Blogs

As this blog may be a resource for aspiring CMOP interns, in addition to discussing my lab work I would like to use this weeks blog as an opportunity to reflect on something that is very important to college students and has been plentiful this week-free food.

This week I have been working on processing samples taken from the ocean during a phenomenon called "red water" and from the Columbia River estuary during an estuarine turbidity maximum (ETM). An ETM occurs when the freshwater flowing out on the surface of the river mixes with the saltwater flowing in from the ocean, stirring up lots of nutrients and sediment particles.

Corny as it may sound, time flies when you are having fun. Yes Paul and Jim, I’m having a blast! Listening to great music in a laboratory, working in a 10 degree Celsius room, what else could I ask for? I’m not joking here. Interestingly though, the highlight from last week occurred outside of the lab. We were privileged to talk/eat lunch with a member of a North West Native American Tribe. During our brown bag discussion we focused on our relationship, as future scientists and productive members of society, with the Native American Tribes in our region. It was great.

This week I completed eight more RNA isolations from samples along a salinity gradient from the estuary. I also attended half of the practice NSF presentations earlier in the week as well as the entire site visit on Thursday. On a side note, I got a new OHSU ID with a photo this time in order to ride the public transportation without a hassle and organized the accumulating literature I've read. I also went over the protocol for creating a microarray with probes and spent a day generating spread sheets and graphs with the data I have thus far.

This week was really busy around the center. We had the NSF visit, which gave us interns a chance to see presentations about all aspects of the center. As far as my own work goes, I've been doing a lot of research about how zooplankton function, move, eat...etc. That way, I can make my model as realistic as possible.

I cannot believe that it is already my third week here at CMOP. Everything is going really well; I could not have asked for a better lab to work in and people to work with. Before I tell you the riveting details of the last week, I would like to issue a correction for last weeks blog. Apparently I was incorrect in my description of how tetrazolium works in regards to cells. I had previously described it as working in the glycolysis pathway, but it seems to actually act as a substrate analogue for reductases and hydrogenases in mitochondria. It seems that by binding preferentially to these enzymes, the cell slowly exhausts itself because it uses up NADH and NADPH, thereby decreasing its reducing power.
Also, the product of this reaction is formazan, which is nasty, and may work to kill off the cells.

This week I felt like I was finally starting to get a grasp on my project. I had read through all of the material that I was given and feel that I have a great conceptual idea of about the ETM.

Later on in the week I started working on the computer. Grant, my fabulous mentor, helped me load various computer programs to get started on modeling the ETM. I discovered that computers are really great when you get them to work correctly but definitely a pain to troubleshoot. Google has become my new best friend in that regard.

Snow!!!
This week was pretty good. It mostly dealt with the NSF site visit. On Monday we watch the various speakers practiced their speeches. I have to admit that I had no idea what they were talking about but I tried to pay attention. On Tuesday, we went to the primate center to have lunch with some of their summer interns on that side of the campus. At least no one Thursday was the actual site visit. I have to say that these people asked some serious questions, but I guess that it was necessary to know exactly what a program that you fund is doing.

It is kind of funny that I have been working three weeks already and I haven't even purified all the protein I need to start my experiments. Who knew separating our one desired protein from the over 2,000 normally expressed in E. coli would be so time-consuming?

Our YjbH protein, which we worked so hard to express and purify, aggregated which means it is now useless. Right now I am attempting to squeeze a little bit more YjbH out of our lysate pellet and I am waiting for my gel to stain as we speak (as I type?).

This week was a little crazy but pretty fun. I continued working with Frontpage to get practice for the real website that I was going to work on for the Estuary Watch. On Tuesday all the us got to go to the Primate Center for lunch. I really wanted to see the monkeys but I was told that we were not going to be able to get a tour...I was sad.