Increasing the efficiency of biofuel production is critical to decrease the dependence and consumption of fossil fuels. In the United States, most car fuel contains about 10% ethanol, the result of fermentation, and 90% gasoline. The process of fermenting sugars into ethanol relies on agricultural stocks, decreasing the area of arable land available for food production. Non-agricultural plant species can be used, but the lignocellulose material from the total plant contains both five and six carbon sugars. Baker’s Yeast can ferment the six carbon sugars, but a novel yeast species is necessary to ferment the five carbon sugars. The goal of my research is to isolate and identify wild yeast species growing in non-agricultural plants that ferment five carbon sugars, such as xylose, into a usable product; xylitol in this case. Xylitol can be sold as an artificial sweetener to subsidize the overall costs of biofuel production, or alternatively, may be converted to ethanol through biochemical pathways that some yeast species have. After attempting to grow yeast from nine different plant species growing in Pack Forest with xylose as their only carbon source, one yeast species from red alder, Alnus rubra, exhibited growth. The other eight species did not show significant growth compared to controls: common Baker's Yeast and PTD3, a previously isolated yeast. Further research of these yeasts was not pursued. Next, AR (for Alnus rubra), was tested for xylitol production. First, AR was grown in a medium with xylose as its sole source of sugar. By placing the growth culture in an air-tight flask, any xylitol production would be prevented from evaporating, making it measurable with a high-performance liquid chromatography machine. The yeast isolated from red alder successfully fermented xylose into xylitol, making it a potential source of efficient biofuel production.

Washington State is home to unique prairie ecosystems that have been invaded and degraded over the last several decades. A habitat restoration study is underway at 4 research sites in Western Washington. Areas at each site were prepared with solarization, burning, or herbicide, and plots were seeded with a diverse mixture of native species following site preparation. I am researching the effect of these treatments on the physiological profile of soil microbial communities and on available nitrogen (N) mineralization. Soil samples were collected from 5 locations at each site: the site preparation treatments, an unseeded herbicide area, and an untreated area. The samples were either inoculated into a Biolog EcoPlateTM containing 31 carbon sources and 3 water well controls, or used to extract a KCl solution for N mineralization amounts. The wells of the EcoPlatesTM contain tetrazolium, which changes color in response to microbial activity. The color development was recorded when plates were first inoculated using a micro-plate reader at a wavelength of 590nm, and were then incubated for 24 hours. Readings were then taken every 12 hours for 96 hours. The normalized data are analyzed using PCA and PERMANOVA.N Mineralization rates are obtained by subtracting the results of time 0 from time 1. PVC tubes were inserted into the 5 treatment plots on day 1 and removed to collect samples for mineralization. To obtain the second sample PVC tubes were left in the 5 treatments plots and collected after 40 days. Samples were mixed with a 2M KCl solution to extract NO3 and NH4 amounts. The resulting amounts of NO3 and NO4 from day 1 will be subtracted from day 40 to obtain mineralization rates. This research is important to the larger restoration project because it is examining how strongly the restoration treatments affect the soil microbial community.

Curiously, Black Cottonwood (Populus trichocarpa) thrives on the rocky riverbanks of Washington under nutrient-poor conditions few other species dare tolerate. Their prosperous lives could be the result of nitrogen-fixing bacteria that inhabit the tree's stems and roots. It is the hypothesis that these endophytic bacteria provide trees with organic nitrogen throughout their lives, where the river side substrate fails to provide sufficient nitrogen for the Poplar to otherwise live. Wild Black Cottonwood seeds were collected from Three Forks Park along the Snoqualmie River in Washington then grown in greenhouses. Endophytes were isolated from these trees and tested for the presence of the nitrogenase gene (nifH) using PCR. The nitrogenase proteins equip bacteria to fix atmospheric nitrogen into forms plants can readily use. Understanding the life cycles, inoculation techniques and genetic make-ups of these bacteria enable us not only to grasp a little better the diversity of life, but to think beyond Black Cottonwoods, to how these bacteria could be recruited to be used on crops and degraded fields. Nitrogen is necessary for plants and often a growth limiting factor; harnessing these nitrogen-providers may help reduce our dependency of energy-intensive industrial ammonia.

Biochar is the product of biomass that undergoes pyrolysis, the process of thermal degradation in the absence of oxygen and is a type of charcoal. Research has shown biochar to be an effective soil amendment but the optimal levels of incorporation are unknown. This study examines if an optimal level for plant growth exists and to determine if introducing a stress factor will alter the optimal point. Five levels of biochar amendments at 0%, 1%, 3%, 5%, 10%, and 15% by volume have been made into root media with high or low nutrient availability as a stress factor. Sweet peppers plants were grown from seed in flats for one month and seedlings were transferred to larger pots with appropriate biochar level. They will be grown for two months and destructively harvested for dry biomass data. We hypothesize the pepper plants will have an optimal biochar level for growth and this level will change with plant stress.

As environmental degradation continues to worsen around the world, finding ways to mitigate the effects is increasingly important. Currently, school systems widely utilize standardized testing as a method of teaching resulting in disconnect between children and nature. Environmental art education is a medium that can be used to develop tangible connections between the youth and the environment. It has even been shown to promote environmental concepts as well as produce more environmentally aware citizens.Through my capstone experience, I will be working with Nature Consortium and the Yesler community center to develop environmental art curricula and evaluate the impact of these curriculum on creating tangible connections between the youth and the environment. I will be developing 10-20 environmental art curriculums and projects. Comparative evaluations of the students that have particpated in the environmental art curricula and the students who have not participated in the lessons will be conducted through surveys. Through this project I will also be responsible for creating plans for an environmentally aesthetic  classroom to contribute and facilitate the connections between the environmental art lessons and the students. My deliverables resulting from this project will include 10-20 environmental art curriculums, annotated bibliography, capstone journal logging my hands-on experience, and research material on the environmental art education. This data will help contribute not only to the organization I am working with, but to the future organizations. Discovering how to engage youth with the enviornment is key to both mitigating environmental degradation and creating adults who are more environmentally aware. 

The modern parents' choice between disposable and reuseable affects not only their child but their global and local community. In exchange for more convient disposable diapers the industry has degraded the environment, introduced public health hazards, strained waste management efforts, and increased monetary costs of diaper consumers. Cloth diapers provide parents a less impactful option and a good value economically. This paper will explore the harmful effects of disposable diapers, the benefits of cloth diapers, why and how parents choose their diapers, and why most parents (90 percents) choose disposables. The motivation behind parents' choice will be studied, and their knowledge of diapers will be assessed. Interviews will consists of parents with young children using either cloth diapers or disposable diapers. Analysis of the interviews will access disparities between the parents and how society might educate parents to choose a diaper that is more ecologically sustainable, financially endurable, and better for their children's immediate health and development.

The American crow (Corvus brachyrhynchos) is believed to practice facial discrimination and incorporate past experiences in its reaction to individuals. To test this neural integration of perception and memory, a pilot study performed by Dr. Marzluff and his colleagues used PET imaging methods in conjunction with an avian MRI to create a global map of the bird’s brain after performing a visual, analytical task. The initial results suggest that individual crows incorporate memory and activate distinct brain regions while evaluating different stimuli, specifically familiar human faces previously associated with either capture (dangerous mask) or feeding (caring mask). Regions of high activity were correlated with high 18F-FDG intake, a radioactively labeled glucose injected into the bird prior to a conducting the scan. These experiments are now being expanded to determine if there are different pathways for fear responses between threats such as humans and natural predators. I have exposed crows to a natural danger stimulus, a taxidermy mount of a common predator, the Red-tailed Hawk. My hypothesis is that the hawk treatment should prompt more of an innate reaction instead of the processing of contextual information; therefore more activity should be centered in the midbrain instead of the striatum and nidopallium. The second objective of this study was to find a difference in brain activity between memory storage and memory retrieval. To accomplish this, I have exposed crows to a novel person and a novel person holding a taxidermy mounted “dead” crow. The brains maps of differential activity from these treatments should highlight the fear learning pathway. My data can help distinguish the facial neural processing from that of a broader perception of danger and promote translational research by allowing parallel analyses of physiological and operative processes of the human and animal brain.

Phytoremediation is the use of specific plants to remove pollutants and toxins from soil and water.  Phytoremediating plants can have problems surviving in highly polluted industrial environments, known as Super Fund sites. The Doty Lab has isolated an endophyte bacteria designated "PD.1" that has shown the ability to give plants the strength to become estabilished and productive in these highly toxic environments.  The term endophyte refers to a class of mutually beneficial, symbiotic microbes, which live in the intracellular spaces between cells of inoculated plants, and have been shown to release growth hormones, provide tolerance to drought, flood and high salt environments and can give plants the ability to break down large human-made chemicals into smaller molecules which the plant and microbes can use as a nutrient source . This presentation will show the results of several experiments conducted in hydroponic solutions, and in soil dosed with the Polycyclic Aromatic Hydrocarbon, phenantherene. Several different species of Salix and Populous trees were dosed with high levels of phenantherene after being inoculated with an endophyte bacteria isolated from a Populous deltoids. Growth, plant mortality rates and plant uptake of the pollutant phenantherene were recorded.  In several of these studies there was a dramatic decline in mortality of inoculated plants in highly polluted environments and also signifigant increases in shoot growth of inoculated plants. This research adds to the growing body of work that is demonstrating that the use of plants, inoculated with a corresponding symbiotic, endophytic bacteria can be a viable tool in pollution remediation of soil and water.

Populus trichocarpa, or Black Cottonwood, form a mutualistic relationship with diazotrophic bacteria, in which nitrogen is provided to the host plant in exchange for protection and energy. Understanding this form of symbiosis is essential in determining how biologically available nitrogen is cycled throughout our planet’s biomes. A well-known diazotrophic mutualism is found between leguminous species and Rhizobia or Frankia bacteria, where colonies are established inside root nodules of the host plant. Black Cottonwoods differ from legumes in that they form an endosymbiosis with nitrogen-fixing bacteria recruited from the environment, where the bacteria form colonies throughout the plant tissue. To determine the endophyte source, bacterial samples were obtained from sand, river water, and seed collected at the Three Forks Park in Washington to determine where in the environment Black Cottonwoods are coming into contact with these endophytes, and which species are found at each source. Nitrogen-fixing species were selected for by culturing bacteria using nitrogen free media, and were then subjected to PCR for amplification of the nitrogenase gene for confirmation. Species identification was performed by amplifying the 16sRNA, followed by sequencing and local alignment matching. Of the 29 samples collected from the Three Forks site, 27 were found to carry the nitrogenase gene, and species identification underway. Black Cottonwoods, in addition to other poplar species, have been found to be very useful industrially as biofuels and in the bioremediation of environmental pollutants. Nitrogen-fixation provides a major benefit for using poplars, where the use of fertilizers is reduced. It is thought that there is a common evolutionary link between more plant species and diazotrophic bacteria than is currently known, and understanding which species exist outside of the plant hosts may lead to the reduction of nitrogen-based fertilizer in other industrially useful plants.

When we decide to go somewhere, we must also decide how we will get there. Any choice, whether it be by car or bike, will have a unique route associated with it. This route can play a role in the decision making process. With this in mind, it is important to understand differences in the routes taken by both bikers and motorists. This study uses Google Maps as a tool used to do just that. 32 Routes were created randomly, and ran for both cars and bikes. The outputs were then compared with regards to length, duration, and complexity. Overall length of the two routes showed little variance, while the duration for automobiles was predictably much shorter. Less predictable was the increased complexity for bike routes, which were calculated to be over 250% more complex than car routes. This increased complexity may have an effect on whether people chose to ride their bike or drive their car. Furthermore, it highlights another challenge that cyclist must face. In the future, communities should plan and invest in the type of infrastructure that fosters transportation equality