They kicked this week off with a very righteous weekend of touring the Oregon aquarium and Hatfield facilities. I was especially excited to broaden my understanding of ongoing research from a different institution and learning more about the Oregon coast. The faculty and interns gave us a very well-rounded introduction to the ongoing efforts being made in sustaining the local oyster population. Something that may escape an Angeleno like myself, is that marine life not only plays a role in the human food chain but it also plays an instrumental role in the ecosystem. When considering how many oysters live throughout the Oregon coast and that they are a keystone species, if they were to one day extinct, the ecosystem could suffer dramatically. This knowledge helped put the research being conducted at Oregon State University in focus and highlighted the importance of the research pertaining to oyster sustainability. Aside from the insight on the research being conducted, it was also great to go through the aquarium and learn more about the marine life across Oregon. It was great to see octopus throughout the aquarium, but it was surprising to see that puffins are also a species common in this area as well! I absolutely adore puffins. For years I would eat my Puffins cereal and think I could only see them in real life if I visited the arctic, but all I had to do was go to Oregon. The following day we lounged by Hall lake, which is a lake situated right next to a dune! The scenery was epic. All-and all the weekend was a good way to unwind and bring my focus back to my week’s research. Troubleshooting had proved to have been one of the more challenging aspects of the project. With almost a week and a half dedicated to just trying to figure out the right annealing temperature and primer sets to set off my reaction I was becoming less and less sure that my samples would ever work. My persistence panned out, and I could get my PCR to work. I needed to get some new reagents to get my reaction working again. One aspect that this research opportunity has given me is the opportunity to wrestle with my challenges instead of just setting my issues down for someone else to deal with them. I can hone in on my issues and plan out a constructive approach. When I hit a point that I am not sure of what my next step should be, I fall back on either Kara or Svetlana (maybe Nicole if I just want to throw darts). They both are much more knowledgeable and could better help me in navigating my issues and sure enough they almost always have advice to push me through the next step. It brings to light the importance of being able to network in any kind of situation—whether it’s work or school life. It was rewarding to see my efforts pan out. Another treat this week was the R workshop hosted by Ross. I have taken computer science classes before and I have to say that he has arguably taught me more in 3 hours than I learned in most of my semester courses. He was very well-organized and really was great at explaining both the syntax and the math of the tools we were operating. This week was an exciting that has left me even more grateful of this summer.
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Avaste ye! There are sequences, ahead! Going into the program, I would say that I was looking forward to the most was having to work with all the sequences. I had done a bit of PCR while I was at community college, but I never had the opportunity of analyzing, trimming, and comparing the sequences to those already uploaded to genetic databases. In fact, those extra few steps are what really what elevates PCR amplification of a gene into DNA bar-coding. What’s great about this opportunity is that I get to use real samples that have been collected in the field. Being that these are samples from an understudied phylum, there is also a higher chance that I may recognize a sequence that has yet to be catalogued (i.e., discover a new species). So far, my lab partner and I have done just that!
Being giving so much autonomy I felt a lot of gratitude when I can discover a new species, but I also feel a lot (maybe a little less) gratitude just getting to where I can compare, or BLAST, the sequences that I PCR amplified. There are a lot of steps to get to that point (and so many ways it can go wrong to get there) but with enough practice you can start worrying less about mistakes you may have made along the way. Even then, there are still sequences that come out poor for whatever reason or, comically, you may have a great sequence of your sample’s dinner! Yes, you may have just PCR amplified what had been lurking in that specimen’s digestive tract! Frustrating but always funny to talk about in retrospect. It’s been great seeing how far we’ve come by the end of week 5, but there is still a lot of work to do! Namely, starting to get ready for the poster! The better part of this week has been consumed by mostly trimming, troubleshooting, and “BLAST-ing” sequences. There was, however, some small moments along the way adding on to the experience of doing research at this unique institution. Yar’, I reckon that a many of us have been feeling a wee bit burned out from our research doing at the OIMB. Tis’ past weekend was a great way of resting our sea legs and wandering about at Cape Arago. I, along with the rest of the REUs spent the weekend camping. At first I felt a bit worried that I wouldn’t have enough time to work on my proposal, but then I figured that I should just roll with it and plug out from the stress of lab work.
There were boatloads of critters we saw down at the tidepool and I would love to post each one of them, but alas this is a blog post and not a photo album. I am however, going to mention how we saw a giant pacific octopus in the tidepools as well! Unfortunately, we could not get a good picture of it as it was dwelling in its den, but its suckers were the size of the nudibranch that I am holding in the following picture. Was quite a lovely site, and I was particularly chipper after I saw it. Especially since I’ve been wanting to see an octopus since the first day I have been in Charleston, Oregon. On our second day we had shared our campground with the UO SPUR students, and we managed to play a game of ultimate frisbee between both camps. As you could imagine, the REUs beat the SPUR students to 10! Not that it needed to be said. On our way back we all got to enjoy ice cream that Richard had bought for all of us. Before you knew it the night-sky was upon us and we got to spend time over the bonfire. When dusk rose, we went tide-pooling one last time before we headed back to OIMB. The following Monday we went back to humming along in our old routine. We did get to spend our Tuesday presenting our proposals (which had ended up turning out fine), and followed it up by celebrating a job well done and Christina’s going away at one of the local dive bars. This entire time that I have been in this program, Christina has been at the helm of the Maslakova lab while Svetlana has been doing research abroad. She did a great job of making sure that the ship did not crash at the hands of two REUs and I can honestly say that I credit her for me being able to pick up PCR as well I have. In all honesty, the ship would’ve only crashed in my bumbling hands, but I can safely say it did not. I may not have perfected PCR (yet!), but I grew much, much more comfortable because of her mentorship. I could not have imagined my REU experience having gone nearly as well without her and I will be forever grateful for her patience and all her sage teachings and advice. Cheers! It’s odd to think about how much I have come to love benchwork. My prior research experience involved me doing a lot of field work and a little bit of benchwork, whereas this research has kept me tied to the bench with very little field work. Although it’s a completely different environment, I learned to love it the same. Being that lab work is in a more fixed setting, it has allowed me to work on refining my technique and approach in a more concise manner. That is not to say that bench work does not have its uncertainties. This week alone has been a never-ending trial of PCR, troubleshooting, purification, and more troubleshooting. Troubleshooting has been one of the more agonizing aspects of this experiment. Especially when you place so much effort into one step of the process and it does not pan out in your favor.
Thankfully, I get to be part of this program and not place too much emphasis on making a home run out of every pitch. I get to strike out and come right back to the plate for another swing. I don’t have to worry about grades, I can just focus on refining my skill set. I always strive to do better than the day before, but I do it knowing that this is done out of my own benefit. Whether it is trying to get a little bit faster at loading gels, being more efficient with timing procedures, or even just getting into lab a little bit earlier and making up a pot of coffee ready for everyone in lab. Another aspect I have come to appreciate while being part of the REU program is collegiality. I have come to value the collegial environment in research settings as it provides an opportunity to have discussions pertaining to one’s research. Or, alternatively it can serve as an outlet to your frustrations. Sometimes we bond over a cup of coffee, and sometimes we bond over a game of hackie-sack. It all just depends on everyone’s availability, but there is a more-or-less a silent mutual agreement between all of us that sometimes we just need a take step away from research and enjoy some casual moments. So as this work week went on it became progressively chaotic. It never quite felt that the results matched the efforts, but my perseverance and many cups of coffee kept me through it. On the Fourth of July I, along with the other REU interns and UO students, took the day off and enjoyed myself at the beach. It was a break well worth pushing for. |
AuthorI’m a first-generation college student. I like enjoying the outdoors and finding new hiking trails. Archives
August 2019
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