Issue 21

ELEMENTS A MAGAZINE FOR SCIENCE AT THE UNIVERSITY OF PUGET SOUND

ISSUE 21 - FALL 2017

SUMMER RESEARCH - REUs

ENVIRONMENT - PHILOSOPHY

“It is only through enlightenment that we become conscious of our limitations. Precisely one of the most gratifying results of intellectual evolution is the continuous opening up of new and greater prospects.�

-NIKOLA TESLA, 1915

FROM THE EDITOR Though often overlooked, the ability to communicate is a strength possessed by great scientists. Being able to articulate something incredibly technical to a wider audience lends lasting, tremendous impact to discovery. However, as information can be accessed almost instantly about any topic conceivable to the human mind, the way in which we communicate is morphing, both for good and bad. Recently, society has struggled with many of the inherent dangers of the rapid dissemination of information.

Facts are frequently distorted, misinterpreted, and falsified.

Through Elements, my hope is that we, as a university ripe with critical thinkers and problem solvers alike, can continue to foster a community that seeks truth and understanding in all aspects of life. This edition of Elements is an amalgam of the efforts of so many individuals: students poured their passions into crafting articles, artists devoted their talents to further those scientific narratives, and my wonderful editors spent countless hours editing and designing the pages that follow.

We have two common trends in this edition – student research and environmentalism. Climate change is often a concern for university students, and is perhaps heightened our current political climate. As such, we have a feature on the role of climate change in causing island hurricanes, an article highlighting the current environmental impact of the university, and the effect of pesticides on worldwide bee populations.

This edition also strengthens our focus on undergraduate research with six research articles: three about research on campus, and three articles from students with NSF grants for Research Experiences for Undergraduates (REUs). We were also able to gather words of wisdom from an alumna who is now a resident physician, gain insight on the link between philosophy and mathematics, and as always, have a bit of fun with the Allium.

Elements hopes that you will continue to learn about the surrounding world, particularly through scientific inquiry. We are always looking for passionate students to submit writing or artwork, and we welcome any topics relating to science, mathematics, technology, and the environment.

If any of this sounds interesting, feel free to get in touch with us at elements@pugetsound.edu. Keep exploring, learning, and pushing the boundaries of knowledge and understanding!

STAFF Tina Chapman EDITOR IN CHIEF

Carly Baxter COPY EDITOR

Melody Saysana ASSOCIATE EDITOR

Megan Tegman ASSOCIATE EDITOR

Shreeti Patel ASSOCIATE EDITOR

Erin Stewart ASSOCIATE EDITOR

Annelise Phelps ASSOCIATE EDITOR

- Tina Chapman

The production of Elements Magazine is possible due to the funding and support of the Associated Students of the University of Puget Sound (ASUPS). We thank Media Board, ASUPS and, by extension, the student body for making this publication a reality. This magazine was printed by Print NW (Lakewood, WA).

Cover illustration by Emma McAllister

Millie Lasky ASSOCIATE EDITOR

In this issue 6

Islands: On the Front of Climate Change

8

REUs: What They Are and How to Apply

11

Van der Waals Heterostructures (REU)

14

Fructose and Copper in Liver Disease (REU)

17

Stem Cells in Regenerative Medicine (REU)

20

Environmental Impact of UPS

23

Interview with a Resident Physician

26

Washington before the Cascades (Summer Research)

28

F-box/14-3-3 Protein Interactions (Summer Research)

30

Green Amide Catalyst Formation (Summer Research)

32

Philosophy and Mathematics

35

Pesticides and the Worldwide Bee Decline

37

The Allium

38

Alkynes of Puns

39

Cosmonerd

40

How to Prepare a Formal Lab Report

42

Anatomy of a Science Student

Islands

On the Front Lines of Climate Change

BY CURTIS W MRAZ

Islands, from a biological stand point, are particularly interesting. In fact, modern evolutionary theory has redefined islands to give them value for their isolative properties. Islands, if truly isolated and independent, are scientifically unique in the sense that factors of change are relatively easy to determine. Historically, the world’s largest nations have done little to refrain from exploiting this inherent scientific value. This trend was exemplified between 1946 and 1958 while the United States test detonated twenty-three nuclear weapons on Bikini Atoll of the Marshall Islands, displacing the 167 permanent inhabitants of the island community and exposing many to unprecedented levels of nuclear radiation (1). The largest of these blasts, ”Bravo”, was a fifteen-megaton blast responsible for vaporizing three of Bikini Atoll’s smaller islands (1). With the pass of time comes humanitarian and biological insight that allows us to “[rethink] ways in which science used the isolated island concept to produce some of the most apocalyptic technologies on earth [and] challenge both the assumption of the primitive ahistorical island and what constitutes the laboratory itself ” (2). Mustn’t we carry this insight forward in the age of a changing climate?

Unfortunately, climate change has brought a unique threat to the front door, both literally and figuratively, of island communities.

It is no exaggeration to say that climate change is waging a disproportionately large ecological and humanitarian war on island communities. The same geographic isolation that advocated for lab-rat scientific policies in the age of nuclear testing now proves to provide the driving forces for natural disasters, extreme ecological disruption, and humanitarian neglect—characterized only by hegemonic distaste for accepting responsibility of global, and economic, petrochemical addictions.

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As climate change rapidly increases the amount of heat stored in the world’s oceans, the biological integrity of ecological island communities experiences novel threats (Figure 1). Many scientists have chronicled the decline of endemic species as they are outcompeted by invasive species introduced by warming waters and variable climatic conditions (3). The impacts of invasive species on island communities, like lion fish and feral pigs, is thought to be more economic than biological by some. With feral pigs leading to the destruction of Hawaii’s coral reefs, ecological tourism takes a hit, ultimately stunting a very necessary sector of island economies (4). The presence of invasive species is only thought to increase in island communities as more extreme storms and weather patterns provide a means to disperse plants and insects over longer distances and through different patterns than before (5).

The same storms aiding in the distribution of invasive species, many of them unprecedented in magnitude, are causing disproportionate humanitarian crises on island communities, amplified by geographical isolation and political stagnation. Typhoon Haiyan devastated the Philippines on November 9, 2013 (6). Many scientists contribute the magnitude of this storm to ocean waters warmed by climate change (7). Most recently, Hurricane Maria quickly elevated from a tropical storm to a category 5 hurricane in 27 hours (8). Maria, the sixth largest storm to hit the United States and the strongest storm to hit Puerto Rico in 80 years, dumped up to 30 inches of rain on parts of the U.S. territory on September 20, 2017 (9). Storms like these, the ones that devastate island communities, build off of warm waters, light winds, well vented rising air, and ample moisture and are often trapped over island communities by mountainous geography (8). Anthropocentric climate

change is generating the perfect recipe for these storms.

Unfortunately, the storms hit the front lines first. These front lines—island communities—are simultaneously being plagued by climate driven ecological destruction and subsequent economic depression.

As a leading polluter and contributor to climate change the United States has a moral obligation to offer these communities culturally and geographically appropriate solutions. Instead, climate denying policies and lobbying seek to dismantle the science that recognizes the disproportionate and unethical effects felt by island populations. More than a month after hurricane Maria struck, two-thirds of the population remained without power (10). Food security continues to be a key issue in the Philippines since typhoon Haiyan struck in 2013 (11). Instead of recognizing this age of climate chaos as a reality and opening doors to climate refugees, the U.S. government has done the exact opposite: closing doors to refugees and restricting financial aid to disaster relief efforts. Biologically, we can not stand to lose the genetic diversity found within endemic island species. Socially, we have an obligation to ensure the safety and security of island civilizations on the front lines of climate change.

Illustration: Emma McAllister Images: Wikimedia Commons

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REU Programs

What they are and how to apply

BY ERIN STEWART

We all know that the very first thing you want to think about after finals week is: “what should I do this summer?”

Good news! If you’re interested in research, the National Science Foundation has a great set of summer research programs under the catchy title “Research Experiences for Undergraduates” (REU). Essentially, REUs are paid, full-

time summer research internships that any United States undergraduate student can apply to. There are a large number of REU sites across the country, from California to New York, and from Florida to Alaska. These sites are generally located at public research institutions, such as universities, and host about ten students each summer. The specifics vary place to place, but REU programs typically last ten weeks; provide housing, a stipend, and funding for food and travel; and are open to any student that hasn’t yet graduated. Most programs also include a number of professional development workshops and excursions (read: field trips), and culminate in a research paper or symposium.

REU programs are offered in all the major scientific disciplines: as of October 2017, there were 143 sites listed for biology, 82 for chemistry, 61 for physics, 93 for computer science, and 57 for math. These programs focus on a wide variety of subjects, such as tropical ecology, epigenetics, green synthesis, food toxicology, astronomy, nuclear physics, artificial intelligence, robotics, cryptography, and quantum computing. Apart from the major fields, there are also sites focusing on social, behavioral, and economic sciences. To check out all the disciplines and sites, Google “search for an REU site” and click on the NSF website.

If this sounds like your idea of an awesome summer, here are some tips on applying:

Illustration: Carlisle Huntington 8 | ELEMENTS

(1) Picking REU sites. REU programs are somewhat competitive (many receive up to 300 applicants for 10 positions), so don’t place all your cuckoo eggs in one host nest. Unlike college applications, no programs require an

application fee, so apply to as many as you can! In addition, try to choose sites based on your academic interest, not based on location or site prestige. Choosing a site you’re genuinely interested in will help you write a stronger, more sincere application essay. Plus, big-name universities usually get more applicants, and are thus harder to get into, so applying to a variety of sites will likely increase your odds of acceptance.

(2) Applying. Once you’ve picked out all your sites, consider putting together an excel spreadsheet to keep track of all the deadlines and application components. The earliest application deadlines are in late January (so maybe start working on them over winter break).

Statement of Interest. This is essentially a short essay in which you outline your motives for applying to the program, as well as any past experience. If you selected programs you’re genuinely interested in, this shouldn’t be too hard! Just talk about what you’re interested in and why. In addition, many applications ask you to select three research mentors that you would most like to work with from a list of ten or more. If this is the case, spend some time reading about each mentor’s research, select those which sound most interesting, and explicitly address those specific research interests in your essay.

(3) Resume/Transcripts. Most programs will ask for a resume and/or a transcript. Don’t be worried if you don’t have previous research experience to put on your resume!

While some of the programs are looking for students with research experience, many are not. Remember – REU stands for Research Experiences for Undergraduates, so the primary goal of these programs is to allow students to engage in research, especially if they haven’t done so previously. And even if you haven’t done formal research, you probably have other relevant experiences and skills, whether they be from classes, labs, extracurriculars, or

jobs. Make sure to highlight those on your resume. In regard to your transcript – again, don’t worry if you haven’t taken many classes in the subject area of interest. If programs are looking for students of a certain class standing or with certain academic credentials, they will usually tell you in the “Eligibility” section of the program description (so make sure to read this section!).

(4) Letters of recommendation. Two letters are a fairly standard requirement for applications. While you can ask for letters from people within your subject area of interest, this isn’t a necessity – I asked my chemistry and anthropology professors, and was accepted into a REU in marine biology. The most important consideration is whether they can write you a strong recommendation!

One last plug: This past summer I participated in an REU at the University of Massachusetts-Dartmouth, which not only enabled me to travel to the East coast for the first time, but also showed me what research looks like at a larger, public university that hosts both undergraduate and graduate programs. Because of this, I was able to learn more about what graduate school is like, which will help inform my post-undergraduate decisions. With regard to the research experience itself, I studied how rockweed responds to run-off, which allowed me to explore my interest in ecotoxicology, and gave me a new appreciation for that weird, lumpy, brown, slimy-looking stuff you see all over Pacific Northwest beaches. Furthermore, I had a fantastic research mentor who provided me with lots of insight regarding careers in science. As a result, I would highly encourage anyone with an interest in research to apply to REU programs, as they’re a great way to explore and define your areas of interest, develop research skills, and meet peers and professionals with a variety of scientific backgrounds.

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Student

“My predominant research experiences at UPS have been solo projects that I undertook with Professor Amy Spivey, and while the one-on-one interactions are valuable in their own way, it’s hard to imagine what it’s like to work in a lab of 10-15 people who share rooms full of equipment, coordinate time using different machines, and come and go on their own schedules. The REU research experience is different from anything I’d done before, and I couldn’t be more grateful for the chance to see that aspect of research.

“I loved my REU for the people I worked with and the people I lived with. . . My REU cohort had physics majors from all over the United States interested in so many different branches of physics, and talking with them about what their life-plans were, what we were doing in lab, and what our frustrations were throughout the summer was one of the best parts of the experience.”

-JORDAN FONSECA

“As with any internship, my experience had its ups and downs, but I learned a lot about myself and am extremely glad I had the opportunity to be part of such a great program. Bozeman, MT was a fantastic place to spend the summer; virtually every weekend was spent exploring the outdoors with my fellow REU members, there was a dog park just a few blocks from campus, and downtown Bozeman is an extremely vibrant place that left me with many fond memories.

“In my opinion, an REU is more about building relationships, learning about how research works in a larger institution, learning new skills and techniques both inside and outside of lab, figuring out if you want to pursue research as a career and what kind of research you want to do, and essentially building your confidence as a scientist. Don’t be intimidated by the competitiveness of REUs; choose programs with research that really interests you, and make sure every sentence of your application lets them know why you want to be a part of their specific project.”

REU

-MEGAN TEGMAN

Experiences

“I have come to appreciate that this past summer was so much more than the sum of its ‘programmed parts.’ I was challenged to think big, and to think forward. I made mistakes, and I was committed to learning from them. I was inspired by the research of experienced professionals, and I gained certainty about pursuing a career in medicine.

“I got to be part of a new discovery that might someday make all the difference for patients suffering from traumatic skin conditions, and that was one of the best things I took away from this experience. Although I am still wholeheartedly committed to a career in medicine, this summer helped me realize that it is possible to keep one hand in the field of research. The prospect of discovery through deep investigation is a powerful image in my mind, and without the GSIP program acting as my guide, I might never have come to this realization.”

-ELENA FULTON

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REU: Optoelectronics Studying a Van der Waals Heterostructure

BY JORDAN FONSECA During the summer of 2017, I participated in a 10-week Research Experience for Undergraduates (REU) at the University of Washington. I worked in Professor Xiaodong Xu’s experimental solid-state physics lab, which addresses research questions in optoelectronics - the branch of physics that explores the interaction between light, electricity, and magnetism in matter. In particular, researchers in the Xu lab search for previously undocumented physical phenomena (new physics) in the nano-scale limit. As a physics lab, the objective of research is not an application of knowledge, but rather new knowledge itself. The results of physics research often have other applications and uses; however, these applications often appear years after research is conducted and are not the motivation of undertaking the research.

In physics classes, new concepts are often introduced first in a single spatial dimension (throwing a ball straight into the air, for example), which simplifies the calculations and makes new topics easier to grasp. As students develop, problems grow more complex, perhaps including up to

three spatial dimensions to better model the “real world,” which we think of as inherently three dimensional. Three dimensions, however, are not always more interesting than two.

In particular, the Xu lab studies materials so thin that they can be thought of as one or two dimensional. The lab employs a host of sophisticated fabrication and characterization techniques, many of which have only been discovered recently and are continually revised.

The “devices” that I assembled in the lab are microscopic-made from materials ranging in thickness from a single molecule (monolayer) to tens of molecules. Although there are potential applications of this research to information storage and energy harvesting, the primary interest of the Xu group is to discover how ultra-thin, complex material structures behave when they are exposed to laser light under different electric and magnetic fields. By experimentally observing this behavior, physicists can develop better understandings of why one- and two-dimensional materials behave they way they do. This knowledge not only informs

Figures: Schaibley et al., with permission (1) FIGURE 1: (a) Monolayers of different materials (left) can be stacked together much like Lego bricks (right) to build a van der Waals heterostructure. (b)On the left, note how an electron that is first excited in WSe2 is first excited into the conduction band (upper blue line), leaving a hole behind in the valence band (lower blue line). After that, the electron moves to the MoSe2 conduction band (upper red line), which is at a lower energy. The figure on the right shows these interlayer excitons stretched across the two materials.

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how humans think about the world, but also how we create new technologies.

In many ways, the well-known discovery of monolayer graphite, or graphene, paved the way for the study of more complex two-dimensional (2D) materials and structures.

Although there are many different materials that can now be obtained in monolayer flakes, the two that I used are MoSe2 and WSe2, chosen for their optical properties, discussed below. Physicists now study monolayer materials not only on their own, but as single layers in larger devices consisting of layers of different materials stacked together into a van der Waals heterostructure (Figure 1a). The term “van der Waals heterostructure” is daunting, but it simply refers to a structure consisting of different materials (hence, hetero-) that are held together by the van der Waals force, a weak “stickiness” that results when electrons in each material re-arrange themselves very slightly so that a weak electric attraction pulls the two materials together.

In part, the lab chose to study monolayers of MoSe2 and WSe2 because these materials can efficiently absorb visible light by using the energy from the light to excite a valence electron into the conduction band (where electrons can move freely through the material as if it were a metal). When an electron moves from the valence band to the conduction band, the previously neutral region it leaves behind is positively charged, and for convenience physicists treat this positively charged, empty region of space as its own “quasi” particle called a hole. Electric attraction between the positive hole and negative electron causes the pair to tend to stay near each other (much like

an electron is attracted to a proton in the Hydrogen atom), and together they are commonly known as an exciton. In a monolayer, the exciton combines with the hole after a brief time, releasing energy as light in the visible spectrum.

When MoSe2 and WSe2 monolayers are stacked vertically (Figure 1b), however, an additional transition takes place between the materials. If a visible photon excites an electron in WSe2, the electron can naturally jump into the other material, MoSe2 because this puts the electron in a lower-energy state (Schaibley et al., 2016). When a hole is in one material and an electron is in the other material, the pair is called an interlayer exciton (see Figure 1b).

To actually study the behavior of interlayer excitons, the MoSe2/WSe2 bilayer must be enclosed in an insulating “sheath” of boron-nitride and surrounded by endcaps of conducting graphite (Figure 2). While it is impossible to address in detail the reasons for this composition and stacking order, the punchline is that the graphite endcaps enable researchers to put the completed device in a circuit and create a controllable electric field around the MoSe2/ WSe2 bilayer. The insulating boron nitride prevents electrons on the graphite from rushing onto the bilayer, which must remain neutral for this study.

To understand how this electric field changes the way light interacts with the van der Waals heterostructure, the Xu lab focuses laser light onto the bilayer and measures the wavelength, intensity, and polarization of the light that the interlayer excitons emit. Comparing the difference

FIGURE 2: Schematic of material position in a completed device. Graphite endcaps can be charged like a capacitor to create an electric field between the graphite pieces, and thick layers of boron nitride prevent the electrons from flowing from the graphite onto the MoSe2/WSe2.

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FIGURE 3: Plot showing how the energy of light emitted by interlayer excitons changes when an electric field is applied. The red curve shows natural emission, without any field, while the black and green curves show a decrease/increase in energy when an electric field is applied parallel/anti-parallel to the exciton dipole moment, respectively.

between the incident laser light and the light emitted by excitons in different electric fields gives researchers an indirect way to study how the electric field changes the materials’ properties. Thus, studying how light changes after interacting with the material gives physicists a clever way to try to understand what’s happening in the material itself.

Figure 3 shows data that I collected on a sample identical to the ones I assembled over the summer. The plot is best understood by focusing on the arrows underneath the three different curves. The brown arrow represents the direction of the external electric field, created by adding electrons to one of the graphite endcaps and removing them from the other. Depending on which plate the electrons are added to, the electric field can either point up or down, or be turned off completely. The purple arrow is technically the “exciton dipole moment,” but just think of it as always pointing from the electrons, which move to MoSe2, toward the holes, which stay in WSe2. Figure 3 shows the intensity of the emitted light plotted versus the energy (which is associated with the color of the light). The red curve represents the “natural” emission of the interlayer excitons, without any electric field present. The black and green curves show how the energy of the emission changes when an electric field is applied. The energy (color) of the light changes for different electric fields, so something must be happening in the material!

When the electric field and dipole moment point the same direction (black curve), the emission energy is lower than the natural emission energy. When the electric field and dipole moment point in opposite directions (green curve), the emission energy is greater than the natural emission energy. This result is qualitatively consistent with the theoretical predictions for a dipole interacting with an electric field, although this theory is not presented here.

The interested reader can explore the Stark effect for a more thorough explanation of why this happens.

The experimental results discussed here are difficult to obtain. From finding usable monolayer flakes of MoSe2 and WSe2 to precisely stacking the different flakes in the right orientation to preparing the complicated laser setup required to collect and interpret the light emitted from such a tiny device, the challenges of undertaking such experiments cannot be overstated. As is so often the case in physics papers, the millions of dollars of equipment, countless precise experimental procedures, and hundreds of hours of work that go into producing even a single figure have been glossed over. On the flip-side, I’ve only discussed (and briefly at that) one of the countless aspects of van der Waals heterostructures that scientists study. The physics of 2D devices remains a rich and rapidly expanding frontier of materials research, and there is certainly more knowledge and technology to come out of what physicists learn from these exotic structures.

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REU: Biochemistry Fructose and Copper: Potential Culprits in the Development of Non-Alcoholic Fatty Liver Disease

BY MEGAN TEGMAN As the Western diet - characterized by high fat and sugar content - has been rapidly introduced in the U.S. and other countries worldwide, metabolic syndrome (MetS) has become an increasingly prevalent global health issue (1).

MetS is a relatively new disease, yet it already affects 1 in 6 Americans, increasing their likelihood of developing type II diabetes, insulin resistance, and cardiovascular disease.

Non-alcoholic fatty liver disease (NAFLD) is considered the hepatic (liver) manifestation of MetS and is implicated in a myriad of metabolic malfunctions, and untreated NAFLD can lead to permanent liver cell damage. One suspected culprit behind NAFLD development is sugar, particularly fructose; as the production and consumption of highfructose foods has risen, cases of obesity and diabetes have concurrently skyrocketed. Is this mere coincidence, or is fructose a key player in the development of MetS?

FIGURE 1:

According to the USDA, the average American consumes over 150 pounds of refined sugar per year, more than 20 times the amount consumed in the 1700s.

Image: Wikimedia Commons

To understand why fructose may be wreaking havoc on our metabolisms, we must dive down into the biochemistry of how we process consumed sugar. Glucose can be used by virtually all cells in the body and acts as our main source of carbohydrate energy. Glycolysis, the metabolic process that breaks glucose down into ATP (energy), is highly regulated by the enzymes hexokinase, phosphofructokinase, and glucokinase, which are controlled by blood glucose concentration and the energy requirements of the cell.

Fructose, on the other hand, is primarily metabolized by the liver, causing it to undergo a completely different metabolic process (Figure 2). Unlike glycolysis, metabolic fructose breakdown (fructolysis) is largely unregulated.

Liver cells will start breaking down fructose into triose-phosphates regardless of whether insulin is present, and this fructokinasecatalyzed reaction is not controlled by negative feedback. This causes ATP depletion in liver cells, which can wreak havoc on other hepatic functions. Triose-phosphates can be converted into pyruvate (a common metabolic intermediate capable of producing energy via the citric acid cycle), but FIGURE 2: Schematic of fructose metabolism in the liver. most of the triose-phosphates produced by fructose Figure: Lustig, R. with permission (2)

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are converted into glucose and safely stored as glycogen.

The real problem occurs when someone consumes too much fructose; after exhausting its other possible metabolic functions, fructose is converted into fatty acids through the process of de novo lipogenesis and ultimately synthesizes VLDL-triglycerides (TGs). De novo lipogenesis is thought to be crucial to NAFLD development, because hepatic TG build up is the main characteristic of NAFLD. In rodent models, a high-fructose diet is a common method of inducing symptoms of metabolic syndrome, and the majority of human NAFLD patients consume excess fructose. Fructose is a simple carbohydrate (sugar) that is found in sucrose (table sugar), high-fructose corn syrup, and fruits. It is important to note that like many other foods, eating fructose in moderation is unlikely to cause MetS or NAFLD. However, when we consume large quantities of fructose over a long period of time, we slowly accumulate TGs in the liver and are extremely FIGURE 3: Proposed interactions between fructose, copper, likely to develop NAFLD. Soft drink consumption is and NAFLD. Figure: Morrell, M. et al. with permission (3) one of the largest contributors to metabolic disease; people who drink soda on a regular basis have a high NAFLD (Figure 3). risk of developing NAFLD in their lifetime, so consumers This summer, my REU project used H-NMR in a must be aware of the high risks associated with chronic metabolomics approach to identify metabolic markers consumption of excess fructose. for NAFLD. “Metabolomics� is the study of small

In addition to high sugar, inadequate copper may molecules (metabolites) and their interactions within a also be an adverse aspect of the Western diet. Copper biological system, and the goal is usually to identify which deficiency (CuD) is thought to contribute to NAFLD metabolites are majorly influencing certain processes or progression by altering lipid metabolism and promoting phenotypes. Combining metabolomics with results from hepatic triglyceride accumulation. Cellular copper proteomics (study of proteins), transcriptomics (study of homeostasis is maintained by copper-specific membrane mRNA), and genomics (study of genes) can build a detailed transporters and intracellular copper chaperones, with picture of what’s happening differently between diseased the liver acting as the main regulatory organ of copper and healthy cells. Though it has limited sensitivity and is homeostasis. Copper is harnessed by the liver and highly pH-dependent, nuclear magnetic resonance (NMR) distributed to other organs via the circulatory system. is an excellent approach for metabolomics research due roper mitochondrial function also requires copper, and to its high reproducibility, quantitative potential, ability to CuD and NAFLD induce similar changes in mitochondrial characterize non-ionizable compounds, and rapid and nonfunction, indicating that the two diseases may be related. destructive sample analysis.

Patients with NAFLD have notably lower hepatic copper

To examine the effects of fructose and copper on concentrations than patients without NAFLD, and copper NAFLD, male and female rats were fed one of four diets: content within tissue has been shown to increase as liver high fructose (30% w/v in drinking water, +F), no fructose steatosis (damage) increases. Some studies suggest that (plain drinking water, -F), adequate copper (12 mg/kg in CuD and high fructose diets may cooperatively contribute food, +C), and deficient copper (>0.2 mg/kg in food, -C). to MetS and NAFLD progression, and fructose may heighten My lab tested the livers of these rats (24 total, 12 male and the effects of a CuD diet, or even induce CuD, contributing 12 female) by extracting polar and non-polar metabolites to increased lipogenesis, inflammation, and oxidative for H -NMR analysis. We consistently identified 54 polar stress. A CuD diet is also shown to induce insulin resistance metabolites in all 24 liver samples, with significant and NAFLD in rodent models. The potential relationship differences in metabolite concentrations among the dietary between fructose, copper, and MetS is still unclear, but groups. Partial least-squares discriminant analysis (PLSmany studies suggest they are all jointly implicated in DA) of female polar metabolites (Figure 4) shows no overlap

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FIGURE 4(A): PLS-DA of female polar metabolites (A) and male polar metabolites (B) determined by 1D 1H NMR. Red(Δ) = +F+C, Green(+) = +F-C, Purple(X) = -F+C, Blue(◊) = -F-C. Each of the four diets was mathematically associated into four distinct groups. A higher amount of distance between two groups means that their metabolite profiles are highly dissimilar. For example, the +F+C and +F-C groups in the female plot show no overlap and are far away from each other, while the same groups in the male plot overlap slightly and are in closer proximity, suggesting that their metabolite profiles are more similar and the one difference between their diets (copper level) doesn’t seem to affect males as strongly as females when combined with high fructose. between the +F+C (red) and +F-C (green) dietary groups. In contrast, PLS-DA of male polar metabolites (Figure 5) shows a noticeable overlap between +F+C and +F-C samples. This suggests that male and female rats metabolize copper differently, where copper has a less significant effect on the metabolite concentrations of high-fructose fed rats when compared to females. One explanation is that copper may exhibit a degree of toxicity in the females; the “adequate” copper provided in the diet may have been excessive for female rats, and therefore induced a different metabolic response than in males. The difference may also be due to the effect of sex hormones on male and female processes.

In some studies, chronic high-fructose diets caused triglyceride levels to increase in male rats, while females rates seemed to be protected by fructose-induced metabolic changes. However, another study suggests that female mice were more susceptible to NAFLD than male mice because high fructose caused more liver damage in females.

-F+C and -F-C diets were expected to group closely in both males and females dues to the absence of a high-fructose effect, but instead exhibited distinct separation, suggesting that copper may still impact metabolic function regardless of dietary fructose content.

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Non-polar metabolite extraction of the male and female rat livers showed no differences between diets, and no differences between sex. These results were unexpected, because high-fructose diets were expected to induce hepatic TG accumulation. Perhaps NAFLD was not fully developed, or may be in an early stage when TGs are still released into the bloodstream and not stored in the liver.

Future experiments will analyze blood serum samples, and may clear up whether NAFLD is present in these rats or not.

There is still a lot of work to be done on this project, and determining whether or not copper deficiency is an aspect of NAFLD that could potentially be treated (e.g. with copper supplementation) is one step towards reducing the dangers of this disease. In an environment ruled by processed foods and high fructose corn syrup, we must have an awareness, as consumers, of exactly what we’re choosing to eat. Fructose itself is not inherently evil, but if we continue to eat it in such large quantities over the course of our lives, the prevalence of NAFLD will only continue to increase. Do your research, be conscious of the ways you’re getting your energy, and remember that the choices you make now will impact your health 10 years from now.

REU: Regenerative Medicine Using Stem Cells to Improve Skin Grafting Technology

BY ELENA FULTON As humans, we are comprised of many unique systems, tissues, and organs, the largest of which is our skin. This layer of cells protecting us from pathogens, chemicals, and UV damage plays such an important role in our survival that it would be difficult, and very unpleasant, to imagine living without it. Given the role of this key player in our lives, it is important to investigate what happens to the people who sustain significant damage to the skin. How do we effectively help people with burns, deep wounds, or inherited genetic conditions? In the medical field, a common solution is the use of skin grafting technology however we are now starting to realize the limitations of this treatment.

Autografts (where skin is taken from a different part of the patient’s body) are very common, however for extensive wound coverage, or genetic conditions, autografts have limitations in terms of how much skin can be harvested without damaging the dermal layer of the donor site (1).

Allografts and xenografts (where skin is donated from another individual, or from an animal) also have risks associated with rejection, and therefore must be replaced within a week to prevent negative consequences (1).

Although grafting is still a very popular technique, recent advancements in stem cell technology are changing the way we think about treatment options. Historically, the conversation about stem cells has centered around the ethical question of whether or not to use embryonic stem cells in biomedical research. In the early days of this field, populations of stem cells had to come entirely from human

FIGURE 1:

Differentiation of induced pluripotent stem cells into unique cell types/tissues.

Image: Wikimedia Commons embryos; this was clearly not a sustainable resource. In 2006, the field began to change when Shinya Yamanaka and his team discovered that normal adult tissues could be “reprogrammed” to create an entirely new category of stem cells (2).

The discovery of “induced pluripotent stem cells” (IPSCs) marked a transition away from the embryonic debate and into a new era of biomedical research that, now, no longer relies on the use of human embryos as the primary source of stem cells. Today, researchers are able to create their own “pluripotent” stem cells from adult tissues such as skin or bone (2). These cells are particularly exciting because they have the potential to become any other cell in the human body (given the right conditions). In a broad sense, induced pluripotent stem cells (IPSCs) are created by exposing adult tissues to four main transcription factors (OCT4, SOX2, KLF4 and MYC), which cause the adult tissues to revert back to a stem cell state (3). By

FIGURE 2: Process of the generation of induced pluripotent stem cellderived skin equivalents.

At the differentiation stage, all necessary skin cells are generated, and then combined to make one, full-thickness graft.

Figure: Bilousova Lab UNIVERSITY OF PUGET SOUND | 17

FIGURE 3: Process of epithelial to mesenchymal transition. Figure: Jakobsen et al. with permission (4) exposing a population of IPSCs to specific growth conditions, it is possible to then differentiate them into tissues such as heart muscle, liver tissue, kidney cells etc. (Figure 1)(3).

Over this past summer, I took part in an 11 week program at the Gates Center for Regenerative Medicine in Denver, Colorado. I was placed in a dermatology lab focusing on how we can use IPSCs to create full-thickness skin grafts that could potentially replace current grafting techniques. These grafts rely on the creation of epidermal skin cells, dermal skin cells, and vascular tissue to be successful, and each cell type must be derived from IPSCs. Donor skin biopsies were reprogrammed into a large population of IPSCs, which could then be used to create the various layers of the skin grafts (Figure 2). My project specifically focused on the differentiation of IPSCs into endothelial cells, which are critical for the survival of these grafts post-transplantation. Endothelial cells create the network of blood vessels found throughout the human body, but they are quite unpredictable when differentiated from IPSCs. Current differentiation protocols (see Patsch C. et al.) result in a stable population of endothelial cells immediately post-differentiation. Unfortunately, these cells lose their endothelial identity within two or three passages. In general, all types of cells possess unique “markers” either on their surface, or in the cytoplasm, that distinguish them from other cells.

Endothelial cells, for instance, possess surface markers such as E-Cadherin which help them “stick” together with other cells. The markers serve a particular purpose in the body (or in

a full-thickness graft) but we can also use them to assess the identity of our differentiated cell population. The differentiated endothelial cells I worked with this summer would consistently lose their standard endothelial markers over time (they would not express the surface proteins/marker that we normally expect any endothelial cell to have), and in general, this creates a huge roadblock for the development of full-thickness skin grafts. We hypothesized that the IPSC-derived endothelial cells were going through a process known as “epithelial to mesenchymal transition,” (EMT) which causes endothelial cells to revert back to a stem cell-like state so they can migrate and proliferate (Figure 3). EMT is a process that facilitates cancer metastasis when tumor cells break away from the main mass and dedifferentiate back to a stem cell-like state. They can then migrate to a different location and begin proliferating.

Over the duration of my program, I tested a small panel of cancer treatment drugs (which had previously been shown to inhibit EMT in breast cancer cells) on different populations of IPSC-derived endothelial cells to see if I could inhibit the process of EMT. With each passage, half the cells were collected and re-plated (moved to a new plate to continue growing) while the other half was analyzed by flow cytometry to assess the expression of endothelial markers (Figure 4). It took many weeks to get the experiment in full swing, but after a few replicates, we discovered that the drug Pyrvinium Pamoate (PP) was able to keep the population of IPSC-derived endothelial cells in

FIGURE 4: Cells tagged with a particular fluorescent antibody are probed with a laser, and each antibody emits a particular wavelength of light. The detected signal is then converted into interpretable data which offers information about marker expression within a population of cells.

Figure: Abcam (5)

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a stable state (Figure 5). This was the first time any lab had been able to keep these cells in culture for more than two passages, and we were able to successfully maintain them past passage four. With a stable population of endothelial cells, the lab was able to continue moving forward with a mouse model for the engineered grafts, which would then continue on to human trials in the future. Not only was this discovery beneficial for process of engineered skin grafts, it also led to an amendment of current differentiation protocols which will hopefully help move the field of stem cell research forward in its ability to mimic the anatomical processes that occur in all humans.

Although a simple amendment seems like a small drop in a very large bucket, the results from this project could

A

potentially cause a much greater ripple effect. The field of stem cell technology is just beginning to unlock its full potential, and in the specific context of grafting, we are getting closer and closer to offering a better treatment option for problems concerning the skin. Countless people are able to benefit from this technology, and the information we gained from this summer will help future researchers generate better cells that will ultimately lead to more stable grafts for the people who need them.

B

FIGURE 5: (A) Flow cytometry results for untreated IPSC-derived endothelial cells after passage two. Cells are negative for both CD144 and CD31 marker expression (CD31 and CD144 are endothelial cell markers while CD90 is a mesenchymal stem cell marker). (B) Data for IPSC-derived endothelial cells treated with PP after passage two. Cells are nearly all positive for both CD31 and CD144. % gated refers to the percent of the total cell population that has a particular marker expression profile. For example, in (B) 2.83% of the total population of endothelial cells express only CD31, but not CD144. This tells us that they are not fully endothelial cells. If they were, they should express both CD144 and CD31 (upper right quadrant).

VOCABULARY LIST Transcription factors: proteins involved in converting, or transcribing, DNA into RNA. Transcription factors include a wide number of proteins (excluding RNA polymerase) that initiate and regulate the transcription of genes (6).

Differentiation: The process by which cells or tissues change from relatively generalized to specialized during development (7). Prior to differentiation, stem cells have not committed to being one type of cell, so they possess no tissue-specific structures or functions.

Passaging/passages: The process of collecting and splitting a population of cells to allow for prolonged growth in culture (culture refers to the state of keeping cells immersed in a liquid “cell food” which contains the necessary nutrients to keep cells alive in an incubator).

Endothelial markers: Proteins expressed on the surface of endothelial cells that can be tagged and visualized with fluorescent antibodies which only bind to their specific target. Marker expression was used to determine the identity of the cell population post-differentiation, and after multiple passages.

Flow cytometry: “Flow cytometry is a popular laser-based technology (Figure 4) to analyze the characteristics of cells or particles” (5)

UNIVERSITY OF PUGET SOUND | 19

University of Puget Sound in its Natural Habitat: The Environmental Efforts and Impacts of Puget Sound

BY ANNA FRYXELL

“Loggers Live Green” is a catchphrase continuously bounced around the campus of the University of Puget Sound. The university prides itself on working towards sustainability and environmental equity by promoting sustainable habits and ethically conscious decisions, and most members of our academic community advocate for such a campus. The Puget Sound student body, staff, and faculty have made significant steps towards a green campus in recent years, but we have more growing to do. How can the Puget Sound community make a difference? How can we continue to make progress and educate ourselves about the sustainable actions that we, as a community, have accomplished?

The first step to solving this issue involves understanding the environmentally relevant actions currently taken by the university.

In terms of food and drink product waste, Puget Sound is off to a good start, but we can do better. About a year ago, members of ECO club and Dining and Conference Services (DCS) worked together to create a new design for the bottled water sold at the SUB in efforts to increase environmental consciousness and reduce sales of disposable bottles. The new labels, designed by former student Sophie Lev, say “DON’T BUY THIS (please)” and have a cartoon picture of a landfill. Since their release last year, there has been a 45% reduction in bottled water sales (1). Another one of the school’s goals is to decrease the amount of “to-go” coffee cups on campus. In response to this issue, Loggers Live Green recently hosted an event called “Sippin’ Sustainability” to educate people about where each of the components of a coffee cup go (recycling, trash, etc.), and the importance of bringing your own mug. ASUPS provides each incoming freshman with a free reusable mug, and students can use these mugs when

they go to Diversions or Oppenheimer Cafe to check off their “cup karma”. If a customer orders at a lucky time, students using a reusable mug may receive a free cup of coffee.

In addition, DCS provides students with the option of both “for here” and “to-go” containers, hoping that students will choose “for here” containers more often to reduce the usage of container materials. However, students frequently choose “to-go” containers even when deciding to eat at the SUB. Knowing whether you want your food for here or to go beforehand can minimize this wasteful occurrence. Also, if students take “for here” dishes outside of the SUB, it is important to eventually return the dishes because not doing so is costly for both DCS staff and students, resulting in even more waste from buying new dishes.

Furthermore, while the “to-go” containers are compostable, they do not end up being composted because Tacoma does not have a composting system; the closest system is in Seattle. The campus garden has a small site for composting, but cannot accommodate all student food waste.

Recently, students have submitted applications for Green Fee grants, funded by $3 of each student’s annual tuition. Thus far, the school has turned down every application related to composting. Despite the composting setbacks, a new implementation called the LeanPath system is reducing waste in the Diner. It consists of machines called “Insinkerators,” which turn food waste into plant fertilizer. In 2016, utilization of this system reduced food waste by more than 10,000 lbs, or 28% (2).

In addition to repurposing food scraps, the University of Puget Sound is trying to stop uneaten food from going to waste. One of these ways is displaying some of the food

How can we continue to make progress and educate ourselves about the sustainable actions that we as a community have accomplished?

20 | ELEMENTS

from the previous day in the “Grab n’ Go” section of the SUB. Another method of eliminating food waste is the Food Salvage program, in which leftover food that has not yet been served is donated to a nearby transitional house. This program is based off of student volunteers from the Food Justice program who package and redistribute food from the SUB three times per week.

A major group on campus that helps manage our school’s environmental impact is Sustainability Services. It has a “Waste Diversion”programinwhichdonatedorcollecteditemsareeither recycled or reused. For example, at Grizz’s Garage Sale, gently used items are sold with the intention of reducing the purchase of new items. In addition, Recycling Club collects cardboard boxes from the mailroom and makes a cardboard castle out of them each spring, collecting more than 1,500 boxes each year.

They then supply the boxes to students moving out of the dorms at the end of the year. Another environmental achievement is that clubs and organizations now have the option of hosting “zero-waste” events, in which all food and plates are composted, and there is minimal usage of paper and other handouts (3).

Currently, one of the most widely-known environmental projects at Puget Sound is divestment. The school’s divestment campaign is a collaboration between ECO club, Loggers Live Green, and other sustainability groups around campus to push towards divesting our school’s investments in fossil fuels. Thus far, 12% of the university’s endowment is invested in fossil fuel companies, which amounts to about 38 million dollars. The motives behind divestment are to live

up to the “Loggers Live Green” catchphrase and to be more environmentally ethical. Since the university prides itself on activism and living amidst the beautiful nature of the PNW, it is our responsibility to live up to those expectations and protect both the surrounding nature and people. Divestment would not only be an accomplishment for our school; it would also send a message to colleges, universities, and other institutions around the country and the world to join the bandwagon.

So, where are we in the process? Have we divested yet? Not really... A couple years ago, the Board of Trustees passed a resolution centered around divestment and ruled that the Board will refrain from investing in coal and oil companies and will not make any new investments with a majority exposure to hydrocarbons. In other words, the Board will likely not choose investment packages containing 50% or more invested in coal and oil companies. That being said, as much as 49% of the money in an investment package could be put towards fossil fuels, and the word “refrain” is noncommittal. This compromise is a promising response from the Board and shows that they are willing to listen to students’ needs. However, we have not yet publicized our achievement for a few reasons: the language in the passed resolution is somewhat vague, and the Board stated that they will “not fully divest” in a statement in the spring of 2016. In order to wholeheartedly feel proud of our achievement as a student-Board collaboration, we need to forge a mutual understanding so we can clarify the language in the resolution.

In the meantime, the conversation continues.

While environmentalism can seem like an endless battle

ABOVE: The “Don’t Buy This” water bottle label designed by Sophie Lev

UNIVERSITY OF PUGET SOUND | 21

at times, remember that a sustainable future begins with a single step. We can all work together at this school and take the responsibility to be part of the solution. Perhaps it’s fostering conversations with your family or peers, voting for like-minded candidates, or getting involved with the campus and/or surrounding community. It is easy to feel hopeless after learning about environmental problems, especially after being told that climate change is an inevitable and neverending battle.

However, the steps UPS is taking to reduce our impact on the environment prove that the fate of the Earth can partially rest in our hands. Whether on an individual level by carrying a reusable water bottle, on a campus level by creating a composting system, or on an institutional level by divesting from fossil fuels, we can all work together to make a difference.

ABOVE: The popular “Divest UPS” sticker

Sustainability at UPS • The introduction of the “Don’t Buy This”

What you can do to help • “BYOM” - Bring your own mug! Reduce

water bottles has reduced their sales by

waste by bringing a reusable mug to any

roughly 45%.

campus cafe and have the opportunity

• ASUPS provides each freshman with a reusable coffee cup to reduce waste and promote sustainable habits.

• The Green Fee fund offers students a chance to implement their own sustainable ideas in the community.

• Sustainability Services provides campus

to get a free drink with the Cup Karma program.

• Order your food “for here.” The Cellar and on-campus cafes offer discounts if you skip the pizza box or paper coffee cup.

• Donate to Grizz’s Garage. Instead of throwing away that lamp you didn’t like,

clubs and organizations the opportunity to

you can donate it to be reused by someone

host zero-waste events.

who wants it!

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INTERVIEW WITH ALUMNA MEGAN ROOSEN-RUNGE Insider Info on a Career in Medicine

BY CARLY BAXTER

I got the privilege of interviewing a UPS alumna, Megan Roosen-Runge, who graduated from Puget Sound in 2009 with a BS in Biochemistry. Now, eight years later, she’s a resident physician at UW Medicine. As of recent, she was moved to work in a clinic in a small town in Alaska for a month, which is when I had the pleasure of doing a phone interview with her to get answers to some of the most concerning questions premed students have at this point in their career.​ CB: How many hours of sleep do you get on average?

MRR: “Well it’s a complicated answer because it’s so dependent on what I’m doing that month. As a resident and intern, you change what you’re doing every four weeks so it’s highly dependent on the job. Right now, I’m getting normal sleep, like 7 or 8 hours, but when I come back to Seattle at the end of the month, I’ll be on a rotation… I’ll spend at least 28 hours at one time at the hospital. And that means I may or may not get a little bit of sleep on that shift, so I might get, if I’m lucky, an hour or two of sleep within that 28 hours. On a typical night in between those shifts, I’d say I probably get 6-7 hours.”

What was the biggest challenge for you in med school and how did you work through it?

“To begin with, one of the biggest challenges I had was this concept of feeling like I was an impostor. I think people across fields feel that at various points in their career developments, but especially in medicine, I think we feel that a lot, and I think it comes in waves. When I first started med school, I felt it and when I started residency, I felt it again. I felt like, you know, how can I possibly be here, there’s so much to know, maybe I made a mistake.

I had really high expectations for myself. Having high

expectations for yourself isn’t a bad thing, but I think you also need to be realistic and learn to forgive yourself for being human and wanting to have friends and a life outside of school. So figuring out how to strike that balance between devoting enough time to studying, something that’s really important, and also being like you know what, I’m going to go hiking this weekend and it’s going to be okay! I don’t have to sacrifice those things that make me who I am for the sake of this school experience.”

How much did you prepare for MCAT? “I took a Princeton review course that was actually hosted at UPS when I was a junior. I also had all the Princeton review study resources and things like that. So I think it was a good five months that was blended in with my normal coursework that I studied in preparation for the MCATS. And certainly, if you decided to study over summer and decided to dedicate more consistent time to it, you could study in a shorter period of time.”

What did you do during your gap years?

“I got my masters in public health at UW and I actually got it in public health genetics.”

UNIVERSITY OF PUGET SOUND | 23

Did you stay where you did medical school for residency? Why or why not?

“For med school, I decided to go away because I had the opportunity to, and I hadn’t been away. For residency, similar to med school, I applied all over the country and had my own biases about where I would be happy living and I think that’s a big factor for most people. I had the added factor that I was couples matching, so I had met my boyfriend in med school and he was applying also so we decided together about where we wanted to apply. I knew I wanted to be closer to my family and it was also complicated by the fact that my dad got very ill when I was a fourth-year med student. So, I found that out in time to help make my decisions about my preferences of where to go for residency. It ended up being that I had a nice list all over the country with high quality training programs. But it’s important to understand that the residency application process is very different than med school because you get to make preferences, but then, in the end, it’s an algorithm that makes the decision.”

Do you know anyone who has taken the military route with medicine? And what is your opinion about that route?

“There has to be something that propels you through that. You just have to have that drive.”

“I don’t know that many people who have done it. And certainly, it’s a great option in terms of a way to make it more affordable.

I also had a friend who had applied for med school and went through a whole round of applying and didn’t get in, so he reapplied to military as another option. I think that - again, I’m not an expert- but the most obvious advantage is the financial one. I think that if you know going into it that you’re someone who wants more choice over where you are and a little more flexibility in that way, you have to think extra hard about that as an option.”

What is the best way to balance a medical career with other things in your life?

“That’s something I have struggled with back into undergrad and all the way through. With most of my colleagues and classmates, we are all really motivated

24 | ELEMENTS

and are this type A type of people but we also have lots of priorities outside of academics and our career path. So I think in medical school, it was important that I found a community. That I found friends that had similar interests to mine and have the similar drive to figure out how to not just be, you know, studying every evening but that we would have some normalcy to our lives. So we made a point to plan fun adventures and it wasn’t every week. But we made sure we did something once a month and put it on the calendar and we all got to have that as the little carrot out there to pull you through studying for tests or some sort of presentation or whatever it was. I am more of an extrovert so I have the natural tendency to make plans with friends and have friend/family dinners and things like that. But I also tried to make a point of having good food and making actual food for myself at least a couple times a week or going to the gym or on runs and that helped keep me sane. I think it was having the ability to pull yourself back and take a step back and remind yourself of what your priorities are. Because for me, if I do that, it’s really obvious. Yes, my career is really important to me but actually my friends and family are the most important thing. And that’s not true for everyone.

“Sometimes, your career is everything and that’s great too, but no matter what your priorities are, the ability to take a step back and acknowledge them is important. And I think you have to do that over and over again through training and that helps keep you on the right path.

“For example, when I was an undergrad, I ended up taking a year off that was unexpected because my grandma got sick and I had grown up with her next door to me my entire life. I had started my sophomore year at UPS and then she got sick and I had this critical window of time where I had to make a decision of whether I would withdraw from the semester now or stick it out. I still relied a lot on my mentors, so I could talk it out. I ended up having a really meaningful time with my family and some really cool experiences. That’s when I volunteered for the Indian health services for a month in New Mexico and wouldn’t have done that otherwise. I had a similar no regret moment when I was applying to residency and when my dad got sick.

I had been entertaining the idea of potentially spending my residency all the way across the country based on some wonderful interviews that I had. But when my dad got sick it was like oh, there’s no way. If I have the opportunity to be closer to my family then I have to do that, otherwise, I’d kick myself later. And that was just true to myself. The no regret model can apply to people with completely different values than my own. It’s pretty airtight most of the time!”

Can anyone become a doctor?

“I definitely think that anyone can become a doctor. You go out and sit down with a bunch of different doctors, you find an entire sector with different personality types. You have to be motivated for sure, like you have to have something that’s going to drive you through the process of the training. Whether that’s the decision of your future career working as a neurosurgeon or as a family doc in the middle of nowhere Alaska, whatever that is, I think the motivation or the drive and the intellectual curiosity about medicine and science has to be there. There has to be something that propels you through that. You just have to have that drive.”

actually can do something. I have something to offer them.

That’s incredibly humbling and rewarding and inspiring all at the same time. And you get to do that every day.”

What is the best advice you can give to an undergraduate on the premed track?

“I would say, be curious and explore. Keep exploring that question of whether medicine is right for me. Don’t be rushed to answer it. There is no reason to have to go barreling into med school straight from undergrad. You don’t have the opportunity to explore in this way at any other point, so I would say take advantage of that and don’t rush yourself through the process.”

What is the most fulfilling part of med school or residency for you?

What is your “why”?

“I think, for me, it’s multiple things.

Initially it was more intellectual curiosity. And, you know, everyone talks about the desire to help people and I think that’s still true. I think it was really the intellectual curiosity and my internal drive to constantly challenge myself was the initial why and then, it was a little bit in med school, but definitely in residency, when you realize that, being a part of the medical profession is such a privilege. Most people innately trust you in a way that is so sacred and it’s very powerful. By the time you get into residency and have a level of expertise and can say oh my gosh, someone really trusts me with their life or their loved one’s life and I can

Illustration: Emma McAllister

UNIVERSITY OF PUGET SOUND | 25

Washington before the Cascades The Magmatic Prequel to the Evergreen State

CAMERON WALLENBROCK Tucked away in the first floor of Thompson, there exist a string of classrooms into which few students ever venture. In these rooms, shrieks of frustration and epiphany echo through the walls at all hours. The air is thick; a permanent fog of dust particles hang overhead from the seemingly archaic methods of sample preparation: hammering, sawing, and pulverizing.

Occasionally, and much to the disapproval of the department, the long, black tables become covered in formulas and diagrams; these chalk scribbles are those of a mad people: geology students. Allow me to now give you some insight as to what exactly unfolds in these hallowed halls.

This summer, I had the pleasure of spending many an hour hunkered down in these dusty rooms exploring the history of modern Washington’s geologic origins. My research focuses on the tectonics driving the creation of our state, before the Cascades, during a geologic epoch known as the Eocene. Before delving into my work, a couple of basic geologic processes must be understood. Principally, the process of subduction; when an oceanic plate collides with a continental plate the oceanic plate folds under, or subducts, underneath the continent. As this plate (also called a slab) descends into the mantle, the intense heat

26 | ELEMENTS

and pressure conditions cause the breakdown of minerals in the slab. Specifically, hydrous minerals break down at 110 km, leaching water into the “mantle wedge” (the space between the subducting slab and the overlying continent).

This causes the mantle to melt and this melt is the magma that rises up through crust creating volcanism. Subduction is the process that created our beautiful Cascades and was also responsible for the chain of volcanoes that preceded our mountain range.

When we look at the Cascades, they align almost perfectly north-to-south and have relatively consistent ages along this axis. However, the rocks proceeding the Cascades act a bit differently. They are oriented in a completely different direction than the Cascades, and as you travel from northeast Washington to central Washington, these Eocene rocks get progressively younger. This indicates that, during this epoch, the oceanic plate was subducting at a different angle and that this 110 km depth was somehow moving to the southwest. A prominent theory is the idea that the subducted slab had begun a process of “rollback” wherein its net motion had begun to descend faster than it could move horizontally, causing the 110 km depth to “move” towards the trench (the collision point between ocean and continent). This helps explain the “younging” of volcanism towards the southwest, but at some point this subduction orientation makes a dramatic shift and the Cascades begin.

To explain this, we geologists Top Left: Diagram of suggest the subducting slab’s dip tectonics: slab rollback became so severe that the slab and breakoff broke off at an unknown point in time, falling deeper into the Left: Stirring a molten mantle but no longer pulling the sample in preparation ocean behind it. A new subduction for chemical analysis. zone began shortly thereafter at a

new orientation creating the Cascades.

This is all very exciting to geologists, I promise, and so my research focuses on a single rock formation, the Taneum Formation, which I believe represents the last subduction zone magmatism created by the former subducting slab, in order to establish some timeline of events for the processes of slab rollback and breakoff. The key to confirming this lies in geochemistry, isotopic analysis, petrography, and some form of imagination.

My summer of work began in the field, south of Cle Elum, where I labored for several hours each day with my co-researchers Jack Randall and Tommy Kimler before exhaustion “forced” us back to our picturesque camp for evenings near a gentle river warmed by campfires and Rainier. Together we made observations of the region and collected samples for future reference and lab analysis.

When we returned to Tacoma, we prepared our samples for ICP analysis; this mainly consists of taking rocks the size of footballs and smashing them with hammers, picks, and chisels until they become about the size of a pea and then placing them in a machine which can turn them into a fine dust. This powder is weighed out and heated to 1000°C until molten where it is quickly removed and dropped in acid, diluted, and bottled. The final product is an aqueous equivalent of the once solid rock, ready to be tested for its chemical and isotopic qualities. Side note: during the heating process, the sample must be stirred to make sure all of the fine particles are included in the melt. This means you get to roll a marble-sized molten rock around a crucible, which is something I never pictured myself doing – pretty sweet!

As the data accumulates, the exciting part of research really begins. Between my colleagues’ and my own formation, a story begins to unfold. The chemical characteristics of my own formation and Jack Randall’s are vastly different even though the geologic units were emplaced atop one another.

Later in the summer, we would fly to the University of Arizona to use their “laser ablation” lab where we would, in simpler terms, zap the mineral zircon with a laser in order date the sample. Our two units were even shown to overlap in eruption dates, making their chemical differences even more significant.

Above: Distribution of Eocene igneous rocks in Washington. Figure: Prof. Jeff Tepper We are still exploring the relationship between these units, and our findings will be published in our theses early next year, but – spoiler alert – we believe that our hypothesis is valid. The chemical and isotopic data seems to suggest that my formation is the remnant magnetism of the older subduction and that Jack Randall’s formation developed as mantle below the old slab and upwelled to fill the void from breakoff, creating its own unique magmatism. Since we have dated the samples, we can begin to prescribe dates to these tectonic shifts furthering our geologic knowledge of Washington state.

This opportunity has been very special to me, and I am incredibly thankful primarily to Professor Jeff Tepper for his unique ability to inspire students to learn and for his seemingly unlimited patience. Furthermore, thank you Jack Randall, Tommy Kimler, and Gloria Ferguson for spending so much time joyfully gallivanting through Washington with me, protecting our camp from small rodents, building trails, dancing around fires, and occasionally working on our project. Lastly, I would like to thank the Agricola Scholarship Fund for making all of this financially viable, without their generosity and support for the sciences I would have spent a summer making lattes.

UNIVERSITY OF PUGET SOUND | 27

Biomolecular Drivers of Phenotypic Plasticity in Plants 14-3-3 proteins regulate the Ubiquitin 26S Protease System

BY RYAN APATHY Weeks before the summer even began, Bryan Thines, PhD, factors, which are proteins that bind to a unique DNA my research advisor and a professor of biology and genetics sequence upstream of a gene to control the rate in which at UPS, challenged me to a beard-growing competition. “I that gene is transcribed. Increased regulation of such like to have friendly games within our labs,” he told me proteins alters the transcription activity of the gene that it after I received my research grant, “it encourages both regulates, therefore controlling the abundance of specific competition and camaraderie.” I had already been pranked proteins at a given time. Additionally, rate-limiting enzymes once by my lab after consistently forgetting the fourth “s” or stress sensors are frequently down-regulated in response in the word “assess” on a poster for a research symposium, to a number of environmental conditions, resulting in so I should have assumed that our summer work would the decreased function of their respective pathway. In be just as mischievous as the previous semester. I learned eukaryotic cells, the process of molecular regulation is quickly that work will become very boring if you don’t take dominated by the Ubiquitin 26S Proteasome System (UPS), time to find humor in the part of the work that is the most a highly complex system of protein degradation. intimidating.

A system as complex as the UPS requires regulation Before I go on, I must pause and provide a little of its own. Countless papers have been published that background information for the project that I undertook characterize the numerous ways in which the UPS is this past summer. To the best of my abilities, I have removed regulated, but there still exist many elements to this the dirty details that are only interesting to those who are process that have yet to be understood. Understanding embarrassingly fascinated by molecular biology. Bear with the factors that regulate this system is necessary to assist me: an organism’s survival against all forms of environmental Plants have evolved to possess incredibly powerful stress (think climate change). My research investigates a mechanisms for responding to external stress conditions. hypothesized form of UPS regulation, namely the unique In the presence of stress, the survival of plant cells interaction between the UPS and 14-3-3 proteins, another is contingent on its ability to adapt to these adverse important family of regulatory proteins. conditions. Each form of stress, from drought and cold to pathogenic invasions, requires an extensive method of cellular response. Often this response is regulated on the molecular level, as stress conditions can result in a cascade of reactions that alter the abundance or function of proteins needed to respond to ever-changing external environments.

For many eukaryotic species, a common method of environmental adaptation is the increased or decreased activity of proteins ABOVE: (A) Quaternary structure of an F-box protein. (B) that participate in all levels of stress response.

The SKP, Cullin, F-Box Containing Complex (SCF) selectively For example, proteins that can be regulated to targets proteins for degradation by the UPS. Specific targets initiate intercellular change are transcription are recruited to the SCF by F-Box proteins.

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Figure: Vierstra, R. with permission (1)

LEFT: Schematic

of the Ubiquitin 26S Proteasome System

Figure: Rahimi, N. with permission (2)

14-3-3s are highly conserved proteins that serve a wide range of regulatory functions, including the facilitation and promotion of intercellular change. There are 13 distinct 143-3 proteins in Arabidopsis, but they all share a large degree of similarity, particularly within the protein domains that facilitate the interaction with client proteins. Specific biological functions of 14-3-3s range from the direct binding of a client protein to prevent its interaction with another protein, or facilitating an interaction by bringing two targets in proximity of one another.

What role does the 14-3-3s perform when it interacts with the UPS? Currently, both the mechanism of the interaction between these two protein families and the extent to which they interact are unknown. By further investigating the interaction that has been demonstrated to occur between these two important and widespread regulatory protein families, attempts can be made to understand the specific function and conditions required for interaction.

Obtaining this knowledge will provide information as to whether the observed interaction exerts a regulatory function that is unique, or is merely the first observance of a broader regulatory mechanism on the entire Ubiquitin 26S Proteasome System.

Simply put, I am attempting to understand the extent in which two important protein families interact with each other. If they consistently interact with each other then we can assume that interaction is significant and serves to regulate a much larger system of cellular survival. If we do not see a larger interaction, then what makes what has been observed unique? These are the questions that I am trying to answer.

There, that wasn’t so bad. Now that I’ve covered my bases

on the technical front, I want to shift to my lab experience in general. This semester I am, along with five other students, working to characterize proteins in Arabidopsis thaliana through molecular, genomics and bioinformatic approaches. Through weeks packed with genotyping, gels, culturing, dessert contests, cloning, harvesting seeds, pourover coffee, and extracting DNA, we have begun to identify knockout lines, develop gene constructs, and locate brand new candidate genes for further study.

For 10 weeks this past summer, Lily O’Connor, Tina Chapman, myself, and Dr. Thines were at the bench working on our individual projects. We all wrote proposals to earn summer funding, and as such, we each had specific goals and results we were striving for. Each week we would meet as a lab to update each other on our projects, discuss relevant literature, write progress reflections, and discuss how to introduce efficiency into all aspects of life, scientific or otherwise. One day we all took a two-hour lunch break and sat in the sun learning what life is like as graduate student.

By the end of my summer tenure I had made considerable progress on a project that was much larger than I initially assumed. Unfortunately, as is often the case in scientific research, I had not produced the results I was hoping for.

Luckily, I still had a year left at Puget Sound to apply the skills I learned over the summer and progress towards a complete project. I am excited to say that the first wave of results are incubating as I write this, and I will be presenting a poster at the Murdock College Science Research Conference in early November, results and all. As anyone who has ever spent time in research can attest, it feels good to know that there is a reward for working your assess off.

UNIVERSITY OF PUGET SOUND | 29

Catalyst Formation: Searching for Greener Amide Synthesis

BY CHRIS ROACH This summer, I had the pleasure of working on a Green Chemistry focused multi-step synthesis project with Professor Luc Boisvert. Specifically, I focused on forming catalysts which would produce of Amides with minimal byproducts. Amides are greatly needed in the pharmaceutical industry as and are present in many drugs such as the penicillins (Figure 1b); they are used in many other products (1). Since amides are so widely used and current amide production forms a massive amount of toxic waste (2,3), a new mode of amide formation is needed. An amide, 1, is a group of atoms comprised of a nitrogen, which has two attached carbon-based groups (R), bonded to a carbon that is doubly bonded to an oxygen (Figure 1a).

The current production method of amides is by the combination of a carboxylic acid 2, which has been transformed into an acyl chloride 3, and an amine 4 (Scheme 1a). While this process is efficient for creating amides, it also produces large amounts of toxic and corrosive waste

Scheme 1.

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(Scheme 1a). A direct amide formation from a carboxylic acid 2 and an amine 4 (Scheme 1b) would potentially be a huge improvement. In such a reaction, water would be the only “waste” product and the use of toxic reagents wouldn’t be necessary!

A catalyst is a substance that can be added to a chemical reaction to speed it up, yet is not consumed in the reaction.

Organocatalysis is the specific use of organic molecules

F igure 1. Structure of an amide and penicillin

to act as catalysts (4,5). This project focused on catalyst synthesis because the use of catalysts could play a major role in developing more sustainable amide formation methods (3). Using catalysts is one of the most important ways to reduce the costs of chemical processes and to decrease the time needed for a reaction to take place along with the amount of waste generated (6, 7).

The catalysts which were formed were bifunctional catalysts, meaning that there are two functions of the catalyst. This makes the carbonyl group of the carboxylic acid 2 a better electrophile through hydrogen bonding form thioureas(3) and makes the 2-hydroxypyridine on the carboxylic acid a better leaving group (the intermediate negative charge is stabilized with hydrogen bond donor groups). From the methods of activation described above, Scheme 2 shows the ways this catalyst makes the carbonyl more prone to nucleophilic attack. By these two methods, bifunctional thiourea catalysts are expected to increase the reaction rate of amide formation.

At the beginning of research, the goal of the project was to synthesize six catalysts via two synthetic routes.

However, this was a tall order, as much of the time of research was spent optimizing initial reactions and attempting new chemistry. Wee ended up synthesizing three quinoline based catalysts (Figure 2a) and making significant progress on the other three hydroxypyridine based catalysts (Figure 2b). With the synthesis and purification of these three catalysts, by the end of the summer, preliminary results were produced, which indicated that the new bifunctional catalysts were indeed faster at performing the amide forming reaction than the previously used monofunctional catalysts.

F igure 2. Catalysts investigated in the Boisvert lab in Summer of 2017

During my research in the Boisvert lab, I learned a lot about having patience for synthesis. The many, many precursors produced before a final product was synthesized outweighed anything which I had worked with before.

Furthermore, the many, many failed synthetic steps were trying in their own way but were also empowering since I knew that few others had worked on trials that were attempted in this project. Being able to synthesize even three catalysts and having them improve upon previous research was a very rewarding experience and was well worth the work that was put into this project.

Scheme 2.

UNIVERSITY OF PUGET SOUND | 31

PHILOSOPHY AND MATHEMATICS: The Humanistic Approach to Numbers

BY MILLIE LASKY

Artwork: Yuki Morgan

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In the minds of many, the humanities and natural sciences

six, one plus five still equaled six. If there was not a sin-

should stay as far apart from each other as the east and west

gle person on Earth to understand and acknowledge that

coasts of the continent. Mathematical knowledge has often

fact, one plus five would still, by fact of nature, equal six. If

been determined to be the parallel of all human knowledge,

five rocks had fallen into the ocean and then another rock

being that the truth as it applies to numeric truth is a vital

had fallen into the ocean, six rocks would still have fallen

piece of human truth. Some of the greatest minds of our

into the ocean, and that is as much a certainty of nature as

century can still have explicit arguments about whether we

the rocks being able to fall into the ocean is. This is mathe-

invented mathematics or discovered it, but regardless of

matical truth. Related to its inveterate ability are its eternal

any of that, somewhere along the line mathematical con-

and necessary qualities. That I happen to be wearing black

cepts became applied and understood in non-mathematical

shoes is not necessary. Five plus one could not be anything

terms.

but equal to six; it is necessarily six.

In several respects, both mathematics and philosophy

But what is it about? If you have five rocks and one rock

require levels of thinking that exist and thrive entirely in

you have six rocks, but that five plus one equals six isn’t

an abstract plane of understanding and execution. Mathe-

about rocks. It’s about numbers. But who can say what num-

matics has furnished philosophy, creating a model of cer-

bers are? It’s one of those questions that has no answer- the

tain knowledge that applies itself -funnily enough, creating the branch of mathematical study that is purely theoretical, climbing away from actual real-world applications of mathematics- to philosophical problems. If everything in the world can be expressed through numbers, the ratio of whole numbers to irrational numbers makes that belief unsustainable. As we know, the square root of two cannot be expressed by two numbers, which as a fact on its own takes away the former known safety of algebraic expression. This creates some sort of numeric turbulence, and suddenly in history, we find geometry standing as the purest form of mathemat-

“Reason has superiority over the things that we can absorb through our own sensations”

more you think about it, the less clear it gets. Numbers seem to be a represent of constant truths. If you say that five plus one equals six, you’re not getting anything from anything; it is objectively true. Somebody might argue that most things we receive objective truths from are objects, so does that then make numbers objects? You can’t see a number, nor touch a number. If it is an object, it is a peculiar object that does not corrode or rot away, it does not exist in space in time, it does not exist in our world. Plato, perhaps most known for his application of philosophical thought to mathematical concepts, thought that numbers are forms, and forms are impartially

ical expression. In geometry you can, in fact, express the

existing objects. This created the theory that reality is for-

square root of two. By drawing and plotting the square root

mal, and that everything we see and everything we touch

of two in a physical plane, the square root of two suddenly

and smell is always open to be revised. Meanwhile formal

exists in that physical plane.

knowledge cannot be changed, and this is why reason has

Mathematics provides a knowledge of a discrete kind.

Philosophers since the ancient Greeks have regarded mathematical knowledge as the focal point for all other knowledge- that decision having been derived from the truth of

superiority over the things that we can absorb through our own sensations. That is why the mathematical truth holds the truth that it does and creates a defined standard for actuality in the modern world.

mathematical facts. If you know that one plus five equals

If I ask a man who has just ordered coffee what color the

six, it is fact, and there is no part of your brain that is going

eyes of his barista were, he might at first tell me green, and

to ponder over why one plus five might not equal six. Two

then five minutes later when I ask again, tell me that he

hundred years from now, one plus five will equal six, and

was wrong, that the eyes were brown instead. In the mem-

two hundred years before you knew one plus five equaled

ory of that man, either of those things look correct; there is

UNIVERSITY OF PUGET SOUND | 33

nothing about the subtlety of eye color that could make that

theory of reality-a proof that there is a different truth. This

mental image deplorable or noticeably wrong. Our truth is

allows for an explanation of application, and a further clar-

able to be bent by our memory, and shortly after we have

ification of what is known and what is not. The answer is

bent the eye color from green to brown, it is accepted as a

simply a construction of theories, a set of definitions and

kind of truth that does not exist in mathematical percep-

thought analysis which lead to a multitude of distinct pos-

tion. Memory has no objectivity- yet it can be molded and

sibilities. That we will ever find one logical, finite answer

changed as we like it to be, whether or not we are aware that

as to where math and its truth came from is unlikely, but it

it is being changed from its original state. By objectivity I

is perhaps the theorizations of these logics that makes the

mean the significant physical state of an object as it occurs

philosophical study as prominent as it is.

in the physical word. In that definition, memory has no objectivity, numbers hold no objectivity- yet, they are as concrete as the actuality of a desk in an empty room, or a cat in a box. We can change memory, accept it as something fluid and expected to change, but no one person sits and decides the there should be a number between five and six, or that five added to one does not equal six. Memory is subjective to humanity. It is flexible and able to be shaped by our preferences or choice, our emotions and whims. Numbers are not, and everything that comes from numbers is inherently separate from humanistic tinkering or sway of direction.

In the philosophical treatment of numbers lies a vast frontier, a treacherous place with inexplicable definitions and uncharted limits. We analyze unrealities with realities; theorizations and proposals using the clarity and stability of a mathematical function, and with each result, we further ourselves in the study of either subject, without too much of the other. There exists in the world of mathematicians and scientists a deeply rooted respect for the medium- the golden mean, if you will. Never can we have too much of either, lest they blot the other out. Too much philosophy and we land too far from numerical understanding to give and

Having determined what defines a mathematical object

appropriate answer, and too much mathematical coverage

and how that object ultimately supports the thought of

and the observer casts away theoretical possibilities for the

mathematical truth, the logical question which follows that

sake of natural law and order. The answer, lies somewhere

description is understanding how we know these things for

in the richly sought middle. Will we find the answer? That

what they are. Are pieces of mathematics a part of us, in-

depends. Are we really searching? Or do we, from an intrin-

nate to our nature and knowledge, or are they abstractions

sic degree, already know?

from humanity, viable to be used if only the proper mind can find the right path of thought to discover them? Do we learn math, or do we remember it? This is the central divide between the philosophical study of mathematics, originally cited in the difference between Plato’s teachings and Aristotle’s beliefs. The categories of the fall out being rationalists and empiricists. These categories separate even the household names of mathematics. John Locke was analyzed to be an empiricist, agreeing that knowledge comes from experience; while Rene Descartes was known to have perpetuated the conviction that mathematics was simply the premier of a clear head- with unobstructed thought, any one problem would be solved with the highest properties of mathematical function in the human mind. By assessing that numbers are abstracted from a physical reality, philosophers can set the state to allow mathematics a sorted space of definite control. That is, to hand over to mathematics a sort of governing ‘Marshall law’ over the relative use of manipulation.

To challenge an equation or finding requires a disparate

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Worldwide Bee Decline Are pesticides to blame?

BY ANNA MARCHAND Bees are the most prevalent group of pollinators worldwide. They are largely responsible for pollinating around 35% of the world’s food crops and 80% of European wild plants, confirming their role as key players in the ecological world (1). Several scientists have attempted to estimate the value of insectpollinated crops that are dependent on honey bees, with conservative estimates predicting that bees are responsible for almost 3.07 billion dollars of fruits and vegetables produced in the United States as of 2006 (2).

As important as they are for both ecology and economy, bee numbers are declining at an alarming rate. One study compared museum records to current bumble bee populations and found that the relative abundances of four prominent bumble bee species have declined by up to 96% and that their geographical range has also decreased by 2387% during the last several decades (3).

The same interdisciplinary study also showed that susceptibility to pathogens is increasing while genetic diversity is decreasing in current bee populations, which are predictors for continued decline (3). This plunge in pollinator populations could have a huge negative effect on worldwide agriculture, even in areas where beekeeping activities are prevalent (4). Fruit and vegetable crops would be among the most highly affected, as these industries are currently dependent on

wild bee populations for free pollination, a necessity for growing and harvesting produce.

There are many potential culprits causing the rapid decrease in bee populations across varied species and geography. Hypothesized causes of decline include: pathogens, pollutants, habitat loss, climate change, and pesticide usage (1, 5). Pathogens in particular have received much media and scientific attention of late, having been connected to colony collapse disorder (CCD). Colony collapse disorder was first reported in 2006, and between 2006-2007 an estimated 23% of beekeepers in the United States lost an average of 45% of their operations to CCD (6). Colony collapse disorder is characterized by mental decline and rapid loss of adult bees from the colony (6). A pathogen called Israeli Acute Paralysis virus is hypothesized to be a contributing factor to CCD, as it was found in a majority of bee populations displaying symptoms, but no causal relationship has been found.

As scientists devote attention to finding the causes and solutions to colony collapse disorder, a new threat has come into the spotlight: pesticides.

One recent study on honeybees found that around 75% percent of the world’s honey is contaminated with pesticides (7). Specifically, three-fourths of the samples tested positive for neonicotinoids, the most widely

UNIVERSITY OF PUGET SOUND | 35

used class of insecticides in the world. The researchers tested for the five most common neonicotinoids: acetamiprid, clothianidin, imidacloprid, thiacloprid, and thiamethoxam (7). Many crops are routinely treated with neonicotinoid insecticides as a seed dressing (1, 8). These compounds are systemic, so that when neonicotinoids are taken up by the plant, they contaminate every organ, including the flower (1, 7, 8). Bees rely on the flower’s nectar and pollen to make honey, which sustains colonies both on a daily basis and through the winter. Therefore, the concentration of pesticides in honey is an indicator of the contamination levels of the surrounding landscape (7). The research article reported that their positive samples contained an average concentration of 1.8 ng/g (7). While this concentration is considered safe for humans to consume, it is well over the minimum exposure required to produce harmful effects in pollinators (0.10 ng/g) (7).

Neonicotinoids are neurotoxic agents (they disrupt the normal functioning of the nervous system), and cause a variety of neurological/behavioral issues, even at nonlethal doses (1, 7, 8). Bees exposed to neonicotinoids experience physical symptoms such as, trembling, uncoordinated movements, and hyperactivity (1).

Chronic exposure to some neonicotinoids have been shown to negatively affect olfactory learning and memory abilities as well as foraging capacity, both of which are essential for worker survival (1). Furthermore, when bumble bees were exposed to imidacloprid

(a neonicotinoid commonly used on sunflower, corn, cotton, and sugar beet crops) in a lab, colony growth and reproduction suffered (8). Colonies across a range of fieldrealistic treatment levels were significantly smaller than control (non-exposed) colonies. The average number of queens produced in pesticide-contaminated colonies was also dramatically lower (8). Scientists hypothesize that this dramatic difference is due to the fact that only the largest bumble bee colonies are successful at producing queens, so even a small reduction in colony size can bring it below the threshold for queen production (8). These results imply that even trace levels of neonicotinoids can have a slew of negative effects on bee populations.

The scientists behind the worldwide survey of neonicotinoids in honey expressed the urgency of the issue in their paper, saying “bee populations throughout the world are exposed to a cocktail of neonicotinoids” and urging national agriculture authorities to be transparent about the amount of pesticides used in public territories (7). So, how can you do your part to “save the bees”?

“Like with any systemic, long-term issue, the power of individual actions resides in the collective,” says Mariah Seller, the leader of our on-campus beekeeping group, “Hiveminders.” She suggests a variety of bee-friendly habits such as, planting a pollinator garden, using pesticides only sparingly, being mindful of the benefits of buying organic produce, and letting your representatives know where you stand on bee-related issues.

Illustration: Kiri Bolles

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Entering the Allium:

A “Lighter Side” of Science

UNIVERSITY OF PUGET SOUND | 37

s n u P f o s e n Alky

What’s an agnostic ester’s favorite holiday?

Easter, but without the “a” man.

BY ALEX GUZMAN & EDITORS

In the 007 quantum (solace) reaction, what is responsible for making reagent M so salty?

Bond, Ionic Bond

What did the mycorrhizae say to the oak tree?

I’m rooting for you!

Student: Is it true that analytical geometry is an integral part of GC-MS analysis?

Lab assistant: As a function with respect to your continuous questioning, yes!

What did the carbocation say to the benzene ring at Denny’s?

I’m really resonating with this pi.

A recent dihydrogenmonoxide spill on Lake Superior has caused a flood of environmentalist to advocate for further safety regulations regarding the compound.

When ecological politics become unpalatable...

Stop copying me!

Photos: Wikimedia Commons 38 | ELEMENTS

d r e COSMOPOLITAN n Why does my plate SMELL? Experts say it’s Geosmin

65

crazy-hot

Streaking Techniques

Make other protists jealous!

How to make it BIG: It’s all about INVAGINATIONS

FINALLY.

Inside: How to tell if symbiosis will last

P2 vs P1000...

Does Size Matter?

Our panel weighs in Help your man find your Ori Site.

Cell Membranes that Diffuse for you!

UNIVERSITY OF PUGET SOUND | 39

In Preparation for Writing a Formal Lab Report...

Guidelines for Such a Lab Report; Criteria for Stating and Analyzing Experiments; A Closer Look at Procedures and Findings; Extrapolation of the Elements of Experimental Design; Why Wait? Extrapolate! ‌in other words, an [exaggerated] “sampleâ€? of rules for organic chemistry lab and lab reports

BY ANNA FRYXELL Rules of Thumb: #1: When multiple steps in a procedure are present, always state the first step before the second step, the second step before the third, and so on. For example, if you would like to convey that you first extracted a mixture into separate components and then washed it to purify, do not state that you washed it to purify and then extracted it. Very simple, really. #2: Make sure that you note which items of clothing were worn throughout the entire duration of the experiment. This is the most important step. If you do not state this, your report will not be considered in the scientific community, and your findings will NOT be contributed to science. You MUST denote the brand, color, type, and length of each clothing piece as well as accessory. If you do not do this, the reader might conclude that you were wearing nothing at all, which is a big no-no in the Organic Chemistry Lab. #3: All reports are to be typed in đ&#x;•ˆď¸Žâ™“︎■︎♑︎♎︎♓︎■︎♑︎⏧︎ font unless otherwise indicated. #4: Take care of yourself. If necessary, provide a brief autobiography before proceeding to the introduction.

Personal anecdotes are never required, but always in good taste and appreciated.

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#5: All schemes, figures, charts, cartoons, pictographs, murals, sketches, self-portraits, (you name it) are to be introduced in the text in the opposite order in which they appear, and if they do not appear in the report than they do not need to be mentioned. If they appear more than once, they still need to be mentioned only once. #6: The Discussion. This is where you bring in all kinds of outside information from other sources, including, but not limited to, newspapers, magazines, advertisements, comic strips, pamphlets, commentary, sound-bites, talk shows, Bill Nye, The Onion, Wikipedia, and perhaps scientific journals like the Scientific American. #7: Sig figs! You probably thought I forgot to mention them! All decimals are to be rounded to include 10E3 significant figures, except in plutificaxion calculations the number depends on the size, relative speed,

or the firmness of a handshake received by an inspector of the lab from the FDA. However, contrary to most chemistry labs and certainly all organic chemistry labs, you will not be expected to wear gloves, goggles, long pants, a ponytail, scissors, Crocs, stamps, gold leggings, a “Mr. Yuck” tattoo, a clipping of a recently published article pinned to your breast pocket, one small gourd carefully strapped behind your goggles, or anything else to that nature. You may wear whatever you want, if you want. You may also arrive approximately five minutes early to lab and not be yelled at for being late.

type of reagent, and NMR spectroscopy for the given compound in standard conditions. It is not uncommon for serious organic chemists to stop, drop, and take stock of the measurement of various objects within their surroundings, thereby recording the results in their laboratory notebook to the appropriate number of sig figs (correct units, please!). If taken seriously and followed correctly, said protocol should be repeated every 15.3334-17.9856 seconds (unless a crucial step in a reaction is taking place, in which case it is best to stare at the reaction with an open jaw until completed). Typical objects you may choose to measure include, but are not limited to, lab coat cuffs, goggle straps, the tiles on the floor, the height of each and every beaker, the uglyvap, your instructor’s ponytail, and the space between your nose and upper lip.

Typical lessons learned from a biology lab are actually (but not surprisingly) quite practical to everyday life. We consider life, examine it closely (sometimes very closely), dissect its components, diagram its structures, and come up with solutions to real “life” problems. We do not perform eleven reactions involving carcinogenic reagents that result in approximately 0.019 grams of product (if we are lucky).

For example, one might look at a cell and say “huh.” Then one might look at a different type of cell and say “interesting.”

Then one might look at yet a different type of cell and say “imagine that.” All of these remarks can be recorded in the lab notebook. A picture of a circle and some squiggles is highly recommended, but again, not required.

#8: Be safe! (Safety is no accident.) #6.02 x 10^-23: Have fun! (You can’t spell “fundamental” without “F-U-N”!) Organic is better for you, and it tastes better…

“Such is Life” Now we are on to biology. Biology may be best described as “the applied and practical version of chemistry” or “the study of the better half of chemistry,” (Haha Bioboy, 2016). In typical biology labs, you may be asked to wear a lab coat. Please do it. This is to ensure the credibility you would attain if photographed for a profile picture

Images: Wikimedia Commons (1) UNIVERSITY OF PUGET SOUND | 41

Illustration by Carlisle Huntington 42 | ELEMENTS

CITATIONS Islands and Hurricanes (Mraz) (1) Davis, Jeffrey Sasha. 2005. “Representing Place: ‘Deserted Isles’ and the Reproduction of Bikini Atoll.” Annals of the Association of American Geographers 95 (3):607–25. https:// doi.org/10.1111/j.1467-8306.2005.00477.x.

(2) DeLoughrey, Elizabeth M. 2013. “The Myth of Isolates: Ecosystem Ecologies in the Nuclear Pacific.” Cultural Geographies; London 20 (2):167–84. https://doi.org/http:// dx.doi.org.ezproxy.ups.edu/10.1177/1474474012463664.

(3) Stachowicz, John J., Jeffrey R. Terwin, Robert B. Whitlatch, and Richard W. Osman. 2002. “Linking Climate Change and Biological Invasions: Ocean Warming Facilitates Nonindigenous Species Invasions.” Proceedings of National Academy of Sciences of the United States of America 99 (24).

(4) Nogueira-Filho, Sergio L. G., Selene S. C. Nogueira, and Jose M. V. Fragoso. 2009. “Ecological Impacts of Feral Pigs in the Hawaiian Islands.” Biodiversity and Conservation 18 (14).

(5) Hellmann, Jessica J., James E. Byers, Britta G. Bierwagen, and Jeffrey S. Dukes. 2008. “Five Potential Consequences of Climate Change for Invasive Species.” Conservation Biology 22 (3):534–43. https://doi.org/10.1111/j.15231739.2008.00951.x.

(6) Carlowicz, Mike. 2013. “Super Typhoon Haiyan Surges Across the Philippines : Natural Hazards.” Text.Article.

November 8, 2013. https://earthobservatory.nasa.gov/ NaturalHazards/view.php?id=82348.

(7) Geographic TV. 2015. One of the Deadliest Typhoon | Haiyan Documentary | Geographic TV. https://www. youtube.com/watch?v=9vjlxDg53zE. (8) Mersereau, Dennis. 2017. “Hurricane Maria Proves How Difficult It Is to Predicta Storm’s Devastation.” Popular Science, September.

(9) Resnick, Brian. 2017. “WHy Hurricane Maria Is Such a Nightmare for Puerto Rico.” VOX, September 22, 2017.

(10) McKay, Tom. 2017. “Puerto Rico Is Investigating How It Screwed Up Restoring Power After Maria So Badly.” Gizmodo.

September 28, 2017. https://gizmodo.com/puerto-rico-isinvestigating-how-it-screwed-up-restorin-1819943571.

(11) Di Nunzio, Jack. 2013. “Long-Term Food Security Risk in Philippines after Typhoon Haiyan.” Future Directions International (blog). November 27, 2013. http://www. futuredirections.org.au/publication/long-term-foodsecurity-risk-in-philippines-after-typhoon-haiyan/.

Monolayer Van der Waals Heterostructures (Fonseca) (1) J. R. Schaibley, H. Yu, G. Clark, P. Rivera, J. S. Ross, K. L. Seyler, W. Yao, and X. Xu. Valleytronics in 2D Materials.

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