Thursday, August 8, 2013

Meet Tiffany

Hi everyone!

I'm Tiffany Armenta, a new-ish graduate student in the Blumstein lab.

I've been at RMBL since mid-April and absolutely love it here. I've done fieldwork in the past but have never been at a field site for such a long time, so this has allowed me to become completely immersed in my work. Plus, the hiking and biking opportunities around here are exceptional :)

In addition to the standard observations and samples we collect when trapping, I am stabilizing RNA from the marmots in order to look at genes expressed in their blood. I aim to compare the expression profiles of different phenotypes in order to see how environmental conditions can affect the genetics of individuals and, in turn, how these profiles may alter an animal's physiology.

For instance, I think it will be interesting to compare marmots that consistently exhibit signs of high vs. low stress (based on behavioral and physiological data). Studies of other (mostly model) organisms show over-expression of anti-inflammatory genes and under-expression of anti-viral genes in stressed individuals so it will be interesting to see if these patterns persist in a natural population.

I am also interested in the underlying mechanisms that occur when an individual prepares to disperse, so I focused on collecting RNA from our yearling marmots this summer. These guys will likely be exposed to new pathogens during this journey and will travel much further than they ever have in their entire life, so I expect dispersers to show a different pattern when it comes to metabolic and immunological genes.

In order to do this, I have to first build the marmot transcriptome, which is basically just the transcribed regions of the species' genome. This may not look like anything special, but it took me months of quality control and program queries to get this figure, which shows RNA sequence data that aligns to the 13-lined ground squirrel genome.

The lowest window here represents the squirrel genomic sequence: exons are blue blocks and introns are the lines with arrowheads. The large middle window displays marmot sequence (from one individual) that aligns to the squirrel genome, with each line representing a unique expression of that sequence.

Note that the majority of the marmot sequences (small gray squares) align with the squirrel exons. This was the highlight of my week because RNA should only be exonic sequences, so this means I've done something right! Success!

The next step is to identify the genes being expressed based on homology in other organisms (such as the squirrel and mouse) and then to quantify expression values. So expect to hear more from me once I make another breakthrough...

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