2018: Yuki Kitanishi

Yuki Kitanishi
Hometown in Japan: Tokyo
Home University: The University of Tokyo, Faculty of Pharmaceutical Sciences, Pharmaceutical Sciences
B3: Junior, Expected Graduation Date: March 2020
Host Lab at Rice University: Laboratory of Biomolecular Engineering and Nanomedicine
Host Professor: Prof. Gang Bao, Depts. of Bioengineering and Chemistry
Research Project Poster (PDF): “Efficiency of SSA Assay in Quantifying CRISPR/Cas9 induced DNA Cutting Activity”
Received Honorable Mention for Joint RCQM-Nakatani RIES Research Poster Symposium


Why Nakatani RIES?

English is a common language in every field of science. All articles are written in English and researchers speak English at most scientific conferences. Without English, scientists cannot share their findings with people around the world. Undergraduate students in my university are offered some English lectures to reach a certain level to be able to talk about scientific ideas in English. However, my English level is still far from the level required to work at the frontline of science. By participating in the Nakatani RIES program and experiencing lab life in U.S.,  I believe I will be able to think and communicate more clearly in English, which would become a great skill for my future. Furthermore, I hope to better understand how to collaborate with people from other countries to solve our shared problems.

I think the Nakatani RIES program is one of the most challenging and stimulating programs for students in all scientific fields. All participants are eager to study outside Japan to improve themselves as a researcher. The laboratories that will host us are all famous and high level. I am so glad that I was selected as one of the 2018 participants.

Goals for the Summer
  • Discuss scientific topics with the members of my host laboratory in English.
  • Catch up with the research being done in my host lab.
  • By the end of the program, have no problems communicating in English.
  • Make many friends.

Meaning of Nakatani RIES: Post-Program 

I found that it is important for students in science fields to be given opportunities to do research abroad. In general, if Japanese university students seek chances to study abroad using their short-term vacation, we will only find programs focused on becoming more familiar with English. Even though we may find some programs where we can study something other than English, they are mostly about humanities and not related to science. However, the Nakatani RIES program is different from other programs in that it is a “science” program and even gives us the opportunity to join in a lab to do research by ourselves. After I finished this program, I learned not only about the lab environment and research culture in U.S., but also how exciting research is.

  • My favorite experience in the U.S. was … To be honest, I cannot narrow down into one episode. I enjoyed going to the party with Sahil. I cannot forget all the places I visited with my friends during Labor Day and the last week of the program. However, it was when I truly understood my research and discussed with other members in the lab that I thought I am really enjoying this experience. After that time, all the experiences were exciting to me and when my research was about to end, I felt I want to do more research.
  • Before I left for U.S. I wish I had … a higher communication skill to enable me to talk fluently with native speakers. Almost every time I spoke English among native English speakers, I interrupted their communication, which meant I had to take time to organize what I wanted to speak. I believe that I am now more fluent than before and even able to talk about everything in my daily life in English.
  • While I was in the U.S. I wish that… I could have asked anyone what I wondered or what I couldn’t understand without caring about what they would think of my questions. Especially when I was in lab, there were many cases where I couldn’t understand what others were telling me. I made the effort to understand them by myself searching the Internet, but some of my questions remained unsolved. When half of the program had passed, I changed my mind and kept on asking about everything, and that facilitated my relationship between other lab members and made it easier for me to do research.

Excerpts from Yuki’s Weekly Reports

Week 01: Arrival in the U.S.

I lived in US for three years when I was in an elementary school and, due to this, I believed I knew a bit more about life in US more than is usual for Japanese students. Prior to departure, we attended some lectures that were held in Japan and got some advice on how to manage our life in US. Then I realized how things have changed in the past ten years. Today, people use credit or debit cards, not cash. Uber and Lyft are the best way to catch a taxi. All of those things didn’t exist ten years ago. I realized that I was totally behind the scene and asked some of the U.S. fellows what I should do to prepare and searched on the Internet more about what it is to live in U.S. In addition, every state in U.S. has its unique culture and tradition. In that sense, talking with one of my best friends in Texas was so helpful for me.

At the Houston Food Festival with Shuhei ~ Yuki Kitanishi

The first week in Houston was all amazing and made me so excited. I actually love to eat local foods when I visit other countries. The most famous local food in Texas is Tex-Mex. Tex-Mex food is a mix from the U.S. and Mexico. One things you must try in your first week is tacos, and I think we all liked their taste. Tomato, lettuce, grilled chicken or beef, guacamole and some other ingredients are folded inside tortilla, which is a flatbread made of wheat or corn. When I first ate fajitas during the welcome lunch, I was so surprised at how delicious it was. However, the thing I was most surprised by was its size. Everything is huge here in Houston. It takes about 30 minutes to eat only one taco or fajita!

On our first day in U.S., we learned about “Intercultural Communication in the U.S.“. It was so useful to learn about some of the cultural differences between Japan and US, and what kind of values do people have in each country. I believe that there may be some times when I may  face some difficulties communicating with people in U.S., especially in my research lab. If I can keep in mind about some of differences in communication styles, I can more easily overcome these barrier. The campus tour was one of my favorite events at Rice University this week. Every building had its own history and unique designs with special meanings and symbols. They were all huge and old and I was overwhelmed at their scale. Finally, “Introduction to Designing a Research Poster” was one of the most useful lectures this week. I have presented a poster once before when I was in high school, but I haven’t thought about the overall impression of the poster and the wording. Considering the fact that audience members will have various backgrounds and different majors, it is essential to make a poster that is understandable for everyone. When I make my own poster, I will review this lecture and make the best of the tips we learned.

I guess most of the Japanese Fellows will talk about the excursions that were part of our scheduled program, so I will write about the things I experienced on Sunday. One of the US fellows, Sahil, texted me asking if I would like to work out together on Sunday. Actually, I promised him to work out together during my time at Rice University when we were in Japan. To have fun in Rice, I strongly recommend to make friends with the Rice University U.S. Fellows prior to the departure. In the morning I called my friend from Japan and then worked out for about an hour with Sahil. After finishing training, he took us to his residential college (dormitory) and showed us around. Then, we ate Tex-Mex for lunch in the cafeteria and had chance to talk with other Rice students. It was a very short time, but through this I learned more about what it is to be a student in a U.S. university.

Reflections on Intercultural Experiences
One of the U.S. core values that I encountered during my first week in US is the value of “Telling it like it is / Speaking up”. Every week on Monday and Friday, our lab holds a meeting in the morning. In this meeting, every group member gives an update on their project. After the presentation finishes, the audience will ask questions about anything related to the report. Of course, not everyone in the lab was asking questions, but it was so surprising to see that when people asked questions, they all asked clearly and directly what they had on their mind. I don’t know whether this is because I’m Japanese or not, but when I ask something to some members in my lab, if not in the lab meeting, I become so awkward that sometimes they ask me to repeat my question. I’m now trying to speak more clearly and be more self-confident even if my question is at a low level. In order to have a constructive and efficient communication, I strongly believe that being explicit and straightforward is the best way.

On the other hand, I experience my ‘Japaneseness’, in the value of ‘Rikai/Understanding’, when I have conversation with my mentor or other lab members. For example, my mentor always kindly teaches me how to use every instrument. Sometimes, I cannot understand what she is telling me, but I react as I am understanding so as not to disrupt her explanation. Then I go back to my office and search on the Internet to make sure of what she has explained to me. I realized that this is so meaningless because my mentor will keep on explaining assuming that I am fully understanding, and I will be left far behind from her explanation. So, I am also trying to ask any question as soon as possible if I have something that I cannot understand.

With my mentor Buhle and senior lab administrator Amy! ~ Yuki Kitanishi

Preparing for Research in the U.S. 
About two weeks prior to departure for the U.S., I sent an email to my host lab to ask about what project I am going to take part in and what articles or textbooks they would like me to review. This was really helpful, because once you arrive in the U.S. you won’t have much time to review all those articles and textbooks. Reading through them also helped make me more comfortable when talk with my lab members about research. When you read these articles, I strongly recommend to also review the basic theories behind them. Even if you believe that you fully understand the content, there might be some mistakes or some questions you have that remained unsolved. In addition, everything will be written in English here in the U.S. Be sure to review the concepts in English and take notes if you encounter some words you don’t know.

First Few Days in Research Lab 
At first, I was so nervous about working in my lab. However, my mentor and other members in my lab were so friendly. It is almost the first time to do research on my own, so I always asked about things that I couldn’t understand. My mentor answered all of my questions so kindly and even offered me some textbooks and some articles that could help me. We also had lunch together every day and talked about foods in Texas or places that are fun to go to. I’m now so excited to go to eat sushi in Texas with my lab members.

Return to Top

Week 02: First Week in My Research Lab at Rice

My mentor’s name is Dr. Buhle Moyo. She is a Postdoctoral Research Associate in the Bao Lab. What I am doing in the lab is the basics of genetic engineering and Buhle instructs me all the process I must follow.

In my lab, two meetings are held every week on Monday and Friday. On Monday, some of the members will share their progress on each project and report to Prof. Bao. After each presentation finishes, the audience will ask questions to the speaker and discuss problems related to the project. On Friday, one article is shared for all the lab members to read so they can discuss its problems or implications for their research. So far, all of the meetings were so difficult for me to understand, but I will do my best to be able to understand what they are talking by the end of the program.

Not only my mentor but every member in my lab is so kind and they teach me what they’re doing if I ask them. During the first week of research, I was given an article that my project is based on. Since it was almost the first time to seriously read a research article, especially in English, it was really difficult to read thoroughly, but by asking my mentor and lab members, I finally made it.

At the Rice Football Game. Nasa T-shirts and Banana ~ Yuki Kitanishi

This week at Rice, we talked with Prof. Seiichi Matsuda during lunch. He is the Dean of Graduate & Postdoctoral Studies and a Professor of Chemistry and Biochemistry & Cell Biology. At the end of the session, I asked whether we are required to have passion in our major. Now, I am studying in a lab in molecular biology. Of course, it is interesting, and I am really excited to learn new things and catch up to the frontline of science. However, I also have a lot of interests in many other fields of science such as computer science and chemistry and felt anxious whether I can continuously keep my passion toward biology and do research in that field. The answer was “not necessarily”. Prof. Matsuda told us that at first, he also wasn’t very fond of Chemistry, but by continuing doing research in a tough lab environment he became a professional at the end. He also told me that it is not necessary to fall in love with one field of science. It doesn’t matter if you like other subjects, and there is no typical answer for this question. I realized that I can keep on having interest in many fields and do whatever research I like to gain variety of experiences.

  • Tip: This is also why so many professors at Rice have joint appointments with other departments.  They love doing research in a variety of fields and so the interdisciplinary nature of their research means that it spans multiple departments and fields. This is very, very common in the U.S. – especially at small schools like Rice. 
With my friends! ~ Yuki Kitanishi

This week, I had a lot of activities outside of research too. I cannot forget the atmosphere of attending my first party in Texas. The Rice University U.S. Fellows told me that it was the first public party of the school year in the residential colleges (dormitories) at Rice University, and most of the students join ed. I was so surprised to see the students dancing on the balcony of Martel College under the night sky. However, people not only danced, but also built their own network. The Rice University students were all kind and if you asked about joining in and having fun, they were all willing to introduce us to many other people and tell us how to enjoy the party. On the next day, we also went to a Rice University football game. This was also one of the most exciting and astonishing events that I have experienced until now. It is so unbelievable in Japan that a university has that huge of stadium in its campus. Once you enter the stadium, you can hear the sound of brass instruments and the cheers of the audience. People have their drinks and food on their knee. When Rice won a goal, they all stood up and you can see some fireworks launching when RICE Owls scored a goal. Rice students can watch the game for free so you can find many students in the stadium and I think this system is making the stadium so energetic.

Parties and football game are one of the main parts of USA students’ life. I really appreciate for Sahil to telling us such exciting events.

Research Project Update:
My group’s theme is Gene Targeting Using Engineered Nucleases. Following the improvement of ZFN(Zinc Finger Nucleases) and TALEN(Transcription Activator-Like Effector Nucleases), Crispr Cas9(Clustered Regularly Interspaced Short Palindromic Repeats – associated protein 9) emerged as an efficient and revolutionary tool to edit genes. Cas9 doesn’t work by itself and needs a guide(gRNA) to help it lead to a specific sequence of the targeted gene.

In order to analyze the efficiency of the guide, many types of assays have been invented, and my project aims to compare those gRNA efficiency by using SSA(Single Strand Annealing) assay. SSA reporter vectors are required for this assay. This vector contains two segments of fluorescent protein (e.g. GFP) gene with an identical sequence of homologous region. Target sequence is flanked by these regions, so when gRNA attaches and Cas9 cleaves this sequence, fluorescent protein is expressed, and it becomes possible to detect the activity of Cas9.

The basics of genetic engineering are all required to complete my project. I will follow the process written below.

  • Cloning of target sequence into target vector backbone: Some sequences of target gene are each cloned into plasmids. To amplify the number of plasmids, cloning is required. Target sequence ligate to a plasmid backbone and be transferred into bacteria(E.coli.). After this so-called ‘transformation’ is done, bacteria get incubated, which means the plasmids are replicated. Some colonies are selected after the positive selection with Ampicillin.
  • Miniprep: This process is done to extract the target vector plasmid from the bacteria. Bacteria get resuspended and lysed so that to be possible to extract plasmids by chromatography. Sequencing the extracted plasmids, it becomes possible to see whether transformation succeeded or not in the selected colonies.
  • HEK293T Cell transfection: CRISPR plasmids (Express Cas9), gRNA plasmids, and SSA vectors are transfected into HEK293T cells. HEK293T cells are usually used in cell biology. By analyzing the fluorescence by cytometry, it becomes possible to see the activity of gRNA targeting and Cas9 cleavage.
  • Analyzing the data

Return to Top

Week 03: Interview with a U.S. Student and Researcher

In this interview, I interviewed Kevin who is a graduate student and Buhle who is a postdoctoral researcher. Kevin planned my project and has always helped me when I needed assistance. Buhle is my mentor. She also planned out my project and taught me from the basics of biological experiments. Every time I asked her question, she always kindly answered them. As I worked with them on my project, I felt that I wanted to know more about them and decided to interview with them.

Kevin is a graduate student at Rice University. Since our lab is doing research on genetics, I first asked him why he decided to study genetics. Genetics is one of the fields in Biology that is developing so rapidly owing to the technology related to gene targeting such as CRISPR Cas9. As a researcher, he told me that doing research on such a developing technology is fascinating. The reason why he chose to join Prof. Bao’s lab from a lot of different laboratories doing research on genetics was also impressive. He had a friend who played basketball with when he was in high school, but his friend was diagnosed with a sickle cell disease and became unable to do sports. Furthermore, he failed to get a scholarship, which he needed to be able to enter university, due to his disease. Drugs and some other treatments that available now can cure some diseases, but not all of them. There are some diseases that we can only alleviate their symptoms, and still remain incurable with drugs, and sickle cell disease is one of them. However, patients with these diseases have problems in the genes, so Prof. Bao’s laboratory aims to cure those diseases by using gene targeting. To achieve his goal to cure incurable diseases, Kevin decided to learn about genetics and chose Prof. Bao’s lab to do research. In fact, every member in the lab is doing research on different genetic disorders and trying to establish treatments by modifying gene.

Then I asked him why he chose Rice University among many universities in U.S. First, Rice University has fewer students compared to other universities, and that makes students closer to their professors. Secondly, while some universities require graduate students to attend lectures instead of doing research in the first two years, Rice offers opportunities to get engaged into research from the first year. In addition, Rice has a research culture to facilitate interaction between different faculties and laboratories. For example, the Bioscience Research Collaborative (BRC), the facility that I am studying now, has many laboratories inside the same building. Researchers share equipment between laboratories and there are even some cases where some laboratories collaborate to on the same research projects. And of course, Rice is located in one of the largest medical districts in the world, the Texasm Medical Center, which means that researchers can access to many medical resources. Kevin is also doing research in Baylor College of Medicine using mice.

Finally, I asked about his future plans as a researcher. He told me that he is wondering which to path proceed, post-doc or industry. Through this program, I was also wondering which is better for my future. He advised me to participate in projects in labs at my university in Japan as soon as possible even though I am an undergraduate student, and ask for some advices from graduate students.

Buhle is a Postdoctoral Research Associate in the Bao Lab. I decided to ask her some different questions. First, I asked how she got interested in gene therapy and why she thinks the Bao Lab is a good lab. Throughout her career as a researcher, her main interests have been virus and cancer related. As gene therapy emerged, it showed great potential for the treatment of any genetic diseases such as certain cancers. Prior to joining the Bao Lab her previous research focus involved using gene therapy to target hepatitis B virus, which is related to cancer. Prof. Bao’s laboratory really attracted her because it had an excellent reputation and publication record into gene therapy. She thought Prof. Bao would be an excellent mentor given his high standing and expertise in the field of gene therapy.  Furthermore, the lab was well funded, which I think is important when choosing which lab as researchers can easily have access to variety of lab equipment.

Then I asked her about her perspective on working in academia versus working in industry. As she has not worked in industry, she could only comment on academia. She said that some of the advantages in working in academia are that researchers have greater freedom to come up and test their own ideas and are able to do their research while enjoying the university culture and environment. Also a lot of opportunities to learn that extend further than one’s own area of expertise are easily accessible within an academic setting. In the Bao Lab every member has their own unique project and has a culture of helping each other and that makes experiments enjoyable. Furthermore, as Kevin also mentioned in his interview, there are even some opportunities to collaborate with other labs inside the department.

Finally, I also asked if she had any advice for undergraduate students thinking of a career in research. One of the things she said was that it is important to get good grades in lectures and courses. Even though I have not yet decided what to do in the future, I will have more options available to me in my career if I have good grades. I have been reluctant to make good grades because most of the lectures I have taken in my faculty were all so boring. But after this advice, I strongly regretted my past attitude. I promised to myself to do my best in future exams to make up for my past grades. Lastly, she encouraged me to participate in anything that I find interesting and not to hesitate to step forward. I will keep this advice in mind.

Reflections on the Interviews
It was so impressive to know that both of them had a strong desire to understand and target diseases through their research. I also decided to go into pharmaceutical science faculty because I thought it would be so great if I can save people from diseases through my own research. I have always kept this in mind, but to be honest, I was not so serious about it. This interview drove me to feel more strongly that I also want to be a researcher that can contribute to patients with diseases, and motivated me to study hard. In addition, both of them gave me practical advice for making career decisions that were so helpful, since I was really wondering about my future as a researcher. I really appreciate that both of them kindly accepted to be interviewed.

Programs and Seminar at Rice University 
This week, the lecture we had by Prof. Akane Sano in the Department of Electrical & Computer Engineering was so interesting. During her lecture she talked about her research on affective computing. Affective computing is like a system of analyzing people’s emotion using devices. Actually, I am now making a program to detect emotion through facial expressions using deep learning, so most of the things she talked about were related to my program and this made me so excited. Using features other than facial expressions, such as the heart beat or communication, to detect emotion was also so interesting. It must be hard, but I thought that I can also use these features to make my program more accurate. Some diseases are said to be affected by mental health, so I believe continuing research on this topic must be useful in my field of study, medicine.

Labor Day Weekend
During the Labor Day holiday weekend, I went to Austin and San Antonio with my friends. Both of the cities were so fun and exciting!

Barton Spring Pool !! ~ Yuki Kitanishi

Since Austin is the capital city of Texas, the atmosphere in Austin was different from that of Houston. Many people were walking on the street even at night and I felt Austin is a little bit similar to Tokyo. We visited all the major tourist spots. We visited the State Capital and learned the long history of Texas. The University of Texas at Austin was close to the Capital, so we went there next to see their large buildings. I cannot explain the difference but the impression it gave us was different from the Rice University campus. The Barton Spring Pool was the last spot we visited. It was the first time I had gone to a pool since I came to US, so it was extremely exciting. Jumping from the diving board was also thrilling and fun. The food we ate in Austin was so delicious. We ate Texas barbecue at one of the most famous restaurants in USA, Franklin Barbecue. We knew this restaurant from a kind man on a shuttle bus from our hotel, so I really appreciated him introducing such a great restaurant to us. For dinner, we ate in a cool restaurant on Sixth Street, which is famous for biscuits. We spent a lot of money on food, but I believe it was worth spending that money.

We are now Cowboys !! ~ Yuki Kitanishi

On the second and third day of the holiday weekend, we visited the historical city of San Antonio. San Antonio was also different from other cities in Texas. We went to the Riverwalk and the Alamo, but what was the most exciting was the farmers market. The day we visited San Antonio was the day they held a Labor Day festival. We fortunately encountered a group that is performing Mexican Jazz/Rock music. We all had fun listening to their music and some audience members even danced while listening to it. Eating authentic Tex-Mex food while listening to authentic Mexican music was so great that I felt like living in Texas in the future may be good.

I must mention that we went through the cities using Electronic electric scooters. It was the first time I had rode them, but I soon got used to it and had fun riding it. I wish it will be introduced in Tokyo before the 2020 Tokyo Olympics.

 

 

Research Project Update

Monday: On Monday, things were harder than in the past weeks. In the first week and the second week of the program, I just shadowed what other lab members are doing and tried to understand the principles of each procedure. From the end of last week, I started doing my own project. Most of the processes were all things that I had learned in the previous weeks, so I did them mostly by myself. At first, I thought it wouldn’t be so difficult because I took careful notes of what I should do in every process, but it was much more difficult than I expected. In biology, experiments require precise control of time in seconds. However, I was too careful and much slower than my mentor in every process and mistakes many times. To make matters worse, I used the wrong agent while extracting the plasmid DNA, which made the result worse than expected. Keeping attention to all the process in a long period is so stressful and I strongly felt that being a researcher is so challenging and people around me are so admirable. I want to be familiar with each process and finish my project efficiently without failure.

Tuesday-Friday: We checked the amount of DNA we had extracted yesterday. The amount was fewer than I expected, so we decided to start to extract DNA from another colony. I did all the process alone from lysing to analyzing the cell density of the liquid. At this time, I was able to do all the process smoothly and finally made it to extract enough amount of DNA.

Next week: We are going to submit the extracted DNA to a company that analyzes the sequence of DNA in order to see whether the plasmid contains the right sequence of target DNA. Once we confirmed that all the plasmid has the expected genome sequence, we are going to proceed to the phase of transfection, which means to introduce designed plasmids into human cells. Then, we can see whether Crispr-Cas9 works using my SSA vector. This will be the last step of my project. I am so excited and a little bit nervous about the result of sequencing.

Return to Top

Week 04: Reflections on English Language & Life in the U.S.

I played squash for fun! ~ Yuki Kitanishi

I feel my English is getting better than it was in the first and the second week in U.S., especially when I am in the lab. In biological experiment, one mistake can ruin all of the process I have done, so I must be careful with every step of the process. If I hesitate to ask anything and do not fully understood, it will lead to a loss of a whole day’s work. In order to finish my project and get a good result, I have to ask about everything that I didn’t understand as soon as possible. Furthermore, I have to read as many articles as I can and have asked about things in the articles that I found hard to understand while also trying to catch up to the conversations between the lab members. I also tried to talk to as many people as possible in the lab so that I can be able to join in on many conversations.

This week, these efforts paid off. I was doing PCR to see whether the target sequence is inserted or not into the plasmid backbone. However, the expected result I was told from my mentor seemed to be strange, so I reviewed the protocol, read through some related articles, and looked through the sequence of both target gene and the plasmid backbone. After all, the expected result was proven to be true, and I was able to have a discussion with other lab members and understand what I was doing now more precisely.

Other Seminars at Rice University
This week we had a webinar about “Career Decision Making”, by Jen Topp, Program Director of Global Engagement at Lehigh University. In this lecture we were taught how to make our own elevator pitch. I even had a chance to practice presenting my elevator pitch, but it turned out to be so long and not well summarized. To make a wider network, I’d like to practice doing my elevator pitch more.

Research Project Update
To make it easier for the readers to understand, this time I will review what I have done up until this week. CRISPR Cas9 is known to be the tool to target genes inside the cells and knock out or alter the genes. Briefly speaking, two major molecules Cas9 protein and guide RNA take part in targeting. Guide RNA has a specific sequence of 20 base pairs, which is called target sequence. Once guide RNA get introduced into the cell and reach the nucleus, it binds to the complimentary sequence in the cell DNA and lead Cas9 to cleave that sequence, which could be the first step of editing specific target gene sequence.

What I have synthesized is called SSA vector. SSA vector is a plasmid designed to contain a target sequence in it, and when the guide RNA binds and Cas9 cut off that sequence it becomes fluorescent. Analyzing the fluorescence, it becomes possible to quantify the function of CRISPR Cas9. To synthesize this vector, we prepared plasmid backbone and target sequence, and ligated each other using enzyme. Then we mixed the vector with chemically competent cells to let the vectors go inside the cells and made them replicate the plasmid. We cultured those cells on medium and selected some colonies to make sure that cells have the same sequence of plasmid and again cultured it in medium.

After that, we extracted the plasmid from the cells, which is called miniprep. To extract only the plasmid, cell membranes are lysed and other molecules such as chromosomal DNA were separated using chromatography. Extracted plasmid were sent to assay to check whether the target sequence is correctly ligated to the plasmid backbone. This week we received the result of its sequence. We used fifteen target sequences for my project and it revealed that two out of the fifteen targets were correctly inserted in the vector. Actually, the sequence of the plasmid backbone tends to make a different sequence from what we had expected.

However, I realized how difficult it is to get an expected result in real experiments that researchers are doing every day. My skills in biological experiments are also still not good enough. After I go back Japan, I will soon join a lab again and enhance my skills so that I can control the condition of every experiment accurately.

Return to Top

Week 05: Final Week at Rice and Research in the U.S. vs. Research in Japan

Working in the Bao Lab

In my project, we prepared 15 sequences for target sequences of gRNA-Cas9 complex. Out of fifteen total, two sequences we correctly ligated to the plasmid backbone and transfected into human cells, which means two were able to test the assay. Since I understood what to do and became faster in every process, I wanted to try ligating the other sequences to the plasmid backbone and increase the number of types of SSA vector. However, the day we realized only two sequences were correctly ligated was just three days before the submission of final poster and we weren’t able to try again. Results showed the expected data, so I felt relieved when I realized that we don’t need additional trials to validate the SSA assay.

I was able to make success in my research owing to the collaboration of other lab members, especially in the final week. Julie provided us with the result of T7E1 assay, which we used to validate the result of SSA assay and Kevin instructed me how to do the quantification of luminescence of luciferase-luciferin reaction. They helped me even though they were both very busy. My mentor Buhle supported me until I finished making my poster. I really want to appreciate again all the lab members for supporting me!

There are no labs that do the same kind of research in my faculty, but there are some labs that use gene editing to do research on certain organs, so I believe that what I have learned will be applicable in my future research in Japan.

Research in Japan vs. Research in the U.S. 
When I was in Japan, I knocked on the door of a lab in my faculty and was kindly accepted as an undergraduate student. However, what I was able to do in this lab was just practice and every time I went to lab, I did the same thing. (Now I realize that this is because I just kept on following what my mentor told me and haven’t proposed anything from myself.) I expected that what I would do in this program would be the same. However, in this program, I was given one project to do, which is not just a practice, but it is a useful project for the lab’s overall research. Of course, I was instructed by my mentor and practiced the basics of genetic engineering, but when my mentor left me alone to do some processes after I took on the basics, I felt so excited.

The Bao Lab has two main projects and many small projects are going on under each of these two projects. Due to the scale of projects, my lab is larger than many other labs at Rice University. I don’t know whether this is because of the size of the lab, but there were kind of rules that people should come to lab every day from 9:30 AM to 6:00 PM and meetings were held twice a week. At first, the atmosphere in the lab gave me the impression that people were doing experiments almost like a job. Not all of them ate lunch together and we didn’t go outside to do fun things together like some other labs did. I guess individualism is stronger here than in some other labs. However, people would freely ask each other if they have problems or questions and there was a culture to collaborate.

One key difference I see between labs in Japan vs. in the U.S. is when it is time to go back home. In my lab in the U.S., it was up to each individual person to decide when to go home and you didn’t need to wait until others left to leave and follow them. In Japan, there still exists a culture that the longer you stay in lab the harder you are thought to be studying. I really liked the U.S. approach where the emphasis is on finishing all the things you need to do until the time you go home and doing things efficiently. Staying in the lab late at night is really exceptional.

Before I joined this program, I was really wondering whether I should go into industry or stay in academia. At the time, the experiments and lectures that I had in my faculty were all so boring for me that I thought being a researcher may be not suitable for me. Through this program, I found the excitement of doing research, and I even had a chance to get engaged in research that has potential to save people’s lives. The reason why I chose Pharmaceutical Science was to accomplish my goal to cure diseases by my research. I remembered this goal and decided to take a bachelor’s degree. If I make success in my project until then, I plan to continue on and take a master’s degree.

As my time at Rice University comes to an end, I will first really miss the members in my lab. All of the Bao Lab members were really kind to me and taught me the basics of genetic engineering. Without their support, I believe that I wouldn’t have been able to find the excitement of doing research. I also miss the Rice University students that talked with me kindly. It was a very short time, but I really enjoyed the culture of US college students through the people I met. I really appreciate all the people that supported me!

Other Activities in Houston

This week we got to tour the TMC innovation Center and this was very impressive for me. Actually, I have attended some lectures about the health care industry in Japan and the around the world and learned how start-up companies are growing up from both the academic and business perspectives. However, it was so surprising to see such a huge and cool building in a great location next to Texas Medical Center. I realized that there is a lot of support in incubating health care companies. It even made me feel that I want to go there.

Return to Top

Research Project Overview and Poster

When the poster presentation began, I was so nervous but as time went by I began to get excited. It was so good that I was able to practice doing my presentation with the other Japanese Fellows before the presentation day. At first, I was got stuck with what words I wanted to use often, but by practicing, I was finally able to make presentation so fluently that I was able to talk about my research even to people who haven’t studied biology. I felt so happy when people who looked curious or people who were only attracted by the word of CRISPR-Cas9 finally understood the purpose of my research and its principle at the end of my presentation. I even felt that questions were so nice, because it means that they’re showing interest in my research. This presentation made me feel that I want to keep on doing research and make some results that are more fascinating and interesting.

Research Project Poster (PDF): “Efficiency of SSA Assay in Quantifying CRISPR/Cas9 induced DNA Cutting Activity”
Received Honorable Mention for Joint RCQM-Nakatani RIES Research Poster Symposium
Host Lab at Rice University:
 Laboratory of Biomolecular Engineering and Nanomedicine
Host Professor: Prof. Gang Bao, Depts. of Bioengineering and Chemistry
Mentor: Dr. Buhle Moyo

Introduction: CRISPR-Cas9 is a system that can be designed to cut a specific target gene sequence. After the cutting, gene repair mechanism can be used to replace the sequence with the correct sequence. In order to see the cutting activity, T7E1 assay was mainly used in my lab, but it takes about a week and has many processes. SSA has less processes compared to T7E1 and takes about three days which means so efficient. In my research, we analyzed the sensitivity of SSA assay comparing to the result of T7E1 and sought for the potential of SSA assay to replace T7E1 assay.

Approach: Cloning, Transformation, Colony PCR, Sequencing, Transfection, and SSA assay were the techniques that I used. Cloning were used to design a vector that contains gRNA-Cas9 targeting sequence. Transformation is a process to amplify the amount of the vector. Colony PCR was used to select the correctly designed vectors. Vectors were injected into human cells by transfection and lysed human cells were used for SSA assay.

Results and Discussion: Out of 15 target sequences, 2 target sequences were correctly cloned into vectors. The cutting activity showed a correlation to the result of T7E1 assay, which is proved to be valid.

Future Research: We expanded the number of guides that are screened by the SSA assay in order to accurately determine the robustness of the assay. If SSA assay proves to be valid, we use SSA assay to screen large numbers of gRNA/Cas9 complexes instead of traditional T7E1 assay and Surveyor assay.

It is also interesting to seek the reasons behind the difference of efficiency between different target sequences. There are many remaining things that should be done, but for my research, it showed a good result.

Return to Top

Week 06: Last Week in the U.S.

Sight-Seeing in Philadelphia 

You should take pictures here! ~ Yuki Kitanishi

I enjoyed Philadelphia from seeing famous places to places that only local people know with Chihiro’s friend Avram as our guide. I felt every building in Philadelphia was large and had a unique history. We visited City Hall, the LOVE monument, the Philadelphia Museum of Art with the famous with the Rocky Steps, an art gallery that has a lot of mirrors so that you can be a part of the art, an observatory where you can see the whole of Philadelphia, and finally the night scenery that Avram really loves. Even though our stay in Philadelphia was short, I really enjoyed sight-seeing in Philadelphia thanks to Avram.

Program at Lehigh University
It was so fun to have dinner with undergraduate students at Lehigh. The students that I talked with were the same age or younger than me, but they were pursuing their interests so hard and it was so stimulating. In particular, it was so interesting that one student is writing a program that converts a sound wave to an electric signal, which makes it easier for the parents of children who have hearing disabilities to understand how their children are listening. I also found that it is special to the USA that students from many countries were collaborating on this project.

Really enjoyed our dinner with undergraduate students at Lehigh University! ~ Yuki Kitanishi

Program in Washington, DC
The lecture at Gakushin (the Japan Society for the Promotion of Science) was so useful. I believe that I have some chances to get support from Gakushin for my research in the future. I think there are few opportunities to talk with people that are responsible for selecting the students who receive awards. I am appreciative for the program for giving us such a great experience. I found that some people that I know are also receiving money from Gakushin, so I will talk with them I after I go back Japan.

Sight-seeing in DC

The last time I came to Washington, DC was when I was in elementary school and I almost forgot what I had done at that time. It was so exciting to go around the city with my friends. Seeing the White House, Lincoln Memorial, we visited most of the famous places, but I couldn’t go to Smithsonian museums. However, the night scenery I saw from the Big Bus tour was so beautiful and it was great way to finish my stay in US in this city.

Kind of sentimental ~ Yuki Kitanishi

I felt both excited and sad leaving the U.S. It was the day I left U.S. that I finally got used to the culture in U.S. including its multiculturalism, that people talk to each other so freely with kindness, and the foods that are all large, delicious and diverse. I made new friends in U.S. and had begun to really enjoy the culture. Even in my lab, it was not until the last week that I fully understood my lab’s research and got friendly with the other members. I feel so sad about leaving U.S. so soon but it drove me to think my future career opportunities in U.S. On the other hand, it was so exciting to meet my friends in Japan again. Many friends encouraged me to do research in U.S., so I will share with them what I have done during my time here. I was also feeling excited to keep on studying and doing research on what I have learned in U.S.

Return to Top

Final Report

Before I joined this program, I was passive about learning new things. I have done all the things in a passive way, not only in lectures but also research in my faculty. Through participation in this program, I found myself being more active than before that I am now trying to find interest in lectures and research. The professors and students that I met were all pursuing their interests very actively! I felt it is just a waste of time to do nothing while I am an undergraduate student. I am now finding some companies to do an internship with that really match my interests and going to a lab to do new research. In addition, I found myself being more competitive than before. Since all the people I met during this program were highly motivated and clever, it was natural for me that I want to work hard to compete at the same level.

I have so much advice that I want to tell the future participants, but I narrowed it down to four points.

  • First, find something that you are really interested in. When you find it, stay hungry about it and go beyond others. I felt that the people who succeeded all had enthusiasm for their research.
  • Second, if you still cannot find any interest, gain as much experience as possible while you are an undergraduate student. I believe that these experiences will shape your future by and by. Keep in mind that you cannot always realize at that time what will be important to your future career.
  • Third, don’t hesitate to fail. During the first week of my research internship at Rice University I was afraid of failure and tried to pretend to be perfect, which led myself feel uncomfortable. There is nothing shameful about failures or setbacks in research. By asking to my mentor everything I had in my mind, even questions that sounded foolish, I began to understand more about my research.
  • Finally, don’t be passive in studying. Whenever you’re taking a class or doing research, if you find something that you cannot understand, find the answer by yourself. It is only when you figure out the answer by yourself that you can get interested in that topic.

What would you tell another Japanese student about why international research experience is important? 

The research environment abroad is totally different from Japan and my lab members came from all over the world. Every member of my U.S. lab was highly motivated, and this was a stimulating environment me as a Japanese undergraduate. What I thought to be the most important thing, however, was the opportunity to think about our future careers doing research or working outside of Japan. Even if Japanese undergraduates participating in this program decide to pursue graduate study in Japan or work at a Japanese company, I believe they won’t regret their decision study abroad.

What would you tell your family members about this experience?

Of course, it is so hard to live as a researcher especially in Japan, but in U.S., researchers can live by the money that are paid by the universities. In addition, for researchers, staying in academia isn’t the only future option – many researchers are planning to go into industry. One of the differences of research environment between universities and industry, is that lab members can be more flexible in universities, while team members are more fixed in industry. This program gave me many perspectives when thinking about my future career.

What would you tell a professor about this experience? 

To Japanese professors, I want to tell them how fun and interesting it was to do research with researchers from all around the world. On the other hand, I also reflected on the research environment in Japan and felt that I also like the Japanese culture to hang out together with all lab members and emphasize the importance of working as a team. Both have good points and bad points.

What would you tell a future employer about this experience? 

In U.S., researchers are funded to make innovation by their research product. For example, the TMC Innovation Institute is an organization with rich facilities that give opportunities to researchers to create companies that impact the health care industry. It collaborates with hospitals and universities around its location and facilitates the innovation eco-system. I know that there are similar environments even in Japan, but I still think that US gives a better environment for this type of innovation.

Return to Top

Tips for Future Participants

I have so much advice that I want to tell the future participants, but I narrowed it down to four points.

  • First, find something that you are really interested in. When you find it, stay hungry about it and go beyond others. I felt that the people who succeeded all had enthusiasm for their research.
  • Second, if you still cannot find any interest, gain as much experience as possible while you are an undergraduate student. I believe that these experiences will shape your future by and by. Keep in mind that you cannot always realize at that time what will be important to your future career.
  • Third, don’t hesitate to fail. During the first week of my research internship at Rice University I was afraid of failure and tried to pretend to be perfect, which led myself feel uncomfortable. There is nothing shameful about failures or setbacks in research. By asking to my mentor everything I had in my mind, even questions that sounded foolish, I began to understand more about my research.
  • Finally, don’t be passive in studying. Whenever you’re taking a class or doing research, if you find something that you cannot understand, find the answer by yourself. It is only when you figure out the answer by yourself that you can get interested in that topic.
  • Pre departure packing: Pack a Boston bag in your suitcase so that you can pack your souvenirs when you leave U.S. Just in case.
  • Preparing for Research in the U.S.: Read some articles that are related to your research in English to understand the terminology.
  • Doing Research or Working in a Research Group in the U.S.: Just keep on asking anything you wonder about.
  • Things to do at Rice University: Make friends with Rice University undergraduates. You may have some chances to see how undergraduate enjoy their college life.

Return to Top

Print Friendly, PDF & Email