Blogs

Week seven of my internship included a lot of reading papers and waiting for bacteria to grow.  This week and next, we are working on conjugating the plasmid containing the delta DNA fragment (the one without the gene of interest) into Teredinibacter turnerae.  However, this step requires aligning the growth of the E. coli and the T.

This week was filled with results! I have had great success with the Nitric Acid digestions, and the lab now has permanent slides for the chironomid gut contents from June and July for all three collection sites! This is great because these results will be compared to Claudia's counts of the same sites to see how the environment compares to the chironomid diet. 

During the seventh week of the program, I discovered that the pHstat system reagent flow rate might be dependent upon the height of the reagent bags above the manifold. In order to discover the range that the manifold maintained similar perturbation times, I experimented with the height of the reagents increasing it an inch at a time until the system could no longer compensate. I tested two different concentrations at the 0.25 pH deviation, this was due to this deviation resulting in the greatest difference in perturbation from the data.

On Monday, I attempted to use the fluorospectrometer to quantify DNA concentrations in various samples as well as standards of known concentrations so we could check their accuracy.  However, I ran into many difficulties when trying to take the nanodrop measurements; when it came time to run the actual samples, an error message popped up for several of them reading "the measurement concentration is outside of the range of reference or standards", and so the concentrations could not be determined for these samples.

​Week 6, with most of the backend finished, I began working on the web interface. During the first week, when Jesse and I discussed this project, we agreed that we wanted to use a Python web framework. We chose Flask, since it was simple to use and quite powerful. Since I haven’t done much web development before, I spent most of Monday and Tuesday getting aquatinted with Flask. I went step by step through a tutorial on Flask, and also brushed up on HTML and CSS.

Week 5, I spent most of my time working on the csv parser and revising my code. Nothing really exciting happened this week; I mainly worked on refining my previous work. I talked to Jesse, who wanted me to present my progress at the group meeting on Friday. Since my midterm presentation was next week, this was a good opportunity to practice for that. I made some mockup images of the web interface for the presentation to give a general visual demonstration on the functionality.

Week 4 was actually quite short, since we went to Bonnevile dam on Tuesday and had a day off on Friday for 7/4. With most of the plotting backend finished, Jesse and I discussed how users would actually use these tools. He suggested that users should be able to upload their own data, in the form of a csv (comma delimited) text file. That file would contain observation data obtained from stations, with time and a variable (such as salinity). Currently my plotting interface worked with data container files, with data in various arrays in a specific format.

This week I remade each of the manganese ligands that I’ve studied so far this summer and tested their stabilities over time. After going through my lab notebook record I picked the method for making each one that had worked the best. I made the manganese oxalate and manganese malate by using the acid version of the ligand combined with ammonium bicarbonate, degasing with argon, and adding manganese acetate.

This week involved a lot of grinding through experiments, one by one. There was a lot to do, and not a lot of variety to it. However, I figure that the more experiments I get done now, the more time I'll have at the end to wrap everything up. I worked on testing the effect of the length of the probe and iron oxide reaction on absorbance.

I began the week with optimism that my Cerc5 primers would be usable for qPCR and that I could get some numerical results confirming it is located in just the Columbia River Estuary. This plan did not work out as my first qPCR run featured significant amounts of contamination in the no template control. This confirmed once and for all that my primers must be contaminated and that I needed to order a new batch. Until the new primers arrive I have begun working on quantifying the distribution of a new protist organism- euduboscquella.