Category: UTRIP

by Emre Discekici — I will never forget the summer 2012 I spent in Japan.  There are no words that can adequately describe what I have learned, the experiences I have had, and most importantly, the people I have met.  It was February of this year when I applied to the University of Tokyo internship program and the FUTI scholarship.  It ended up being the only summer internship program that I applied to.  I was well aware that the chances of getting accepted were extremely slim.  With 315 applicants and only about 20 spots, I was not very confident about getting in and naturally did not expect too much.  However, with that being said, I convinced myself that out of those 315 applicants, I wanted to go to Japan more than the any of the other 314 applicants.  It just was a matter of whether or not I was able to express that sentiment in my application.  There truly was nothing I wanted more at the time than to get accepted.  Part of this indescribable desire to get accepted is attributed to the cancellation of my study abroad program at Waseda University due to the devastating March 2011 earthquake.  I was told to come back by my home university and my 11-month program was cut short to just about 5 and half months.  As a result, I was also forced to withdraw out of the 2011 spring semester at my home university before reenrolling again in the fall.  Not knowing whether I would graduate on time because of my withdrawal was a very unsettling and difficult time for me.  However, thinking that I needed to do my best to move forward, I became determined to turn something bad into something good.  I was more motivated to work harder than I ever had before and I made it a huge goal of mine to be able to return back to Japan someday.  Now as I sit here writing this report, I realize again that with hard work, luck on my side, and the FUTI scholarship, I was able to reach that goal. It meant the world to me when I found out that I would spend my 2012 summer with the Tachibana group researching natural product chemistry at the University of Tokyo.  The research focus of the Tachibana group is far different than what I researched back at the University of Illinois, so I was ecstatic at the opportunity of immersing myself into a new field of chemistry.  I became further excited the moment I first met the members of my lab.  Upon the first exchange of greetings, I had no doubt that I would have a very productive and enriching experience.  Furthermore, it was the first time that I could use my knowledge of chemistry and proficiency of Japanese simultaneously.  After getting to know each and everyone of my lab members, I began the research process.  My specific project involved the synthesis and search for potential biosynthetic precursors to 6-membered polycyclic ether rings.  Many important natural products contain polycyclic ether backbones and as a result, the potential for discovering biosynthetic pathways to polycyclic ether rings via enzyme catalysis have long been of interest to biologists and chemists alike.  Though a current group member worked on a similar project, my goal was to expand on this research by synthesizing new precursors, subjecting them to incubation with enzymes from a dinoflagellate known to produce 6-membered polycyclic ether rings, and to ultimately determine whether or not a potential biosynthetic pathway to the desired 6-membered exists.  Though my results suggested no evidence of the desired biosynthetic pathway, extremely interesting results involving the oxidation processes of the synthesized precursors and the dinoflagellate extracts were observed, and as a result, progress has been made towards understanding interactions between the extract and the precursors tested to date.  New questions have also been raised and research in the group will continue in an attempt to find some answers.  Before starting the research process, I was well aware that 6-weeks was hardly enough time to make any significant advances in any field of research, but with some determination and the help of my surrounding lab members, I was not only able to complete my project on time, but also acquired some very interesting results. As for what I did with my time outside the lab, the list goes on and on.  From dinners with professors, to sitting in on graduate classes, to late night karaoke outings, to taking hot spring baths, to evening walks in the park, to watching fireworks light up a night sky beyond your wildest imagination, to cheering on Japan in the Olympics, to attending concerts on a sun setting beach, to barbeques by a river, to the tastiest late night dinners I have ever had, to swimming in the Pacific in some of the bluest of waters in Japan, to spending time with my grandma and enjoying her wonderful cooking, I experienced a summer like I never had before.  My time outside the lab still consisted of hanging out with my lab members, and also included spending time with friends from my study abroad experience, and spending time with my grandma.  Thinking back on it, it truly has been a very productive, incredibly fulfilling, tremendously enriching, and indescribably enjoyable summer.  The time I spent in Japan this past summer will remain an unforgettable chapter of my life.  Even though it was only 6-short weeks, I am proud to say that I will forever be a part of the UTokyo family.  My time in Japan this summer reiterated my love for the country, its people, and its culture.  I will do my best to find a way back to Japan again someday.  Thank you, UTRIP and FUTI, for providing me what has truly been an experience of a lifetime.

by Gulnara Fayzulina — This past summer I have participated in University of Tokyo Research Internship Program (UTRIP). For six weeks, I got an opportunity to live in Japan and to do research in Dr. Kuroda’s Laboratory at the University of Tokyo. Dr. Kuroda’s Laboratory, part of the Biophysics and Biochemistry department in Graduate School of Sciences, works on research in the field of Systems Biology, which is an emerging field that incorporates an interdisciplinary approach to study biological systems holistically combining experimental data with mathematical modeling. The complexity that requires mathematical models and computer simulations to keep track of arises from the fact that communication from the surface of the cell down to the DNA in the nucleus is carried out by myriad of proteins, which form signal transduction pathways. The complex networks of signaling pathways regulate a number of cellular functions such as gene expression, enzyme activity, and ion channel-activity. Dr. Kuroda’s Laboratory works to understand how signal transduction pathways regulate cell-fate determination, synaptic plasticity, and insulin action, and how information is propagated by the pathways. In the first week and a half of the program, the professors gave us morning lectures, introducing us to their research. I found these lectures to be incredibly informative; as I learned about fields of science I didn’t know anything about and the current hot topics in science. From the lectures I learned about why earth quakes occur and the challenges to tsunami warning system, the history of green fluorescent protein (GFP), graphene, and much more. Meanwhile, in the laboratory for the first two weeks, each laboratory member talked to me individually, introducing his research to me. In addition, Dr. Kuroda’s Laboratory taught a week long introductory summer class to Systems Biology for third year undergraduate students. I attended the class and thanks to graduate students willing to translate for me, I was able to keep up and gained more experience with mathematical modeling. In my research project I studied the activation mechanisms of extracellular signal-regulated kinase (ERK), a key protein in cell fate decision. Sustained ERK activation leads to cell differentiation, while transient ERK activation leads to cell proliferation. Extracellular stimulation by Endothelial Growth Factor (EGF) triggers transient ERK activation, because EGF stimuli activate EGF receptors, which in turn activate a fast ERK activation pathway, while activating a slow ERK inhibitory pathway. As part of my research I have created a simple mathematical model to simulate ERK activation by EGF. An experiment was first carried out using Western Blotting, and the model parameters were fit to the experimental data. Then using my model, I did various simulations to find out that a certain temporal pattern of EGF stimuli produced sustained ERK activation, which was quite counterintuitive, as it has been thought EGF only produces the transient ERK activation. To translate the simulation to practice, I stimulated cells every five minutes within an hour, and then lysed them at the time points for which I wanted to collect data. In my experiment, I observed twenty minute sustained ERK activation using EGF. This summer, for the first time, I performed laboratory experiments. I learned how to handle cells and how to do Western Blotting, a popular method in biology used to detect protein presence in cells. At the end, I made a presentation on my research topic, and will be submitting a research report. UTRIP is a great program. Not only did I learn more about science, but I learned more about Japan. UTRIP organized cultural activities for us, where we got a chance to practice calligraphy and Japanese flute, Shakuhachi. Even though, I wasn’t able to get my flute to produce much sound, it has been fun to try a new instrument. In addition, UTRIP sponsored a field trip to world heritage site Nikko and University of Tokyo Botanic Gardens. On the weekends, I got a chance to explore Tokyo and even take a trip to Hakone and Niigata. I was blown away by the beauty of the countryside in Japan. Also, I got to meet amazing new people who just like me by incredible chance came to Japan this summer through UTRIP. And talking in Japanese to the graduate students in my lab has helped improved my Japanese conversation skills and make friends. Ever since I studied abroad in Japan in high school, I enjoyed learning about Japan and its culture, and I hoped that one day I could go back. Coming back to a country where I have spent one year that has had a profound effect on me has led me to look back on my memories in Japan and then look forward to the new memories I will make. Seeing new places, meeting new people, learning new things has led my thoughts to new ideas, opening me up to new interests and new possibilities. UTRIP has been really special experience to me, as it combined both my research interests and my interest in Japan, to make one unforgettable summer. Thank you Friends of UTokyo, Inc., as this wonderful experience would have never happened without you.

by Olivia Waring — This past summer, I had the great fortune to spend six weeks in the laboratory of Professor Takeaki Ozawa as part of the University of Tokyo Research Internship Program. I arrived at an auspicious point in the group’s research trajectory, and was given the opportunity to participate in its first three-color fluorescence imaging experiment. The skills I acquired and the confidence I gained while in the Ozawa Lab far surpassed anything I had hoped to derive from the experience, and I am deeply indebted to Friends of UTokyo, Inc. for making this remarkable trip possible. Since the discovery of GFP, fluorescent proteins have revolutionized the field of molecular imaging, allowing researchers to tag specific molecules with glowing reporters and thereby track their progress through living cells.  The study of subcellular components has also benefited greatly from the advent of super-resolution microscopy, which exploits the blinking and photobleaching of single molecules to circumvent the diffraction limit of visible light. By combining fluorescent reporting with super-resolution microscopy, we have at our disposal a powerful methodology for probing subcellular processes. The phenomenon of immediate interest to the Ozawa Lab is clathrin-mediated endocytosis, during which the plasma membrane engulfs extracellular particles and pinches off to form a vesicle. A number of proteins are implicated in this process: most notably clathrin itself, which assembles on the cytosolic surface of the cell during vesicle formation; but also transferrin receptor, a transmembrane protein that binds selectively to iron-bearing transferrin; and dynamin, a GTPase thought to mediate vesicle scission by mechanical twisting. In order to more precisely characterize the interactions between these three proteins, the Ozawa group sought to tag each target molecule with a fluorescent reporter and quantify colocalization via super-resolution microscopy. During my six-week stay, I assisted in the preparation of three fluorescent systems: clathrin-light-chain cloned to photo-activatable mCherry; transferrin receptor cloned to EYFP; and dynamin linked to AlexaFluor 647 via antibody conjugation. The two plasmids were co-expressed in monkey fibroblast cells, followed by immunostaining with the antibody construct. We first used confocal microscopy to validate the expression of the target proteins and their associated fluorophores. We then observed the samples on a total internal reflection microscope at a sampling rate of about 30 microseconds per frame. Once data had been acquired, images were processed using ImageJ software with the Octane plugin. PALM analysis was performed, after which clustering and colocalization were qualitatively verified. In order to subject our data to more rigorous, quantitative treatment, I proceeded to implement Ripley’s K function and a standard pair-correlation algorithm in MATLAB. These cluster analysis techniques confirmed that localization had indeed occurred. Throughout the coming months, I plan to improve upon this software, rendering the code more robust, versatile, and conducive to the Ozawa lab’s specific requirements. Although research was undoubtedly the highlight of my six weeks in Tokyo, my adventures were by no means confined to the sample prep room or the microscopy lab.  FUTI’s generosity also afforded me the opportunity to immerse myself in a culture that had been hitherto unknown to me. I cleansed my hands at a chouzuya in front of Nikko’s Toshogu Shrine; I studied Japanese beside Shinobazu Pond in Ueno Park, lulled by the distant chiming of furins; I bathed in a steaming onsen at Hakone; I browsed for books in Jimbocho, cameras in Akihabara, and teapots in Kappabashi; I marveled at the yumomi water-mixing ritual in Kusatsu; I discovered the gastronomical delights that are sashimi, tempura, and zaru soba; I tried my hand at the shakuhachi (and decided I should probably just stick to stringed instruments after all); I overnighted in a capsule hotel, a ryokan, and a mangakissa; I braved the Tower of Terror at Disney Sea and the Tokyo metro at rush hour (I’m still not sure which required more guts); and all in all, I had the time of my life. I am not being hyperbolic when I say that my experience in the Ozawa Lab was utterly life changing. I had been entertaining grave doubts about my desire to pursue a scientific career, but my UTRIP experience inspired, galvanized, and empowered me in a way that none of my previous research experiences had before. I am indescribably grateful to Friends of UTokyo, Inc. for financing this invaluable opportunity. My post-graduate plans are still uncertain, but I have no doubt that Japan, the University of Tokyo, and quite possibly the Ozawa Lab will figure prominently in my future endeavors.

Jose M. Lobez Ph.D. Candidate Swager Lab – Department of Chemistry Massachusetts Institute of Technology — Project This summer I did a research stay at the Aida Lab within the Department of Chemistry and Biotechnology Engineering at the University of Tokyo, UTokyo (Hongo Campus). The Aida Lab is an organic chemistry lab focused on new materials development to mainly study supramolecular interactions, and how we can make use of those interactions to create new materials relevant for fundamental social issues in the fields of energy and health. This lab has a very unique work philosophy, which makes use of a combination of heavily synthetic chemistry with a strong focus on applications for energy, biomaterials and organic electronics. The project I carried out under the supervision of Prof. Aida was centered on the development of new liquid-crystalline side-chain functionalized polymer brushes to study their nanomorphology and 3D macroscopic assembly capabilities. I used the synthesized polymers as a model to understand liquid crystalline assembly in the thin film and later apply this knowledge to the design of organic solar cells. The information obtained from these studies will be crucial in the rapid development of more efficient systems capable of exhibiting a better performance for harvesting energy from the Sun. This is paramount to achieve access to more efficient alternative energies. During my time at the University of Tokyo, I also helped understand the behavior of complex organic liquid crystalline systems and coordinated research efforts while developing new research directions for organic photovoltaics. Accomplished goals The work carried out at the University of Tokyo has helped me hone my lab techniques and Japanese language skills, while broadening my scientific knowledge. This work will be included in my Ph.D. thesis at MIT, and we are also currently collaborating on the creation of a manuscript for publication of this work in a high impact scientific journal. On a personal and intellectual level, I have really enjoyed learning about different work ethics and alternative ways to approach problem solving, from the perspective of a completely different culture. During my time here, I also greatly increased my network of colleagues and friends. In this time I gave a lecture at the University of Tokyo on my Ph.D. work, and I also had the opportunity to visit and give lectures at Osaka University, Kyoto University, and Nagoya University. This was a magnificent occasion to discuss my science with very well respected Japanese professors and young Japanese researchers. Furthermore, I was also very active in re-establishing connections with Japanese scientists who had carried out research at MIT in the past, and are now professors at Universities, principal scientists at Japanese companies (Sumitomo Chemical, Toray) and students at Japanese Universities. Future After completing this program, I truly feel like I would like to work in a position after graduation where I can make a difference and help solve global problems. I want to make use of a combination of my scientific background, language skills and also my personal network to make a difference. This is even more evident to me now after having spent this time in Japan. Message for prospective students I would encourage future recipients of this fellowship to not only make the most out of their courses and scientific work while in Japan, but also to explore other possible connections at other research institutions in different locations within Japan.