Digital Commons Network^™

Fxr Agonists Induce Distinct H-12 Structural States, Vikash Kumar

Graduate Student Theses, Dissertations, & Professional Papers

The nuclear receptor ligand-binding domain (LBD) is a highly dynamic entity. The FXR LBD shows multiple low-energy conformational states of the activation function-2 (AF-2) coregulator binding surface upon ligand binding, indicating the complexity of FXR activation. However, it is unknown how ligand binding leads to different conformational states within the AF-2 region centered on helix 12 (H-12) of the LBD. Here we observe the conformation of the coregulator binding surface (H-12 specifically) of FXR upon ligand binding in solution using fluorine-19 (19F) nuclear magnetic resonance (NMR) and simulations of this surface using molecular dynamics. Fluorescence anisotropy of fluorescein-labeled coregulator peptides …

Investigations On Novel Cyp26a1/B1 Inhibitor, Dx308: Using Atra Response As A Theraputic Target For Traumatic Brain Injury And Parkinson’S Disease, Jacob Morgan Leatherwood

Graduate Student Theses, Dissertations, & Professional Papers

Neurodegenerative diseases (NDs) take a wide spectrum of pathologies and have a tendency to present themselves later in life. Neurodegenerative diseases affect 6 million Americans annually with ~1 million currently living with Parkinson’s disease (PD). One of the greatest contributors to the pathogenesis of neurodegenerative diseases is the occurrence of a traumatic brain injury (TBI) during life.

All-trans-retinoic acid (atRA) is the active metabolite of Vitamin A. The retinoic acid pathway is known to be activated following TBI and is reduced in PD patients. Previous studies found a decrease in inflammation and behavioral deficits following administration of Vitamin …

Species Selection And Plantation Management In Enrichment Planting With Native Timber Species In The Panama Canal Watershed, Abigail A. Marshall

Graduate Student Theses, Dissertations, & Professional Papers

Large areas of the Panama Canal Watershed have been converted to monocultures of teak (Tectonia grandis), a non-native timber species that is generally not providing hoped-for economic and ecological benefits of Forest Landscape Restoration. Enrichment planting offers a potential strategy for revitalizing these underperforming plantations through the addition of high-value, native species to the understory, but more information is needed to guide implementation and management in this region and other tropical areas. I assessed the performance of six promising native species (B. crassifolia, D. retusa, D. oleifera, H. alchorneoides, P. pinnatum, T. amazonia) as an enrichment …

Towards Evidence-Based And Data-Driven Recommendations Promoting Independence In Later Life: Gait Speed, Falls, And Activities Of Daily Living In Older Adults, Claire Elaine Adam

Graduate Student Theses, Dissertations, & Professional Papers

Background: Falls in older adults are a significant public health challenge. Fall prevention as well as intervention after a fall both are critical to reduce the negative consequences and improve quality of life in older age.

Purpose: 1) Quantify the association between gait speed and fall risk in a cross-sectional analysis for older adults with and without cognitive impairment. 2) Determine if there is an association between change in gait speed and fall risk in a longitudinal analysis including older adults with and without cognitive impairment. 3) Quantify the association between falls and difficulty with activities of daily …

A Reintroduction Retrospective: Comparative Fisher (Pekania Pennanti) Survival And Prey Habitat Use In The Cascade Mountains Of Washington State, Tanner S.T. Humphries

Graduate Student Theses, Dissertations, & Professional Papers

Increasing human impacts on biodiversity highlight the global need for ecological restoration. For many wildlife species, reintroduction is necessary to re-establish populations in parts of their historic range where they have been extirpated. Reintroduction efforts are commonly used to help restore ecosystem integrity, but are often expensive, time consuming, and unsuccessful at generating self-sustaining populations. Thus, a more complete understanding of the factors affecting restoration success is important for ensuring successful outcomes and responsible stewardship. Fishers (Pekania pennanti) are one of the most commonly reintroduced carnivores in North America, but the success of such efforts is highly variable, …

A Moral Influenza: An Historical Archaeological Investigation Of The Prohibition Era In The United States 1920-1933, Kelli Michele Casias

Graduate Student Theses, Dissertations, & Professional Papers

The following exploration of National Alcohol Prohibition in the United States employs an interdisciplinary approach to understand the impetus of the large-scale defiance of liquor laws and to identify the physical manifestations of the social process of mass resistance in the archaeological record. Historical documentation, newspaper publications, oral histories, landscape analysis of road development in Montana, and an archaeological survey of a mountain homestead site where manufacturer of illicit alcohol took place are used to contextualize the Prohibition Era from the perspective of the offender. The research goals of this work are varied and include documentation of the archaeological footprint …

Benthic Invertebrate Paleontology Of The Late Mississippian (Serpukhovian) Bear Gulch Limestone, Central Montana, Amy Elizabeth Singer

Graduate Student Theses, Dissertations, & Professional Papers

The Bear Gulch Limestone of the late Mississippian central Montana is a significant Konservat Lagerstätte known and a part of one of the most complete mid-Carboniferous stratigraphic sections in the world. Despite containing a well-described fish fauna, the most diverse and abundant Carboniferous fish fauna known, nothing was known of the invertebrate assemblages, and many aspects of the geology remained enigmatic. With few rocks of this age available for study worldwide, the Bear Gulch Limestone contains an important record of life and Earth history near the Pennsylvanian boundary, a time of climatic change.

Using new outcrop data combined with subsurface …

Adult Perspectives Of Kaleidoscope Connect: A Social Emotional Program Aimed At Promoting Resilience Among Youth, Samantha Cody Russell

Graduate Student Theses, Dissertations, & Professional Papers

Purpose. The current study explored the perspectives of adults who participate in Kaleidoscope Connect, and specifically, to understand how effective adults perceive the program in its attempt to promote resilience, school safety, and the psychological well-being of youth.

Background. Youth who encounter stressful life circumstances or experience trauma often experience negative life outcomes, such as lower academic achievement, mental illness, and perpetrating violence (Liu, Reed & Girard, 2016). Research, however, has demonstrated that some youth who have these experiences have more positive outcomes, including psychological health, strong academic achievement, and financial stability (Zolkoski & Bullock, 2012). Resilience is a dynamic …

Transboundary Marine Management In The Sulu-Sulawesi Seascape, Lindsey G. Ellett

Graduate Student Theses, Dissertations, & Professional Papers

Transboundary conservation aims to facilitate environmental conservation and management at the ecosystem level by operating across political boundaries, through the cooperation of two or more countries. Though there is increased interest and advocation for transboundary conservation initiatives around the world, there remains a limited understanding of how they function on-the-ground. Within this study, I address these gaps in knowledge through two phases of research, both focusing on the Sulu-Sulawesi Seascape as a case study site. Phase I involved a policy analysis of Indonesian, Malaysia, and Philippine policies related to fisheries, coastal zones and protected areas, and environmental quality. Through this …

Conservation And Conversation In The Anthropocene, Brittany Alyse Garner

Graduate Student Theses, Dissertations, & Professional Papers

The driving questions of this dissertation consider both the scientific and communicative understanding of conservation and extinction in the Anthropocene. Overall, this dissertation portfolio explores this topic via genetic and genomic data, international policy, big data analytics, human values, and the performing arts. Chapter 1 analyzes the use of genetics and genomics in conservation, finding multiple case studies within and outside of peer-reviewed journals. Chapters 2 and 3 quantify and describe the use of genetic principles and tools in a global species extinction risk assessment, the IUCN Red List, and finds low overall use but high potential for genetics to …

Fun Ctional Implications Of Dual Transmitting Neurons On Aggression, Lewis Michael Sherer Ii

Graduate Student Theses, Dissertations, & Professional Papers

No abstract provided.

The Effect Of Test Difficulty On Perceived Memory Performance, Phoebe S. Bean

Graduate Student Theses, Dissertations, & Professional Papers

Neuropsychological testing is a critical element of the assessment and treatment of a host of neurological disorders, such as Alzheimer’s Disease, stroke, and traumatic brain injury. Certain non-neurological variables may also affect an individual’s test performance. Such secondary factors may include current psychiatric issues, chronic pain, sleep, and the effort put forth during testing. Little is known, however, about the effect the testing process itself has on people’s actual and perceived cognitive abilities. For example, the process of undergoing memory testing may, through a variety of mechanisms, influence memory performance and impact the person such that their view of their …

Characterization Of Nucleocapsid-Rna Interactions In Rift Valley Fever Virus Infection, Miyuki Hayashi

Graduate Student Theses, Dissertations, & Professional Papers

Rift Valley fever virus (RVFV) is a mosquito-borne virus that infects humans and livestock and exhibits potential for global spread. No vaccine or treatment is currently available for human use. The nucleocapsid protein (N) in RVFV is a multifunctional RNA-binding protein that is necessary for viral replication and dissemination. Because of its essential roles, N is a promising candidate to be targeted for anti-RVFV therapy. The goal of this dissertation is to characterize N-RNA interactions in RVFV infected cells. To achieve this goal, two methods, strand-specific reverse transcription and quantitative PCR (RT-qPCR) as well as multiple reaction monitoring mass spectrometry …

Generation, Characterization, And C-H Bond Activation Reactivity By Mononuclear High-Valent Cobalt(Iv) And Nickel(Iv) Non-Oxo Complexes, Yubin Maria Kwon

Graduate Student Theses, Dissertations, & Professional Papers

The study of terminal high-valent transition metal-oxo complexes has increased significantly over the years as it is believed that they are key reactive intermediates for a wide range of biological and industrial catalytic processes. These complexes are powerful oxidants for the activation of strong C-H bonds. The chemical and physical properties of these complexes remain elusive. It is therefore desirable to study the properties and function of these complexes through synthetic models. There have been many efforts and reports of synthetic high-valent metal-oxo complexes of early and middle transition metals (up to group 8 on the Periodic Table of Elements), …

Management And Conservation Of Westslope Cutthroat Trout In An Impacted, Connected River System, Troy Weant Smith

Graduate Student Theses, Dissertations, & Professional Papers

Westslope cutthroat trout Oncorhynchus clarkii lewisi (WCT) is a native species of high conservation value that historically exhibited partially migratory behavior throughout its range. Long-term persistence of WCT is threatened by human habitat modification, fragmentation, introduction of non-native species, and hybridization. As a result of these changes, remnant populations in Montana have shifted toward resident populations in headwater systems and away from migratory populations in larger connected river networks. This is compounded by the historic introduction of rainbow trout O. mykiss (RBT) that hybridize with WCT, especially in larger river habitats. Rock Creek in western Montana, USA was historically managed …

Policy And Collaborative Governance: Case Studies Of Three Wildlife Crossings, Nicholas Maya

Graduate Student Theses, Dissertations, & Professional Papers

Over the last several decades, the number of wildlife-vehicle collisions in North America has significantly increased, driving substantial loss of human life and wildlife and economic costs. The most effective wildlife-vehicle collision mitigation is wildlife crossing structures (undercrossings and overcrossings), with some studies suggesting they can reduce wildlife-vehicle collisions by 97% when paired with wildlife exclusion fencing. However, cost, funding, jurisdiction, land ownership, and local support are limiting factors in constructing these crossing structures. This paper presents case studies of three crossing projects in Snoqualmie, Washington, Teton County, Wyoming, and Summit County, Colorado, to illustrate the similarities and differences in …

Wildlife-Friendly Fence Policy On Federal Public Lands Managed By The U.S. Forest Service And Bureau Of Land Management, Joshua D. Elliott

Graduate Student Theses, Dissertations, & Professional Papers

Many wildlife species are negatively impacted by the presence of fences on the landscape. Climate change is only exacerbating the problem as home ranges shift and species face heightened levels of stress. In recent decades, wildlife biologists have studied these impacts and devised ways of constructing fences to increase habitat connectivity and significantly reduce fence-related injury and mortality rates. Conservationists attempting to address this issue on a landscape level face significant challenges resulting from complex land ownership patterns, specifically across the western United States.

The two largest landowners in the U.S. are the Bureau of Land Management (BLM) and the …

Sustainability In A Changing Landscape: Identifying The Effects Of Land Use On Vegetation And Mammal Communities, Christopher Paul Hansen

Graduate Student Theses, Dissertations, & Professional Papers

Increases in habitat loss and fragmentation from anthropogenic disturbance present substantial threats to global biodiversity; thus, sustainable land management will be crucial to support current and future generations of humans and wildlife. In the western United States, approximately 70% of the land is grazed by domestic cows (i.e., “cattle”), and urban development is increasing rapidly. These land uses may affect vegetation composition and mammal communities, which could alter ecosystem function through bottom-up or top-down processes. Therefore, understanding the responses of vegetation and mammal communities to these practices is important when considering socio-ecological sustainability.

In this dissertation, I evaluated how cattle …

Using Formulation To Unlock Vaccine Adjuvant Efficacy For Toll-Like And C-Type Lectin Receptor Agonsts, Kristopher Kenneth Short

Graduate Student Theses, Dissertations, & Professional Papers

Ligands for pattern recognition receptors (PRRs) have been isolated or synthesized for use as adjuvants in order to improve the magnitude and quality of the immune response of vaccines. In particular, basic research of toll-like receptor (TLR) and C-type lectin receptor (CLR) families has culminated in the production of novel ligands with agonist activity. To use these PRR agonists as vaccine adjuvants, it is necessary to properly formulate them in delivery systems to unlock their agonist activity. The objective of this work was to develop liposomal and oil-in-water (O/W) emulsion formulations for TLR4 and TLR7/8 agonists and to develop O/W …

Monitoring The Wetland Landscape: White-Faced Ibis (Plegadis Chihi) Breeding Habitat As A Model Assemblage, Shea P. Coons

Graduate Student Theses, Dissertations, & Professional Papers

Wetlands structure landscape biodiversity by providing critical habitat to numerous fish and wildlife species. However, climate change, growing human populations, and shifting land use practices strain limited water supplies that sustain wetlands in the semi-arid western US. Conserving a wetland network with prominent value to wildlife is paramount to ensure future security of habitat and ecosystem processes. Here, I use white-faced ibis (Plegadis chihi; hereafter ‘ibis’) breeding colonies as a model system to identify and monitor a landscape-scale wetland network across the semi-arid western US. Ibis serve an important role in marking ecologically important wetland networks because they require a …

Ensemble Protein Inference Evaluation, Kyle Lee Lucke

Graduate Student Theses, Dissertations, & Professional Papers

The Protein inference problem is becoming an increasingly important tool that aids in the characterization of complex proteomes and analysis of complex protein samples. In bottom-up shotgun proteomics experiments the metrics for evaluation (like AUC and calibration error) are based on an often imperfect target-decoy database. These metrics make the inherent assumption that all of the proteins in the target set are present in the sample being analyzed. In general, this is not the case, they are typically a mix of present and absent proteins. To objectively evaluate inference methods, protein standard datasets are used. These datasets are special in …

Transient Tertiary Interactions And Persistence Of Interhelical Turns In The Denatured State Of A Helical Protein, Dustin Corey Becht

Graduate Student Theses, Dissertations, & Professional Papers

Protein folding is the natural process through which a linear polypeptide, originally encoded by a gene, adopts a distinct, three-dimensional structure capable of biological function. Over the last several decades, the denatured state ensemble (DSE), one of the two major populations adopted by a protein along with the native state, has been a topic of interest. Classically, the DSE has been interpreted as a collection of random-coil conformations devoid of any structural features. However, numerous studies have demonstrated that residual structure persists in the denatured state of proteins and may dictate the earliest stages of the protein folding process. Characterization …

Concentration And Composition Of Nanoparticles And Colloidal Particles In A Mine-Waste Contaminated River, Kaitlin Rose Perkins

Graduate Student Theses, Dissertations, & Professional Papers

Metals and metalloids (metal(loid)s) in aquatic ecosystems are often described through measures of their concentrations in whole and filtered waters. The filtered fraction is operationally defined as “dissolved,” and assumed to be primarily composed of free metal(loid) ions or of ions bound by low molecular weight organic matter. This definition ignores that the dissolved fraction also likely contains colloidal particles (1 to 1000 nm) that can pass through commonly used filters. This colloidal fraction can also be preferentially removed from the water column by algae and other aquatic organisms compared to free metal(loid) ions and organic bound metal(loid)s. Though they …

Tropical Plant-Animal Interactions: Linking Defaunation With Seed Predation, And Resource-Dependent Co-Occurrence, Peter Jeffrey Williams

Graduate Student Theses, Dissertations, & Professional Papers

Plant-consumer interactions can be critical for regulating populations of both plants and animals. In the tropics, many trees rely on animals to disperse their seeds, but many of these dispersers are disappearing, with potentially disastrous consequences for tropical tree species and global carbon storage. Defaunation—the loss of large animals due to factors such as overhunting—can also affect seed fates, either by increasing or decreasing seed predation. We know that defaunation alters these plant-animal interactions, but we still do not know how these changes at early life stages will ultimately affect tropical tree populations. Furthermore, we do not understand how defaunation …

The Impacts Of Integrating Interdisciplinary, Introductory Computer Science In High School Courses, Jan Roddy

Graduate Student Theses, Dissertations, & Professional Papers

No abstract provided.

All In Due Time: Multi-Trait Assessment Of Elk Acclimation To Translocation, Ellen Marie Pero

Graduate Student Theses, Dissertations, & Professional Papers

Wildlife translocation – the intentional movement of animals – is a crucial conservation tool for restoring species and halting global biodiversity decline. However, this practice is challenging for wildlife, and animals must adjust to their release landscapes for restoration to be successful. The period following release is a vulnerable time for translocated wildlife and determining when and how animals eventually acclimate following releases allows researchers to efficiently tailor post-release management to each species’ needs, thus maximizing the success of translocations while minimizing costs of an already expensive conservation practice. In this dissertation, I investigate changes in the physiological, behavioral, and …

Collaborative Conservation And Backcountry Weed Control: A Case Study Of The Great Burn Proposed Wilderness, Christopher James Prange

Graduate Student Theses, Dissertations, & Professional Papers

Noxious weeds have become a management priority on public lands in the United States. Managing invasive weed populations in natural areas with complex ecosystems presents issues that need a systems-wide approach over long temporal and spatial scales. This broad-scale problem increasingly demands collaborative efforts. While collaborative conservation has become a tool in natural resource management during the 21^st century, it is less commonly applied in weed control in backcountry wilderness areas. Programs that have been initiated are understudied. Accordingly, this research was conducted through semi-structured interviews to gather perspectives of weed professionals involved in a collaborative backcountry weed program …

Evaluating The Effectiveness Of A Transgender-Affirmative Care Training On Healthcare Workers’ And Trainees’ Attitudes Toward And Knowledge Of Routine Care And Transition Support For Transgender Individuals, Oakleigh Marshall Reed

Graduate Student Theses, Dissertations, & Professional Papers

Objectives: Transgender individuals, often highly stigmatized and discriminated against, face challenging barriers regarding seeking routine- and transition-related physical and mental health care (James et al., 2016). What has been consistent throughout time is that contact as an intervention (i.e., personal contact, contact with educational materials, and/or contact with general media outlets) has been found to be associated with improved attitudes toward and knowledge of marginalized communities (Braun et al., 2017; Click et al., 2019; Reed, 2018; Stroumsa et al., 2019). The aim of the current study was to explore the impact contact with a transgender-affirmative care training may have on …

Ecotoxicological And Physiological Effects Of Salinity On Amphibians, Brian James Tornabene

Graduate Student Theses, Dissertations, & Professional Papers

Salinity is a persistent anthropogenic contaminant that negatively effects freshwater species, communities, and ecosystems. High-salinity wastewaters from energy extraction (wastewaters) and road salts are major contributors to increased salinity (NaCl; sodium chloride), but most studies focus on effects of NaCl roads salts. Amphibians are particularly vulnerable to contaminants such as increased salinity because of their porous skin, dependence on freshwater, and poor osmoregulatory capacity. We investigated the relative effects of wastewaters and NaCl on three species of larval amphibians with acute toxicity experiments (Chapter 1). Effects of wastewaters on larvae were predominantly due to high concentrations of NaCl and both …

Uncovering Cooperation In Housepit 54, Bridge River, British Columbia, Canada, Megan Denis

Graduate Student Theses, Dissertations, & Professional Papers

There is a significant amount of literature regarding the theory of cooperation, as well as ethnographies and data from modern populations that clearly show cooperation, yet it is difficult to tease that information out of the archaeological record. My thesis will focus on floors IIi to IIc of Bridge River’s Housepit 54 in British Columbia, Canada, which extends from the Bridge River 2 period to the Bridge River 3 period and includes two incidents of resource stress and one of resource plenty. These times of fluctuating resource availability should result in the population utilizing different approaches to social organization. By …