Category: 2011

Deposition Bias in the Late Miocene McKay Reservoir

Presenter: Kelsey Stilson, Geology

Poster: C-7

Mentor: Samantha Hopkins, Geology

Fossils found in association have the potential to tell us about the ecology of a specific time and place in geologic history, suggest 9something 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.

Genetic Basis of Evolution of Armor Phenotypes in Threespine Stickleback

Presenter: Taylor Wilson, Biology

Poster: D-6

Mentor: William Cresko, Biology

Differences in physical traits among species arise first as variations within and among populations. Studying this intraspecific variation provides important new knowledge about the process that gives rise to biodiversity. To better understand this variation and its genetic and developmental basis I am studying a small fish, the threespine stickleback (Gasteroseus aculeatus). The threespine stickleback is undergoing rapid evolution in bodies of water recently formed by uplift and glacial melt, diverging into very different anadromous and freshwater life history forms. With each saltwater-to-freshwater evolutionary transition, there is a reduction in the stickleback’s bony armor plates and characteristic spines. In order to discover the genetic basis for the diversity of armor phenotypes, I am measuring variation in the size and number of lateral and pelvic armor structures of 148 stickleback collected from the McKenzie River in Springfield, OR. The genetic variation in these same individuals has been measured using high-throughput sequencing techniques.

We are correlating these genetic data with specific aspects of the armor variation, such as spine lengths and plate sizes. This is the first such study in stickleback, and is providing us with key information on which genes are responsible for the rapid evolution in some of the phenotypes of the threespine stickleback. My results will have general importance beyond stickleback by providing new knowledge about the genetic and genome basis of evolution in the wild.

Effect of Mutations Within the DNA Binding Domain on Ancestral Steroid Hormone Receptors’ Specificity to DNA Response Elements and Protein Stability

Presenter: Greg Hanak, Biology

Poster: B-3

Mentor: Joe Thornton, Biology

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.

Optogenetic Silencing of Parvalbumin-expressing Interneurons in Mouse Auditory Cortex: Mechanisms of Gain Modulationology (Neurobiology)

Presenter: Alexandra K. Hartman, Biology (Neurobiology)

Poster: B-4

Mentor: Michael Wehr, Institute of Neuroscience

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.

Enhancer-GAL4 Database Yields Subsets of Gene Expression

Presenter: David Bauer, Kris Haenderson, Allison Wilbur, Biology

Poster: A-2

Mentor: Chris Doe, Biology

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 hemisegment. 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.

Oak Habitat Mapping and Monitoring in the Southern Eugene Ridgeline

Presenter: Alexandria Russell, Matthew Silva, Matthew Liston, Environmental Science

Poster: C-5

Mentor: Peg Boulay, Environmental Science

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.

Reversing the Homeless Trend: A Case Study of the Homelessness Prevention and Rapid Re-Housing Program in Lane County, Oregon

Presenter: Korrin Bishop, Planning, Public Policy and Management

Poster: D-8

Mentor: Laura Leete, Planning, Public Policy and Management

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. currently showing at the Princeton University Art Museum.

Solar Reflector Prototype

Presenter: Jared Barak, Josie Baldner, Architecture

Poster: A-1

Mentor: Alison Kwok, Architecture

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.

Exploring Rome through Guiseppe Vasi’s Eyes

Presenter: Jesus Fernandez, Architecture

Poster: A-9

Mentor: James Tice, Architecture

Guiseppe 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.

Theoretical Study of the Molecular Dynamics of Diubiquitin

Presenter: Kimberly Davidson, Chemistry

Poster: A-5

Mentor: Marina Guenza, Chemistry

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.