Warning: extra long blog
To wrap up the internship, the interns wanted to make sure we completed all the activities that were on our checklist. This included going to the South Slough Visitor Center and hiking on the trails (again), and picking berries. We also wanted to have a charcuterie on the beach. This week marked the grand finale. We wrapped up posters and any lab work. In the lab, all sequences and trace files for Oman and Red Sea were uploaded. The lab fridge and freezer was also cleaned out and all samples were organized. We also streamlined our data and spreadsheets, making it more convenient for handing off the data. Ethan and I also submitted our abstracts to the SICB conference in January (yay!) In terms of posters, the finalized product was due on Tuesday at 3 pm and printed on Wednesday. The interns spent the whole weekend and Monday working on our posters and addressing feedback we got from our mentors, Richard, and Maya. To continue our almost daily movie tradition, we watched two horror movies: Us and Get Out. We also watched Glass Onion and Howl's Moving Castle. This meant many trips to Davey Jones to stock up snacks for the movies. To celebrate that our posters were complete and printed, and Tara, Madison, and Randi came back from their trip, we had a charcuterie at Bastendorff. Naia is a pro and worked her magic to make a beautiful board. We got cold so we played ninja and it was really nice to not worry about any work. This week felt really slow and unproductive because after finishing our posters, there wasn’t much left we needed to do. It also felt strange not having any work or deadlines. The poster presentation on Friday went better than I thought. On Wednesday we did elevator pitches to help us prepare for the poster presentation. I found this exercise helpful as it allowed me to arrange the information in a comprehensive manner for the audience. I was less nervous than my elevator pitch and found my groove. We ended off the program with a potluck at Richard’s house. We made another charcuterie board courtesy of Naia working her magic. We ended off the night with a celebratory potato gun. I can’t believe we are all done! This has been a very special summer! The interns kept saying how Maya and Richard did a good job selecting the interns because of how well we got along with each other. When I first got here, I wasn’t used to the schedule so each day felt like two days. After a week of adjusting it felt pretty normal, but after the second week, time flies by so fast. Before you know it, the internship is complete. Even when writing the blog it still hasn’t fully sunk in that the nine weeks are over. It is crazy going from all of us meeting in the van and having an awkward two hour drive to having to say goodbye and possibly not seeing each other again. This has been one of the best summers. Being able to breath and live marine biology, making such great friends, and being able to work under amazing mentors was such a valuable experience. If anyone reading this is going to be an intern, here are a few things you should know:
Here are a couple activities I recommend!
A little note to the other interns hehe: I will miss all of you so much! Please keep in touch and I hope we can meet up again! Thank you for making it such a great summer <3 I'll miss each and every one of you so much! Please stay in touch, and I hope we can meet up again soon. Thank you for making this summer so incredible ❤️ Naia, you're incredibly sweet and thoughtful. I hope you know how much we appreciate you, our movie curator, theater manager, and snack provider ❤️. Shreyaan, we might not miss your "your mom jokes," but we'll miss your lively and down-to-earth personality that always made meal times fun. Madison, you've been like an older sister, driving us around and offering a shoulder to lean on. Always so kind ❤️. El, your impeccable timing and funny jokes, along with your encyclopedic knowledge, have been a constant source of entertainment. You're amazing! ❤️ Tara, your bubbly and friendly personality has made you someone we can always talk to when we're feeling down ❤️. Chloe, your outgoing and funny nature has made mealtime so fun❤️. Devin, you're the cool uncle who drove us around and put up with our shenanigans. Thank you for being so chill. Ethan, our camp counselor, thank you for your responsibility and for being an awesome lab partner. Randi, thank you for being so cool and chill. It's always fun being around you. And Pigg, you adorable little munchkin, you're an instant serotonin boost for everyone 😊🐷❤️.
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The public outreach activities at the CMLC this weekend went pretty smoothly! I was a bit nervous about how many visitors we would get, but it turned out better than I expected. Ethan and I set up 3 activities: extracting blackberry DNA (explained in the last blog), a sorting game to categorize the nemertean into groups, and live animals. The children really liked the DNA extraction activity and looking at the worms (touching them, not so much). The matching game was hard, even to marine biologists. This week, the campus was hit with COVID. Ethan was sick, so I was the only one in the lab for a few days. It worked out fine because our sequence processing can only be done by one person at a time. I finished uploading all sequences and trace files to BOLD for both Oman and Red Sea - woo! It took a while for the last plate of samples because some of the samples are new sequences that have to be entered into BOLD, while others were sequences combined from previous plates and needed to be updated in BOLD. A few weeks ago I thought I wouldn’t have enough time, but I feel like the data entering and uploading files to BOLD is going a lot quicker than I expected. We shall see! A rough draft of my poster was due on Monday so I could get feedback from my mentor before she left for a trip. She gave me a lot of helpful comments and made me feel better about the content. When I was first working on it, I felt like the poster was unbalanced. Some areas had too much text and others had too much empty space. However, with suggestions from my mentor, Richard, and Maya, I feel a lot better about the design of my poster. I am excited for the poster session next week! On Tuesday night we went to get Indian food and had dinner on the beach. It was nice to take a break for a bit and enjoy being outside before our posters are due. For the past couple of weeks (since week 6 I think) we have been watching movies at night to decompress and relax a bit. Naia has been recommending the movies, and they were always a hit! Overall, the week in the lab felt pretty slow (hence the shorter than usual blog and lack of photos). Most of the time was sequence processing, uploading them to BOLD, and triple checking that 1) all “redo” samples were combined with previous sequences to see if it produced a higher quality and length 2) all combined sequences were in the final analysis folder 3) no duplicates in the final analysis folder 4) Oman and Red Sea master spreadsheets were up to date. I had to redo ASAP analysis at least 4 times because either some samples had duplicates or were missing from the final folder. I associate productivity with lab work, so this week felt extra non productive because I only did computer and poster work. Next week is our last week! I cannot believe how fast 2 months went by! It still has sunk in that we are all leaving soon. See you next week for the last blog, the finale. We started off the week with going to the mudflats and tidepooling to hunt for nemerteans. Ethan and I wanted a live specimen for visitors to see when they visit our table at the CMLC. We reached our peak for hunting nemerteans at the mudflats early on, so we felt unsuccessful for not finding any more nemerteans after that. We went to two mudflats to find the nemerteans and only found a Cerebratulus. Ethan and I weren’t sure if nemerteans liked the mud better or the rocks better. Our success wasn’t any better when tidepooling the next day. We found two Tubulanus rubar, but one of them broke, so we were afraid it would die before the CMLC (which is a week away). I slipped into one of the tidepools, causing my boot and socks to become soaking wet. Definitely not the best feeling to have wet socks and boots while climbing over rocks. Something strange happened to the Cerebratulus (the only good one we found). When I was transferring it to a dish, it broke in half. The next day, Ethan and I found chunks of the body and decided to move the head to another container. Shortly after, some white stuff was coming out of the posterior end, causing us to think it was a parasitic worm since it was moving. It turned out to be the proboscis of the Cerebratulus. We went another two times to hunt for nemerteans during the week. We went back to the mudflats as we were told by multiple people that nemerteans were on the surface of the mud at low tide. However, when Ethan and I went back to the mudflats (for round 2) we were disappointed to come back with 1 nemertean. At the end of the week, we went one last time to find nemerteans. Since the low tides were not low enough, we went to F-dock and scrapped off the barnacles. With the help of my mentor, we finally found some nemerteans, Emplectonema viride. Success! We wrapped up lab work this week! Since Ethan and I got Qubit to work last week, we measured the DNA concentration for all the purified samples we wanted to send out. We ran into some issues with not having enough purified product for samples we wanted to resend. Previously, we had trouble with rerunning samples as they would fail the second time we ran them. This time we used all new primers and it seemed to work well (phew). The last plate was sent off on Thursday. There was also an Inverts Ball where everyone dresses up as their favorite invertebrate. I planned on being a Sea Bunny, Jorunna parva, however I couldn’t find anything at the thrift store. Naia let me use her red pipe cleaners, so I made crabs to pin onto my dress. Ethan and I were on decorating duty, which was a lot of fun since it was my first time decorating. I was impressed by everyone’s costume! On Friday, Ethan and I prepared our activities for the CMLC. We performed a test run of extracting DNA from blackberries using a buffer made from dish soap, water, and salt. Here are the steps for an at home experiment:
I hope our activities are fun and a success to the visitors! Tune in for next week’s blog to see how it went! Each week feels faster and faster! I can’t believe there are only 2 weeks left :0 Next week the plan is to finish processing the sequences, make a rough draft of the poster (due Wednesday), and enter the rest of the sequences to BOLD. Hopefully we will have all the results ready by then. When you hit rock bottom, the only place to go is up (or stay there but let’s ignore that)! Maybe I am being a bit dramatic but last week was our worst week. However, on Friday night (7/28) Ethan and I bit the bullet and finished loading the plates. We were able to send off the plates on Monday- woohoo! Although it took an hour to determine DNA concentration based on gel images, 2 hours for setting up the spreadsheet and plate map, and another almost 3 hours of pipetting and praying that I can maintain my focus (and not mess up), I can say with a sigh that we did it! It wasn’t as bad as I thought. Since each step had room for error, I was afraid that we would mess up. Luckily, everything went pretty well! Thank you to my mentor, Svetlana, for going through the trouble of finding a new company for us so we can get results back in time! In the lab this week we mainly did computer work, so it feels like we didn’t do as much as previous weeks. However, we submitted the sample from our first two plates to the BOLD database. We also managed to figure out why the Qubit wasn’t working. It turned out that during the previous attempt, we hadn't properly diluted the reagents with the buffer, rendering the instrument incapable of reading the standards. Since switching to the new sequencing company, we noticed that more samples have low quality reads. Ethan did some calculations using the Qubit DNA concentration to figure out how much we actually sent. Turns out we didn’t send enough DNA, so Ethan and I made a priority spreadsheet for which samples to send. I compiled the low quality sequences to figure out if we needed to resend the sample. The priority list's criteria include the quantity of high-quality strands available and the uniqueness of samples, determined by the initial field ID count. I understand that in the realm of research, data tracking is crucial, but I didn’t realize how much spreadsheet work and data management we had to do. I feel like we do more spreadsheet work than hands-on laboratory work. I also thought we had ample time to finish the project, but I am starting to feel like we are in a time crunch. Because we want to resend samples, our schedule is a lot tighter. We want the samples to make it back in time for us to include in the poster. This means that we have to send off the last plate by next Wednesday, which means that any samples that need to be re-PCRed have to be completed on Monday and Tuesday. We finally went crabbing this week, which is something I have been wanting to do since I got to Oregon. My mom said it is a must do activity. We used fish heads as bait to attract the crabs. We set 2 crab traps out, but most of the crabs we caught were Dungenese that were too small (and they actually slipped through the trap). We ended up catching 2 Red Rock Crabs, 2 Green Crabs and one Dungenese. The goal was to catch enough to eat, but I don’t think it was enough to cook it for a main meal. On Thursday, the interns gathered for a potluck organized by Maya, the OIUMB educator program coordinator. We picked berries at OIMB’s parking lot and took it over to her house to bake it into a pie. I sculpted a turtle, snail, and pig (tribute to Randi’s pug, pig) as a pie topper out of dough. We also played on the zipline and got transported back to our childhood playing double dutch. It was a slower week, but I feel like it was much needed. I think everyone is reaching a point where we are getting a bit tired and need to have a lighter week to reset. Next week the goal is to have all samples sent off to wrap up our lab work. |
AuthorHi everyone! I am Audrey and a rising junior at Boston University majoring in Marine Science and minoring in Biology. I am super excited to be participating in Dr. Svetlana Maskalova’s nemertean research this summer. Over the nine weeks, I hope to expand my experience with PCR. In my free time I like to go hiking, sewing, making jewelry, and baking. ArchivesCategories |
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