Life Sciences Commons^™

Computational Analysis Of Antibody Binding Mechanisms To The Omicron Rbd Of Sars-Cov-2 Spike Protein: Identification Of Epitopes And Hotspots For Developing Effective Therapeutic Strategies, Mohammed Alshahrani

Computational and Data Sciences (PhD) Dissertations

The advent of the Omicron strain of SARS-CoV-2 has elicited apprehension regarding its potential influence on the effectiveness of current vaccines and antibody treatments. The present investigation involved the implementation of mutational scanning analyses to examine the impact of Omicron mutations on the binding affinity of four categories of antibodies that target the Omicron receptor binding domain (RBD) of the Spike protein. The study demonstrates that the Omicron variant harbors 23 unique mutations across the RBD regions I, II, III, and IV. Of these mutations, seven are shared between RBD regions I and II, while three are shared among RBD …

Trophic Assessment Of The Invasive Hydrozoan Gonionemus Vertens Using Stable Isotope Analysis : You Are What You Eat, Diana Sisk-Gritz

Theses, Dissertations and Culminating Projects

Gonionemus vertens, commonly known as the clinging jellyfish, is a small hydrozoan known for their conflicts with humans due to their neurotoxins that can lead to paralysis. Native to the Pacific Ocean, it has now invaded numerous ecosystems in the coastal waters of the Mediterranean Sea, Europe, and the United States. In the United States, it has flourishing populations from New Jersey to Maine. However, many questions remain as to how it arrived and spread, but equally important is what impact this species may have in the invaded communities they now reside. Research suggests that G. vertens actively feeds on …

Assessing The General Public's View Of Direct-To-Consumer (Dtc) Genetic Testing And Their Interpretation Of Dtc Website Disclaimer Messages., Madison Ruehl, Shelly Hovick, Alisdair Philp, Kevin Sweet

Medical Education Articles

The general public continues to show increased interest and uptake of Direct-to-Consumer (DTC) genetic testing. We conducted an online survey (N = 405) to assess genetics knowledge, interest, and outcome expectancy of DTC genetic testing before and after exposure to a sample DTC disclaimer message. Descriptive statistics were used to analyze the relationship between previous genetic knowledge, attitudes and self-reported systematic processing of a sample DTC disclaimer message, outcome expectancies, and interest to pursue DTC genetic testing. Increased genetic knowledge and more positive attitudes towards DTC genetic testing were associated with increased self-reported systematic processing of the DTC disclaimer message. …

Investigation Of Orthohantavirus Genetics In Rodent Reservoirs And Clinical Samples, Samuel Melvin Goodfellow

Biomedical Sciences ETDs

Orthohantaviruses are negative-sense, single stranded RNA viruses with trisegmented genomes that can cause severe disease in humans and are carried by several host reservoirs throughout the world. In the United States, Sin Nombre orthohantavirus (SNV) is the primary cause of hantavirus cardiopulmonary syndrome (HCPS) with a fatality rate of ~36% and the highest cases occuring in the southwest region. The primary SNV host reservoir is thought to be the western deer mouse, Peromyscus maniculatus, however it has been shown that other rodents can carry different orthohantaviruses. We designed a pan-orthohantavirus detection tool to survey several small mammal populations throughout New …

Proceedings Of The 2023 Berry Summer Thesis Institute, University Of Dayton. University Honors Program

Proceedings of the Berry Summer Thesis Institute (2013-Present)

Thanks to a gift from the Berry Family Foundation and the Berry family, the University Honors Program launched the Berry Summer Thesis Institute in 2012. The institute introduces students in the University Honors Program to intensive research, scholarship opportunities and professional development. Each student pursues a 12-week summer thesis research project under the guidance of a UD faculty mentor. This contains the product of the students' research.

Contents:

• “How Porous Materials Affect the Boundary-Layer Transition of Hypersonic Flight Vehicles” (Megan C. Sieve)
• “Ultra-Stretchable, Self-Healing, DLP 3D-Printed Elastomers for Damage-Resistant Soft Robots: A Review” (Robert M. A. Drexler)
• “Extrapolation of Scalar …

Mapping The Binding Site Within Integrin D2 For Carboxyethylpyrrole (Cep)-Modified Proteins, Afia Prema

Electronic Theses and Dissertations

Neutrophils and macrophages accumulate at sites of inflammation and cause chronic inflammation leading to various diseases. Therefore, to better understand chronic disease pathways it is important to investigate the properties of macrophage accumulation in inflamed tissues. The I-domain of the macrophage receptor integrin a_Db₂ plays a vital role in macrophage retention by binding to CEP (carboxyethyl pyrrole), a ligand available at inflammatory sites. This thesis mainly focuses on evaluating the binding site within integrin a_Db₂ that binds carboxyethyl pyrrole (CEP)-modified proteins. So, a recombinant plasmid construct containing the integrin I-domain was developed. Seven non-conserved …

An Early Pliocene Fish Assemblage From The Southern Appalachians: Ichthyofauna Of The Gray Fossil Site, Shay Maden

Electronic Theses and Dissertations

The Gray Fossil Site (GFS) preserves an early Pliocene sinkhole pond that accumulated a rich flora and vertebrate fauna. Fossils of fish are incredibly common at GFS, representing thousands of specimens recovered to date. Comparison with extant species reveals a depauperate freshwater fish fauna consisting of only two species: Lepomis sp. and Micropterus sp. The absence of fishes that are ubiquitous in modern streams suggests no perennial surface hydrologic connection between the Gray Fossil Site and the nearby Holston River. Limited opportunities for dispersal into the pond and deleterious conditions such as eutrophy and high competition may have resulted in …

Microsporidian Spores And The Integrin Binding Loop Of The Madam Protein Are Important For Integrin Signaling And Attachment To Host Cells, Cindy L. Barrett

Electronic Theses and Dissertations

Microsporidia are a distant fungal pathogen that have severe clinical consequences for the immunocompromised. Previous work identified a microsporidian pathogen protein termed Microsporidian ADAM or MADAM. This protein has close sequence homology to other ADAM proteins (A Disintegrin and Metalloproteinase) in two microsporidian species, Encephalitozoon intestinalis and E. cuniculi. ADAM proteins have a wide range of functions, including binding to integrins and host signaling. It is known that many pathogens manipulate integrins to invade host cells, and it is predicted that microsporidia are also exploiting this host target. Previous work with the MADAM protein demonstrated that this protein has a …

How Does Increasing The Darkness Of A Plate Affect The Perception Of Both Bitter And Sweet Flavors?, Jessica Williams

Food Science Undergraduate Honors Theses

Extrinsic cues like plate color have been shown to effect taste perception. Previous studies conducted show a consensus that plate colors can modulate taste perception (Piqueras-Fizman et al., 2012, Stewart & Gross, 2013). No studies, however, have investigated varying color hues and their effect on taste perception. This study aims to determine whether the change in the black to white ratio of plate color can affect consumer perception of sweetness or bitterness.

We presented a group of volunteers two different brownies on plates varying from 100% white to 0% white in 25% increments. A 30:70 male to female gender ratio …

Development Of New Cotton Defoliation Sprayer Using Unmanned Ground Vehicle And Pulse Width Modulation Technology, Jyoti Neupane

All Theses

Chemical spraying is one of the most important and frequently performed intercultural agriculture operations. It is imperative to utilize appropriate spraying technology as a selection of ineffective one leads to waste of agrochemicals to the non‐target area. Several precision technologies have been developed in the past few decades, such as image processing based on real‐time variable‐rate chemical spraying systems, autonomous chemical sprayers using machine vision and nozzle control, and use of unmanned aerial and ground vehicles. Cotton (Gossypium hirsutum L.) is an important industrial crop. It is a perennial crop with indeterminate growth habit; however, in most parts of the …

Photodynamic Therapy To Treat Triple Negative Breast Cancer In Vitro, Hunter S. Warren

All Theses

Triple negative breast cancer (TNBC) is the most resilient form of breast cancer, being one of the leading causes of death for women and making up 7% of all cancer deaths. Photodynamic therapy (PDT) offers a minimally invasive solution to TNBC as a passive-targeting treatment that reduces the need for other well established yet harsh treatments that can be taxing on the patient. PDT involves the use of a high-energy red light on the area of a tumor injected with photosensitizers (PS) that generate reactive oxygen species (ROS) in the tumor, triggering cell death. The PS tetra(hydroxyphenyl)chlorin (m-THPC) was used …

Study Of Morphological And Physiological Properties And Pollinators Of The Invasive Callery Pear, Prabina Sharma

All Theses

Callery pear is an invasive tree in 15 states of United States and is currently present in 37 states. Its management has challenged landowners and land managers. Despite being listed as a noxious weed in four states, its study is limited. The accurate estimation of Callery pear biomass will give a clearer picture of the level of invasion and help land managers develop different strategies to control its population. Similarly, identifying possible pollinators of Callery pear is essential to have some insights on pollinators associated with this tree. Hence, the objectives of this study are 1) to calculate total above-ground …

Effects Of Antagomir-22-3p On Muscle Size In Older Lambs Using Computed Tomography Imaging, Anna Brewer

All Theses

Background

Texel sheep are known for their double-muscling phenotype and extraordinary meat production (Miar et al., 2014). Satellite cells are essential for this desired muscle growth. MicroRNAs can silence target genes by binding to the target messenger RNA (mRNA) (Horak et alk., 2016). Antagomirs are miRNA inhibitors and are used for loss of function studies. MiR-22-3p is known for inhibiting skeletal muscle growth and directly targets HDAC4, TGFBR1, PAX7 mRNA expression. Computed Tomography (CT) imaging is now growing in popularity in the animal science field to record changes in muscle characteristics.

Materials and Methods

Texel x Suffolk lambs (n=4) were …

Utilizing The Land-Based Learning Model For The Clemson Agricultural Safety, Growing Safe Tigers Program, Maryann Lovern

All Theses

The Clemson Agricultural Safety, Growing Safe Tigers program was developed in 2019 with the goal of increasing the awareness of agricultural safety in South Carolina. By utilizing the land-based learning model, a need for agricultural safety education was identified through incident surveillance strategies. Agricultural incidents were quantified using AgInjuryNews.org and recommendations were made for the program to provide more tailored information to the four regions of South Carolina, based on the primary cause of incident for each region.

Educators’ understanding of place and interconnected systems was determined pertaining to agricultural safety to provide a baseline for how agricultural education teachers …

Heat Stress-Induced Lipid Alterations In Peanut, Walker Spivey

All Theses

Peanut (Arachis hypogaea) is a globally important crop cultivated for human consumption and for the production of seed oil. As anthropogenic climate change continues to challenge global crop production with extreme environmental conditions such as high temperatures, the development of heat-tolerant varieties is crucial to meet peanut production demands. At the cellular level, one of the fundamental causes of yield loss at high temperatures (HT) is membrane damage. This work reports the investigations on a subset of a peanut recombinant inbred line population demonstrating that the membrane lipid remodeling occurring at HT is consistent with homeoviscous adaptation to …

The Effect Of Package Types On Fresh Peaches In The Direct-To-Consumer Distribution Environment, Brennan Lytle

All Theses

The direct-to-consumer (DTC) shipping mode presents new opportunity for fresh peach sales in North America where demand over the past four decades has steadily declined. The hazards in this distribution mode are severe, and fresh peaches are fragile emphasizing the need for proper protection. A full analysis that not only encompasses the effects of the direct-to-consumer distribution environment, but also incorporates analyses of the environmental and economic impact of the packages utilized for transit of peaches is necessary. In this study, we use the metrics of peach grade, firmness, soluble solids concentration, and percent softness before and after the distribution …

An Investigation Of The Impact Of Entrepreneurship Programs On Student Interest In Entrepreneurship Competitions, Toni Sharp

All Theses

According to a survey by ACNielsen International Research, over half of Americans want to start their own business to build wealth and achieve independence (Bygrave & Zacharakis, 2011). In the research community, most entrepreneurship education research happens in business schools (Matlay, 2006). As a result of continually researching one form of entrepreneurship, less attention has been paid to other forms contributing to the “definitional obscurity with important consequences for the direction of the field” of entrepreneurship (Baker & Welter, 2017). This has created a need for research on entrepreneurship at the college level in fields outside of business.

Clemson University …

Use Of Biorational Products For Botrytis Management In Floriculture Crops, Josselyn Calidonio

All Theses

Botrytis cinerea is an important pathogen that has a significant economic impact on the floriculture industry from propagation to the postharvest environment. Chemical fungicide applications have been one of the main approaches that growers use for botrytis blight management; however, studies have shown that the indiscriminative use of these chemicals leads to fungicide resistance (Brent and Hollomon, 1998; Fillinger and Elad 2016). This thesis explores the potential use of biorational products for botrytis blight management. Biorationals are defined as compounds that have low or no direct mammalian toxicity and few effects on the environment (Paulitz and Belanger 2001). A review …

Identifying Genetic Sources Of Anthracnose Resistance In Global Sorghum Lines, Mary-Frances Behnke

All Theses

Anthracnose of sorghum (causal agent: Colletotrichum sublineola) is the most detrimental disease of sorghum (Sorghum bicolor) worldwide, significantly reducing grain yield. This study includes a literature review of the disease and a meta-analysis of genome-wide association studies (GWAS) of anthracnose-resistance in sorghum as means to elucidate genetic sources of the trait. The meta-analysis includes genotypic and phenotypic data from 5 unique studies and 1,071 sorghum lines. Original genotyping-by-sequencing data from were obtained primarily from National Center for Biotechnology Information’s Sequence Read Archive (NCBI-SRA) and prepared and processed using the Tassel 5 GBS v2. pipeline. Phenotypic data were …

Reduced Growth Mindset As A Mechanism Linking Childhood Trauma With Academic Performance And Internalizing Psychopathology, Lucy A. Lurie, Emily J. Hangen, Maya L. Rosen, Robert Crosnoe, Katie A. Mclaughlin

Neuroscience: Faculty Publications

Background

Despite the high prevalence of childhood adversity and well-documented associations with poor academic achievement and psychopathology, effective, scalable interventions remain largely unavailable. Existing interventions targeting growth mindset—the belief that personal characteristics are malleable—have been shown to improve academic achievement and symptoms of psychopathology in youth.

Objective

The present study examines growth mindset as a potential modifiable mechanism underlying the associations of two dimensions of childhood adversity—threat and deprivation—with academic achievement and internalizing psychopathology. Participants and setting Participants were 408 youth aged 10–18 years drawn from one timepoint of two longitudinal studies of community-based samples recruited to have diverse experiences …

A Comparison Of Pm-Nato3’S Influence On Neural Progenitors And Mature Dopamine Neurons, Mary E. West

Masters Theses

This thesis presents significant findings regarding the role of PM-Nato3 in its interaction with developing neurons in the context of Parkinson's disease (PD) and regenerative medicine. We investigated the effects of PM-Nato3 on dopamine (DA) neurogenesis under different culture conditions, both in vitro and in vivo. In the standard dopaminergic culture condition, PM-Nato3 potentially increased the speed of DA neuron production but did not significantly increase the yield of DA neurons. In a minimal culture condition, there was no notable difference between the control and PM-Nato3 conditions, suggesting minimal impact on DA neurogenesis. In vivo studies using a mouse model …

Modeling The Egyptian Goose (Alopochen Aegyptiaca) Invasion; And Future Concerns, Percival Matzinger Marshall

Graduate Theses and Dissertations

In an increasingly interconnected world, the ecological and financial cost of invasive species is expected to continue to climb through the movement of exotic biota. Understanding the driving forces behind how a species invades, what environments promote their establishment, and what impacts they are likely to have on the invaded environment are all critical for management. Waterfowl, order Anseriformes, are one such category of invasive species of concern due to their popularity of accidental introduction, ease of movement, and propensity to affect both terrestrial and aquatic ecosystems. The Egyptian Goose (Alopochen aegyptiaca) is a native to the African continent that …

Evaluation Of Biochar Rate And Hemp Cultivar For The Phytoremediation Of Heavy-Metal-Contaminated Soil From The Tar Creek Superfund Site, Dietrich Thurston

Graduate Theses and Dissertations

Soil contamination by cadmium (Cd), lead (Pb), and zinc (Zn) at the Tar Creek Superfund site in Northeast Oklahoma remains a threat to the environment and local ecosystem. Phytoremediation by industrial hemp (Cannabis sativa L.) and the use of biochar (BC) have been independently shown to be effective methods to remediate heavy-metal-contaminated soils. The objective of this greenhouse study was to evaluate the effects of industrial hemp cultivar (‘Carmagnola’ and ‘Jinma’), BC rate (0, 2, 5, and 10% by volume), soil contamination level (low, medium, and high), and their interactions on above- and belowground (AG and BG, respectively) plant dry …

Shedding In The Timber Rattlesnake: Natural Patterns, Endocrinological Underpinnings, Temporal And Energetic Effort, And Integration As A Reptilian Life History Trait, Maxwell D. Carnes-Mason

Graduate Theses and Dissertations

The semi-frequent replacement of the epidermis (ecdysis) is a characteristic trait of reptiles. Whereas all reptiles regularly engage in some degree of skin shedding, skin morphology in snakes necessitates the synchronous replacement of the entire epidermis and facilitates the subsequent removal of the old layer as a single sheet. To date, the ubiquitous process has garnered little attention from researchers because snakes shed with unpredictable timing and frequency and are exceedingly cryptic during ecdytic cycles; previously impeding detailed physiological or ecological investigations of the process in the clade. Because of the lack of study, ecdysis is often viewed as a …

Runoff Water Quality And Crop Growth As Affected By Wastewater-Derived Struvite, Machaela Morrison

Graduate Theses and Dissertations

Mined phosphate rock, used to produce phosphorus (P) fertilizers, is a finite resource. Struvite (MgNH4PO4 • 6H2O) that has been synthetically produced from a stock solution of known P and nitrogen (N) concentrations has been shown to be an effective, alternative fertilizer-P source for various crops. However, little is known about the runoff-water-quality implications from and the crop response to soil application of struvite created from an actual municipal wastewater source. This study consisted of two objectives: i) to evaluate the effects of soil [i.e., Creldon (Oxyaquic Fragiudalf), Dapue (Fluventic Hapludoll), Roxana (Typic Udifluvent), and Calloway (Aquic Fraglossudalf) series], fertilizer-P …

Investigation Of Consumer Freezing Practices, Condition And Duration On Palatability Of Beef, Elizabeth Sue Neal

Graduate Theses and Dissertations

The objective of these studies was to determine: the impact of extended periods of frozen storage duration and packaging type on palatability traits of cooked beef steaks from two muscles and the impact of freezing type and storage duration on objective and subjective measures of ground beef palatability traits. In study 1, no differences were elicited from any of the possible interactions (P= 0.95) for SSF or CL: package × muscle × freezing duration, package × muscle, package × duration or muscle × duration. However, freezing duration did impact both SSF (P < 0.01) and CL (P < 0.001). Generally, for both SSF and CL steaks that were frozen for 9-months elicited both the highest SSF values as well as the greatest percentage of CL among all treatments. In comparison, EM was impacted by the interaction (P = 0.059) of packaging type  muscle  freezing duration. Samples from OW GM stored for 9-months elicited the highest percentage of EM while fresh OW LL samples resulted in the lowest. Additionally, expressible moisture was impacted by the interaction (P = 0.047) of muscle  freezing duration. Among all treatments, GM steaks that were frozen for 9-months elicited the highest EM values and fresh LL samples the lowest EM values. Contrastingly, there was no significant difference observed in expressible moisture for the interaction (P  0.18) of package type  freezing duration or for the interaction (P = 0.70) of package type  muscle. Generally, fresh OW GM steaks resulted in the greatest concentration of lipid derived volatile compounds such as aldehydes, hydrocarbons and alcohols which contrasted sensory ratings of trained panelists that indicated oxidized and refrigerator-stale ratings increased as storage time increased for OW steaks. In study 2, The interaction of freezer treatment × storage duration impacted gumminess (P = 0.05), a TPA attribute. In greater detail, samples stored in RF for 6-months resulted in the greatest gumminess values (P < 0.001), while those stored in the CF for 12-months elicited the lowest (P < 0.001). Similarly, flavor development was also impacted by the interaction (P = 0.05) of freezer treatment × storage duration. Three lipid derived compounds were of greatest concentration among RF patties stored for 1-month. In contrast, the interaction of freezer treatment × storage duration elicited no impact on consumer ratings, SF or TBARS. Nonetheless, frozen storage duration impacted TPA, flavor development, consumer ratings, SF and TBARS as a main effect (P < 0.05), especially in regard to tenderness and juiciness. Moreover, beef flavor development, tenderness and juiciness are impacted by freezing duration, muscle, freezer type and packaging, however these factors are not necessarily independent of one another. Furthermore, the retail display period is a critical period for fresh beef steaks, especially when packaged in aerobic conditions. For optimal eating experience, beef products should be stored for extended periods in a vacuum packaging, in a designated freezer that is not opened frequently to allow for optimal air flow regulation and minimize freezer burn to improve tenderness and juiciness.

Securing Rice Safety Through Innovative Radiative Heat Treatment And Proper Storage, Faith Achieng Ouma

Graduate Theses and Dissertations

Securing the microbial safety of rice is a rising priority within the food industry, especially when used as an ingredient to manufacture ready-to-eat, minimally-processed products. Mold contamination is typically the most problematic for rice because certain species of Aspergillus produce toxic secondary metabolites known as aflatoxins, rendering the grain unfit for human and animal consumption. The objectives of this study are to: (1) investigate the effectiveness of using high-power (915 MHz frequency), short-duration microwaves (MWs) to inactivate microbes on rough rice; (2) use a three-level screening design to determine which storage factors, such as temperature, relative humidity (RH), storage duration, …

Dietary Effects On Cardiac Lipid Composition And Subsequent Phenotype In The American Lobster (Homarus Americanus), Melissa Colette Butler

All Theses And Dissertations

Lipids are fundamental components of many biological structures and compositions of these molecular species can alter with diet. Differences in lipid membrane composition can impact the functioning of membranes and proteins subsequently altering the organism’s ability to respond to stressful conditions. American lobsters (Homarus americanus) are an economically important shellfish in New England and are sometimes kept intermittently in lobster impoundments (pounds) for months where they are often fed herring, which differs from the assumed natural diet of wild-caught lobsters. In this study, we compared the lipid composition of lobsters obtained from the wild and pounds that were …

Recreational Fishing For Western Rock Lobster: Estimates Of Participation, Effort And Catch In 2022/23, Claire B. Smallwood, Karina L. Ryan, Alissa C. Tate, Lucy J. Rudd

Fisheries Research Reports

The Western Rock Lobster (WRL) (Panulirus cygnus) is the most commonly caught Rock Lobster (RL) species in Western Australia. Catches from the commercial and recreational sectors are required to determine and monitor Total Allowable Commercial Catch (TACC), Total Allowable Recreational Catch (TARC) and proportion of Allowable Harvest Level (AHL) achieved. The TARC is set at 5% of the AHL and evaluated in the harvest strategy based on a 5-year average. Data for the recreational sector are obtained using phone-recall surveys to provide estimates of participation, fishing effort and retained catch (by numbers) from recreational fishers who hold a RL licence. …

Visual Complexity Of The Time-Frequency Image Pinpoints The Epileptogenic Zone: An Unsupervised Deep-Learning Tool To Analyze Interictal Intracranial Eeg, Sarvagya Gupta

Graduate Masters Theses

Epilepsy, a prevalent neurological disorder characterized by recurrent seizures, continues to pose significant challenges in diagnosis and treatment, particularly among children. Despite substantial advancements in medical technology and treatment modalities, localization of the part of brain that causes seizures (Epileptogenic Zone) remains a difficult task. Intracranial EEG (iEEG) is often used to estimate the epileptogenic zone (EZ) in children with drugresistant epilepsy (DRE) and target it during surgery. Conventionally, iEEG signals are inspected in the time domain by human experts aiming to locate epileptiform activity.

Visual scrutiny of the iEEG time-frequency (TF) images can be an alternative way to review …