Blogs

On Monday I took more samples of the Leap tank sediments for both 2-CAP and TNT. I then spent the rest of the day running Leap tank samples on the HPLC. The HPLC was actually behaving quite well on Monday. 

Pyoverdine is a organic ligand that binds to iron molecules. At a low iron environment, Pseudomonas putida and some other bacteria produce pyoverdine to find iron for uptake. On top of our manganese research, we were also interested in looking at the pyoverdine secretion for this week’s experiment. I grew the P. putida in minimal medium A with 100uM manganese, Mn(II), and different concentration of iron (0.37, 18, and 100uM). There was only four time-points collected for this week.

This week I spent a lot of time working on DNAN to try to figure out what is going on at the end of the reaction. 

Each week I've been looking forward to completing the qPCR of the cave samples, but each week, it has been delayed for one reason or another. Last week, I was finally able to do it. The qPCR is a way to amplify DNA samples and figure out how many copies of DNA were in the tube before the amplification began. It's fun to use, because it creates real-time graphs showing the amount of DNA present after each cycle. The lines on the graph start off horizontal as the PCR begins and the amplification is slow. Then, they begin to rise sharply in a curve and, finally, level off.

Monday: Prepared to write final paper, re-researched symbolic regression.

Tuesday: Started writing final paper starting at symbolic regression section, and changed code on main file.

Wednesday-Friday: I continued going over the Field Guide to Genetic Programming, implementing code that Charles and Tuomas suggest, and asking questions about genetic programming to Charles and Tuomas.

This has been a good week to understanding more about what symbolic regression is about.

The last two weeks have been very busy, it's crazy to think I only have 3 weeks left now.  I spent most of my time doing more PCRs, growing cells, and analyzing sequences.  As I mentioned a few weeks ago, I have some new primers that I've been working with, rather successfully.  Nicknamed "Dub 2" primers, these amplify the variable d2 region plus a non-variable region on each end.

I started off this week by running a touchdown qPCR with the archaeal primers to see how similar the numbers were when compared to the qPCR, that way we would know if the we numbers we get with the touchdown qPCR for bacteria are an accurate representation of what we would see with a normal qPCR. Although the numbers for the touchdown qPCR were higher and statically different it was not by a great amount.

Week eight has been pretty slow I’ve had steady cell counting hours and my weekly culture transfers where done as usual, I haven’t had much data to put in but since we will be collecting Pam data from the part of the experiment we just set up I’ll have more Data to put in a few days. The other thing I did this week was make more media since we used up so much of it during our experiment, and acid wash all the bottles we used last week.

Week six was rather uneventful, I spent most of my time cell counting and entering data into an excel sheet. I managed to finish counting all of the cell samples from June and some from May I am still not quite done with those but hopefully they will be done by the end of the summer. I also entered all the PAM (fluorescence) data from June I’m not sure if I’ll be doing the ones from May since there were some issues with those data sets, but I will be collecting the ones from the next part of the experiment.

The culture tubes I started last week with various P.putida mutants growing in the presence of various carbon sources did not much change from when I checked them on Friday. This makes me wonder if maybe there is a limit on how much of the carbon source the bacteria are capable of breaking down and digesting.