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Mail Buoy
April 22, 2001

My name is Rick Anderson. I’m a student in Mrs. Heidenreich’s Life Science class.(Chinook Middle School, Lacey Washington). You talked about comparing animals in the Indian Ocean with animals in the Pacific. We are studying Genetics now and I was wondering what process you go through to analyze the DNA to see if the species are closely related.

Thank you.

Hi Rick,
Thanks for the great question. The process we go through is similar to what most scientists use to genetically identify and type of organism, whether it is a microbe, a plant, or an animal. After collecting our animals from the sea floor we dissect them and put their tissue into the freezer (at minus 80°C, which is 4x as cold as your freezer at home) or we put the tissue in alcohol.

At that point we need to extract the DNA and we can either do that out here at sea or we can wait until we get back to the lab. Essentially, it’s a procedure in which we rupture the cells in order to get the DNA out, and then we capture the DNA on special membranes while the rest of the cellular components get washed away. Then, we have to decide on what section of the DNA we want to sequence. In order to compare animals from one ocean basin to the next, we need to pick a section of DNA that has been sequenced before by other researchers, to build up a database of DNA fingerprints that can be compared.

To start, scientists in our lab usually sequence a 600 base pair region of the mitochondrial cytochrome oxidase gene. A gene is a section of DNA that codes for something, usually a protein. There is DNA (and genes) in both the mitochondria and the nucleus, but cytochrome oxidase is an enzyme that most organisms have in the mitochondria that helps to generate energy for cellular processes. The DNA that codes for this enzyme is what we target in the next step of our procedure.

After extracting the DNA, we only have a few copies of the DNA segment that we need. In order to sequence it. we artificially make more copies. We do this through the polymerase chain reaction (PCR), maybe you’ve heard about this in class. In this reaction, we use an enzyme known as polymerase to create new copies of our DNA and special primers designed for the COI gene to tell it where to start copying. The reaction takes anywhere from 3-5 hours, and requires special temperatures and other components in the reaction mixture.

After that we have to clean up our product to make sure that it is pure DNA (we usually use a kit to do this) and then we are ready to sequence the segment. In order to sequence the segment, we use fluorescently-labeled chemicals to light up the four different bases (A, G, C, and T) in the segment of DNA differently. Then we use a special machine that “reads” the sequences for us based on the kind of fluorescence it sees. In the old days, scientists used to label the bases with radioactivity and read them by hand, but we don’t have to do it that way anymore, thank goodness.

After we have our sequences, we go back to our database and compare our animal to others. In this case we will be comparing our animals from the Indian Ocean with others of similar species in the Pacific and Atlantic Oceans hydrothermal vents. In general, the more differences in their sequences, the less they are related. If two organisms have almost the exact same sequence, they are likely to be the same species. We have software programs that help us figure out these differences and make phylogenetic trees that help us visualize those relationships.

I hope this helps and that you can learn more about genetics from your teacher. It’s a very interesting and powerful tool that scientists can use to learn about organisms.

Keep following us on the website; there is more excitement to come.

Shana Goffredi

Hi Susan,
Hope things are going well there. I have a biology question (maybe for Tim Shank). I saw on the April 18 slide show, slide 5, the “Phymorynchus” snail. It looks very similar to the intertidal snail, Nucella lapilus. (dog whelk-formerly Thais, I think). Could you find out if this vent snail and the intertidal snail are related at all? Does this deep sea snail have a ‘drill’ like Nucella - the same groove is there in the shell. Wild!!

Carolyn Sheild
Clarke Middle School, Lexington, MA

Hi Carolyn,
There about 2 dozen families of marine snails living in deep sea and intertidal environments. The vent snail Phymorhynchus is in the family Conidae (Cone shells), and Nucella is in the family Muricidae (Rock shells). Both of these families have a radula (drill) with one to three teeth in each row. They are both scavengers.

Through comparisons of DNA sequences between these two families, we could address your question of how they are related. It’s is generally believed that the deep water Phymorhynchus has evolved from shallow water ancestor, but it is also possible that the invasion into vents occurred via deep-sea lineage. We observe Phymorhynchus at the periphery of dying vents, probably predating on molluscs and scavengers.

During our first days of exploration at the recently-discovered site at 24 degrees South, we have observed very few Phymorhynchus snails.

Thank you for joining in our discoveries at 25 degrees South and stay tuned for more as we begin bringing biological samples up from vents at 24 degrees South.

Tim Shank