Student research grants

Sky Button, Cell biology: Using aquatic eDNA to inform the conservation of a rare and secretive terrestrial amphibian. Mentor: Jonah Piovia-Scott, WSU Vancouver.

Environmental DNA (eDNA) is a critical modern tool in conservation science due to its ability to detect rare and secretive species that would be infeasible to study otherwise. For example, species with low populations or limited visibility often go undetected using conventional (e.g., visual) surveys, which can make eDNA the only reliable tool for studying them. For example, the Van Dyke’s salamander (Plethodon vandykei) is one secretive, fully terrestrial salamander whose watercourse-adjacent life history makes it detectable using aquatic eDNA. This species is also difficult to detect using visual survey and is a potentially at-risk species in Washington. My objectives are to: (1) use aquatic eDNA to determine how current P. vandykei occupancy is related to long-term forest clearing and other anthropogenic disturbances at historically occupied localities, and (2) determine how eDNA-based detection of the species varies across habitat and land use gradients. This research will serve as the first ever demonstration of aquatic eDNA as a tool for enhancing the conservation of a fully terrestrial salamander, and will enable key inference about the potential for aquatic eDNA to detect non-aquatic species. (2021 October)

Malcolm Peavy, Systematics / Evolutionary Biology: Vitamin D exploration of the mTOR pathway in Austrofundulus Limnaeus. Mentor: Jason Podrabsky, Portland State University.

Annual killifishes live in ephemeral ponds and survive through the dry season as diapausing (dormant) embryos encased in the drying mud. Recent data support a role for vitamin D signaling in the control of dormancy in annual killifishes, entrance into diapause is controlled by blocking the synthesis of vitamin D. Dormancy in other systems, including in pre-implantation mammalian embryos, if known to be dependent on regulation of the mechanistic target of rapamycin (mTOR) pathway. I propose to investigate the importance of the mTOR pathway to the regulation of dormancy in annual killifishes and to explore a potential link between the vitamin D and mTOR signaling pathways. I will block mTOR signaling by incubating embryos in two distinct inhibitors: rapamycin and Torin 1. I will test for an interaction between mTOR and vitamin D signaling by incubating embryos in a mixture of mTOR inhibitors and vitamin D. I hypothesize that inhibition of mTOR signaling will induce embryonic dormancy and that the addition of vitamin D will reverse this inhibition. This research is foundational to understanding the role of the mTOR pathway in development and the potential for Vitamin D signaling to regulate mTOR function. The mTOR pathway plays an indispensable role in cell biology by regulating cellular growth and metabolism, and thus a better understanding of this pathway may have many important biomedical applications including combating aging and modulating immune system function. (2021 March)

Rebecca Talbot, Hydrology / Geomorphology: Spatial and seasonal variations of microplastic concentrations in Oregon’s freshwater. Mentor: Heejun Chang, Portland State University.

Microplastics are a pollutant of growing concern, capable of harming aquatic organisms and human health. The majority of microplastics research to date has been conducted in marine waters, and little is known regarding the sources and delivery pathways of microplastics in urban rivers. Two watersheds in the Portland metro area representing an urban-rural gradient have been selected to assess microplastic concentrations and potential links with land cover, population density, flow rate, and seasonality. Samples will be collected from the Clackamas River and Johnson Creek in both wet and dry seasons, and statistics and GIS analyses will be used to describe variations in microplastics and identify landscape and hydrometeorological variables that are associated with microplastic concentrations. The findings of this research can be used to inform management decisions regarding microplastic waste and identify hotspots of microplastic pollution that may benefit from remediation. (2020 March)

Amy Ehrhart, Ecology: Effects of Exposure to Coastal Wastewater Treatment Plant Effluent on Pacific Oyster Health and Survival. Mentor: Elise Granek, Portland State University.

Pharmaceutical and personal care products (PPCPs) are increasingly detected in marine environments worldwide and pose unknown risks to ecological communities. Municipal wastewater treatment plant effluent is a primary source of PPCPs to the marine environment as most are not fully removed during the treatment process. Continual discharge from treatment plants in coastal areas exposes organisms to a suite of PPCPs on a regular basis which may act as stressors. This project addresses effects of mixtures of PPCPs through a lab experiment where Pacific oysters were exposed to effluent from coastal wastewater treatment plants of different discharge capacities, to represent different population sizes in Oregon. The goals of the experiment were to determine concentrations of various PPCPs in effluent from two different sized treatment plants in Oregon and examine their effects on Pacific oyster growth, feeding rate, health, and survival. PPCP accumulation in oysters and effects on their fitness may have implications for the commercial fishery, human health, and coastal ecosystem resilience, especially with increased urbanization, pharmaceutical usage, and resultant discharge into estuarine systems.Knowledge of these effects could elucidate potential harm to ecological functions provided by oysters, such as water filtration and provision of habitat for other species, and inform future coastal water quality regulations, especially near oyster growout areas. (2019 October)

Lara Jansen, Ecology, The Effects of Temperature, Nutrients and Non-native Fish on Harmful Algal Blooms in Mountain Lakes. Mentor: Angela Strecker (Portland State University, Western Washington University).

Often harmful cyanobacteria blooms are considered a growing environmental health issue limited to lowland lakes in developed regions from increased nutrient runoff by human activity. Yet remote mountain lakes are also experiencing such blooms. Many high elevation lakes are vulnerable to not only increased atmospheric deposition of nutrients like phosphorus due to adjacent industry and agriculture, but also warming trends with the changing climate. Yet the repercussions of these environmental shifts on the prevalence and composition of cyanobacteria in mountain lakes remains unclear. Therefore, this project aims to characterize cyanobacteria communities of mountain lakes, using DNA sequencing, across a gradient of temperature and phosphorus to examine the possible relationships with bloom-forming and toxin-producing strains. (2019 October)

Colin Wakeham, Cell biology / biochemistry: Trophoblast glycoprotein: A novel PKCα-dependent phosphoprotein in retinal rod bipolar cells. Mentor: Catherine W Morgans, Oregon Health & Science University.

Rod bipolar cells (RBCs), the first excitatory interneurons in the rod visual system, receive light-dependent synaptic input from rod photoreceptors and contribute to retinal output through synapses with downstream neurons. Though the rod pathway is generally associated with low-light vision in mammals, RBCs actually operate under a wide range of light intensities and serve different functions depending on luminance conditions, from complete darkness to daylight. Therefore, RBCs must have mechanisms to modulate their sensitivity to various light intensities, and compelling evidence suggests it involves protein kinase C-alpha (PKCα) phosphorylation. In the retina, PKCα is primarily expressed in RBCs, and genetic knockout of PKCα results in a significantly amplified RBC light response to bright flashes, suggesting that PKCα may be suppressing the RBC light response to bright light. Using a phosphoproteomics approach, we have identified trophoblast glycoprotein (TPBG) as a major target of PKCα-dependent phosphorylation in RBCs. TPBG is a transmembrane leucine-rich repeat protein that is strongly localized to the dendrites and synaptic terminals of RBCs, and our proteomics data identified two serines within TPBG’s intracellular C-terminal tail that show PKCα-dependent phosphorylation. I have shown that, similar to PKCα, genetic deletion of TPBG also results in an amplified RBC light response. Since phosphorylation is a common means by which protein interactions and activity are regulated, I hypothesize that PKCα modulates the RBC light response via phosphorylation of serines within the C-terminus of TPBG. Identifying the function of TPBG, a novel PKCα-dependent phosphorylation target in RBCs, will increase our understanding of how the retina adapts to changing light conditions and may aid in the development of effective therapies to combat retinal diseases and restore vision. (2019 March)

Madeline Lewis, Cell biology / biochemistry: Uncovering small RNAs in Streptococcus mutans, an agent of dental caries. Mentor: 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. Mentor: 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)