Tag Archives: Research

Cloning, Harvesting, 117 Grilled Cheese … and Counting

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Ryan Apathy photo Grand Park, Mt RainierWeeks before the summer even began, Dr. Bryan Thines, PhD, my research advisor and a professor of biology and genetics at Puget Sound, challenged me to a beard-growing competition. “I like to have friendly games within our labs,” he told me after I received my research grant. “It encourages both competition and camaraderie.” I had already been pranked once by my lab after I misspelled the word “assess” on a poster for a presentation, so I should have assumed that our summer work would be just as mischievous as the previous semester.

I and two other students, Lily O’Connor and Tina Chapman, are working hard to characterize F-box proteins in Arabidopsis thaliana through molecular, genomics and bioinformatic approaches. Through weeks packed with genotyping, gels, culturing, cloning, harvesting seeds, and extracting DNA, we have finally begun to identify knockout lines, develop gene constructs, and locate brand new candidate genes for further study.

Throughout the hard work we’re putting in at the bench, our lab has found additional ways to entertain ourselves. Any given day often alternates between lab meetings discussing research progress, thesis writing sessions, miniature genetics or molecular biology lectures, bench work, and discussing how many grilled cheeses we have each eaten since our research began (I’m in the lead with 39).

Lily, Tina and I are entering our final year at Puget Sound, and we collectively decided to capitalize on our mentor’s time by bombarding him with questions about scientific writing, life after college, applying to and attending graduate school, how to make the best cup of pour-over coffee. As we enter the penultimate week of our ten-week grant program, our lab has collectively grown countless pots of plants, run dozens of gels, eaten 117 grilled cheese sandwiches, and grown two significant beards.

Ryan Apathy’s summer science research at University of Puget Sound is supported by the M.J. Murdock Charitable Trust’s Science Research Program.null

Recruitment Struggles

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Undertaking a long, multi-step project or process often involves unforeseen difficulties. While these challenges can be similarly frustrating to experience, combating them often necessitates a very different set of skills. Some problems require patience, while others require rapid ingenuity; other problems are best viewed through a creative lens, while some should be addressed as methodically as possible.

However, solving problems effectively can often default to a simple formula: one tries various solutions, fails, and subsequently bases future attempted solutions off of previous failures.

In the context of my research project, the largest challenge that I have had to deal with is recruitment. Participation in my study is limited exclusively to students at UPS, and since a large percentage of students go home during the summer months, I have a small potential sample size to draw from. However, there are still more than enough students for me to reach my minimum goal of 40 participants, as well as my ideal (and wildly optimistic) goal of a sample size of 80 participants. Despite the fact that I am offering $5 as compensation for participation, it has been difficult to find a steady flow of participants.

I initially thought that it would be sufficient to advertise solely via flyers placed around campus that advertised my study. Theoretically, the allure of getting $5 for 30 minutes of participation would be too much for some students to resist, and I would be overwhelmed by potential participants clamoring to get a piece of the action. In reality, the experience thus far had been vastly different. I’d be lying if I were to say it wasn’t a little bit of a letdown when, after putting up my flyers, I received little to no interest in the first week.

However, I also knew that in order to optimize the number of potential participants, I needed to undertake a more active, personable, and tangible recruiting process. The frenetic pace of daily life makes it difficult for a student to pay attention to every poster or flyer that they see, much less consciously decide to consider the information that it displays. By deciding to go around to summer classes and actively present about my research to students, I knew I had a much better chance of engaging them.

If I were going from classroom to classroom, handing out surveys, and simply asking students to fill them out, I would have no problem; people are not inherently opposed to participating in research studies, nor are they inclined to not want $5! However, participation in my study is different – it requires conscious effort – potential participants have to clear space in their schedule, contact me to set up a time, and show up and participate. That’s a significant amount of work, with a relatively small incentive; I can completely understand how other concerns and interests can make prioritizing research participation an afterthought.

Despite these initial setbacks, I am determined to continue working to get as many participants as I can. While it can be difficult at times, every single person that I get counts, and I frequently have to remind myself that, quite literally, “they all add up”. Hopefully the coming weeks will see steady, progressive participation as I look to reach my goal of 40 participants!

Research Reflections

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A brief demographic questionnaire from the study.

A brief demographic questionnaire from the study.

 

Hi everyone! I’m Stephen Baum, a rising senior and psychology major. This is my first ever blog post, as well as my first summer conducting research independently, which, initially, was a slightly daunting prospect. While I was incredibly excited and humbled to have received a summer research grant, I was anxiously aware of the challenges that lied ahead. Somewhere along the line, I visualized myself drowning in a sea of journal articles that I was hopelessly inept at trying to interpret. However, thanks to the support of my advisor, Jill Nealey-Moore, (Ph.D, Psychology) I have neither downed nor am I (completely) inept at reading and analyzing articles; thus far, the research process has been fantastic and extremely rewarding, albeit challenging.

While I can’t speak entirely about the specifics regarding my research, as I am still running participants and don’t want to compromise the scientific validity of what I am testing, my research generally examines how an individual’s mood alters as a function of various tasks that they perform. Participants in my study come into the lab, complete several written exercises and questionnaires, and are then compensated for their participation. The study in its entirety takes around 35 minutes, which, figuratively speaking, is in a “sweet spot”; long enough to comprehensively examine how the tasks influence mood without leaving a participant overly fatigued and potentially compromising their ability to concentrate.

As a whole, my reflections on conducting research thus far are positive. It is very apt to characterize a considerable portion of the research process as unglamorous; for every significant finding or “eureka” moment, there are hours and hours spent in the lab, at the computer, or the library, meticulously sorting through the world of online publications, struggling with the margins on a set of questionnaires, and agonizing over the heading on a written activity. Research is inherently painstaking, and it highly prioritizes attention to detail; those that put in extra effort will be rewarded with the most fruitful, and often, most unexpected findings. Since a significant portion of the validity in experimental psychological research rests in ensuring that each participant in the study has as identical of an experience as possible, minutia cannot be ignored. In this way, routine is a researcher’s best friend, as the experimental procedure for each and every participant follows a pre-drafted “script” that standardizes language and controls for deviations. While some may find this monotonous, the process is incredibly inherently satisfying for me, as I get a certain gratuitous please out of agonizing over organizational details and running a participant directly according to the script.

Additionally, being able to work in such close proximity to Jill and pick her brain has considerably advanced my academic development. The axiom “work smarter, not harder” comes to mind – while research does require you to work (very!) hard, which Jill demonstrates, it rewards innovative, critical though and harnessed spontaneity. Observing Jill’s careful and analytical reasoning has enabled me to grasp the value of such traits in an experimental setting.

Watching my thought process systematically evolve from when my research project was in its fledgling stages has been incredibly gratifying and empowering. I believe that largely due to the help of those around me, I’ve been able to progressively develop a variety of skills that will benefit me even outside of an academic research setting, such as the ability to problem solve in difficult situations, or ration time and resources in an advantageous manner.

So that is about it! Hopefully I can keep everyone up to date with my adventures in the lab as my study progresses. I’m looking forward to being able to speak more freely about the semantics of my research and the theory behind it. Stay tuned!

Fun fact: the TCI Department for the Environment and Marine Affairs has twelve officers nationwide.

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There’s nothing like the feeling of being done with exams – which I now have been for several delightful days.  So here I am on my tropical island, no more classes, and two weeks until I go home to DC; clearly, all I’m doing with my life right now is tanning and swimming in the clear, warm, turquoise ocean, right?

Actually, right now I’m sitting in my room wearing a fleece jacket and looking through the window to grey, Tacoma-esque skies.  I just got back from a snorkel at a site called the South End of Long Cay, and for some reason the elements never cooperate when we go there.  Last time, there was a huge current; today, it bucketed rain.  But hey, an eagle ray swam right next to us, so there’s that.

Lectures are over, but we’re still collecting data for our directed research (DR) projects (thus the necessity of the stormy snorkel).  Our papers are due a week from tomorrow, which is an absolutely terrifying thought, and then we spend a few days presenting our research to the community and the rest of the Center.  And then we return to the world of normal winter (as opposed to winter here, which means sleeping under a sheet and without a fan on).

DCIM100MEDIA

But before that, we have to get these papers written.  It’s already looming over my head, and we haven’t even finished collecting data – and then there’s the analysis of said data.  I’ll be creating a management plan based off of my group’s findings regarding the abundance of the invasive lionfish Pterois volitans, which basically means that I’m acting as a middleman between the scientists and the policy-makers, synthesizing and interpreting our results to suggest methods for controlling the lionfish invasion.  Think about it as a report for a government environmental agency, giving them scientific knowledge in a way that gives them a basis for creating policy – because may be what it turns out to be.  Fun things can happen when you’re at a prestigious field station in a small island nation.

Fun fact: lionfish create jets of water to orient their prey for headfirst consumption.

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Back in September, we were taken to a site called Admiral’s Aquarium for our first snorkel of the semester.  There wasn’t much of a current, but there was more than we were used to, and the swell was pretty big – as in every time you lifted your head to try and listen to the intern showing you around, you got a face full of water.  My first night snorkel here was at a site called Shark Alley, which is really quite spectacular, except that we had no idea what we were doing and ended up on a shallow shelf of coral, turning it into a mind game that went along the lines of “if I suck my stomach in enough I won’t hit those corals.”  My bazillionth snorkel here had both big swells and shallow reef – and I was carrying a laboratory.

This is the usual amount of scuba gear - bulky, yes? Now add several additional pieces of equipment. Carabiners are basically the most useful thing ever. (Side note - look closely for a shout-out to UPS Crew.)

Okay, not quite, but it was our second time collecting data for directed research and we hadn’t gotten used to the equipment yet.  Directed research projects started last week, and the resource management professor and three other students and I are studying the proliferation of the invasive lionfish, Pterois volitans, at various sites near South Caicos.  When we go out for a research dives or snorkels, we carry underwater slates, pencils, transect tapes, clip weights for the end of the transect tapes, and plastic T-bars with centimeter increments.

Besides the fact that it means I get to dive between four and eleven times a week, this is a fascinating and relevant research project because it involves the world’s most ecologically-harmful marine invasion ever.  You know the stereotypical look-at-this-reef-and-all-the-pretty-fish-isn’t-nature-amazing type of picture?  A lionfish will eat pretty much every single fish in that picture as long as it can open its mouth wide enough.  They eat up to 6% of their body weight per day (even as a rower, I can’t eat nine pounds of food a day); not only that, but native reef fishes haven’t figured out an effective defense mechanism to avoid their predation, and the only fish that eat them are the hugely-overfished grouper.  Also, they’re venomous.

The environmental morals of the story: don’t let your cool aquarium fish out into the ocean because they will take over everything, and use reusable water bottles instead of buying those single-use plastic ones.  That latter part was absolutely unrelated to lionfish, just something I thought I’d throw in there after a recent lecture on pollution and marine debris (remember that campaign on campus last spring with the plastic jellyfish hanging in the SUB?).  I’ll get down from my soapbox now.