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The Interview:

Karen:Tell me about your current research, and how you initially got involved in research at Stony Brook.

Trinity: I’m working with Dr. Siu Chiu Chan in the Dept. of Medicine to investigate the molecular mechanism that regulates the transcription of this necessary factor, HNF-1B, that if improperly regulated or absent, typically leads to chronic kidney disease in most mammals, including humans. Our group investigates the genomic interactions with different factors that might lead to the dysregulation of this factor, and specifically, we are looking at the arrangement of chromatin in mouse models through these methods called chromatin conformation capture. We use bioinformatics to analyze the results. Knowledge of the regulatory mechanism of HNF1B transcription may guide the development of more effective treatments for patients suffering from HNF-1β-dependent nephropathy. 

I found my current position initially through an application on Handshake: I was interested in the techniques that my Lab Advisor posted that they would be using during that time. I joined in February 2024. And this summer, I will be able to commit to full time research through the URECA summer program.  

Prior to this experience, I was a member of Stony Brook University's International Genetically Engineered Machine (iGEM) team (2023). As a part of this ten-month research competition, I worked along with a fourteen-person team to investigate the integration of a positive and negative feedback system and the nitrogenase gene cluster into E. coli colonies. We designed these engineered bacteria to provide an alternative to synthetic nitrogen-based fertilizers, the overuse of which has been linked to hazardous algal blooms. This formative experience was my first exposure to how synthetic biology could be used to tackle complex environmental challenges, and to the field of bioinformatics. 

How difficult was it to get started in this area of research, and to learn the techniques necessary to conduct experiments? 

There was a lot of new information, and I think that's one of the things I enjoyed most about it. But it was also one of the most daunting things about getting started in a lab. I'd never worked with mice before, and I don't have any sort of medical background. So a lot of it was just brand-new information. I had some background in coding from iGEM, but that was more from doing website design rather than computational stuff. So it was a very new playing field. To be able to do the analysis, I've been learning and using programs like R Studio and Command Line to analyze the sort of feedback that we get back from RNA and chromatin immunoprecipitation sequencing datasets.

That there is always something new to learn is intimidating, but also exciting. And I think that what I love about my mentor’s approach is that he really pushes me to learn as much about different fields as I can, so I never feel like there's sort of one thing that I'm doing every day. There's always some new technique, some new and useful sort of procedure that he's encouraging me to look more into …So even though it was all new at first, it’s also been very valuable.

Are you working with other undergraduates in your research group?  

We have several undergraduates, and we all are working on related projects. But we're also all working more or less directly with our mentor—focusing on different aspects of one big project.

What would you say is your favorite part about doing the research?

I love how creative it is!  It’s different than learning things in the classroom where you are presented with information as a final packaged product: this is what we know. When you’re doing research …  you are presented with some bits and pieces, and clues about how this mechanism functions, but the actual arrangement of the information, and how you can predict that these different transcriptional factors interact ,and the effects that they cause is creative. And I like that. There's so much that's still under investigation. And you have to put forth “This is our guess. This is the evidence that supports it. This is the evidence that doesn't. . . ” and the arrangement of those different things is a very creative process.

Did your previous work on the iGEM team help prepare you for doing this kind of research?  

That's a good question. In terms of the actual project and the work that we're doing, it was very different. But I think what iGEM prepared me for most, in addition to working as part of a big team and being able to communicate--both very, very valuable aspects of working with iGEM!--was just being able to approach something that you don't know anything about  and having the willingness to jump forth into a topic that you don't know anything about. One of my major contributions to the 2023 team was the coding of the website. And prior to joining the team, I I had never coded before and didn’t know anything about this topic when I started. But I was willing to start from zero. And that experience has been something that's very valuable in research too, because there's always going to be a situation where you don’t know what's going on. So, to be able to know how to reach out to people and talk about it, and how to look for the information that's out there to sort of build yourself up from having zero background has been helpful.

What advice do you have for other students about getting involved in research and creative activities?

My biggest piece of advice, cliche as it sounds, is: don't be afraid to apply, even if you don't feel that you know how to do everything yet. From my experience, professors and faculty research mentors are very willing to teach as long as you're willing to ask. But you have to ask the questions. So don't be afraid of learning something new. 

I started learning more about bacteria for the iGEM team. And now I'm doing completely different work.  I didn't think I'd be doing bioinformatics, and I'm loving it now. So try different things, and just learn as much as you can. As a college student who's interested in doing research, I think you should try and learn as much as you can from as many different fields as you can. Research is so much more interesting when it's interdisciplinary. There's so much out there, and there are so many people who are willing to help you get there if you're willing to take the first step and ask.

How has your faculty mentor helped on your research path?

I think that one of his major strengths as a mentor is that he gives us a lot of space to learn different things. When I first started in the lab, I was primarily doing tabletop molecular biology techniques. And he said, “it would be really amazing if we had an undergraduate who could learn more about bioinformatics.” And even though I didn't really know much about that at the time, that didn't stop him from encouraging me to learn more about it. He's very encouraging, and he expects the best, and that really reflects on the people in his lab, because people are more willing to take that next step because they know that he has faith in the graduate students and undergraduate students in his lab.

How do you think your involvement in research and previously with the iGEM team has helped enhance your overall education at SBU?

It’s helped in a very practical sense. I've taken exams where I know the answers not from what I've done in class, but from what I learned in the lab. But also, I think the background in research provides a different way to think. When you are doing research, there's a lot of missing information. And you have to learn how to organize that and think stepwise logically from one thing to another in order to try and get a picture that makes sense. I think that's helped in my coursework, and also just in being more confident in myself. I've learned these new techniques that I couldn't imagine myself learning 2 years ago. So I'm able to be a little more tenacious with my coursework and less overwhelmed on it. Becoming comfortable with uncertainty is a big thing. Just being comfortable saying “I don't know how to do this” can be a really big step. Because if you're trying to convince yourself that you know how to do everything, you're not going to ask for help. You're not going to ask for clarification, and you're not going to go through the process of learning more. 

Are you looking forward to this summer? 

I'm so excited! It’s been difficult balancing doing research and coursework and clubs and all that stuff. So I'm excited to just have free time to just do research this summer and just focus on it. I'm very grateful for the URECA program for being able to help facilitate me doing this research over the summer!