Emily Guo, Week 7, Hanging Up the Lab Coat


Some good news: the plasmids Anna and I made a few weeks ago were sent off for sequencing, and they came back with the correct sequence! The plasmids can now be used in the next round of electroporation. 

We are currently still troubleshooting the bisulfite conversion process. I ran a PCR for the DNA samples (non-converted) that we were using on Monday with two sets of primers that we knew would work, and we did indeed have bands of DNA show up on the gel afterwards. Therefore, the quality of the DNA that we were converting wasn’t the problem. I found a bisulfite conversion guide by Zymo Research – which deals a lot in epigenetic research in addition to providing biology research tools for DNA and RNA research and analysis – that provided some tips that we could try out. One was a way to analyze the DNA after bisulfite conversion, which we didn’t do before, by running the gel with the bisulfite-converted product. However, because the DNA becomes so damaged through the conversion process, the DNA will appear as a long smear.

So after we ran the bisulfite converted DNA (we used the QIAGEN kit instead of the one from Zymo) we chilled it on ice. I checked the gel after ten minutes to see no DNA, but when I checked after another ten (for a total of twenty minutes chilled) I saw very faint smears, confirmed by Isabella (another lab technician). However, since I didn’t have a USB drive and Isabella needed to check her gel, I put the gel back on ice for another ten minutes until she was done. Unfortunately, I could no longer visualize the smears when I checked the gel again, even after running and chilling the gel for another ten minutes. So, at the end of it all, I wasn’t able to take a picture.

Because it took such a long time for the smears to appear (the guide recommended chilling the ice for only a few minutes) and because the smears were so faint, it could be because the kits are not yielding enough DNA as expected or we were not using enough DNA. Regardless, we would need to think about redesigning the primers (because our positive control was not successfully amplified), which the Zymo guide also has a few helpful tips for.

Friday was my last day at the lab, and so Anna and I decided to throw a little party. This was expanded to include the other students in the lab (Lucas and Noah, who were working with Cathy and Martha). Anna baked brownies and I the cookies – Lucas supplied the sodas – and we set up everything in the lunch room downstairs. Anna and I went out that morning to get a dozen assorted donuts from Dunkin' Donuts. She'd also emailed Dr. Tycko, who has been away the last few weeks preparing for the move. He came in today, but was unable to join us as he suddenly had to go to a meeting downtown. In a way, it was a sort of surprise party by the students, and I was happy to say that it was very well received! Alyssa liked my raspberry thumbprints, which were my sister's favorite as well. 


Alyssa also got me a parting gift!
Because Alyssa will be leaving the lab, it is most likely that Dr. Tycko will hire a post doc in Hackensack to continue our project. Hopefully, he or she will be able to make use of everything that we've done and benefit from all the problems that we've sorted out along the way.

Many thanks to Dr. Tycko for allowing me the opportunity to work in his lab and learn from his experience! I am also extremely thankful to Alyssa for taking the time and effort to mentor me throughout her research and all the ups and downs that we've encountered in this project.

In addition to being exposed to the amazing scientific background surrounding the project, I've received some great advice and learned some valuable life lessons as well. This experience will be sorely missed!

Taking off my lab coat for the last time

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