Past Projects

Interactions Among Wolves and Mesopredators in Washington
​​Rebecca Windell, Research Scientist
Dr. Laura Prugh, PI, SEFS

This project examines the movements and population dynamics of two common mesopredators, coyotes and bobcats, in response to wolf recolonization in Washington state. Noninvasive fecal genotyping will be used to estimate coyote and bobcat population densities in areas of varying wolf presence. In addition to genetic methods, GPS tracking and remote wildlife cameras placed at kill sites will be used to examine the facilitative and suppressive effects of wolf presence on coyotes and bobcats.  More information on the fecal genotyping for this project can be found here.
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Ungulate-Predator Dynamics in Northern Washington
​​Taylor Ganz, PhD Student
Dr. Laura Prugh, PI, SEFS

As a part of the Washington Predator-Prey Project, we are examining how carnivores influenced the mortality rates and movement of mule deer, white-tailed deer, and elk in 2 regions of Northern Washington occupied by recolonizing grey wolves. When radio-collared ungulates die by predation, we swab lethal bite wounds to identify the responsible predator species. Combined with additional data on ungulate vital rates, movement, and nutrition, we seek to determine what factors most strongly influence these deer and elk populations.

Vashon Island Coyote Pilot Study
Collaboration with the Vashon Nature Center

The Vashon Nature Center is providing funding to the SEFS Genetics Lab for a pilot study to determine if quality DNA can be extracted from scat swabs taken by citizen scientists. If successful, the genetic data will be used to assess the population size of coyotes on Vashon island and their level of inbreeding.
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DNA and Protein Analysis from Pollen
Lila Westreich, PhD Student
Dr. Patrick Tobin, PI, SEFS 

The introduction of non-native species can have a direct and dramatic effect on the function and structure of native ecosystems and biodiversity. Pollinators search for specific groups of flowering species to find the most nutritionally dense food sources during different times of the year. The effect of pollen introduced by non-native plant species on pollinator fitness and food supply is not well understood. Recently, there has been economic and environmental interest in understanding the importance of ecosystem services and the management of sustainable ecosystems. Specifically, research focused on pollinator food sources and the effect of non-native pollen sources on native pollinators is lacking. My goal is to determine the effects of non-native plants on native bees in the Pacific Northwest and urban Seattle area. My project will consist of three main experiments. The first is a survey of local bee species to identify pollen being used for food throughout the flowering seasons, and the second is a series of semi-controlled experiments to understand the effect of non-native pollen on larval emergence and development in native orchard mason bees. The third experiment will create a test area containing native and non-native plants to understand bee larval emergence and development on an ecological level. This work is necessary to the conservation of native bee species and the future of invasive plant treatments.    
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Mesocarnivores in Alaska
Dr. Laura Prugh, PI, SEFS

As top predator populations decline worldwide, the role of mesocarnivores is becoming increasingly important, yet we have a poor understanding of how these top-down forces ripple through food webs. We are examining interactions among wolves, coyotes, and other mesopredators (wolverines, foxes, lynx, and marten) in Denali National Park and Preserve using a combination of GPS collars, snow tracking, fecal genotyping, and modeling.
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Nitrogen-cycling Bacteria and Archaea
Anna Simpson, PhD Student
Dr. Darlene Zabowski, PI, SEFS

Nitrogen deposition has the potential to cause eutrophication and increases in nitrogen leaching in the pristine alpine meadows of the Pacific Northwest. This project examines shifts in abundance of genes that code for N-cycling enzymes (for example, ammonia monooxygenase) in soil with fertilization treatment, mountain range/site, and type of vegetation.
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Domestic Pig Microbe Detection
Donia La Fazia, Undergrad Capstone Project
Dr. Laura Prugh, Supervisor, SEFS

The Buffalo National River in Arkansas is under threat by a 6500-head hog operation causing high E.Coli counts and large algal blooms. The hog farm sits 6 miles from the river along one of the main tributaries. Since the operation began in 2013, millions of gallons of liquid hog waste has been sprayed onto pastures and fields and some of which lie in flood zones. Despite protests and evidence that water quality is being impaired from the farm, the operation is continuing to operate. The Buffalo River Watershed Alliance is providing funding to the SEFS genetics lab to detect microbes that are specific to domestic pigs in the river water. The developed assay for the microbe will be optimized for more sensitive detection using the droplet digital PCR machine. 

Cancer Detection using Aptamers
Meilyn Sylvestre, PhD Student
Dr. Suzie Pun, PI, Bioengineering

Over 12 million people in the US are affected by cancer. Cytotoxic chemotherapies are used to treat this disease with varying results. Due to the non-specific nature of these therapies, patients suffer from treatment-related side effects that severely compromise patient quality of life. We are developing technologies to target certain cell populations within the cancer environment, increasing therapy specificity and effectiveness. To do this, we are identifying aptamers (singe stranded DNA) that can bind these cell populations with high affinity and specificity, while offering the economic advantage of affordability over antibodies. Our goal is to translate these therapies into the clinic to improve patient quality of life and prognosis. ​
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Interactions of Colonizing Endophytes in Populus trichocarpa
Sam Scharffenberger, Undergraduate Capstone Project
​Dr. Sharon Doty, Pierre Joubert - PI/Supervisor, SEFS

 Microbes that live within plants, called endophytes, are being heavily researched on their ability to assist host plants in processes from nitrogen accumulation to drought tolerance. Two endophyte strains named WP5 and WP9 are known to colonize Populus trees. Previous research has shown that the presence of WP5 in a host plant allows for greater colonization by WP9 subsequently. This research is directed at replicating these results with more robust molecular biology techniques. Methods for experimentation include the growth of the endophytes in selective media and varying the optical densities of these liquid cultures before inoculating the poplar clones. The plants co-cultivate with the inoculum for 24 hours, at which point they are removed, washed and placed in limited nutrient media. After removal from the inoculum as well as at 7 and 14 days hence, the host plants will be sampled by performing genomic DNA extractions and subsequently analyzed through Digital Droplet PCR to quantify endophyte presence. Additionally, these strains have been marked with fluorescent tags to enable imaging under a microscope. The two endophytes were labeled with different colors, one red and one green, so that they could be visualized concurrently. Along the same sampling timeline, root samples will be taken to image through microscopy in order to visually investigate the colonization process of the two strains. The results of this research will help to shed light on the colonization abilities of these strains, and allow for the optimization of bio-fertilizers comprised of endophytic consortia.  ​

Gender Identification of Crows
Dorian Overhus, Undergraduate Capstone Project
​Dr. John Marzluff, Supervisor, SEFS

The purpose of my study is to determine the gender of nine American crows in John Marzluff's and Loma Pendergraft's research experiment. In doing so, I will be able to decide if there is a significant difference between gender and (1) ability to learn Aesop’s fable paradigm task, (2) ability to pull chicken up on string, and (3) crow personality. The outcome of my study will add well-needed depth to Marzluff and Pendergraft’s study, and will later allow them to compare gender with the brain scans of the crows before and after the study. The outcome of my study also serves useful for future avian and wildlife gender comparison studies. 
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High-severity Fire effects on the Community Composition and Succession of the Microbiota of Ponderosa Pine
Fabiola Puliodo-Chavez, MS
​Dr. Ernesto Alvarado, PI, SEFS

Healthy forest maintain a diverse microbial community which play a significant role in the cycling of  nutrients, the recycling of living material and procurement of resources. However, soil communities are not static and are highly susceptible to alterations within their environment. In the Pacific Northwest, decades of fire exclusion have exacerbated the severity and intensity of wildfires, and ecosystems, such as Ponderosa pine ecosystems, which traditionally burned at low-severity, are now burning at high severity, leading to the removal of all soil organic matter. This alteration to the soil has led to a growing concern about the effects and recovery of the belowground community in wildfire affected environments, specifically in areas which have burned at high-severity. In this study, I will examine the community composition and succession of the microbiota of a chronosequence of four Ponderosa pine stands in Central Washington, that were affected by high-severity fires between 2006 and 2015. Soil samples from burnt and adjacent non-burnt forest will be analyzed using shotgun metagenomics analysis to sequence the microbial DNA and profile the taxonomic composition of the soil microbial communities. Succession of the microbiota will be examined via statistical analysis comparing the community composition of each fire (2006-2015). This information will help elucidate the effects that high-severity wildfires have upon the soil microbiota and increase the knowledge of microbial succession in highly disturbed ecosystems. Additionally, the results of this study can help guide management decisions in disturbed ecosystems.
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Understanding the Microbiome of Puget Prairies: Community Composition of Endophytes in a Hemiparasitic Plant System
​Victoria Fox, MS Student
​Dr. Jon Bakker, PI, SEFS

Recent advances in the field of metagenomics have allowed for a boom of research in the field of microbial community ecology. Using a combination of shotgun genomics, Illumina sequencing, and advanced statistical software, scientists are now able to examine the community composition of microbiomes existing throughout the world. My research examines the microbial communities of Puget prairie plants, which have remained largely unexplored until now. I performed a field study to identify the endophytic communities that comprise the microbiomes of 16 native prairie plant species. I discovered that the bacterial endophyte communities within Puget prairie plants often differ significantly between plant species. However, the microbiomes of some plants belonging to the same family do not differ from one another. Additionally, I found that these bacterial communities did not reflect disturbances applied several years prior to sampling, nor to disturbance regimes applied continuously to research plots. I also used genomic information from this study to examine if the endophytic microbial community could be influenced by Castilleja levisecta, a hemiparasitic plant that attaches root connections to other prairie plants. I found no consistent effect of plant parasitism on the microbiomes of parasitic plant Castilleja levisecta or its hosts. This research provides valuable information about the types of endophytes that exist in native Puget prairie ecosystems, and insights about how parasitic plants may contribute to the colonization of endophytic bacteria across a Puget prairie plant community.
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Epidemiology and Evolution of a Common Plant Pathogen
​Michael Bradshaw, PhD Student
​Dr. Patrick Tobin, PI, SEFS

My project will focus on the epidemiology of a common plant pathogenic fungi (powdery mildew) in the Pacific Northwest. This research will:  1) Evaluate the epidemiology and biology of powdery mildew species accruing on the University of Washington (UW) campus, Washington State Arboretum, and Western Washington forests. 2) Examine the relationship between host divergence and host resistance to powdery mildew. 3) Develop a network based model of the spread of powdery mildew throughout American botanical gardens and nurseries.
 
Botanical gardens have extensive maps and databases of their plant specimens yet the fungi on their properties have never been thoroughly tracked. In this proposed project, we will identify and map the vast array of powdery mildew pathogens in the Pacific Northwest as well as in botanical gardens throughout the country. The proposed research will facilitate our understanding the dynamics of fungal spread in urban and forest environments, examine the role of botanical gardens in contributing to the spread of plant fungal diseases, and guide the development of improved management protocols. Furthermore, the relationship between host plant divergence and resistance to fungal pathogens will be quantified to better understand the host range and the severity of non-native pathogens. A keystone component of this research is the accurate identification of plant fungi; To accomplish this to the species level sequence work will need to be conducted.
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Investigating the Impact of Increasing Numbers of Wolf Packs on Coyote Diet in Northeastern Washington
Anna Malesis, Undergraduate Capstone Project
​Dr. Laura Prugh, Supervisor, SEFS

This study compared coyote diet between two sites in the northeast portion of Washington—one overlapping with two wolf pack territories and one overlapping with four. Coyote scats collected from each site and identified using DNA extraction methods were dissected and prey items were identified. The diets were compared with contingency tables and Shannon’s diversity index to discern the effects of wolf presence on coyote diet, and scats found inside of and outside of wolf pack territories were also compared. 
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Estimating Coyote Population Density following Wolf Recolonization in Eastern Washington 
Iona Rohan, Undergraduate Capstone Project
​Dr. Laura Prugh, Supervisor, SEFS

The objective of this study is to investigate the effects of wolf recolonization on coyote (Canis latrans) density in Washington State. Coyote scats were collected in two field seasons, summer 2018 and winter 2019, from northeastern Washington and the Okanogan, regions with higher and lower wolf densities respectively. Fecal genotyping was employed to generate consensus genotypes for use in a spatially explicit mark-recapture model to estimate coyote density in both field sites. Data from both seasons was pooled, and a closed population capture-mark-recapture method was employed to estimate density inside and outside of wolf pack home ranges.