Using distance sampling to estimate population size of black-tailed deer on Blakely Island, WA
(Sponsor: Eric Long)

Columbia black-tailed deer (Odocoileus hemionus columbianus) are a subspecies of mule deer primarily located in low-land coastal regions east of the Cascade Mountain range in Oregon, Washington, and British Columbia. There have been very limited studies of small island populations of these deer. Blakely Island (17.8 km2) is a privately owned island in the San Juan archipelago of Washington State. The only predation of deer on Blakely is limited hunting by humans. During June-September of 2007, and again in summer 2008, I used distance sampling to estimate population density of black-tailed deer on Blakely Island. Data from both years were compiled and stratified. Using DISTANCE 5.0, I estimated a population density of approximately 45.5(95% CI: 37.2-55.5) deer per km2. Compared to mainland studies (7 deer per km2) and other island studies (28.5 deer per km2), this populati on density is very high. It is important to study this isolated island population to get a better understanding of what the population capacity of the island is, and future studies will also investigate the impact of such high density deer populations on the island's ecosystem.

Deconvolution May Provide Quantitative Evidence of Zinc Co-localization in Hemocyte Lysosomes of the Pond Snail, Lymnaea stagnalis
(Sponsor: Richard Ridgway)

Hemocytes of the pond snail, Lymnaea stagnalis, are capable of sequestering zinc within vesicles when exposed to ZnCl2 solution; however, the specific mechanism is unknown. Previous experiments, which used the fluorescent probes FluoZin-3 (to label Zinc) and Lysotracker Red (to label lysosomes) suggest that once in the cytosol, the zinc-containing vesicles enter the endosomal-lysosomal pathway. In order to establish a more quantitative data set, we are currently deconvolving these images (acquired with a CARV II confocal system from BD Biosciences) and calculating Pearson's coefficient of co-localization using the analytical software, Huygens Essential 3.3 (Scientific Volume Imaging). With this numerical means for comparison, we will not only be better able to look for significance when compared to controls, but we will also be able to measure the changes in these vesic les over time quantitatively.

Measuring recombination efficiency in Agrobacterium tumefaciens
(Sponsor: Derek Wood)

Generation of insertional mutations in bacteria is facilitated by homologous recombination, a process mediated by the recA gene. In Agrobacterium tumefaciens C58, recombination requires a minimum of 1,500bp of homologous DNA. In contrast, efficient recombination in Azotobacter vinelandii requires only 300bp. In order to improve recombination in C58 we are replacing its recA gene with that of Azotobacter. To test the effectiveness of recombination in this strain we are constructing three test vectors that contain 0.5, 1.0, and 1.5kb of homologous DNA flanking a kanamycin resistance gene cassette. The vectors are designed to replace gene Atu0944 and the efficiency of this replacement will be tested for all three vectors in both wild type recA and recA:Avin C58 backgrounds. Generating a recombination efficient C58 strain will support the development of functional genomics tools in this model organism.

Endochondral ossification is required for haematopoietic stem-cell niche formation

Little is known about the formation of niches, local micro-environments required for stem-cell maintenance. Here we develop an in vivo assay for adult haematopoietic stem-cell (HSC) niche formation1, 2. With this assay, we identified a population of progenitor cells with surface markers CD45-Tie2-V+CD105+Thy1.1- (CD105+Thy1-) that, when sorted from 15.5 days post-coitum fetal bones and transplanted under the adult mouse kidney capsule, could recruit host-derived blood vessels, produce donor-derived ectopic bones through a cartilage intermediate and generate a marrow cavity populated by host-derived long-term reconstituting HSC (LT-HSC). In contrast, CD45-Tie2-V+CD105+Thy1+ (CD105+Thy1+) fetal bone progenitors form bone that does not contain a marrow cavity. Suppressing expression of factors involved in endochondral ossification, such as osterix and vascular endothelial gro wth factor (VEGF), inhibited niche generation. CD105+Thy1- progenitor populations derived from regions of the fetal mandible or calvaria that do not undergo endochondral ossification formed only bone without marrow in our assay. Collectively, our data implicate endochondral ossification, bone formation that proceeds through a cartilage intermediate, as a requirement for adult HSC niche formation.

Impact of Stress on Metabolic Rate

Chronic stress has been linked with health problems including reduced immune function, hypertension and cardiovascular disease; however, less is known about the effect of stress on other physiological processes like metabolic rate. Here we examine the effects of prolonged stress exposure on resting metabolic rate (RMR) during the course of a 10-week academic term, comparing pre-nursing and non-nursing students. Oxygen consumption, stress surveys, and blood pressure were collected from 19 female participants once weekly for ten weeks. Our data show a significant relationship between both nursing and stress on metabolic cost.

The effects of depth on nitrogen and carbon content of Ulva lactuca and Ulvaria obscura at three sites off Blakely Island, WA.

Macroalgal blooms can be detrimental in the Pacific Northwest because they can cause anoxia, shading, decreased primary productivity, decreased colonization of algae and animal species, and loss of sea grass meadows. Two species involved in these blooms in Washington State are Ulva lactuca and Ulvaria obscura (Ulvophyceae). Macroalgal blooms are usually caused by an influx of nutrients, including nitrogen, which is a main limiting resource for these algae. The nitrogen and carbon content of these two species of ulvoids were measured from samples grown at three different depths and at three locations surrounding Blakely Island, WA. Tissue nitrogen content was significantly higher in deeper water and at sites with higher dissolved inorganic nitrogen in the seawater. These results reiterate the importance of nitrogen as a key factor in macroalgal blooms.

Undergraduate Genome Sequencing of Agrobacterium rhizogenes A4 via 454 and Sanger Methods

Agrobacterium rhizogenes is a bacterium of special interest to the industry of Biotechnology, but as yet has not had its genome sequenced. In order to rectify this, undergraduate researchers in the microbiology lab at Seattle Pacific University work to sequence the genome of Agrobacterium rhizogenes. 454 whole genome sequencing technology produced most of the genome sequence in the form of "contigs." Contigs are large swaths of DNA that have a known sequence in the genome. These contigs were organized using optical mapping technology and comparative scaffolding techniques in order to create an accurate map of the Agrobacterium rhizogenes genome. Primers were designed to anneal to the ends of adjacent contigs so that each "gap" region of unknown DNA could be amplified and sequenced. In this study, 27 contig gaps are closed via the Sanger method.

Immunolocalization of dopamine in the marine alga Ulvaria obscura differs with use of monoclonal and polyclonal antibodies.

The temperate green alga Ulvaria obscura secretes dopamine as an anti-herbivore defense molecule in response to tissue damage. The mechanism for dopamine release, however, is not well understood. Because the thallus of U. obscura is monostromatic it is an ideal candidate for whole-mount confocal microscopy, by which optical sectioning of the tissue is possible. The purpose of our study was to localize dopamine in the cells of U. obscura by pairing this technique with immunohistofluorescence. Tissue samples were fixed, permeabilized by partial enzymatic cell wall digestion, and then incubated in either commercial polyclonal or monoclonal antibodies generated against a dopamine conjugate. The polyclonal antibody stained numerous vesicular structures along the inside of the cell membrane. The monoclonal antibody, however, stained larger granular structures throughout th e cytoplasm, as well as the starch plates surrounding pyrenoids. The variation in dopamine distribution suggests that differences in specificity may exist between the two dopamine antibodies. In both cases, staining was limited to cells near the cut edges of tissue samples. A parallel study using a monoclonal antibody to α-tubulin showed similarly restricted staining, suggesting that this phenomenon is due to an inability of our probes to penetrate further into the tissue rather than a limited distribution of dopamine itself. Further studies are aimed at more effectively localizing dopamine in U. obscura tissues while preserving cellular structure.

Comparative prevalence of Baylisascaris procyonis between raccoon (Procyon lotor) populations on Blakely Island, WA, and mainland western Washington.

Baylisascaris procyonis is a roundworm of the family Ascarididae and the common intestinal parasite of raccoons (Procyon lotor) in the United States. The propensity of B. procyonis larvae to encyst in the central nervous system makes this zoonotic pathogen a health concern for those in close proximity to raccoon populations. Higher contact rate among individual raccoons is expected to result in a greater prevalence of parasites. Fecal samples were collected from mainland and Blakely Island, Washington. Samples were processed through fecal flotation and analyzed using light microscopy. Roundworm prevalence was compared between the two sampling areas along with total parasite loads. Baylisascaris procyonis was more prevalent in mainland samples suggesting a higher epidemiological concern for mainland Washington.

Comparison of parental behavious in inexperienced and experienced Peromyscus californicus parents.

The California mouse, Peromyscus californicus, is a monogamous species in which both males and females show a significant amount of parental care toward their offspring. Previous studies have suggested that species differences in paternal care are associated with variation in patterns of arginine vasopressin-immunoreactive (AVP-ir) staining and receptor patterns within the brain of male rodents. Because less is known about the relationship between vasopressin and female behavior, this study examined the relationship between AVP and female parental care. This project examined whether AVP levels in female P. californicus differed between first-time and experienced mothers. We hypothesized that a mother learns how to respond to her offspring's needs in response to food availability or environmental conditions with each additional generation of pups. Ten virgin females were paired with males chosen at random from a laboratory population of P. californicus. In order to compare parental care in inexperienced and experienced females, each female and her offspring were videotaped every other day for 30-minute segments. Reviewed videos determined the amount of time the female spent huddling with the pups, retrieving pups, grooming pups and nest building. Differences in maternal behavior between inexperienced and experienced mothers will be presented. From this experiment I am able to effectively discern the outcome of certain levels of AVP and their direct correlation to parental care in female P. californicus. This could draw a parallel with humans as to why parenting skills may increase as a mother has more offspring.

Agrobacterium tumefaciens C58 Redundant Genes

Agrobacterium tumefaciens C58 contains redundant biosynthetic pathways for both arginine and proline. Though the enzymatic activity that allows arginine and proline to be synthesized is well documented, it is less understood if the redundancy for either amino acid gene creates the same end product. The purpose of this research is to use functional complementation to determine which genes code for a functional protein.

Foot arch morphology variation among humans and energetic cost to running and walking

The purpose of this research is to study the effects that arch shape may have on force impact and energy efficiency of human locomotion; that is, the energy used during running and walking due to either a more or less efficiently shaped arch. It was predicted that the development of the plantar arch in the foot enabled more efficient walking and especially running in humans and that the difference in efficiency will be shown between humans with high, medium, and low arches. The results suggest that arch size is inconclusive which is most likely due to a small sample size. It was also shown that subjects burn significantly more calories wearing shoes while running than without, this is most likely due to the extra weight (shoes) on the distal limbs.

Effects of Vasopressin on Behavior in Female California Mice (Peromyscus californicus)

Peromyscus californicus, the California mouse, is an unusual species because they provide a substantial amount of biparental care to offspring. One neuropeptide that may be stimulating this high level of parental care is arginine vasopressin (AVP), a neuropeptide found throughout the brain of most animals. Although this neuropeptide has been most strongly associated with aggression and parental care in male animals, it may also play a key role in regulating female behavior. In females, limited evidence suggests that AVP may be linked to maternal care, including behaviors such as grooming pups, nest-building, and huddling with pups. Expression of AVP also is prominent in the olfactory bulb, which transmits information about odors from the nose to the brain. We hypothesized that first time mothers would have less AVP-immunoreactive staining and slower olfactory processing du e to their inexperience and would provide less maternal care that experienced mothers. In this study 10 male and 10 female mice were paired and were assigned randomly to the first-time or experience mother group. After the birth of pups each mother and her pups were transferred into clean Plexiglas cages for behavioral observations of maternal care. In order to test olfactory processing times in first-time and experienced mothers, an olfactory recognition test was performed on day 7-8 after the birth of pups. In this test, a cotton ball dipped in vanilla was placed in the cage and we recorded the latency before the mother acknowledged the cotton ball. After video recording of the first litter (first-time mothers) or second litter (experienced mothers) was complete, immunocyctochemistry was used to reveal the distribution of the AVP-immunoreactivity (AVP-ir) within the brain. Comparisons of the amount of AVP-ir staining between four inexperienced and four experienced mothers i n the paraventricular nucleus (PVN), bed nucleus of the stria terminalis (BNST), supraoptic nucleus (SON), and the medial amygdala (MA) will be presented.

Stories from Skulls: Morphological measurements and tooth wear patterns exhibited in the Blakely Island black-tailed deer population.

The isolation of Blakely Island and small human presence has made the black-tailed deer an especially interesting subject to population studies. Over the years, SPU students have collected numerous skulls of naturally expired deer. These skulls are going to undergo an extensive set of measurements to document the morphological characteristics of each with the goal of creating a dataset extensive enough to determine the fluctuating asymmetry (FA) of the population. Fluctuating asymmetry is the random deviation from the expected symmetry in left/right features on an organism. An emerging theory holds that when a phenotype is subject to stress, asymmetry develops over an organism's lifespan. Establishing such a dataset will allow us to determine if this theory fits this isolated population and the level of stress and coping ability of the population. In addition to all this, the teeth of the skulls will be studied based on the current aging techniques to determine the age at which the individuals expired. This will create another dataset that will prove to be invaluable for future research. These estimates will be compared to studies that will happen at a later date where the skulls will be aged based on cross-sectioning.

Assessment of Puget Sound Beaches: The Effect of Marine Reserve Policies on Biodiversity

The Puget Sound houses a variety of organisms making the west side of Washington State an icon for conserving biodiversity. In 2001 marine protected areas were established on seven local beaches in hopes to conserve biodiversity and the health of the ecosystems. Through research with the Seattle Aquarium Citizen Science program, analyses of indicator species amounts from seven beaches were analyzed. General trends include three beaches with higher amounts of biodiversity, one neutral, and three slightly lower biodiversity counts. Based on the data, marine reserves may play a role in helping conserve local biodiversity in short periods of time and help determine local conservation acts.

Rational design of enhanced affinity at the MICA-NKG2D

MICA is an MHC-like protein expressed on stressed cells. It binds the NKG2D immunoreceptor and activates natural killer cells. Our research seeks to enhance binding affinity at contacts between MICA and NKG2D. Previous research has focused on mutating the area beneath the binding site, an indirect design strategy that has increased the association and affinity between MICA and NKG2D by more than an order of magnitude. We currently aim to increase binding affinity directly by designing point mutations at MICA-NKG2D protein-protein contacts. RosettaDesign was used to predict which contact mutations would be most beneficial at the MICA-NKG2D interface. We have produced multiple point mutants of MICA in an undergraduate research environment and measured NKG2D binding kinetics and thermodynamics using surface plasmon resonance. In the first round of design, 4 out of 6 mutations enhanced NKG2D affinity by 0.5 kcal/mol or more, up to 1.2 kcal/mol. This success rate is similar to published accounts of antibody-antigen design and other protein design strategies. Once a panel of point mutations is complete, we will investigate the kinetics and thermodynamics of combining mutations, from direct and indirect design strategies.

Parallel Computational, and Experimental Analysis of Symmetric Hotspot Residues on the Binding Surface of NKG2D

Immune responses are largely governed by tight, highly specific protein-protein interactions. This study focused on one such interaction between the homodimeric immunoreceptor NKG2D, found on natural killer cells, and its MHC-like ligands, which are expressed on stressed cells. Previous research has shown that the NKG2D-ligand interface structure is dominated by 4 central tyrosine residues at positions 152 and 199. We mutated these residues to smaller and larger amino acids in order to investigate the role of these tyrosines in NKG2D-ligand complexes. Eight tyrosine mutants were tested for binding to MICA, MICB and a high-affinity MICA mutant using surface plasmon resonance. For example, mutating Y199 to phenylalanine had a larger detrimental effect on binding than did Y152F, implying that the former tyrosine is more sensitive to the removal of the hydroxyl. Alanine mutati ons were most detrimental to complex affinity but we were still able to detect binding. We found the Vant Hoff enthalpies of each mutant NKG2D-ligand interaction. We correlated observed binding energies with those predicted by a fixed-backbone Rosetta Design mutation simulation. Even simple fixed-backbone Rosetta Design provided qualitative agreement with results for 14 of 15 mutant NKG2D-ligand interactions, and quantitative agreement for 11 of those. To complete this study we plan to investigate the hydrophobic effect in the center of the site by making an additional 3 mutations (I,L, and V) at each residue.

Classification of Mammals by Chemometric Analysis of Scat Samples

Scat samples of three species of canines were analyzed by GC-DMS. This produced 2-dimensional data, which was then processed chemometrically in order find any volatile compounds which produced a unique signal that could distinguish one species from another. The data was first baseline corrected, normalized, and aligned, which was difficult to do with 2D data. Various algorithms were used to classify the data, including anova, IPCA, IPLS. In total, 2 unique volatile chemicals were found. One separated the first species from the other two, and the second was found when just looking at the second and third species, as it could only differentiate between them, and not the first.

No Title Provided

The ability for yeast Saccharomyces cerevisiae to adapt to cold temperatures is still largely not understood. Previous research by Loerstcher et. al. has shown that proteins associated with endoplasmic reticulum-associated degradation (ERAD) are required for cold adaptation as well as the increased production of sterols. In preliminary testing, some deletion mutants associated with endoplasmic reticulum-related proteins exhibited notable sensitivity at 10 °C. The deletion mutants left to be characterized are the orm2∆ and the orm1∆ with comparison to a wild-type cell. Sterols extracted from yeast with the deletion mutants are quantified with Gas Chromotography-Mass Spectrometry (GS-MS). Sterols are challenging analytes due to solubility properties and low natural concentration. We optimized a GC-MS method to provide precise percent total signal quantification of sterols from mutant orm1, mutant orm2 and wild-type cells. Haploid cells showed an increase in Squalene production and a decrease in Ergesterol production for orm1 and orm2 relative to the wild-type cell

Dynamic Surface Tension Detection Studies of tetrabutylammonium compounds

The surface active properties of tetrabutyl ammonium compounds of standard proteins and coffee components are studied using liquid chromatography coupled with a dynamic surface tension detector.

oChem Hammer
(Sponsors: Elaine Weltz and Kevin Bartlett)

oChem Hammer is a computer program designed to help instructors and students of organic chemistry. The program was designed by Mark Boatman, Tavis Bohne, Chris Carlson, and Tara Hodges using Visual Studio 2008 and the .Net 2.0 Framework. It features the ability for instructors to easily create graphic representations of molecules and their resultant reactions. It allows for students to step through the reactions their instructor has graphically created. It gives feedback to the students throughout the reaction and allows the instructor to provide additional instruction as well. Ideal use of oChem Hammer would include an instructor creating a study assignment, in file form, comprised of multiple reactions. The instructor could then disperse the assignment to the students via email or a Blackboard system. The students, with oChem Hammer installed on their personal PC, could then open the assignment in the program and work through the reactions in the assignment. The projected outcome of this program is more efficient and better learning of the organic chemistry material for students, and easier assignment of study materials for instructors.

Website Media Publisher

The Website Media Publisher is a software system. It easily uploads media to a website, regardless of the users' technical ability. The WMP has a desktop application and website players, which communicate with each other to relay files from the users' computers to website servers. Once the files are on the servers, web surfers can view/listen/watch them via the players. We used Java and JavaFX to write the program.

The Engedi System: An Alarm Clock For Modern Living
(Sponsor: Don Peter)

The Engedi System is the next generation in alarm clocks, designed to maximize comfort and flexibility. Rather than jolting the user awake with obnoxious beeping, it contains an extensive suite of customizable features that provide a more natural and healthy way of waking. These include a gradually increasing light to simulate sunrise, a gently vibrating mattress pad with integrated heating and cooling, MP3 player compatibility, and a remote outlet control for appliances such as a coffee maker.

Mimicking Robotic Arm
(Sponsor: Don Peter)

Our project is a robotic arm that mimics the movements of a human operator's real arm which is fitted with sensors. The movements are intended to have the same freedom as a real arm. It is also designed to have the maximum possible precision given our resources. The project involves several Cypress PSoC microcontrollers, is battery powered, and will communicate wirelessly. The robotic arm is intended for use in environments where a person would not want to put their real arm.

A Basic Data Logger
(Sponsor: Don Peter)

We are in the process of designing a data logger that will record light flux and temperature within an environment for a user-specified period of time. After the sensor data is properly conditioned, it is converted to digital information and passed to the PSoC CPU Core. Once our device is connected to a computer, it will transmit its data for later analysis. Our team's primary goal in this project is to provide usable information that can later be mined for trends, dependencies, and definitive characteristics of the environment of interest. This presentation will describe our work and research.

Examining Human Force Control: Adaptation to Deceptive Visual Feedback
(Sponsor: Melanie Plett)

Brain disorders often impair a person's ability to control their body naturally by impacting the motor control system that controls contact forces and motions in free space. This study investigates how healthy humans adapt their force control when presented with deceptive visual feedback. The results confirm that when a healthy person is given misleading visual feedback, their proprioceptive faculties are deceived. Thus, the body's sense of its position in space can be fooled. The results also indicate that the human motor control system relies on proprioceptive information for controlling contact forces by showing that deceived proprioception alters human contact forces.

Energy Vampires: Idle Power Elimination System
(Sponsor: Don Peter)

Our Junior Design project is to design and build a working prototype of an idle power system that will effectively reduce the power consumed by a simple appliance. We will be presenting on why there is a need for our product, the research we have done as to similar products already available and a description of our current design. We will also discuss how we will be expanding on our current design for our next year's Senior Design.

Improve Your Home Garden
(Sponsor: Don Peter)

The goal of our project is to design a system that analyzes temperature, light, and moisture conditions for use in home gardening. Users will be able to make educated decisions on growing certain plants, as well knowing whether temperature/moisture/light modification is necessary. All of this will be based on their personal garden statistics, available through a computer interface. Our project will also include planting recommendations based on statistics.

Coxswain's Mate

The Coxswain's Mate is an engineering Senior Design project intended to help crew teams in training and competition. It consists of a voice amplifier for the coxswain, a heart rate monitor for each rower, a stroke counter, a programmable practice timer, and an interface for a walkie-talkie and audio recorder.

The Verna System

Our poster is an electronic pill dispenser that allows for programmable alarms and multiple dosages. In addition, the system has networking compatibilities that allows for remote status updates through the network.

A "Greener" Seattle Pacific

An honors project exploring what SPU can do to move towards their goal of becoming a more sustainable university. The project focuses on designing a solar photovoltaic system to be installed on Otto Miller Hall.

How computers hear music
(Sponsor: Lane Seeley)

From an engineering perspective, the music industry goes on at the interface between digital and analog. Innovation is driven by the need for more accurate ways of representing music and more possibilities of what to do with it. Imagine a computer that can listen to music and then play it back using real instruments rather than speakers. Although this may seem more historic than futuristic, as player pianos predated cell phones, the ability for a computer to "hear" music still poses a challenge similar to that of speech recognition. However, methods for digitally representing music in a way that a computer can communicate with have been established (MIDI). So, how can we translate music as we hear it into MIDI using only a microphone? Much of this problem has been dealt with by others, except for as it pertains to percussive instruments. This research seeks to answe r this question as it applies specifically to percussion instruments such as those found in a drum set.

Research on a permanent atomic electric dipole moment in mercury
(Sponsor: Stamatis Vokos)

The existence of nonzero permanent electric dipole moment(EDM) of a particle or an atom would violate time reversal symmetry(T), and wound also imply the violation of the combined charge conjugation and parity symmetry(CP) through the CPT theorem. The Standard Model(SM) of Particle Physics predicts EDM to be too small to be detected in a lab; however, the extension theories of SM,such as supersymmetry, predict EDMs within experimental reach. The EDM experiment on 199 Mercury at University of Washington places four mercury vapor cells in parallel magnetic and antiparallel electric fields and emits a linear laser through the cells to observe the spin precession frequency. Their new reported result on mercury EDM is |d(199Hg)|<3.1*10^(-29) e cm, which improves the previous limit by a factor of seven.

Nikola Tesla: Genius or Alien?

Nikola Tesla, an often-overlooked physicist and inventor of the early 20th century, was not just a brilliant man; he also suffered from undiagnosed mental illness. This mastermind behind things as outlandish as a "death ray" and as fundamental as AC power and wireless communication also believed his inventions could be used to communicate with extraterrestrials. A following even developed that claimed Tesla was from Venus. This project provides a short biography of Tesla's life and explores his seemingly runaway mind, to the end that Tesla, who gave so much to society, died broke and alone in a New York hotel room.