Blogs

 This last week (week 4) was characterized by a scarcity of vials, meaning that the number of runs I could start was limited. I already had several going that I started on Monday, and I still had the cold runs going through their second week of sampling. I think some of them might need another 2 weeks to fully finish... But, at the start of the week, we did look at some new compounds to try to see what method to use to analyze them. The nitrobenzene method is apparently pretty comprehensive, so we just decided to continue using that, since it gave us a nice peak.

This week was, for the most part, pretty uneventful.  We started a new experiment last week, so most of the beginning of this week just involved testing nitrate/nitrite concentrations each day.

On Thursday, we collected our day 7 sediment and extracted DNA.  We also tested the day 7 nitrate/nitrite levels.

       I can’t believe we are already halfway through! It’s gone so fast. I guess time flies when you’re having fun. After all, my notebook is already more than halfway full.

 This week, I've started to analyze the data I've gradually collect in the last 5 weeks. Analyzing all the 2011 DNA sequences I've collected so far and aligning these extremely large DNA sequences are a lot of work. After all the alignments and continuously making phylogenetic trees, I have finally gotten some prelimary results.

This week definitely had its ups and downs, but I am going to focus on the positives J.  I finally have had all four of the plasmids I’ve been constructing come back clean from sequencing!  On Monday I had received the news that once again the plasmid pFS1, which was prepared by the highschool intern Felicia, had yet again failed to come back clean from sequencing.  Dejected, since I really was hoping I would be successful this time and begin the transformation into Bacillus subtilis with all of my

 Monday, I finished running our preliminary trials of DNAN and looked at the data I had collected to try to see how long I would need to run each experiment for. I think I have times ranging from 24 hours to 3 or more weeks! But, I couldn't start those right away, since we went on a fun field trip to Astoria on Tuesday(more on that later). So, I started them all on Wednesday, taking sample after sample, and running them all. I was very glad I brought my sweater that day - standing in the cold room all day without it would not have been fun.

Alrighty, this was yet another busy week with lots of traveling.  We were able to go up to Astoria to gain a better understanding of SATURN and the instruments involved in monitoring the estuary.  I also went back out into the field to collect more sediment samples to run some more tests on our archaea and bacteria.