Week 6: ESP deployment prep

This week was by far the busiest week of my internship thus far.  Monday and Tuesday I ran full plates of qPCR with variable results.  The first run displayed an efficiency of 107%, which was within the accepted range.  In effect, this data was viable, and displayed some interesting results.  We had ran samples that had been taken from the ESP and compared them to samples taken from the Oceanus (ship-based collection), and the amoA gene abundance was comparable between samples; this was exciting in that it showed we could take samples from slightly different water masses and get the same results, supporting the reliability of the ESP as a viable means of sample collection.  The second run of qPCR on Tuesday however was less successful; the data could not be used unfortunately because the efficiency for the run was too low.  Wednesday was a long day because it was a sampling day, which meant making the roadtrip out to the coast.  However, the weather was nice, and we didn't have to collect as many samples as we did previously, so sampling went relatively fast.  I was in charge of taking subsurface samples and then distributing some sediment into DNA and RNA tubes for extraction.  On Thursday, I ran another full plate of qPCR, but we didn't have time to analyze the data yet, so we will see if the run yielded viable results next week.  Thursday was also the day all the interns delivered their mid-term presentations, which I had been prepping for all week.  I found it especially hard to consolidate all of the background information of my project into a 5 minute presentation as well as choosing which results I wanted to share because I had just recently been getting a lot of exciting data.  However, my mentor helped me make a clear and concise powerpoint, which I later presented on Thursday.  It was nice to have actual results to share as well as to learn a bit about the other interns' projects.  Friday was a big day because Lydie and I headed out to Astoria to prep the ESP for deployment next week.  I had been working with samples collected by the ESP for so long, and I was excited to finally get to see and work with the machine itself.  Just to reiterate a summary of the ESP, ESP stands for Environmental Sample Processor and can collect samples at preprogrammed time intervals or when certian predetermined conditions are met in which case sensors are triggered by certain threshold values being reached.  In this way, the ESP can capture transient, re-occuring events that occur due to the dynamic nature of the estuary.  Lydie and I first did some general maintenance on the ESP and ran it through some commands to make sure that it was working as it was supposed to.  Everything looked fine, and surprisingly the biggest problem we came across was a leaky tube, which took a significant amount of time to troubleshoot because we didn't have the necessary tools to fix it.  We then ran the ESP through a test protocol, which involved picking up a sample of water, filtering the water, adding a nucleic acid fixative, and storing the filter in a puck.  The whole process took about a half hour, but luckily everything ran smoothly.  Then we prepped the pucks in the ESP so they were ready for sample collection, replaced the flush bag, and discarded the waste.  At that point we were ready to go. It was great to see that everything was working properly, and hopefully deployment and sample collection goes smoothly starting next week.