Diversity of Animals in the Ocean
Most of us are aware of the great diversity of animal life that we see around us. The vast majority of animal diversity however can be found in the ocean, and we are often unaware of the types of animals that live there. Each year many new species are found living in the oceans. Many of these animals are benthic as adults and so live on the ocean floor, or other substrates in the sea. For example, a new species of bristle worm was recently described that lives on whale carcasses!. These benthic animals however often have a larval stage that swims within the plankton, sometimes for many months, before undergoing a dramatic metamorphosis into their adult forms. The larval forms often look completely unlike the adult forms.
When trying to understand the relationships among these animals, it is important to include all of the life stages in the analysis. Often times the adult stages can appear very derived and different in morphology from the other members of their group. In these cases the larval form can provide important information about the relationships among these animals. For example, the similarity of barnacle larvae to the larvae of crabs was the clue that allowed scientists to realize that barnacles were crustaceans.
Many marine larvae are easy to grow in the lab and so have become model systems to understand development. We can observe their development under the microscope and manipulate the embryos in various ways to help understand more of their normal development. Thus many marine animals, including sea urchins and sea stars are model systems for understanding the genetic control of development and cell morphogenesis.
The Visit to the Labs @ Carnegie Mellon University
During your visit you are going to have a look at some marine larvae. These have been obtained from a plankton tow from around the Cape Cod region collected by the Marine Biology Laboratory staff. A fine pore size net is towed behind a boat through the water column in the ocean. We’ll take a look and see what was recovered.
In the Microscope Room
You will look at embryos and larvae in the sea water dishes. As these larvae are very small, usually less than 1mm, we will observe them using a microscope. You can have a look at this website http://virtualurchin.stanford.edu/microtutorial.htm to get an idea of what we will do. You should see many different types of larvae. Can you identify any of the species?. What similarities can you see between some of the different larvae?
You can spend some time looking at these larvae. Then pick one type that you would like to examine more. Take some time to look at it, document what you see and then photograph it. Keep all of this information.
You will then pick one individual of your larvae to use for a DNA extraction.
You will also have a chance to look at some of the adult invertebrates that we have on display. Also take a small tissue sample from these animals to use for DNA extraction.
In the Molecular Biology Lab
Extract DNA from your sample
You will then extract DNA from this sample. Follow the procedure provided by your lab teacher carefully. We are using a quick method that won’t produce a very pure preparation of DNA but it will be good enough for our purposes. For more details you can look at this website http://www.sigmaaldrich.com/life-science/molecular-biology/dna-and-rna-purification/extract-n-amp-tissue.html
Amplify the 18s ribosomal gene
All living things use common sets of genes for some of their basic cellular processes. You are going to use a polymerase chain reaction (PCR) to amplify two regions on the 18s ribosomal gene. This gene is found in all organisms as it is encodes a protein that is needed to translate RNAs into proteins. You will set a PCR with two set of PCR primers to amplify a 400bp region and 600bp region of this gene.
Follow the directions of your lab TA closely as you set up the polymerase chain reaction with your extracted DNA
Look at the PCR amplification using gel electrophoresis
If there is enough time you will get a chance to look at the amplified product. If we run out of time, we’ll look for you and send the pictures onto school.
Sequencing your PCR amplification product
We will set up a sequencing reaction using your PCR amplification product and obtain the sequence during the week.
Back at School
We will give you files of the sequence that we obtained for your 18S genes. The 18S gene is quite conserved, i.e. it is very similar in different species. However like all genes, 18S will slowly acquire mutations. The longer it has been since any two species last shared a common ancestor – the more time there has been for mutations to arise in the sequence. Therefore more closely related species will have more similar sequences. We should be able to identify your larval species based on its 18S gene sequence.
We will use this website (http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastHome) to find out what your sequence best matches to and to find out a little more about the organism that it came from.