Thursday, April 28, 2011

Early season field work!

This is my favorite time of the year, everything around is so white and quiet that you can almost hear the beat of your heart!

Photo: Adriana Maldonado

Every day, when the snow storms give us a chance we go out to look if the marmots have wake up. This is our first day working, we manage to go out and recognize some marmot's burrows under a very snowy day.

Friday, April 22, 2011

April: time to go to the field

Every year by mid-April we start to look for marmots. However, our study site is around Gothic, Colorado and our lab is at UCLA, Los Angeles, California. So April is also the time of our migration from Californian beaches to Colorado mountains. The trip from LA to Gothic is approximately 1000 miles and take two days.
As the landscapes along the road are so beautiful, some of us take their time and enjoy their trip.
I took 6 days to go from LA to Gothic.During the trip,
I slept in Mojave National Preserve,
I drove along the road 66,
I was amazed by the Grand Canyon,
I hiked around Sedona,
and I enjoyed the Painted desert.
Since we arrived in Colorado, we have not see any marmots and we had 2 snowstorms but this is for another post.

Photos by Julien Martin

Wednesday, April 13, 2011

From marmots to hermit crabs!

My introduction to marmots occurred in the Fall 2010 quarter as I contributed to Matt’s study, watching videos of marmots in an open field experiment and scoring their behaviors. Working on this project inspired me to think about the entire research process, including the steps it took to create all the videos I was watching as well as the steps that would follow after all the marmot behavior had been scored. My project was only a small part of this complex process. I made a decision that before I graduated, I wanted to conduct my own research and experience the whole process from beginning to end.

Since it would not be possible to work with the adorable marmots, at the beginning of the Winter 2011 quarter, Professor Blumstein suggested an animal behavior project with hermit crabs, and as a huge fan of crustaceans, I could not have been more excited. My own hermit crab project focuses on animal personality and behavioral syndromes. Animal personality is not the same “personality” we use when referring to humans; instead, animal personality refers to consistent behavioral differences between individuals. Personality has been identified in many vertebrates and invertebrates, including aquatic hermit crabs. In my experiment, I am looking for evidence of animal personality in the terrestrial hermit crab (Coenobita clypeatus). I am in the process of performing four separate experiments in which I will quantify their behavior in order to study the variation between individuals and the consistency of this variation over multiple trials. In addition, I will look for evidence of behavioral syndromes, which refer to correlations of the consistencies in the behavior of the population across different contexts.

I am working in the lab of Professor Aaron Blaisdell. With the help of Professor Blaisdell, Professor Stahlman, grad students and post-docs, and of course Professor Blumstein, I aimed to study personality in this species of hermit crab and identify correlations that may exist in their responses to the various situations I expose them to.

My first experiment was a manual inversion test. I flipped the hermit crabs over, so the aperture of their shell faced upwards, which caused them to retract into their shell. I measured the time it took for each crab to emerge from its shell.

This is a screenshot from an inversion video. The white box shows that the detector program identifies enough red pixels of the crab to determine the crab has re-emerged. My second experiment was an open field test. I placed the crabs in a 100 x 100 cm open arena and measured variables such as the latency to emerge, distance travelled over 5 minutes, and maximum speed.

This is a picture of the path that one of the crabs travelled in the open field test.

My third experiment was a visual predator habituation test. I placed the crabs in front of a monitor which displayed an image of a hawk that appeared to swoop upon the crab. Each subject received repeated trials until they habituated to the hawk and did not display a hiding response. I measured the latency to emerge between trials, latency to hide after the hawk first appeared, and how many trials it took for crabs to habituate to the predator.

This is a picture of a crab that emerged from its shell in front of the monitor.

This is a picture showing the crab hiding because it saw the image of the predator (huge picture of hawk on right).

I have not yet completed my fourth experiment, which is a shock test. I will give hermit crabs a light electric shock using a Skinner box to initiate a withdrawal response. I will then measure the latency of the crabs to re-emerge.

I am beginning to analyze my data, which does seem to suggest consistency in individual behavioral variation across trials, i.e. personality, as well as some cross-contextual correlations. I look forward to further analyzing my data and finding more interesting correlations in hermit crab behavioral responses. I feel proud that my experiment is a small step on our way to understanding why this behavioral variation is maintained. Taking advantage of the opportunity to do an independent research project was a great decision. It has been a lot of work, but an extremely rewarding experience and I am excited to continue working with the hermit crabs and share this experiment and my results at multiple upcoming poster sessions.

Monday, April 4, 2011

Attack of the clones!

As I've discussed in previous blog posts, I am working in the lab to characterize major histocompatability complex(MHC) genes in yellow-bellied marmots. These genes code for molecules that recognize and bind proteins floating around in and around our cells. The MHC complex distinguishes between self and non-self proteins, and initiates an immune response when a non-self protein (e.g. pathogen) is detected.

MHC proteins must therefore be able to accurately differentiate a wide array of molecules and pathogens specific to the population of interest. These genes are therefore the targets of enormous selective pressure (making them a great model for evolutionary genetics studies) with numerous, ecologically important consequences. An individual's MHC geneotype may determine how it chooses mates, how it responds to parasites, and even how long it lives.

So, that all sounds great. But how do we actually determine MHC genotype? Well, we have to sequence the DNA of each individual marmot at this particular locus (i.e. site on the genome). However, when we sequence using traditional Sanger sequencing methods, both copies of the gene (the one you inherited from mom and the one you inherited from dad) are pooled in the same reaction. So, if your alleles at this locus looks like this...

from mom AGATT
from dad AGAAT

...the sequence I'm viewing after Sanger sequencing looks like this...

AGA?T where ? is T and A

If I then asked you (after showing just the Sanger sequencing output), what are the possible sequences for this locus? You could easily reconstruct mom and dad's individual alleles based on simple ideas of segregation. But what if I showed you this sequence...

AGA?T? where ? is T and A...becomes a bit more complicated, right?

There are more than two possible alleles in this case, so was mom AGATTT and dad AGAATA? Or was mom AGATTA and dad AGAATT?

Now imagine that you are working with
sequences that are hundreds of base pairs long with 10-20 variable positions. How could you possibly figure out the alleles present in an entire population of marmots?

The answer is cloning. I take my PCR product (containing many copies of both sets of alleles) and stick it into bacteria that only accept a single copy of the gene at a time. I plate and grow these bacteria into colonies (i.e piles and piles of clones containing the same, single allele from my PCR product) and sequence this DNA to determine individual alleles. To ensure that I have sequences of each individual allele, I must grow, pick, and sequence many many colonies (see below for a small fraction of my clone army!)

Conveniently, the bacteria we use are designed with the PCR product insertion site in a gene that causes them to produce a blue color. Therefore, colonies that have accepted the insert (and are now part E. coli part marmot) turn white, while colonies that have not accepted the insert retain their blue color (see below). This makes the clone screening process much more efficient, though it is still a time consuming and labor intensive process.

And in the end, if all goes according to plan, I am left with sequences of individual alleles that can be used in analyses, as well as lots and lots of marmoty bacteria.