National Science Foundation East Asia and Pacific Summer Institutes

Markita Landry, Japan 2009

As with many other EAPSI participants, my EAPSI experience began with the decision to apply for a research fellowship to form a collaboration with another research group, and help advance my Ph.D thesis project. My research involves the study of protein- DNA interactions using single molecule, high resolution optical traps. However, the particular protein-DNA pair under study displayed binding forces and behaviors that were largely unexpected and inexplicable, mostly because the protein, responsible for identifying a specific binding sequence prior to undergoing its catalytic activity, was found to bind strongly and indiscriminately to any double stranded DNA sequence. With the goal of imaging this protein at a single molecule level, to visually observe its behavior during its interactions with DNA, I chose to pursue an EAPSI fellowship to study protein-DNA interactions using TIRFM (Total Internal Reflection Fluoresence Microscopy) with Dr. Toshio Yanagida at Osaka University’s graduate school for frontier biosciences.

My time in Osaka, Japan, began surprisingly well. Never one to forego a cultural opportunity, I opted to search craigslist to find local urban housing, rather than to stay at the Osaka University student housing. It is as such that I found myself sharing an apartment with two Japanese women in the heart of downtown Osaka. Despite a slight communication barrier (science experiment and accident are the same word in Japanese), morning commutes to the university campus on the crowded Osaka metro, and one too many loads of laundry accidentally washed in fabric softener instead of detergent, living with my Japanese roommates was the cultural highlight of my EAPSI experience. I visited each of their hometowns to celebrate Obon with their families. They were glad to show me the most authentic local restaurants and museums, and in turn I was glad to teach them to tango and salsa dance, and cooked some Bolivian dinners for them and their friends.

With the help of my new colleagues at Osaka University, my project also advanced as steadily as my acclimatization to Japanese culture. TIRFM videos of my protein interacting with DNA showed that, unlike previously imaged proteins, this particular protein did not slide along DNA in a loosely bound conformation as it searches for its recognition sequence. This perplexing new information led to a series of additional experiments that helped us conclude that our particular protein may be part of a protein family that interacts with DNA in a manner that is distinct from previously studied protein-DNA interactions. These findings would not have been realized without the collaboration established through the EAPSI/ JSPS program.

After months of Japanese bath house trips, traveling, traditional Japanese Matsuri festivals, seafood barbecues, lab group outings, late night conversations on our apartment balcony, and even a trip to the top of mount Fuji, saying goodbye to my roommates and lab mates was by and large the most difficult part of the EAPSI experience. However, the cultural and academic lessons I learned over the course of 10 weeks continue to enrich my day to day life, both in and out of the lab.

Last Updated: July 15, 2010 01:31 PM

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