GIAR archive
Kelsi Ramos, Chemistry: Characterization of Pre-Transition Droplets in Liquid-Liquid Systems with Magnetic-Susceptibility-Matched NMR Tubes. Mentor: J. Charles Williamson, Willamette University.
The Williamson group has developed methods to determine the coexistence curve of a partially miscible liquid-liquid system with high accuracy and precision. An interesting anomaly has been observed in some systems: two liquid-liquid phase transitions are observed, with one occurring 0.2 K above the other. The upper transition is unexpected, characterized by droplet formation, and only occurs on one side of the critical point. Characterization of these droplets will increase the understanding of liquid-liquid equilibrium dynamics and could be relevant to the many industries that utilize liquid-liquid systems to synthesize and purify chemical products. Nuclear magnetic resonance spectroscopy could be used to characterize the droplets. Each unique proton will exhibit two resonances when a liquid-liquid system is in two phases, as each phase provides a different chemical environment. Therefore, during droplet formation, the components in the droplets should exhibit resonances separate from those arising from the bulk phase, allowing the droplets to be characterized. The droplets rise to the top of the liquid-liquid mixture, however, where the magnetic field is no longer uniform due to the difference in magnetic susceptibility between air and the liquid system. The creation of a uniform magnetic field at the top of the sample is crucial if the droplets are to be observed with NMR. This could be achieved with magnetic-susceptibility-matched NMR tube plugs, which reduce the magnetic susceptibility discontinuity at the top of the sample, resulting in a uniform magnetic field. How effectively the plugs increase detectability of a droplet at the top of a sample will be determined. The aniline + 2-methyl-2-butene system will be the liquid-liquid system of interest, as the system exhibits droplet formation and has a convenient critical temperature. Additionally, each component has a magnetic susceptibility that matches available plugs. An accurate phase diagram of the system will be determined using established laser-light-scattering methods in order to accurately determine the compositions and temperatures of droplet formation. Then, a sample equipped with magnetic-susceptibility-matched plugs will be brought to the temperature of droplet formation while in the NMR probe. The droplets may be observed in the resulting spectra. (2017 October)
Tetiana Korzun, Chemistry: Effects of Vaping on Ocular Health: Analysis of Selected Alcohols, Acids and Their Derivatives as Major, Yet Underestimated E-cigarette Vapor Toxicants. Mentor: Robert M. Strongin, Portland State University.
More recent evidence suggests that short-term effects of vaping result in e-cigarette-related ocular injuries due to vapor components functioning as irritants. However, the long-term health effects of e-cigarettes are not yet conclusively known. Formaldehyde and formic acid are the final products formed in the process of thermal decomposition of e-liquid components, including solvents (propylene glycol and glycerol), flavorings and other ingredients. Chronic inhalation of methanol, formic acid and formate derivatives is responsible for raising the risks exacerbating the burden of vision impairment and blindness. Considering the trends of e-cigarettes surpassing combustible cigarettes in popularity and the increasing number of young e-cigarette users, there is a need for the analysis of aforementioned toxicants in e-vapor. Our preliminary 1H NMR data show that formic acid and its formate esters are major toxicants found in e-cigarette aerosols that have been overlooked to date. The lack of chromophores, overlapping resonances, low molecular weights and the high volatility of the analytes hinder their quantification via HPLC and qNMR methods. To overcome these obstacles, the experiments will be performed by the combination of GC-MS, GC-FID and 13C NMR techniques using 13C-labeled standards. This study will represent an excellent initial step toward the assessment of the chronic and subchronic effects of e-vapor containing ocular toxicants as not only their exposure levels, but also their known propensity to accumulate over time in the body, could potentially lead to vision impairment. (2017 October)
Brian M. Wendel, Cell Biology / Biochemistry: Determining the mechanism by which DNA replication completes. Mentor: Justin Courcelle, Portland State University.
To accurately duplicate a genome, a cell must have the ability to enzymatically initiate, maintain elongation, and complete replication of the DNA accurately and efficiently. A failure in any stage can cause chromosomal instability, resulting in a range of deleterious outcomes for the cell. In order to complete replication cells must recognize and join newly replicated strands at a point in which every sequence has exactly doubled. As replication forks converge, a cell must be able to enzymatically process the complex DNA structures that arise into discrete molecules without altering the sequence. Despite the significance of this final stage of DNA replication to the accurate inheritance of genetic material, only recently has completion been widely studied.
The goal of this work is to define the molecular mechanism of completion in Escherichia coli. Using next-generation sequencing techniques combined with PCR-free library preparation methods, DNA replication profiles in identified mutant strains will be generated and compared to detect DNA intermediates formed during the completion reaction. The results of these studies will likely define a novel and fundamental step required to maintain genome stability with potential conservation among other evolutionarily divergent organisms. This work would not only advance our understanding of the molecular pathway of completion during the normal cellular process, but also when impaired how this process could contribute to mutation and cancer. (2016 December)
Adam Baz, Conservation Biology: Habitat use and minimum area requirements of woodpeckers in an urban landscape. Mentor: Michael Murphy, Portland State University.
Urbanization has contributed to the fragmentation and alteration of natural habitats around the globe, and is rapidly increasing. In this context, urban parks can play a critical roll for many species by providing patches of usable forest within the urban matrix. These habitat islands may be particularly valuable to forest-specialists such as woodpeckers (Family Picidae). As primary cavity excavators, many woodpeckers are keystone species– functionally linked to a suite of organisms that rely on tree cavities for shelter and breeding. Thus, determining habitat requirements of urban woodpeckers would improve the guild’s potential to persist in urban-fragmented landscapes and, importantly, benefit a broad network of species.
Despite the recognized value of woodpeckers as bioindicators, almost no research exists on woodpecker ecology in urban areas. As rates of urban development continue to increase, it is imperative that this gap in knowledge be filled. Consequently, I am assessing habitat use and area requirements of woodpeckers in parks throughout Portland, Oregon. My research objectives are: (i) describe the distribution of woodpeckers in Portland’s greenspaces; (ii) identify the ecological, anthropogenic, and biogeographic drivers of woodpecker abundance in urban landscapes; and (iii) estimate minimum area requirements for each species. This information is essential to understanding and conserving woodpeckers in an increasingly urban world. (2016 March)
Jess Millar, Cell Biology/Biochemistry: Horizontally acquired tRNA facilitates adaptation to an extreme environment. Mentor: Rahul Raghavan, Portland State University.
Coxiella burnetii is an obligate intracellular bacterium that lives inside parasitophorous vacuoles (PV) derived from lysosomes. The PV is acidic (~4.5 pH) and Coxiella is the only bacterium known to thrive in this extreme environment. However, the metabolic adaptations that allow Coxiella to replicate in this niche are unknown. Coxiella has a highly reduced genome due to lack of selection pressure to maintain superfluous genes; however, it has retained an extra copy of tRNAGlu. Horizontal gene transfer is the likely origin of the additional isoacceptor (tRNAGlu2) present in Coxiella as it is not present in other Gammaproteobacteria. tRNAGlu not only has a role in protein biosynthesis, but it’s also the starting point for heme biosynthesis. Many bacteria obtain heme from their environment using heme transporters, however these are missing in Coxiella. The high expression of both heme biosynthesis genes and tRNAGlu2 during intracellular growth highlights its importance. This leads to our question; is the non-translational function of tRNAGlu a widespread mechanism essential for microbial adaptation to extreme environments? We hypothesize that heme biosynthesis is necessary for intracellular growth and selectively maintains the extra horizontally acquired tRNAGlu in Coxiella. We will study the impact of tRNAGlu2 on Coxiella’s fitness by creating tRNAGlu2 knockouts. Heme content and growth rates will be measured and compared to our wild type strain. Our study will provide first insights into whether a bacterial tRNA confers an adaptive advantage in an extreme environment. (2015 October)
Caitlin Maraist, Ecology: The effects of phyllospheric fungi on sexual effort and chemical cues in the dioecious moss, Ceratodon purpureus. Mentor: Sarah Eppley, Portland State University.
Mosses have been shown to harbor a diversity of fungi, yet the physiological and ecological context of their interactions have been relatively unexplored. This represents a significant shortcoming in the current state of knowledge for plant-fungi interactions because bryophytes – including moss, hornworts, and liverworts – were likely the first plants to colonize land. Fossil evidence suggests that endophytic and mycorrhizal fungi associated with early land plants may have contributed significantly to plant terrestrialization. Past studies in our lab have found that male and female C. purpureus differ in fungal abundance and composition, but whether fungal community structure is influenced by the moss or influenced by complex interactions within the microbial community is unknown. Furthermore, although male and female C. purpureus differ in their production of volatile organic compounds (VOCs) that attract micro-arthropod pollinators (Collembola), the extent to which VOCs reported in the latter study were produced by the moss and/or moss-dwelling microbes is also unknown. However, fungal mycelia have been demonstrated to produce unique fragrance profiles that attract foraging Collembola. The goal of my project is to determine whether symbiotic fungi differentially affect the reproductive effort of male and female C. purpureus and their interaction with micro-arthropod pollinators by altering sex-specific VOCs. Understanding the role of the phyllospheric mycobiota in determining the reproductive success and chemical ecology of moss can further elucidate potential drivers for the diversification of early land-plants. (2015 October)
Ariana Chiapella, Ecology: The fate of contaminants in mountain lake food webs. Mentor: Angela Strecker, Portland State University.
The atmospheric transport of industrial contaminants results in the accumulation of compounds like mercury and polychlorinated bophenyls (PCBs) in high elevation ecosystems, particularly lakes.These toxins consequently bioaccumulate in the tissues of organisms in mountain lakes. Many of these lakes are stocked with trout, and anglers visit annually to take advantage of this seemingly pristine resource. However mercury and PCBs are known to cause adverse health effects to both human and aquatic life, and preliminary surveys indicate alarmingly high levels in fish from mountain lakes in Washington's National Parks. It will be important for those who manage lakes to understand the factors which are responsible for uptake of contaminants into the food webs, and are associated with high contaminant levels in fish. My research seeks to understand the variables that influence high contaminant levels, determine pathways of uptake, and assess the effects of fish stocking on levels of mercury in macroinvertebrates and zooplankton. By identifying the major predictive factors of contaminant levels, managers should be able to estimate which lakes are at the highest risk for contamination, which will be important for the health of the ecosystems, as well as for those who consume fish from the lakes. (2015 March)
Timea Deakova, Ecology: Biogenic Volatile Organic Compound emissions by mosses and the role they play in local atmospheric chemistry. Mentor: Sarah Eppley, Portland State University.
Mosses are some of Earth's most species rich, ancient and stress-tolerant "ecosystem engineers". Through emission of isoprene and other Biological Volatile Organic Compounds (BVOCs), moss may locally engineer the atmosphere. This can cause changes in the atmospheric hydrological cycle by encouraging the production of Secondary Organic Aerosols (SOA) that often become cloud nucleation particles. These contribute to a localized negative feedback on atmospheric warming by increasing the local albedo. Efflux of isoprene from mosses combined with the high reactivity of isoprene with OH radicals also has the localized effect of modulating the oxidation capacity of the atmosphere. My intentions are to improve our basic understanding of BVOC emissions in mosses and to improve upon the BVOC/SOA parameterization and coupled biosphere-atmosphere modeling necessary to examine the range of BVOCs emitted and their impact on atmospheric chemistry. I plan to better quantify total moss isoprene emissions from mosses; and more broadly BVOC emissions using two-dimensional gas chromatography/time-of-flight mass spectrometry. Despite their potential evolutionary and ecological significance, BVOC emissions are extremely poorly characterized in mosses, creating a fundamental gap in our understanding of the chemical ecology of these ubiquitous plants. (2014 October)
Sydney Gonsalves, Ecology: Evaluating the effects of habitat elements on beetle diversity of urban greenroofs. Advisor: Catherine de Rivera, Portland State University.
Despite being simpler than ground level habitat, greenroofs support a surprising diversity of invertebrates, including rare and endangered species in urban areas. Invertebrates are beneficial as they perform ecosystem services such a decomposition, pest control, and pollination. It has been proposed that roofs intentionally designed for biodiversity, through added habitat elements such as logs or stones, or use of native soils and plants, would create microhabitats and therefore result in greater invertebrate diversity, however minimal peer-reviewed data exist to support this. My research will investigate the difference in habitat quality between five greenroofs designed primarily for stormwater management and five greenroofs that were designed for biodiversity in the urban core of Portland, Oregon. On the roofs I am pitfall trapping and identifying beetles to species level since previous studies have found beetles to be good indicator species due to their ease of observation and sampling, taxonomic stability, well-known life history, habitat specificity, and high correlation with difficult to study species. I am also monitoring vegetation cover, substrate depth, temperature, and moisture on the roofs to help understand how beetle community is mediated by such factors. This project will shed light on whether greenroofs designed for biodiversity, often at additional expense, support a greater abundance, richness, and diversity of native and ecosystem service providing invertebrates in urban areas. (2014 October)
Zecong Fang, Engineering: Ultrasensitive pH sensor based on two dimensional atomically layered MoS2. Advisor: Feng Zhao, Washington State University Vancouver.
As one of the most important chemical parameters, pH of a solution or substance often needs to be carefully and accurately measured in lots of areas, such as medicine, biology, chemistry, agriculture, food science, nutrition, water treatment and purification. Unfortunately, commercially available high accuracy (±0.001pH) pH meters are either costly or cumbersome. Therefore, a highly sensitive, cheap, and portable pH sensor is badly needed. Here we introduce a simple, cheap, and ultrasensitive pH sensor based on atomically layered MoS2 crystals. MoS2, a two dimensional (2D) single atomically thin (less than 1 nm for a single layer of MoS2) material, has shown the greatest potential as a nanosensor. MoS2-based photodetectors and gas detectors have been studied in the literature. However, more investigations are required to study their performance in an aqueous environment. In addition, effects of geometry, morphology, and thickness, which we believe are deterministic factors of these sensors, are not thoroughly studied. In this project, I will investigate these new MoS2 pH sensors more systematically and comprehensively. Key parameters of MoS2 flakes, such as thickness and morphology will be characterized. Sensitivity at different pH values, sensing repeatability, hysteresis of sensing, sensing response time, long-term stability of sensing, and influence of contamination on sensing will be experimentally and analytically studied related with the basic physical properties of the MoS2 flakes. (2014 October)
Eve Wiggins, Neuroscience: The effects of 24-hour total sleep deprivation on the neural mechanisms of selective attention. Advisor: Courtney Stevens, Willamette University.
Sleep deprivation is detrimental to human health and cognitive function in a myriad of ways. Selective attention is a key aspect of cognitive function, and particularly essential for learning. The present study assesses the effect of sleep deprivation on selective attention in volunteer college students by randomly assigning them to one of two conditions for the night before testing: sleeping as normal or staying up all night. In the morning, participants complete a dichotic listening task, a classic exercise used to assess selective attention. In the version of the task used in this study, participants have one story playing in each ear; they attend to one story and ignore the other. The neurological impact of sleep deprivation on selective attention is assessed using event-related brain potentials (ERPs) time-locked to auditory probes occurring at different times in each ear. Peak magnitude and latency for ERPs time-locked to attended and unattended probes are compared between sleep conditions. (2014 March)
Christine Kendrick, Environmental Science: Aerosols in the Urban Roadside Environment. Advisor: Linda George, Portland State University.
Vehicular combustion exhaust is the primary source of particulate matter emissions in many urban areas. Compared to larger more ubiquitous particles in the urban atmosphere, ultrafine particles (UFP, <100nm) have increased toxicity and reactivity in human lungs. In partnership with the Portland Bureau of Transportation, we have established a unique roadside monitoring station that continuously measures traffic-related pollutants such as nitrogen oxides (NOx), PM2.5 (particulate matter with aerodynamic diameter ≤ 2.5µm), local meteorology, traffic volumes and measures of traffic congestion along with episodic measurements of UFP. The main thrust of my research is to understand how optimization of traffic signals affects roadside pollutant concentrations in order to evaluate how cities can reduce roadway emissions through a cost-effective mechanism. This project will be used to help improve our particulate matter measurements through the addition of a diffusion dryer as our measurements are significantly impacted by relative humidity due to particle hygroscopicity. It is important to evaluate UFP against accurate PM2.5 since it is a regulated parameter under the National Ambient Air Quality Standards (NAAQS). (2014 March)
Brittney Davidge, Cell Biology / Biochemistry: Examining the role of the Cul3 ubiquitin ligase in cell cycle progression and exit from quiescence. Advisor: Jeffrey Singer, Portland State University.
Cyclin E is an important cell cycle regulator which signals the cell to begin DNA replication, driving the cell cycle forward. Cyclin E levels are controlled in part through ubiquitin-mediated degradation. In this pathway a ubiquitin molecule is attached to a target protein by a ubiquitin ligase. This signals the target protein to be degraded. Two ubiquitin ligases, Cul1 and Cul3, are known to degrade cyclin E. However, it remains unclear at which point in the cell cycle each ligase works to degrade cyclin E. The goal of my project is to determine at which point each ligase is responsible for cyclin E degradation. I am using MEFs (mouse embryo fibroblasts) to make comparisons between MEFs that are deficient for Cul3 and wild-type MEFs. I am comparing cell cycle profiles as well as levels of cyclin E and other proteins responsible for cell cycle control. (2013 October)
Miguel Correa, Chemistry: Exploring Pre-Transition Droplet Formation and the Effect of Secondary Isotopomeric Abundance Percentage. Advisor: J. Charles Williamson, Willamette University.
Liquid-liquid coexistence curves of partially-miscible systems can be measured with good precision from laser light scattering. For a given composition there should only be one transition temperature at which a solution changes from one to two phases, but recent work in the Williamson group shows evidence of two transitions taking place. These transitions are only about 0.2 K apart, and indicate that the binary system is not truly binary. The effect appears to happen only on the side of the coexistence curve in which the dominant species has the higher secondary isotopomeric percentage. In this study the phase diagrams of 2,2′-dichloroethyl ether (chlorex) + n-hexane will be determined. Due to the chlorines on chlorex, the natural secondary isotopomer percentage is 36.7%, significantly greater than other systems studied thus far. This experiment will help elucidate whether or not naturally-occurring isotopomers are the source of the two phase transitions. (2013 October)
Erin Shortlidge, Biology: Testing mutualism theory in the ancients: Exploring a scent-based plant pollinator-like relationship between the mosses and microarthropods. Advisor: Sarah Eppley, Portland State University.
In mosses, sexual reproduction requires that free-motile sperm travel across the landscape from male to female reproductive structure. Microarthropods are prevalent in moss patches worldwide and recent data suggest that microarthropods disperse sperm in mosses, significantly increasing moss fertilization rates, and highlighting the importance of biotic gamete dispersal in moss mating success. Additionally, we found that the tissues of the cosmopolitan moss Ceratodon purpureus emit volatile scents, similar in complexity to those in pollination mutualisms and that the volatile metabolomes are sex-specific. Common moss-dwelling microarthropods (springtails) are differentially attracted to these sex-specific moss volatile cues, preferring female mosses. Taken together, our results indicate the presence of a scentbased ‘plant–pollinator-like’ relationship between two ancient terrestrial lineages, mosses and microarthropods. My research further investigates the factors influencing and sustaining this relationship by testing for benefits that each partner may gain from engagement in this understudied, yet likely ubiquitous transport-mutualism. (2013 March)
Jianlong Gao, Mechanical Engineering: Experimental and analytical studies of superhydrophobic surfaces on polymer films. Advisor: Wei Xue, Washington State University Vancouver.
Previous research has shown that micro pillars on a polymer can critically change its surface wettability. While the selection of related dimensions for micro pillars is somewhat random. Our ongoing experiments have shown that the realistic results and previous analytical outcomes cannot be perfectly matched. Our initial analysis shows that the contact states of the liquid-solid interface cannot be fully explained by either Wenzel or Cassie-Baxter models. A thorough investigation on such polymer features is therefore needed. The objective of this project is to explore the optimum conditions for superhydrophobic surfaces on polymer. Photolithography and soft lithography will be done using SU-8 and PDMS respectively. Afterwards micro pillar arrays with different pillar diameters and center-to-center distances will be then coated on the surface of SU-8 and PDMS. Experimental and theoretical analysis will be done to deeply explore the possible relationship between the contact states and micro structure dimensions. (2013 March)
Benjamin Coder, Engineering: Leidenfrost Levitation Beyond Droplets. Advisor: Jie Xu, Washington State University - Vancouver.
The Leidenfrost Effect occurs when a droplet of liquid comes into contact with a surface that is significantly above its boiling point. The resulting pressure difference causes the droplet to levitate above the heated surface, creating a near-frictionless contact. The initial proposition was to see if a load could be placed on top of the droplets and transported across the surface, and was achieved. This first step in the work has been accepted by the ASME IMECE conference for presentation and by the Nature Publishing Group for publication. Currently, we are working on the ratcheted surface concept, where a droplet will travel parallel to the ratcheted surface when under the Leidenfrost Effect. (2012 March competition)
Manjari S. Kulkarni, Engineering: Memristor Based Reservoir Computing. Advisor: Christof Teuscher, Portland State University.
In today's nanoscale era, scaling down to even smaller feature sizes poses a significant challenge in the device fabrication, the circuit, and the system design and integration. On the other hand, nanoscale technology has also led to novel materials and devices with unique properties. The memristor is one such emergent nanoscale device that exhibits non-linear current-voltage characteristics and has an inherent memory property, i.e., its current state depends on the past. Both the non-linear and the memory property of memristors have the potential to enable solving spatial and temporal pattern recognition tasks in radically different ways from traditional binary transistor-based technology. We explore the use of memristors in a novel computing paradigm called "Reservoir Computing" (RC). RC is a new paradigm that belongs to the class of artificial recurrent neural networks (RNN). However, it architecturally differs from the traditional RNN techniques in that the pre-processor (i.e., the reservoir) is made up of random recurrently connected non-linear elements. Learning is only implemented at the readout (i.e., the output) layer, which reduces the learning complexity significantly. We use pattern recognition and classification tasks as benchmark problems. Real world applications associated with these tasks include process control, speech recognition, and signal processing. This presents an important step towards computing with memristor-based nanoscale systems. (2011 October competition)
Estella F. Yee, Chemistry: Investigation of a phase diagram anomaly in the o-toluidine + n-hexane binary liquid-liquid system. Advisor: J. Charles Williamson, Willamette University.
Temperature-dependent changes in light scattering behavior are used to delineate liquid-liquid coexistence curves. Using semi-automated laser light scattering instrumentation, the measurement of coexistence curve temperatures is accurate to 0.01 °C. However, in several liquid-liquid systems, an anomaly is observed for mixtures richer in one chemical: light scattering data suggest two transition temperatures differing by approximately 0.1 °C. In these compositions, droplets form at a higher temperature than the temperature of maximum critical opalescence. The anomaly is not observed for mixtures richer in the other chemical. This current research investigates the source of the anomalous droplets in the o-toluidine + n-hexane system through the use of light scattering and variable temperature 1H and 13C NMR experiments. Findings will contribute to a better understanding of liquid-liquid phase behavior. (2011 October competition)
Alireza Goudarzi, Computer Science/Mathematics: On the effects of heterogeneity in random dynamical networks. Advisor: Christof Teuscher, Portland State University.
The high cost of processor fabrication and approaching physical limits in processor scaling have motivated researchers to look for alternative computing paradigms. One proposal is to use the intrinsic dynamics of an excitable dynamical system, called the reservoir, to perform computation. In this approach, an input signal will stimulate the system and leave a trace in its internal dynamics. If the dynamics can be interpreted correctly, then one can compute the desired output for the input signal. The system dynamics is due to their interacting parts and therefore studying this phenomena lend itself to network modeling. However, much of the research in the area focus on homogeneous networks. We use two classical network models to study this phenomenon: Random Boolean Networks(RBN), a model of gene regulatory networks, and Liquid State Machine (LSM), a model of cortical microcircuits. We will systematically introduce heterogeneity in the node functions, in-degrees, and wire length to study the effects of heterogeneity on systems dynamics of RBN and LSM. We find the two models behave very differently. In RBN, increasing in-degree and node-function heterogeneity reliably produces rich dynamics for computation, whereas increasing wire length heterogeneity makes the dynamics poorer. In LSM, increasing in-degree and wire length heterogeneity makes the dynamics poorer for computation. We also find that LSM dynamics is completely independent from node-function heterogeneity. (2011 October competition)
Daniel O. Hassumani, Physiology/Functional Morphology: The CCAAT/enhancer-binding protein δ and its response to hypoxia in the zebrafish, Danio rerio. Advisor: Bradley Buckley, Portland State University.
The generally conserved ability of organisms to mount rapid changes in gene expression during perturbation from environmental stress is known as the cellular stress response (CSR). During the CSR, broad-scale gene expression patterns can change significantly, particularly for genes involved in cytoprotective mechanisms and cell cycle regulation. The CCAAT enhancer binding protein δ (C/EBP-δ) is a transcription factor that has been shown to be involved in both cell cycle arrest and apoptotic pathways. Heat shock can induce C/EBP-δ expression at both the mRNA and protein levels in the longjaw mudsucker (Gillichthys mirabilis) and Antarctic rockcod, Trematomus bernacchii, however, its expression has not been studied during hypoxic conditions. My research will use the zebrafish, Danio rerio, as a model organism to determine if exposure to low oxygen stress results in increased levels of C/EBP-δ, thereby integrating the expression of this transcriptional regulator into our understanding of how cells sense and respond to abiotic factors in their environment. (2011 March competition)
Tanya Cheeke, Ecology: Evaluating the effects of transgenic Bt maize on arbuscular mycorrhizal fungi in the soil ecosystem. Advisor: Mitch Cruzan, Portland State University.
Crop plants genetically modified for the expression of Bacillus thuringiensis (Bt) insecticidal toxins have broad appeal for reducing insect damage in agricultural systems, yet few studies have evaluated the impact of Bt crop cultivation on symbiotic arbuscular mycorrhizal fungi (AMF) in the soil environment. My research examines whether symbiotic plant-fungal relationships are reduced in transgenic Bt maize and assesses the effects of Bt maize cultivation on the abundance and diversity of arbuscular mycorrhizal fungi in the soil ecosystem. A sustained reduction in AMF colonization could lead to a decrease in the abundance and diversity of AMF propagules in the soil ecosystem, potentially impacting soil structure and function in areas where Bt crop cultivation is high. (2011 March competition)
Jason Juhala, Electrical Engineering: A comparative analysis of transistors based on dielectrophoresis-aligned carbon nanotubes (CNTs) and self-assembled random-network CNTs. Advisor: Wei Xue, Washington State University Vancouver.
In order to continuously improve electronic devices, carbon nanotube (CNT) devices must be further explored. It is particularly important to obtain an improved understanding of the physical and electrical properties of CNTs to successfully use them in electronics. The purpose of this project is to compare the field effect of carbon nanotube transistors, based on two separate fabrication methods. The first will be achieved by the use of dielectrophoresis (DEP) in the deposition and alignment of CNTs to fabricate transistors. The second method is to fabricate transistors based on self-assembly of CNT random networks. The study will compare the two devices, indicating important characteristics of the two forms of CNTs. This will provide crucial information on how the CNTs can be used in future research and practical devices. (2011 March competition)
Skye Anderson, Biology: Evolutionary Control of Mitochondrial Mutation Heteroplasmy. Advisor: Suzanne Estes, Portland State University.
Mutations that impair mitochondrial functioning are associated with a variety of metabolic and age-related disorders. Such disease-causing mutations are often heteroplasmic, meaning that wildtype and mutant mitochondrial genomes can co-occur within the same individual. The evolutionary forces that influence whether mitochondrial mutations will be transmitted across generations remain mysterious. Similarly, the forces that determine among-population variation in mutation heteroplasmy levels are unknown. Until recently, the progress of research into the evolutionary inheritance patterns of such mutations was hampered by lack of appropriate experimental systems. Caenorhabditis briggsae nematodes provide a powerful system in which to study mitochondrial deletion dynamics. (2010 October competition)
Arpita Sinha, Computer Science: Neuromorphic non-linear networks. Advisor: Christof Teuscher, Portland State University.
The goal of the project is to evolve the functionality of an associative memory from analog circuits by using memristors and other novel non-linear time-dependent devices. Arpita proposes to use an evolutionary optimization framework combined with cutting-edge circuit simulators. She hypothesizes that associative memories using memristors and other novel non-linear time-dependent circuit elements are more efficient than traditional associative memories. The approach is novel in that it will rely on novel time-dependent circuits as opposed to classical neural networks. (2010 October competition)
Sam Smith, Biology: Effects of Oxidative Stress on Somatic Nuclear Mutation Rate and Aging in Caenorhabditis elegans.Advisor: Suzanne Estes, Portland State University.
Endogenous oxidative stress, primarily originating through the creation of reactive oxygen species (ROS) by natural inefficiencies of the mitochondrial electron transport chain, is thought to be a primary cause of macromolecule damage within the cell. Sam is using paraquat, a commonly used herbicide which generates ROS in vivo, to test hypotheses which predict that increasing oxidative stress will result in an increase in somatic nuclear mutation rate and an increase in general macromolecular damage. (2010 March competition)
Timothy M. Davidson, Environmental Science / Marine Ecology: The prevalence and effects of native and non-native wood-borers in Panama mangroves. Advisor: Catherine de Rivera. Portland State University.
The morphology and structure of habitat forming species, such as trees and coral reefs, can be extensively modified by the animals that inhabit them. Marine wood-borers (crustaceans and mollusks) alter the morphology and performance of mangrove trees by reducing aerial root growth and inducing root-branching. Such effects are likely density-dependent, but this has not been explored. Using field surveys and experiments, I am characterizing the distribution and prevalence of non-native and native root-boring crustaceans and mollusks among the mangroves of Caribbean and Pacific Panama. These surveys are being supplemented by a manipulative field experiment, which seeks to determine the density-dependent effects of burrowing damage on mangrove root growth and morphology. This study will reveal the extent of mangrove borer effects and how root damage alters mangroves. (2010 March competition)
Sophia Trieu, Biology. Increase in adhesive bond strength during dental restoration. Advisors: Randy Zelick and Sean Kohles, Portland State University; Tom Hilton, Oregon Health and Sciences University.
Over 200 million dental restorations are performed each year in America. Dental restorations require a strong bonding of restoration to tooth structure and rely on dental adhesives to create this mechanical and chemical bonding. Sophia is working to increase the restoration longevity by examining the clinical methods of adhesive application to create a stronger bond of restoration to tooth structure. Enhancing adhesive bonding may help reduce problems such as postoperative sensitivity, marginal staining, and recurrent caries that may lead to more invasive dental operations. (2009 October competition)
Sarah Bortvedt, Biology: New Approaches to Huntington’s Disease Therapy: Investigating Combined Drug and Intracellular Antibody Treatments in a Drosophila Model. Advisors: Ami Ahern-Rindell, University of Portland; William J. Wolfgang, Wadsworth Center, Albany, NY.
Huntington’s disease is a neurodegenerative disorder characterized by age-dependent, neuronal degeneration and early death, for which there is no effective treatment. Sarah is using a Drosophila model that faithfully recapitulates many features of the disease to evaluate the ability of combination therapies against Huntington’s disease to reduce neurodegeneration and prolong survival. Identifying effective treatments in the fly may be the first step towards a human therapy. (2007 October competition)
Sarah Courbis, Biology: Population Structure of Island-Associated Dolphins. Advisor: Deborah Duffield, Portland State University.
This project focuses on genetics and photo-identification of pantropical spotted dolphins near the Hawaiian Islands. Sarah is exploring movement patterns and gene flow. This work is in collaboration with Cascadia Research Collective and the National Marine Fisheries Service. Sarah is also working on a project to study population structure of odontocetes near the Marquesas Islands in French Polynesia in collaboration with Hawaii Pacific University, Te Mana O Te Moana, and Gump Research Station. (2007 March competition)
Lisa D. Karst, Systematics / Evolutionary Biology: Do pollinator shifts and floral character evolution correlate to large area radiations in Sisyrinchium (Iridaceae)? Advisor: Carol Wilson, PSU.
We will investigate Sisyrinchium, a New World genus that is used as an ethnobotanic material and ornamental plant, and is also an agricultural weed. The research examines hypotheses of evolutionary history, character evolution, and corridors of dispersal for Sisyrinchium using fifty species, representing its morphological variation and geographic distribution. (2004 March competition)
Joshua J. Picotte, Ecology: Responses of the parental and hybrid genotypes of the Piriqueta caroliniana complex to calcareous soil conditions. Advisor: Mitchell Cruzan, PSU.
Gene flow between genetically similar taxa, known as introgression, frequently produces low-fitness hybrids, but occasionally may produce vigorous hybrids that out-compete their parental genotypes. Hybrid genotypes may outcompete their parental counterparts under particular environmental conditions. This field investigation of one such system, over a range of Florida landscapes, reveals genetic adaptation to drought. (2004 March competition)