Life Sciences Commons^™

Mechanistic Investigations Of A Novel Braf Regulatory Switch And Braftide, An Allosteric Peptide Inhibitor Of Braf, Alison Yu

Theses and Dissertations

RAF kinases (ARAF/BRAF/CRAF or Raf-1) are serine/threonine kinases in the MAPK (RAS-RAF-MEK-ERK) pathway. The MAPK pathway is crucial in development and normal cell function. These same roles are dysregulated in cancer; BRAF is the most frequently mutated isoform in cancers and in particular, activation loop mutants BRAF V600E/K mutants have the highest mutational incidence. Three FDA approved inhibitors potently inhibit BRAF V600E/K mutants. However, these same inhibitors fail to address the non-V600E/K mutations and result in paradoxical activation of the MAPK pathway. Two strategies were employed to address the limitations of the FDA-approved inhibitors: provide novel regulatory details of RAF …

Combining Expert Opinions To Assess Risk Of Change In Earth Systems: Permafrost Collapse, Global Wildfire, And Water Security, Sayedeh Sara Sayedi

Theses and Dissertations

In a world of uncertainty and change, leaders should base their decisions on best available scientific evidence. However, history has shown that science is often inadequately incorporated into the decision-making process. This dissertation investigates three environmental issues to identify the challenges of considering Earth system dynamics in policymaking and management. I also propose solutions for improving the two-way exchange of knowledge and values between researchers and policymakers. In chapter one, I investigate subsea permafrost carbon sensitivity to climate change using an expert assessment. The analysis revealed that subsea permafrost contains significant carbon stocks and is already contributing to climate change …

Sctiger: A Deep-Learning Method For Inferring Gene Regulatory Networks From Single-Cell Gene Expression Data, Madison Dautle

Theses and Dissertations

Inferring gene regulatory networks (GRNs) from single-cell RNA-sequencing (scRNA-seq) data is an important computational question to reveal fundamental regulatory mechanisms. Although many computational methods have been designed to predict GRNs, none work on condition specific GRNs by directly using paired datasets of case versus control experiments, common in diverse biological research projects. We present a novel deep-learning based method, scTIGER, for GRN detection by using the co-dynamics of gene expression. scTIGER also employs cell type-based pseudotiming, an attention-based convolutional neural network method, and permutation-based significance testing to infer GRNs from gene modules. We first applied scTIGER to scRNA-seq datasets of …

Development Of An Antibiotic Resistance Breaker To Combat Staphylococcus Aureus Pathogenesis Skin Infections Ssis A Multidisciplinary, Gopalakrishnan T Mr

Theses and Dissertations

Problem Statement: Staphylococcus aureus is a highly adaptable and tenacious pathogen known to cause a wide range of infections. The survival characteristics of the pathogen in different host niches are due to their ability to produce various pathogenic determinants. Although there lies the first line of treatment regimens with antibiotics, the pathogen defends at various levels to cause the waves of resistance - a silent pandemic “AMR”.

Notable strategies are through the protective layer, biofilm that enables the inter-/intra species communication (Quorum Sensing; QS) and emerges as a battleground to withstand host-immune response and antibiotic pressure. In parallel, several research …

Gene Dive: Assessing The Diversity Of Perchlorate Reducing Genes In Mars Analog Environments, Colin Michael Robinson

Theses and Dissertations

Biotic perchlorate reduction, a metabolic process that potentially occurs on Mars, has long been the subject of speculation in astrobiology. To determine whether it could be a viable metabolic strategy on the Red Planet, we sought to determine whether biotic perchlorate reduction could evolve and persist in Mars-analog environments on Earth. In this study, we introduce Gene Dive, a novel computational methodology that leverages profile hidden Markov models, sequence alignment, phylogenetic tree construction, and Faith's phylogenetic diversity to probe the prevalence and diversity of perchlorate reducing genes in metagenomes. To determine whether biotic perchlorate reduction persists in a wide range …

"The Trees Act Not As Individuals"--Learning To See The Whole Picture In Biology Education And Remote Sensing Research, Rebeka A.F. Greenall

Theses and Dissertations

To increase equity and inclusion for underserved and excluded Indigenous students, we must make efforts to mitigate the unique barriers they face. As their knowledge systems have been historically excluded and erased in Western science, we begin by reviewing the literature on the inclusion of Traditional Ecological Knowledge (TEK) in biology education and describe best practices. Next, to better understand how Native Hawaiian and other Pacific Islander (NHPI) students integrate into the scientific community, we used Social Influence Theory as a framework to measure NHPI student science identity, self-efficacy, alignment with science values, and belonging. We also investigated how students …

Food Web Of Icy Strait, Alaska: Comparison Of Position, Size, And Overlap Of Trophic Niche Among Fish Species, Andrew D. Suchomel

Theses and Dissertations

The Icy Strait of southeast Alaska, USA is an ideal system to study how ecological diversity is maintained. This area has historical ecological significance and supports diverse assemblages of fish species that are easily sampled. We used stable isotope analysis using δ13C and δ15N stable isotope ratios. Using these isotope ratios, we quantified trophic niche position, size, and overlap and compared how those trophic niche metrics varied using ecological and evolutionary perspectives. For ecological variation, mean total length, and δ13C trophic niche position has positive relationships with trophic niche size while total percent trophic niche overlap had a strong negative …

Taxonomic Revision And Phylogenetic Analysis Of The Philadelphicus Group In The Genus Proctacanthus (Insecta: Diptera: Asilidae), And Key To All Proctacanthus North Of Mexico, Teagan Marie Mulford

Theses and Dissertations

Proctacanthus (Macquart 1838), an elegant genus of robber flies within the Asilidae family, plays a significant ecological and economic role. However, the lack of a comprehensive taxonomic treatment hinders their identification and thus their use in evolutionary and behavioral research. This study focuses on the taxonomic revision of the Proctacanthus, identifying the features used in recognizing the philadelphicus Species Group and the rufiventris Species Group. By providing systematic and biological data, describing new species, and offering a key for identification, this research contributes to understanding the ecological significance and geographic distribution and history of Proctacanthus. This work will enhance future …

Feasibility Of Rna-Based Pathogen Detection In An Infant Formula Matrix, Gweneth Claire Gustafson

Theses and Dissertations

Background: The dairy processing industry is currently hindered by slow, antiquated testing for high-risk pathogens, including Listeria monocytogenes and Cronobacter sakazakii. Powder infant formula's low water activity and substantial fat content enhance the survival and thermotolerance of such foodborne pathogens. As DNA-based detection methods can produce false positives even after cell death, a more accurate approach is needed. The objective of this study is to evaluate the suitability of an RNA-based platform for the detection of pathogens in a dairy powder matrix. Materials and Methods: A unique phenol-chloroform extraction method was used to obtain total RNA from heat-killed and unheated …

Spatiotemporal Variation Of Alfalfa Leaf Area Index And Crop Water Productivity In An Irrigated Alfalfa Field, Keegan Dillon Hammond

Theses and Dissertations

Throughout the world, there continues to be increasing demand for freshwater resources. With urban expansion, increased demand from a growing population, drought, and climate change, growers must produce more crops using less water. One approach to water conservation is with a variable rate irrigation (VRI) system. VRI technology allows growers to irrigate crops according to site-specific within-field variation instead of a uniform rate across the field. This thesis addresses aspects of within-field variation of irrigated alfalfa as it relates to the potential for VRI. Chapter 1 examines measurement of within-field variation of leaf area index (LAI) to inform variable-rate irrigation …

Potential Clean-Label Astringency Maskers For Acidic Whey Protein Beverages, Jozxelle Tongson Gao

Theses and Dissertations

Whey Protein Ready-to-Drink (RTD) beverages are popular nutritional products due to their high protein content, complete amino acid profile, convenience, and flavor. However, astringency imparted by whey protein at low pH (pH <4.5) can significantly reduce consumer liking. Astringency is a complex problem, so it may require a multi-faceted solution. Samples were created through Response Surface Methodology (RSM), utilizing parameters determined through literature review and preliminary testing. There is evidence that sucrose may help to reduce astringency in wine. Various natural sweeteners like stevia, monk fruit extract, and sweet proteins: thaumatin and brazzein were evaluated to observe if they may reduce the astringency in acidic whey protein RTD beverages. Samples were assessed by trained quantitative descriptive analysis (QDA), consumer acceptance, and focus group panels. Formulas were instrumentally measured for pH, brix, zeta potential, and particle size. pH and brix were useful measures for monitoring processing consistency, but neither related to level of astringency of samples. Zeta potential instrumental data coincided with results of previous studies finding that a decrease in zeta potential within the range of pH 3-5 correlated with less astringency with whey protein isolates. Particle size relation to astringency is dependent on the zeta potential. A large particle size measurement does not lead to higher astringency if the molecules do not interact due to electrostatic repulsion. Analytical measurements of the samples were statistically compared for differences that may relate to less astringent beverages. The QDA panel determined the combination of 0.20% thaumatin and 0.22% stevia rebaudioside M to most reduce astringency, however this did not correlate with higher acceptability as its acceptability remained as a neither like nor dislike rating. Consumers evaluated thaumatin, brazzein, and monk fruit to be clean-label ingredients after learning about their natural sources and flavor functionalities. More research about thaumatin, monk fruit, and especially brazzein is needed to find the ideal usage levels in AWB formulation. Brazzein was least preferred according to the focus group panel, who felt it did not reduce astringency. Future research could evaluate whether a higher concentration would be more effective. These findings aim to help sensorially improve acidic whey protein beverage formulations and provide the dairy beverage industry insight on creating and marketing more clean-label products.

Exploring The Role Of Salt-Tolerant Halomonas Inoculant In Altering Plant Gene Expression To Improve Salt Tolerance In Alfalfa., Ashley Kay Miller

Theses and Dissertations

Soil salinity is an increasing problem facing agriculture in many parts of the world. Climate change and irrigation practices have led to decreased yields of large areas of farmland due to increased salt levels in the soil. Irrigation introduces salts to the soil that with time accumulate and threaten crop yield. In arid climates like Utah, the practice of irrigation is especially threatening to salt-sensitive crops including alfalfa (Medicago sativa). Plants that have tolerance to salt are needed to feed livestock and the world's population. One approach to address this problem is to introduce genes encoding salt tolerance into the …

An Assessment Of Cattle Traffic On, And Seed Dispersion Patterns Of, Sclerocactus Wrightiae, David D. Lariviere

Theses and Dissertations

Cattle grazing has been a historic use of rangelands in Utah since Pioneer settlement in the mid 1800's. Wright fishhook cactus is a small globose cactus endemic to an area of 280,000 ha in south-central Utah and was listed as endangered in October of 1979, by the U.S. Fish and Wildlife Service (USFWS). By 2010, concerns were expressed that soil compaction in proximity to the cactus posed a threat to this species, though there was no empirical data to support such concern. In order to assess the impact of cattle traffic on Wright fishhook cactus, we used an imprint device …

Using De Novo Transcriptomes To Decipher The Relationships In Cutthroat Trout Subspecies (Oncorhynchus Clarkii), Andrea Leena Kokkonen

Theses and Dissertations

Cutthroat trout (Oncorhynchus clarkii) is a salmonid native to Western North America. For almost 200 years, the taxonomy of these species has fluctuated as ichthyologists and fisheries managers alike have tried to understand the diversity seen within these fishes. In the 1950s, Robert Behnke reexamined the cutthroat trout and identified 14 subspecies based on morphological observations, Pleistocene events, and modern geographic ranges. These designations were instrumental in preserving the remaining diversity of cutthroat trout. Over time, molecular techniques (i.e. karyotypes, allozymes, and mtDNA) have largely replicated Behnke's phylogenies. However, these studies have revealed that some of these relationships are consistently …

Evapotranspiration In Urban And Agricultural Systems With Interacting Irrigation And Nitrogen Fertilizer Treatments, Samantha R. Shumate

Theses and Dissertations

Nitrogen (N) fertilizer and irrigation are important inputs for all managed plant species, especially in arid and semi-arid climates. The interaction between N management and irrigation can lead to more sustainable practices. This is true for both agricultural and urban environments. Precision nutrient management has been widely adopted by producers in recent decades, and water conservation has become an important goal for turfgrass managers. In urban systems, our goal was to evaluate Kentucky bluegrass (Poa pratensis L.) to determine response to three N fertilizer rates and three irrigation rates in all possible combinations. The main and interacting treatment effects were …

Characterization Of Phage-Host Interactions And Its Impact On Tail Fiber Evolution, Jessica Marie Lewis

Theses and Dissertations

Beyond the scope of what our unaided eyes can see is a diverse and rich microbial community that greatly impacts each of our lives. Bacteria are microscopic organisms that can grow, develop, divide, and even rapidly evolve to adapt to new changes in their environment. Because of this, bacteria have gained the ability to thrive in extreme biological niches ranging from the high temperature and pressure surrounding hydrothermal vents to the harsh acidic conditions of our stomachs. One adaptation attracting attention, however, is their capability to survive in the presence of common and even last-resort antibiotics. The WHO recently reported …

Loading Force In Recreational Runners And Its Effect On Achilles Tendon Biomechanical Properties, Joshua K. Sponbeck

Theses and Dissertations

Background: Achilles tendinopathy is a common debilitating running related injury. Achilles tendon loading force has been hypothesized as a contributor to Achilles tendinopathy. Loading force through the Achilles tendon during running is impacted by many factors such as footwear and foot strike pattern. Achilles tendon biomechanical (Achilles tendon cross-sectional area, thickness, echogenicity, stiffness, and T2*) responses to loading forces are variable and measurable in vivo. These responses impact the physiologic function of the tendon. Aims: 1) To evaluate baseline Achilles tendon biomechanical characteristics associated with a runner's habitual foot strike pattern. 2) To evaluate single running bout Achilles tendon biomechanical …

Regulation Of Stress Responses And Membrane Morphology By Dspa In Synechocystis Sp. Pcc 6803, Rebekah Kathryn White

Theses and Dissertations

In the world of microorganisms, cyanobacteria are a uniquely skilled powerhouse. They participate in global nutrient and carbon cycling. They have the ability to photosynthesize, which allows them to use sunlight and carbon dioxide to produce cellular energy. However, photosynthesis has a lot of points were environmental stresses can interfere, increasing the chances of oxidative stress and nutrient imbalances that can amplify deleterious effects. One regulator in particular will be the target of this study. DspA, also known as Hik33, is a histidine kinase that perceives and regulates multiple overlapping stress responses. In this project, abiotic stress effects will be …

Maximum Size-Density Relationships In Mixed-Species And Monospecific Stands Of The Southeastern United States, Maxwell Robert Schrimpf

Theses and Dissertations

Maximum size-density relationships (MSDR) are used to quantify differences across sites in the number of trees of a given size and species that can be supported per hectare. These relationships are important to managers who are trying to maximize basal area and wood volume. In my study, I examined MSDR across Alabama, Georgia, Louisiana, and Mississippi using US Forest Service, Forest Inventory and Analysis (FIA) data. I determined the impact of species-specific, specific gravity, functional traits, and environmental factors on MSDR using a quantile regression approach. Overall, I found that climatic factors had the greatest influence on MSDR, and that …

Evaluation Of The Virulence Potential Of Avian Pathogenic Escherichia Coli Isolated From Broiler Breeders With Colibacillosis In Mississippi, Jiddu Joseph

Theses and Dissertations

Avian pathogenic Escherichia coli (APEC) is a bacterium that is responsible for colibacillosis in birds. However, information about broiler breeder APEC isolates is limited, but the data is critical due to the transfer of this bacteria down the production pyramid to progenies resulting in high mortality. Therefore, we evaluated the phenotypic virulence characteristics of 28 isolates using embryo lethality and day-old chick challenge assays. Also, the in vitro adhesion and invasion potential of selected nine isolates were identified. Results showed more than 1/3^rd of the isolates were highly virulent and the virulence increased as the number of virulence-associated genes …

Evaluation Of Heat Abatement Use, Vaginal Temperature, And Activity Of Pregnant, Lactating Holstein Cows Housed On Pasture With Or Without The Choice Between Shade And Sprinklers For Heat Abatement., Kevin M. Braman

Theses and Dissertations

The objective of this thesis was to determine how pregnant, lactating Holstein cows on pasture interact with shade and sprinklers when offered a choice or no-choice between methods. Authors hypothesized that cows would use shade more then sprinklers, but sprinklers would be more effective at cooling cows. Additionally, authors predicted cows using shade more would have decreased lying bouts and steps and an increase in time lying, compared to cows choosing sprinkler. Results indicate cows will use both methods when offered alone or together. However, cows will choose to be exposed or in shade at lower temperature humidity index values, …

The Interaction Between Predation And Sound Pollution On The Internal And External Microbiome Of The Grasshoppers Melanopus Sanguinipes, Alanna Bond

Theses and Dissertations

Anthropogenic activities such as construction and agriculture directly affect its surrounding environments. Many studies have focused on how megafauna and flora are impacted by human activities, however, relatively little is known how new occupation of land affects smaller organisms such as insects and microbes. Additionally, other stressors such as predation can impact host physiology. The grasshopper species Melanopussanguinipes was chosen to be used in a study to measure how stress caused by artificial sound and predation can alter exoskeleton and gut microbiomes once exposed to these stressors.

Molecular Mechanisms Of Novel Brain-Penetrating Oxime Acetylcholinesterase Reactivators On Sarin Surrogate-Induced Toxicities, Darby Caroline Stanford

Theses and Dissertations

Organophosphorus compounds (OPs), both nerve agents and insecticides, may induce damage leading to long-term neurological deficits. Oxime 20, the lead compound from a platform of substituted phenoxyalkyl pyridinium oximes (US Patent 9,227,937), is an oxime that reactivates OP-inhibited acetylcholinesterase (AChE) and has displayed neuroprotection within the brain of rats in in vivo tests where the currently approved treatment, pralidoxime (2-PAM), has not. This research investigated the neuroprotective effect of novel oxime therapy. Gene expression in rat piriform cortex was analyzed to determine if neurotoxicity, stress, and synaptic plasticity-associated genes were down-regulated by Oxime 20 following a sublethal dose of sarin …

Leaf Area Index And Aboveground Biomass Estimation Of Populus And Its Hybrids Using Terrestrial Lidar, Surya Adhikari

Theses and Dissertations

Short rotation woody crops (SRWC) eastern cottonwood (Populus deltoides) and hybrid poplar plantations were established in 2021 in Pontotoc and Oktibbeha counties of Mississippi to study the biomass potential of SRWC for biofuel production. We used a novel backpack LiDAR system to measure forest metrics and harvested sample trees to build aboveground biomass (AGB) and leaf area index (LAI) equations. The results showed that LiDAR-derived variables accurately estimated aboveground biomass (R² =0.81 and 29.22 % RMSE). However, the LAI estimation results showed that the LiDAR metrics moderately explained field measurements of LAI (R² =0.31 and 18.05% …

Pre-Emergence Herbicide Programs For Weed Control In Soybean (Glycine Max) And The Effect Of Rainfall Amount On Herbicide Activity, Caleb Knox Meyer

Theses and Dissertations

Preemergence (PRE) herbicides are used to control weeds and reduce pressure on postemergence (POST) herbicides. However, knowledge of length of control each herbicide provides, as well as the amount of activation rainfall required for adequate weed control, is unknown in Mississippi soybean production. Twenty-one PRE applied soybean herbicides were evaluated for their duration of residual control for five weeks over twelve site years on three weed species from 2021-2022. Some differences in control following herbicide application used on certain weed species were observed at different times. However, most PRE herbicides resulted in adequate (greater than or equal to 90%) control …

Nanoscale Modeling Of Membrane Systems Under Mechanical Deformation In Traumatic Brain Injury Using Molecular Dynamics, Anh Thi Ngoc Vo

Theses and Dissertations

Neuronal membrane disruption and mechanoporation are nanoscale damage mechanisms that critically affect brain cell viability during traumatic brain injury (TBI). These nanoscale cellular impairments are elusive in experiments and necessitate in silico approaches such as molecular dynamics (MD) simulations. Implementing MD, this research aims to investigate the effects of different key factors related to membrane deformation and damage, including force field resolutions, lipid compositions, and loading conditions.

To examine the impact of force field resolution, MD deformation simulations were conducted on 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidylcholine (POPC) lipid bilayer membranes, using all-atom (AA), united-atom (UA), and coarse-grained Martini (CG-M) force fields. The mechanical responses …

Isolation And Culture Of Epichloё For Reinfection Of Endophyte-Free Southeastern Wildrye (Elymus Glabriflorus), Bryna Joann Haile

Theses and Dissertations

Mutualistic relationships between endophytic fungi and grasses have shown to improve the hardiness of the host. This relationship is common in grasses, including North American native grasses that are important in both forage and grassland ecosystems. Elymus species, such as Canada wildrye (CWR), commonly host the endophytic fungi, Epichloё, while southeastern wildrye (SEWR) may not. In this study, seed of CWR and seed and leaves from local SEWR were assessed for endophyte infection. Infection status was confirmed via histological analysis of seed squashes and leaf peels. Presence/absence of endophyte was determined by scanning for mycelia within seed and between leaf …

Soil Health As Influenced By The Integration Of Cover Crops And Poultry Litter In North-Central Mississippi, Nikitha Reddy Kovvuri

Theses and Dissertations

Soil health-based agricultural management practices are widely promoted to improve soil structure, infiltration and reduce erosion. This study was conducted at two locations in North-Central Mississippi to evaluate the influence of different cover crop species and poultry litter on soil health that can impact crop production, climate change, and resilience. The results indicated that the cover crops showed a little effect on some soil health indicators compared to control treatment. However, in one location, rye, and a mixture of cover crops decreased bulk density and increased available water content and organic matter. The poultry litter had a positive effect on …

Nutritional Strategies To Reduce Salmonella Enteritidis Infections In Laying Hens: Prebiotic, Probiotic, And Precision Biotics, Ishab Poudel

Theses and Dissertations

Salmonella Enteritidis (SE) infections in laying hens is a significant cause of foodborne illness linked to the consumption of contaminated eggs. This dissertation encompasses novel strategies aimed to explore appropriate in-vitro and in-vivo models to evaluate the effects of these novel strategies to reduce SE in laying hens. Firstly, we investigated the potential probiotics, prebiotics, and essential oil combinations to reduce SE in-vitro. The results showed that probiotics and prebiotics are equally effective to reduce SE. In subsequent studies, we evaluated the role of vaccination history on cecal microbiota and SE infections with various doses of oral SE challenge. …

Effectiveness Of Intervention Studies Based On Diet And/Or Physical Activity In Treatment, Prevention, And Management Of Diabetes Among South Asians: A Systematic Review, Ishaan Arora

Theses and Dissertations

The purpose of this study was to describe diet and/or physical activity-based interventions and their control in cardiometabolic risk factors of diabetes for the South Asian (SA) population. A systematic review was conducted in accordance with the PRISMA guidelines. Seventeen randomized control trials meeting the inclusion criteria were included for analysis. Interventions with type-2 diabetic SA showed significant improvements in HbA1c% (4/5 studies), fasting blood glucose (3/4 studies), and postprandial glucose (2/2 studies). Interventions with at-risk/prediabetic and non-diabetic SA showed a modest change in overall outcomes, with significant change reported for post-prandial insulin (3/4 studies), BMI and weight (2/4 studies), …