Week 3: Rerunning reactions from Week 2 and finalizing synthesis of the diketopiperazine

The elimination, isomerization, and Diels Alder reaction from last week did not progress as expected. After workup, 1H NMR analysis showed many different impurities with very little product formed. This could be attributed to remaining impurities in my starting material, resulting from ineffective purification of previous reactions.

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Visual Analysis & Structural Coloration

This past week, field work proceeded as usual. We conducted assays, nest box checks, banded birds, and collected feather samples. I also begun visual analysis of the feather samples! Visual analysis will be used to get more information on how CORT levels impact individual condition, and will be overseen by Casey McLaughlin.

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Summer Research Week 3 Update

It was during the second week that the control variables were narrowed down to the poverty or unemployment rate, overall drug use (or opioid abuse if the first was not feasible), and the number of black persons per state. I then needed to find a data set for each variable that was separated by year and state in the U.S. on the government census website or the CDC Wonder database. As mentioned in the second week blog, I realized that information on all the control variable was not collected for each year within the research timeline, 1998-2017. Therefore, it was decided by my instructor that the control variables would be constricted to a median year in the timeline, 2010. This year is not the centermost within the timeline, however, since some of the control data came from the government census database, that holds information collected decennially, it was the closest possible year.

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3rd Week of Research

Good Afternoon Readers,

In my third week of research in the Shakes’ lab, I worked with a fellow student researcher in the Kerscher lab to utilize their UTAG protocol on my nematode gonads. The kmUTAG protocol is developed from one of the SUMO proteases, Ulp-1; further, kmUTAG is a useful tool of evaluation because it has less affinity to bind to free, unconjugated SUMO. A quick note about the SUMOylation pathway, three enzymes are required for a protein to be SUMOylated. The three enzymes are known as the activating enzyme – E1, the conjugating enzyme – E2, and the ligase E3 – in nematodes, the enzymes frequently studied for their localization throughout nematode gonads, especially during the meiotic divisions are the conjugating enzyme (E2) UBC-9 and the ligase (E3) GEI-17. I have included a pathway depiction developed by Dr. Shakes at the bottom of this post.

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2nd Week of Research

Good Afternoon Reader,

In my second week of research, I began trying to formulate some co-staining protocols, which would allow us to evaluate the location of SUMO in relation to other cellular components, such as tubulin and actin: because we are hoping to publish our findings, we need to be able to combine SUMO staining with antibodies for different proteins. There has been quite a bit of trial and error, but I am learning a lot about being able to evaluate your own methods and making changes to better the results of my preps.

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