Portland-area students have received Grants-in-Aid of Research (GIAR) through Sigma Xi’s national competitions. The GIAR competitions are held twice a year, with deadlines of March 1 and October 1 for research proposals. The Chapter encourages students to apply. The Chapter also provides a modest supplemental grant to local students whose proposals have earned a GIAR. For general information on the awards and requirements, visit Sigma Xi’s national website. Here is an example of a successful proposal, by Sarah Bortvedt. Recent local winners of these grants are featured below, and earlier winners in the archive.
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)
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. Advisor: Ragul 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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
The Columbia-Willamette Chapter awards a supplemental grant to each of the above students in further support of their research. These supplements are funded with income from the Chapter’s MacCannell Endowment, and with current operating funds. The Endowment honors Earle MacCannell, who made generous donations (with Julie Blume and others) to endow student grants and public science lectures. Donors are encouraged to endow new educational and scientific projects for the Chapter, such as additional student research grants or our annual student research symposium.