Friends of UTokyo Inc. Internship Report

by Jacob Albritton

In Nara with a deer

I have been researching under Professor Ichizo Kobayashi in the Laboratory of Social Genome Sciences at the University of Tokyo for about 6 weeks now.  At a glance, Kobayashi-sensei et al. have been researching restriction-modification systems and DNA recombination machinery, with a focus on the role of these biological phenomena in shaping the genome and epigenome of bacteria. My internship began in July with a projected end date in July 2013, and was organized through the MISTI-Japan program and supported by both Friends of UTokyo Inc. and MISTI-Japan.
Much of the research here at the Kobayashi lab is geared towards investigating Helicobacter pylori, a stomach pathogen that has infected over 50% of the world population and is one of the leading causes of stomach cancer. One of the reasons for H. pylori’s “success” in chronically infecting humans is its extreme genome plasticity, or ability to alter itself genetically, which enables H. pylori to effectively compete with the immune response.  Until now much of the Kobayashi Lab’s research on H. pylori’s ability to infect humans was focused on the genome, but currently the lab is approaching this problem from a different angle – through its proteome (all proteins capable of being produced).

At a temple

Proteomics or the study of protein structure and function is a branch of biology that has been experiencing rapid growth due to innovations in mass spectrometry (MS) and bioinformatics technology.  Mass spectrometers are able to identify proteins or protein fragments and are commonly used for proteomics studies, but until the past five years or so, proteomic studies have been bottlenecked by the labor-intensive preparation stage and limited by MS technical capabilities.  However, recent advances have led to a faster and more “stream-lined” analysis of proteins by reducing preparation time and increasing MS processing speed and resolution. Even with a faster method of processing proteins though, there is still the problem of analyzing the enormous amount of data generated.  Advances in bioinformatics, or applying algorithmic methods to biological problems, have also contributed to proteomics analyses by providing formalized programs to successfully “mine” data from the MS output.
In my project thus far, I have been developing methodologies for generating and analyzing proteomic data.  Initially, a small group of the lab and I have been creating a preparatory protocol for MS analysis in collaboration with the Medical Proteomics Laboratory, specialists who possess a next-generation MS machine. Additionally, I have been researching current bioinformatics techniques for analyzing the proteomics data we will obtain from the MS machine.  Tentatively, the goal is to finalize our preparatory protocol and generate some preliminary MS data by the end of September.  Based on these preliminary results, we will spend time refining both the initial protocol and the data analysis procedure before generating more data.

At a temple

The internship so far has been a great learning experience for me both in terms of expanding my technical skills and in terms of broadening my horizons to include a top-tier Japanese university perspective on research.  As well, my time living in Tokyo has and I fully expect will continue to be a fascinating glimpse into Japanese society and metropolitan life.  So far, I have only seen the festival and fireworks-ridden summer-side of Tokyo life, but I can hardly imagine what new cultures and traditions I will encounter in the coming seasons.
The University of Tokyo has many labs involved with cutting-edge research and is a major contributor to scientific progress. I greatly appreciate the support I received from the Friends of UTokyo and think that this organization offers a great access point to experience this world-renowned university in addition to the Tokyo lifestyle. I have enjoyed my time in the Kobayashi lab and look forward to seeing my new project through to completion.