Fernanda's Blog

First Blog

The sentence starter that I chose is "From my experience at Stanford, I've been thinking on my way home about..." The appeal comes from the fact that I spend about one hour transporting from home to Stanford and vice versa. So one could say I have plenty of time to think. But it's worth it.

Factually, I thinking about the phytoplankton located at the Western Antarctic Peninsula (WAP, http://www.eoearth.org/view/article/150106/). That remote and fairly small amount of land is helping scientists predict the effect of climate change. The south is becoming more populated by larger diatoms (specific type of phytoplankton, http://tolweb.org/Diatoms/21810) and zooplankton. Whereas the north is favoring smaller phytoplankton and zooplankton. Palmer station, one of the three United States own stations in the Antarctic, is located directly in the middle of both of these zones. It's close to this station where the samples the head of research team, Shellie Bench, has collected and will be using to explore her research questions. These include identifying the phytoplankton species located at WAP in relation to the time of the year and other weather factors. Just from looking under the microscope, which recently has been most of my job, some differences can be clearly identify.

On the other hand, I'm also thinking about other abstract subjects. For example, I understand that there was a technology barrier that prevent scientist from proving the existence of phytoplankton before recently. But I can't wrap my head around the idea that we thought we knew how the world worked without having studied these basic organisms. Phytoplankton are called the "plants of the sea" and produce about half of the world's oxygen. Yet it wasn't until recently that they were discovered. It doesn't surprise me the large amount of studies are researching phytoplankton. If these small, yet beautiful, organisms are changing then it can cause a snowball effect that eventually would get back to us. By studying them it can be predicted the effect of larger trophic level organism, such as penguins or whales or seals. I'm still amazed at how important the smallest organism—phytoplankton, bacteria, and viruses—can be towards the well-being of almost any other organism.

Second Blog

It has been brought to my attention that my previous blog post didn't describe the research I have been helping with. In order to fix that, I have included an introductory paragraph plus a reflection on my new experiences and thoughts.

I am currently working with Shellie Bench, a post-doc researcher, to identify the species of phytoplankton in the Western Antarctic Peninsula (WAP). We are also investigating any correlations between the types of phytoplankton during the year and during blooming seasons. To support such research there are two ways in which we asses the inhabiting phytoplankton. The first is looking at sample slides through the microscope and keeping record of our observations through photographs. Because phytoplankton obtain most of their energy by using chloroplasts to covert sunlight and nutrients into food and oxygen, by shining fluorescence light the individual organisms light up. In the few samples that we have been examining, we see mainly four types of organisms: centric and penate diatoms, cryptophytes, and flagellates. Just looking at the photographs it's hard to determine the exact type of organisms within each of those four larger families. This is where the second process--PCR--rises. The process involved in PCR allows us to extract and observe the actual DNA of the organisms living in WAP waters. After the DNA has been extracted successfully, it is send to a lab were it's read. From that lab we obtain the actual sequences that can be compared to current database to confirm the species of organisms that live there.

As an intern I have been involved in doing a lot of microscope photographing, DNA quantification, and have recently started doing PCR reactions. Because the main focus of the last two weeks have been in the DNA quantification and PCR reactions area, those will be the topic I will cover in this blog post.

Since the actual samples are hard to obtain, for practice we collected bay water. In the building we are currently working on, there are three devices that can read the amount of DNA present in all of our samples. Two of them use 450 and 515 fluorescence and another uses 420. The difference is that 450/515 only read organisms with chloroplasts where as the 420 can also read contaminants in the water. Our results showed low variation for small quantities of DNA but significant variation between larger quantities of DNA.

During this process I didn't quite understand the usefulness of knowing how much DNA is present in your sample. If the same question has risen in your head the answer is quite simple. It all has to do with the fact that a certain amount of DNA needs to be present in order for a company to be able to read your DNA. Even though the results we obtain sometimes had wide ranges, the overall results was enough DNA that if we wanted to we could send it to be read.

The second process we have been recently working on is PCR, the extraction of the DNA. Previous to this internship I had experience with PCR, but due to the limit of class periods my teacher had to shorten the amount of explanation needed for the process. For PCR, as well as with DNA quantification, most of the work done us is preparation. These process in reality take place inside a machine, some like PCR takes three hours and others like DNA quantification take three minutes. The overview of PCR is having a section of the DNA replicate itself multiple times. That can be achieved by having a solution with your DNA, primers and nucleotides, and then heating and cooling the DNA for separating and binding. After the three hours have past, a gel can be created, and ran with out solutions. The overall result should be a thick black band in each section where the solution was put plus an empty section in the negative control.

But it techniques and procedures are not the only lesson I have learned.

The first day we did DNA quantification, we decided to grab lunch while the samples incubated. We had planned to eat at Ike's sandwich, but we hadn't been aware that is had been closed for a while. The next closest open restaurant to was Cupa's cafe. When we got there the line was long and the whole cafe was overloaded. Apart from the long time it took to order, the machines were malfunctioning and the bread was running out. In overall it was a chaotic lunch, that ended with a nice salad and burnt caramel gelato bar. But the lesson was not that even though lunch started badly everything would turn out fine in the end, rather something Shellie mention. She said [paraphrasing] "All this bad luck from lunch will translate to a good result in the lab." That is what I took out of such experience. What's even better is it actually came true. For the second part of the process, there wasn't any mistakes or accidents that happen. Maybe scientist should have bad lunches more often.

Third Blog

Since this will be my last blog post, these will also be my lasts words about my experience as a summer intern at Stanford school of earth science. I’m glad I got to be part of such great community and experience.

There are two main aspects about working the science field that I will take away from this internship. These lessons are: the importance of accurately presenting your information and the usage of simple techniques.

1. Accurately presenting information. My supervisor, Shellie Bench, kept mentioning that the most important part of being a scientist is presenting your results. Results can be presented either by a presentation or a paper or both. Well-presented results will lead to others acknowledging the research you have been working on. Shellie compared research papers to the monetary equivalent in the science community. For my lab’s presentation, we worked through nine versions until we were satisfied with the content. But it was hard balancing background with the more advance procedures and results.
2. Common usage of simple techniques. For clarification when I say “simple” techniques, I mean techniques that high school students and even some middle school student would know about. For example my lab conducted PCR, which I was well acquainted with because of my genetics class in high school. But other labs used spectroscopy, which most students learned in chemistry of high school or even the second year of middle school. I know Jenny mentioned this after the presentation; I thought that she had a great point and I will keep learning techniques with this new mindset.