Presenter: Andrew Delapaz, Biology
Poster (Morning Session)
Mentor: Braedan McCluskey, Biology
Zebrafish and Related Species as a Model of Evolutionary Development
Out of the nearly 60,000 species of known vertebrates, fish comprise nearly half of the group. Natural selection has created the spectrum of sizes, shapes, and colors seen in fish. However, the developmental mechanisms underlying these differences are still unknown. The zebrafish (Danio rerio) is a common model for development and genetics. Our specific purpose is to understand differences in anatomical structure development between zebrafish and related species. The sensory “whiskers” found on fish, also known as barbels, differ greatly within this genus and therefore are ideal to study. To investigate the genetics behind barbel development in Danio, we measured and compared barbel size and number in different species and hybrids between these species. These hybrids can be used to determine if a characteristic is inherited in a dominant or additive fashion. The species we used were zebrafish (D. rerio), and dwarf zebrafish (D. nigrofasciatus). We chose these species because in addition to clear differences in body size, D. rerio has two pairs of barbels, while D. nigrofasciatus has only one. The hybrids obtained from crossing these species had a single set of barbels, which were intermediate in length compared to the two parent species. These data indicate that barbel length and number are not determined by the same mechanism. / By further researching barbels and other traits among this genus, we can deepen our understanding of how species diversity of vertebrates evolves.
Presenter: Patricia Macqueen, Geological Sciences
Poster (Afternoon Session)
Mentor: Katherine V. Cashman, Geological Sciences
Using Forward Modeling to Optimize the Geometry of Geophysical Networks at the Summit of Kilauea Volcano: A Matter of Great Gravity
Minute changes in the gravitational field of a volcano can give early warning of subsurface magma accumulation or withdrawal long before other more traditional precursors (e.g., seismic and deformation) and provide a valuable data set that is complementary to other data sets. Scientists have been monitoring gravity changes at the summit of Kilauea Volcano, Hawaii for decades, and these data sets have yielded valuable insight into volcanic activity at Kilauea. However, we currently have a poor understanding of the bias imposed by network geometry. My work focuses on using forward models of three known magma storage areas beneath Kilauea’s summit to test the resolving power of the current network. This forward modeling indicates that the current network can distinguish changes from sources near Halema`uma`u Crater and Keanakakoi Crater very well, but that additional station coverage is needed to decrease bias from network geometry in the south caldera region — known to be the primary magma storage reservoir beneath the summit. To this end I have suggested 5 new station sites in the south caldera area and evaluated the improvement that these stations would bring to the network. Forward modeling has also clarified the ability of the network to resolve sources with different mass changes and depths, and given insight on which stations are most useful for monitoring known sources of subsurface magma storage.
Presenter: Kimberly Davidson, Chemistry
Poster (Morning Session)
Mentor: Marina Guenza, Chemistry
Theoretical Study of the Molecular Dynamics of Diubiquitin
In eukaryotic cells, polyubiquitin chains attach themselves to proteins that are ready for proteolysis. When the proteolysis pathway is disturbed, diseases such as cancer can result. This study focuses on the molecular dynamics of diubiquitin on a small time scale. Diubiquitin contains two ubiquitin chains connected by an isopeptide bond between Gly76 and Lys48. We used GROMACS to simulate the protein chain for ~10 ns with an average RMSD of ~0.2 nm. A change in RMSD was observed at ~4 ns indicating a conformational change in diubiquitin. Calculation of T1 and T2 values revealed the theoretical spin-relaxation time for each residue. Further study of diubiquitin will be useful in understanding the proteolysis pathway and how disruption can occur.
Presenter: Tracy Zapf, Spanish
Poster (Afternoon Session)
Mentor: Karen McLaughlin, Communication Disorders and Sciences
Acquisition of Second Language Vocabulary for Kindergartners with Speech Sound Disorders
Researchers and educators alike have raised concerns over the potential lack of inclusion of children with speech and language disorders in immersion programs. The purpose of this study was to determine if children with speech sound disorders acquired Spanish vocabulary at a similar rate as a typical peer when learning in an immersion program, and if there was a difference between rates of acquisition for expressive versus receptive vocabulary. Participants included five kindergartners attending a partial, early elementary immersion school, one control participant and four participants with speech sound disorders. Expressive and receptive vocabulary probes were used to test the number of Spanish vocabulary words children could produce and comprehend within an eight-week period. Results showed that children with speech sound disorders acquired expressive Spanish vocabulary at a similar rate as their typical peer, but had lower levels of acquisition overall; rates of receptive vocabulary acquisition varied across participants. The results of this pilot study suggest that children with speech sound disorders are able to acquire Spanish vocabulary and, as a result, should continue to be included in immersion programs in the future.
Presenter: Jesus Fernandez, Architecture
Poster (Morning Session)
Mentor: James Tice, Architecture
Exploring Rome through Guiseppe Vasi’s Eyes
Giuseppe Vasi (1710 – 1782) created over 240 vedute or city landscape views of Rome during his lifetime and in the process provides us with a vivid document of the city and its people during the period. Vasi methodically and accurately depicts every corner of the city from impressive monuments to more humble quarters. His views of daily life also provide a fascinating social commentary rendering all classes with a witty and candid eye. The research project in which I have been involved highlights five spectacular panoramas that Vasi created at the height of his career. The largest of these, the Panorama of Rome taken from the Janiculum Hill, is over 9 feet long and shows 390 individual monuments that are carefully keyed to an index on the print. Working with faculty in the Department of Architecture and the InfoGraphics Lab in the Geography Department on campus, my research has been to carefully analyze and create a multi-media display, allowing the viewer to understand the wealth and breadth of the information, portrayed. The resulting work was formatted into an innovative iPad installation and included in the recent exhibition, “Giuseppe Vasi’s Rome: Lasting Impressions from the Age of the Grand Tour” sponsored by the Jordan Schnitzer Museum of Art last fall. The exhibition is currently showing at the Princeton University Art Museum.
Presenter: Kelsey Wahl, Chemistry
Poster (Afternoon Session)
Mentor: Hui Zong, Institute of Molecular Biology
Investigating Early Effects Following Glia Cell Ablation in Medulloblastoma
Medulloblastoma is the most common type of malignant brain tumor in children. During cerebellar development, granule neuron precursor cells (GNPs) proliferate along the external germinal layer in response to the sonic hedgehog signaling pathway. In our lab, medulloblastoma is modeled in mice by inducing heterozygous mutations in both the sonic hedgehog signaling receptor patched (Ptc) and the tumor suppressor gene p53. These mutations lead to a brain tumor in the cerebellum through over-proliferation of GNPs. From previous research, it is shown that unipotent GNPs in a tumor can somehow give rise to glia cells. In order to determine the role of glia cells within the tumor, they were selectively ablated through thymidine kinase (TK)-mediated cell ablation with administration of Ganciclovir (GCV). Amazingly, the proper dosing regime of GCV leads to complete tumor regression. To further understand the ablation process, we studied early time points during GCV injections to observe cellular processes within the tumor.
Presenter: Korrin Bishop, Planning, Public Policy and Management
Poster (Morning Session)
Mentor: Laura Leete, Planning, Public Policy and Management
Reversing the Homeless Trend: A Case Study of the Homelessness Prevention and Rapid Re-Housing Program in Lane County, Oregon
The Homelessness Prevention and Rapid Re-Housing Program (HPRP) is a $1.5 billion stimulus program that came out of the 2009 American Recovery and Reinvestment Act. Funds were distributed to qualifying communities to provide Housing First and housing stabilization services. Lane County received a total of $1,490,050 from combined City of Eugene and Oregon state grant funds to coordinate HPRP services for the Lane County community. As a locally active participant in the HPRP, Lane County lends itself as a case study for exploring this new federal policy. The research question explored through interviews with HPRP staff members and an analysis of reported program data follows: Despite its time limitations as a short-term, stimulus program, is the HPRP building upon long-term, sustainable solutions to homelessness in Lane County, Oregon? Upon completion of research, highlights of the program focused on positive collaborative efforts and forward changes in organizational thinking, while challenges centered on burdensome reporting requirements and struggles with low funding and time. Overall, the HPRP has helped to build upon long-term, sustainable solutions to homelessness both in Lane County and nationwide. However, a commitment to collaborative efforts and the establishment of a substantial funding source are vital for continued sustainability. This research is significant to the field, as it explores best practices for ending the homelessness epidemic and discusses the challenges they face in implementation.
Presenter: Kelley Mabry, Architecture
Poster (Afternoon Session)
Mentor: James Tice, Architecture
Nolli, Lanciani, and the Spatial History of Rome
Giambattista Nolli’s 1748 Baroque Map of Rome remains one of the most engaging and accurate maps of the city ever created. Rodolfo Lanciani’s 1902 archeological map of Rome, based on Nolli, depicts the city as a series of layers extending from antiquity to the beginning of the 20th century. By carefully comparing these two cartographic sources, one can create a clearer understanding of Rome’s spatial history and how, among other things, Rome’s famous seven hills have influenced the city’s growth over the centuries. By using the geo-database software, ArcGIS, both the Nolli and Lanciani maps can be further geo-rectified with recent satellite imagery and data to achieve an even richer, layered, spatial understanding of the city. This enhanced layered approach opens new possibilities toward the understanding of Rome’s spatial history and its evolution over two millennia.
Presenter: Alexandria Russell, Matthew Silva, Matthew Liston, Environmental Science
Poster (Morning Session)
Mentor: Peg Boulay, Environmental Science
Oak Habitat Mapping and Monitoring in the Southern Eugene Ridgeline
The prevention of fire regimes, in combination with increasing urbanization, has led to a drastic decline in woodland oak habitats over the past 150 years in the Pacific Northwest. Currently, less than 2% of pre-European settlement oak habitat remains in the Southern Willamette Valley. Oak habitats are home to a wide range of rare plants and animals. As a result, the City of Eugene made conserving oak habitats one of their top priorities. As members of the Ridgeline Oaks Team, we collected data within these native oak habitats to help the City of Eugene implement a future management plan and protocol. We compared the accuracy of previous habitat delineations to the data we collected in the field and found that the former habitat delineations were only 55% accurate. We collected baseline data as well as data on heritage trees, which are mature trees that are important for their ecological and historical value. We also modified the protocol to adapt to the conditions in the field and improve efficiency. Our implementation of the original protocol helped us to develop more efficient ways to collect the data. The ecological data will assist the City in determining priority restoration and management areas within the Ridgeline. In addition, the data we collected will serve as a baseline against which future changes can be compared.
Presenter: Angela Stelson, Political Science, Mathematics, Physics
Poster (Afternoon Session)
Mentor: Daniel Ho Sang, Political Science
Affirmative Action and White Males: A Study of the Impacts of Framing
Ballot measure campaigns have served as a discursive battleground for various arguments (or “frames”) of affirmative action. Using this historical backdrop, this study tests three models designed to predict the success of frames using demographic attributes: liberal vs. conservative, group dominance, and parent morality. The study used a survey of 104 Caucasian males to analyze the relationship between demographic factors, political ideology and morality models for frames found in the campaigns for affirmative action ballot measures. The survey was based around a fictitious ballot measure which the respondent could vote on, and then change their vote based on exposure to frames. The findings ascertained that no one model could completely explain the effect of the frames. However, different model predictions correlated positively with different types of frames; the parent morality model best described frames which addressed the same socioeconomic group (“in-group”), and the liberal-conservative model best fit frames which were oriented toward other demographics (“out-group”). These results help to contribute to the body of framing knowledge by providing a comparative test of these models and indicating their flaws, while providing an alternative model which combines the strengths of each model.
Presenter: David Bauer, Kris Haenderson, Allison Wilbur, Biology
Poster (Morning Session)
Mentor: Chris Doe, Biology
Enhancer-GAL4 Database Yields Subsets of Gene Expression
Enhancers and suppressors are major controls in the tempro-spatial expression of a gene. Prior work has shown that enhancers may be made up of small modules, each driving only a small subset of expression in an overall pattern that we associate with a gene. The Rubin lab at Janelia Farms Research Center created over 70,000 fragment sequences from more than 1,100 neural gene regions. These fragment enhancer sequences were used to generate site-specific transgenic GAL4 expressing Drosophila lines. These lines are currently being screened by several collaborating labs for their ability to function as transcriptional enhancers to drive limited subsets of UAS-GFP expression. Our lab’s role is to screen Drosophila embryos for neural expression patterns of the transgenic enhancer fragment lines. As a test analysis, we took a subset of 82 individual fragment enhancer lines derived from seven gene regions in embryonic nerve cords (VNC). These 82 lines produced 77% of fragments with expression in the VNC. Within that expressing set, 62% drove small patterns of less than ten cells per hemi-segment. This data complements the screening results collaborative labs are finding in Drosophila larval brains. Together, these results show that the theory of enhancers being a set of modules acting in concert to yield an overall pattern of gene expression seems quite likely. The end result should be a valuable tool that can be used for studies of gene control, patterning, and neuronal circuitry.
Presenter: Brianna McHorse, Biology
Poster (Afternoon Session)
Mentor: Samantha Hopkins, Geology
Biostratigraphy of Miocene Camelids in the Juntura Formation
Paleoecological research relies largely on the accuracy with which fossil specimens can be identified. Species-level identifications provide the most precise data for measuring diversity and communities through changing environments, space, and time. While cranial (skull) fossils allow a researcher to quickly identify specimens to the species level because of the density of characters (teeth, foramina, sutures, etc.), postcranial elements tend to be less diagnostic. However, postcranial material is favorably preserved in the fossil record. Previous studies have shown that the dimensions of camelid metapodials (cannon bones) tend to cluster in a species-specific way, as well as provide some indication of the presence or absence of a pacing gait. This study carries out measurements on Miocene camel metapodials from the Black Butte site in the Juntura Formation to identify each specimen more precisely, suggest the presence or absence of pacing, and examine whether sexual dimorphism was likely. A more precise understanding of the Juntura camel paleoecology will help to place them in ecological context relative to the other animals with which they lived. Preliminary results suggest that the two different camels present in this fauna had similar but distinct patterns of locomotion.
Presenter: Jared Barak, Josie Baldner, Architecture
Poster (Morning Session)
Mentor: Alison Kwok, Architecture
Solar Reflector Prototype
Skylights are a lovely addition to most rooms, but they are also major contributors to building heat loss in cold weather. Because glass is such a poor insulator, an improperly placed skylight can make a room retain heat poorly, resulting in a chilly space and an expensive utility bill. In an attempt to increase the solar penetration into one such room, a prototype solar reflector was constructed and placed above a skylit bathroom. Temperature and light intensity data collected from beneath the retrofit skylight indicated that the additional reflected sunlight significantly increased the brightness of the room, but had a negligible effect on the temperature. The study implies that reflecting additional sunlight through an existing aperture could make a skylight perform as if it were a larger skylight without any additional building heat loss.
Presenter: Braden Larson, Biology, Russian and Eastern European Studies (REES)
Poster (Afternoon Session)
Mentor: Charles Kimmel, Institute of Neuroscience
Genetic Interaction in the Developing Danio Rerio Jaw
Genes act in concert during animal development to form complex anatomical structures. For example, the jaw skeleton requires precise expression and interaction of a multitude of genes to develop correctly. Our research focuses on the gene endothelin-1 (edn1), which encodes a signaling molecule required for ventral jaw development in the zebrafish, Danio rerio. Because elements of the jaw remain in the edn1 mutant, we hypothesized that other genes function within the edn1 genetic pathway. To test this, we generated double mutant zebrafish, pairing the edn1 mutant allele with mutant alleles of candidate genes based on previous literature. We then analyzed the double mutant skeletons for evidence of genetic interaction, and discovered an enhanced phenotype in one of the double mutants. Specifically, mutants for edn1 and fibroblast growth factor-8a (fgf8a), a gene that encodes another signaling molecule, are missing a portion of their upper jaw, a phenotype not present in either single mutant. To investigate the cell biology behind this phenotype we imaged the cells that constitute the jaw precursor tissue in live transgenic zebrafish. Strikingly, the cells that give rise to this structure appear missing in double mutant fish. Furthermore, we used Fluorescent In Situ Hybridization to observe gene expression of edn1, fgf8a, and potential shared target genes in wild type and mutant embryos. We conclude that cross talk between edn1 and fgf8a signaling is required for development of the jaw skeleton.
Presenter: Alexandra K. Hartman, Biology (Neurobiology)
Poster (Morning Session)
Mentor: Michael Wehr, Institute of Neuroscience
Optogenetic Silencing of Parvalbumin-expressing Interneurons in Mouse Auditory Cortex: Mechanisms of Gain Modulationology (Neurobiology)
Mammalian sensory systems detect relevant stimuli with remarkable sensitivity. This holds true in both high-and low-contrast sensory environments—that is, both when the signal an organism is trying to isolate (say, a pure tone or a visual object) is the strongest signal detected, or is detected in the context of irrelevant signals of equal intensity. The firing rate (‘output’) of a typical auditory neuron increases with stimulus intensity (‘input’). The rate-intensity function is not fixed: gain adjustments—an increase or decrease in response magnitude, relative to baseline—depend on the context in which the stimulus is presented. Contextual gain modulation is thought to be regulated by synaptic input from inhibitory interneurons, but little is known about the connection patterns and cell types that enable it. We use optogenetic tools to address this. Archaerhodopsin is a proton pump activated by yellow-green light. When illuminated, these pumps generate dramatic outward currents that hyperpolarize —or ‘silence’—the neurons in which they are expressed. We will obtain in-vivo recordings from single units in the auditory cortex of anesthetized transgenic mice, in which Archaerhodopsin is expressed in conjunction with Parvalbumin, a protein specific to cortical GABAergic interneurons. The shift in the rate-intensity function of pyramidal cells—before and after Parvalbumin interneurons are dropped from the network—will reveal the physical target(s) of synaptic inhibition.
Presenter: Dylan Udy, Biology
Poster (Afternoon Session)
Mentor: Alice Barkan, Institute of Molecular Biology
Determining the degree to which chloroplast genome copy number limits the expression of chloroplast genes
The relationship that exists between chloroplasts and the plant cells they occupy is very complex. Chloroplasts evolved from a cyanobacterial endosymbiont, and throughout evolution many of the ancestral bacterial genes have been transferred to the plant nuclear genome. The proteins from many such nuclear genes are sent back to the chloroplast where they perform a variety of functions. We identified a non-photosynthetic maize mutant that accumulates reduced levels of several chloroplast mRNAs. We showed that the causal mutation is a transposon insertion in a nuclear gene encoding a protein that is closely-related to bacterial DNA polymerase I. Angiosperm genomes include two closely related paralogs encoding this protein. These have been studied in Arabidopsis (a dicot plant), where they are dual-targeted to both the mitochondria and chloroplast and have redundant functions. I have shown that our maize mutant has a 10-fold reduction in chloroplast DNA but normal levels of mitochondrial DNA, suggesting that the two paralogs have become specialized for either chloroplast or mitochondrial DNA replication in maize (a monocot plant). I am using the maize mutant to investigate the degree to which the abundance of chloroplast DNA limits chloroplast gene expression. I have found that the abundance of some chloroplast mRNAs decreases in parallel with the abundance of chloroplast DNA, whereas the abundance of other mRNAs does not. These results show that different factors limit the expression of different genes in the chloroplast.
Presenter: Greg Hanak, Biology
Poster (Morning Session)
Mentor: Joe Thornton, Biology
Effect of Mutations Within the DNA Binding Domain on Ancestral Steroid Hormone Receptors’ Specificity to DNA Response Elements and Protein Stability
The steroid hormone receptor (SR) family is a group of proteins that activate transcription via the binding of DNA response elements. We believe that the present day SRs found in animals, which include the estrogen, androgen, progestagen, mineralocorticoid and glucocorticoid receptor, all evolved from one ancestral receptor protein (ancSR1). The ancSR1, which had the ability to activate transcription via the binding of DNA estrogen response elements (EREs) in response to estrogens, gave rise to another ancestral receptor (ancSR2) that carried the ability to bind the DNA response elements associated with all the SRs except the EREs that were recognized by ancSR1. Examination of the ancSR1 and ancSR2 on a molecular level showed a number of differences in the amino acid sequence between the two receptors, some being within the P-box of the DNA binding domain (DBD). The question then becomes how are these P-box mutations contributing to the specificity of the ancSR2 protein. We predict that the derived P-box in ancSR2 is eliminating positive contact with EREs. To prove this, biophysical and biochemical experiments such as thermal melts, guanidine melts and DNA binding assays will be run on the DBDs of these two ancestral proteins and two different supposed intermediates of ancSR1 and ancSR2. The data gained from these experiments and the inferences made will help us better understand the series of events leading up to the formation of the current, distinct SRs and, more importantly, how and why they function as they do.
Presenter: A.J. Risenmay, Biology
Poster (Afternoon Session)
Mentor: Jim Remington, Physics, Institute of Molecular Biology
Investigating an Unusually Bright Variant of the Red Fluorescent Protein mKeima.
mKeima is a monomeric red fluorescent protein (λem¬¬max ~620 nm) that is maximally excited in the blue (λex¬¬max ~440 nm). This extraordinarily large stokes shift can be significantly reduced following chromophore deprotonation under acidic conditions. By designing mutants to exploit the varying excitation species of mKeima, our lab was able to develop a redox-sensitive red fluorescent protein to be used as a quantitative reporter of the thiol/disulfide status in reducing subcellular compartments. This ratiometric variant was identified as mKeima M159K_TDCC and was found to be unusually fluorescent under green light (580 nm). Further examination revealed that mKeima M159K_TDCC is colorless when expressed in the dark, but irreversibly becomes pink when exposed to blue light. Here we combine x-ray crystallography and fluorescence/absorption spectroscopic techniques to investigate the fascinating chemistry behind this mKeima mutant.
Presenter: Taylor Wilson, Biology
Poster (Morning Session)
Mentor: William Cresko, Biology
Genetic Basis of Evolution of Armor Phenotypes in Threespine Stickleback
Genes act in concert during animal development to form complex anatomical structures. For example, the jaw skeleton requires precise expression and interaction of a multitude of genes to develop correctly. Our research focuses on the gene endothelin-1 (edn1), which encodes a signaling molecule required for ventral jaw development in the zebrafish, Danio rerio. Because elements of the jaw remain in the edn1 mutant, we hypothesized that other genes function within the edn1 genetic pathway. To test this, we generated double mutant zebrafish, pairing the edn1 mutant allele with mutant alleles of candidate genes based on previous literature. We then analyzed the double mutant skeletons for evidence of genetic interaction, and discovered an enhanced phenotype in one of the double mutants. Specifically, mutants for edn1 and fibroblast growth factor-8a (fgf8a), a gene that encodes another signaling molecule, are missing a portion of their upper jaw, a phenotype not present in either single mutant. To investigate the cell biology behind this phenotype we imaged the cells that constitute the jaw precursor tissue in live transgenic zebrafish. Strikingly, the cells that give rise to this structure appear missing in double mutant fish. Furthermore, we used Fluorescent In Situ Hybridization to observe gene expression of edn1, fgf8a, and potential shared target genes in wild type and mutant embryos. We conclude that cross talk between edn1 and fgf8a signaling is required for development of the jaw skeleton.
Presenter: Wade Sugden, Nathan Johnson, Biology
Poster (Afternoon Session)
Mentor: Mark Sasaki, Institute of Neuroscience
The Use of Gateway® Cloning and Modified BAC Trangenesis to Study Zebrafish Craniofacial Development
Transgenesis techniques have revolutionized the study of cellular, developmental, and molecular biology by allowing researchers to visualize the proteins they study and manipulate the expression of genes in vivo. Through the use of genetic regulatory elements, transgenes can be tailored to over-express genes of interest, label tissue-specific cell types, and express genes in atypical locations. When expressed in skeletal elements of the zebrafish (Danio rerio), transgenes can be used to explore cell behavior and the genetic pathways involved in craniofacial morphogenesis. Two methods in particular have streamlined the process of creating transgenic animals: Gateway®-mediated and BAC-mediated transgenesis. Here we discuss the use of both techniques to create zebrafish that express transgenes in craniofacial elements using the runx2b, sp7, col11a2, and sox10 promoters. These promoters were chosen because runx2b and sp7 mark bone at different time points during development, while col11a2 and sox10 serve as cartilage markers. In the future, these fish will be vital tools for conducting cell tracking experiments, distinguishing cell types, and expressing genes of interest in craniofacial structures to determine their function.
Presenter: Kelsey Stilson, Geology
Poster (Morning Session)
Mentor: Samantha Hopkins, Geology
Deposition Bias in the Late Miocene McKay Reservoir
Fossils found in association have the potential to tell us about the ecology of a specific time and place in geologic history, suggest something about the changing prehistoric world, and give clues about the effects of present-day anthropogenic climate and habitat change. However, this is no simple process of counting up the number of bones found. A community is rarely, if ever, fossilized in the same proportions as it lived. This study suggests ways to measure the preservation bias in a system and extrapolate the composition of original fauna. My site is McKay Reservoir in north-central Oregon, where fossils were deposited by fluvial transport in the late Miocene (5.5 million years ago). Current approaches to depositional bias in such systems use the shape and evidence of postmortem damage to the bones in an assemblage to estimate the degree of sorting due to river flow. Voorhies diagrams, which use bone type (e.g. radius or metapodial) to determine the degree of sorting, indicate the McKay bones were transported at high velocity and were deposited relatively close to where they entered the water. Another method suggests that the bones were not exposed to air for long (little to no weathering) and rolled a medium distance along the stream bed (moderate abrasion). These results show that the bones came from nearby, perhaps as little as a mile from the site of desiccation to the site of final burial, and would therefore be relatively accurate indicators of ancient local species distribution.
Presenter: Christina Wilson, Geology
Poster (Afternoon Session)
Mentor: Samantha Hopkins, Geology
Climate Change and Preservation Bias in the Pliocene Ringold Formation
Fossils found in association have the potential to tell us about the ecology of a specific time and place in geologic history, suggest something about the changing prehistoric world, and give clues about the effects of present-day anthropogenic climate and habitat change. However, this is no simple process of counting up the number of bones found. A community is rarely, if ever, fossilized in the same proportions as it lived. This study suggests ways to measure the preservation bias in a system and extrapolate the composition of original fauna. My site is McKay Reservoir in north-central Oregon, where fossils were deposited by fluvial transport in the late Miocene (5.5 million years ago). Current approaches to depositional bias in such systems use the shape and evidence of postmortem damage to the bones in an assemblage to estimate the degree of sorting due to river flow. Voorhies diagrams, which use bone type (e.g. radius or metapodial) to determine the degree of sorting, indicate the McKay bones were transported at high velocity and were deposited relatively close to where they entered the water. Another method suggests that the bones were not exposed to air for long (little to no weathering) and rolled a medium distance along the stream bed (moderate abrasion). These results show that the bones came from nearby, perhaps as little as a mile from the site of desiccation to the site of final burial, and would therefore be relatively accurate indicators of ancient local species distribution.
Presenter: Catherine Ituarte, Biology
Poster (Morning Session)
Mentor: Bill Cresko, Biology
Differences in Acute Stress Response between Lab Adapted and Non-Lab Adapted Caenorhabditis remanei
Organisms can adapt to the environments they inhabit in amazing ways, but sometimes adaptation to one environment can lead to a decrease in fitness in another environment. One example of this phenomenon is the potential difference in an organism’s ability to respond to stress depending on if the organism is kept in laboratory conditions or in its natural environment. I used the small nematode worm, Caenorhabditis remanei, to address the interplay between lab adaptation and stress response. I hypothesized that populations that have adapted to laboratory conditions would be less stress resistant than non-lab adapted populations. Six populations of C.remanei were maintained under standard laboratory conditions for four months while six populations did not have prolonged exposure to laboratory conditions. These populations were then assayed for their resistance to acute heat and oxidative stress. The populations that were in the lab for four months had a lower average percent survival after an acute stress event than the populations that were not, supporting my hypothesis. These results suggest that evolving under laboratory conditions compromises an organism’s ability to respond to environmental stress, highlighting the importance of considering adaptation to laboratory conditions when designing experiments. My experiments form the basis for studying the complex relationship between an organism and its environment in this model organism, opening the possibility of identifying the genetic basis of this laboratory adaptation.
Presenter: Katharine Dwyer, Ian Austin, Aidan Tart; Architecture
Poster (Afternoon Session)
Mentor: Allison Kwok, Architecture
Glazing Peanuts
In our consumer society the ultimate and most lasting product is, without a doubt, the landfill. We produce massive amounts of materials and products that have a functional lifespan of a month or a year and then discard them as waste to decompose for hundreds or thousands of years. Our goal is to discover which materials can be reused so that such destructive cycles can be slowed or even reversed. Responding also to the inefficiency of buildings, we have honed in on Styrofoam. We believe that this material, which is otherwise thrown away, can be used to add insulative value to double pane windows. During the night, hot days, or whenever views are not desired, Styrofoam peanuts would drop from within storage units in the walls to fill the gap between the panes of glass to add extra insulation. We tested our theory by building a custom hotbox that contained a 3” double paned window section in the center. With the help of HOBO data loggers, we then tested for the insulative value of our window with and without Styrofoam peanut filler. Our tests resulted in an insulative value of the Styrofoam peanuts to be about R-8, a significant improvement over the glass panes alone. Glazing makes up a significant percentage of a building envelope, and is a main source of heat loss for a building. By implementing simple insulative technologies such as this, great amounts of energy can be saved with virtually no effort or sacrifice.
Presenter: Alex Goodell, Biology
Poster (Morning Session)
Mentor: Janis Weeks, Biology
Scaling Up: Expanding Community Health Worker Programs for Refugees and Internally Displaced Persons in the Bururi Province, Burundi, East Africa
Burundi, a small and often-forgotten country in East Africa, lies directly south of Rwanda. Though poorly covered in the media, Burundi suffered a similar conflict as its northern border, with ethnic-driven violence plaguing the nation for 13 years. When the conflict officially ended in 2006, Burundi was ranked as the poorest country in the world. Its health statistics are equally low. According to the WHO, one in five children die before their fifth birthday, half of those driven by malaria. Only 200 doctors serve the population of 8 million and most of the poor have no access to healthcare. In some areas, days of walking are required to reach the closest physician. Additionally, hundreds of thousands became refugees or internally displaced persons during the conflict and have little access to resources. In this setting, the use of “Community Health Workers” (CHWs) is appropriate. Village Health Works, a small clinic in the rural Bururi province, has implemented a small CHW program similar to Partners in Health. Over a six-month period in 2009 and 2010, data was collected on 10000 patients regarding their medical status, location, and demographic information at VHW. Additionally, GPS data was collected on the location of the CHWs. This presentation looks at the history of CHW programs worldwide and analyzes the health metrics of the area surrounding VHW. It then makes a series of suggestions on how VHW could better serve its patients with CHWs, specifically focusing on refugees and internally displaced persons.
Presenter: Margo Werner, Ingo Braasch, John Postlethwait; Biology
Poster (Afternoon Session)
Mentor: Ingo Braasch, Biology
Genomic News From an Old Fish: Understanding Gene Regulation by Sequencing the Genome of a Living Fossil, the Spotted Gar (Lepisosteus oculatus)
Cis-regulatory elements (CREs) are important regions of the genome that modulate the expression of nearby genes. However, their role in the evolution of genes is not yet well understood. To examine the function and evolution of CREs in fish, we study the spotted gar (Lepisosteus oculatus). The gar is a ‘living fossil’ that diverged from teleost fishes just before a teleost-specific whole genome duplication. Comparing the genome sequence of gar to teleosts allows us to investigate the appearance of CREs in relation to this genome duplication. We screen a genomic library of the gar in order to find regions of the genome containing developmentally relevant genes and their CREs. These genomic regions are then sequenced using next generation sequencing techniques. The results will potentially help us to understand the evolution of gene regulation in fish.
Presenter: Shannon Ladner, Gina Realmuto, Ayla-Mae Vedder; Architecture
Poster (Morning Session)
Mentor: Alison Kwok, Architecture
Lack of Ventilation – Intoxication: Studying Carbon Dioxide Levels in a Student’s Apartment
As building technology increases, buildings are being sealed tighter to reduce heating and cooling costs. With this increase in energy efficiency comes a decrease in quality. Air quality, specifically, has become a major concern as people spend more time indoors. In a student’s small apartment near the University of Oregon, ventilation has become a pressing problem. Our team set out to test the build-up of the highly known chemical compound carbon dioxide in a four-hundred square foot apartment. The American Society of Heating, Refrigerating, and Air-Conditioning Engineers has set the ventilation standard at a maximum of one-thousand parts per million of carbon dioxide. After testing the apartment with carbon dioxide meters, we found the average amount of carbon dioxide to be one thousand six-hundred and fifty parts per million. Determined to find a solution to this ventilation problem, we decided to test the effectiveness of a common remedy: opening a window. Our hypothesis was that an open window would bring in enough fresh air to reduce the apartment’s carbon dioxide level to one thousand parts per million within four hours. The results were a success and in fact only took an average of forty-five minutes. However, it being winter, this method of ventilation sacrificed the residents’ thermal comfort. This research jump-started our interest in finding more convenient and passive ways to ventilate spaces as an alternative to mechanical ventilation systems.
Presenter: Christina Wickman, Marine Biology
Poster (Afternoon Session)
Mentor: Chuck Kimmel, Institute of Neuroscience
What is the genetic basis of evolution? Looking at the shape of the opercle bone in Alaskan stickleback fish.
What is the genetic basis of evolution? For this study, we used the three spine stickleback fish, which is a model for evolution as both the ancestral and derived populations can be gathered, and crossed to form viable offspring. Our study concentrated on the facial bone known as the opercle and we hypothesized that the shape of the opercle was controlled by Mendelian genetics in a co-dominance relationship. To test this hypothesis a model was created and both the parent and F1 populations were land marked choosing 12 points along the bones edge and the variation between the points were graphed using Principle Component Analysis. From the land marking of the F1 progeny it appeared that the alleles were expressing a dominance relationship and based on our findings we revised our hypothesis proposing this. To test this hypothesis the F2 progeny were landmarked, but did not show a dominance relationship, so we again revised our hypothesis proposing that quantitative genetics are at work: where multiple genes are acting to form different regions of the opercle bone. From this we concluded that the opercle shape is specified by multiple genes acting on different areas of the bone and we can infer that the changing of these genes provides the basis for evolution of the opercle, which provides for more skeletal variation, which can be advantageous evolutionarily.
Presenter: Anna Crist, Biology
Poster (Morning Session)
Mentor: Patrick Phillips, Biology
Effects of a Natural Environment on Caenorhabditis elegans
The nematode Caenorhabditis elegans is an important model organism in the field of biology and yet little is known about how it lives in its natural environment. In order to study C. elegans in a more naturalistic setting, we created artificial soil microcosms. Populations of C. elegans were estimated over time by taking small periodic samples. We were able to maintain large, stable populations for over one month, or twelve generations. This methodology could be a useful tool in many areas of C. elegans biology. We are investigating the effects that this naturalistic environment has on a known aging mutant, daf-2. The effect of this mutation, although well characterized in a laboratory setting to have an extension in lifespan, is unknown in a natural environment. Artificial soil microcosms will aid future C. elegans studies in determining the effects of a natural setting on lab-characterized traits.
Presenter: Andrew Mckay, Biology
Poster (Afternoon Session)
Mentor: Kryn Stankunas, Institute of Molecular Biology
Determining roles of Wnt signaling in mammalian heart valve development
Heart defects occur in 2% of live births, and of these, valve defects are the most common. By studying normal heart valve development we hope to find the genetic causes of these defects. Our primary question is: what signals direct the remodeling of embryonic heart valves into thin, elongated leaflets? We hypothesize that local Wnt signals direct heart valve remodeling by regulating cell proliferation and morphogenesis through activation of the NFATc1 transcription factor. To accomplish this, we use transgenic mice that allow us to block Wnt signaling during narrow time windows of embryogenesis. We inject transgenic mice with doxycycline, a molecule that causes the transgenes to temporarily express the Wnt antagonist Dkk-1 and inhibit Wnt signaling in particular cell types. I helped determined which of three transgenic lines best inhibits Wnt signaling and produces the most consistent and robust phenotype for valve defects. This line will be used for future experiments in which we will stain the sections for various cell type markers, indicators of proliferation, and localization of the transcription factor NFATc1. We will then use these results to determine if Wnt signaling affects cell proliferation and NFATc1 localization in targeted cell types in the developing valve.
Presenter: Matthew Garish, Biology
Poster (Morning Session)
Mentor: Kyrn Stankunas, Institute of Molecular Biology
Chromatin regulation during fin regeneration in zebrafish
Vertebrate organisms such as the Zebrafish have developed molecular processes to regenerate their fins after amputation by epigenetic cell reprogramming. An insight into the molecular processes could prove clinically useful in addressing such problems as tissue repair. The transcript of KDM6B.1, a histone demethylase (me3K27H3), has already been established in caudal fin regeneration in zebrafish via in situ hybridization. I hypothesize that KDM6B.1 plays a crucial role in zebrafish fin regeneration. I propose to spatially and temporally establish expression patterns of KDM6B.1 during fin regeneration. To address this question, I have purified a KDM6B.1 antigen and antibodies against the antigen. I performed techniques to surgically remove a portion of the Zebrafish’s fin. I have characterized the antibody using such in vitro methods as affinity purification and immunocytochemistry (ICC) analysis. After characterizing the antibody, I performed studies on the zebrafish such as immunohistological analysis during fin regeneration. The results concluded higher expression of KDM6B.1 specifically in regenerating tissue. I believe that understanding the results of a histone demethylase during fin regeneration has given insight to the ability of a cell to reprogram itself in response to injury which will give insight to tissue repair.
Presenter: Emily Ebel, Biology
Poster (Afternoon Session)
Mentor: Patrick Phillips, Biology
Quantitative Mapping of Male Traits Affecting Female Longevity and Fecundity in C. Remanei
Differing reproductive interests between the sexes can manifest in surprising ways, including a conflict, or tradeoff, between female reproductive effort and longevity. In some species, including the soil-dwelling nematode Caenorhabditis remanei, the act of mating has been demonstrated to reduce female lifespan by up to 50%. Interestingly, males from different genetic backgrounds affect female longevity—and fecundity— to varying degrees. To understand the genetic basis of these differences, and why they may have evolved, I am cataloguing the effects of males from 30 unique C. remanei strains on female lifespan and reproductive output. When this phenotypic data is combined with Restriction site Associated DNA (RAD) marker data from each line, I will be able to generate a Quantitative Trait Loci (QTL) map to approximate a genomic region that may be responsible for the male effects. Gaining this insight into the “battle of the sexes” in C. remanei will elucidate how sexual conflict, as an evolutionary force, can shape the morphology and behavior of many animals.