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 😊🐷❤️.
0 Comments
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. I can’t believe it is already week 5! The week started out great and slowly got more… well you will see when you read the rest of the blog. I didn’t get a chance to mention it in the last blog, but we saw the movie Barbie last Friday. It was highly anticipated among the interns since the beginning of the internship and it did not disappoint. We started week 5 with a boat trip on the OIMB’s new 48’ boat — R/V Megalopa! The weather was foggy, but the wind was only 10-15 knots, and the waves were relatively small. Check out the gallery to see what organisms we dredged up from 100-300 ft of water! Between looking down at the sea tables and the stench coming from the dredge, I got a bit sea sick. We also witnessed breaches in the water. One breach was from a seal, but we couldn't identify the second animal with certainty. We speculated that it might be another seal or its prey. At first, we considered porpoises, but their breaches were not consistent. This week in the lab was rough to say the least. It finally hit me how many times our PCR failed. Especially on Tuesday, none of the PCRs we ran worked. We have tried everything. From changing the primer combinations, decreasing the annealing temperature, diluting the samples, and doing a combination, none of the samples amplified. Some of the primer combinations, like LF/jgHCO, were new to us, and we only used them because we were running out of solutions and desperate for any progress. We've dubbed the 20 samples as our "problem children". We suspect that the problem might be our DNA concentration. However, theoretically, PCR doesn't require a large amount of DNA; it should work with just one strand. At this point, we are starting to feel like we're beating a dead horse if we continue to troubleshoot because it would lead us into an endless spiral of trying every possible combination of primers, temperatures, and dilutions. It would be a waste of time and resources to test out numerous combinations when the chances of success are low. The last solution to try is to re-extract if there is tissue left. It feels like we are treading water without making any progress and seem to be stuck in the exact same spot. We have made our way into the 600 zone for PCR tube numbers, 677 to be exact. This entire week Ethan and I stayed late in the lab hoping that our PCR would work. Our fruitful efforts were unfortunately not enough. There is more. On Thursday, we encountered a setback when the sequencing company, Sequetech, abruptly closed its operations after 30 years. As a result, we had to search for a new company to handle the sequencing of our samples. My mentor found a core facility at the Oregon State University's core lab, which seemed like a great option. However, there's a catch (as expected, it wouldn't be that easy). The DNA must fall within a certain concentration range and we need to pre-mix 1.2 ul of primer into the wells, totaling 12 ul. Unfortunately, it didn't end there. We couldn't determine the DNA concentration using our lab’s fluorometer (called Qubit), so we had to go with the second method, which is using a gel to estimate concentration based on the brightness of the amplified bands. We selected a range of samples to run on a gel and visually assess their brightness. However, since this process relies on subjective judgments, it introduces the potential for errors. If we fail to find another company to handle the sequencing, we'll be left with the task of reviewing all the gel images of the 96 samples we plan to send in order to estimate their concentrations. From there, we'll have to calculate how much we need to dilute each sample, adding further complexity to the process. To top it all off, I had high hopes that changing my laptop battery would work. To my disappointment, my laptop is still dead and useless. I think this is the trend this week: nothing is working :( We also had presentations this week. It went okay and it was fun to hear about the other intern’s progress. I was super nervous and I am glad that it is over. As a reward, all the interns went hiking after dinner! We went to the South Slough Trails and hiked to a saltmarsh. There were so many ripe blackberries, thimble, and salal berries. I really hope next week is better and we can send off the plates for sequencing. This week, the interns started off the week with a treasure hunt! We visited antique, vintage, and thrift stores at Coos Bay Boardwalk, where everyone found items that suited their style. As my mom would say, it was a productive trip! Personally, I love tiny things, particularly china teacups and trinket boxes, so I am definitely looking forward to returning. We also went back to the 7 Devils Pub and Brewery to see a band called Three for Silver. I personally liked this band better than the last band. Oregon State University interns came for a tour of our campus and the Charleston Marine Life Center (CMLC). We gave them a tour of our lab and tagged along the CMLC trip. On Monday, I joined the 20-plus-year-long larval crab project led by the OIMB Professor Emeritus Dr. Alan Shanks. We went to the docks to collect what was in the traps, recording the numbers of the Dungeness crab megalopa larvae and any other bycatch we came across. The catch turned out to be quite diverse, including isopods, rockfish, and shrimp! It was my first time at the docks and I was excited to see so many jellyfish there. Another new experience was plankton towing! Chloe allowed me and Ethan to join her for a plankton tow at the docks. We also went digging in the mud flats, where we discovered various organisms, such as clams, tube worms, phoronid worms, polychaetes, annelids (shimmy worms), and an ascidian. In the lab this week, we received more samples from Oman, courtesy of my mentor's colleague, Dr. Gustav Paulay. Just like the previous weeks, we extracted DNA, performed PCR, troubleshooted, ran the PCR samples on a gel, and purified the samples. We've already processed PCR tube number 400, and we're getting close to 500 :0! I wonder if we'll reach 1000 PCR tubes by the end of the project. Last week, we sent our samples for sequencing, and this week we got the results back. We found 7 new operational taxonomic units (OTUs — putative species) from Oman and Red Sea! Among them, there was a new species from the genus Gorgonorhynchus , 2 new species of Baseodiscus, 1 species from the family Lineidae, 1 Reptant polystiliferan, 1 species of Nipponnemertes, and 1 species of Tetrastemma. We believe that we'll discover many more Tetrastemma species, and overall, we expect to find numerous new OTUs. Unfortunately, my laptop broke this week, which couldn't have come at a worse time, as my proposal was due on Wednesday and I had a lot of edits to make. I made efforts to work on it in the lab early and after dinner. Additionally, I've been compiling all the species found in the Indian Ocean, which requires a lot of computer work. I have never done something like this before so it makes it a little inconvenient to have to reopen my sources every time I want to add to the list. Hopefully, after replacing the battery, my laptop should be up and running again! On Thursday, we were informed that Wallace the friendly porcupine that had been hanging around the OIMB campus had been removed by the Oregon Department of Fish and Wildlife (ODFW) to be relocated to the nearby hills. Sadly there won't be any more weekly Wallace photos to bless your feed. Compared to other weeks, this one feels less eventful, but time is flying by faster and faster! The highlight of the week was discovering numerous new OTUs, and I'm excited to send off another plate of samples for sequencing (hopefully next week). We started the week three off with camping at Camp Arago for 2 nights. On Saturday morning we went tidepooling and found a bunch of cool animals. My favorite was Antiopella fusca, a white-and-orange-tipped nudibranch. I was so surprised because I thought they were typically found in eel grass or on substrate, but this particular nudibranch was floating on the surface. Additionally, I saw a lot of bright orange-red nemerteans, Tubulanus ruber, and collected two to bring back to the lab. I saw lots of starfish (Pisaster ochraceus), purple urchins (Strongylocentrotus purpuratus), and a green anemone. We also went hiking and spotted some seals, a salamander, and several crabs. I grilled hot dogs for lunch and prepared hamburgers for dinner. The plan was to wrap up the camping trip by watching the sunset from the beach, but we got carried away digging holes in the sand in search of critters, paying little to no attention to the sunset. A few lessons I learned from camping: always remember to bring a pillow, make sure to have padding for your bed, and have enough layers or blankets as it can get really cold. Our sequences arrived this week! I learned how to process the sequences using Geneious Prime. First, the primers get trimmed, and low quality bases are removed from the ends. If there are two strands (one for each primer), they are aligned to make a double-stranded DNA. Then, a consensus sequence is created from the aligned strands and compared to sequences publicly available through GenBank, a database maintained by the National Center for Biotechnology Information, to find the best match. This step helps us confirm whether we indeed got a sequence from the phylum we expected (e.g. a nemertean, and not an annelid or crustacean, common prey items of nemerteans). A tree was constructed based on the relationship between the neighboring samples and provides us with a visual representation of the identified Operational Taxonomic Units (OTUs) and their relationships to one another. This also helps us determine which samples are cryptic species (there are a lot!). I was really excited to continue troubleshooting PCR, as we were able to send off another plate this week! I can’t wait for the results to come back so that we can add more individuals to the tree. Some of the previously sequenced samples showed amplification of a prey item, requiring us to try different primers. Our hope is that these new primers will better match nemertean sequences. Additionally, we encountered the same issue this week as we did last week with the presence of double bands. We have two potential solutions: first, purifying the PCR solutions in the hopes that it won't affect the sequencing process; or second, increasing the annealing temperature to eliminate the fainter second band. I started working on my project proposal this week, and it is progressing okay. However, I'm uncertain about the level of detail and development required due to the page limit. Fortunately, since we began searching for citations in the first week, it reduced the workload for this week. My mentor has also provided us with awesome resources and an outline to follow, which has been super helpful. She is the best! While searching for citations, I got to read more about the biotoxins found in nemerteans. Some of these toxins include tetrodotoxin and neurotoxic peptides. Interestingly, other organisms such as the blue-ringed octopus and pufferfish also possess tetrodotoxin. It is believed that this toxin is produced by endosymbiotic bacteria. Tetrodotoxin is 1,200 times more potent than cyanide, functioning by blocking sodium channels and interfering with the transmission of signals from nerves to muscles. So cool! I hope to learn more about it. Next week, we expect to receive more samples, and the process will repeat: DNA extractions, PCR, PCR troubleshooting, gel imaging, and sequencing. To start off the second week, the REU interns went kayaking at Hall Lake and climbed up sand dunes. Fortunately, the weather had warmed up just in time to go swimming! This week in the lab, I continued performing PCR. However, I noticed that my positive control was faint, making it difficult to observe. The positive control is a previously successful sample used to assess the viability of the master mix. This issue arose on two separate occasions, and I'm uncertain about its cause. To ensure thorough mixing of the DNA, which is not homogenous, I made sure to flick the positive control. Additionally, I fully incorporated the sample into the master mix and centrifuged it using the tabletop centrifuge. After discussing the matter with Ethan, we decided to switch our positive control to a more recent sample taken from the first PCR we conducted. We hoped that the positive control bands would be more pronounced, and indeed, they were brighter. Aside from the finicky positive control, I conducted PCR troubleshooting due to samples failing the initial PCR run. There are a couple of methods available for troubleshooting. The first approach involves diluting the DNA by using a ratio of 1:10 of DNA to nuclease-free water, which helps decrease the presence of PCR inhibitors. We found that a good amount of the samples worked after dilution. In some cases, an additional dilution of 1:100 may be necessary. Some of the samples yielded positive results using this method. The second troubleshooting method includes changing the primers. Currently, we are using Folmer primers, which serve as universal primers for a standard barcoding region of the Cytochrome Oxidase I gene for many metazoans. However, there are instances where the primers may bind to the DNA of a prey item in the gut instead of the predator (the specimen of interest to us), so in case of nemerteans one sometimes gets an annelid or a crustacean sequence instead. For the samples that were unsuccessful after the dilution, we tested out different primer combinations. The LF/ DR primer and LF/ HCO combination failed for most samples we were troubleshooting, so we are trying LCO/ DR and a set of degenerate primers. Since we had enough purified samples this week, we loaded them into a plate and shipped them off for sequencing. I am super excited to get the results back! My literature search has been yielding more progress since I expanded the scope of my search to the entire Indian Ocean, rather than just Oman. Unlike other species, nemerteans are not a hot topic in marine biology; however, they are in desperate need of attention. Ribbon worms, as top predators, play a crucial role in ecosystems by feeding on other organisms, like crustaceans and annelids. At most, the literature might contain descriptions of a couple dozen species, but many still await discovery, description, and classification. I am always amazed by how much science has developed. It used to be that histological sections were the best way to assess nemertean morphology and classify species, because the color of the live nemerteans would fade away after preservation. Now, DNA sequence data is routinely used to distinguish between species. I have always wondered how scientists developed procedures such as DNA extraction and PCR and how they determined the necessary chemicals for the reaction. This week, we went fossil hunting. The interns were hiking to a beach when we ran into a man carrying a fossil. At the beach, we were searching for fossils and only managed to find a small one. When we left the beach, the man had left the fossil on the trail with a note saying "Free." It felt as if it was meant to be, so we traded and left the small fossil for someone else to discover and keep. Additionally, at the same beach, we dug a channel to connect the freshwater with the ocean. However, the freshwater kept drying up, so we had to dig deeper as we approached the water. In the end, it was successful! On Wednesday, I attended my second seminar where two PhD candidates talked about their experiences on a research cruise. They even brought jellyfish for us to hold and pet, definitely one of the highlights of my week! Next week in lab we are continuing to do PCR troubleshooting, DNA extractions, and hopefully get to data analysis! I am excited to see the progress of the project. As a brief introduction, hello! My name is Audrey and I am majoring in Marine Science and minoring in Biology at Boston University. Ever since I was little, I thought cuttlefish and octopus were fascinating and have been interested in Marine Biology ever since. I hope to explore regeneration and stem cell research in marine organisms in the future. At Boston University I had the opportunity to work in a population genomics lab conducting research on coral to determine if the symbiont composition is impacted by environmental variation and if it affects the thermal tolerance of coral. I also worked in the wet lab feeding coral and conducting water quality tests. This summer, I will be conducting Polymerase Chain Reactions (PCR) on the Cytochrome Oxidase subunit 1 (CO1) gene under the mentorship of Dr. Svetlana Maslakova. Through the use of genetics, we aim to improve the knowledge of nemertean species diversity in Oman and the Red Sea, and to distinguish between cryptic species - organisms that share similar appearances but belong to different species. This week, Ethan and I completed 68 DNA extractions, consisting of 48 samples from Oman and 20 samples from the Red Sea. The extraction process involved lysing the tissues, binding the DNA to spin columns, and eluting the solutions to obtain liquid-form DNA. Unlike the other REU interns, our samples were already collected by our mentor. Next, we performed PCR to amplify a specific gene, the Cytochrome Oxidase subunit 1 which is a mitochondrial gene. CO1 is a highly conserved gene with specific regions that vary enough among species, allowing us to differentiate taxa. To assess the quality of the samples, we conducted gel electrophoresis and examined the resulting gel images. Additionally, negative and positive controls were used to detect contamination and evaluate the master mix.The successful PCR samples were purified. Next week we are aiming to send off a plate to get the samples sequenced. Aside from lab work, we were given readings and videos to enhance our understanding of the classification of nemerteans and their distinguishing features. There are three classes in the phylum Nemertea: Hoplonemertea characterized by stylets in their proboscis, Palaeonemertea, and Pilidiophora which is named after the pilidium larvae. One scientific article I read written by my mentor discussed how a nemertean species Micrura alaskensis is actually a complex of five different but cryptic species. I am currently in the process of finding literature, and I must admit that it is proving to be quite challenging. The topic I am exploring is largely unexplored, and narrowing it down to a specific location adds to the difficulty. During my freetime this week, I went to Davey Jones Locker, the pottery store, the OIMB beach, and the Charleston Marine Life Center. If I had more time, I would have volunteered in their aquarium. The campus has a lot of animals roaming around, so hiking is super fun. The REU interns and the summer students have a synchronized schedule because the meals are served for only 30 minutes. Breakfast is served at 7:00 am, which is something that I still have to get used to, but it makes the days seem a lot longer and more work can be done. All the interns check in with each other’s progress and it is so fun to hear what the others are doing. I wish there was more time so that I could spend nine weeks on each project. I would also like to go to the mudflats and experience collecting samples. I am excited to go on more hikes and check out the docks to see if I can find harbor seals. I am also looking forward to starting data analysis. |
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 |
Proudly powered by Weebly