Life Sciences Commons^™

Prochlorococcus Death By A Ubiquitous Zooplankton Filter Feeder, Avery E. Harman

University Honors Theses

Prochlorococcus is a globally abundant cyanobacterium that can help reveal the ecology of microorganisms in the ocean. Specifically, mortality by zooplankton such as appendicularians is globally important and Prochlorococcus can help reveal some of the choices made around feeding for this ubiquitous filter feeder. Two ecotypes of Prochlorococcus were introduced to appendicularians to determine if appendicularian feed selectively between these ecotypes. Further, a single ecotype of Prochlorococcus was fed to appendicularians over a variety of life stages to determine if retention rate changed with appendicularian life stage. My results reveal that there is no significant selection between the two Prochlorococcus …

Hell’S Tails: Localizing The Tail Proteins Of The Hyperthermophile-Infecting Virus Ssv1, Jane M. Arterberry

University Honors Theses

The tail of Saccharolobus spindle-shaped virus 1 (SSV1) has long been thought to be composed solely of viral protein 4 (VP4), but recent SSV1 structural studies have implicated the presence of additional structural proteins C166 and B78 in SSV1’s unique tail. The exact locations of these proteins have not been confirmed. Structural proteins VP4 (C-terminus) and B78 are hypothesized to contribute to an adapter region bridging the viral capsid to the tail, whereas C166 is thought to comprise the majority of an internal extended structure, respectively. SSV1 structural proteins lack cysteine residues providing targets to determine their locations in the …

Exploring How Factors Affecting Exercise Adherence May Inform Strategies To Increase Adherence In General And Depressed Populations: A Literature Review, Henry D. Link

University Honors Theses

Background: Exercise is associated with numerous physical and mental health benefits; however, many people struggle to exercise a sufficient amount and thus do not reap the benefits. Exercise is recognized as an effective treatment for depression with few risks. Professionals must understand the factors affecting exercise adherence to assist individuals of different backgrounds with adhering to exercise over the long term and to avoid common pitfalls that could hinder an individual’s progress.

Objective: This literature review aimed to identify factors affecting exercise adherence and to explore how those factors could inform strategies to increase exercise adherence among depressed …

Varecia Rubra (Red Ruffed Lemur) Diel Activity And Calling At Andranobe, Masoala National Park, Madagascar, Hannah Elena Hilden-Reid

Dissertations and Theses

With respect to the natural variation in abiotic and biotic conditions present between daytime and nighttime periods, many animal species show evolutionary adaptations specialized for diurnality, nocturnality, or crepuscularity. Biologists have traditionally viewed categorizations of this kind as fixed within taxonomic groups, emphasizing how intricately species’ survival is contingent on the ability to adapt to low light, high light, or twilight conditions. However, movement away from such distinct temporal niche categories began within chronobiological studies following the discovery of more flexible patterns of activity in numerous taxa during the late 1970s. This shift generated increased interest in elucidating the complex …

Genome Editing Using Crispr-Cas9 In Annual Killifish Species, Keria Moritsugu-Vandehey

University Honors Theses

CRISPR-Cas9 genome editing has been used successfully to knock out genes in model organisms such as zebrafish, turquoise killifish, and cichlid fish. CRISPR-Cas9 genome editing has not been verified in the annual killifish, Austrofundulus limnaeus. We hypothesize that targeted editing of the tyrosinase gene in embryos of A. limnaeus will lead to fish without the ability to produce black pigment. Embryos at the 1-cell stage were injected with a Cas9 cocktail containing a mix of guide RNA molecules that target the genomic sequence of the tyrosinase gene and either an mRNA coding for the Cas9 protein or Cas9 protein. …

Supply Is Not Limulus: Research Review Of Horseshoe Crab Conservation In The Face Of Intense Pharmaceutical Demand, Zoya Galeev

University Honors Theses

Horseshoe crabs are being used by the pharmaceutical industry to conduct endotoxin tests using LAL derived from the organism’s blood to ensure safe medical practice. Their annual collection and bleeding, while not always leading to mortality, affects horseshoe crab behavior and health. This research seeks to understand how the American horseshoe crab, L. polyphemus, is being used by pharmaceutical agencies and the implications that their harvesting has on the industry and the conservation of the species. Studies were collected from the past decade across two databases, Web of Science (WOS) and PubMed, to assess present conservation techniques to reduce …

The Discovery Of Diverse Picophytoplankton Populations In The Columbia And Willamette Rivers Using Flow Cytometry, Kylee Brevick

Chemistry Undergraduate Departmental Honors Theses

As important primary producers, picophytoplankton determine the flow of carbon and energy in aquatic ecosystems. Picocyanobacteria are one picophytoplankton group known to be dominant in oceans and lakes, but they are still poorly understood in river systems. This project examined picophytoplankton communities in two distinct river systems: the Columbia and Willamette Rivers in Portland, Oregon. I aimed to characterize and quantify the picophytoplankton populations in the context of the environmental conditions of the two rivers. I used flow cytometry to detect cells based on their relative size and pigment fluorescence. I sampled nearly weekly for ten months to capture population …

How Beavers (Castor Canadensis) Affect Habitat Availability For Two Native Oregon Turtles: Actinemys Marmorata And Chrysemys Picta Bellii, Rodé Krige

University Honors Theses

Oregon is home to two native freshwater turtle species: the northwestern pond turtle and the western painted turtle. Both turtles are Oregon conservation strategy species with a status rating of sensitive, indicating declining populations. Oregon’s decline in these turtle’s populations is thought to be predominantly due to loss and degradation of habitat that results from development and urbanization. Beavers’ ability to dam streams and create ponds may be creating habitat usable by turtles, but the relationship is under-studied. This study assessed water temperature, basking habitat, and overall turtle habitat suitability at beaver-dammed and control ponds in Portland, Oregon. Average basking …

Using Biometrics, Behavioral Observations, And Multiple Molecular Techniques To Assess The Impacts Of Changes In Temperature And Salinity On The Common Bay Mussel (Mytilus Trossulus), Casey Martin

Dissertations and Theses

The intertidal zone is a place of rapid and frequent change that is home to a variety of creatures who are essential to the integrity of the habitat. Mussels are robust sessile bivalves that anchor to the rocks of the intertidal. The prominent species on the Oregon Coast, the Common Bay Mussel (Mytilus trossulus), plays an essential role as a coastal food source, water column filter, and barrier to prevent erosion due to wave action. Mytilus trossulus withstands daily shifts in temperature, salinity, and tide, as well as seasonal changes. Global climate change due to excess carbon emissions …

The Influence Of Polystyrene Microplastics On Juvenile Steelhead Trout (Oncorhynchus Mykiss), Kaitlyn Marie Baker

Dissertations and Theses

Mass production of plastic within the past decade has led to over 100 billion tons of plastics being added to the world’s oceans through rivers and effluent disposal and decomposition. For marine environments, the sudden and constant growth of microplastics (plastics 1 µm to 5 mm in diameter), is of particular concern to top-predatory fish such as steelhead trout (Oncorhynchus mykiss), who passively or actively uptake microplastics while consuming prey. Previous research has demonstrated clear detrimental impacts of microplastic accumulation in bivalves, seabirds, and zebrafish, including decreased diet, reproduction rates, and metabolism, as well as increased rates of …

Instructors At A Crossroad: Perceptions Of Collaboration And Support Intersect With Intentions To Implement A Cure, Justin Berl

Dissertations and Theses

An ongoing crisis of student drop-off from undergraduate science, technology, engineering and mathematics (STEM) education has led to a sustained call over the last 15+ years for the increased implementation of updated practices in undergraduate STEM education. Though over the past few decades many researchers have developed and analyzed the efficacy of various evidence-based teaching practices (EBTPs) designed to improve the state of undergraduate STEM education throughout the country, the rate at which these EBTPs are implemented in undergraduate STEM classrooms remains low.

In order to better understand the specific factors that affect individual instructors' efforts to implement EBTPs, we …

Resistance To Dna Interstrand Crosslinks In Escherichia Coli Arises Through Prevention Rather Than Repair, Travis Kim Worley

Dissertations and Theses

DNA interstrand crosslinks are particularly lethal lesions that form in DNA when certain molecules intercalate between complementary strands of DNA and form covalent bonds with both strands. Once formed, these lesions present an absolute block to replication and transcription, ultimately resulting in cell death. Because of this lethality, chemicals that form DNA interstrand crosslinks are found in nature as defensive chemicals produced by plants and microbes. Moreover, crosslinking agents have proven effective the treatment of dysplastic conditions and are often first line chemotherapeutics.

However, cancer cells can become resistant to DNA interstrand crosslinks. Unlike other DNA lesions, the double-stranded nature …

Drivers And Dynamics Of Phytoplankton Communities And Harmful Algal Blooms In Mountain Lakes, Lara Stephanie Jansen

Dissertations and Theses

Harmful cyanobacterial blooms (cyanoHABs) are a complex and widespread disturbance in freshwater water bodies, impacting water quality for wildlife and human populations. While cyanobacteria often bloom in warm lakes impacted by human development like agriculture, blooms are increasingly reported in cooler waters with limited development in the surrounding watershed. As much of cyanoHAB research has focused on lakes in highly developed watersheds, the understanding of factors leading to cyanobacteria dominance and blooms in the absence of major development remains limited. Mountain lakes can serve as ideal systems to study bloom-forming cyanobacteria in watersheds with minimal development. In addition, mountain lakes …

Let Kids Sleep: The Role Of Interdisciplinary Neuroscience Outreach In Stimulating Brains And Developing Research-Informed Approaches To Community Concerns, Marc Chenard

University Honors Theses

Northwest Noggin (NW Noggin), an all-volunteer neuroscience education outreach non-profit, serves its community by bringing students, artists, scientists and other participants together for artistic collaboration and learning. The outreach takes place in K-12 schools and other institutions (such as museums, coffee shops and correctional facilities) all over the Pacific Northwest. Neuroscience education outreach generates discourse surrounding community concerns through illuminating the brain-centric qualities of issues and by drawing on neuroscience research to create solutions. The neuroscience research-informed perspectives on these concerns stimulate awareness, create momentum towards evidence-based reform, and can result in policy interventions. This thesis details how NW Noggin …

Pleurotus Spp. As Agents Of Mycoremediation: A Review, Colin Innes

University Honors Theses

Elemental and molecular contaminants of anthropogenic origin represent an increasing threat to virtually all terrestrial and aquatic environments as well as their surrounding atmosphere. The decontamination and restoration of these environments pose a significant and expensive challenge. Although chemical treatment or physical removal of contaminated substrates often is the most direct response to eliminate contaminants, due to the complexity and sensitivity of many natural systems, technologies involving biological remediation can provide viable alternatives. While plant, bacterial, and fungal organisms have the abilities to accumulate or to metabolize toxic compounds, fungal organisms are uniquely suited to do so. Their fast growth …

Resistance Training And Running Performance And Economy: A Literature Review, James Bottrill

University Honors Theses

Running performance is largely determined by maximal oxygen uptake (VO₂ max), velocity at VO₂ max, fractional utilisation of VO₂ max and running economy. Running economy is relatively under-researched and could be improved by resistance training because of its neuromuscular underpinnings. However, existing research on this topic is quite unorganised and inconclusive and is yet to prove a direct linkage between resistance training, running economy and performance. This literature review aimed to provide an organised overview of the existing literature, identify and address confounding variables and provide recommendations for future research. A search for studies was conducted via …

Genetic Considerations For The Conservation Of The Red Junglefowl, Courtney Lee Mcpheron

University Honors Theses

The undomesticated wild populations of our domestic species deserve heightened consideration when it comes to their conservation. Not only do they carry significant socio-cultural and economic roles, but they offer an exceptionally unique case study for population genetics. The red junglefowl (Gallus gallus) of southern and south-eastern Asia is considered to be the living ancestor and progenitor of the domestic chicken. This literature review examines how published research has evaluated its genetic relationship with the chicken and implications for its conservation. A special emphasis is given to the threat of genetic introgression with domestic and feral chicken populations …

A Policy Proposal For Agricultural Data Governance, Ana Sofía Castellanos Santamaría

Dissertations and Theses

As the digital economy continues to grow and data becomes increasingly important, effective data governance is essential. A data governance framework enables the efficient management, sharing, and integration of data, resulting in better decision-making, increased productivity, and enhanced innovation across industries, including agriculture. However, the agricultural sector in the United States is lagging behind other industries in the adoption of effective data governance practices. Agricultural data governance presents a unique set of challenges due to the wide range of stakeholders involved and the ever-increasing volume of data generated by digital technologies in farming. One key challenge to achieving the benefits …

Investigating The Mammillary Bodies As An Early Target Of Alzheimer's Disease, Cole Martinson

University Honors Theses

Alzheimer's disease (AD) is the most common form of dementia. With minimal treatment options and no cure, developing a deeper understanding of the pathology of the disease is crucial. For nearly four decades, the accumulation of beta-amyloid (Aβ) plaques has been correlated with the disease and its progression. Previous studies mapping this accumulation show that the mammillary bodies (MB) are an early target of the disease. Glutamatergic neurons are of key interest due to their prevalence in the central nervous system, specifically the MB. To understand the effects of AD on the glutamatergic system, we used vesicular glutamate transporter 2 …

Investigating The Role Of Holoenzyme C In Restoring Replication Following Uv-Induced Dna Damage In Escherichia Coli, Rahul Shimpi

University Honors Theses

The recovery of replication following UV-induced DNA damage in Escherichia coli correlates with the time at which the lesions are repaired, suggesting that the two processes may be coupled. holC encodes the Chi-subunit of replicative DNA polymerase III, and is nonessential for viability, but renders cells hypersensitive to UV-induced damage when mutated, suggesting it may play a specific role in restoring replication when it encounters DNA damage. Here, I characterized the role of HolC in restoring DNA replication following disruption by UV-induced damage. I found that survival following UV in strains deleted for holC was similar to that of strains …

The Influence Of Microorganisms On Human Health, Tiffany Bui

University Honors Theses

The purpose of this thesis is to explore the interplay between the environment, lifestyle, and composition of human microbiomes across different communities, with a specific focus on immune and digestive health. This literature review investigates three distinct types of communities: isolated/traditional, transitional, and urban/industrialized communities, each characterized by unique environments, societal structures, and interactions. These factors contribute to the distinct microbial populations and compositions within each community. It is impossible to avoid contact with microorganisms as they are present in every aspect of our lives, from the air we breathe, the water we drink, the soil we walk on, the …

An Examination Of The Current Knowledge Of Contaminants In Mangroves: Hawaii And Globally, Geoffrey Szafranski

Environmental Science and Management Professional Master's Project Reports

The geographic range of mangrove forests is shifting quickly as they expand poleward in response to climate change while simultaneously being removed from their native extent to clear space for anthropogenic land-uses. Mangrove forests are also known to be sinks for anthropogenic contamination. Yet contamination research is under-researched in mangrove ecosystems, specifically the environmental fate, effect on biodiversity, and risk to human populations from contamination in the context of these changing conditions requires further research. The goal of this thesis is to address this data gap through analysis of contamination in the literature and through an investigational survey of mangrove …

Management Plan For The Western Painted Turtle At The Sandy River Delta In Troutdale, Oregon, Emma Scott

Environmental Science and Management Professional Master's Project Reports

This management plan has been prepared for the Lower Columbia Estuary Partnership and is intended to provide guidance for the improvement and protection of western painted turtle (Chrysemys picta bellii) habitat at the Sandy River Delta in Troutdale, Oregon. The Sandy River Delta is a 1500-acre natural area situated where the Columbia and Sandy Rivers meet. Its dynamic floodplain habitat supports a diverse assemblage of species, including the western painted turtle, an Oregon Conservation Strategy Species. A small, unknown number of western painted turtles utilize the wetland habitats of the Sandy River Delta, and the frequency in observations …

Comparison Of General Population Vs. U.S. Military Veterans Eating Disorder Prevalence, Micah Callahan

University Honors Theses

Eating disorders disrupt the psychological wellbeing, work ability and daily functioning of many individuals. There is currently no data to compare the prevalence of eating disorders in the general public compared to the military population. The hypothesis was that the military population would be significantly higher in prevalence compared to the general population within the general eating disorder, subcategories of eating disorders and between sex. To analyze the data collected from two studies, sixteen two-proportion Z tests were conducted to determine if the proportions of DSM-V eating disorders differed within and between sex for total incidence and sub-category incidence for …

Urban Nesting Biology, Population Viability And Ecology Of The Willow Flycatcher, Empidonax Traillii, Stephanie Alexandra Byrne Doorly

Dissertations and Theses

Reproductive success, in any species, relies both on the habitat utilized to reproduce and on the successful reproductive output of individual animals within a population. Populations in turn rely on the reproductive fitness of the individual. Whether populations remain stable, grow, or decline ultimately relies on the combined reproductive output of the individuals within that population.

We studied the Willow Flycatcher (Empidonax traillii; henceforth WIFL), a well-studied Neartic-Neotropical migrant passerine whose breeding range extends from the east to west coast of North America. Across much of their range, and in particular in the western regions, breeding population are …

System Design For The Quantification Of Microbial Motility In Extreme Environments, Megan Marie Dubay

Dissertations and Theses

Motility of microorganisms is understudied but provides useful insights into their behavior. Organisms' ability to move autonomously changes how they interact with their environment--finding nutrients, interacting with other organisms, and avoiding unfavorable conditions. Understanding motility features can also be used to identify specific species, such as the identification of Vibrio cholerae in human samples. Motility might also be used as evidence of life existing in even the most extreme environments on Earth, and possibly beyond. Specialized microscopy systems can be required to examine the motility of microorganisms due to the nature of the environments to which the instruments are exposed. …

Post-Fire Erosional And Hydrological Processes Promoting Debris Flow Initiation In A Douglas Fir And Western Hemlock Forest In The Riverside Burn Area, Oregon, Morena Nicole Hammer

Dissertations and Theses

Post-fire debris flows initiated by overland flow in the Pacific Northwest (PNW) are largely undocumented. Instead, debris flows are typically initiated by shallow landslides that result in a mud slurry of water and sediments traveling downhill under the force of gravity. However, because of the Fall 2020 fires in Oregon, the typical initiation style and erosional patterns in burned catchments may have changed because of unusually high burn severity. Due to the intensity of these fires, we set out to determine how hydrologic processes and erosion occurred, when they occurred, and what process was primarily responsible for the erosion that …

Orthotrichum Lyellii As An Active Moss Biomonitor: Examining The Interplay Between Ambient Pm10, Bulk Deposition And Heavy Metals In An Urban Environment, Scott Bradley Kiel

Dissertations and Theses

The importance of monitoring and preventing pollution in the environment is a globally recognized issue. Of the criteria pollutants outlined by the United States Environmental Protection Agency, particulate matter is among these least understood in relation to toxicity and most wide-spread. Many governments have employed continuous air quality monitoring networks to track ambient levels of particulate matter, but are often too widespread to capture the heterogeneity of the urban environment, especially for heavy metal deposition. In Portland, OR, the epiphytic moss Orthotrichum lyellii was successfully used as a low-cost passive biomonitor to increase the spatial resolution of pollution around the …

The Role Of The Gut-Brain Axis In Alzheimer's Disease: A Narrative Review, Leila Karout

University Honors Theses

The importance of the gut microbiome in health has become increasingly recognized as more research points to the strong association between an imbalanced gut microbial composition and a diseased state. Alzheimer's Disease burdens millions, and the rate of growth is expected to increase. However, current treatment methods are less than ideal and do not offer a substantial benefit to patients' quality of life. Additionally, there are gaps in the current understanding of Alzheimer's Disease pathogenesis. Research on the relationship between gut microbiota and neurodegeneration provides a different perspective on the pathogenesis and treatment methods for dementia, such as Alzheimer's Disease. …

The Relationship Between The Gut Microbiome And Sleep Examined Through Associated Human Disease, Jessica Flikkema

University Honors Theses

The crosstalk between the gut microbiome and sleep affects many aspects of human health. This paper looks at metabolic disorders affected by sleep deprivation, sleep disorders affected by the gut microbiome, and other disorders related to both systems. The possible mechanisms of disease are examined for obesity, diabetes, and irritable bowel syndrome as examples of metabolic diseases. Insomnia, narcolepsy, and obstructive sleep apnea as examples of sleep disorders. And hypertension, Alzheimer’s disease, and psychiatric diseases as examples of diseases related to both systems. Understanding of these mechanisms is then used to support probiotics, fecal microbiota transplants, and regulated sleep schedules …