Expression Patterns of Codon Usage and Homopolymers in the 13-Lined Ground Squirrel

Introduction Why Squirrels? The 13-lined ground squirrel, scientifically labeled Ictidomys tridecemlineatus, is a furry squirrel abundant in Minnesota and much of the Midwest. Named for the alternating stripes down its back, the 13-lined squirrel is the namesake of the University of Minnesota Golden Gophers [1]. It lives in tunnels underground rather than in trees like its cousins the tree squirrels. The 13-lined squirrel is slightly larger than a chipmunk in size. Most interestingly to scientific researchers, the 13-lined ground squirrel is a true hibernator that sleeps from October to March in their underground den [2]. University of Minnesota Duluth, has long centered on hibernating mammals, especially the 13-lined ground squirrel. Dr. Andrews' lab is currently looking at identifying genes that are responsible for regulating the physiological characteristics of hibernation in the heart, skeletal muscle, and white adipose tissue (WAT) of the thirteen-lined ground squirrel [3]. The hope is that learning what genes are responsible for hibernation can benefit humans in areas such as hypothermia, ischemia/reperfusion injury, cardiac function, and organ preservation [3]. Squirrels are easy to study because of their relative abundance in the area and their size. They are particularly interesting to study because of the extremes their bodies go through during hibernation. Right before going to sleep (torpor), they pack on fat at a rate as high as 4 grams per day [2]. During torpor, their body temperature drops to around 0°C, oxygen consumption is 1/30 to 1/50 of the aroused condition and heart rate can be as low as 3-10 beats/minute, compared to 200-400 beats/minute when awake and active [3]. When they awake in March, they have lost as much as 1/3 of their body weight [2]. These extreme conditions would be deadly to humans, making their study of great interest. Since many of the genes identified in the squirrel also exist in humans [3], comparing the DNA that makes up these genes could shed light on what allows the squirrels to go through such massive physiological changes. For biologists or those in a medical field, this could lead to the development of new drugs or procedures to aid humans when bodies undergo similar physical stresses. Biology Background Even though 13-lined ground squirrels posses many of the same genes as humans, it is thought that they are expressed differently to allow the animals to hibernate [3]. Gene expression refers to the " detectable effects of a gene …