We are past the halfway mark, and everyone’s projects are in full swing! Adrian and I are spending our time in the lab troubleshooting pesky DNA samples. This is the less glamorous side of DNA barcoding. Sometimes, PCR reactions do not work correctly, meaning they do not amplify the correct section of DNA, on the first try. This requires changing the variables of the reaction, one at a time, little by little, until you finally get a enough of the same segment of DNA that is the right length. Why is the length of the DNA segment important? The length of the DNA segment is how we tell whether we have amplified the correct section of DNA, in my case the CO1 gene. We use a technique called gel electrophoresis. This method begins with placing the PCR-amplified DNA in the well of a gel. Next, an electrical field is introduced. Because DNA is negatively charged, it is moved through small pores in the gel by the electrical field. The smallest DNA segments move the fastest through the gel’s pores while longer DNA segments take more time to be pushed through the gel. When we take a picture of the gel after some time has passed, we know that the segments of DNA that have traveled the farthest, are the smallest. We use a “ladder” that is full of DNA segments of known sizes to compare our samples to and quantify their lengths. Using this technique, we can tell which PCR reactions worked (there is a band of DNA approximately 658 base pairs long – the size of the gene CO1) and which did not (the band of DNA indicates a segment too long or too short, there are multiple bands, or there is no band at all). We REALLY want there to be a single, bright band of the correct size, but if there is not, we keep trying until we achieve that result from our gel electrophoresis. We spent some time crabbing in the evenings this week. It turns out permits very inexpensive for Oregon residents (thank you Steven) and you can catch quite a few crabs, mussels, and other shellfish. It was fun to watch the crabs and throw the smaller ones back. Renee is teaching us all about crabs because her project requires catching a lot of them. She is doing a predation experiment where she observes which species of smaller crabs (Dungeness or invasive green crabs) that a larger species (red rock) prefers to eat, by putting them in containers and waiting until they eat each other.
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AuthorHi! I’m Megan Powers, a fourth year Biology and Environmental Sciences student at the University of Iowa. Throughout my summer at OIMB, I will be working with the Maslakova lab to assess Nemertean diversity in the Caribbean. Archives
August 2019
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