Undergraduate Research

Kyogo Nagashima '24

OUR Featured Researcher: Kyogo Nagashima '24

Portrait of Kyogo Nagashima.
Photo credit: Tanya Rosen-Jones

Kyogo Nagashima (he/him) is a Biochemistry major conducting mentored research under Professors Lisa Ryno. His project is titled “Influence of pentose sugars on biofilm formation and composition in E. coli". 

Please describe your project: 

Microorganisms such as bacteria are everywhere, whether that’s on your teeth or in a nearby pond. These floating microorganisms can attach to surfaces and accumulate, forming biofilms. 

Biofilms are a collection of microorganisms that are surrounded by a gooey substance called the extracellular matrix. Biofilm formation can be affected by a number of factors including temperature, the material to which biofilm attaches, and available nutrients. 

The goal of my current project is to understand the influence of certain sugars, specifically pentose sugars (sugars that contain five carbon rings) on biofilm quantity and composition in E. coli. By doing so, we believe that we can further our understanding of the pathways that control sugar uptake in E. coli which has the possibility of impacting biofilm formation greatly. 

A brief summary (the elevator speech) of your research project: 

My research project investigates the characteristics of biofilm formation, specifically on how pentose sugars affect its growth. This may further elucidate the pathways and mechanisms in which biofilm formation occurs in E.coli. 

Why is your research important?

One of the main reasons for studying biofilms comes from their significant role in antibiotic resistance. Compared to free-floating bacteria, bacterias in their sessile form are way more resistant to antimicrobial agents because the biofilm serves as a protective layer. Therefore, the study of biofilms and their relation to antibiotic resistance is both important for medical and industrial settings.  

What does the process of doing your research look like? 

I go to my lab usually every day in the afternoon. Because my experiments are based on E. coli, they require about one to two days of incubation and they usually need to be taken care of every day. Then, after incubation, I will perform various assays to measure specific characteristics of biofilm for each sample. Then, I will analyze those results to plan for my next experiment. While it may feel repetitive to some people, I truly enjoy finding out and solving problems as I go, as there is usually no immediate success. 

What knowledge has your research contributed to your field? 

I have found that adding pentoses have the potential to drastically increase biofilm growth. My current focus is to further investigate whether different types of pentoses may affect biofilm growth differently under several different control variables. 

In what ways have you showcased your research?

A paper that I am involved in may be published in the near future but because it is currently in the review process, I will not be able to discuss it. 

How did you get involved in research? 

I got involved in research during the summer right after I finished my first year in college. I was very eager to do research in biochemistry and molecular biology and therefore contacted professor Ryno as her research project was very interesting to me. After I started doing research, I further started to enjoy the process more and more and I am very thankful for the experience I am given now. 

What is your favorite aspect of the research process?    

My favorite aspect of the research process is solving problems. Often times, experiments do not work out as planned and the majority of the time is used to trouble shoot for certain problems in order to establish a research protocol that is reproducible and reliable. I truly enjoy this problem solving process as it requires you to think objectively about failure.     

How has working with your mentor impacted the development of your research project? How has it impacted you as a researcher? 

I was initially working on another project that similarly investigates another aspect of biofilm growth. However, during that process, we observed the phenomenon that biofilm growth significantly increases depending on the availability of certain sugars. After this key finding, my mentor guided me to shift the scopes of my project. 

Like this, my mentor has provided me with key advice that has largely influenced the focus of my projects. Weekly meetings with my mentor have provided me with the fundamentals of conducting research from design, techniques, to certain problem-solving techniques. Not only that, but she has also influenced how I approach problems. Working closely with my mentor allowed me to learn her ways of thinking that she has developed over the years of research experience which is very valuable for my development as a researcher.

How has the research you’ve conducted contributed to your professional or academic development?   

Not only has doing research increased my understanding of research methods in microbiology and biochemistry, but it has also inspired me to become a researcher in the future. This interest in research that I have developed here is something I am wishing to pursue after Oberlin.

What advice would you give to a younger student wanting to get involved in research in your field?      

One piece of advice I would give to another student who is wanting to get involved in research is to give it a try. It may be intimidating to contact a professor about doing research in their lab. However, Oberlin has a lot of opportunities for students that want to do research and so I would really recommend giving it a try.