Week 2: A glimpse of TE evolution by analyzing the ratio that the query TE sequences match the referential sequences

In the post of week 1, I summarized how I got the raw data of some key features of the Mimulus TE sequences. I aligned the query sequences with the referential genome sequences using ReapeatMasker. Based on the data in the output files, I wrote python programs to make tables and plot frequency histograms for each of the TE families. In the second week, I moved forward to focus on the matching ratio of sequences in each TE family. That was, the ratio that a detected region of the query sequences matched the corresponding sequences in the referential genome file. To achieve that, I first calculated the length of each transposon in the referential file. After that, I assigned the referential length of each TE to the ones that I found in the plant genome file, using the name as index. Then, I constructed a csv file that contained the name, the family it belonged to, the number of bases matched, and the matching ratio of  every single TE in the plant genome file. This file would serve as the data frame to generate frequency histograms of matching ratio of every TE family. All those procedures were achieved by self-written python programs.

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Training in the Lab

The first two weeks in Dr. Hinton’s lab have gone by quite quickly! Mostly, I have been helping to train some of the newer members of the lab. Because we have so many students working in the lab this summer, it has been happily chaotic. So far, I’ve been reminded a lot of when I was first being trained at my old lab. There were eight of us who had to share one small bench, so everyone got very close very quickly. Being able to be in a space that feels the same, with everyone working together has been extremely nostalgic for me.

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Week 2: Successes and Challenges in Initial Reactions

This week in lab provided both challenges and successes in my project. The goal for the week was to produce enough of the core material so that I could run new reactions in the upcoming weeks. While I was able to synthesize the product, the yield for the three reactions was smaller than hoped for and set me back a little bit. However, the point of research is to try many things in order to determine what works best, so the bumps in the road will help me to determine efficiency for these reactions.

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Summer Research Week 1

The first week has been a great learning experience and has allowed me to put my time and focus on my project. I continued to perform PCRs on the DNA strains of Migrant and European strains of S. Paradoxus (my yeast of interest). My advisor, Professor Murphy, ordered new primers that we added into our cleaned PCRs and sent them to get Sanger Sequenced.

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Greetings From Blandy Experimental Farm! Blog Post 1

The first week and a half of research is off to a great start! We spent the first half week learning about lab protocols, milkweed plant care, and the spectroradiometer. We used this instrument to take absorbance readings for leaves from all 122 of our common milkweed plants in the greenhouse. We also collaborated with Professor Williamson’s lab on an experiment to see if cardenolides (a compound in milkweed) have antimicrobial properties. The initial results showed that they do not, but we are going to revise some elements of the experiment and try it again.

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