Blogs

This week I have been extracting RNA from the samples that we thought were good candidates for our project. My technique for RNA isolation is pretty good and is becoming more routine the more I practice it in the lab. Once we have enough samples isolated, we will start to hybridize them. Next week, we will probably hybridize them so that we can finally use the microarray.

Until next time...

This past week was fairly uneventful as we had our fair share of setbacks early in the week. On Monday I set up batch reactors that would equilibriate over night and be used in the morning for new tests on 1,2-DCP, 1,3-DCP, or allyl chloride (it wasn't decided yet). Unfortunately, on Tuesday morning, after running some preliminary tests on where each reactant would peak on the GC, I found that the noise from the hexanes was in direct conflict with all three of the reactants we were going to look at and therefore the results would not be very accurate.

Some experiments are working better than others.

 This week we started the infection experiment and continued to try and get a good PCR and gel run to be able to begin sequencing. For the infection experiment we have 18 bottles set up- 12 experimental and 6 with dye as controls. Half of the bottles are shaken to simulate turbidity and the other half are not. Half of each of the bottles in shaken/not shaken have parasites while half do not. We will take a small sample from each bottle and measure RFU values and fix the samples to do cell counts, as well as measure for chlorophylls and nutrients.

Phoebe is now making her way south and making about .34 m/s. Her heading is 46 dergrees and she is about 4 km from her next waypoint.

Wow, week four already; my time here is just flying by.  This week started with going over my data analysis with one of my mentors.  We compared my analysis with the known composition of the samples themselves to see if there was noticeable agreement.  I also tried to look for seasonal patterns in my statistical analysis of some water samples over about a year’s time.  I have been utilizing my PCA MATLAB code to its fullest and have developed another code which graphically displays the variance, a result of executing PCA

 This week was all about testing different concentrations to see which would give a better signal.  Monday, we received a SLA sensor in our lab! Now we will be able run tests here in the lab when we are not at Sharp.  After attending a meeting with Andrei, Mariya and Holly, Vena and I traveled to Sharp to run tests on multiple and single probe dies using a high concentration of DNA at 0.1 ug/ul. On Tuesday, we tested the dies at a lower concentration of  0.01 ug/ul to see whether the signal was better.