Thursday, May 14, 2015

Mission Possible

Mod 3 Goal: Develop a research proposal.

Vipul and I decided on our exact idea in a kind of backwards way. Vipul had found a technology that he found really interesting -- the Spinach aptamer had been recently developed to bind to a fluorophore to fluoresce. Spinach could be conjugated with an aptamer for some other small molecule to act as a sensor for that small molecule. We both agreed that this system could have a lot of useful applications.

We had an idea of what the technology we would use, but we really struggled with figuring out an effective and useful application. Our first thought was to something with metabolites in cancer. Maybe Spinach could be used as a detection system? But the aptamer was really good for looking across several time points, and detection is often just concerned with one time point. Next, we brought our idea to Leslie, who offered some ideas in direction we could take. Thanks to Leslie's advice, our next line of thinking focused on research out of the Vander Heiden lab, which dealt with the differences in metabolism in cancer cells compared to normal cells. Perhaps a way to look at levels of metabolites over time would be useful? We toyed with this idea for a full day, before discarding after taking a more closer look at papers the lab produced. We had found that their current methods were already sufficient because they did not need to look at multiple time points, just only up/down regulation of a particular gene. 

Finally, we decided on an idea that Vipul had on the first day of brainstorming -- development, in which small molecule morphogens dictate cell fate based on local concentration. While initially, I was not really sold on the idea because I honestly had no interest in embryonic development, I thought that it actually was the most promising direction. We settled on the small molecule morphogen retinoic acid because Vipul already knew of it off the top of his head (?). We did things kind of backwards in that we came up with the application after we decided on the 'solution'. Furthermore, for us, I think the hardest part was just coming up with the idea itself. Because all the technologies and protocols already existed, and the novel part was just the way we put things together, all the details just fell into place after reading a few more articles. I am convinced that our idea is completely feasible and could very realistically be someone's master's thesis, if they were so inclined. 

This experience reminded me of when I was in 11th grade, I participated in iGEM (trying to compete in the college competition as part of Duke University.) iGEM had absolutely no infrastructure, and at that point in time, I had never worked in a lab before. When they told us that we had to come up with our own project related to synthetic biology and carry it out on our own with no guidance from grad students, I definitely floundered and eventually dropped out, and instead, worked in another lab that summer under a grad student (thankfully). I am more convinced that I was incapable as a high school student with absolutely no lab experience to come up with a feasible project on my own. However, after a few summers of traditional lab work and this 109 project proposal, I am definitely equipped to come up with a feasible research project now that I have the background in what research is actually like. 

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