Digital Commons Network^™

Hypoxic Incubation Chamber, Simone Lisette Helfrich, Makenzie Nicole Jones

Master's Theses

This paper describes the design, manufacturing, and testing of a novel controllable hypoxic incubator with fully functional oxygen gas control and temperature control in a humid environment. On the current market, a majority of the few hypoxic incubators use pre-mixed gas that does not offer precise control over gas concentration. The objective for this project was to create a chamber that allows the user to set the O2 concentration to varying set points of % O2 while maintaining the chamber at a constant body temperature, CO2 level, humidity, and sterility. To start the project, multiple concepts were developed for the …

Quantifying Pain: A Ratio Of Cortisol, Substance P, And Pituitary Adenylate Cyclase-Activating Polypeptide As Biomarkers For Pain In Animal Cruelty And Neglect, Danielle Sherer

Master's Theses

Understanding the relationship between cortisol, Substance P, and PACAP during experienced pain and recovery, as well as the contrast between expression levels and serum levels, will provide an objective measure of pain and suffering to aid in the prosecution of animal cruelty and neglect cases.

There is no consensus at this time as to a recognized biomarker for pain experienced by an animal. Cortisol, Substance P, and Pituitary Adenylate Cyclase-Activating Peptide (PACAP) have been investigated separately in various animal and human studies with regard to stress, pain, and injury. Cortisol is a steroid hormone in the glucocorticoid class that has …

Fabrication Of Thin-Film Composite, Reverse-Osmosis Membranes With Polyethylenimine Modifications For Enhancing Membrane Fouling Resistance, Stephanie N. Hamilton

Master's Theses

Increasing water reuse opportunities for communities has become increasingly important as access to clean water is becoming more scarce. Reverse Osmosis (RO) is an advanced treatment technology used in water recycling wastewater for potable reuse applications. RO is a promising technology; however, the membranes have limitations including their high energy demand and their susceptibility to membrane fouling. The main objective of this study was to develop a reproducible method for the fabrication of RO membranes with enhanced flux and reduced susceptibility to fouling. Literature contains numerous publications on fabrication of thin film composite (TFC) RO membranes with high performance. However, …

Exploring The Role Of Lactobacillus Jensenii And Lactobacillus Mulieris In The Urogenital Tract, Adriana Daniela Ene

Master's Theses

Lactobacillus is a predominant species of the urogenital tract and it has been found in females with and without lower urinary tract symptoms. The Lactobacillus genus is thought to be beneficial to the host due to its capability to produce hydrogen peroxide, secondary metabolites, and lactic acid. L. jensenii is an organism frequently isolated from the urogenital tract. In March 2020, a new sister taxon of L. jensenii was described, L. mulieris. Shortly thereafter we produced a genomic analysis of all publicly available genomes (n = 43) which reclassified some L. jensenii as L. mulieris. This motivated the in-depth study …

Phylogenetic Relationships Among Fishes In The Order Zeiformes Based On Molecular Data From Three Mitochondrial Loci, Lindsay Scarpitta

Master's Theses

The Zeiformes (dories) are mid-water or deep (to 1000 m) marine acanthomorph fishes with a global, circumtropical, and circumtemperate distribution. Some species have a near-worldwide distribution, while others appear to be regional endemics, e.g., near New Zealand. Six families, 16 genera, and 33 species are currently recognized as valid. Relationships among them, however, remain unsettled, especially in light of recent proposals concerning the phylogenetic placement of zeiforms within the Paracanthopterygii rather than allied with beryciforms or percomorphs. The present study uses mtDNA characters to investigate zeiform interrelationships given their revised phylogenetic placement and attendant changes to their close outgroups, carried …

Polyomavirus Jcpyv And Its Role In The Urinary Tract, Rita Lauren Mormando

Master's Theses

Polyomaviruses are the smallest closed-circular supercoiled double-stranded viruses found in the human microbiota. The polyomavirus JC (JCPyV) is most commonly found within the urinary tract, and prior studies estimate that 20-80% of older adults carry JCPyV. In very rare cases, JCPyV leaves the kidneys, causing progressive multifocal leukoencephalopathy. However, the role of JCPyV within the urinary tract remains an open question. In a prior study conducted by our group, the bladder microbiota of females with and without overactive bladder symptoms (OAB) were sequenced. Interestingly, JCPyV was only detected in females with OAB; none of the control (“asymptomatic”) microbiota contained JCPyV. …

The Impacts Of Framework Mutations On Steady-State Kinetics Of An Aldolase Abzyme, Charles Andrew Mettler

Master's Theses

During affinity maturation, antibodies acquire point mutations that lead to enhanced binding strength to a particular ligand while simultaneously becoming more conformationally restricted as they become increasingly complementary to their ligand’s electrostatic geometry. This property has catalytic potential in transition-state (TS) stabilization whereby kinetic barriers (i.e., the energetic gap between the substrate and its TS) are reduced and reaction rates are enhanced. This basic mechanism is thought to underlie the majority of the rate enhancement observed for enzymes. A key integration of antibody binding specificity and strength with enzymatic catalytic strategy is the development of catalytic antibodies (“abzymes”). Abzymes are …

Cataloging And Engineering Temperate Coliphages Of The Human Urinary Microbiome, Elias Crum

Master's Theses

In the US, around 60% of females will be diagnosed with a Urinary Tract Infection (UTI) in their lifetime, and Escherichia coli is the most implicated etiological agent in UTIs. Despite its frequent association with lower urinary tract symptoms, recent studies have found that the urinary microbiome (UMB), the viral, bacterial, and fungal resident members of the urinary tract, of healthy females can also consist of E. coli. While most research has focused on the bacterial constituents of the UMB, bacteriophages, viruses that infect bacteria, are far more abundant. Bacteriophages (phages) of other human microbiomes have been shown to play …

Interplay Between Human Microbiota And Celiac Disease, John James Colgan

Master's Theses

Celiac disease is an autoimmune disorder of the small intestine in which gluten, an energy-storage protein in wheat and other cereals, elicits an immune response leading to villous atrophy. Despite a strong genetic component, the disease arises sporadically over the lifetime leading us to hypothesize the microbiome might be a trigger. Here, we re-examined 16S data from 3 prior studies examining celiac disease and the microbiome with newer computational tools: the dada2 and PICRUSt 2 pipelines. Our results both confirmed findings of previous studies and generated new data regarding the celiac microbiome of India and Mexico. The datasets were also …

Interrogating Antagonistic Differences Among Pseudomonas Aeruginosa Cdia Alleles, Haotian Yang

Master's Theses

Bacteria are complex social organisms that live within mixed communities where microorganisms compete for limited resources. We studied Contact-Dependent Growth Inhibition (CDI), a particular type of competition mediated by a type 5b, or two-partner, secretion system that is widely spread among Gram-negative bacteria. CdiB and CdiA make up the two-partner secretion system that mediates CDI. CdiB translocates CdiA to the cell surface, and CdiA delivers its C-terminal toxin domain to the target cell. The C-terminal toxin (Tox) domain of CdiA is highly diverse. We studied Tox domains of various Pseudomonas aeruginosa clinical isolates. We found different strains that contain unique …

Integrating Current Analyses Of The Breast Cancer Microbiome, Sidra Sohail

Master's Theses

Breast cancer is the leading cause of cancer death for women in the US. Many cancertypes have significant associations with their resident microbial communities - emerging evidence suggests that breast cancers also interact with the local tissue-associated microbiota. Studies have examined the relationship between breast cancer and its microbiome, however, the studies varied in their approaches used to evaluate these relationships. Microbiome research advances rapidly and analysis pipelines and databases are updated frequently. This dynamic environment makes inter-study comparisons and superficial evaluations challenging as no two studies are using the same standards for evaluation. Researchers have observed the microbiota of …

Role Of Tetraspanins In Sars-Cov-2 Fusion And Entry, Marcos Saul Santiago Figueroa

Master's Theses

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for the pandemic the world has been facing in recent years. Even as new countermeasures are developed, there is still much we don’t know in terms of its entry into host cells. Tetraspanins are transmembrane proteins that are near ubiquitous amongst cell types. They fulfill numerous roles, including that of a viral co-receptor. Here, we considered whether tetraspanins, specifically CD9, CD63, and CD81 influence SARS-CoV-2 fusion and entry. Using ACE2-LgBit and tetraspanin overexpressing EVs and HeLa cells, we find that the presence of excess tetraspanins inhibit fusion and entry. However, we …

Migration Across Institutions Of Race: How Immigrant Women From Latin America Construct Ethnoracial Self-Identities In Sending And Receiving Societies, Juanita Vivas Bastidas

Master's Theses

How does immigration affect perceptions of self? In this study, I explore the processes by which immigrants construct ethnoracial self-identities in sending societies, an individual’s country of origin, and receiving societies, an individual’s country of destination. For my exploration, I conduct eleven life history and cognitive interviews of immigrant women from Spanish-speaking countries located in Latin America. Mainly, I find that the women in my study construct ethnoracial self-identities throughout their lives informed by their socialization into myths of racial democracy present in both locations and contradicting interactions, which take place in local organizations such as families, schools, and workplaces. …

Removing Soluble Phosphorus From Tertiary Municipal Wastewater Using Phosphorus- Deprived, Filamentous Microalgae, Aloysia Ahern

Master's Theses

Harmful algal blooms (HABs) can be detrimental to ecosystems, human health, and economies. The low levels of phosphorus remaining in the effluent of municipal wastewater treatment plants can contribute to HAB formation. To achieve more complete phosphorus removal, an effluent treatment method has been proposed that uses phosphorus-deprived, filamentous microalgae to quickly assimilate soluble phosphorus to low concentrations. This study investigated two parameters that influence the feasibility of such a system: (1) the biomass growth productivity of algal cultures during the phosphorus deprivation period and (2) the correlation between the duration of this period and the phosphorus uptake rate by …

An Integrated Approach For Controlling Verticillium Wilt Of Strawberry, Jack T. Koster

Master's Theses

Strawberry (Fragaria x ananassa, Duch.) is an important crop in California, with more than 35,000 acres planted in 2018 resulting in a farm gate value of $3.1 billion. In 2020, California strawberry production accounted for more than 85% of national strawberry production and faces serious threats to production due to various soil-borne diseases. One such disease, Verticillium wilt, is caused by the fungal pathogen Verticillium dahliae and is commonly found in temperate zones around the world where strawberries are grown. Due to the phase-out of efficacious fumigants like methyl bromide, alternative disease management methods have become necessary to …

Determination Of Fungicide Resistance In Botrytis Cinerea On Wine Grapes In California's Central Coast Region, Evelyn Alvarez-Mendoza

Master's Theses

Botrytis bunch rot, caused by Botrytis cinerea, is a fungal disease that primarily affects the fruit of wine grapes. Infection of fruit consequently results in reduced yields and wine quality. These factors lead to significant economic losses for growers which prompts the implementation of management practices to control the disease. One objective of this study was to evaluate the level of resistance that populations of B. cinerea in the Central Coast region showed to various chemicals. A fungicide assay was conducted to determine resistant phenotypes to six fungicide active ingredients (pyrimethanil, iprodione, fenhexamid, fludioxonil, trifloxystrobin, boscalid). Thirty-five (2020) and …

Mechanisms Of Substrate Selectivity And Transport By Escherichia Coli Atp- Binding Cassette (Abc) Transporter Metni, Yuchun Chen

Master's Theses

ABC transporters are central in many cellular functions including nutrient uptake, signal transduction membrane assembly, and cellular detoxification. Both structural and functional studies have revealed insights into the high-affinity uptake mechanism of the MetNI methionine ABC transporter. Using the energy from ATP binding and hydrolysis, the MetNI-Q system can import L-Met, D-Met, and other methionine derivatives against concentration gradients. Many mechanistic studies of ABC transporter propose a model in which cognate binding proteins sequester substrates in the periplasm and deliver them to the transporter. In contrast, recent in vivo and crystallographic studies of MetNI-Q suggest that some substrates may be …

Thermodynamic And Structural Quantification Of Metal Ions Binding To The Antimicrobial Peptide Calcitermin, Sohee Choi

Master's Theses

Over the past several decades the number of antibiotic resistant bacteria has grown dramatically, in part due to the over-prescription of antibiotics. This rise in antibiotic resistance has led to development of novel antibiotics. An attractive alternative to treat bacterial infections may be the use of antimicrobial peptides due their little-known resistance from bacteria. One such peptide is calcitermin (VAIALKAAHYHTHKE), a 15-residue peptide found in human airways. Calcitermin has antimicrobial properties that target Gram-positive bacteria and is most active in acidic buffer (pH 5.4) due to protonation of its three histidine residues, which allows it to interact with the negatively …

Synthesis And Analysis Of Short Antimicrobial Peptides: Rr, Rika Igr, And Hq, Kathleen Pierce

Master's Theses

A significant impending threat to the public health system is the rise of multidrug resistant bacteria. An attractive potential option to combat this is antimicrobial peptides (AMPs). AMPs are peptide chains with lengths that range from 10 to 70 amino acid residues that show antimicrobial activity. AMPs tend to have less toxicity than other antibiotic therapies, have a broader range of activity, and have a decreased resistance development by the target cells. Short AMPs are especially attractive due to their stability as well as their ability to penetrate cell membranes. With a wide range of possible AMPs available, further characterization …

Effects Of Shoreline Development And Freshwater Discharge On Nekton Assemblage And Trophic Structure In A Northern Gulf Of Mexico Estuary, Glenn Schumacher

Master's Theses

Coastal salt marshes support a diversity of nekton and facilitate critical ecosystem functions but are threatened by shoreline development and climate change. Therefore, coastal ecosystem managers have begun incentivizing the use of living shorelines (LS), erosion control structures incorporating native plantings, to mitigate ecological consequences of marsh loss. However, post-restoration climate changes may shift habitat templates and negate positive effects of ecosystem restoration. I evaluated the ecology nekton along LS, natural marshes, hardened shorelines and greyed shorelines within Biloxi Bay, Mississippi, during a high freshwater discharge (HFD) period by comparing nekton assemblage (using species richness, Shannon-Wiener diversity, and relative abundance), …

Investigation Of Dead Ocean Quahogs (Arctica Islandica) Shells On The Mid-Atlantic Bight Continental Shelf, Alyssa Leclaire

Master's Theses

Ocean quahogs, Arctica islandica, are a long-lived, widely dispersed, biomass dominate in the Mid-Atlantic; therefore, quahog shells are valuable resources for studying climate change over time. Recently, dead ocean quahog shells were discovered south and inshore of the present biogeographic range of this animal. The presence of ocean quahog shells outside the current range is presumably a consequence of past regressions and transgressions of the Cold Pool, the bottom-trapped, cool body of water that allows boreal animals to live at lower latitudes. Dead ocean quahog shells were collected offshore of the DelMarVa Peninsula then radiocarbon-dated, evaluated for taphonomic condition, …

A Bioarchaeological Investigation Of The Courtney-Anderson Cemetery, Lauren Scott

Master's Theses

Located in Perry County, Mississippi, the Anderson Family Cemetery represents an abandoned turn-of-the-century Piney Woods cemetery. The cemetery is located on land once owned by the Courtney and Anderson families, who farmed the area until it was taken under eminent domain by the United States government in 1942. The purpose of this thesis is to present three osteobiographies created from human remains and material culture recovered from three graves excavated from within the cemetery in 2022 to explore the lifeways of rural Piney Woods families of Mississippi at the turn-of-the-century.

Among the graves explored, one did not contain evidence of …

Evaluating Traditional And Novel Modalities Of Self-Monitoring In Females With Low-Literacy & Obesity: A Feasibility Study, Anita H. Kelleher

Master's Theses

This study aimed to determine the feasibility of three distinct self-monitoring modalities employed as part of a weight-loss intervention among Spanish- and Mixtec-speaking women with low-no literacy who were overweight or obese (body mass index, BMI> 25). Primary outcomes assessed include self-monitoring adherence, weight, body composition, and diet quality. Participants (n=18) were recruited from the Cal Poly Women and Infants Mobile Health Unit, and contacted if they had a BMI> 25 and did not attend school beyond elementary level (6th grade). Upon enrollment, participants were asked to attend a weekly meeting at which the lifestyle intervention was delivered by a …

Mercury-Mediated Cyclization To 2-Isoxazolines, Abigail Palmer

Master's Theses

The isoxazoline ring has been utilized in many therapeutic agents. For example, it is the key structure in ISO-1, an anti-inflammatory agent with unique anti-Type 1 diabetes activity. There are two primary methods used for the synthesis of isoxazolines: transition metal free cycloadditions and transition metal-mediated cycloadditions and cyclizations. Most transition metal-mediated syntheses employ the use of palladium, gold, silver, or copper complexes as catalysts. The syntheses often require long reaction times and result in low yields with many impurities. In general, mercury-mediated syntheses typically have shorter reaction times and result in products with higher purity. This research investigated the …

Using Portable X-Ray Fluorescence To Predict Physical And Chemical Properties Of California Soils, Micaela D. Frye

Master's Theses

Soil characterization provides the basic information necessary for understanding the physical, chemical, and biological properties of soils. Knowledge about soils can in turn be used to inform management practices, optimize agricultural operations, and ensure the continuation of ecosystem services provided by soils. However, current analytical standards for identifying each distinct property are costly and time-consuming. The optimization of laboratory grade technology for wide scale use is demonstrated by advances in a proximal soil sensing technique known as portable X-ray fluorescence spectrometry (pXRF). pXRF analyzers use high energy Xrays that interact with a sample to cause characteristic reflorescence that can be …

Infidelity And The Bioecological Protective Factors For Mental Health: A Longitudinal Investigation, Lindy Williams

Master's Theses

Infidelity is an important topic of research due to the profound effects on the individual experiencing the trauma. Through the lens of bioecological systems and betrayal trauma, the impact of infidelity on mental health is examined in relation to the most proximal systems to an individual which include personality traits such as agreeableness and neuroticism as well as support from friends, family, and community. This research explores the hypotheses that more support leads to more positive mental health outcomes after the experience of infidelity and the possibility that support from friends, family, and community may buffer specific personality traits and …

Digital Pastoral, Rebecca Holifield

Master's Theses

Digital Pastoral is a collection of original poems and a creative nonfiction essay, accompanied by a critical introduction.

Topo-Climatic Effects Of Fuel Loading In Ponderosa Pine (Pinus Ponderosa) Forests Of The Colorado Rocky Mountains, Justin Yow

Master's Theses

A key restoration focus is the mitigation and prevention of intense wildfires. This is done using a regularly prescribed fire regime and forest thinning practices to reduce surface fuel loads. Prediction of fuel loads at the forest floor is pivotal when assessing the hazard level a forest fire may present. Scientists already have much data correlating fuel characteristics to fire effects and behavior. However, links between montane climate variability and relative effects on fuel load characteristics have not been extensively explored in the Front Range and southwestern Colorado. This study system was uniquely located along a North-South monsoonal gradient and …

Understanding Species Boundaries Between Penstemon Acaulis And Penstemon Yampaensis: Implications For Conservation And Management, Juliet Simpson

Master's Theses

Effective conservation management relies upon accurate taxonomic information and an understanding of the genetic health and population structure for each species. Penstemon acaulis and P. yampaensis are endemic species to Colorado, Utah, and Wyoming, and have been considered for listing under the Endangered Species Act (ESA). There is little biological data published about either and there remains taxonomic uncertainty surrounding the two. Phylogenetic analyses showed P. acaulis and P. yampaensis to be distinct, monophyletic lineages and morphological data further supported taxonomic recognition of both species, however these results did not support the previous species boundaries. Eastern populations of P. acaulis …

Fabrication Of Lab-Scale Polymeric And Silicon Dioxide Nanoparticle-Enabled Thin Film Composite Reverse Osmosis Membranes For Potable Reuse Applications, Timothy J. Dinh

Master's Theses

Reverse osmosis (RO) is widely used for water reclamation and is one of the most feasible technologies for addressing water scarcity around the world. RO membrane fabrication procedures are continually being optimized and modified to enhance the treatment performance and efficacy of the RO process. A review of the existing literature published on membrane fabrication revealed that a detailed and reproducible methodology consistent among prior studies was not available. Therefore, the primary objective of this study was to utilize techniques from prior research to develop a reliable lab-scale membrane fabrication process for studying the potable reuse applications of TFC RO …