea that took both of their ideas into account. I saw the respectful attitude in them and think it was based on the value of equality.

Question of the Week
Students at Rice University seem to be studying alone more than in group. Is this observation correct and why they do so?

  • They do both ways, individual study and group study. Since students in the U.S. can take classes both within and outside of their major, no two students will take all the same classes at the exact same time.  So, a lot of times your friends may be studying something different than you and it is easier to focus/think/work if you are studying alone.
  • However, many students do also study in groups too if they are preparing for exams or working on a group project.  They often do this in the common room/servery of their residential college or they will reserve small group/study rooms in the upper floors of the library and meet up there.
    You probably just didn’t see where/when students were studying in groups because places like the first floor of the library, Pavilion, and Coffee House/Student Center are usually places people go when they want to study alone or with just one other person.

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Final Research Poster Presentation

Host Advisor: Prof. José Onuchic, Dept. of Physics and Astronomy
Host Lab: Center for Theoretical Biological Physics
Research Poster (PDF): “Homo Dimer Structure Prediction of Bacterial Signaling Protein Utilizing Structural and Sequence Information”

With my host professor and mentors in my office at Rice University ~ Mayu Shibata

I worked on the project “Homo Dimer Structure Prediction of Bacterial Signaling Protein Utilizing Structural and Sequence Information” at the Center for Theoretical Biological Physics (CTBP) under the supervision of prof. Onuchic and two mentors.

I computationally predicted a homo dimeric structure of bacterial protein using experimental data of monomeric structure and sequence. The protein of interest is called Response Regulator, a transcriptional factor which regulates gene expression in bacteria. The value of this research lies on

Because knowledge of it will be useful in antibiotic drug designing. If you know the structure, you know the function. If you know the function, you know the mechanism. And knowledge of bacterial gene expression will suggest potential target of antibiotic drug.

To predict the dimeric structure, I used two methods. One is direct coupling analysis, DCA, and the other, structure-based modeling, SBM. DCA is a bioinformatics approach that tells pairs of amino acids that are close in 3D structure of the protein from the protein sequences. SBM is a simulation which shows the trajectory behavior of the proteins based on known structure. By integrating sterically close couplings into SBM constraints, I achieved two things. One is to reproduce anti-parallel dimeric structure shown in the previous work. and second is capturing conformational change of the dimer. After calculation of energetic frustration, these newly observed structures are evaluated to be reasonable structures as proteins.

The future work will be exploring homo dimeric conformations of other protein families of response regulator by applying the same method as used in this project.

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Week 05: Science & Technology Policy Study Tour

With Lehigh University students ~ Mayu Shibata

Among the program activities this week, I was inspired a lot by the talking with a female graduate student Howard University. This activity gave us an opportunity to get “real-world” advice and experiences of what we are keenly interested in from who someone who is achieving something that is a goal for most of us – to be a female researcher. The graduate student we talked with was a black female student whose major was physics. During our talk, she said that total number of black women with PhDs in physics throughout the history was just 77 and they are called “purple elephants” because they are rare and almost like imaginary organisms. This was quite surprising for me because I believed the scientific research environment in the U.S. was diverse. As for being a member of a minority group in the STEM, she said that we should always need to try to be the best. What she meant was that females in the STEM environment should be the best version of themselves because they will be the representatives of other women in the area and their impressions will affect the way people look at researchers in the same category. I was inspired by her comment. It was something that I hadn’t thought of, but something that is true and very important. The word “leadership” always sounds strong and reminds me of image of doing something actively, but I thought that this could be one way of showing leadership in encouraging minority people to come into STEM area because in spite of its quietness, doing your best opens door of opportunities to other underrepresented people. Now my future goal is not just to become a female researcher in STEM area but also to always do my best and be able to contribute to opening the door to opportunities for others too.

Ice cream by the river in DC ~ Mayu Shibata

During our final week we also visited several museums in the National Mall in DC such as National Gallery of Art, National Museum of Natural History and National Air and Space Museum. The number of exhibits they have and the greatness of each of them overwhelmed me. I was able to see works of Leonardo da Vinci, Rodin, van Gogh, Gaugin, Monet, Manet, Mondrian and Lichtenstein. It was really surprising for me to see pieces of great artists of various time and countries in one place. At the same time, I was also surprised by the distance of art work and people who are looking at them. In most cases, there was no glass between them, whereas there are often thick glass barriers in Japan. I found the closeness between visitors and exhibits in another museum as well. In the Natural History Museum there were a lot of “touch me” exhibits. Japanese museums have these types of exhibits as well, but I felt the number of them are bigger in the U.S. and I thought this style of exhibitions would encourage children to be interested in science/arts.

We got to see some cherry blossoms! ~ Mayu Shibata

One of the things that I found out about myself that was very Japanese throughout this program was to expect public transportation to be punctual. Throughout this program, there were not many things that were frustrating, but it was little awkward when I first experienced American standard time. Growing up in Japan, I took punctuality for granted but in the U.S., even public transport is often late and I was surprised by it. I still think public transportion should be on time, but I gradually came to like the American sense of time. Maybe this is because I was a never-to-waste-just-a-second kind of person, but I liked the way people are not in rush all the time and have enough time to have small talk with others.  I am glad to be back at home and meet my family after five weeks, but I find myself missing small talk and the American standard time concept.

Question of the Week
How do people in the U.S. work so efficiently? I was not able to detect the working/time management tips that are characteristic to the U.S. people during this stay, but is there any habits/tips that are commonly used among people in the U.S.?

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Final Report

This program was full of surprises. Every opportunity during this program inspired me a lot.

My favorite experience in the U.S. was the research internship at Rice University. One of the significant lessons I learned there is that the researchers I met have a very conscious desire and want to make contributions. It might be for the world, the community they belong to, the lab they work for, or the people they care about. However, they all had a strong sense of contribution and I thought this is one of the core values that informs the way they work. Because of this value, they focus on the big picture of how their work impacts other researchers and people’s life. Because of this value, they try to communicate a lot with others in order to make use of their strengths/professional expertise to help other researchers who have different strengths. Although I noticed this at Rice, I also saw a strong sense of contribution everywhere in the U.S. For instance, the people we met at Dow Chemical were also motivated to make the world better place by inventing new materials. This attitude will bring better results no matter what people are working on, and generates a positive loop of helping contribute to new achievements. Being exposed to people with this mindset, I have come to think about how I can make good use of myself for others more frequently.

Another important lesson I learned is the way people in the U.S. respect various cultures. I noticed three communication skills shared by most of people I met in the U.S. people that reflect their respectful attitudes toward multiple cultures. First, they listen to others until they finish. Second, the ask questions about whatever they do not understand. Finally, they accept what others said at least for the first sentence of your response. Different cultures have different ways of communicating. Listening and asking for support and for people to understand each other’s thoughts correctly and accepting different viewpoints shows respect to others. It is easy to interrupt when others’ are talking, not ask question, or immediately oppose or disregard others’ thoughts from the beginning if they are different from your own. I sometimes did these things. However, now that I’ve learned more about respectful communication skills, I am absorbing these so I can cultivate better communication capabilities.

This five-week program inspired me far more than I have expected. I gained a lot of knowledge. I realized my academic capabilities. I learned about my personality. I was connected to a lot of wonderful people. I am sure that all of them are great gifts that I can take back home with me. What I can do now is not to just put these gifts on a display shelf, but to make use of them to get closer to my career goals. I am reading papers that are related to my project at Rice, learning computational skills to extend my academic capability, thinking of the ways I can contribute to the society with my strengths in my current position and in the future, and I plan to maintain my connections with people I met using the communication skills I learned. These are mere baby steps but I believe they will take me closer to the my mid-term career goal of being an independent graduate student and my long-term goal of pursuing the mystery of life.

Now I am 100% sure that there are things that can only be learned firsthand, and some of the things I learned on the TOMODACHI STEM program are definitely examples of them. I have come to be convinced that undergraduate overseas research experience is extremely important not only because it broadens your horizons to enrich your remaining school life, but also because it allows you to have more time to think about your career and life and consider different options. I believe this is the greatest benefit of this program for female STEM undergraduate students and I am grateful to be given such an enlightening opportunity at this early stage of my career.

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Tips for Future Participants

Food: My advice for future participants is to raise your cooking skill as much as possible. This might not sound convincing, but food is the key of well-being and time management. I was not a complete beginner at cooking by myself, however, I wish I could do it more quickly, because I wanted to use more time working on research/sightseeing. You will encounter difficulties in English communication and with research project no matter how well-prepared you are. On the other hand, once if you raise your cooking skill before you leave, you won’t have as much trouble with this. I think getting ready for cooking on your own is just as important as English conversation and lab research will make a good practical preparation.

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