by Pramodh Ganapathy
Few people can say they spent their summer throwing a plankton net, but that was just one of many things I learned how to do over my summer at the University of Tokyo as part of the University of Tokyo Research Internship Program (UTRIP). I interned at the Nozaki Laboratory of Origin of Eukaryote Biodiversity from June 12th to July 24th, and my project was titled “Molecular identification of gender based on analysis of OTOKOGI and HIBOTAN genes in natural populations of Volvox carteri.”
Going into the program, I had very little experience with the specific subject matter of the lab and of my project. I majored in evolutionary anthropology as an undergraduate, so the evolutionary biology aspect of the Nozaki lab interested me and seemed to be a good opportunity to expand my knowledge. The learning curve was even steeper than I had expected, but I was very touched that every single individual in the Nozaki lab—undergraduates, graduate students, and Professor Nozaki himself—made every effort to make me feel comfortable and to really make me feel like I was part of the lab community. I was also able to practice my Japanese with them, so I feel very fortunate and grateful that I was able to learn not only about science but also improve my Japanese as well.
In this environment, I was ultimately able to complete a project of which I could be very proud. The first step of my project was to establish new strains of Volvox carteri, a colonial algal species. This may have been my favorite part of the project, as it involved field sampling trips in which we would take samples of algae from bodies of water with plankton nets. The first trip we took was to Lake Isanuma in Saitama Prefecture. While we were there, we were also able to do a little bit of sightseeing as well as go to a souvenir shop.
I was also able to go to Lake Biwa near Kyoto for sampling. While we unfortunately did not have time to go to Kyoto for sightseeing, we were able to sightsee around Lake Biwa and go to the Lake Biwa Museum. While I was very clumsy with the plankton net at Lake Isanuma, I was able to get a lot of practice and improve my technique at Lake Biwa.
Once the samples were collected, we had to return to the University of Tokyo the same day in order to isolate the specimen of interest, in this case Volvox carteri, to allow it to proliferate for further study. Unfortunately, I was unable to isolate any of the target species from the samples, so I instead used cultures graciously lent to me by the Nozaki Laboratory for the next steps of my project, which involved determining the formae of the Volvox carteri strain being studied as well as the determination of its gender. To do this, DNA was extracted from each strain and run through polymerase chain reaction (PCR) with primers designed for an identifying DNA sequence. The amplified DNA was then sequenced and analyzed using a software program in order to determine that the formae of all strains were f. nagariensis.
Once this was done, gender was determined for strains for which gender was unknown by running the extracted DNA through PCR with primers for OTOKOGI and HIBOTAN genes, gender-specific genes for male and female Volvox carteri f. nagariensis, respectively, that I designed. The PCR products were then run through gel electrophoresis to determine presence or absence of OTOKOGI and/or HIBOTAN genes, which would indicate gender.
The last step of the project involved determining if there was any recombination of the sex chromosomal region in the Volvox carteri strains analyzed—this would be represented by bands indicating the presence of both OTOKOGI and HIBOTAN genes in a single strain. There were some strains in which this was observed, but after retesting, bands indicating the presence of either OTOKOGI or HIBOTAN genes, not both, were observed, suggesting that the previous presence of both bands was an error. The study therefore indicated that there was no evidence of recombination, but more gender-specific genes and a larger sample size would be necessary for further study.
The project was definitely challenging, and even frustrating at times. I would sometimes have to arrive quite early in the morning and would not be able to go home until the last train. However, everyone in the lab was right there beside me and supported me through all of the challenges. I definitely would not have been able to see the project on to its finish without them.
I was also able to enjoy my stay in Tokyo in ways unrelated to my work in the lab as well. In the summer of 2013, I participated in the Japan-America Student Conference (日米学生会議) and was part of the Executive Committee for this year. Therefore, I was able to spend time with a lot of my friends from the conference who were in Tokyo.
Ultimately, I cannot think of any better way I could have spent my summer. It was definitely challenging and came with a lot of hardships, but I also had a lot of fun, and I think all of my experiences came together in the end to create an unforgettable time of growth and reflection. Thank you once again to Professor Nozaki and everyone at the Nozaki Laboratory, and a special thank you to FUTI as well for giving me this opportunity.