The Anticipation Builds: Preparing Data for Analysis

Hey y’all!

I’m so excited to send out my first research update! During my time in the lab thus far, I have been conducting an in-depth literature review of mentoring studies. The bulk of the literature focuses on youth characteristics that influence the mentoring relationship. These characteristics include youth environmental stress and behavioral challenges. I have only found one study that touches on mentor emotional background so I hope that I will be able to meaningfully contribute to the mentoring literature at the conclusion of my research! I will analyze mentor stress using two scales: The Risky Families Questionnaire, which measures early life and familial stress, and the Student Stress Scale, which measures previous or ongoing stress in multiple aspects of life. Combined, these two scales will allow me to not only measure mentor stress, but also will allow me to better understand the effects of different types of stressors on mentoring relationships. I will measure mentor depression using the CESDR-10 scale, and I will run analyses analyzing the relationship between mentor’s reported depression and stress levels.

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Creating the Processing Pipeline

The early stages of my research have been comprised of creating a pipeline of computer scripts that can process the large amounts of genomic data I have. Because the files I’m dealing with are incredibly large (10gb text files) none of the data cleaning and processing can feasibly be done by hand. I’ve tried several strategies to do this, and after weeks worth of failed attempts, I was able to get the major file processed and broken down into much more reasonably sized files that I now have to work on further to fully process to the point where I can use them to create a phylogeny.

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Seven days, Population eight, and Nine Ball

In the lab this week, I continued to transfer beads for my first cycle of evolution this summer. I was really impressed with myself because I managed to go the entire week without dropping a bead. It can be so difficult at times to get the beads out of the glass tubes, to wash them, and then put in the microcentrifuge tubes without dropping one or messing up at a single step. I am typically holding my breath the entire time because I am so anxious about it. This is such a huge accomplish for me and am glad that I have the opportunity to document this eternally. Other than my project, this week I helped out Dr. Murphy with some of her ongoing projects. I learned how to streak and made YPD glycerol plates.

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PCR and sequencing HMY7

Hello readers! (of which I am sure there are many)

Well, I have reached the end of the second week of summer research. So far, I have been working on the project that I have been on since the Spring semester. It isn’t my allantoin pathway work yet, but it will lead into that project, so I am excited to finish up this stuff so I can look into the allantoin research. I have been doing PCR, PCR, and some more PCR! I did PCR for all of the genes previously found to be significant to plastic adherence for the strain HMY7. In the Spring, I worked on the genes in the strain HMY355. PCR proved…difficult. Many of the genes in these two strains are particular to say the least. So, I ended up with a bunch more PCR hours under my belt, but only about 50% of them worked. But! That’s okay. I pushed on and did PCR clean-up for the genes and the corresponding segregants (high and low plastic adherence segregants) that did work. I then did a big push for sequencing and just submitted the samples. Hopefully the sequences will be back in a few days and I can begin analysis! What I will be looking for is a systematic difference (an SNP or change in allele) between the high and low segregants because this means that that difference is probably crucial to determining whether or not the segregant will have high or low adherence.

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