Blogs

spent time re-writing the introduction for the tribal portal and cleaning up my writing about the four tribes. spent a lot of time writing interview questions for Elizabeth Furse, Roy Sampsell, Charles Hudson, and Antonio. also talked with Jeff about the lay out of portal and it's content.

7/29
So far this week I am finishing up hybridizing the rest of the selected PCR products. Some of the chips are still hard to work with and require very careful handling and cleaning.  The chips aren't guaranteed to, but they should work for about 4 uses.  So far two out of 8 chips are not working after about 2-3 uses.  However, we have enough to finish up the rest of the hybridizations this week and start analyzing the results.
7/31

I cannot believe this internship is coming to an end! I spent this last week wrapping up my project at the bench: I extracted DNA from B.pacifica one last time and amplified genes that will reveal the identity of the bryozoan we are working with. This is being done to be sure that we are, in fact, working with B.pacifica and not a similar bryozoan of the Bugula spp. I sent those sequences off on Monday (7/27/09) and those results should come back to us by the end of the week (just in time to throw it into my presentation/paper!) 

It seems impossible that it is already Friday. This week has flashed past in a blur of boats and special projects. We began on Monday with a dive at Saturn03 to retrieve an outdated cage of instruments. It was the first surface supplied air dive that I’ve been privy to this summer and it was pretty cool. We could talk to Michael from the surface since his helmet had a microphone in it. Once we retrieved the instruments we had to go back to the shop and prepare all the things we were going to need to do the Oceanography camp on Tuesday and Wednesday.

This week I have been tying loose ends that I have been working on for the last few weeks.

7-27
-Inoculated all 7 mutant strains (E1, E2, E3, C1, C3, F1, D1) for 5 hours starting at 10:21am then plated onto YE% screening plates.
-Made LBKan (with proper amount of Kan - I used 6µl for the previous plates for some reason instead of 600µl) and YE% plates again. YE 225µl did not mix terribly well. It appeared to solidify too quickly.
-Repeat transformation (plated onto wrong amount of LBKan plates, so this will be redone tomorrow)
- O/N cultures for two transformants which did grow correctly (F1, D1).

 The Amoa primer reaction was somewhat successful since the bands indicate a definite presence of the Amoa gene in 2/3 of the cDNA samples. However, the locations of the bands on the gels indicate strands are present that are longer than expected. I had been about to investigate this a little more but the primers I designed arrived and I had been excited to use those in an experiment. The initial reaction run showed a slight amplification in only one of the six new primers which is very frustrating.

This week has been focused solely on finding the clearest graphical interpretation of the data that we have so far. I had to compare the Light scattering data to tides, salinity, nitrate levels, and temperature. Unfortunately, the time stamp of the data sets did not have the same format so I had to manually insert one. Below is one of my super awesome graphs.

This summer is definitely flying by!! Week 7 already! This week I worked at WetLabs with my senior mentor, Andrew. This was a good opportunity to update him and inform the company's software team of my project and ponder some possible suggests for improving my interface. So far my GUI's main functionality is complete. It can connect to the database, allow the user to graph some variables and flag the data, and updates the database including the qc flags. One of the things Andrew wanted my interface to include was an automatic flagging for some of the variables.

Sorry Vanessa, I should really start doing these on Friday. No new project this week. I’ve actually managed to stay on the same project for more than a week. Haha! I’ve continued characterizing the reduction of nitrobenzene by nano iron. After much experimenting I have settled on an optimal pre-exposure time. Now I have to make up multiple different samples varying concentrations of either nom, xanthan gum, guar, or other real world materials. So far I have characterized nom, with some interesting results.