Peddie EXP 2017

Hey everyone! The next three weeks in my EXP experience take a really interesting turn. I had initially planned to be done with my EXP on July 29th, but in case you haven’t read my last blog post, I decided to extend it to further my understanding and get my hands on some more projects. I chatted with my post-doc Kayla on the 29th and she advised me to operate remotely and do things from home for two weeks, work on the coding course and the proposals, while her and the PI, Nick, craft a project for me to do with some of the knowledge I’ve picked up on coding. The lab uses this great interface called Slack to communicate with each other, there are group chats, individual direct messages, and you are also able to send snippets of code! So that’s what I did for that 7th week, continued editing and revising the medical documents and made sure that they were all ready to be sent off the IRB. I worked on my online coding course, which was really interesting, but a learning curve is definitel...

As my week came to an end so did a lot of the summer students. Because so many students were ending and the PI had come back from paternity leave we had a lab presentation where all the summer students presented their experiments and findings from their time there. Having finally finished analyzing and recording all the pup calls I was assigned to do, I could graph the information and make some conclusions. Jenn was at a conference in Brazil for my last week so I was stuck trying to use the graphing program by myself. I use Graphpad prism on windows 98 which I had honestly never seen before. I had no idea what to do or how to even start and the wifi in Brazil was basically useless. But after a few frustrating hours, I was able to input the data and make some helpful graphs.  I made two each for frequency, interval duration, and motif duration (one separated by age and one covering all pup calls). I was looking for any kind of variation either between the ages or ...

This past week was my final week at the Seale Lab. It started quite slowly, but the last two days were perhaps the busiest days I had during my time at the lab. So what happened? Monday was quite a slow day. I arrived at the lab at 8:30 AM as usual, and began working on my poster. I continued working until 10:30, when I realized my supervisor still wasn't at the lab. In fact, almost no one was at the lab except me and two undergraduates. I was a bit confused, but I continued working on my poster. Finally, at 1:00, I left the lab. I later got an email from my supervisor saying that I didn't need to be there that day.  On Tuesday, I had a good amount of work to do. I transfected the virus-infected HCT116 cells with p53 and empty pcDNA plasmids. Besides that, I genotyped 20 more mice, and worked on my poster. Wednesday was much like Monday, in that it was a slow day. I worked on my poster once again, and genotyped another 15 or so mice. Additionally, I spent about an hour pre...

My final days at the Bissig lab have turned out to be the most eventful yet. In the past days, I've harvested the livers from the mice injected with my gRNA constructs, harvested the DNA from those livers, and analyzed that DNA. In addition, I learned to split live cell cultures and infect human cells with viruses, and continued cloning gRNA constructs for other lab members.  Of the above, the dissection and harvesting of the livers was by far the most interesting experience. My constructs targeting the Agt and Ddc genes were injected into several mice each, and since it had only been a little less than two weeks since the injection, we couldn't preform many of the assays to determine what the effects of cutting into the genome had been. However, what we could do was harvest the livers of just one of the mice, and determine if my gRNA had been successful in leading the cas9 to cut in the right place. Essentially, whether or not what I had spent about 8 of the last nine wee...

The Lee Lab!!! My eighth and final week at the Lee Lab was finally here. After finishing up the analysis of my remeasurements and new data from my fourth run, I compiled it all into a presentation file for Dr. Lee. After going over the data I had collected with Dr. Lee on Tuesday, I came out of the meeting thinking that after making some changes to the model I used for ellipsometry, the results came out very close to what we expected. After to going over my final results for my project, Dr. Lee also gave me some “homework” to do. As my time at the lab is coming to an end, I was busy revising my poster in the meantime, but in addition to that, he wanted to make a short video of how I performed my experiments. I didn't have to include every single step - just those that were unique to what I did. Since there was a new high school student coming next week, I am guessing it is probably for that high school to reference as she will be conducting very similar experiments to what...

After having injected the gRNA constructs I made with the cas9 to see if I could successfully knock out my target genes, I've mainly been focusing on helping out with other projects around the lab, mainly with Mercedes' project in synthesizing some other constructs. In addition, Collin has been instructing me on how to actually figure out how to pick genes to target in various metabolic pathways, and how to make up the gRNA construct on the computer. Since my gRNAs are for the murine (mouse) model, he has assigned me to creating one for a human model (which, when synthesized, will go into humanized mice , not actual humans).  This mostly involves research into the genes and metabolic pathways of interest and figuring out which exons are most important, and through using a few fancy programs on the lab computer, how to alter them in a way that can generate a frame shift mutation to knockout the gene. Although the computer work has still been interesting and no doubt important,...