My Final Week!

It is hard to believe that it is the tenth and final week of my internship. I am spending it on the island, reminiscing with the other interns on the summer we have had as well as finding things to do to fill our time left. On Tuesday evening we presented our summer work to two classes at the lab right now: one being a high school class and the other incoming college freshmen. The presentations went well and it was a relief to give them. In addition, it was nice to describe what we have been working on all summer to people who have been somewhat in the dark on our projects.

This week has been warm so we have spent it swimming off the dock and trying not to move around too much to stay cool. We have noticed that many of our belongings feel a bit moist, an indication of the high humidity that has plagued us the past several days. Luckily, it broke in a thunderstorm last night that cooled the air to our delight. It was not as exciting as the storm that shook this island to its core a few weeks ago. It was during that storm we realized none of the buildings on this island are sealed against water. Clever details (or lack of details, one could say) put forth by the builders. Kudos to them.

It is a bittersweet ending. I will miss the serenity and the distance this place maintains. Being the only group (aside from a few private residences) residing here, we enjoy consistent peace and quiet. One of the very first days the assistant director, Jim, who has become a great friend to all of us, said that observing the nature here was better than any reality TV show. While I don’t watch reality TV, I agree with his statement. Watching the gulls interact with each other, even when they viciously attack baby chicks, is fascinating. We get to be up close and personal with the wildlife here, which is unique.

We had our last Sunday brunch, famous for its size and calorie content, this morning. Tomorrow we take the boat from the island to Portsmouth and depart for home. It is exciting but I leave a piece of myself in this place.

Some photos from our last week:

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A juvenile gull who we’ve called, Snacks, hanging our in our lair. This gull was abandoned by her parents, her father passing away from old age and her mother going senile. Snacks takes refuge from her crazy mother with us and looks for food.

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One of the private residences at dusk. The house looks a little sinister to me. I think it would make a great setting for a story.

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Addison, one of the interns, hugging a giant terrarium she made. She wants to take it home with her, but it is heavy and we are not sure if the staff will let us put it on the boat. But we are concerned no one will water it if we leave here!

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Ossian, one of our captains, showing us how to tie up the sail on the lab’s sail boat. He took us sailing yesterday, my first time ever going!

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Another picture of us sailing. In order from closest to the camera: Meg, me, and Mila. It was a little cold and rainy, which explains the grey skies behind us and our frizzy hair.

It has been an honor working here this summer. I am sad to say goodbye, but hopeful for an opportunity to return in the future. Thanks for reading!

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My 9th week! (and a summary of weeks 5-8)

Hi everyone! I apologize for my recent lack of posting. Exciting things have occurred in the last few weeks. I have wrapped up doing DNA extractions with a grand total of over 100 samples of DNA to be sequenced. This was achieved by doing 24 extractions per day, which takes about 8 hours at Sarah pace, meaning being unnecessarily careful and slow yet still capable of making mistakes. I have a few photos of the lab work I’ve been doing that I thought would be interesting to share!

 

 

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Here is a photo of a gel than I ran. I explained previously that we run gels to see the length of the DNA. Shorter DNA pieces will travel farther than longer pieces in the same amount of time because smaller sections can travel more easily through the pores of the gel. Loading the gel is a therapeutic exercise for the perfectionist. It involves mixing buffer, dye, and DNA into a bubble and then steadily pipetting it into the well. The well is simply a hole in the gel and is what you see where the blue squares are.

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Here is a photo of the bubbles in which we mix the buffer, DNA, and dye.

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As I mentioned before, we create an electric field through the gel to separate the DNA. Here is a picture showing the DNA after several minutes of generating the field. The blue squares look blurry because some of the DNA has moved.

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We also took photos of each of the shells from individuals we collected at our sampling sites. This was the set-up of the photoshoot. The idea was to maintain the same settings for each photo so as not to bias the color because the lighting was changed or there was a shadow in the photo. The set-up is a white weighing dish with two “octupus” lights (I call them this in my head) that we use to illuminate dishes we look at under the microscope. The dish is sitting on a styrofoam box I found in the room to get the shell closer to the camera. Rather ingeniously we poked a hole in the white dish and the box so we could insert the test tube that have the shell identification number label on top so when we later reference the photo we know which individual we are photographing.

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Here is another angle of the photo staging.

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Unrelated to my project, here is a picture of an awesome crab we had in our sea tables at the island lab. We have sea tables that are filled with salt water so we can collect organisms from the ocean and study them later. We return them to the ocean after researching them, usually. This crab was collected to feed a gull chick whose was abandoned by its parents. Well, to clarify, one of its parents passed of old age and the other seems to have gone senile and is unable to care for its chick. I like this picture, though, because I didn’t zoom in at all on the crab. It was leaning against the wall of the table and I faced my phone camera directly down at it so it appears the camera and the crab were very close in proximity, because they were!

Gulf of Maine Storm

This summer has also been a very dry one. We haven’t been receiving a lot of rain. Fortunately, a couple weeks ago was a massive storm that brought sheets of rain, hail, and high wind speeds. In turns out the houses on the island are not well sealed so we watched in astonishment as water seeped in cracks between windows and the wall and splashed in from under the door. It also turns out not every window closes very easily. Needless to say, it was fun to watch but water had to be swept out of the rooms after the storm ended. Check out the video above, made by Daniel, a TA for one of the classes being taught at the island, who set up a time lapse. Notice in the beginning a boat traveling towards the storm and upon sight of the unfriendly clouds made a U-turn and zipped off.

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A nice sunset ­čÖé The photo does not capture the various hues of yellow and orange but there was quite a range! I love this view.

 

Thanks again for reading my blog ­čÖé

 

 

 

 

My fourth week (and into my fifth!)

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A ship seen from the boat going back to the mainland from Appledore!

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Sunset on Star Island, which neighbors Appledore. We visited to buy ice cream (and sorbet). There is a hotel on Star that seems to be very popular.

Hard to believe I am already midway through my fifth week! Last week and this week has been consumed with DNA extractions. A few days ago I ran through the protocol alone and hit a few bumps in the road along the way, leading to a failed attempt at an extraction. Luckily, the day was not wasted because I am feeling increasingly more comfortable going through the steps by myself!

We have run into an interesting problem, though. After extracting the DNA, we check the concentration. Our threshold for a feasible concentration is 100 ng/╬╝L. After checking the concentration, we run the samples on a gel to see what how long the DNA is that we have retained from the snail and visualize how much of it. Unusually enough, we are not always seeing bands! This is odd because we have measured the amount of DNA present, so we are confident that there is a considerable amount in the sample.

We have a few theories going into this:

  1. While loading the DNA mixed with buffer and dye into the gel, we missed the well. When we make a gel plate, we add a plastic fixture that creates dips in the gel. In these dips, we pipette the colored sample. We have 10 of these dips that run along one edge of our square gel plate, creating 10 lanes. When we run an electric current, the DNA should move along the lane. If we missed the well, the sample will diffuse throughout the 1XTAE buffer which we have poured all over the plate. This would cause us not to see a band.
  2. The NanoDrop machine incorrectly read the concentration of our samples and it is really much lower than we originally measured.
  3. Before loading the gel (pipetting the sample into the well), we add 1μL of DNA to a 9μL drop of buffer and dye. Then we pipette the entire 10μL drop into the gel. We are now trying mixing the drop before we load. Perhaps the DNA was not properly mixed with the dye and was moving in the gel without it, causing us to not see anything when we shine UV light on the plate.

Otherwise, we have no other competing theories. Today we have isolated the samples that didn’t show up in previous attempts and we are running them altogether. Will update with the results!

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Example of a lane with any band, despite the sample having DNA present. The names of the extractions represent the site sampled from and the number of the snail. Notice the 6th lane looks as though it has a smear. This indicates a high amount of DNA. My mentor, Dave, says smears are characteristic of running genomic DNA on a gel.

UPDATE:

I’m sure my audience is on the edge of their seat waiting for the results and HERE THEY ARE!

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So oddly enough, all the samples produced bands. This is great news! Except that we threw a couple samples away because they didn’t show up on the gel. Besides that, it is good news. The fourth lane is really bright because we doubled the amount of DNA that we added and it showed up very clearly. We are thinking the concentration of that one was comparatively lower to the other samples but I will have to double check.

My third week here

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Beach rose in the Celia Thaxter Garden on the island!

Hello again! I am back to update you with my project’s progress. This week I finished up processing samples. We now have 6 boxes of snail flesh from each of our sampling sites and six boxes of their corresponding shells. The next step is extracting DNA from the individuals we want to send off to the lab for sequencing.

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The processed sample from the tide pool on Appledore Island by the Dive Locker (DL).

DNA extraction involves a few steps:

  1. First, we slice off a small piece of the body and clean off the ethanol it has been stored in. We add Proteinase K, an enzyme that breaks down the proteins in the sample. This must incubate for a little while until all the proteins have been completely digested. You can tell this has occurred when you can no longer see the piece you placed in the test tube.
  2. After digestion, we add Phenol, an aromatic chemical that we use in the hood to prevent inhalation. Phenol purifies the nucleic acid by further eliminating the proteins and lipids in the sample.
  3. Afterwards we centrifuge the test tubes. This creates two layers: a lower phase of lipids and proteins and an upper phase of nucleic acid (DNA). The DNA ends up in the upper phase because it is less dense than the proteins and extraneous material. We carefully pipette the nucleic acid off so as not to get any of the lower phase in the pipette.
  4. Then we add isopropanol. DNA is insoluble in isopropanol so when we subsequently centrifuge the samples the DNA forms a pellet. After this we can decant the isopropanol, leaving just the pellet behind.
  5. Then we suspend the pellet in TE buffer, which prevents changes in pH from occurring.
  6. To see how well our DNA extraction turned out, we remove a small amount from the solution, add dye, and run on a gel. Gel electrophoresis involves adding DNA into lanes in gel over which a charge is run. DNA is negatively charged so it is attracted to the positive end of the charged gel. Small pieces of DNA travel faster than larger pieces of DNA because they can fit through the spaces in the gel. After you run the gel you can see the lengths of the DNA pieces and get an understanding of how much DNA you added.

The upcoming weeks will involve mostly doing DNA extractions. In addition, the assistant director of Shoals Marine Lab, Jim, managed to find some Bryozoans! This is exciting because I found some but they were not very clean which could affect DNA extractions, making them impure. We will transport the bryozoans from Appledore in sea water and peel them off the kelp in the lab! We plan on sequencing these Bryozoans, as well. They have not been previously sequenced before.

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My favorite color morph of obtusata snails. I like the stripes! I am curious what causes such a strange morphology.

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Membranipora, a genus of Bryozoan under the microscrope!

Bryozoans form colonies which serve different purposes, such as feeding, reproduction, or excretion. These colonies are called zooids. They use a lophophore for feeding, which is made up of cilia that catch particles in the water and bring it back to the organism. Lophophores are typical of Lophophorata, a collection of three major animal groups. Lophotrochozoa is the phylum to which Lophophorata belong (thank you, freshman general biology).

I will update more next week! Here are some photos that I have taken this week (unrelated to my project):

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Pretty sunset

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Gull chick

My first week on land! (Well, at the lab to be specific)

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View from the porch hammock on a rain storm over the water. Very cool to see from the island! Rain on the island is welcomed to add to our store of freshwater. Unfortunately, the rain can negatively affect the young gull chicks who are susceptible to hypothermia after a rain storm.

Hi everyone! After spending one full week on the island, I returned to the mainland to move into UNH where I would be spending the majority of my summer working in my mentor, Dave’s, lab. I brought back my six samples in test tubes frozen on dry ice. We stored them in the -80 degree centigrade freezer to preserve them.

I spent most of this week processing my samples. This involved removing an individual gastropod from a test tube and separating the body from the shell. I placed each in a test tube and wrote corresponding numbers to keep the pair together. I was surprised at my reaction to the removal of the body. I did not expect to be repulsed by the body but it was a procedure to which I needed to become acclimated. Imagine pulling a just-frozen blob of mucus out of a shell with a pair of forceps. Unpleasant, yet necessary.

The bodies were stored in 95% ethanol and placed back in the freezer, whereas we stored the shells in no particular medium and also stored them in the freezer. This was done to prevent discoloration of the shells, which we want to keep for later so we can use them to help us decide which individuals to sequence. In addition, we want to look at the shells to quantify their color. We are still in the process of deciding our method of giving their shells color values.

This week I also practiced extracting DNA and running it on a gel. I have included a picture of the resulting gel:

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The left-most lane is our ladder. The next four lanes are two individuals from two different sites. The second lane from the left does not show any DNA, indicating that we made a mistake. Luckily, the other lanes came out pretty clear, which was nice to see. The middle lane is pretty smeared, probably because we sliced off just a bit too much off that particular body. We realized our mistake after waiting overnight for the DNA to digest and seeing that it was still not complete. We moved forward anyway but something to keep in mind when we do more DNA extractions in the future.

Right now I am expected to go back to the island once a week for intern meetings in which we talk about our progress and practice giving presentations to the group. I expect to be back on the island this weekend!

Thanks again for reading this week ­čÖé More next week!

 

 

 

 

 

 

 

My first week on the island!

IMG_0712.jpgThe sun behind the clouds as seen from the shores of Appledore

This post marks the end of the first week of my internship! Four of the other Shoals Marine Lab (SML) interns and I arrived on Monday and began exploring the beautiful shores and woods of Appledore. We quickly learned to avoid the unfriendly gulls who currently have baby chicks scampering about or are incubating their eggs. I got to meet my mentor, Dr. Plachetzki, and we discussed the intricacies of this project. We agreed I would spend most of the week collecting samples to bring back to the University of New Hampshire (UNH) where we would begin extracting DNA to be sequenced. We decided upon five organisms we were interested in collecting: Littorina obtusata, two Bryozoan species, a Haliplanella anemone, and some Chaetognaths.

This week I collected obtusata at different locations around the island. I observed that sheltered locations harbored more yellow-shelled snails whereas the snails of exposed locations were remarkably darker. In exposed locations, the yellow individuals I collected were usually much smaller in comparison to the darker individuals. My main concern has been keeping them alive and in separate containers in the lab. I had a couple frights caused by snail escape attempts and knocked-over bins but have seemed to keep the snails in their rightful places overall. Tomorrow, Dr. Plachetzki will travel to Appledore with dry ice so we can freeze them. Then we will bring them back to UNH and start working on extracting their DNA in his lab.

Here are a couple pictures of the snails from different sites in their  respective observation dishes:

IMG_0752I must have taken the photo immediately after transferring them from their container to the dish because none have managed to crawl up the sides yet. The tide pool I sampled these individuals from is a sheltered location so the shells seemed to be of a lighter color in general.

IMG_0754Half-Tide Ledges is an exposed site. Most of the snails I collected there were darker. It is harder to ascertain the differences in color when they are crawling all over each other.

Hope you enjoyed my first post! I will share more with you as my internship progresses. Have a wonderful week!