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Growing PLOS Synbio Blog Community

Hello PLOS Synbio community! Our online forum is growing! Last month we welcomed the addition of a new editor, Sam Million-Weaver, and now I get to introduce myself as a regular contributor. My name is Aaron Dy and I’m a PhD student at MIT in Biological Engineering. I’ll be adding to the conversation with posts a couple of times a month on news, events, and hot topics in the field of synthetic biology. I hope to go beyond rambling on my own expertise and actually engage with more of you on what excites you in synthetic biology.
So who am I? For starters, I am from Evansville, Indiana USA. For most of you who have no idea where that is, that’s roughly in the middle area of the Unites States. I did my undergraduate degree in physics at Indiana University (Go Hoosiers!). While there I did research using microfluidics for biological applications and rooted tirelessly for Hoosier basketball. You can spot me in the lab still representing IU as an alum.
As a graduate student I currently work in synthetic biology with Jim Collins and Domitilla Del Vecchio, both professors at MIT, as my research advisors. I’m interested in some foundational synthetic biology problems like the resource limits of host cells, and also more applied problems like designing new sensors for the gut microbiome. Like a lot of people in the field, I mainly use the bacterium E. coli as my workhorse. Check out E. coli hanging out with my cat Dr. Watson (named after Dr. John Watson of Sherlock Holmes, not James Watson).
Dr. Watson and E. coli lounging at home. Note that they have very similar eyes.
My roommates and I spend a lot time talking about Dr. Watson and he might make some more appearances with his other favorite stuffed microbes. As a graduate student, I spend most of my time focused on experiments for my research. I try to combine mathematical modeling and wet-lab experiments to create new synthetic biology tools for interacting with the human gut microbiome.
A lot of my mathematical modeling looks at problems in synthetic biology from the point of view of control theory which studies how feedback can affect the dynamics of a system. For instance, imagine having a heater and a thermometer to bake a cake. You could look at your thermometer to see if you need to turn the heat on or off, but you would also have to think about the dynamics because you might not want to overshoot and burn the edges (unless you like crispy cake). You wouldn’t want to be too cautious either or you’d get awfully hungry waiting for your cake to finish baking. Control theorists have analyzed these types of problems and had huge impacts in the advancement of traditional engineering. Many of us think there are applications for engineering biology as well to help build predictable synthetic biology. I want to combine this theory with expertise in our lab to engineer microbes so we can improve treatment and diagnosis of gut microbiome related diseases.
Schematic of my framework for using synthetic biology for the gut microbiome
Schematic of my framework for using synthetic biology for the gut microbiome
I won’t bore you too much more with my specific research here, but contact me on Twitter or via email if you want more about that or your interests in the field. While I’m somewhat new to blogging, I’m very excited for the opportunity. I want to talk to you about what you find so interesting in synthetic biology. We hope that you will help us continue to grow our online synbio community. Tell us what topics we’re missing. Contribute a post on your passion in synthetic biology. Feel free to contact me or the editors with your ideas.
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