Blogs

Loading of Wecoma for the July 2010 CMOP cruise got a late start due to an unexpected drydock delay in Portland.  All gear did get loaded and put in place quite quickly thanks to the abundant help of the MarTech group (Dave^2, Toby and Daryl).  Pushed off from the dock 4 or so hours later than originally planned.  On the way out of the estuary, a problem developed with the bow thruster.  Thought it was a problem with the power supply but no luck.  A swap with a spare proved it still doesn't work.  And so, we just made the turn around and are headed back in

7-26-10
Completed alterations to poster and re-submitted to Wendy.

Completed reading / note taking on essay questions. Began brainstorming for various means of organization, finally resolving to follow a pattern similar to the order of questions asked. Certain sections will be answered throughout as opposed to being limited to pre-determined distinctions. This was decided to allow for better continuity throughout the essay

7-27-10

     My fourth week at CMOP consisted mostly of me monitoring the subcultures from Roberto’s PC2 experiment from April, waiting eagerly for them to oxidize. With the Halomonas LOB-5 it's been the same story, waiting to see manganese oxidation, waiting to see the colonies turn orange or brown. I did look at a handful of the cultures under a microscope, mostly the RA26A subcultures, and determined that within those there are at least two different types of cells, one that is motile and another that isn't.

Throughout this internship I’ve felt very out of my element, as I’m sure I’ve made fairly clear throughout my blogs.  I’m very new to laboratory work, biology, microbiology, and especially genomics.  But I have still found some connections from what I’m doing here to my chosen career path in environmental engineering.  Science and engineering are not normally closely linked, but there are some main similarities that permeate both professions.  The one that I’ve experienced the most is problem-solving.

This week I was working on a variety of little projects in order tobe ready to mail the mass cloning plates away and to help Suzanne prepare for the sampling cruise that she will be going on next week.  On Monday, Suzanne and I got packing material from Nancy Christie and got dry ice from the primate center.

7/19/10
     Katie, Greta, and I went to the Tansy Station and retrieved the CT sensor for cleaning. The sensor was attached to a rope, so we were able to retrieve it simply by pulling it up. We brought the sensor into the boat and it was covered with barnacles. We made a quick trip to the Desdmona Station to check for comorrant chicks. We won't work on a station if there are chicks because the chicks become frightened, throw themselves into the river, and drown. To check for chicks, I had to scurry up one of the stations poles in a way that Greta found comparable to a gecko.
     Then I got to drive the boat back to port, and later, I got to clean the sensor.

This week consisted of many more tests of titanium dioxide and a lovely surprise in one of them. I photodeposited more pieces of titanium dioxide with platinum with varying deposition times and tested them under the solar simulator with caffeine as a model contaminant. Unfortunately despite varying deposition times, the platinized TiO2 degraded the caffeine much slower.

 Since the primers that Pete and I have been using start from the ITS 2 region, the sequences that we receive only account for about the first 400 base pairs of the 28S sequence. Pete and I developed internal primers so we could possibly obtain the full 28S sequence. After using these primers in PCR we could see that we were not getting the right size fragment. Next week we will try and optimize the PCR program to give us the right product.

Hello!  This week was more of a book and writing research week than lab work.  I am doing a lot of online and textbook research to really solidify the concepts of my lab work, as well as starting an outline and write-up for the ASE Symposium on August 20th.