Life Sciences Commons^™

Development Of An Enhanced Sampling Workflow To Accelerate Molecular Docking With Sparse Biophysical Information, Zachary Stichter

Masters Theses & Specialist Projects

Rapid docking of flexible biological macromolecules remains a significant open challenge in protein structure determination. While rigid docking is relatively simple with toolkits such as TagDock, a key obstacle to rapid flexible docking is the complexity and roughness of the free energy surface associated with protein conformational motion (often termed the many-minima problem), meaning conventional molecular dynamics methods do not effectively sample protein conformations near the interaction complex in accessible timescales. Methods such as metadynamics and replica exchange molecular dynamics exist to ameliorate this obstacle, yet these methods use nonphysical biases or random swaps to enhance sampling. In contrast, high …

The Effect Of Mindfulness Training On Muscular Endurance Exercise Performance, Mindfulness, And Mental Toughness, Donte Mcgee

Masters Theses & Specialist Projects

INTRODUCTION: Mindfulness training is a method of mental training becoming increasingly popular and has been positively associated with mental toughness, which may be valuable in highly fatiguing and stressful activities, like endurance exercise. Mindfulness training has resulted in increased endurance performance, but limited literature exists on a similar modality, muscular endurance exercise. The purpose of this study is to examine the effect of an acute bout of mindfulness meditation on muscular endurance performance, mindfulness, and mental toughness. METHODS: Participants (n=24) completed two sessions, a week apart, of three planks until fatigue, with one-minute rest intervals. Immediately following each plank, RPE …

Synthesis Of Gold Nanoparticles Via Pulsed Liquid Ablation For Use In The Photodynamic Therapy Of Bacteria, Justice Ben Yosef

Masters Theses & Specialist Projects

With the ever-increasing threat of antibiotic resistant bacteria, alternative treatment methods have been developed including photodynamic therapy (PDT). Within the PDT process, photosensitizers are used to generate reactive oxygen species (ROS) and facilitate the cell termination process. This work lays the conceptual foundation for the functionalization of the photosensitizer methylene blue (MB) with gold nanoparticles (AuNPs) and INF-55 as a potential inhibitor of the AcrAB-TolC efflux pump to enhance the effectivity of the PDT process.

AuNPs were synthesized using pulsed laser ablation in an aqueous citrate solution. Both nanosecond and picosecond pulse durations, as well as both 532 nm and …

Acl Bracing: Is It Still Being Done Clinically And Does It Influence Confidence And/Or Biomechanical Performance During A Drop Vertical Jump?, Bailey Watson

Masters Theses & Specialist Projects

Introduction: Anterior cruciate ligament (ACL) ruptures account for 60% of sports-related injuries and the gold standard for treatment is surgical intervention to replace the damaged ligament to restore function of the ACL. Braces are typically used to return to previous physical activity levels; however, there are no clear guidelines on their utilization. Beyond the physical consequences of undergoing ACL reconstruction surgery, the psychological component is often ignored.

Purpose: The aim of this study is to better understand the impact of knee bracing on both biomechanical factors and confidence following ACL reconstruction. Two aims comprise the overarching purpose; the first is …

Cannabidiol (Cbd) And Resistance Training: Does Cbd Attenuate Acute Pain?, Guillermo Pacheco

Masters Theses & Specialist Projects

INTRODUCTION: Resistance training (RT) is an advantageous form of physical activity for health and performance benefits; these benefits are maximized when done strenuously. However, strenuous RT can induce acute inflammatory pain which can lead to delayed-onset muscle soreness (DOMS). Common analgesics like non-steroidal anti-inflammatory drugs (NSAIDs) can block protein synthesis, so other alternatives are needed for exercise and athletic communities to maintain physiological adaptations. Cannabidiol (CBD) is a non-psychotropic cannabinoid with purported anti-inflammatory, anti-oxidative, and analgesic properties. One of the main reasons for the use of CBD in exercise is pain alleviation; however, research in humans is limited. Therefore, the …

Grey Relational Analysis And Canonical Correlation Analysis Of Air Pollution In Three Kentucky Counties, Sarah Hartman

Masters Theses & Specialist Projects

Air pollution is a crucial factor that affects both the environment and public health. Various methods are available for assessing air quality and pollution levels, such as regression models, principal component analysis, and factor analysis tools. However, some of these methods present issues in multicollinearity and the nature of collected data. It is important to recognize that air pollution data is often uncertain, incomplete, and contains limited valid data points. Weather conditions and economic activities are also factors that can affect air pollution. With growing communities in Kentucky (KY), it is essential to address these factors as the state has …

Towards The Quantification Of Estrone And 17Β-Estradiol Conjugates In Dairy Cattle Urine Sorptive Stir Bar Extraction And Gas Chromatography-Mass Spectometry, S.M. Istiak Ahmed

Masters Theses & Specialist Projects

The global concern regarding the presence of compounds with estrogenic properties in the environment has grown significantly. Endocrine-disrupting compounds (EDCs) are environmental pollutants that disrupt the endocrine systems of both wildlife and humans. Estrogens, with their potent estrogenic effects, are particularly noteworthy among the various substances with endocrine-disrupting properties. They are of concern due to their prevalence in the environment, especially due to dairy waste contamination. These lipophilic compounds can accumulate in livestock fat tissues, potentially entering the human food chain. Sulfated forms of estrone and β- estriol, which exhibit a higher degree of saturation than their non-conjugated counterparts, have …

Liquid Chromatography Mass Spectrometry Method Development For The Determination Of Β–Defensins In Bovine Milk, Elisha Ogbebor

Masters Theses & Specialist Projects

Bovine mastitis is caused by a wide range of pathogens which results in a substantial economic loss for the dairy cattle livestock industry. β-defensins are a part of the innate immune system and act as the first line of defense against mastitis in bovine. β-defensins (~6- 10kDa) are antimicrobial peptides that contain about 28 to 67 amino acids, the presence of six cysteine residues results in their three disulfide bonds and a β-sheet structure. A few β- defensins have been identified in cows based on the site of occurrence and time of expression in tissue, but not in milk. A …

The Role Of Leaders In Implementing Effective Leadership Strategies Towards The Educational Barriers Of Us-Based Refugee Students: A Qualitative Case Study Of Congolese Refugee Students, Faustin Busane

Masters Theses & Specialist Projects

This qualitative research study explored the experiences of three families of refugee school students, two school officials (a Superintendent and a Principal), three teachers, and one humanitarian agent all living in a Southeastern U.S. city. The results of the study revealed that the language barrier is the main academic challenge that refugee students encounter when they enroll in U.S. schools. The study also found that educators conceptualize their responsibilities toward refugee children by emphasizing the importance of high-quality teaching, and establishing through establishing strong relationships between parents, school officials, and exercising patience in the process. This study poses important implications …

Mammalian & Avian Community Response To African Elephant (Loxodonta Africana) Habitat Modification In Southeastern Kenya, Dakota Vaccaro

Masters Theses & Specialist Projects

African elephants (Loxodonta africana) play a significant role in the modification of their habitat, foremost by decreasing woody vegetation cover and density and in some parts of Africa high elephant densities damage small sanctuaries and preserves. For wildlife that depend on forested patches, this increased modification could lead to displacement and/or decreases in abundance. If suitable habitat is not available elsewhere, elephants and other wildlife may move closer to humans in search of resources, which can result in increased human-wildlife conflict. Evaluating this impact was one of the goals of the Elephants and Sustainable Agriculture in Kenya (ESAK) …

A Comparison Of Computational Perfusion Imaging Techniques, Shaharina Shoha

Masters Theses & Specialist Projects

Dynamic contrast agent magnetic resonance perfusion imaging plays a vital role in various medical applications, including tumor grading, distinguishing between tumor types, guiding procedures, and evaluating treatment efficacy. Extracting essential biological parameters, such as cerebral blood flow (CBF), cerebral blood volume (CBV), and mean transit time (MTT), from acquired imaging data is crucial for making critical treatment decisions. However, the accuracy of these parameters can be compromised by the inherent noise and artifacts present in the source images.

This thesis focuses on addressing the challenges associated with parameter estimation in dynamic contrast agent magnetic resonance perfusion imaging. Specifically, we aim …

Characterization Of Legionella Pneumophila Effector Proteins, Lneb And Mava, Kayode Adeyemi

Masters Theses & Specialist Projects

The crucial virulence factor of accidental human pathogen Legionella pneumophila during the course of Legionnaire disease is the over 300 effector proteins secreted from its Dot/Icm secretion system. Eukaryotic host cells usually elicit an arsenal of immune responses against invading L. pneumophila. Nonetheless, the bacteria unexpectedly subvert these defense mechanisms to survive and proliferate unhindered in the host. Although some effector proteins have been proposed to play a significant role in this host-pathogen interaction, many still need to be characterized. The LneB and MavA proteins are examples of those effectors that need characterization. Thus, this study aimed to investigate the …

Microglial Response To Glucocorticoids During Chronic Sleep Fragmentation, Christian Chelson

Masters Theses & Specialist Projects

Sleep is one of the body’s greatest and most basic needs. Chronic sleep loss (<6 hours a day) is linked to many cardiovascular issues, diabetes, and inflammatory conditions and has been shown to lower life expectancy. Obstructive sleep apnea (OSA) is a complication that causes sleep fragmentation in >8% of adults from developed countries, and many with OSA may be unaware of their condition. Having long-term OSA is linked to neuroinflammation caused by activated microglia in the brain, but the mechanics of this inflammation are not well understood. It is known that glucocorticoids, steroid hormones produced and released from the adrenal glands, have a suppressive effect on microglia. The purpose of this study is to explore the role that glucocorticoids have upon microglia activation induced by chronic sleep fragmentation (SF). C57BL/6J mice were …

Effects Of Exercise When Transitioning From Free Choice Tall Fescue (Lolium Arundinaceum) Grass Diet In Late Summer To Free Choice Tall Fescue Hay Diet In Late Fall On Plasma Fructosamine Concentrations, Insulin Levels, Body Weight, And Body Condition Scores Of Stock Horse Mares And Gelding, Riley Brown

Masters Theses & Specialist Projects

Equine exercise may influence a horse’s metabolic and physiological functions. Studies can help to prove this linkage, and to better understand the nutritional requirements of the horse. The parameters that are being evaluated are plasma-fructosamine concentrations, insulin levels, body weight (lbs.), and body condition score (BCS) as a measurement of obesity. Eight horses used in this study were split into two groups; Worked horses were exercised three times a week while the unworked horses were not exercised. All eight horses were fed an ad libitum diet of tall fescue grass and hay for 127 days.

Forage samples were collected to …

The Effects Of Attentional Focus Instructions On Approach Jump Performance, Hanwen Liu

Masters Theses & Specialist Projects

Introduction: Attentional focus is a crucial factor that impacts motor learning and performance. Instructions that direct performers’ attention externally (i.e., toward the effects of movements) have been shown to enhance performance compared to those that direct attention internally (i.e., toward the body’s movements). Research has also demonstrated that novices perform better when they are instructed to focus externally on the process of skill execution versus the outcome. However, this effect has not been tested in complex jumping skills that are important in many sports.

Purpose: The aim of this study was to test the effects of internally and externally directed …

Rapid & Sensitive Detection Of Antibiotic Resistance Genes By Utilizing New Diagnostic Probe Tales With 2d-Nanosheet Graphene Oxide, Jihye Kang

Masters Theses & Specialist Projects

As antibiotic resistance is one of the major health concerns in infectious diseases because of reducing the efficacy of antibiotics, rapid and sensitive detection of antibiotic resistance genes is critical for the effective treatment of infectious diseases. Polymerase chain reaction (PCR) is widely used to detect nucleic acids, but it requires additional steps involved in DNA denaturation and subsequent hybridization. A new class of DNA-binding domains called transcriptional activator-like effectors (TALEs) provide a novel scaffold for designing versatile DNA-binding proteins due to their modularity and predictability. Here, we developed a simple, rapid, and sensitive system for detecting antibiotic resistance genes …

Functional Analysis Of Legionella Pneumophila Effector Protein, Shreya Neupane

Masters Theses & Specialist Projects

Legionella pneumophila is a gram-negative bacterium that causes Legionnaire’s disease (a severe form of pneumonia) in humans. L. pneumophila can cause infection by utilizing its Type IV secretion system, a protein secretion system that transports proteins from the bacterial cytosol into the infected macrophage. Effectors released from the Type Iv secretion system allow L. pneumophila to create a safe environment to survive, replicate and cause infection. One such effector, RavQ, inhibits cell proliferation of mammalian HEK 293T cells and localizes to the cell’s nucleus, leading us to hypothesize that RavQ interferes with cellular activity in the nucleus. To detect its …

Functional Characterization Of Mycobacterium Smegmatis Phage Moomoo Gene Products: Identification Of Toxic Genes, Whitney Heard

Masters Theses & Specialist Projects

Mycobacteriophages are a group of phages that infect members of the genus Mycobacteria. Previous studies have conducted extensive comparisons of the mycobacteriophage genomes and amino acid sequences to establish different phage families. MooMoo is a singleton mycobacteriophage that has been characterized due to its lack of appreciable homology to other phages. Some of its unique properties include its structure and the isolation of a mutant that causes clear plaque phenotypes. The experiments described in this thesis identified three MooMoo phage (gp87, gp90, and gp91) encoded proteins that are toxic to the bacterial host, Mycobacterium smegmatis.Through the use of a …

Description, Diversity, And Phylogeography Of The North American Spider Beetle (Coleoptera: Ptinidae) Genus Coleotestudo, Robert Chambliss

Masters Theses & Specialist Projects

A new genus, Coleotestudo, is proposed for the American species currently placed in the genus Niptus LeConte and are transferred herein. Two new species from Mexico are also described as C. potosi n. sp. and C. nahua n. sp. Distinguishing morphological characteristics for the North American Coleotestudo species are given. The combined set of morphological evidence, DNA sequence data, and a Western New World distribution strongly support the hypothesis that Coleotestudo does not share a recent common ancestor with N. hololeucus and both represent unrelated clades of spider beetles.

During the summer of 2021, Coleotestudo was collected mainly from …

Evaluation Of Silver Nanoparticles Attached To Methylene Blue As An Antimicrobial Agent And Its Cytotoxicity, Somon Hakimov

Masters Theses & Specialist Projects

Antibiotics resistance is considered as one of the greatest public health challenges of our time. In this work, we have synthesized silver nanoparticles (Ag NPs) using pulsed liquid ablation in different medium of growth and later combined with methylene blue (MB) to evaluate its potential as an effective photodynamic therapy agent. Ag NPs were synthesized by pulsed laser ablation technique in Polyvinylpyrrolidone (PVP), citrate, and Polyvinyl alcohol (PVA). The Ag NPs were characterized using transmission electron microscopy (TEM), UV-Visible (UV-Vis), and photoluminescence (PL) spectra. Next, Ag NPs were coupled with MB and used to deactivate the Gram-negative bacteria, Escherichia coli …

Diversity In Darkness: Shedding Light On Cryptic Species In The Cave Beetle Genus Darlingtonea Valentine Using 3rad Sequencing And Consequences Of Climate Change Based On Thermal Tolerance And Dehydration Resistance, Athanasios S. Apostolopoulos

Masters Theses & Specialist Projects

The relationship between geographic distribution and phylogeny is pronounced in patchy, discontinuous habitats that limit gene flow, such as cave ecosystems. The isolating nature and selective pressures of cave environments can result in relatively high levels of endemism and cryptic speciation in cave faunas. Cryptic speciation exhibited in cave faunas is poorly studied, though it is an integral aspect to consider when discussing conservation efforts.

Our study employed the 3RAD genomic sequencing technique and robust population sampling across the distribution of a monotypic genus of cave beetle, Darlingtonea Valentine, that inhabits karst systems in a nearly 200 square mile range …

Effects Of Glucocorticoids Upon Pro-Inflammatory Responses To Acute Sleep Fragmentation, Hunter Weaver

Masters Theses & Specialist Projects

Sleep loss is a common problem in humans who suffer from obstructive sleep apnea. Sleep aids in the regulation of immune responses, some of which induce inflammatory responses. Cytokines regulate the inflammatory process and are released in response to sleep fragmentation (SF) in mice. Glucocorticoids are hormones that are released from the adrenal cortices during a stress response and are considered to be anti-inflammatory and immunosuppressive at high doses but may stimulate immune function on an acute level. The first hypothesis tested was that normal physiological expression of glucocorticoids (Sham) will display increased IL-1β and TNFα expression levels, while high …

Towards The Determination Of Estrone And 17Β-Estradiol In Dairy Cattle Waste Using Solid Phase And Stir Bar Sorptive Extractions With Liquid Chromatography-Mass Spectrometry And Gas Chromatography-Mass Spectrometry, Pallavi Ragi

Masters Theses & Specialist Projects

Steroidal hormones are naturally produced as a part of many physiological processes and are excreted in the urine and feces of animals and humans. Farm animals in concentrated animal feeding operations (CAFOs) are routinely implanted with synthetic and natural hormones to enhance growth and production, contributing significantly to environmental steroid hormone contamination. Every year around 49 tons of estrogens are generated by livestock waste in the United States alone. Due to rainfall and runoff, these steroid hormones reach the environment when animal waste is applied as manure. Studies show that estrogens and other steroidal hormones present in the surface waters …

Agriculture Education Teacher Perspectives On Stem In Secondary Classrooms -A Delphi Study, Nicholas Kyle Porter

Masters Theses & Specialist Projects

Recent statistics tell us that the number of jobs in Science, Technology, Engineering and Mathematics (STEM) related fields are growing at a rapid rate, it is projected that STEM related careers will grow 17% between 2008 and 2018 (Langdon, n.d.). Within these areas lies agriculture. Given the shift of career opportunities, such as in the areas of research and development, a change has to be made in the way students are educated within agriculture. The ultimate goal of all educators is to better prepare students for their future careers and endeavors because these students are the future of our food …

Factors Influencing Tree Growth In A Bottomland Hardwood Along The Green River In Kentucky, Caleb Miller

Masters Theses & Specialist Projects

In bottomland hardwood forests, large fluctuations in moisture availability can lead to stress from both flooded and drought conditions. These forests can have a complex species composition with different water use and drought strategies. The bottomlands in which these species co-occur can have a complex spatial distribution of alluvial sediments due to the meandering and migration of river or stream channels, which may impact the hydrology, nutrient dynamics, and productivity. At Western Kentucky University's Green River Preserve, approximately 9 ha of bottomland hardwood forest were planted in 2006. Although these hardwoods have received equal amounts of sunlight, rainfall, and wind, …

Liquid Chromatography With Tandem Mass Spectrometry Method Development For The Determination Of Β–Defensins In Bovine Milk, Symone T. Whalin

Masters Theses & Specialist Projects

Bovine mastitis, caused by a wide array of pathogens, results in a substantial economic loss for the dairy cattle livestock industry. β-defensins are a part of the bovine’s innate immune system and act as the first line of defense against mastitis. Only foundational research has been done on β-defensins’ ability to treat and prevent mastitis. There have been no analytical methods reported in the literature for analyzing β-defensins in bovine milk. This research aims to create an analytical approach to determine β-defensins in bovine milk. It is challenging to determine an analyte in a complex sample matrix, and milk is …

The Validity & Reliability Of The Repetitions In Reserve Based Rating Of Perceived Exertion Scale In Single Joint Exercise, Grant Malone

Masters Theses & Specialist Projects

Introduction: Intentional regulation and individualization of resistance training schemes are imperative when structuring a resistance training program. Optimal adaptation cannot be expected without proper manipulation of training variables such as load and volume. Load is traditionally prescribed by testing a given exercise’s repetition maximum and basing intensity from that load. This method of intensity regulation may be limited, considering it fails to recognize the day-to-day undulation of individual performance which can be impacted by several variables. A flexible method of regulating load and volume would be of use for those undergoing a resistance training program. The repetitions in reserve-based rating …

Do Changes In The Navy Physical Readiness Test Impact Performance?, Alison Colao

Masters Theses & Specialist Projects

The fitness level of our service members is of utmost importance due to the nature of their occupation. This study investigated whether changes to the Navy’s Physical Readiness Test (PRT) impact performance on the fitness test. Participants were college-aged males between the ages of 18 and 29 (n=20; 21.05±2.01 years; BMI 24.85± 2.74). Participants performed both the New PRT and Old PRT at two separate randomized visits. Protocols included push-ups, curl-ups (old version) or a forearm plank hold (new version), and a 1.5-mile run. At the end of each exercise, the participant’s heart rate and rating of perceived exertion (RPE) …

The Validity Of Perceptual Recovery Status On Monitoring Recovery During A High-Intensity Back Squat Session, Nicholas Buoncristiani

Masters Theses & Specialist Projects

Adaptations to resistance training and subsequent performance can be undermined by inadequate inter-set recovery. This time between sets is often uniformly prescribed based on desired training outcomes; however, there is demonstrative evidence that recovery is highly individualized. Methods typically used to monitor recovery were developed for longitudinal use, making them cost- or time -inefficient within a bout of exercise. If valid, the perceptual recovery status (PRS) scale may be used as an efficient and inexpensive recovery assessment tool to monitor individual recovery as well as appropriately modify rest periods. Purpose: The aim of the current study was to assess the …

Alleviating Human-Elephant Conflict Through Deterrent Fences And Environmental Monitoring In Southern Kenya, Sophia Carmen Corde

Masters Theses & Specialist Projects

Human-wildlife conflict is present across the world. In areas where human settlements overlap with elephant habitats, human-elephant conflict can result from crop raiding events, compromising farmers’ food and economic security, and putting humans and elephants in danger through farmer retaliation. Elephants raid crops primarily at night, when detection by humans is lowest, and during the dry season, as crops are developing towards harvest and natural forage quality drops. People living in these areas facing HEC have developed mitigation strategies to lessen the impacts and move towards coexistence. As a team member on the Elephants and Sustainable Agriculture in Kenya project, …