Week 2: learning R

To improve my data analysis skills, I have been trying to teach myself how to code in R.  This is my first foray into coding so the going has been rough.  Part of the challenge is that I have no idea what is or isn’t possible to do while coding in R.  I started out by watching some videos on the basics of R coding language.  Honestly, the videos weren’t very helpful.  They went very in depth on the theory of everything and what R was doing behind the scenes.  I spent a long time watching one video explaining logical vectors.  Eventually I gave up on the watching videos method of learning and turned to old fashioned googling all of my problems.

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Week 1: reading papers

My summer research started out with reading a ton of papers on all aspects of the monarch butterfly life cycle.  I thought I knew most of it pretty well after researching the monarch and milkweed interaction for three years, but there is always more to learn.  The idea behind my project is that there was a change in the monarch butterflies’ diet over the past century as prairie was replaced by farmland and eastern forests were cleared.  I hypothesize that they are now less chemically defended because their main food plant is Asclepias syriaca which contains low levels of weakly emetic cardenolides.  This may have led to an increase in mortality during their overwintering period due to greater numbers being eaten by birds.  In the process of writing a grant proposal to fund this project, I have read about 30 papers on monarchs and milkweed.

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Results from Trial 1/ Starting Trial 2

At the beginning of this week, I looked at my Trial 1 slides for no treatment/ chloroquine that I made the week before. I examined the twelve chloroquine slides and took pictures of those slides. I need to perform statistics on the slides but I will do that throughout this week. In general, the majority of the cells on the chloroquine slides were not viable and the cells that were alive were scarce. One explanation for this could have been forceful washing during the cell fixation process. This week when I do cell fixation, I will make sure to be careful when washing the cells using the autopipette. I have also done cell culture for Trial 2 of no treatment/chloroquine. I will add my DNA conditions to my cells today and add the autophagy inhibitor drug, chloroquine, to the cells tomorrow.

Week 5: Modifying the density plots and grouping the TEs by family when conducting the alignment

Last week, I did the alignment of transposons using a series of programs. I had got the alignment file and the distance matrix for each DNA subfamily. This week, I continued on this track but modified the grouping of the TE families. Instead of grouping them by the really tiny unit–subfamily, I regrouped them by their family. There were only six major families of DNA transposons. In this way, we could now see a phylogenetic hierarchy within the families.

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