"Conversation with myself or a couple of strangers …."
by Dasia Simpson
"Poetic justice… poetic justice", the sweet sounds of Kendrick Lamar flowing through my headphones as I franticly decipher this extraterrestrial language called "R."
What am I doing exactly? Oh, it's just some differential gene expression analyses, haha. Okay, now you wonder how I got here and what EXACTLY I am doing. Okay, let's start from the beginning. Do you know stressful environments like climate change affect your "insides?" For example, "Insides," meaning your DNA, the molecule that is vital for your health, reproduction, and growth? My research focuses on the conceptual idea that organisms around us, like lizards, are experiencing natural stressors that can affect their insides. Another way to look at it is something like that 6:45am alarm clock that has the intention for you to make it to 8am lab meeting or game day traffic that contributes to your increased levels of cortisol (known as the stress hormone, another type of "inside"). The concept of stress is difficult to study because there are so many factors that can contribute to a stressed individual. Nevertheless, it is important to understand stress and how we respond to stress.
So long story short, I heated up some lizards or unleashed an avalanche of fire ants unto them…. okay, this sounds like torture, Nah. I'm really a good person. Here is what I really did. I'm interested in how genes respond to environmental stress, such as that annoying clock or never-ending traffic. Specifically, I'm interested in how genes respond to stressors in natural environments in fence lizards. These little critters are native to the United States' southeastern region are constantly exposed [CU1] to increasing temperatures or subtle yet excruciating fire ant apocalypses. On a gene level, how animals like fence lizards respond to different types of stressors is still poorly understood.
In a recent experiment led by collaborators, fence lizards exposed to acute heat stress of 109.4°F (which is considered to be hot for lizards) for up to 3 hours, or fire ant stings (receiving ~10 stings) had elevated hormone levels compared to control groups (the "unbothered"). My research builds upon these results to test whether these same stressors at the gene level show similar patterns seen at the endocrine level (elevated hormones) or whether each stressor's stress responses yield entirely different outcomes. To do this, I isolated RNA, a single-stranded molecule that basically stole DNA's prom dress look with a few different alterations from each lizard liver. After some data sequencing and processing steps, those isolations allowed me to perform RNA-sequencing, a method to analyze "big amounts of data" to address biological hypotheses or questions. Oh, I hinted at where my interests lie, but my actual research hypothesis is whether Fire ant envenomation and acute heat stress will have different gene-level responses.
Finally, I told you a brief introduction, why it is important, and what I am testing… now, back to Kendrick and differential gene analyses. I fed my RNA-seq data into R, a computer program for statistical analyses and data visualization. This program, along with an R "package," think of it as Mario party cartridge (R package) to your Nintendo DS (R or R studio), allowed me to do a data analysis method called differential gene analysis, where I compared and contrasted the expression of different genes in each lizard in response to both stressors relative to the control group (hint-- the unbothered lizards).
My results were pretty interesting. Lizards who were heat stressed had many genes expressed, whereas lizards exposed to fire ants had little to no response. Was I absolutely, positively shocked? Yes. Did I validate my samples and their corresponding treatments? Yes. Did I re-analyze my data one more time to make sure Kendrick didn't steer me wrong? Yes. These very different stress responses add to the ever-progressing field of stress research. It is important to have an integrative approach such as combining multiple techniques or observing different types of your "insides” to gain a full perspective of stress responses.
Acknowledgement: This work is supported by Auburn University Startup funds and was done in the lab of Dr. Tonia Schwartz in the department of Biological Sciences, Auburn University.