The focus of this thesis is to design, characterize, and apply novel computational methods and molecular systems to interrogate heterogeneous human gut microbiome-related phenomena. In Chapter 2, I design, implement, and characterize a method for embedding co-occurrence patterns derived from massive 16s amplicon datasets. I use this method to 1....
Fission product yields (FPYs) are used for a wide range of applications including nuclear fission theory, nuclear reactor design, reactor antineutrino anomaly, stellar nucleosynthesis, and nuclear forensics. These applications rely on FPYs that were last evaluated in 1993, which included measurements from all over the world up until 1993. In...
In this dissertation I explore the Arms representation and activities for teaching quantum mechanics invented at Oregon State University. In the Arms representation students embody quantum states. The Arms activities are presented as an exemplar of the unique physics classroom culture of the upper-division Paradigms in Physics program. In the...
Immobilized proteins are integral components of a number of important technologies, including the principal component of many biosensors, as functional coatings in various implants, as catalysts is industrial biosynthesis, and as the building blocks of next-generation nanotechnologies. Despite their ubiquity, relatively little is known about the processes that shape immobilized...
Wastewater treatment plants are considered one of the main sources and reservoirs of antimicrobial resistance (AMR). This study investigated the prevalence of 8 different phenotypes of AMR, multi-drug resistant (MDR), and extended-spectrum beta-lactamases (ESBL) producing E. coli in 17 wastewater treatment plants across Oregon in winter and summer of 2019...
Physics sensemaking is a growing topic of study within the physics education community. Many lenses have been used to study sensemaking but few have considered how time and instruction can impact student sensemaking practices and ideas. In this dissertation, I present four studies that address four major questions: What sensemaking...
Modern plant pathology benefits from integrating methods and concepts from evolutionary biology. For example, evolutionary concepts are used to identify and examine species boundaries of plant pathogens, recognize processes underlying pathogen biogeography, identify traits that characterize emerging species, and discover new molecular interactions that originate under processes of selection. In...
Bioenergy is a rapidly growing subsector of the emerging global bioeconomy, with the potential to create a substantial number of jobs and mitigate climate change. In order to develop bioenergy into a viable industry, capable of providing valuable energy and employment, there is an immediate need for a skilled workforce...
Phenylketonuria (PKU) is a genetic inborn metabolic disorder which inhibits the functional production of the enzyme phenylalanine hydroxylase (PAH). It currently affects one in 15,000 Americans and is the most common amino acid metabolism error found in newborns. Individuals affected with PKU are incapable of metabolizing the amino acid, phenylalanine...
Many ecologists and environmental scientists witnessing the scale of current environmental change are becoming increasingly alarmed about how humanity is pushing the boundaries of the Earth’s systems beyond sustainable levels. The world urgently needs global society to redirect itself toward a more sustainable future: one that moves intergenerational equity and...