Blog Post: “CSI” for the Marine Ecologist 

powdered seagrass
Powdered seagrass tissue suspended in a detergent solution during the early stages of DNA extraction.

By Nicole Kollars

A patch of a seagrass meadow in Bodega Harbor, CA.  A patch this size may contain many different genetic clones, but you won’t be able to distinguish which clone is which just by looking at the plants.

The popular television show CSI: Crime Scene investigation follows the day-to-day drama of a team of investigators whose job it is to determine whodunit.  While watching the show, it is common to see forensic scientists in lab coats using a variety of oddly-shaped tools and instruments to extract DNA (i.e., deoxyribonucleic acid - the building blocks of life) from hair or saliva samples collected at the scene of the crime. After extracting and visualizing the DNA, the scientists can then compare their results to samples collected from suspected persons and oftentimes, solve the mystery. 

Fictional television aside, the advent of DNA technologies has changed numerous aspects of modern life.  For example, scientists study genetics for the purposes of solving crimes, advancing human medicine, conserving endangered species, and managing food production (i.e., agriculture and fisheries).  As a marine ecologist, I use these same DNA technologies to identify clones of seagrass, a flowering plant that lives in shallow coastal bays and harbors.

Seagrass populations reproduce through seeds and by producing genetic clones of the plants already present in a seagrass meadow.  Nearly two decades of research has shown that the genetic identity of a seagrass plant matters.  Some clones grow faster than others, while other clones are more resilient to stresses in the environment (e.g., high temperatures or a hungry goose eating the plant’s leaves).  Furthermore, seagrass meadows that have a higher number of clones in the population are overall healthier than seagrass meadows made up of only one or two clones. Healthy seagrass meadows translate to benefits for human communities such as healthy populations of commercially important fishes, reduced water pollution, and increased protection from coastal storms.     

Using a tool called a pipette to add a known amount of alcohol to each extraction sample.

However, a scientist cannot know the clonal identity of a seagrass plant by just looking at it.  Here is where DNA technologies become incredibly useful tools for the marine ecologist.

The first step is to extract the DNA from a ~ 1cm2 clipping of the seagrass leaf.  Extraction involves grinding the leaf piece up into a powder, adding a detergent-based solution to get the DNA out of the cells, and using various types of alcohols (i.e., isopropanol and ethanol) to get rid of any non-DNA material that hitched a ride out of the cell alongside the DNA. After extraction, we use a technique called the polymerase chain reaction (or PCR for short) to make many, many, many copies of the DNA.  Having many copies of the DNA makes it easier for an instrument to determine the unique DNA code for that individual sample, similar to how it is easier to tell the type of tea your drinking by taking a long sip versus a tiny taste. We repeat this process for any sample we are interested in, knowing that clones will have the same genetic code.  By using these techniques, we know that a 1m2 patch of seagrass can have anywhere from 1 to 15 clones!

CSI ("clonal seagrass identification") for the marine ecologist may not solve crime, but like our scientific counterparts in the forensics department, we can use DNA technologies to solve mysteries of identity.



Blog Post: Into the Deep End

Helen Killeen on RVMP night cruise

By Helen Killeen

The rest of the crew and I have various nicknames for the gear we use to collect fish plankton from the depths, and none of them are particularly complementary. Two months ago I found myself securing our nets for another deployment one last time. It was around 2am and I was thrilled that I would not have to scramble over nets and lines and hitch up the four heavy nets for another round of fishing. This was the last deployment of the last station of the last cruise for the year. Even with the rocking of the boat and the choppy seas, it only took me about five minutes to get things squared away. What a relief.

RVMPOnce I stepped away from the rig, ready to deploy the nets one more time 25 miles from shore, it flashed through my mind that doing this used to be much more difficult. On the very first cruise, a year before, it took three of us upwards of twenty minutes to get the stupid nets to hang correctly. To make things worse I was so seasick I could hardly keep myself upright for more than a few minutes at a time, let alone manage a crew much more seasoned than myself to conduct a complicated scientific sampling protocol. When we docked at the end of those first few trips, I felt sure that I was not the right person for the job and was sorely aware of my inadequacies as a scientist and leader.

What helped me through those first few trips was recalling moments when I’d felt similarly unprepared and inadequate. After college I took a position as a high school teacher. The first few months were similar to what many first-year teachers experience: a total mess. I couldn’t manage the class, I struggled to craft lessons, and stay afloat in a sea of paperwork. However, as the months wore on, I stopped making the same small (and sometimes big) mistakes over and over again. Prior failures turned into valuable experience that gave me the confidence to make and carry out my decisions. I desperately hoped that the same would happen if I could stick it out through just a few more night cruises.

catchThe only way I was going to make it though was if I stopped sweating every little mistake. If I stopped feeling like a failure every time I didn’t set the computer up right, or didn’t hit the right target depth for a sample, or made the wrong call on the weather. So I decided that I would need to make a conscious, painful effort to let the mistakes go. I would focus on lessons-learned, and take time to reflect on what I was doing right.

There are many elements to success in graduate school: a network of peers, strong mentors, and an inclusive academic community. But I am learning that no one escapes without a healthy dose of failure. And it is in part how we choose to respond to these failures that determines whether we are able to overcome obstacles and become better scientists. While I’m glad I won't have to clamber around a boat in the middle of the tumultuous nighttime sea for a while, I’m grateful for the opportunities to fail that doing so over the last two years has given me.