Posted by: Date: May 5, 2014 In: ,
Associate Professor of Biology Jacob Egge works with students during a summer semester research project. (Photo by PLU Photographer John Froschauer)

Associate Professor of Biology Jacob Egge works with students during a summer semester research project. (Photo by PLU Photographer John Froschauer)

Faculty-Student Research Provides a Cornerstone of the PLU Mission

By Pacific Lutheran University Marketing & Communications and the Office of the Provost

This year’s 2013-14 celebration of Student-Faculty Collaborative Research and Creative Projects will take place on May 8 from 11:30 a.m. to 1 p.m. in the Regency Room of the Anderson University Center. This event will feature research projects from the three divisions of the College of Arts and Sciences—Humanities, Natural Sciences and Social Sciences.

The posters, articles and videos on display will provide a window onto activities that are at the core of Pacific Lutheran University’s mission: scholarship and student learning. These projects make visible what too often is invisible: the intellectual activity that is central to discovery, interpretation and artistic production.

Division of Humanities

Charles Bergman, Ph.D., and Nevis Granum
Department of English
Kelmer-Roe Fellowship

Our research has three components: First, we joined Dr. Jane Goodall in a four-person team—Bergman, Granum, an ornithologist from the World Parrot Trust and Dr. Goodall—on a research excursion in Uganda in which we released 17 “laundered parrots.” The final remnants of about 200 smuggled birds, these parrots were historic—the first such release ever of parrots in Africa. They had been trapped in the wild, smuggled to Lebanon, give forged documents, confiscated almost by luck in Cyprus. Second, we studied African grey parrots as paradigmatic of the problems in the global problem of wildlife trafficking. Between 2 and 2.5 million African grays have been trapped for the wildlife trade in the last 20 years. They are among the most popular animals in the global wildlife trade, largely because they are so intelligent. Dr. Goodall told us of one African grey parrot with a vocabulary of 1,600 words, as large as a human teenager’s. Third, we used the narratives of our experiences and our photography to write several articles, exploring complex relations between the legal trade and the illegal trade. The legal trade, for example, offers cover for the illegal smuggling of birds, and the same people are often involved in both.

Seth Dowland, Ph.D., and Clayton Bracht
Department of Religion
Sports, Christianity, and Manliness:  Evolving Notions of Christian Manhood in the YMCA
Kelmer-Roe Fellowship

Founded in the mid-19th century, the Young Men’s Christian Association (YMCA) grew rapidly in the early decades of the 20th century. During this period, the YMCA built facilities and offered programs that would develop the “mind, body and spirit” of young men—most of them white and middle-class. During the 1940s and 1950s, the YMCA increasingly served women, children, nonwhites and non-Christians. This broadening of scope demonstrated the YMCA’s adaptability and ultimately led to the 2010 decision to rebrand as the “Y,” notably dropping both “men’s” and “Christian” from the organizational acronym.
In order to narrate the Y’s transformation from muscular Christian outpost to multicultural gym, we draw on a rich trove of YMCA documents, collected during three week-long visits to the YMCA Archives in Minneapolis. This paper contends that the YMCA leaders decided to move away from single-minded focus on developing “muscular Christian” men because they increasingly prioritized service to women and minorities in the decades after WWII. As the YMCA included more minorities and women, it found it harder to promote a coherent understanding of Christian manhood. This shift unintentionally shed light on the racial and class stereotypes built into Christian understandings of masculinity.

Pauline Kaurin, Ph.D., and Peter Joyce
Department of Philosophy
Moral Considerations in Jus in Bello
Kelmer-Roe Fellowship

This project seeks to apply philosophical methods and insights to the examination of what the crucial moral considerations in the Jus in Bello portion of just war theory are. We are seeking to bring the discipline of philosophy, and ethical theory in particular, to bear on the issue of how soldiers make decisions on the battlefield. This is an emergent issue in military ethics that has implications relative to what actions in war are morally permissible, based on the knowledge soldiers are capable of obtaining amidst the chaos of war. This project would further and sharpen discussion on this topic in military ethics, by providing sustained philosophical reflection and discussion of the moral ramifications based on epistemic limitations. This project is also designed to reflect the progression of scholarship from question-asking to research and written scholarship submitted to the academic community for discussion and critique, and finally to publication of findings.

Division of Social Sciences

JoDee Keller, Ph.D., and Ashely Hill
Department of Social Work
Ten Years After: Assessing the Development of Community in Mixed-Income Housing
Severtson Fellowship

Salishan is a public housing development on the eastside of Tacoma that historically had high rates of poverty and reputation of crime. Despite these challenges, the community came together across language and cultural barriers. Tacoma Housing Authority received a grant to redevelop Salishan to replace outdated, poorly constructed housing and create a mixed-income community. The community continues to undergo changes in types of housing, expectations of residents, ethnic & socio-economic makeup of the community.
This research examines the development of community in New Salishan and utilizes partnership with community members, soliciting their input in research design. The primary methodology utilizes focus groups co-facilitated by Community Health Advocates and university research team. The goal of the research is to provide feedback to community residents and leaders and in partnership, guide next steps in development of community ties. Data collection is still in process, but preliminary findings show that residents continue to feel dissatisfied with security, lack of programming for children, lack of educational resources. They also missed recreational activities for children and families that allowed for greater interaction.

Laura Kemmer, Ph.D., and Geena Pfeninger
Department of Psychology
Agreement and Attraction:  What kind of distance matters?
Severtson Fellowship

Language is produced using cues to determine the appropriate next words. Participants made grammatical decisions in order to investigate aspects of calculating subject-verb agreement in language comprehension and determining influencing factors. Stimuli included three intervening nouns before the verb varying in number, single or plural. For example, “The dogs (single) with the balls (plural) in the street (single)…” It was hypothesized that if linear distance from the verb mattered most, there would be decreased errors and response times in the conditions where the subject noun (dogs) and the local noun (street) match in number; conversely, more errors and increased response times are expected if syntactic distance impacts agreement errors. Repeated measure analyses of variance were run to analyze response times and accuracy revealing a clear difference in response types dependent on the number of the subject noun (single or plural). Within the single head noun condition there was support for an interaction of both the linear distance hypothesis and syntactic distance hypothesis. The primary body of research focuses on the syntactic distance hypothesis whereas the results of this study point to an interaction of both, predominantly supporting linear distance.

Laura McCloud, Ph.D., and Andrea Capere
Department of Sociology
Whither the Redneck:  Symbolic Violence in ‘Redneck Media’
Severtson Fellowship

We show that “redneck media” is a cultural product of the Great Recession. Given that many formerly middle-class Americans lost their jobs, homes and savings during the Great Recession, cultural products created during this time work to distance the middle and upper classes from the working and lower classes by emphasizing class as a cultural distinction versus an economic distinction. We use data from the popular television program Duck Dynasty. We content code each instance of social class defined by economic position and social class defined by cultural tastes and behavior. We pay special attention to overlap between these portrayals. We find that Duck Dynasty highlights the importance of cultural capital in determining social class and purposefully minimizes the economic position of the Robertson family. This process, we show, encourages high cultural capital audience members—many of whom lost financial capital during the recession—security in their position in the social strata. The cultural place of “redneck media” is to show the lower class as having a distinct habitus, through committing symbolic violence against low cultural capital individuals. This process reminds “rednecks” that they are a valid target of mockery and are at the bottom of the social class hierarchy.

Christine Moon, Ph.D., and Katrina Graven
Department of Psychology
The Power of Teaching Your Fetus
Severtson Fellowship

In this paper we explore the concept of teaching your fetus and assess the validity of various popular claims regarding the effectiveness of prenatal learning systems, and types of talk utilized during pregnancy. Specifically, we examine the comparative evidence between fetuses exposed to talking while in utero versus those who aren’t, to decide which methods are most beneficial, or if in fact it is not necessary to capitalize on a fetuses prenatal learning ability at all. Overall, this paper calls into question the idea that imparting knowledge directly to the womb is essential to a higher functioning neonate, which challenges many current products aimed at new parents. Additionally, these revelations illustrate how the power of teaching one’s fetus is a much more complex and contested issue than originally thought.

Ami Shah, Ph.D. and Jared Wright
Department of Political Science
Negotiating Development in a Neoliberal State:  The Work of Amextra in Oaxaca, Mexico
Severtson Fellowship

Neoliberalism, understood as a political project promoting the preeminence of the market for allocating goods and handling social issues, has had a profound impact on the practice of development in Mexico, removing trade barriers, opening investment flows and aggregately reducing the provision of social services and support to rural and poor populations. A prominent feature of the neoliberal political-economy has been not only the increase of migration as an economic strategy, but also the elevated presence of nongovernmental organizations (NGOs) doing work in development, with a diverse spectrum of practices and philosophies. Through my experience in Pacific Lutheran University’s Oaxaca study abroad program in 2013, I had the opportunity to work with an NGO called Amextra, focused on community development and combating marginalization. My research project focused on Amextra as a case study for development in Oaxaca, as I sought to answer how development is understood by local people in the communities where Amextra works, and how Amextra fits into the larger political-economic context of the region. Combining data from guided interviews and quantitative sources, I conclude that Amextra is a stabilizing and transforming force in Oaxaca, but that it is limited in its developmental scope by its apolitical nature.

Marianne Taylor, Ph.D., and Darla Avis
Department of Psychology
When Jack & Jill Switch Brains: How Development Affects Gender Identity
Severtson Fellowship

Do children and adults view gender identity as residing in one’s body or one’s brain? Previous research has used a hypothetical brain transplant between different animals to measure how children understand identity (e.g., if a pig gets a cow brain, will it say “moo” or “oink”?; Gottfried et al., 1999; Johnson, 1990). Only one study has examined gender identity using this kind of task, and it focused on adults (Mahalingam & Rodriguez, 2003). In the present study, kindergarteners, third-graders and adults considered a brain transplant between male (Jack) and female (Jill) characters. They made predictions about changes across four domains: physical body, appearance, activities and occupational choices. We coded the percentage of category-based (rather than brain-based) responses. Kindergarteners made significantly more category-based predictions than adults, across all domains. Adults provided significantly more category-based responses for physical traits than all other domains. Adults also had more flexible views of gender identity than third-graders and kindergarteners, acknowledging both the body and brain’s influence on gender identity. Finally, all age groups provided more category-based responses more for Jack than they did for Jill, suggesting that they view male gender identity as more resistant to outside influences.

Teru Toyokawa, Ph.D., and Donyale Sanchez
Department of Psychology
Emerging Adults’ Goal Engagement in the Transition from School to Work
Severtson Fellowship

This study examined the relationship between barriers college students foresee as likely to occur and the control they believe they will have in overcoming the barriers, in the school-to-career transition. Although previous research has examined the barriers that college students foresee in the school-to-career transition, none have examined the differences in barriers and control between students closer to the transition and those further from it. The three barriers categories were discrimination, social support and personal. I predicted that junior and senior students, who are closer to the transition period than freshman and sophomore students, would foresee themselves as having more control over barriers. This prediction is based on the motivational theory of lifespan development, which posits that people closer to major life transitions should be high in primary control striving (e.g., a control orientation were one believes they can exact change in their environment to meet their needs) as they optimize opportunities that can help them transition successfully.

Division of Natural Sciences

Michael D. Behrens, Ph.D., and Kristin R. Neuneker
Department of Biology
Olympia Oyster (Ostrea lurida) Settlement in Fidalgo Bay, Wash.
Natural Sciences Undergraduate Research Endowment

The Olympia Oyster (Ostrea lurida), the only native oyster found on the west coast of North America, has been depleted over time due to overharvesting and other environmental factors. Recently interest has surfaced in re-establishing these populations, including a restoration project in Fidalgo Bay, Wash., begun in 2002. In order to assess the distribution and success of this population we investigated variation of settlement of juveniles in space and time. Through placing oyster shells modified to collect settlers at 42 locations within seven sites, an assessment of their distribution was possible. There was a late July peak in settlement during the sixth week of study; however, this peak was only detectable at the intertidal locations. The results indicate that O. lurida larvae preferentially settled at two intertidal sites, which were nearest to each other and the site of the 2002 restoration seeding effort. This may point to the success of the restoration site as well as support the hypothesis that larvae may settle preferentially to locations with suitable habitat or adult populations. Additionally, rates of settlement were lowest at the mouth of the bay suggesting there may be little dispersal of organisms out of the bay.

Jacob J. D. Egge, Ph.D., Erinn M. Kuest and Dakota M. Rowsey
Department of Biology
Evolution of External Taste Buds in Fishes
Natural Sciences Division Undergraduate Research Program

Gustation, the “taste sense,” represents a major chemosensory system in vertebrates. Taste buds, the primary gustatory sense organs, are generally thought of as being restricted to the mouth, where they play a discriminatory role during ingestion. Unlike other vertebrates, many fish lineages have evolved extraoral taste buds on other surfaces, including gill epithelia, lips, barbels, head, fins, and, in some cases, across the entire body surface. In order to gain a better understanding of extraoral taste bud distribution and evolution in fishes, 24 species representing 24 families and all four major orders of otophysan fishes were surveyed. A combination of light microscopy (LM) and scanning electron microscopy (SEM) was used to search 15 body regions for the presence of extraoral taste buds. Taste bud morphologies and distributions were then mapped onto an existing phylogeny of otophysan fishes, allowing for inferences regarding evolutionary history. Results suggest that extraoral taste buds may have evolved multiple times within otophysans. Minnows and catfishes demonstrate the most widespread distribution of taste buds, but also the most variability among lineages.

Rosemarie C. Haberle, Ph.D., Seanna L. Hewitt and Stephanie J. Stromberg
Department of Biology
A Comparative analysis of pastimes of Asyneuma and Trachelium (Campanulaceae) reveals both shared and unique genome rearrangements
Natural Sciences Undergraduate Research Endowment

Members of the bluebell family Campanulaceae display highly rearranged chloroplast genomes with respect to other plant families. Previous comparative analyses of Campanulaceae plastomes have shown that significant rearrangement events occur not only deep within the phylogeny, but also between closely related genera. We report the completed plastome of Asyneuma virgatum, which we compare to the previously published chloroplast genome of its sister taxa, Trachelium caeruleum. Using the Nicotiana plastome as a reference, we observe interesting genome rearrangements that are unique to Asyneuma, including multiple duplications of trnL-UAG in the small single copy region, the loss of infA and the presence of an ndhF pseudogene. Additionally, we note a shared disruption of the psbB operon (with different outcomes) in both Asyneuma and Trachelium. The present comparison further sheds light on the evolutionary history of the Campanulaceae and contributes to a larger effort to elucidate the location of destabilization and rearrangement events in the Campanulaceae phylogeny.

Julie W. Smith, Ph.D., Hannah L. Lansverk and Benjamin R. Sonneberg
Department of Biology
Red Crossbill Syllable Catalog Comparison: Song as a possible isolating barrier in ecological speciation
M.J. Murdock Charitable Trust—Life Sciences Program + Natural Sciences Division Undergraduate Research Program

The Red Crossbill (Loxia curvirostra) is a unique species of nomadic finch that has evolved a crossed bill, a key innovation allowing it to specialize on an unexploited resource: seeds of closed conifer cones. Crossbills forage by biting between overlapping scales and laterally abducting the lower mandible, thereby prying the scale apart to expose the seed at the base. North American red crossbills are categorized into 10 call types that differ in body size, bill size and palate structure, and non-song vocalizations. The structure of the conifer cones on which each call type specializes is the agent of selection driving the evolution of bill and palate structure between the different call types. This divergence has been rapid and recent within the last 5,000 to 12,000 years, making it an ideal system to study speciation. Our goal was to examine whether the songs of the different call types have diverged and whether this maintains reproductive isolation. Song is a likely reproductive isolating barrier between the call types because birdsong is used in mate choice and species recognition. Additionally, we hope to identify mechanism(s) responsible for the observed differences in songs between call types through syllable catalog comparison.

Mary J. Ellard-Ivey, Ph.D., and Drew B. Huff
Department of Chemistry
Cloning, Recombinant Expression, and Characterization of CrFADS
Washington State University

The term vitamin B2 refers to the compound riboflavin along with its two derivatives, the cofactors flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD). Both FMN and FAD are active cofactors for a range of enzymes. These cofactors are essential for photosynthesis, fatty acid oxidation, DNA repair and mitochondrial electron transport, alongside other metabolic processes. Little is known about the biosynthetic mechanisms associated with vitamin B2. It is known that enzymes called FAD synthetases convert FMN to FAD, while FAD pyrophosphatase enzymes convert FAD to FMN as needed by the cell. The protein CrFADS from algae is a potential enzyme with both FAD synthetase and FAD pyrophosphatase activities. Therefore, it is believed to play an important role in flavin metabolism. Through cloning this algal gene, recombinant expression using yeast, and biochemical characterization of CrFADS, we will confirm whether or not CrFADS is an FAD synthetase or FAD pyrophosphatase. This research will reveal whether CrFADS is an active component in flavin metabolism, and lead to a better understanding of the biosynthesis of flavins as a whole.

Mary J. Ellard-Ivey, Ph.D., and Amandeep Kaur
Department of Chemistry
Determine the role of putatively cytosolic phosphatases in maintaining homeostasis levels of phosphate
Washington State University

Inorganic phosphate is a key ingredient for all organisms; it is required in metabolic activities as well as present in sugar, nucleotide, and co-factors such as adenosine triphosphate (ATP), Flavin adenine dinucleotide (FAD), Flavin nucleotide (FMN). Most plants obtain inorganic phosphate from soil, but it is not available in unlimited quantity due to its immobility and strong fixation in soils. Plants adapt to cope with limited phosphorus availability in the soil. This project focuses on five putatively cytosolic phosphatases (At2g38740, At2g32150, At3g62040, At5g02230, and At5g59490) belong to haloacid dehalogenase (HAD) superfamily. T-DNA insertion screening and western blot assays are performed on transgenic plants with overexpression and RNAi lines for each gene. These transgenic plants will help determine the role played by these genes in maintaining homeostasis levels of phosphate in the cytosol in specific conditions.

Eric E. Finney, Ph.D., and Elizabeth A. Kaley
Department of Chemistry
Forensic Analysis of Biodiesel
Charles and Ann Laubach Student Research Fund

The analysis of four different biodiesel blends, as well as homemade biodiesel prepared from vegetable oil, has been performed using gas chromatography-mass spectrometry. The identification of methyl esters within the biodiesel along with any background components is made possible by recognizing their mass spectral fragmentation patterns. These fuels were subjected to typical fire scene environments (weathering, evaporation, and burning) to investigate how these environments affect the analysis. The data obtained herein will provide the forensic science community with the data needed to help recognize these increasingly common ignitable liquids.

Eric E. Finney, Ph.D., and Blair K. Troudt
Department of Chemistry
The Synthesis and Reactivity of Pyridine Substituted Cobaloximes
Fred L. and Dorothy A. Tobiason Endowment for Faculty-Student Environmental Research

Cobaloximes have been studied for decades as model compounds for vitamin B12. More recently, the chemical behavior of cobaloximes in general has been the subject of focus. The chloro(pyridine)cobaloxime is very stable and can be used as a precursor to many other cobaloximes. Specifically, the reduction of chloro(pyridine)cobaloxime gives a very nucleophilic Co- ion, which can react to form new cobalt-carbon bonds. The cobalt-carbon bond can be broken either thermally or photolytically, producing a reactive carbon-based radical. Our aim was to study these reactions with the long-term goal of using cobaloximes as thermal or photolytic catalysts for various transformations, including the reduction of carbon dioxide.

Adam Glass, Ph.D., Gregg Lowery and Austin Erler
Department of Chemistry
Functionalized benzofulvenes: Coupling synthesis and computational chemistry to develop small molecule inhibitors at a primarily undergraduate institution
H. Eugene LeMay, Jr., Summer Chemistry Research Fund + Natural Sciences Division Undergraduate Research Program

Human thioredoxin reductase 1 (TrxR1) is an enzyme of therapeutic interest in cancer treatment due to its involvement in regulating the redox-signaling enzyme thioredoxin 1. Interestingly, cancerous cells can attribute many of their negative clinical features as a result of thioredoxin 1’s interaction with the cellular redox cycle. Reduced (activated) thioredoxin is involved in a host of intra and extra cellular signaling pathways that can lead to increased cellular proliferation and decreased apoptosis. Predictably, thioredoxin has also been shown to be overly expressed in cancerous cells, particularly the most malignant (e.g., pancreatic, liver and breast). We are currently working towards a small molecule inhibitor developed to target TrxR1, the only known enzyme that reduces and activates thioredoxin. Current research suggests that inhibition of TrxR1 leads to decreased cancer cell fitness through interaction with the previously discussed mechanisms, (i.e., cellular growth control). Encouragingly, computational modeling has demonstrated the possible effectiveness of highly functionalized benzofulvene moieties. We have determined quite high in-silico binding affinities (i.e. >10 kcal/mole) to the TrxR1 active site and have developed effective synthetic protocols to generate various functionalized benzofulvenes.

Adam Glass, Ph.D., Austin S. Erler, Valerie A. Lesniak and Gregg C. Lowery
Department of Chemistry
Functionalized Benzofulvenes: Coupling Synthesis and Computational Chemistry to Develop Small Molecule Inhibitors at a Primarily Undergraduate Institution
H. Eugene LeMay, Jr., Summer Chemistry Research Fund + Natural Sciences Division Undergraduate Research Program

Human thioredoxin reductase 1 (TrxR1) is an enzyme of interest in cancer treatment due to its involvement in regulating the redox-signaling protein thioredoxin 1. Cancerous cells can attribute many of their negative clinical features as a result of thioredoxin 1’s interaction with the cellular redox cycle. Reduced thioredoxin is involved in many signaling pathways that can lead to increased cellular proliferation and decreased apoptosis. Thioredoxin has also been shown to be over-expressed in cancer, particularly the most malignant (e.g., pancreatic and breast). We are working towards a small molecule inhibitor developed to target TrxR1, the only known enzyme that reduces thioredoxin. Current research suggests that inhibiting TrxR1 leads to decreased cancer cell fitness. Computational modeling has demonstrated the possible effectiveness of highly functionalized benzofulvene moieties due to high in-silico binding affinities (i.e. >10 kcal/mole) to the TrxR1 active site.
From readily available indanone a pharmaceutically relevant synthetic route for the benzofulvene scaffold has been developed. We can access highly functionalized benzofulvenes using reduced toxicity solvents while avoiding heavy metals and cryogenic conditions. Currently, we have synthesized twelve novel benzofulvenes with various functional properties. We will apply this route to synthesizing in-silico directed target molecules that could possibly inhibit TrxR1.

Justin C. Lytle, Ph.D., Marshall T. McNally, M. Reed Pueringer, Hannah C. Seal, and Mark C. Walsworth
Department of Chemistry
Carbon Nanofoams as Porous Scaffolds for Iron-Air Battery Electrodes
Research Corporation for Science Advancement + NSCI Division Undergraduate Research Program

Metal-air batteries store more energy per mass (specific energy) and per volume (energy density) than Li-ion batteries, but cannot discharge that energy as quickly as modern electronics need because metal anodes oxidize too slowly. We hypothesize that the specific power of metal-air batteries, as a class, would increase if the electrochemically accessible interfacial areas of metal anodes were greatly increased by supporting the redox-active metal component on nanostructured, porous current collectors. In such a design, a greater percentage of a metal’s atoms would be expressed on an electrode’s surface and would be simultaneously accessible to a liquid electrolyte that transports ions through a continuous pore network that is coupled with electronically conductive pore walls. We report a method to prepare sheets of carbon nanofoams that comprise a nanostructured carbon skeleton and micron-sized macropores within a bed of interleaved carbon fibers. Our work focuses on depositing a uniform coating of FeOx onto the pore walls of carbon nanofoams, and then electrochemically charging this “rust” into iron metal. We demonstrate that these electrodes reversibly discharge and charge, and that FeOx-coated carbon nanofoams discharge more energy than similarly prepared, but nonporous electrode analogues at current densities between 0.01 – 1 mA cm 2.

Tina M. Saxowsky, Ph.D., and Gavin C. Nixon
Department of Chemistry
The Role of the Retromutagenesis Pathway in the Acquisition of Drug Resistance
Natural Sciences Division Undergraduate Research Program

We report the use of a novel assay and replica plate system for the characterization of Saccharomyces cerevisiae that acquired drug resistance to the arginine analogue canavanine. This new technique allowed us to calculate the early mutation rates of clones in a wild type (WT) strain and a strain deficient in a DNA repair glycosylase (ogg1∆), and late mutation frequencies of clones that potentially acquired drug resistance by the Retromutagenesis pathway. Comparison of the late mutation frequencies between the ogg1∆ and WT strains reveal that the ogg1∆ strain experiences a higher rate of mutations per cell in stationary phase (6.96E-07) compared to the WT strain (1.51E-07)

Tina Saxowsky, Ph.D., and Richard H. Mackey
Department of Chemistry
Yeast cell survivability in the presence of Canavanine
Natural Sciences Division Undergraduate Research Program

The acquisition of drug resistance post treatment of said drug by a bacteria, microbe or tumor cell is of great public interest.  Knowing more about these acquisition processes can lead to better drug therapy treatments for infections and cancerous cell growths.  Adaptive mutagenesis occurs in Saccharomyces cerevisiae (budding yeast cells) when selective pressure causes a state of suspended growth. In this research we wanted to know the survival rate of yeast cells in Canavanine.

Tina Saxowsky, Ph.D., and Alicia Worley
Department of Chemistry
Biochemical Characterization of Truncated Mitochondrial DNA polymerase Pol β-PAK from Trypanosoma brucei
Natural Sciences Division Undergraduate Research Program

Trypanosoma brucei has two polymerase beta enzymes that participate in mitochondrial DNA replication within its kinetoplast DNA network (kDNA). These two proteins, Pol β and Pol β-PAK, are found to localize to different regions of the kDNA and have different optimal polymerase activity conditions in regards to pH and KCl and MgCl2 concentrations. Within the polymerase region, these proteins are ~30% identical. However, Pol β-PAK additionally contains an unusual N-terminal extension rich in prolines, alanines, and lysines and a short C-terminal tail. A recombinant protein, ∆PAK∆CT, containing the polymerase region of Pol β-PAK but omitting the PAK region and C-terminal tail was utilized to determine whether the functional differences between Pol β and Pol β-PAK could be attributed to these interesting structural features. ∆PAK∆CT was found to be primarily insoluble when expressed in E. coli but could be solubilized in high salt. Additionally, despite being a primarily positively charged protein, ∆PAK∆CT was found to associate with both positively and negatively charged chromatography columns.

Dean A. Waldow, Ph.D., and Victoria L. Richmond
Department of Chemistry
Synthesis and characterization of dicarboximide-functionalized oxanorbornyl homopolymers with ethylene oxide side chains
Robert C. Olsen Student Research Fund

Polymers may offer a safer alternative to liquid electrolyte supports in lithium ion batteries. We are investigating dicarboximide-functionalized oxanorbornyl homopolymers as potential solid polymer electrolytes. To that end, we have synthesized dicarboximide-functionalized oxanorbornyl polymers with varying ethylene oxide (EO)n side chains with 2, 3, and 4 EO units polymers via a ring opening metathesis reaction under living conditions using a Grubbs third generation catalyst. The polymers were characterized with 1H and 13C NMR as well as GPC. The molecular weights of the polymers are on the order of 36000 g/mol with narrow polydispersities of less than 1.1. Further characterization will include impedance spectroscopy to measure lithium ion mobility, and solid state NMR to measure polymer dynamics.

Neal Yakelis, Ph.D., Alex W. Wisbeck, Marisa R. Cuffin, Thomas J. Kolibaba, and Joy C. Murphy
Department of Chemistry
Tuning decomposition for controlled drug release: Diene effects on the rates of retro-hetero-Diels-Alder reactions
Robert C. Olsen Student Research fund + Fred L. Tobiason Endowment for Faculty-Student Science Research

Diels-Alder reactions involve the reaction of a four-atom diene and two-atom dienophile to form a new unsaturated six-membered ring. The reverse process – the retro- Diels-Alder reaction – has traditionally been very difficult to study due to requisite high temperatures imparted by the stable six-membered ring products. The hetero-retro-Diels-Alder reaction of N-carbamoyl-3,6-dihydro-1,2-oxazines is of particular interest because the reactions can proceed at much lower temperatures.  The unstable nitroso (N=O) dienophile that is revealed upon a retro-Diels-Alder reaction quickly breaks down in water. The retro-Diels-Alder/nitroso hydrolysis sequence is seen as a potential way to trigger the release of an amine leaving group at specific temperatures. The decomposition rates were measured by UV-visible spectroscopy by monitoring the appearance of a colored product. The kinetic profile of this reaction turns out to be strongly affected by the identity of the diene component. The strain imposed by cyclic dienes in the Diels-Alder products correlates with the rates of decomposition. For instance, the strained adducts formed by cyclopentadiene decompose more quickly at lower temperatures than the less-strained adducts formed by cyclohexadiene. Identifying dienes which decompose at physiological temperatures may have application as thermally-activated trigger units in new methods of polymeric drug delivery.

Claire E. Todd, Ph.D., and Taylor M. Christensen
Department of Geosciences
Suspended Sediment Concentrations and Erosion Rates on Mount Rainier, Washington
Natural Sciences Division Undergraduate Research Program

Tracking suspended sediment concentrations in glacial meltwater has important implications for the erosion rate of a rock body and can signify downstream instability, increased flood risk and potential effects on the hydroelectric industry (Stott and Mount, 2006). In order to characterize suspended sediment transport on Mt. Rainier, samples were collected from meltwater of five of Rainier’s glaciers. Samples were taken at the estimated maximum and minimum discharge times during the diurnal cycle, as close to the terminus as possible. Preliminary results indicate that, most often, more sediment is transported during the maximum discharge time, as seen in the 64% increase in sediment concentration between maximum and minimum discharge times at Carbon glacier. Data from a 24 hour sampling period at Emmons glacier report similar results. An interannual study of Emmons and Carbon glaciers indicate that a significantly larger amount of sediment was transported in 2013 compared to 2012. Future work will consist of simultaneous sampling at Nisqually glacier to examine potential downstream variation in sediment transport, as well as intra-annual sampling in order to track sediment concentrations as the ablation season continues.

Claire E. Todd, Ph.D., and Reed C. Gunstone
Department of Geosciences
Understanding Factors of Ecosystem Development in the Pro-Glacial Areas of Mount Rainier
Natural Sciences Division Undergraduate Research Program

Emmons Glacier in the Northeast corner of Mount Rainier National Park has a diverse pro-glacial ecosystem. The purpose of this study was to deconstruct the pro-glacial environment to understand what key factors play the largest role in ecosystem growth and development. Sediment samples were compared to quantitative vegetation and detrital wood debris data to try and determine links between data sets. Specific species of flora were consistently present in the pro-glacial environment along with trends of increasing densities of vegetation the further away from the terminus of the glacier and from the wetted edge of the river. This study brings to light another way to track and understand the activeness of a pro-glacial environment. Future work will include a refined approach that can be applied to more glaciers within the park.

Claire E. Todd, Ph.D., and Isaac S. Moening-Swanson
Department of Geosciences
Catastrophic Flooding on Mount Rainier: Are We Safe to do Our Research?
National Science Foundation

Mount Rainier has a history of outburst flooding centralized on its southwestern flank. In this study, I examine boulder bars as evidence of these catastrophic flooding events. I found boulder bars in five proglacial areas on the mountain, ranging in length from 95 meters to 25 meters, with boulders ranging from 260 mm to 1800 mm. All of the boulder bars demonstrated a discharge at least 100 times that of normal diurnal flow (Christensen, 2013). Future work could map boulder bars in more proglacial areas to gain a better understanding of the fluvial regimes found on Mount Rainier.

Claire E. Todd, Ph.D., and Riley K. Swanson
Department of Geosciences
The Effects of Rapid Glacial Retreat on the Proglacial Area: Mapping Geomorphological Landforms on Mount Rainier, WA
Natural Sciences Division Undergraduate Research Program

Mount Rainier, the most glaciated peak in the contiguous United States, provides an excellent location to study the effects of retreating glaciers on the proglacial sediments. Mapping these proglacial areas we are able to study how rapid retreat is changing the proglacial landforms. Research was conducted in valley transects parallel to the terminus to measure and classify the deposition pattern and origin of the sediments. Fluvial reworking was found to be the major geomorphic process in the deposition of the sediments. It was also found that both supraglacial and subglacial sources are delivering sediment to the valley floor. This shows that the retreating glaciers are leaving large amounts of material that is being reworked and moved by fluvial processes.

Bret Underwood, Ph.D., and Y. Michelle Zhai
Department of Physics
Dawn of Our Universe: Reheating and Resonance in the Very Early Universe
Natural Sciences Division Undergraduate Research Program

The night sky has inspired and intrigued humanity for thousands of years. As a young scientific subject, cosmology now has allowed us to comprehend our cosmos through observational data and detailed theories. With the support of increasingly precise data, cosmology keeps perfecting the model of our Universe and probing further back into the past. After decades of development, cosmologists are able to understand the evolution of our Universe all the way back to the billionth of a second in time, which we call the very early Universe. During this time, the Universe went through a phase called reheating, where much of the matter and radiation of the Universe was created. The physics of reheating is much like a more common phenomenon—resonance. To understand reheating better, we study the physics of resonance in some detail, such as including the effect of special relativity.