University of Oregon (UO) Summer Program for Undergraduate Research (SPUR)
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The University of Oregon (UO) Summer Program for Undergraduate Research (SPUR) provides fellowship opportunities for undergraduate students from other Universities and Colleges to participate in ongoing research in Life Sciences laboratories at UO during the Summer months. Each project is a rigorous and rich immersion in a mentored, high profile science research project with a lab mentor under the direction of a research professor. We are very interested in enhancing the creativity, diversity, and talent of the next generation of life scientists in research communities. We stress active, experiential learning, because a true understanding of scientific ideas requires immersion into the processes of discovery, and it is reflected in the ability to communicate these ideas. SPUR training stresses active learning for interns and their mentors in experimental approaches, methodological skills, strategic design, creative and critical reasoning, and scientific communication. Professional and social interactions with active researchers at all levels helps interns boost personal confidence. In selecting summer interns, we seek talented, motivated, adventurous, and hard-working undergraduates who would benefit from what our program has to offer, and who perhaps would not otherwise have such opportunities.
Visit the website for more information about the program: http://spur.uoregon.edu/
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Item Open Access Role of the gene Ncad in neuronal circuit formation(2017) Sahin, Hatun MineItem Open Access Odor-Guided Navigation Strategies in Mice(2017) Cramer, JenniferOur sensory systems allow us to navigate dynamic environments. For example, the olfactory system plays a key role in foraging behavior, such as the localization of an odor source. We will study sensory navigation in the sensitive olfactory system of the mouse. The primary navigation strategies observed in mice include bilateral nostril comparisons at a single sniff (stereo olfaction), and bilateral comparisons across multiple sniffs (serial sampling). While these sampling strategies have been observed, the overall sampling behaviors used by mice to locate an odor source is largely unknown. Our lab has developed a behavioral assay for studying freely moving odor-guided navigation in mice. In this system, mice receive a reward for correctly navigating towards an odor released from one of two odor ports. The aim of this study is to define the navigation strategies used by mice to locate an odor, and determine if this sampling strategy generalizes across multiple odorant identities. We hypothesize that a mouse’s sniff rate and body movements will slow when introduced to a novel odorant, and that there will be increased serial sampling. Identifying and analyzing these sampling behaviors will create the foundation needed to discover the physiological mechanisms underlying these behaviors. In future studies, we will record from the olfactory bulb to access the neural representation during odor-guided navigation.Item Open Access Evolution of a photoactivatable GFP-like protein(2017) Hernandez, JocelyneUnderstanding how new protein functions evolve is crucial to rationally engineering proteins with desired functions. One way we can begin to understand this is to compare the biochemical properties of ancestral and extant proteins whose functions have changed over an evolutionary interval. An evolutionary interval in green fluorescent protein-like (GFP-like) proteins from corals has been identified where an ancestral green state evolved to an extant photoconvertible red state. Irradiation of photoconvertible fluorescent proteins with light of a specific wavelength, intensity, and duration causes distinct changes in their fluorescence properties. I developed experimental photoconversion assays and biochemically characterized the photoconversion process for a natural evolutionary transition in the Kaede GFP-like protein family. Developing a deeper understanding of the biochemical properties that lead to the natural evolution of a photoconvertible protein will allow better design of markers that can be used in imaging and microscopy.Item Open Access Using a Sequence-Specific Chromatin Remodeling Protein to Alter Heat Shock Response in S. Cerevisiae(2017) Jean-Baptiste, UrielEukaryotic DNA is packaged into chromatin to fit in the nucleus. One of the organizational subunits of chromatin are nucleosomes, which are composed of DNA wrapped around histone proteins. These nucleosomes can be rearranged by proteins called chromatin remodelers. For this project, we looked at the nucleosome remodeling protein Chd1. It has been shown that the Chd1 protein fused with a foreign DNA binding domain (DBD) can remodel nucleosomes toward the specific site of that foreign DBD (McKnight et al. 2011). We are using this knowledge to design fusion proteins where the DBD of Chd1 has been replaced with a variety of different domains, targeting Chd1 to different sites in the genome. The specific fusion for this project used the DBD of Hsf1, a protein that recognizes a conserved heat shock element (HSE) motif in the yeast S. cerevisiae. When induced, Hsf1 turns on stress genes that allow the cells to survive in stressful environments. With this foreign DBD fused to the Chd1 remodeler, we aim to target nucleosomes to genomic HSE sites, blocking access for Hsf1 and thereby modulating the heat shock response. This project will demonstrate the feasibility of using engineered nucleosome positioning to control a physiological response in vivo.Item Open Access Item Open Access Auditory Cortex Mediates Hearing-Guided Prey Capture in Mice(2017) Kelly, LaurenHoy et al. found that vision was necessary for accurate prey pursuit and capture in mice through observing their behavior under various sensory conditions (2016). Although vision was crucial for successful captures, it was found that mice were able to catch their prey in the dark, demonstrating that hearing can aid in prey capture when vision is obstructed (Hoy et al., 2016). In this specific research project we are interested in the role that the auditory cortex plays in prey capture. The experimental design isolates the auditory cortex by using a sound proof and dark chamber in which the mice are placed in an arena and presented with crickets. We observed that mice are able to successfully capture prey using auditory cues. In order to further investigate this in a more controlled setting, we set up speakers around the arena, which played pre-recorded cricket sounds. The mice responded to sounds played from these speakers, but the response was not robust. Additionally, using optogenetics to suppress the auditory cortex significantly increased overall capture time. This implies that auditory cortex mediates hearing-guided prey capture in mice, but it does not appear to be necessary for successful prey capture.Item Open Access Quantification of Synapse Number for Identification of Molecules Influencing Cholinergic Synapse Formation in Drosophila(University of Oregon, 2017) Sweet, Serena; Ackerman, Sarah; Sales, Emily; Doe, Chris Q.Synapses are chemical junctions between neurons that allow signals to be transmitted from one neuron to another. Although disruptions to synapse structure and function contribute to symptoms of most neurological disorders, not much is known about the molecular mechanisms that are responsible for synapse formation and maintenance. Glial cells are a group of non-neuronal cells in the nervous system known for protecting neurons and mediating neuronal function. Astrocytes are glial cells that secrete synaptogenic compounds required for synapse formation. Here, we combine the reverse genetic technique of RNAi and light microscopy to identify novel secreted and cell surface molecules from astrocytes that influence understudied cholinergic synapses in Drosophila melanogaster. I studied two established techniques for labeling the active-zone protein Bruchpilot (Brp) in cholinergic dorsal bipolar dendritic (Dbd) neurons to quantify synapses: 1) Brp-short and 2) Synaptic tagging with recombination (STaR). I used light microscopy to quantify Dbd-synapse number at three larval (L) stages: L1, L2, and L3. We will use this information to identify novel regulators of synapse development by performing an astrocyte-specific RNAi screen choosing genes that are predicted as cell surface or secreted, are highly conserved in humans, and are highly expressed by astrocytes. This screen will allow us to identify new genes that instruct synapse formation and maintenance that could ultimately contribute to the establishment of therapies for neurological disorders.Item Open Access The impact of physical activity and sleep in physiology following a mTBI(2017) Lindsey, GarrettA mild traumatic brain injury (or MTBI) is a common occurrence in many individuals across a range of disciplines. The purpose of this study is to better understand how physical activity and or sleep impacts physiological outcomes following MTBI. Sleep has been regarded as the most effective remedy to restore impaired function in those who have undergone MTBI. However, recent data shows that physical activity post-MTBI can lead to positive physiological outcomes in subjects compared to an increase bed rest. Individuals of similar backgrounds have been evaluated using primarily the triaxial GT3X activity monitor to measure daily activity within 72 hours of initial injury for 5 days. Physiological measurements were also taken within 72 hours post-injury and again at 2 months. There are common trends between the two groups but the results suggest that there is no relationship between the activity and physiological measures, which is expected due to a low n value.Item Open Access Characterization of Colonic Apoptosis Following DSS Induced Colitis in the Absence of Lrig3(2017) Long, CameronResearch in the Powell lab focuses on the epithelium of the small intestine and colon during homeostasis and disease. Homeostasis within the gut requires intricate control of stem cell proliferation, differentiation, migration and controlled cell death. Previous research in the Powell lab has shown the transmembrane protein and intestinal stem cell marker Lrig1, may play both a protective and restorative role in the colon of injury induced mice. Another member of the family, Lrig3, is also expressed in the intestines and localized to the stem cell compartment. In my project, I examine how a structurally similar protein, Lrig3, may play a role in the protection of the colonic epithelium of injury induced mice. My experiments examined the intestinal pathology of ulcerative colitis, that is characterized by inflammation of the colon, by using Dextran Sulfate Sodium (DSS) to induce colitis in an Lrig3 transgenic mouse model. Apoptosis in the cells of the colonic epithelium is a normal result of DDS-induced ulcerative colitis. Understanding if the loss of the Lrig3 affects cell death in the presence of an inflammatory response, is an important step towards potential recovery and/or protective methods for colitis and other inflammatory bowel conditions. Thus, we wanted to investigate if the loss of Lrig3 prior to induced injury would influence this response. To accomplish this, I used a transgenic mouse model with a tamoxifen inducible cre-lox recombination system controlled by an Lrig1 promoter, to allow for specific spatial and temporal excision of Lrig3, only in Lrig1 expressing cells. The experimental cohort was injected with tamoxifen for 3 days and then treated with 3% DSS for 7 days, allowing us to examine molecular and morphological changes in the absence of Lrig3 during DSS-induced colitis. The tissue was co-stained with a TUNEL assay and Beta-catenin antibody to visualize apoptotic cells and adheren junctions, respectively, in the colonic epithelium. The amount of apoptosis present in the colonic epithelium of mice with and without Lrig3 was quantified and analyzed. Although a two tailed t-test revealed no biological statistical significance, we did observe a slight decrease (p=0.0655) in the number of apoptotic cells per mm of colon analyzed in the Lrig3 mutants when compared to the DSS treated control animals. From these results, we will next analyze changes in proliferation, inflammation, and morphology to determine if Lrig3 participates in the protection or recovery of the colonic epithelium following induced injury.Item Open Access Assessing the role of the SMC-5/6 complex in meiotic double strand DNA break repair(2017) Clark, CordellMeiosis is the specialized cell division used to form haploid gametes. During meiosis, endogenous double strand DNA breaks (DSBs) are induced. A subset of these DSBs must be repaired as crossovers with the homologous chromosome to ensure proper chromosome segregation. Although repair is required for proper chromosome segregation, use of the homologs as a repair template for DSB repair is restricted to a specific time window during meiotic prophase I. DSBs incurred outside of this window must be repaired to ensure genomic integrity. Multiple lines of evidence have suggested that these homolog-independent repair events utilize the sister chromatid as a template in repairing DSBs. Utilizing Caenorhabidits elegans, the Libuda lab has developed a genetic assay for intersister repair, directly demonstrating the occurrence of intersister repair events during meiosis; however, the molecular mechanism of intersister repair remains unknown. Previous studies have implicated multiple proteins in promoting homolog-independent DNA repair during meiosis, including the structural maintenance of chromosomes (SMC) 5/6 complex. Utilizing this assay, I will determine whether the SMC-5/6 complex is required for intersister repair during meiosis. Specifically, I will place an smc-5 null mutation in the intersister repair assay and examine the frequency of intersister repair events at a specific locus in the genome. If SMC-5 is required for intersister repair, I expect to observe a lowered frequency or elimination of intersister repair events compared to wild type controls. Determining the precise role of smc-5 and other candidate genes in DSB repair will provide insight into the mechanisms underlying DNA repair decisions during meiosis.Item Open Access Transition in Adolescent Girls(2017) Rubalcava, KarenAdolescence is an important stage in the transition from childhood to adulthood this is when many physical, cognitive, and social changes occur. This stage is associated with an increasing range of problems, such as depression, suicide, and substance abuse (Dahl, Gunnar, 2009). Studies have shown that cortical and subcortical areas, which are involved in emotional reactivity and regulation, undergo significant structural changes during this period. While much research has focused on age-related development, this study will focus on the role of puberty on brain development of adolescent girls. In order to do so, a neuroimaging study of females aged 10-14 years will be conducted, including three waves of data collection. Each point will be separated by 18 months. At each time point, pubertal stage, hormone levels, and brain structure will be assessed. This study will specifically relate pubertal development and brain structure using data from wave one of the larger project. The purpose of this study is to better understand the role of pubertal changes on brain regions underlying emotional and behavioral functioning. We hope to ultimately be able to predict disorders in the future and create interventions and prevention strategies.Item Open Access Effects of histamine-receptor blockade and exercise on blood-glucose concentration(University of Oregon, 2017) Raqueno-Angel, Sabrina; Ely, Matt; Sieck, Dylan; Halliwell, JohnHistamine has been found to be an important component during the exercise recovery period, particularly in mediating vasodilation, hyperemia, and hypotension. Blocking H1/H2 histamine receptors produced altered outcomes during recovery, including a decrease in interstitial glucose concentrations and reductions in blood flow and whole-body insulin sensitivity. It is unknown if blood glucose concentrations change with histamine receptor blockades, specifically during the exercise period. PURPOSE: To determine if H1/H2 histamine receptor blockades decrease blood glucose concentrations during exercise. HYPOTHESIS: It was hypothesized that histamine receptor blockade would decrease blood glucose concentrations during exercise. METHODS: Nine competitive cyclists performed 120 minutes of cycling exercise at 50% VO2 peak. 60 minutes prior to exercise, subjects were given either a placebo or histamine receptor blockades (540 mg Fexofenadine and 300 mg Ranitidine). Blood glucose concentrations were measured using a handheld Precision Xtra Blood Glucose Monitoring System (Abbot Diabetes Care INC, Alameda CA). Measurements were taken from the earlobe pre-exercise and three times during exercise at 15, 60, and 120 minutes. A repeated-measures two-way ANOVA (RM ANOVA, Group X Time) was used for statistical analysis. RESULTS: No differences were found between placebo and histamine receptor blockades groups (p = 0.801), and no Group X Time Interaction was determined (p = 0.881). Blood glucose levels at 15, 60, and 105 minutes were lower than the pre-exercise levels (p<0.001). CONCLUSION: No significant differences in blood glucose concentrations were found between placebo and histamine receptor blockade groups.Item Open Access Investigating plant diversity patterns of Eastern Oregon's arid rangelands(2017) Gee, AlexiaItem Open Access Investigation of Pore-Forming Transmembrane Toxins using Native Ion-Mobility Mass Spectrometry(2017) Young, IsabellaAntrhax toxin (ATX) and Alpha-Hemolysin (AHL) are examples of large transmembrane pore-forming toxins that are similar in structure and are proposed to have specific protein-lipin interactions. Due to the difficulty of studying these structures in solution, native mass spectrometry (native-MS) was used to examine the structure, stoichiometry, and lipid-binding of these membrane protein complexes and ion mobility (IM) analysis was used to further study the complexes' shape and size.Item Open Access Linking transcription factors to neuronal connectivity in the Central Complex of Drosophila(2017) Budhathoki, RashikaEvery neuron in the brain has a specific identity including a key feature called neuronal connectivity, which is defined as how neurons form synaptic pairs. Neurons innervate certain regions of the brain through an attribute of neuronal connectivity known as target specificity. We hypothesize that proteins called Transcription Factors (TFs) bind to DNA to regulate gene expression that determines target specificity. More than 750 TFs are present in the fruit flies, Drosophila melanogaster, but antibodies for only 200 TFs are available. The study was done in the Central Complex (CX) of adult Drosophila. Located in the midbrain, the CX is an ancient conserved brain region critical for insect navigation. The purpose of our study was to identify the post-mitotic TF profile of neurons innervating the adult central complex using antibody screening in flies driven by the binary CX GAL4-UAS system to relate to neuronal connectivity in the CX. Here, we screened 85 TF antibodies in the Central Complex of adult brains. Our results show that 22 TFs from 85 antibodies express in differential densities in the CX. We additionally discovered at least two specific TFs that label single cell types innervating the central complex. This will provide a primary basis for further research on the relationship between specifying neuronal identity and establishing neuronal connectivity. Thus, the results could enhance our understanding of the underlying causes of neuropathological disease.Item Open Access Climate Change Impacts on the Productivity and Community Dynamics of Pacific Northwest Prairie Systems(2017) Okotie-Oyekan, AimeePreservation of Pacific Northwest prairie ecosystems depends on our understanding of how climate change will impact levels of biodiversity within these systems. In the PNW, climate change models have predicted significant increases in precipitation during the winter months and higher temperatures as well as an increase in drought incidence during the summer months. As the vegetation responds to this enhanced seasonal precipitation cycle, primary production may change alongside shifts in community dynamics in terms of functional group composition, potentially altering overall levels of biodiversity. In this study, we questioned how experimental climate change in a series of restored prairie plots in three sites across a 520 km latitudinal Mediterranean climate gradient will impact the overall productivity of species common to Pacific Northwest prairies. Our experimental treatments included ambient conditions as a control, warming by 2.5 C year-round, drought by a 40% reduction in precipitation, and finally warming with irrigation to offset the drying effect of warming. We hypothesized productivity to differ across the latitudinal gradient, with levels of primary production decreasing as we move from north to south. We also hypothesized that the effects of the treatments on productivity will vary by functional group composition (annual grasses, annual forbs, perennial grasses, perennial forbs, and nitrogen-fixing legumes). There should be higher annual plant productivity in response to warming treatments compared to their perennial counterparts, due to their ability to withstand hotter and drier climates. Lastly, we anticipated discrepancies in overall productivity depending on the treatment used. Heating and heating with added irrigation should have a positive effect on productivity, while drought will have a detrimental effect. I quantified changes in composition and productivity by clipping above-ground productivity at peak biomass, sorting by functional group, and measuring the dry weight of these functional groups. The study showed the northern site had significantly greater biomass present compared to the central and southern site, supporting the productivity gradient hypothesis. Also, annual grasses were the only functional group to show a significant positive response to the heated treatment compared to control across all three sites, lending support to the idea that heat has a favorable effect on overall productivity and annuals fare better in higher temperature conditions compared to perennials. Further studies like this that give insight on specific climate change effects within ecosystems can provide information on how to prevent biodiversity loss and protect ecosystems on a regional scale.Item Open Access Investigation of an Uncharacterized Aeromonas Protein involved in Host Colonization(2017) Ngo, JuliaThe gut microbiota consists of a diverse community of microbes, living within the digestive tracts of humans, animals, and insects. While some microbes can cause infectious diseases, other microbes are vital for the development and physiology of the host. Although it is known that microbes affect host health and development, the colonization dynamics of these microbes are still unknown. In the Guillemin lab, we study these host-microbe interactions using zebrafish as a model organism to understand how microbes colonize the host gut. Aeromonas is a normal bacterial resident of the zebrafish gut that we recently discovered produces an uncharacterized double cache domain containing protein ZOR0001_03237 (3237). This protein, 3237, affects the colonization of Aeromonas in zebrafish by decreasing the rate of colonization. To further explore how 3237 could be involved in colonization, we investigated the predicted structure for clues. Based on sequence, 3237 is hypothesized to have a periplasmic sensing region that contains tandem cache domains, a transmembrane region and a cytoplasmic diguanylate cyclase signaling domain. This study focused on identifying ligands that bind to the periplasmic region of 3237. A thermal shift assay was utilized to screen over 200 possible ligands. The amino acids proline, valine and isoleucine were identified to bind to the periplasmic region and increase the melting temperature of 3237 12-19 degrees Celsius. In addition, Aeromonas strains that have loss-of-function mutations in 3237 show increased swimming behavior over wild type in soft agar swim plates and have decreased growth in defined media. These phenotypes suggest that 3237 is involved in aiding Aeromonas to sense environmental cues and dictate motility. The identification of specific amino acid ligands and preliminary characterization of Aeromonas phenotypes when lacking 3237 have provided new insight on how this novel protein might affect colonization of the zebrafish gut.Item Open Access Lrig1 + Stem Cells and Their Role During Colitis Recovery(2017) Jahahn, NicholasThe intestine is a highly regenerative organ in humans and mice in which epithelial cells are replenished weekly and damage is rapidly repaired. Lrig1 protein has been shown to mark a population of quiescent stem cells residing in the base of the crypt that may be important for the recovery of the intestine from a disease state. Current knowledge about the stem cell populations involved in colonic injury and repair is sparse. To address this, we used Lrig1 as a marker for lineage tracing of the stem cells that reside at the base and the middle of the intestinal crypts. Lineage tracing of Lrig1-Cre/ROSA26-YFP mice was induced in animals treated with DSS to simulate ulcerative colitis in the distal colon. We performed immunohistochemistry analysis for lineage tracing and proliferation to examine the location of Lrig1-based cellular contribution in recovery after DSS-induced colitis. We hypothesize that Lrig1 positive stem cells participate in the recovery of the intestine from damage caused by DSS induced colitis.Item Open Access Odor Concentration Change Sensing(2017) Munoz, AntonioMice rely on their sense of smell for spatial navigation in their environment. Navigation with regards to smell relies on using odor concentrations to home in on an odor source of interest. Olfactory neuron populations exist that are sensitive to changes in odor concentration. However, the olfactory sensory processing that mediate this behavior in mice is not fully understood yet. The overall goal is to understand how the brain tracks changes in stimuli. We focus on how the olfactory system processes change in odor concentration. Our paradigm involves the use of trained head-fixed mice. The use of head-fixed mice allows for precise control over the odor stimuli. Our equipment allows me to present a concentration of odor directly when a mouse inhales. This allows me to manipulate the concentration of odor to which the mice will be exposed between various sniff cycles. Using a behavioral paradigm, I will test how sensitive mice are to detecting a change in odor concentration. This behavioral task will demonstrate how mice track stimulus changes over time and will lay the groundwork for determining how perception relates to neural activity.