Thoughts on Theses: Namita Khajanchi

Namita Khajanchi is a chemistry major. Her thesis examines the function of the protein mitoNEET. Her thesis advisor is Associate Professor of Chemistry Sheila Jaswal.

Q: What is your thesis about? A: My thesis is about a protein called mitoNEET. The protein has implications in Alzheimer’s and Parkinson’s, as well as possibly type two diabetes. The reason we think its type two diabetes is because there is a human-made drug that attached to mitoNEET, and that’s how it was first discovered in 2004. In terms of proteins, that’s pretty newly discovered. My thesis project was looking at the confirmation of the protein. This is how it may unfold or fold, because proteins inherently open and close all of the time since they’re insolvent and just moving about. We use this technique called hydrogen exchange mass spectronomy. The first step was to see this protein on the mass spect. The mass spect uses ions that may be in the sample — aka the protein — and then it sprays and we can look at its molecular weight. The protein is actually a metallic protein, and we were looking at the iron sulfur cluster. Prior research has shown that the release of the cluster is induced at acidic pHs, and so I used a couple of denaturants and hoped that I could see the protein on the mass spec. That was the first step. It was really hard to see the protein on the mass spect, and the reason that I figured out three-fourths of my thesis through, was because of the buffer of the protein that was sent to us, which was potassium phosphate buffer. I then had to do buffer exchange, and after buffer exchange I finally saw the protein. Not particularly new discoveries, but it’s the first time we’re testing this protein.

Q: Why did you want to write your thesis? A: I wanted to write a thesis because I really like to do research in a lab. It’s really hands-on in terms of classes. You might learn something new in your classes, but the labs are really the hands-on work. So I thought, “I could either work for a professor for no credit, or do it for credit.” Plus later on, I knew I wanted to do graduate school. Writing a thesis is good in preparing me for graduate school. Professors look and say, “Oh, she wrote a thesis, so she has the motivation to continue,” since you also write a thesis in graduate school.

Q: What has been the most rewarding part of writing your thesis? A: The best part about seeing this protein, which is a dimer and has two similar parts. You have the dimer with the metal in it, and then that dimer goes through a mechanism that makes the solution more acidic. Eventually, with the pH drop, it’ll lose its luster. mitoNEET is a very dynamic and flexible protein, so in terms of functionality we can’t say that we saw it doing this. Just seeing it on the mass spec was really big. I also think that when I finally thought I was almost done with my thesis, I thought “Yeah!’”I printed out two copies and I was ready to turn it in. The rewarding part was when one of my lab partners told me, “You’re not done yet!”, which you’d think would be a “Wait, what?” kind of deal because it sounds like more of a challenge. They told me, “You should add more to your abstract.” I think that really helped me realize that I need to look at it step by step and have other people look at it. Having people look at it in full was really rewarding.

Q: What challenges did you have while writing your thesis? A: The hardest part about writing my thesis is that I came up with two disabilities this year and things that slowed me down. First was carpal tunnel. With the machine we used, we usually have to move our hands in a manner that would hurt my wrist. I also have a back problem. Going through those two things, I always had to lean on my lab manager to help me. There were times where I was like “I just want to get done with my experiment.” Afterwards, I thought, “I’m kind of tired.”

Q: What advice would you give to future thesis writers? A: Start writing down what you’re reading about earlier. Just a little blurb of summary about papers and other things you read would be enough. Also, with Zotero, format as you go instead of waiting until the end. I had someone to help me format, but I think a lot of students at the end are like, “Oh no, I need to add my Zotero references.” If you had started in the middle or even in the beginning it would be much better. So start Zotero early.