Blogs

On Monday, Tuesday, and Wednesday I did RNA isolations. Thursday I read and learned about microarray analysis. On Friday, I installed the necessary software for microarray analysis and tried to analyze (for the second time) the 12K microarray scans on my own and it was a success!

The (Mariya's) procedure for analysis goes like this:
1. Using combimatrix imager, open your image (the scan of the chip) and the probe design.
2. Use a template to align a grid to spots and extract data and save to desktop.

Last week, we ended up getting back our results from both the MS/MS, and the genetic sequencing lab.

The MS/MS gave us fairly strange results which suggested that the column in our lab may have been contaminated with proteins from a strain of bacteria 9A1 (arantimonus). This seems unlikely since great care was taken to clean the column, but to ensure reliable results, more investigation will be necessary; more samples will be run through the FPLC and the results of the MS/MS of these samples will be compared to the original results. Hopefully it turns out that the bacteria we are studying have Mn-oxidizing protiens that are similar to arantimonus, as opposed to contaminated with 9A1.

This week everything started to come together. At the beginning of the week Grant and I realized that the program I had been modifying for the last week and a half would not work even without my modifications. It was a bit frustrating to essentially throw out something you had spent a bunch of time troubleshooting. Oh well such as life I guess. At least I would no longer have to figure out why it wasn't working quite right.

It's August! And its rather scary how quickly the end of my internship is coming up, especially since I don't think I've come up with a whole lot except for finding out what doesn't work well. It feels like my project is becoming more method development--to find a decent, reproducible way to make MnO2 electrodes that can consistently measure H2O2. Only when this method is developed can the differences between the biogenic MnO2 and synthetic MnO2 really be observed.

I can't believe it is already week 7! I'm just getting into the swing of things and now I have to leave pretty soon :(

This week has been busy and exciting. I repurified two of my proteins and repeated a bunch of my experiments (results pending). Me and Garg (my mentor) also came up with a few new experiments to try out which include cross-linking experiments and yeast-two hybrid assays.

I'm back on land! Interestingly enough I spent a good part of yesterday afternoon feeling like I was still out at sea. It really set in in the shower and bed. Who doesn't love lying in bed at night feeling like you are rocking back and forth, constantly. Just to make sure this was common, ok I know this is common but I wanted to know why, I did a bit of research. According to Elizabeth Svaboda, of the International Herald Tribune, "Landsickness" or "reverse seasickness" is familiar to many people who have taken long cruises.

Well this has been a hectic week. I have been running between Pierre's lab which houses the fluorometer I use to get excitation emission data and ours to analyze the data on the computer. Anyway I knew things would be rushed after I spent two weeks on the cruise so oh well...

I’d have to admit that this week went by much better than last week. I had great success in the lab and well, I my friend said that he’s getting better.

For lab this week we tried another method to measure the acetaminophen concentration where we added ethyl acetate, sodium sulfate, sodium carbonate and Folin- Ciocalteu to my standards to create a standard curve. Unfortunately, this experiment almost failed. But, I returned to my faithful experiment and for the first time, tried it with the liquid waveguide capillary cell (LWCC) and was very successful. My r2 was 0.9989 which was so cool!! Because of this, we decided to try a sample taken from the Willamette River. We left it over the weekend to filter through the solid phase extraction. I hope that this helps us to get a good concentration of acetaminophen.

It seems that I've been getting the hang of MATLAB a little bit this past week, so I actually made decent progress. I added a growth function to the model and also allowed for the diatoms to reproduce. (The diatoms reproducing is pretty generic at this point, but they aren't the main focus of the model. If I had more than ten weeks to work on this model, this would be one of the things that I'd like to make more realistic.) So that leaves the zooplankton reproduction function and then the model will be done!