[:en]Yumiko Kimura
Hometown in Japan: Tokyo
University in Japan: Tokyo University of Science
Major & School Year: Pharmaceutical Sciences, B3
Host Advisor: Prof. Gang Bao, Dept. of Bioengineering
Host Lab: Laboratory of Biomolecular Engineering & Nanomedicine

Why TOMODACHI STEM @ Rice University?

As soon as I knew and read about TOMODACHI STEM, I immediately got interested in and there are three main reasons for this. First, I could experience cutting-edge research as an undergraduate student in the U.S. where a lot of innovations occur. This is the point which I am mostly looking forward to in this program. I would like to conduct research and discuss various topics with like-minded students who have different backgrounds. Second, this program is held in Rice University, which is a prestigious university and has highly motivated and talented students who bring a variety of intellectual excitements. The rich diversity is one of the greatest strengths of Rice University and that is what greatly attracted me. Lastly, it is held in the U.S. which is a leading country in scientific fields as well as many other fields. I feel so passionate about experiencing various aspects of American culture, and I would like to compare with those of Japan.

The experience I will gain in this program will change, stretch, stimulate and enable me to significantly deepen my scientific knowledge and skills, and ultimately help me to achieve my career goals as a researcher.

Goals

• Experience cutting-edge research and learn various procedures used in research, logical thinking and discussion with other members of the laboratory
• Deepen my understandings of various aspects of American culture
• Develop my understanding and ability to communicate in English used in daily life, as well as English used in academic and research-oriented fields
• Meet people with various backgrounds and enjoy talking with them

Excerpts from Yumiko’s Weekly Reports

• Week 01: Arrival in the U.S.
• Week 02: First Week at Research Host Lab
• Week 03: Interview With a Female Researcher
• Week 04: Research in the U.S. vs. Research in Japan
• Final Research Poster Presentation
• Week 05: Science & Technology Policy Study Tour
• Final Report & Tips for Future Participants

Week 01: Arrival in the U.S.

On February 26, the TOMODACHI STEM 2017 members arrived at San Francisco International Airport. Coming out from the airplane, I felt the nice sweet smell specific to the U.S. In addition, the scenery that came into my eyes for example signs written in English and big stuff made me realize that I was in the U.S. I was strongly moved by it because it has been one of my dreams to study and experience research in U.S. We left San Francisco to Houston by airplane. The moment I reached Houston, I felt that it was humid and warm. I was so happy because in February it is winter in Japan so it is so cold and dry. I felt so comfortable with this condition.

Before coming to Houston, when I knew about the busy schedule of this program for the first time, I was not sure that I would have enough physical strength to overcome jet lag and complete all of these schedules. But the days here in Houston were very exciting and stimulating because of opportunities to meet wonderful people, daily discoveries and surprises, so I did not feel tired in fact.

As I expected, the campus of Rice University was fantastic. It was much larger than the campus of my university. It had many picturesque buildings, big stadiums, well-equipped gymnasium, concert hall and even it had its own police department. It was rich in nature and I often see cute squirrels.

Through the talks given by Prof. Kono and the Japanese graduate students, I learned that if you pursue a graduate degree in U.S, you can earn money instead of paying academic fee. It was so surprising for me. I was going to get a master’s degree and find a job in Japan, but hearing these talks, I became to consider I have choices to study in U.S. to get Ph.D after I finish my master’s degree. Sarah told us about Cross-Cultural Communication, this talk helped me know how I should behave in U.S. culture.

The site visit to Dow Chemical and their Leader Panel Discussion was most helpful for me. It was impressive that each of the panelists had their own unique background and pathway and everyone was satisfied with their work. One of the panelists advised us ‘You know what you like’, so you can choose your future on your own. Those words were memorable to me because I was lost in what I want to be in the future.

On Saturday, some of my fellows and I went to seeing Houston Rodeo Parade. We went there by METRORail. Every time METRORail stopped at a station, many people who were dressed up to go to the parade rode on it so I felt like I could not wait to arrive at the destination. As soon as we reached there, the parade started. I was so excited to see so many cow boys, cow girls and high school marching bands. I was so moved by high school students who were performing hard. We enjoyed the parade with waving American flags. After the parade finished, we went to watch ‘Cinderella’ performed by Houston Bullet, because as a part of this program we visited Houston Ballet on Thursday and we experienced behind the scenes tour so I was so looking forward to seeing this performance. The ballet was wonderful. On that day, we also went to Galleria by bus. Bus passed 49 stops before we got there. The Galleria is such a big shopping mall and there were a variety of shops in it. We ate dinner there, enjoyed shopping and went home by Uber. It was such a productive day.

On Sunday, Dona Cole, our kind big supporter, invited us to professional woman’s networking lunch in her home. There was amazing panel discussion. All of the panelists gave us tips to work as woman. It was so helpful and I was so encouraged the existence of such wise and strong professional women. I strongly felt I would like to be like them.

Question of the Week
I met some undergraduate students at Rice University this week. As Question of the Week, I would like to know more about their lives at Rice University. I cannot have enough time to talk with them so I will try next week.

Research Internship Update
Prior to arriving in the U.S., I communicated with my host professor, mentor and the lab manager in advance by e-mail. From my professor, I had received two papers to read before I arrived here at Rice University. I started reading those papers in Japan to prepare research internship experience. However, I soon found that it was so difficult and took a long time to read them because I had little experience reading papers before. There were technical words I could not understand in the papers and they were so long.

Therefore, I decided to try to understand the background of the article in the beginning. My project was related to genome editing and papers were about it, so I read some books about genome editing in Japanese. After I read those books, I was able to understand the papers more easily than before and then I continued to read them. But I could not understand all of them. Also, I have never had experience doing research before so I was very anxious. On the first day in the laboratory, I met my mentor and talked with him. I told him that I could not understand all of the articles, then he explained about genome editing from basics so politely and kindly with using some slides. His explanation helped my understanding.

In my opinion, it is so helpful to communicate with the professor and mentor in advance, ask them what your project will be and learn the overview of that using books written in Japanese. At the same time, I think I should have studied in advance how I can say technical terms in the field I will learn in English.

TOMODACHI STEM Tip: If you aren’t sure how to start reading a scientific research paper review the section on “Reading and Understanding Scientific Research Papers” in the Research In the U.S. resources page.

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Week 02: First Week at Research Host Lab

We arrived in Houston on Sunday, and on Tuesday I met my professor Prof. Gang Bao and my mentor Dr. Ciaran Lee for the first time. I was so nervous before I met them. First, I visited my mentor’s room. He welcomed me with smile. He is a postdoctoral researcher and director of genome editing core. After we talked some, he explained the basics of genome editing clearly and politely and took me to the laboratory and showed me the facilities and machines there. He was kind and gentle. I thought I was fortunate to meet such a mentor. And I met my professor, Prof. Bao. He was a bright, energetic and a kind person. I asked him basic questions about the laboratory and the project. He answered each question so politely. At the end of the conversation, Prof. Bao told me ‘Here we start’. I was so excited to experience research here.

On Wednesday I spent all day in the laboratory for the first time. Throughout the day, I shadowed technicians in the laboratory and they showed me the preparation of electrophoresis and cell cultures. It was so interesting to see each procedure. I was pleased to have daily conversations with people in the laboratory but it was challenging for me to understand the technical words because I learned them in Japanese and even if it is said as same in Japan, it has a different pronunciation. It was also hard for me to translate something using technical words. But as the time has passed, it has become a little easier to understand. I think it is important to get used to it.

 

On Saturday, we went to NASA. It was spread out over a large area and there were many scattered buildings. Some of the TOMODACHI members are studying subjects relating to aerospace so, it goes without saying, that everyone was so excited to be at NASA. At NASA, I saw many exhibitions and I participated in the tour to see the training center of astronauts. It was a special experience to see it. Also, I saw the huge space shuttle ‘SATURN.’ I am not familiar with space but I was surprised how big it was and I was moved so much when I think of the amount of wisdom and effort that have been needed and spent until people could launch such a huge rocket.

After we came back, some of the members and I went to shopping at ‘Target’, a large store near the hotel. We enjoyed shopping there. When we were on our way to the hotel and waited for the last traffic light to change, someone in the car spoke to us. How surprising was it to see that the person speaking to us was Ozaki-sensei from Rice! She is a wonderful Japanese teacher at Rice University. She picked us up and took us to a fashionable coffee shop. She treated us to delicious coffee and sweet bread. We enjoyed talking with her so much. She gave us many tips to study foreign languages. I appreciated this happy coincidence.

On Sunday, some of our members went sightseeing in Austin. It took 3 hours from Houston to Austin by bus. In the beginning of sightseeing, we had lunch because it was almost noon when we reached there. We ate Tex-Mex cuisine such as tortilla chips with salsa dip and burritos at the restaurant. After lunch we walked to the Texas Capitol. It was a big quaint building. There we participated in a guided tour and saw the beautiful rotunda, Senate chamber and House of Representatives chamber. We also could get souvenirs of Texas. After that we visited the Bullock Texas State History Museum and learned about the history of Texas. We were going to ride a bus that left Austin at 5:00PM but the bus was delayed for 3 hours and surprisingly we got extra time to go around the city. So we walked through downtown and enjoyed the atmosphere of SXSW, the musical event which was on season. We saw the event venues all around city. We also could see the Colorado River at the end. It was such a productive day. On that day, what made me surprised most was that Daylight Saving Time began. As soon as we got up, we noticed that we lost one hour while we were sleeping. I felt so surprised and strange because Japan doesn’t have it.

Research Project Update
I discussed the research project with my mentor Dr. Ciaran Lee and shadowed researchers in the laboratory of Prof. Gang Bao. During this research project I will survey the efficiency of genome editing by a small Cas9 orthologue derived from Campylobacter jejuni (CjeCas9). The ability of the CjeCas9 nuclease to recognize different protospacer adjacent motifs (PAMs) and the efficiency of DNA targeting with different guide RNA (gRNA) lengths will be assayed. To measure CjeCas9 efficiency we have designed gRNAs targeting the GFP sequence. CjeCas9 activity will be measured by the level of GFP knock-out achieved in a cell line engineered to express GFP (HEK293-GFP).

Week 2
On Tuesday we received DNA oligos and plasmid DNA. Each DNA oligo has different gRNA sequences with two complimentary oligos for each gRNA sequence. The DNA oligos were phosphorylated and sense and anit-sense oligos were annealed prior to cloning into the expression vector.  To facilitate cloning of gRNA sequences downstream of the RNA pol III promoter U6, the CjeCas9 expression plasmid was digested using the restriction enzyme BbsI.

On Wednesday the annealed oligos were cloned into the digested plasmid using T4 DNA ligase IV and the resulting ligation products were transformed into chemically competent E. coli and plated onto LB agar plates supplemented with ampicillin.

On Thursday, we picked up 2 colonies from each plate and inoculated into 3 mL of LB culture medium supplemented with ampicillin and cultured overnight.

On Friday CjeCas9 plasmids were extracted from E.coli and sent for sequencing to confirm the presence of the gRNA sequence.

Question of the Week: I heard next week, undergraduate students have spring holiday but other workers do not have it. So I would like to know whether workers in academic field has enough rest time and take work-life balance.

This is a good question. It is also important to know that in the U.S. there are holidays (that all workers get to take), sick leave (that some companies give to employees to use as needed when ill), and vacation days (that you accrue over time and can be used at any time of the year with the approval of your boss). Sometimes, sick leave and vacation leave are combined into one category of ‘Paid-Time Off’ which is used both for when you are sick and for when you want to take vacation. Rice uses the Paid-Time Off method for staff. The amount of sick, vacation, or paid-time off you accrue varies by company/school.

In terms of whether people get Spring Break week off, it varies by level of school and the school/institution you work at. For example, if you are an elementary, middle, or high school teacher in the U.S. you will typically get Spring Break week off, the summer break off (mid-May to August), and winter break off which is usually 2 – 3 weeks in December and early January.  However, if you work at a university as a staff member you typically do not get the Spring Break week or summer break off. Faculty are usually on 9-month teaching contracts so they technically could take the summer break off but usually they secure external grants to pay for their 3 months of summer salary and continue to work during this time. For staff members, it is not uncommon for people (especially parents) to ‘save up’ their vacation leave so they can take extra time off during the Spring Break or Summer school break periods to take care of or spend time with their children.

You may also notice that during Spring Break week you see more kids on Rice University campus.  This is because it is not uncommon for faculty and staff to bring their children with them to work during this week and there are often sports clinics or other special activities that parents can enroll their children in. This way, parents can still work but they don’t have to leave their children home alone.  Rice University is also very welcoming and accepting of families and that sometimes working parents do need to bring their kids with them if the schools are closed, they are sick, or if they have to take their child to a doctor’s appointment during the day. At other companies or universities this may not be so common; but it is one of the reasons many people like to work at Rice as the university is known for having a good ‘work-life’ balance and family atmosphere.

At Rice, the entire university does close for about 10 – 12 days from late December to early January for Winter Break but not all universities do this.  This is pretty common for many private universities in the U.S., but public universities often do not have a 1 – 2 week staff holiday in the winter.  For example, at the University of Hawai‘i, staff only get Christmas Day (Dec. 25) and New Year’s Day (Jan. 1) as holidays and if they want to take more time off during the Christmas/New Year’s season they may need to use vacation days.  However, it is often very quiet and not too busy during this time of the year so many people may be able to leave work a bit earlier than normal or be a bit more relaxed.

There are 9 federal holidays in the U.S. and many companies and universities do observe most of these holidays.  Some states also have special, state holidays in addition to the federal holidays. If you work at a public university or for the state or federal government you are very likely to get all 9 of these days off. If you work in the private sector, either in industry or a private university, you may get some – but not all – of the federal holidays.  Each institution/company is a bit different in the U.S. regarding holiday and vacation leave so when you start working you need to ask your boss or the Human Resources department what the holiday and vacation policy is there.

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Week 03: Interview With a Female Researchers

Female Student: Yidan Pan
She is a graduate student in the laboratory of Prof. Gang Bao. She is in the 2nd year now. She is from China.

Academic Background
Since she was a child, she has been curious about living creatures, thinking ‘All living things are interesting’ and she liked taking care of animals. When she became an undergraduate student at the South University of Science and Technology of China, she decided to study Biology. After graduation, she chose to come to U.S. and study at Rice University to learn advanced technology and get her Ph.D. When she was a junior, she did a research internship at Rice University for 2 months. It was a wonderful and important experience for her. She liked Rice University so much because of its large campus and beautiful nature. Thus, she was so excited to come back to Rice University.

In her department, System, Synthetic and Physical Biology, she visited 3 laboratories in the rotation when she was in the fall semester of the 1st year. After finishing this she decided to belong to the Bao lab and from spring semester she started her research there. When she was an undergraduate school student, she participated in a summer school at the Chinese University of Hong Kong, where she joined a seminar on genome editing using CRISPR and she got so interested in it. This experience had a big impact on her life. She chose Prof. Bao’s lab and now she is doing research about CRISPR/ Cas9.

Future Career Path
After she gets Ph.D. degree, she would like to apply for a position as a postdoctoral researcher or work in industry. For that, she will try to do an internship while she is a graduate student.

Lab Experience
She is so satisfied with the environment here. It is rich in a lot of ways. When she was an undergraduate student, she was doing computation and simulation using PCs because her laboratory was just set up so it was not equipped to do experiments. So, after coming to U.S., she started to do experimental research and she is enjoying it. She thinks both of them have advantages and disadvantages. When doing computation, it can be done anywhere and anytime with a PC at least. Also, time can be used freely and flexibly. If doing experiment, it is needed to properly arrange the experiment. She likes both of them.

International Experience
She participated in the International Genetically Engineered Machine (iGEM) competition. It is a worldwide Synthetic Biology competition. This experience grew her interest in Synthetic Biology.

Rice University is famous for its diversity, but as a Ph.D. student in a laboratory which has many Asians, she does not feel the diversity so much. She thinks undergraduate students have more opportunities to experience diversity through taking classes and participating in extracurricular activities.

Being a Woman in STEM
Her message is ‘Be strong’. She thinks men and women can do the same thing. In STEM fields, women tend to be the minority. But being strong and confident in yourself, because all are created equal.

Female researcher: Linlin Zhang, Ph.D.
She is a postdoctoral research associate of the laboratory of Prof. Gang Bao. She is from China.

Academic and Career Background

Linlin was born and raised in China. Her hometown is in North China. She got her bachelor’s degree at Nankai University in Tianjin, China in 2011 and got her Ph.D there last year. When she was an undergraduate student, she learned Biological Sciences and in her Ph.D course her major was Cell Biology and her research focused on cytoskeleton, cell motility and their relation to cancer and other diseases.

She decided to study at Nankai University because it is a prestigious university and Enlai Zhou, the first Premier on the People’s Republic of China is one of alumni of that university. Also, the College of Life Science at Nankai University is very new. There are many professors and students from overseas and it has a creative environment. Her supervisor is a very creative professor. He became a professor at the young age of 29. He was smart and hard-working. She had been engaged in research at his laboratory for 6 and a half years.

Chinese students decide their undergraduate major immediately after they graduate from high school. She chose Biological Sciences. In fact, one third of the students in her department changed to different departments like economics after the first year of study. With only a bachelor’s degree in Biological Sciences, it is difficult to get a satisfactory job. To get a position like an instructor or a professor in China, one not only needs a doctoral degree but also overseas experience.

She came to Prof. Bao’s laboratory  in 2014 as a Ph.D student because of the collaboration between her supervisor and Prof. Bao. The initial purpose was to learn the CRISPR/Cas9 technique. However, whens he joined the lab, Prof. Bao has just decided to move his lab from Georgia Institute of Technology to Rice University and the whole lab was reorganized. Thus, she followed Dr. Sheng Tong who is an associate research professor in the Bao lab to learn nanotechnology. She got an extension of her visit and returned to China until the defense of her doctor’s thesis. After graduation, she came back to Rice University to continue her work as a post-doc.

Career Path
She would like to stay and continue research in the U.S. as long as her visa allows. In the future, she plans to go back to China, work in industry and look after her parents.

Lab Experience in the U.S.
In her opinion, the U.S. is a pretty good country for research in many aspects.

First, she can get reagents for her experiment more quickly. For example, while in China it takes 3 weeks to get an antibody in the U.S. it only takes 3 days. Second, she can arrange her experiments according to her schedule and time is more flexible here. Lastly, she thinks there are more resources in the laboratory in the U.S. In her previous lab, resources were often limited and one needed to wait until the others had finished using some instrument. But here, the resources are adequate and one can use the equipment whenever he or she wants to. For example, the hoods for cell culture here is not as crowded as those in her previous lab.

She feels the environment of the laboratory in the U.S. is so comfortable.

International Experience
She has attended some international conferences related to her research before. However, all the conferences were held in China. In 2014, she went abroad, to the U.S. for the first time. She thinks it is good to communicate with people from different backgrounds. When she collaborates with other professors and discusses with them, she learns a lot from them.

Being a Woman in STEM
She basically thinks men and women are equal in the scientific field. On the other hand, she sometimes feels that in the U.S., women tend to have better opportunities to get a good position in academia, especially for women from minority groups. But for men from Asian countries, getting a good position in academia is more challenging.

Her message to women in STEM is to balance the relationship between family and research. Do not forget your families when you are busy with your research. To learn how to manage your time is never a more important issue.

Reflections on My Interviews
I sincerely enjoyed my interview with each of them. They answered my questions so kindly and politely. They also came to U.S. from foreign countries so what they talked about was very helpful for me. Both of them are from China so I could learn more about China in terms of its educational system and the environment of research. It was interesting.

During the interview, both of them mentioned the visa. Unless you have a green card, it is a bottleneck for foreign students and researchers to apply to universities in U.S. to study and do research.

Question of the Week: As question of week, I want to know more about visa needed for foreign students and researcher?

See the U.S. Department of State’s Student and Exchange Visitor overview for more information. You’ll see there are different visas by class/category such as ‘Student’, ‘Exchange Visitor’ and ‘Visitor’ and the type of visa you get depends on what you will be doing/studying.  For example, degree-seeing international students often come to the U.S. on an F-1 visa but a J-1 visa may also be used for graduate students.  For an academic research internship program like the TOMODACHI STEM program you had to obtain a J-1 Non-Degree Student visa to come to Rice for this internship program.

The university you are applying to will typically tell you want type of visa you should apply for once you have been accepted into the school or program and if you aren’t sure what you might need you can always email or call the university’s Office of International Students and Scholars.  Each university will have an office like this and they are very helpful and are the experts on what the current legal requirements are for the various types of visas to enter the U.S. for study or research at a university. .

See the the Department of State’s Employment Visa overview for more information.  The most typical employment visa is an H1-B and your employer must apply for and sponsor this visa on your behalf.  In some cases, a J-1 visa can also be used for a short-term, time-limited appointment such as a post-doctoral research position, short-term research scholar, or short-term internship.

If you want to stay in the U.S. long-term, it is usually a good idea to apply for permanent residency status (a green card) so that you can live and work freely in the U.S. without the need for a visa. If you want apply to become a U.S. citizen, you must first obtain a green card/permanent residency status. However, this is a long and complicated process and not everyone who applies for a green card is successful.

In addition, in front of BRC building, there are the sculpture of a compound. I am curious to know what compound it is.

You might want to review the Public Art website of Rice University. You can look at the map on this website and click on the pins by the BRC to learn more about the art and sculptures in and around this building and in other buildings on campus.

Research Update

On Monday, HEK293-GFP cells were seeded in 24 well plates in preparation for transfection 24 hours later.

On Tuesday, we measured concentration of plasmid DNA and made them the same concentration as preparation for transfection. After that, we did chemical transfection.

On Wednesday and Thursday, as I should wait until I check the result, I wrote the draft of poster presentation.

On Friday, we checked the expression of GFP using Flow Cytometer. We are going to check it again on Monday and Wednesday.

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

I am a junior student, and I don’t have experience of research. But I have already chosen my laboratory for graduation research in Japan. To select one laboratory, I visited many laboratories. Thus, I would like to compare the laboratory in U.S. with them.

First, I think the laboratory in U.S are larger than that in Japan in many points. The height of ceiling and benches was obviously higher. Each of the members has his or her own desk in office, on the other hand, the students of my faculty in Japan have desks in the laboratory. The space to use is obviously larger in U.S.

Second, both laboratories in U.S and laboratories in Japan have a group meetings several times a week. What I felt about it is that people in U.S. ask questions even while the presentation is on the way. In Japan, members ask a presenter questions after the presentation is finished. After coming to U.S. I strongly feel that American people practice both ways of communication not only on casual situations like greeting and daily conversations but also on formal situations like these meetings and seminar talks. I think both ways of communication is so valued because both ways of communication produce more new ideas.

Last, American people arrange their schedule on their own and use time more freely than in Japan. For example, they don’t have a regular time to come and go home and their supervisors don’t mind about the time. I think it is so flexible and comfortable.

I got the my final data and could start writing ‘result’ and ‘conclusion’ on Wednesday, but I should submit the final version of the poster on that day. So that day was such a busy day for me. Owing to kind corporations of my mentor Dr. Lee, Sarah and Aki-san, I managed to complete the final version of my poster. On Thursday, I considered what should I talk about and practiced for the presentation all day. On Friday, I was nervous because it was my first experience presenting a poster. My office mate, Lin, gave me some advice about poster presentations and encouraged me. My mentor answered the questions I had. They helped me relax so much. Prof. Bao invited me to farewell luncheon at noon and I was so glad to meet the lab members before I left Houston.

As at the room we would use for the poster presentation a class was held until 15 minutes before the presentation started, we should prepare for it in hurry, which eased my tension. After I finished setting up my poster, one woman came to see my poster and listened to my presentation. I was so pleased that I explained about the project including background and she understood me even though she did not have basic knowledge in this scientific field. Also, after I introduced my presentation, I talked with her. I really enjoyed talking with her. I felt it was good point of poster presentation that we can talk to each other. I realized that in a poster presentation, I can change what I talk depending on person who I talk to and I enjoy conversations with them. I enjoyed the experience of explaining my poster to her and her interest in my project gave me confidence. Owing to this experience, I enjoyed the rest of poster presentation. I was glad that my mentor came to the presentation.

I miss Houston so much. First of all, I miss people I met in Houston. I encountered many wonderful people in Houston and I will never forget them. I hope to see you them in the future again. I loved Rice University campus, I remembered its rich green nature, picturesque buildings and cute squirrels. I missed warm humid weathers in Houston, Houston Rodeo and Houston Rockets.

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Final Research Poster Presentation

Poster Title: The efficiency of genome editing by a small Cas9 orthologue derived from Campylobacter jejunin(CjeCas9) (PDF)

My research project title is ‘The efficiency of genome editing by a small Cas9 orthologue derived from Campylobacter jejuni (CjeCas9)’. I experienced research at the laboratory of Prof. Bao and my mentor is Dr. Ciaran Lee who is the director of genome editing core.

CRISPR/Cas9 is one of engineered nucleases and it is creating a revolution in genome editing because it is a fast, cheap and efficient method for editing DNA. It is complex of guide RNA and Cas9. It is discovered as the immune system in bacteria. Different species of bacteria have different types of Cas9.

In my project, I surveyed the efficiency of genome editing by CjeCas9. CjeCas9 is Cas9 derived from Campylobacter jejuni. It is smaller than other Cas9 which it is delivered to living cells. Also, protospacer adjacent motifs (PAMs) it recognizes is longer than others so it has more specificity.

First, we designed guide RNA. After we got DNA oligos and plasmid, the DNA oligos were phosphorylated and sense and anti-sense oligos were annealed prior to cloning into the expression vector. To facilitate cloning of gRNA sequences downstream of the RNA pol III promoter U6, the CjeCas9 expression plasmid was digested using the restriction enzyme BbsI. The annealed oligos were cloned into the digested plasmid using T4 DNA ligase IV and the resulting ligation products were transformed into chemically competent E. coli and plated onto LB agar plates supplemented with ampicillin. We picked up 2 colonies from each plate and inoculated into 3 mL of LB culture medium supplemented with ampicillin and cultured overnight CjeCas9 plasmids were extracted from E.coli and sent for sequencing to confirm the presence of the gRNA sequence. CjeCas9 plasmid were chemically transfected into HEK293-GFP cells. On day 3, day 6 and day 8, we measured GFP expression by using Flow cytometry. The level of GFP knock-out achieved reflects the efficiency of genome editing by CjeCas9.

As a result, on day3, day6 and day8, all samples express as much GFP as the cells which don’t have CRISPR/Cas9. We cannot see any drop of GFP expression. This means CjeCas9 is not active Cas9.

Again, there are many kinds of Cas9 and each has advantages and disadvantages in terms of efficiency, utility and specificity.

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Week 05: Science & Technology Policy Study Tour

During our final week in the U.S., we went sightseeing in National Mall and visited the Japan Society for the Promotion of Science (JSPS), the National Science Foundation (NSF), the American Association for the Advancement of Science (AAAS), and Howard University from Sunday to Tuesday. The stories I heard at each place were so interesting. I learned there are a variety of research funding to support researchers. I think if you do not know about the existence of these organizations, you cannot get benefit from it. To know about their support is essential to live as a researcher. It is so meaningful for me to know about them. On Wednesday, we visited the Department of Energy (DoE). I have never been to any ministry building of Japan, so it was such a valuable experience for me to visit a government agency. I heard various presentations about U.S. policy for nuclear energy there so I could understand it from many point of views. For Japanese, nuclear energy is controversial topic because of Fukushima nuclear accident. Thus, it was so interesting to know U.S. perspectives on nuclear energy. Also, I knew more about U.S. corporation with Japan in Fukushima emergency and I appreciated it and I felt strongly the importance of the corporation between two countries.

On Thursday and Friday, we visited Lehigh University. There we heard about the experiences of professional women and undergraduate students of Lehigh University and we had the chance to directly talk with them. For me it was impressive to know about ‘double degrees’. In the U.S., it is not rare for undergraduate students to get double degrees such as science and art or science and business in 4 years. I think to get double degrees make students acquire broad knowledge and flexible mindset. Also, it provides students more options for their future. I think this system is so attractive. I hope it also becomes common in Japan. On Thursday night, we went to bowling with some undergraduate students of Lehigh University. We enjoyed not only bowling but also talking to each other. It was so fun.

On April 2, after a long flight (about 14hours), we finally came back to Japan. As soon as arriving at Japan and getting off the airplane, I was surprised to see advertisements written in Japanese and many people who were talking in Japanese because I got used to the life in U.S. What excited me most about returning to Japan was I could meet my family after so long. I talked about what I experienced in U.S. to them and gave them souvenirs. I was happy because they were so pleased. After spending a few days in Japan, sometimes I felt I missed U.S. In the U.S., everything is so big and I felt people in U.S. don’t mind minor details. I like its free and unconstrained atmosphere so much.

This was the third time visiting the U.S. for me. Two times before, I had just traveled so this was the first time I studied and spent such a long time in U.S. Before I came to U.S. actually I was not sure I could live for a long time in U.S., so I brought to U.S. even daily stuffs as well as Japanese food. However, when we first went shopping at a supermarket in U.S., I found that I could get all kinds of things in U.S. I was surprised that I saw a lot of organic food. I found that I was worrying for nothing. I was really enjoying life in U.S. I ate American food and Tex-Mex food many times during my stay. Every day, I look forward to having American breakfast at the hotel. I ate hamburger or pizza at least once a day. I loved blackberry that we rarely see at supermarkets in Japan. I changed my mind and now I think I can live in U.S. even if it is a longer time.

Question of the Week
It was cold in Bethlehem, Pennsylvania where Lehigh University exists. I saw many beautiful architectures and leafless trees there and I felt like I was in Europe. On the other hand, in Houston where Rice University exists, it was warm and we usually got sunshine and there was rich nature. As U.S. has a big land, weather and vegetation of each university is various depending on where it is located. Do the students in U.S. usually consider these conditions when they decide which university they will go?

• Good question, and I think sometimes yes, weather and the location of the university are a consideration that some students make when choosing an undergraduate college.  Often though, students’ primary consideration is if the college is close or far from home.  Some students prefer to stay closer to home, other students want to move far away (even as an 18-year old) and experience life in a different city or state. I would guess that the location/weather of the graduate university is a bit less of a concern, as the first choice is always (or should be always) about what type of research you can do there as PhD student.  But yes, sometimes students who really dislike winter might not choose to even apply to universities that have cold winters or students that really want to live in a more rural area might not even apply to universities in big cities (or vice versa). It really is a personal decision and I think that yes, the location is something that many students think of, at least in part, when deciding where to go to school for 4 years (for bachelor’s degrees) or up to 7 years (for a PhD).

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Final Report

Time flies and about one month has passed after I came back to Japan. In this one month, I talked about what I experienced and felt through this program for uncountable times to my family, friends and professors. I considered many times how this program had impacts on my life.

I think this program definitely has changed me. Now I feel I am enjoying my life more than the old me. I think this is because I learned the positive way of thinking, I felt the possibility of myself and noticed what I need to improve.

Through this program, I had many chances to encounter wonderful people and hear from them. I guess the number of people I met through this program is more than the number of people I met for the whole of last year. Each person I met shared a lot of unforgettable words with me. The people I met through this program are my treasure.

I do like to talk to people, but actually I am originally shy and sometimes hesitate to talk to people have just met and I am lost in what should I talk to them. However, in this program I could really enjoy each meeting. That is because one word given by Ayako Kameda in Networking Brunch with Japanese Professional Women in Houston reminded me the very important thing. She said ‘don’t ‘try’ to be interesting to the person, just be interested to him or her’. Whenever we meet a person for the first time, we don’t know who he or she is. We should naturally come upon what I want to ask that person. I remembered from her word the significant mindset to be honest with what I feel.

The members of TOMODACHI program also changed my way of thinking. They have a variety of interests not only science but also people, culture, social problems and daily news. Their ability to take actions to what they have interests in was amazing. For example, I visited a variety of places when we have free time in this program because always each member made proposals to visit somewhere. In Houston, on weekends some of us went to the downtown to see Houston Rodeo Parade, Houston Ballet ‘Cinderella’, the musical ‘the King and I’, NBA basketball games. On one Sunday, we took a day trip to Austin. We saw Texas State Capitol and Texas State History Museum and felt the circumstances of the music festival ‘SXSW’ there. On museum day when some museums are open until late at night, we visited the Museum of Fine Arts, Houston. On weekdays we went to hear some interesting seminar talks. And, during our last night in U.S., some of us went to skating at local ice skate center. I enjoyed not only the schedule of the program but also free time owing to my dear members.

I am inspired by them because they had concrete dreams, they started actions to make them happen and they said them aloud. I tend to hesitate to talk aloud about what I want to do in my future. However, my roommate taught that me by saying it aloud, we can get tips to make it happen from others. I thought it is exactly to the point. I would like to be more open-minded and share what I think to others.

For me, it was just a ‘dream’ to one day study in U.S., the country where many innovations have occurred. But by experiencing the real life in the laboratory in U.S., meeting the Japanese students who are actually studying at Rice and knowing the higher education system in U.S., I was able to consider that studying in U.S. is no longer just a ‘dream’ but a possible ‘ choice’ of my future. The Japanese students I met at Rice were hard-working and friendly and they really liked to do research. After I complete my bachelor’s degree, I have already decided to go on to pursue a master’s degree at my university in Japan. If I could have passions to do research like them, I would like to then consider to go on to pursue a doctoral degree in the U.S.

My favorite part of this program was the life in the laboratory. It was stimulating and fruitful and my intellectual curiosity was satisfied through it. There I learned a variety of things and at the same time I knew many points I need to improve. My mentor gave me one project and I could learn the series of flow of the experiment. I really enjoyed it. He was a knowledgeable person and I liked talking with him very much. However, I had difficulty understanding and make use of technical terms in English because I learned them in Japanese. Also my English speaking speed was slow and I was not good at talking concretely. I was often frustrated because I could not express what I mean. Also, I sometimes felt my lack of knowledge when my mentor asked me questions. I was depressed by these experiences but they highly motivated me and I did my best to acquire as many new words as many as possible and speak positively. These experiences made it clear what should I do to grow.

The last day in Houston, the TOMODACHI STEM members participated in the poster presentation. It was the first time for me to do poster presentation and it was hard to prepare for it, but on that day I could enjoy presenting my project. The sense of accomplishment after it was beyond description and this experience gave me a big confidence.

Before I participated in this program, I set just the improvements of some abilities as goals. However, what I got from this program was definitely much more than I expected. I think not only it helped me to acquire some knowledge but also it changed my view of life positively. When reflecting it, I think every day of this program was splendid and those days are the essential part of my life. I sincerely thank everybody who gave me opportunities to participate this program and whom I encountered through it.

Tips for Future Participants

Prepare for Daily Life in the U.S.: I think you do not need to bring much from Japan because you can buy almost anything from daily stuffs to food in U.S. In addition, you will buy souvenirs in U.S. so you had better to have some space to your baggage when you leave Japan. In fact, the baggage of the most of members were overweight when we got on the plane to return and we struggled with packing.

It was mostly warm in Houston. However, in the morning and at night it got chilly so you must bring a light down coat. Sometimes it rained so you should bring a folding umbrella.

Prepare for life in the laboratory: I had a difficulty in communicating with using technical terms so I highly recommend you to learn the basic technical terms in your field in English.

Before I went to U.S., my professor at Rice sent me article relating to the project. This was the first time to read a full article and it took a lot of time to read through it. After knowing the way to read article my mentor at Rice and my seniors at my university practiced, I found that I took mistakes. I concentrated on reading sentences one by one but they are mainly saw figures to understand articles. They let me know figures are the core of articles.

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