Life Sciences Commons^™

Development Of A Rhizobium Seed Coating To Establish Lupine Species On Reclaimed Minelands, Bridget May Calder

Theses and Dissertations

Symbiotic interactions among various organisms are often necessary for one or both individual's survival. These symbiotic relationships must be considered in restoration projects to allow for the successful establishment of the species. Rhizobia are nitrogen-fixing bacteria found in symbiotic relations with legumes. By utilizing this relationship, restoration practitioners can establish native legume species more successfully while repopulating soil microorganisms into degraded soils. Despite the potential benefits a rhizobium inoculant can have on restoration efforts, minimal research has been done to understand the impacts this treatment has on specific species and the systems they are employed within. Our research goal was …

Qualitative Proteomic And Genomic Analysis Of Klebsiella Pneumoniae Bacteriophage Kaomega, Emilee Carr

Undergraduate Honors Theses

Klebsiella pneumoniae is a Gram-negative Enterobacteriaceae that is a common nosocomial pathogen causing pneumonia, infections in the bloodstream, wound infections, and meningitis. It has developed natural resistance to multiple antibiotics, most notably carbapenems which are often seen as the last line of defense against multi-drug resistant pathogens. Bacteriophages are being investigated as a promising alternative treatment to antibiotics in fighting these resistant pathogens. KaOmega, a Klebsiella pneumoniae bacteriophage, was isolated, sequenced, and annotated to characterize and understand its potential for use in a phage therapy. Characterization included Phyre2 analysis to predict putative protein functions based on structural homology, burst size …

Sequencing The Guts Out Of Covid-19; The Evolution Behind The Covid-19 Pandemic, Madelyn Purnell

Undergraduate Honors Theses

The global COVID-19 pandemic has led to an urgent need for scalable methods for clinical diagnostics and tracking of virus variants. In this paper, we attempted a novel method of sequencing using Large Reverse Transcriptase-based cloning (LRTC). Although our methodology ended up not working due to high amount and fast degradation of RNA, we were able to sequence multiple variants of COVID-19 Positive samples from the BYU Student Health Center and 4 sewage samples to check for variant outbreaks in corresponding times. We were able to find several corresponding variants and track the progression of mutation in our local population.

Introgression Or Incipient Speciation? Using Geometric Morphometrics And Gene Expression To Characterize Mouth Development In Larval June Sucker And Utah Sucker, Peter C. Searle

Theses and Dissertations

Understanding how biodiversity evolves is a major goal in evolutionary developmental biology because changes in developmental processes are tightly linked with evolutionary diversification. Heterochrony--alteration to the rate or timing of development--can significantly alter the appearance of descendant species. Heterochronic shifts in gene expression and associated morphological change may explain the morphological divergence between the threatened June sucker (Chasmistes liorus) and the sympatric Utah sucker (Catostomus ardens) in Utah Lake, UT, USA. June sucker are endemic to Utah Lake and have subterminal mouths adapted for pelagic feeding, while Utah sucker (Catostomus ardens) have ventral mouths adapted for benthic feeding. As larvae, …

Use Of Seed Coating Technologies To Improve Cercocarpus Ledifolius (Curl-Leaf Mountain Mahogany) Seed Germination And Emergence To Reclaim Mine Lands, Emily M. Nielson

Theses and Dissertations

Globally, mining is vital to human interests, but its practice can cause landscape alteration which may look unnatural or engineered. The reintroduction of native plants to these areas is needed to restore the visual appeal and ecological function back into these altered mine lands. Cercocarpus ledifolius (curl-leaf mountain mahogany) is one desirable native species in the Intermountain West that is prized for its potential to grow on step and rocky hillsides and for the habitat it provides for wildlife. Unfortunately, C. ledifolius does not establish well from seed, which has been attributed to seed dormancy. The first objective of this …

Estimating Age In Mule Deer: Accuracy And Influence On Reproduction, Morgan S. Hinton

Theses and Dissertations

Accurate estimates of parameters and demographic rates of wildlife populations are crucial to management and conservation. One parameter of interest is age because it influences multiple demographic rates and behaviors including reproduction, dispersal, migration, and disease transmission. There are a number of methods used to estimate ages of wildlife. One of the most common methods used for mammals is evaluation of patterns in dental eruption and tooth wear. In the first chapter, we evaluate the accuracy associated with estimates of age from dental eruption and patterns of tooth wear for mule deer (Odocoileus hemionus). In the second chapter, we use …

The Effects Of Polymorphisms Of Viral Protein R Of Hiv-1 On The Induction Of Apoptosis In Primary Cells And The Characterization Of Twelve Novel Bacillus Anthracis Bacteriophage, Jacob D. Fairholm

Theses and Dissertations

Viral protein r (Vpr) of Human immunodeficiency virus type 1 (HIV-1) plays an important role in the ability of the virus to infect cells and cause disease. Two polymorphisms to Vpr have been shown to result in differences in disease progression in infected individuals. R36W tends to result in rapid disease progression while R77Q results in long-term non-progression. In order to better understand how these polymorphisms result in these different disease phenotypes, our lab has recently shown that in cell culture, the R36W polymorphism results in increased viral replication and greater induction of cell death. On the other hand, infection …

Anatomical And Biomechanical Factors Related To Running Economy In Uphill And Downhill Running, Mckenna Taylor

Theses and Dissertations

Much is known about running economy while running on level ground surfaces. However, with the dynamic of elevation changes during running, more research is needed to understand how various grades that will favor respective mechanics. PURPOSE: In this study, we focused on determining whether certain running mechanics and anatomy would predict a runner's oxygen uptake between downhill versus uphill running. METHODS: Twenty-one experienced runners completed six 5-min running trials (1 shoe x 3 grades x 2 visits) in a Saucony marathon racing shoe model (Type A) on level (3.83 m/s), uphill (+4% grade at 3.35 m/s), and downhill ( ˆ’4% …

Catharanthine Modulates Mesolimbic Dopamine Transmission: A Potential Treatment For Alcohol Use Disorder, Benjamin M. Williams

Theses and Dissertations

Catharanthine is derived from the Catharanthus roseus plant and is an analog to ibogaine, a drug that reduces opioid and alcohol withdrawal symptoms and decreases drug self-administration in both animals and humans. Catharanthine has promise to be an alternative pharmacological treatment for addiction without the adverse side effects associated with ibogaine. The objective of this study was to evaluate catharanthine’s effects on dopamine (DA) transmission in the mesolimbic DA system as well as determine its effects on both ethanol withdrawal induced anxiety and drug-seeking behaviors in mice. We hypothesized that catharanthine would inhibit evoked DA release in the nucleus accumbens …

A Comprehensive Phylogeny Of Stick And Leaf Insects (Insecta: Phasmatodea) Reveals Widespread Taxonomic Incongruence, Jackson B. Linde

Theses and Dissertations

Stick and leaf insects (Insecta: Phasmatodea) are a mesodiverse order of insects distributed across the world. These masters of masquerade crypsis are riddled with analogous morphological characters and lack a robust taxonomic framework. It seems that convergent evolution and the re-evolution of complex traits like wings and ocelli is perhaps the rule rather than the exception in stick insects. To investigate the re-acquisition of traits in this unique study system, a robust phylogenetic framework is essential. Our analyses combine traditional Sanger data with a transcriptomic backbone to provide the most corroborated phylogenetic analyses to date. To accomplish this, we employ …

Elucidating The Relationship Between Self-Reported Disability And Functional Movement In Individuals With Chronic Low Back Pain, Kelsey Ampudia Clark

Theses and Dissertations

INTRODUCTION: Low back pain (LBP) is often exacerbated by movement and, during functional movements, people with LBP tend to inherently modify their posture and movement patterns to avoid aggravating their pain further. Therefore, analysis of spinal movement in people with LBP is necessary and may lead to the identification of movement-based clusters for optimal treatment. PURPOSE: The overall purpose of this study was to investigate how movement patterns in people with chronic LBP relate to their subjective level of pain-related disability. First, we determined which spinal movements best discriminate between people with chronic LBP and asymptomatic controls; second, we ascertained …

Acceptance Finds A Way: How To Teach And Use Evolution's Explanatory Power, Daniel George Ferguson

Theses and Dissertations

The theory of evolution is the central combing theory that brings together all the tenets of biology that bring about a solid understanding of life. It is also one of the most controversial scientific theories of all time and is widely rejected by about 40% of the general public in the United States. One of the biggest reasons for low evolution acceptance is the perceived conflict between evolution and religious beliefs. Educators and researchers have been working hard to improve how we teach evolution in the classroom; some methods, such as focusing on evolution knowledge, have shown to be mixed. …

Genomic Analysis And Therapeutic Development Of Bacteriophages To Treat Bacterial Infections And Parasitic Infestations, Daniel W. Thompson

Theses and Dissertations

Microbiomes are an extremely vast and complex network of microorganisms. Bacteriophages are a key factor in the microbial health of an ecological system and impact the evolution of pathogenic bacterial strains. Bacteria and the phages that infect them have an intricate relationship due to the dependency on the bacterial host for phage replication, the ability of the phage to lyse and kill its host, and the horizontal gene transfer between the host and phage. This thesis aimed to understand how bacteria and the bacteriophages that infect them impact an ecological system, with a focus on disease states. By analyzing all …

Quantifying Protein Quality To Understand Protein Homeostasis (Supplemental Data), Hsien-Jung Lavender Lin

ScholarsArchive Data

This data set includes the supplementary data for chpaters 3 and 4 in the dissertation Quantifying Protein Quality to Understand Protein Homeostasis. It includes various excel worksheets that were used to generate the data reported in the dissertation. We make this data available to the public so anyone who wants to reproduce the results has the resources and access to other perspectives that weren't discussed in depth in the dissertation. Chapter 3 used mass-spectrometry to quantify the surface accessibility differences in human serum albumin (HSA)between patients with and without rheumatoid arthritis (RA). We found certain residues are less reactive …

Micronutrient Fortified Soymilk Processing Supplemental Data Tables, Michael L. Dunn, Oscar A. Pike, Bradley J. Taylor, Dallin M. Hardy

ScholarsArchive Data

This data set contains Supplemental Tables (created using Microsoft Word) for the following manuscript submitted for publication:

Vitamin stability and sensory acceptability in micronutrient-fortified soymilk prepared by small-scale batch processing

Authors: Dallin M. Hardy, Oscar A. Pike, Bradley J. Taylor, Michael L. Dunn

The above manuscript was prepared with modifications from portions of the M.S. thesis of Dallin M. Hardy, which can be found at: https://scholarsarchive.byu.edu/etd/8284/

The data set includes five supplementary tables containing data values for vitamin retention during processing and sensory acceptance of micronutrient fortified soymilk. The data in these tables had no statistically significant differences between treatments.

Enhanced Force Field Analysis (E-Ffa) Templates, Alisha Redelfs, Leah D. Whigham

Faculty Publications

Evaluation is an essential component of public health practice to understand the reach and impact of a program or the functioning of a system. We propose that Enhanced Force Field Analysis (E-FFA), incorporating strategic planning (force field analysis), participatory approaches, and elements of Appreciative Inquiry, is a powerful and versatile tool for evaluators, program developers, and community organizations to optimize programs, understand systems, or assess innovations. E-FFA can work with large or small groups and is flexible enough to work in many contexts.

These E-FFA printable templates include a facilitator's guide, a participant handout (2 per sheet), and scorecards (8 …

Exploring Melatonin As A Treatment For Oral Ulcers, William H. Sutherland

Undergraduate Honors Theses

The hormone melatonin is best known for its role in the sleep-wake cycle, but its anti-inflammatory and antioxidant effects have significant implications that have not been fully explored in oral health. Some studies use melatonin to treat gastrointestinal ulcers, including duodenal ulcers and oral mucositis, but we found no study reporting its effects on more common oral ulcers, like aphthous stomatitis. We hypothesize that the anti-inflammatory and antioxidant characteristics of melatonin could effectively prevent and heal oral ulcers. In this paper, we review the literature on melatonin to propose its use as a treatment for oral ulcers. We also include …

International Water Quality: Global Patterns Of Water Pollutants And Pathogens, Leslie Lange

Theses and Dissertations

Water quality is an essential component of vibrant societies and ecosystems. For decades, researchers, managers, and policymakers around the world have struggled to accelerate societal progress while preserving and enhancing water quality and human health. This thesis consists of two studies that I hope will contribute to better understanding, policy, and management. In the first study, I evaluated spatial and temporal patterns in global water quality and their relationship to gross domestic product (GDP) per capita, as a metric of socioeconomic development status. Using global water quality datasets containing over 2.7 million observations, I tested the Environmental Kuznet Curve (EKC) …

Two New Late Quaternary Avifaunas From The East-Central Great Basin With The Description Of A New Species Of Falco, Steven D. Emslie, Jim I. Mead

Western North American Naturalist

We report 2 new late Quaternary avifaunas from cave deposits in Snake Valley, White Pine County, eastern Nevada, that provide new records of extinct and extant species in the east-central Great Basin. These avifaunas collectively represent at least 24 species, including the most northern inland record of California Condor (Gymnogyps californianus) in western North America and a new species of kestrel (Falco sp.) described herein. Two extralimital living species also were identified—the Harlequin Duck (Histrionicus histrionicus) and Snowy Owl (Bubo scandiacus)—and are the first fossil records of these species in the Great Basin. …

Amino Acids As Alternatives To Emulsifying Salts In Processed Cheese Analogues, Jeremy Thomas Pack

Theses and Dissertations

Background: Manufacturers have used emulsifying salts universally in the processed cheese industry since James L. Kraft patented the first processed cheese in 1916. My objective was to find alternative ingredients to replace emulsifying salts in processed cheese formulations; the product would follow "clean-labeling" trends and lower the final formulation's sodium content. Materials and Methods: My experiments followed conventional processed cheese formulations to create experimental batches, which were compared to positive and negative controls for significance. Textural, rheological, and melting tests evaluated objective cheese parameters. We observed subjective sensory properties through qualitative descriptive analysis, consumer acceptance panels, and focus groups. Results: …

The Regulation Of Atg9a-Mediated Aggrephagy By An Ulk1-Independent Atg13-Atg101 Complex, Joshua Youngs

Undergraduate Honors Theses

Aggrephagy, a type of autophagy, is an essential cellular process by which protein aggregates are collected and broken down in the lysosome. Protein aggregates are implicated in several diseases including Alzheimer’s disease, diabetes, and cancer. Here, we investigate the ATG13-ATG101 protein complex, a sub-complex of the canonical ULK1 complex whose regulatory role in aggrephagy is not completely understood. We also develop a protein fragment complementation (PFC) assay using the biotin ligase TurboID to study the functions of the ATG13-ATG101 complex with increased specificity. We demonstrate that ATG13 is required for optimal degradation of p62-ubiquitin condensates. We also show that a …

Examining Limbic Sexual Dimorphisms In Schizophrenia, Kennedy S. Madrid

Undergraduate Honors Theses

Schizophrenia is a mental disorder that affects a significant number of individuals in the United States and can have numerous different symptoms. Recently, interest in the differences between the neuroanatomy of individuals with schizophrenia and individuals without schizophrenia has emerged, specifically the sexual dimorphism in individuals with schizophrenia. This study aimed to gain a better understanding of the sexual dimorphisms of two structures in the limbic system: the hippocampus and amygdala. Data was harmonized and analyzed from two datasets to determine the sexual dimorphic factor of these structures in healthy controls and individuals with schizophrenia. Demographic features were also taken …

The Dna Methylation Landscape Of Five Pediatric-Tumor Types, Alyssa C. Parker, Badí I. Quinteros, Stephen Piccolo

Faculty Publications

Fewer DNA mutations have been identified in pediatric tumors than in adult tumors, suggesting that alternative tumorigenic mechanisms, including aberrant DNA methylation, may play a prominent role. In one epigenetic process of regulating gene expression, methyl groups are attached at the 5-carbon of the cytosine ring, leading to 5-methylcytosine (5mC). In somatic cells, 5mC occurs mostly in CpG islands, which are often within promoter regions. In Wilms tumors and acute myeloid leukemias, increased levels of epigenetic silencing have been associated with worse patient outcomes. However, to date, researchers have studied methylation primarily in adult tumors and for specific genes—but not …

Isothermal Inactivation Studies Of Listeria Monocytogenes, Salmonella, And Enterococcus Faecium Nrrl B-2354 In Almond, Peanut, And Sunflower Butters, Ruo Fen Liao

Theses and Dissertations

Vegetative, non-sporeforming foodborne pathogens show notable survival and uncanny thermotolerance in low water activity (aw) foods. Controlled studies on Listeria monocytogenes, Salmonella spp., and Enterococcus faecium NRRL B-2354 (a Salmonella surrogate) in a variety of food matrices support thermal process validation studies required to achieve global food safety objectives. In this study, we determined and compared thermal inactivation rates using independent six-strain cocktails of pathogens in three plant-based butters. Direct determinations of decimal reduction times (D-values) for L. monocytogenes, Salmonella, and E. faecium, in corresponding butters were inoculated using peanut oil, almond oil, or sunflower oil. Thermal Death Time (TDT) …

Climate Change And The Global Nutrient Overload: The Microbial Response Of Extreme Waterbodies To Environmental Change, Samuel P. Bratsman

Theses and Dissertations

One of the defining characteristics of our current epoch—the Anthropocene—is modification of nutrient cycles. At regional to global scales, humans have fundamentally reshaped the availability of carbon, nitrogen, and phosphorus. These changes are particularly apparent in freshwater ecosystems, which receive surface and groundwater inputs of nutrients from agriculture, fossil fuel use, and wastewater. In this thesis, I investigated how the addition of nutrients affects microbial community and biogeochemistry in two extreme environments: the hypereutrophic shallow Utah Lake and nutrient-limited Arctic permafrost streams. In my first chapter, I used bioassay and dilution bioassay experiments to identify what factors control harmful algal …

Relationships Among Aa-Genome Chenopodium Diploids And A Whole-Genome Assembly Of The North American Species, C. Watsonii, Lauren Amillicent Young

Theses and Dissertations

Chenopodium quinoa Willd., an ancient Andean pseudocereal almost exclusively consumed in South America, jumped onto the global stage when Western cultures noted quinoa's advantageous nutritional profile. Quinoa seed's high protein content, nutritionally balanced amino acid profile, low glycemic index, and high fiber, vitamin, and mineral content, make it a highly sought-after 'superfood'. Pitseed goosefoot (C. berlandieri Moq.), a closely related North American species sharing quinoa's genome composition (AABB), grows across the North American continent, inhabiting diverse environments including the saline coastal soils of the Gulf of Texas and the drought-prone regions of the Southwest. Quinoa and pitseed goosefoot, along with …

The Default Network And Autism Spectrum Disorder: Characterizing Sub-Networks And Behavioral Correlates, Alyssa K. Kozlowski

Theses and Dissertations

The default network (DN), and specifically its sub-networks default network A (DN A) and default network B (DN B), has been strongly implicated in social cognition. This study examined its role in predicting social behavior, and also differences that may exist across diagnostic groups that may explain discrepancies in social cognition and behavior. One of the popular methods of study is functional connectivity, or analyzing correlated activity in the brain. Autism Spectrum Disorder (ASD) is a disorder characterized by social impairment and abnormal social behavior. To date, much of the functional connectivity research in ASD has focused on global connectivity, …

Mapping Auditory And Vestibular Response Neurons In The Optic Tectum Of Larval Zebrafish, Erika Marks, Arminda Suli

Undergraduate Honors Theses

Cellular mapping of the sensory receptive fields of brain structures is a critical step in understanding function and dysfunction in development. Deficits in the ability to receive, process and integrate the senses leads to difficulties recognizing and responding appropriately to stimuli. To understand how the senses are integrated, it is first necessary to map the neurons receptive to inputs from individual senses. The optic tectum of zebrafish is a structure known for its homology to the superior colliculus of mammals and is a center of multisensory integration – including visual, auditory, and somatosensory stimuli. However, the microcircuitry of this important …

The Power-Duration Relationship Is Just As Reproducible In Females As Males, Despite The Presence Of The Menstrual Cycle, Jessica Joy Linde

Theses and Dissertations

PURPOSE: To investigate the effect of the menstrual cycle (MC) on exercise performance across the power-duration relationship (PDR). We hypothesized females would exhibit greater variability in the PDR across the MC than males across a similar timespan, with critical power (PCRIT) and Work prime (W') being lower during the early follicular phase than the late follicular and mid-luteal phases. METHODS: Eumenorrheic, endurance-trained females (n = 10, age = 24.1 ± 5.59) performed multiple constant-load-to-task-failure and maximum-power tests at three time points across the MC (early follicular, late follicular, midluteal phases). Endurance-trained males (n = 10 age = 29.5 ± 9.18) …

Biophysical Factors Control Invasive Grass Hot Spots In The Mojave Desert, Tanner Corless Smith

Theses and Dissertations

The social, economic, and ecological costs of plant invasions are vast, through their ability to alter ecosystem structure and function. Invasive annual grasses are a nuisance in the American Southwest through promotion of the grass-fire cycle. Annual grasses such as Bromus rubens, Bromus tectorum, Schismus barbatus, and Schismus arabicus have invaded the Mojave Desert and increased fire occurrence, thus it is important to identify and characterize the areas where persistent invasion has occurred and subsequently fire risk is increased by understanding the distribution of these invasive grasses. Previous plot and landscape-scale research has revealed anthropogenic and biophysical correlates with the …