The Tenth and (almost) Final Week – Reflecting

If I have learned anything here, I’ve learned how to feed bacteria. In fact, I know the recipe for LB and lept media by heart. And I can murder and mutate them too. But really, I have learned a lot, and am still learning. Kati has taught me a ridiculous amount of biology and lab techniques that I never would have gotten had I not come here and I am so grateful that she was so patient with me. I’ve really enjoyed learning all of this new stuff and taking in the entire research experience.
 

On Monday, I took a field trip to the primate center to get my mutants sequenced. I almost feel like they’re my babies, not monsters. I had to isolate them from E. coli bacteria in the morning and use the fancy nanodrop spectrophotometer that I learned to use last week to quantify how much DNA we had. Then Kati and I drove over and dropped them off with a label saying where we wanted them to sequence the DNA (what primers to use) and how much of our sample there was. And then we waited for the magic to happen and be reported back to us. This week we got back our sequences and then it was time to try to put the puzzle back together, which I thought was so much fun. Kati explained how DNA sequencing works, which I learned a little bit about in chemistry last year. Then, we took our sequence results and compared them to the actual gene to find the mutation. There was a single base pair change in each of our mutants. I’m fascinated by the fact that changing a single base pair that codes for a single amino acid in one gene that affects the formation of one protein has increased oxidation in P. putida GB-1. And we have no idea why. We determined that the base pair change in our first mutant is a change from a “gtg” to “gag” sequence which translates to a change from Valine to Glutamic acid. Valine is hydrophobic and non-polar, whereas glutamic acid is polar, meaning the folding of the protein could be changed significantly from this mutation. This change is in the portion of the MnxR gene that is thought to encode something in the sigma-interaction domain. The other mutant is another mutation in the sigma-interaction domain of MnxR, which isn’t what Kati was expecting… so more reading to do to try to solve the mystery of this gene and these proteins. Silly, puzzling bacteria.
 

This week, however, was mostly preparing for final presentations and preparing my final paper. In the morning, I would come in and do a little bit of lab work, and then set right to work on my computer. I have definitely missed writing and editing, which is why I have written so extensively in my blog. So, this week working on my presentation and paper was pretty fun, although I ran out of stuff to do several times. My paper is at a stage that is acceptable to turn in, although I believe no paper is ever completely finished and can always be improved upon. I did my presentation this afternoon so that really is finished. I think it went well, at least I know people liked the cookies I baked. So now I am sitting here writing my blog, reflecting on these past 10 weeks and everything I’ve learned and experienced.
 

I feel almost nostalgic thinking about my first day, coming in to meet Kati and be introduced to the lab and actually learn about my project and my bacteria, P. putida GB-1. I have been very welcome here in the Tebo laboratory and it’s something I couldn’t have expected, but I definitely appreciate. I have sort of taken over Kati’s desk here in the lab… so I’m sure she’ll be happy to have that back when I leave. I’m just very thankful for this experience and it’s crazy to think I’m getting paid for it. I know the experience I got here is very unique, especially for a young engineering student like me, and I’m grateful to have had it. I’ve learned far more than how to feed, kill, and mutate bacteria.
 

And it’s not over yet! I’m coming back at the end of the month to finish up some research and get my 400 required hours of research. But these 10 weeks have been wonderful and I do feel that I am coming to the end of a special experience.
 

And thanks for reading, whoever you are :)