Author Archives: Cody Jenkins

Life Aquatic with Team Labby (feat. Team Transcriptome)

Today (8/19/14) we continued to work on our paper. Evidently at one point Casey came looking for me and I missed her. Supposedly this is not the first time something like this has happened to which my colleagues responded by asking each other “Where’s Cody?” As it so happens this question has been asked by enough colleagues to “catch on” as it were. I find this surprising. As we were watching life Aquatic Last Night someone in the movie said “Where’s Cody?” A good time was had by all. All this is to say that I don’t remember actively seeking out places where people will not be able to find me so I don’t really know what the solution to this predicament would be. Suggestions?

Puzzlin’ Away With Team Labby

Today (8/18/14)  We continued to work on all of our projects. Casey and I made a video. I thought it turned out well. We continued working on all our puzzles depicted below. And of course, we continued working on summarizing the results of our experiment. On the whole it is coming along nicely and I am learning lots by reading through so many different papers. It is really fun to be able to put faces to the names of people who have written the papers I am reading. The RCN meeting was really eye opening in that sense. Taking a step back for a moment, the RCN was not only a really exciting opportunity to meet many different scientists involved in really cool project it was also just a really cool way to cap off an amazing experience here at Friday Harbor Labs.

This is a puzzle of a shipwreck

This is a puzzle of a shipwreck

This puzzle shows 2 different views of surface of the Earth. This is also one of those puzzles that is made up of many tiny little pictures. Cool. But difficult.

This puzzle shows 2 different views of surface of the Earth. This is also one of those puzzles that is made up of many tiny little pictures. Cool. But difficult.

This puzzle, to my knowledge, has not yet been assembled but depicts a turtle.

This puzzle, to my knowledge, has not yet been assembled but depicts a turtle.

This puzzle is currently in the process of being assembled. More to follow.

This puzzle is currently in the process of being assembled. More to follow.

RCN

Today (8/16/14) was not only very informative it was also one of my elementary school friend’s birthday so I would like to begin by wishing him a happy birthday. Anyway I learned a lot at the talks today. One thing I did not know was about Pathogen Persistence and Perpetuation in Pacific Herring. But know I do thanks to Paul Hershberger. What was most alarming to me was the enourmous number of virus particles that can be shed by 1 individual. I wish I documented the talk better but I think he said that there is enough farmed herring in the Salish Sea to produce 1 virus particle for every liter of sea water. That is alarming. To be honest, I heard a lot of alarming facts today. I think it is important to understand how to keep yourself happy and optimistic amidst a great deal of doom and gloom.

Workin’ On the Labby

Today (8/15/14) was spent working on the project presentation. On the whole it is coming together nicely. Talking with different scientists (both other students and instructors) has really opened my eyes to the importance of multitasking.It is important to know how to discipline yourself in a way that you are productive but it is also important to have time to do things like relax at Herbs with your close friends. It is a fine act of balancing you want to be productive but you don’t want to be racing to nowhere 24-7. I have learned much about this idea this summer and hope to learn even more in grad school

Team Labby Assembles

Today (8/14/14) was not only my brothers birthday it was also the day that team labby assembles the final experiment and Maya taught us about models. It started with a great lecture that had me 110% convinced that I needed to know about modeling. Then I got to try it out for myself. We modeled the effect of elephant walking paths on vegetation regeneration as well as the effect of oyster filtration on disease. Modeling is very new to me I have never done it before but I can see how it could be benificial to some of the research I have done with mate choice in vertebrate populations. For my senior research thesis I examined the MHC diversity between mated pairs in different populations and compared the nucleotide diversity of the different populations to see if populations in which mates tend to choose individuals that genetically different from themselves with respect to MHC loci had less nucleotide diversity than populations in which mates tended to choose individuals randomly with respect to MHC loci. Although it would be a tricky thing to wrap my brain around I could definetly see how modeling could help us understand the role of MHC diversity in mate choice and immunocompetence. I think one potential obstacle might be, however, that not enough data has been collected to generate a meaningful model. That could just be my inexperience with modeling. Afterwords Amanda, Casey, Rachel and I set up a labby filtration experiment and I learned more about qPCR. I found out that yes qPCR only directly quantifies the amount of DNA that has been replicated for a given step, but it does this by generating an equation that explains the changes in florescence (and thus DNA). This equation can then be used to calculate the amount of DNA that was present at the beginning of the experiment. I suspected that qPCR was able to quantify the amount of DNA somehow but I just wasn’t able to conceptualize it until Amanda and Casey patiently explained it to me. After setting up the filtration experiment we used hemocytometery  to count labyrinthula cells in the sea water. I did not see any. All in all it was a very productive day.

TEAM LABBY!

Today (8/13/14) team Labby went down to the lab to prepare our experiment we had to measure out the little oysters that we love so much and they had to be between 25 and 28 mm. I thought I did a good job with that. Then I got some seawater. Needless to say I did a good job with that. However, something I thought was interesting was the use of controls for our experiment. Because we want to make sure that it is an actual biological process the oyster facilitates that reduces the amount of Labby in the water column we shucked a group of oysters and sealed the shells with nail polish. If it is a biological process that facilitates the reduction of Labby in the water column then the water samples with these oyster shells in them will show significant signs of Labby reduction. Alternatively, the labby might just naturally store themselves in the shells of the oysters and netting that suspends them in the water column. Then we went our separate ways to do some research on Labby. At the end of the day we listened to Carolyn’s and Steven’s presentation to Friday Harbor. I think  I need to take another chemistry class but I would be interested to learn more about how CO2 is thought to affect calcium shell formation. I will ask Carolyn next time I see her and writing it down in this Notebook post will help me seal this commitment in long term memory.

qPCRin’ Day 2

Today (8/12/14) We just finished up some stuff (regular house keeping chores that help us keep moving forward like a well oiled machine). I also noticed a much more amiable skull than yesterdays (see figure 2). After lab we made a stop at the Ballard Locks to check out the fish and there were some really big Salmon there, although I don’t remember what kind. It was really cool. I don’t ever remember going there before. This is kind of an embarrassing realization but it should be a good test of how closely this post will be examined. Here it goes…Mechanically it wasn’t until I saw the locks in person that I realized how it was possible to transport a boat vertically. But I realized its just like putting a boat in a giant tube and controlling how fast the water goes in at the same time you are controlling how fast the water goes out. So if you slow down how fast the water goes out the water surface will rise and push the boat upward. If you speed up how fast the water goes out naturally the water surface will lower and take the boat with it. I don’t know why I was not able to conceptualize that until actually seeing it. IMG_1557

Figure 2. A much more friendly skull and cross bones that is kindly advising his friends to refrain from consuming food or drinks in the lab for their own  safety.

Figure 2. A much more friendly skull and cross bones that is kindly advising his friends to refrain from consuming food or drinks in the lab for their own safety.

Seattle. Receiving its annual 3-4 rays of sunlight.

Seattle. Receiving its annual 3-4 rays of sunlight.

qPCRin’

Today (8/11/14) I showed up bright and early to the School of Aquatic Science and Fisheries at the UW campus in Seattle. I was surprised by how close it was to the NOAA facility. Maybe I shouldn’t have been. Anyway’s after getting the lay of the land and acclimating myself to this very creepy scull (see figure 1). We began work. I focused on extracting Labby DNA. It was pretty straight forward but it was my first time using these kind of pipettes and so it took me a moment to get used to. On the whole the qPCR looked like it turned out great but we are still in the process of interpreting the data. I am very excited to learn more about the data we have collected. Perhaps the most unexpected part of today was how straight forward qPCR is. I was expecting it to be super high tech and very complicated with lots of blinking lights and whizzing machines like something you might see in Dr. Frankenstein’s lab (side note/creative writing idea: would it be cool to be a grad student with him? Also what granting agency do you think he applied to to fund his experiment? If he didn’t have any grad/undergrad students what did he say were the broader impacts of his grant?) anyway all that is to say that the qPCR machine was in fact the exact opposite. It was a very modest little black box with a computer screen connected to it. It worked just like a normal PCR except you didn’t have to run a gel. As I understand it (and it would really help me if someone corrected me where there are apparent gaps) we are using qPCR to quantify the amount of Labby DNA during different points of the replication process of the template DNA. That makes sense to me and I understand how regular PCR that is visualized on a gel doesn’t tell us how much DNA is there only the size of the DNA. But what information about Labby infections in eelgrass can we glean from our qPCR experiments? Why can’t we extract DNA and do a regular PCR and then measure the concentration of the DNA in a NanoDrop Spectrophotometer? Wouldn’t that also theoretically give us an idea of how much DNA results from a PCR? We could even stop the PCR at different points during the run in order to plot multiple points on a graph of PCR product over time.

Fig. 1. Creepy scull found outside Lisa and Carolyn's lab. Perhaps this inspired my creative writing prompts about Dr. Frankenstein.

Fig. 1. Creepy scull found outside Lisa and Carolyn’s lab. Perhaps this inspired my creative writing prompts about Dr. Frankenstein.

A different type of pipette that I have not seen before but have now figured out and am excited to use again at some point in the future.

A different type of pipette that I have not seen before but have now figured out and am excited to use again at some point in the future.

Lisa and Amanda looking at the qPCR output.

Lisa and Amanda looking at the qPCR output.