Student research grants
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.
Madeline Lewis, Cell biology / biochemistry: Uncovering small RNAs in Streptococcus mutans, an agent of dental caries. Advisor: Rahul Raghavan, Portland State University.
Tooth decay (dental caries) is a common childhood disease and affects over 90% of the U.S population. Streptococcus mutans is one of the primary contributors to caries formation. The pathogen’s cariogenicity is due, in part, to its ability to rapidly adapt to environmental stress within the oral cavity. Previous studies have investigated the roles of proteins in S. mutans’s stress response; however, the potential roles of small RNAs (sRNAs) have remained mostly unexplored. sRNAs regulate gene expression by binding to and blocking the translation of mRNAs. Because they are less costly to produce than proteins and can act downstream of previous genetic responses, sRNAs represent an efficient means of rapid stress response for oral bacteria. As a first step in understanding the function of sRNAs in stress tolerance, we conducted preliminary analyses of S. mutans growing in the presence of xylitol, a common component of dental care products that causes sugar-phosphate stress. We discovered 15 novel sRNAs (named SmsR1 to SmsR15) that were expressed under xylitol; of these, SmsR4 displayed the greatest level of upregulation. In silico prediction of sRNA-mRNA interactions suggests that SmsR4 regulates the gene SMU_115, a likely component of the xylitol transport system. However, the function of SmR4 in stress pathways remains unknown. We hypothesize that SmsR4 is important for adaptation to sugar-phosphate stress in S. mutans. The role of SmsR4 will be determined through functional analysis of the effects of SmsR4 gene deletion, as well as the identification of the mRNA binding targets of SmsR4. This work will provide a fundamental contribution to knowledge of sRNA utility in stress response within oral microflora. (2018 October)
Scott Kiel, Climate Science: Moss as a Human Health Biomonitor: a calibration study linking moss heavy metal accumulation and human exposure. Advisor: Todd Rosenstiel, Portland State University.
High-resolution air quality data are critical for assessing fine-scale pollution events and associated human health risks, especially in urban areas. However, deploying the necessary number of air quality sensors to effectively capture the heterogeneity of urban environments is both expensive and labor intensive. In natural systems, mosses and lichens are often used as a biomonitors for air quality as they readily accumulate pollutants over time, are inexpensive to collect and analyze, and are usually well dispersed across an ecosystem. To increase the quality of data collected using biomonitors, a long-term, high-frequency calibration study linking bioaccumulation measures to traditional measures of human exposure has been established in partnership with the US Forest Service. Sampling with a mix of tradition air quality instruments along with co-located moss treatments, this research will produce a fine-tuned air quality dataset that will inform the calibration of heavy metal accumulation in moss tissue, and allow a better understanding of how a moss biomonitor may be used to determine human exposure of heavy metals in an urban landscape. (2018 October)
Kelsi Ramos, Chemistry: Characterization of Pre-Transition Droplets in Liquid-Liquid Systems with Magnetic-Susceptibility-Matched NMR Tubes. Advisor: 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. Advisor: 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. Advisor: 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. Advisor: 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. 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)
Caitlin Maraist, Ecology: The effects of phyllospheric fungi on sexual effort and chemical cues in the dioecious moss, Ceratodon purpureus. Advisor: 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. Advisor: 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. Advisor: 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)
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.