Slowly but surely, we are finishing up the PCR portion of the project. There are a few nemertean DNA samples that we are still struggling to amplify, but we have also started to analyze the data we have received from the company that sequences, or reads, our DNA barcode segments. When the DNA segment is sequenced, the data that we receive is in the form of two chromatograms per sample. We get two results per sample because DNA is double stranded, and the reaction that we use to sequence DNA, Sanger sequencing, only reads one strand at a time. We take these two complimentary strands and line them up using software called Geneious to ensure that they match, and no mistakes have been made. Once we have lined up the two strands in a “consensus sequence”, we check the sequence against Genbank. Genbank is a public, online database of DNA barcoding segments and the organisms that they belong to used by scientists all over the world. If another scientist has found the same species of worm as us and entered it into Genbank, we will find that our DNA sequence matches and know the identity of our sample. Unfortunately, most of our samples represent species that have not even been described, so we get very few species-level Genbank matches. We then turn to the database of Caribbean nemertean DNA sequences that the Maslakova lab has been compiling for the past few years. We compare our sequences to those that have already been categorized by Dr. Maslakova and her colleagues and are able to identify many more worms. The best part is when our worms do not match anything from Genbank or the unpublished Maslakova lab database. When this happens, we have found a new species of nemertean! So far, of the approximately 75 samples that I have sequenced for the gene CO1, I have found 30 different OTUs (operational taxonomic units, or what we call a species before it is officially described). Of those thirty OTUs, NINE represent new species that have never before been sequenced! I can’t wait to see what I find in my last 25 samples. Last weekend we visited Oregon State University’s Hatfield Marine Science Center in Newport, Oregon. All of us enjoyed watching a giant pacific octopus feeding at their visitor’s center as well as seeing their classroom and lab facilities. They have a particularly cool room dedicated to the microalgae that they feed their oysters with giant tanks of different algae species that were all different shades of green and brown. While in Newport, we also visited the Oregon Coast Aquarium where we all geeked out about the cool marine animals.
0 Comments
Leave a Reply. |
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
Categories |
Proudly powered by Weebly