Blogs

One of th other interns, Jean-Paul, came back to the lab with sediment samples from nearby, so we began this week by running tests on his samples. I spiked two samples of the sediment with 2-CAP to see how it would react with this particular sediment type. For each sample, I would spike with 2-CAP, shake the tube for about a minute, withdraw about 1.5 mL to fill a microfuge tube, centrifuge the sample, then withdraw the supernatant to run on the HPLC. Dimin said that we should also filter the samples to make sure that nothing clogs the HPLC.

Week 5 (July 8 – July 12, 2013):

This week we attempted so solve all the problems we had been having with the qPCR for our different samples:

Hi everyone!  It seems like I either forgot to write or forgot to post a blog for week three, although nothing too exciting happened.  I was a 4-day work week because of the holiday, although it really turned into just 1 day of work because we were waiting for an enzyme to come.  Normally it ships overnight but we got it 3 days after we sent in the order, so I wasn't really able to do any lab work.

It turns out that streaking for single colonies of bacteria is even trickier than I thought! Monday is the third time I’ve streaked the mutants obtained from my conjugation experiments I did over the past few weeks. I now have 30 potential mutants where Mn oxidation has been restored, out of around a couple hundred thousand colonies of bacteria. In these oxidizing colonies, my mentor and I hypothesis that the transposon disrupted the gene encoding the negative regulator because of where it randomly inserted itself into the bacteria’s genome.

The highlight of this week was preparing a presentation to give on Wednesday to the other interns and their mentors. The biggest challenge was designing a presentation that I could get through in less than 5 minutes. Despite my doubts, I actually had a lot of fun designing my presentation, which went through several drafts as I got a better idea of what I should say.

Here we are at week five already..... my how time flies...

I have learned alot about resaerch project development.  Project scope can be a tedious process that can lead to many directions and redirections. The key to successful project development is in organizational skills and in obtaining adequate background info to build upon.

On Monday of week 5, Dr. Tratnyek, Ali and I had a meeting to discuss the results I obtained from my TNT trials. I ran six different trials two times each with six different concentrations of iron porphyrin, and I made a graph of the observed rate constant (k-observed) versus the concentration of iron porphyrin ([FeP] (M)).

 To determine whether bioconcentration of BPA and NP by phytoplankton may occur under field conditions in the Columbia River, we collected water samples at Beaver Army Terminal (with the help of the US Geological Survey team). We brought the samples back to the lab and filtered them through a mesh that excludes cells larger than 300μm, to exclude most zooplankton and keep our phytoplankton cells. We transferred these samples to glass Erlenmeyer flasks and added BPA to three of the flasks and NP to three other flasks (both BPA and NP were tagged with the isotope Carbon 13).

This week was a short week because of the Fourth of July! I hope everyone had a great holiday. This week I finished up completely with the second round of TNT trials, we did two trials because the data on the first trials was slightly off. TNT has a much shorter half-life in iron porphyrin than NB does, so irregularities in the method, or preparation of the samples has a much bigger effect on the resulting data. However, I am getting better and more accurate at the experimentation processes.