Tyler Bradstreet's blog

Well it's the end of the internship and to say the least I had an awesome experience. The final presentation went well and I think everyone who attended had a good idea of the basis of my project and the results obtained.  Overall the compliance between everyone at CMOP was very helpful especially from my mentor Mariya, senior scientist Holly and the rest of Simon lab (they were great).  To be honest I didn't expect to develop such a close friendship with the other interns but we all had a great time together.

This week I finished up hybridizing the last 12 samples so now we have all the data we need for a paper.  Mariya is gone this week so I started my paper once done with the lab work. In addition, I also helped Michelle Maier from Tawnya Peterson's lab with PCR product labeling and hybridizing as she will be performing these steps on board in September when the team goes out on a research cruise. So for next week I will finish up the paper and collaborate with Mariya for data analysis.  Also my final presentation is Fri the 14th!

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

Week 7 and I am still loving this job. As I mentioned last week we were able to move on to hybridizing Pseudo-nitzchia samples and we were very successful. Each chip worked this time after some carefull cleaning.   The reliability of the chips is proving to lessen after about two uses but luckily we have enough potential uses to get all the hybridiztions done.  To end the week off I mostly labeled PCR products with Biotin...that was about 36 total which should conclude all samples need to be prepared for hybridization for my ten week period.

To start off week 6 we selected more Archaea and SAR 11 samples to be hybridized.  12 samples were selected, labeled and hybridized but only 8 samples were read by the Electrasense platform.  One of the chips had a faulty sensor so our samples were lost., we may have to go back and run PCR amplification on them again at a later time.

This week we were finally able to isolate, amplify and purify 88 total samples to be hybridized.  This was a huge leap in progress because we can now spend the rest of the next five weeks hybridizing and analyzing microarray data.  Monday and Tuesday were the last days of isolation and PCR, so Wednesday we moved on to labeling 12 samples with Biotin to get them ready for the hybridization process.  These 12 samples included 6 Marine Archaea products and 6 SAR 11 products from Aug 2007 samples.  The entire process is pretty lengthy because there are many incubation steps,

I can't believe this summer is going by so fast already.  4 weeks into it and we're almost half way done with the internship!

So now into week three I am definitely getting a tighter grasp on the project and the techniques we're using to gather data.  Tuesday I met with my senior scientist, mentor, and a few others from the lab to discuss some more long term goals for the project.  This proved to be very effective in boosting my understanding of the project vs just the literature review on the project.  Communication is key!

Week 2 started off great with a visit from the NSF site visit team Monday.  There they gave some background on the aspects of their funding and also assessed each individual project within CMOP to see how they were going.  Each intern had the opportunity to speak with an NSF representative during lunch.  I spoke with an engineer from the University of Florida who had some insightful things to say about his studies with ocean currents and turbulence.

Unfortunately I had to finish 3 final exams this week down at OSU so I was only able to attend the orientation on Monday and a few hours in the office today (Friday).  Today I had the opportunity to meet with my mentor Dr. Mariya Smit and read over a literature review of the research topic we will be dealing with this summer- Using biosensor technologies to monitor and map out microbial communities in the Columbia River plume on a year-to-year and seasonal basis.