How strange to call this planet 'Earth' when quite clearly it is ocean. Arthur C. Clarke

Friday, April 28, 2017

Winter and Spring quarters

It's time for some much-needed updates on my dissertation progress!

This winter I completed my third quarter as a TA for my favorite course: Invertebrate Zoology. Not only did I lead seven animal dissections, but I also baked seven animal-themed desserts for my lab students and held my own review session with lemon coconut doughnuts. I may be the only person in the state (or the country, or the world) who regularly uses snail-shaped muffin tins.

Animal-themed desserts I made last quarter; chocolate cupcake snails, ginger crabs, and assorted fruit tarts.

I worked hard to figure out how to extract and amplify DNA from all the snails from my field study so I can ID them by sequencing characteristic genes. Unfortunately, only two weeks ago did I get the PCRs working—I was hoping to do that much sooner. Thankfully, now the PCRs work, I have lots of amplified DNA, and I'm almost done with that project now. Next week I'll know which of two cryptic species were at my field sites.

Gel electrophoresis with long-awaited amplified 
snail DNA! You can see the DNA as the bright pinkish
dashes near the top of the gel. This gel is on a UV 
light so the amplified DNA, treated with ethidium 
bromide, fluoresces. Before winter quarter this
year, I had no idea how to extract snail DNA and 
use polymerase chain reaction to copy it a bunch
so I had enough to send to a sequencing facility. 
Now I've done it for weeks and weeks, and it's
really rewarding to see bright bands like that!
Notice how not all the blue dashes have bright 
pinkish dashes above them; that is because not all
the DNA samples amplified, and I have to figure
out (or guess) why.

This is a mini centrifuge for PCR tubes. The amplified DNA is 
in the green solution in those tubes. It took me only (ha) a 
month to figure out that only this special green reagent works 
with my snail DNA! Before that, I was trying other reagents 
with zero success.

I have an amazing team of efficient interns, and they collected lots of data on mussels from my OA experiment. After about 12 weeks, most of that collection is done, and now my two paid interns are preparing to present at a malacology conference with me in June! I'm excited to go with them and be marine scientists/ecologists/evolutionary biologists together. One of them just accepted graduate admission to UC Santa Barbara, so soon enough she'll be my colleague!

Planning field work has been a little stressful. I'm currently simultaneously planning two trips: one in Oregon in May and the other over the summer in California. On the Oregon trip, my collaborator (and great friend) and I will be collecting the last bits of info we need to finish a paper modeling the foraging behavior of dogwhelks. Once we have that info, we'll do a few lab experiments and then the model will be fully parameterized! I think it will not take long to write after that. This chapter of my thesis is particularly exciting to me because I came up with it apart from the direct suggestions of my main advisors, and it is my first attempt at using a computer model for something other than statistics. Usually, when I use models, the model gives credibility to the result; this time, the model is the result. 

My other field work will be executing a reciprocal transplant experiment in the intertidal zones at two sites. I am still not completely sure about what sites yet because I need to know what species I'm dealing with, so I'll need the DNA data first. As the clock ticks, the pressure builds, because I have to submit a scientific collection permit before I can do anything. Those can take months to get approved, but I basically only have June and July to do the experiment because the low tides are terrible in August and September. Luckily I have an intern working on writing up the methods for that because I am stressed and swamped preparing a paper for my committee members to read in a week!

A simple diagram of the reciprocal transplant design. Colors indicate site. There will be snails from each site at each site. The grids represent the cages containing the snails. Grey grids are control cages with no snails.

I have my first post-quals committee meeting in mid-May, and I really want feedback on the paper I'm writing about my field survey. I need to make it good because the more work I put into it, the more meaningful our discussion will be. I really want to submit the paper in June so it's out of the way. Since I'm not TAing this quarter, now is the time! 

More updates will come after my Oregon field work and the field experiment get started!