Life Sciences Commons^™

Probing Prebiotic Rna Oligonucleotide Polymerization On A Mg-Fes Catalyst Using Microfluidics, Gabriella Garza

Theses and Dissertations

Non-enzymatic polymerization under aqueous conditions has long been viewed as unfavorable, due to product (H2O) inhibition in abiotic settings (Damer & Deamer, 2015); despite its efficiency in biology through ATP monomer activation. Geochemically sustained pH gradients may provide free energy for condensation of organic monomers (Martin & Russell, 2003). Here, we investigated a biologically analogous non-enzymatic mechanism for RNA oligomerization, by probing the catalytic properties of a Mg-rich FeS mineral under aqueous conditions. FeS minerals promote a diverse prebiotic reaction (Wächtershäuser, 1988) and would have precipitated at Hadean submarine hydrothermal systems (Sojo et al., 2016). Natural pH and redox gradients …

Population Structure Of Red Drum (Sciaenops Ocellatus (Linnaeus, 1766)) In Two Systems In The Northwestern Gulf Of Mexico, Sandra Antonia Leal

Theses and Dissertations

Red drum (Sciaenops ocellatus) are an economically significant species of fish inhabiting the Gulf of Mexico. There are limited studies assessing S. ocellatus population structure focused on the southern coast of Texas. A total of 1,008 fish were collected over one year on a quarterly basis at South Bay (SB) and Holly Beach (HB) in the Lower Laguna Madre (LLM) of Texas to assess population structure. Juvenile S. ocellatus utilize the water systems of the LLM as a nursery ground and were more abundant at SB (n = 718) than HB (n = 290). The most abundant age classes were …

Applicability Of Cementochronology To Estimate Season-Of-Death In Humans: Insights From Modern Documented Collections, Olga Ibarra-Sanchez

Theses and Dissertations

Dental cementum is characterized by lifelong deposition of alternating opaque annuli in fall/winter and translucent bands in spring/summer. This study aims to test the applicability of cementochronology to estimate season-of-death, by observing the properties of the last layer, with direct implications for forensic anthropology and bioarchaeology. The sample includes canine teeth from 146 adults (84 males, 62 females), age-at-death ranging from 20-97 years (mean=61.7 years, SD=18.6 years), from two contemporary skeletal collections. Of these individuals, 78 (53.4%) died in spring/summer and 68 (46.6%) died in fall/winter. Overall accuracy was low at 64.4% (94/146). Accuracy was higher for spring/summer deaths 100.0% …

Engineered An Ultrasmall Curcumin Oral Nanoformulation Restores Intestinal Integrity And Gut Microbiota Dysbiosis, Vivek Sharma, Prateeksha Prateeksha, Balwant Paliya, Sateesh Gupta, Sarvendra Singh, Anand Anunay, Sushil Agrahari, Shailendra Singh, Chandana Rao, Saroj Barik, Brahma Singh

Department of Biochemistry and Molecular Biology Faculty Papers

Antibiotic therapy for bacterial infections often disrupts gut microbiota (GM) and intestinal integrity, inducing chronic inflammation and inflammatory bowel diseases. An effective therapeutic intervention is urgently needed to alleviate the aforementioned adverse effects of antibiotics. Curcumin (CUR) reveals great potential to restore intestinal integrity and GM dysbiosis due to its strong antiinflammatory and prebiotic effects. However, the weak solubility and stability of CUR result in limited bioavailability and a short half-life, which restricts its clinical uses. An ultra-small CUR oral nanoformulation was created using a carboxylated galactomannan (cGM), facilitated by hydrogen bonding between the phenolic hydroxyl groups of CUR and …

Explaining The Association Between Kittlitz's Murrelets (Brachyramphus Brevirostris) And Tidewater Glaciers: Which Habitat Factors Influence Spatial Distribution?, Brendan Higgins

Marine Biology

The Kittlitz’s Murrelet (Brachyramphus brevirostris) is a rare and cryptic seabird species that inhabits Alaska and Eastern Siberia. Populations of Kittlitz’s Murrelets that occur in areas with tidewater glaciers are tightly associated with tidewater glaciers and are only found in close proximity to them. The Kittlitz’s Murrelet is a species of conservation concern, but specific habitat associations are poorly understood. I conducted a multidisciplinary investigation to better understand associations between Kittlitz’s Murrelets and tidewater fjord physical structure. I used remotely sensed spectral indices to model change in abundance of suitable nesting habitat, and a long-term oceanographic dataset to quantify changes …

Investigating Mariculture-Associated Ecosystem Services Across The Northern Gulf Of Alaska, Josianne Haag

Oceanography

The rapid expansion of mariculture in Alaska can drive physical and chemical alterations to the marine environment by introducing non-native organisms or artificially increasing the biomass of a native species. Currently, the main mariculture products grown in Alaska include the Pacific oyster (Crassostrea gigas), the Pacific blue mussel (Mytilus trosuslus), and three macroalgae species: ribbon kelp (Alaria marginata), sugar kelp (Saccharina latissima), and bull kelp (Nereocystis luetkeana). This dissertation examines how these species can impact their surrounding environment to better inform management practices for this growing industry. This research characterized the resource use of C. gigas and M. trossulus seasonally …

Ontogenetic Analysis Of Parasaurolophus Braincases (Ornithischia, Hadrosauridae) From The Kaiparowits Formation (Upper Cretaceous) Of Utah, Usa: Comparing Juvenile And Adult Morphology, Amanda "Billie" C. Guerrero

Electronic Theses, Projects, and Dissertations

This study documents the ontogenetic development of the braincase in Parasaurolophus, a lambeosaurine hadrosaurid dinosaur known for its distinctive cranial crest. Whereas the crest has been extensively examined for its roles in communication and display, the braincase remains less understood, despite its structural and functional relationship with the crest. This research compares the braincase morphology of a juvenile specimen (RAM 14000, "Baby Joe"), a subadult specimen (RAM 17000), and an adult P. tubicen (NMMNH P-25100), to investigate how developmental changes influenced sensory systems, neurocranial architecture, and biomechanical adaptations across ontogeny.

Detailed morphological analysis reveals progressive changes from juvenile to …

Bricks, Bushes, And Bones: Urbanization Influence On Western Fence Lizard (Sceloporus Occidentalis) Morphology And Performance, Daisy P. Xiong

Electronic Theses, Projects, and Dissertations

With increasing urbanization due to rising human populations, organisms may be forced to adapt rapidly to changing environments. Urbanization is replacing natural surfaces with more impervious substrates which can result in morphological changes affecting organismal locomotion, then also impact fitness. This study compares urban and natural habitat impact on Western Fence Lizards (Sceloporus occidentalis) and their adaptations in such settings. We captured lizards from three locations in inland Southern California with both urbanized and natural habitats in order to compare the morphological differences between lizards, and then measured their performance to determine the possible impacts from their morphology. …

Analyzing The Impact Of Diet On Dusky Gopher Frog (Lithobates Sevosus) Development In Head Start Programs, Mckalyn Nelson

Honors Theses

Species are constantly impacted by human activity, directly or indirectly. One critically endangered species under investigation is the dusky gopher frog (Lithobates sevosus), which is an endemic species of frog found in the southeastern United States. Historically found from Louisiana to Alabama, a drought in 2002 narrowed the dusky gopher frog range even further. Head start programs have been shown to be effective in increasing population numbers; however, there is not much published data on the effectiveness of captive rearing diets for these programs. The dusky gopher frog head start program at the University of Southern Mississippi’s Lake …

Functional Characterization Of The Hssb1 K94q Mutation, Isaiah Singleton

All Theses

Genome stability depends on precise DNA repair pathways such as homologous recombination (HR), where human single-stranded DNA-binding protein 1 (hSSB1) stabilizes single-stranded DNA (ssDNA) intermediates and recruits repair complexes. Post-translational modifications, including acetylation, are known to regulate hSSB1 activity, but their molecular effects remain poorly defined. This study examined the role of lysine 94 (K94) acetylation using a glutamine substitution mutant (K94Q) that mimics the acetylated state. Recombinant hSSB1 wild type (WT) and hSSB1_K94Q were expressed in Escherichia coli and purified using Ni–NTA affinity chromatography. Biochemical analyses, including electrophoretic mobility shift assays (EMSA), single-strand annealing assays, and displacement loop …

Reproduction And Larval Development Of The Invasive Asian Longhorned Beetle In South Carolina, Lindsey A. Stone

All Theses

The Asian longhorned beetle (Anoplophora glabripennis Motschulsky; ALB) is a major threat to forest health due to the damage done by larval feeding in host trees. In 2020, ALB was discovered in Charleston County, South Carolina, which presents a novel climate for this invasive pest in North America. I investigated the reproductive biology and larval development of ALB to support detection and management efforts. By exposing 19 host trees to mated pairs of adults, I was able to determine rates of oviposition success (55%), egg viability (55%), and early larval survival (56%). On average, females chewed nearly 1 egg …

Investigating The Impacts Of Azole Antifungals On Growth Of Cryptococcus Neoformans, Gnanambika Sindhe

All Theses

Cryptococcus neoformans, an opportunistic fungal pathogen is responsible for cryptococcosis, leading to approximately 181,000 deaths annually, predominantly in regions such as Sub-Saharan Africa. Fluconazole, a widely used fungistatic azole, is often administered due to its relative affordability and lower toxicity. However, resistance to fluconazole in C. neoformans can arise through aneuploidy, complicating treatment efforts. This study aims to deepen our understanding of resistance mechanisms to azole drugs by comparing fluconazole with other azoles, including both clinical and agricultural azole antifungals. Disk diffusion assays were performed to evaluate the ability of C. neoformans to develop resistance to these compounds, focusing …

Citrullus Amarus Drought Tolerance: An Above And Below Ground Analysis, Ben A. Hyland

All Theses

Ever rising environmental temperatures threaten global food security by worsening severity and increasing the occurrence of drought. Commercially cultivated watermelon (Citrullus lanatus), have reduced drought tolerance due to a narrow genetic base caused by breeding for desirable traits such as sweetness, size, and flesh/rind color. Comparatively, the crop wild relative desert watermelon variety (Citrullus amarus), while more drought tolerant than their commercially cultivated relatives (C. lanatus), still require large amounts of water to grow and produce reliable fruit yields. Watermelon root morphology plays a key role in their ability to tolerate drought, with more …

Plant Community Responses To Wildfire, Timber Thinning, And Bison Reintroduction On The Northern Great Plains, Ethan H. Van-Derpoel

All Theses

The Northern Great Plains (NGP) is one of the largest intact grasslands remaining in the world. These two studies examine a few of the ecological concerns on the NGP today. First, the woody encroachment of conifers into grasslands and the effects of wildfires. Second, the effects of bison (Bison bison) reintroduction on plant communities. In Chapter 1, this study aims to examine the effects of wildfire and mechanical timber thinning, using a two-by-two factorial design, on plant community responses and forage quality in the Bull Mountains area of central Montana, USA. We found that our treatments had varying …

Soundscapes Of Alaska's Arctic Coastal Plain: Implications For Wildlife, Maxwell Plichta

Biological Sciences

Passive acoustic monitoring is an effective tool for collecting baseline acoustic data in remote locations and for advancing our understanding of soundscapes, the sound that emanates from a landscape. Terrestrial Arctic soundscapes remain understudied. The Arctic Coastal Plain (ACP) of northern Alaska is an ecologically, culturally, and economically significant region, containing a mix of land-uses and management practices. This study leverages a spatially large (~8,000 km2), multi-year dataset of acoustic recordings and paired images collected across the ACP to investigate how natural and anthropogenic factors influence the soundscape (Chapter 2), and how acoustic metrics influence the behavior of caribou (Rangifer …

Serum Concentrations Of Inflammatory Markers And Selected Nutrient Metabolites In Holstein And Jersey Cows Across The Transition Period, Avery Orr

Master's Theses

The transition period, spanning the weeks surrounding parturition, requires dairy cows to undergo synchronized metabolic, endocrine, and immunological adjustments that support the onset of lactation but also heighten disease susceptibility. Although individual inflammatory or metabolic biomarkers have been extensively studied, the integrated immunometabolic dynamics that occur across this period and the difference between breeds is not fully understood. The objective of this study was to characterize longitudinal patterns in key nutrient metabolites and inflammatory markers in Holstein and Jersey cows and assess how these systems interact across the transition period.

A total of 63 Holstein and Jersey cows were sampled …

Testing For Local Adaptation In Sympatric Monkeyflowers Growing In Serpentine Seeps And Adjacent Rock Outcrops, Avin Niknafs

Master's Theses

Divergent selection across heterogeneous environments can drive ecological differentiation and the evolution of locally adapted populations, even when gene flow occurs. We tested for local adaptation between two sympatric monkeyflowers, Erythranthe guttata and E. serpentinicola (formerly Mimulus), which co-occur on the central coast of California. Erythranthe guttata is a perennial species primarily found in moist serpentine seeps, whereas E. serpentinicola is an annual species restricted to adjacent serpentine rock outcrops. Using a reciprocal transplant experiment with second-generation, greenhouse-derived seed, we quantified germination, survival, and reproductive success across contrasting microhabitats. We further evaluated the relative contributions of species, lineage, …

Robustness Of Network Inference Algorithms Under Network Class Misspecification, Roberto Ceja

Electronic Theses, Projects, and Dissertations

Inferring phylogenies in the presence of hybridization remains a difficult problem. As a result, many current methods for reconstructing phylogenetic networks are restricted to a simple class of networks known as level-1. This restriction arises from theoretical considerations rather than empirical evidence, with real data possibly arising from complex networks. In this work, we evaluate the robustness of two level-1 network inference methods, SNaQ and NANUQ+, through a simulation study, when the input data originates from a more complex network. Specifically, we investigate whether these methods can accurately recover important features of the true species network, such as the circular …

Requirement Of Prepiilin Peptidase Activity For Variovorax Paradoxus Eps Flp/Fap Pilus Assembly, Jenny L. Lanthripp

Electronic Theses, Projects, and Dissertations

Variovorax paradoxus is a Gram-negative aerobic bacterium present in both soil and the human oral microbiome. This species contributes to biotransformation of xenobiotics and promotes plant growth. Interestingly, although the genome of strain EPS lacks the flagellum operon annotated in strain S110, the microbe remains motile, and flagella can be observed microscopically. To investigate this unexpected phenotype, motility mutants were enriched from a Tn5 mutant library using a liquid culture settling strategy. A total of 122 isolates were screened for motility defects, and 57 exhibited significantly reduced motility compared to the wild type. Rescue cloning revealed that over 60% of …

Interactions Between Black, Brown, Blue And Green Carbon From Terrestrial To Marine Ecosystems: A Critical Review, Allison White, Richard Kline, Md. Saydur Rahman

School of Earth, Environmental, & Marine Sciences Faculty Publications

Black and brown carbon are byproducts of the incomplete combustion of biomass or fossil fuels. These light-absorbing aerosols influence climate by altering the radiative balance through the absorption and scattering of sunlight, exacerbating global climate change. Their subsequent deposition on terrestrial and marine environments affects surface albedo, snow and ice melt, and biogeochemical processes, leading to further environmental consequences. In contrast, green and blue carbon refer to carbon stored in terrestrial vegetation and marine ecosystems, respectively. These ecosystems play a crucial role in mitigating climate change by sequestering atmospheric carbon; however, they are increasingly threatened by climatic disturbances, anthropogenic activities, …

Leptinotarsa Texana Schaeffer And Gargaphia Arizonica Drake & Carvalho As Potential Biocontrol Agents For The Noxious Weed Solanum Elaeagnifolium Cav, Samikshya Subedi, Stephanie L. Kasper, Alexis Racelis, Greg Lefoe, Rupesh R. Kariyat

School of Earth, Environmental, & Marine Sciences Faculty Publications

Silverleaf nightshade (Solanum elaeagnifolium Cav.; SLN) is a perennial forb native to the southern United States, Mexico and South America that has become a serious agricultural weed across the world. Biological control has emerged as a significant alternative for the management of (SLN) due to the challenges and high costs associated with chemical and mechanical controls. In this study, we used a combination of field and laboratory studies to (1) explore the fundamental and realized host ranges of two North American insects, Leptinotarsa texana Schaeffer and Gargaphia arizonica Drake & Carvalho and (2) assess their suitability as potential biological …

Fast & Forensic: Rapid Detection & Quantitation Of 30 + Emerging Novel Psychoactive Substances In Hair Using Lc-Ms/Ms, Seokjin Hwang

Student Theses

The continuous emergence of novel psychoactive substances (NPS) poses a significant challenge for forensic and clinical toxicologists, due to their structural diversity, rapid turnover on the illicit drug market, and limited toxicological information. Hair is a powerful matrix for retrospective drug exposure assessment and monitoring NPS worldwide. Not only does it provide a broad window of detection but also a simple sample exchange amongst laboratories. However, the extraction of multi-class NPS in a single method remains an analytical challenge. Therefore, there is an urgent need for extraction techniques and analytical methods that are both rapid and capable of multi-class quantitation …

Context Dependent Regulation Of Dicer Function During Oocyte-To-Embryo Transition, Nick A. Newkirk

Dissertations and Theses (Open Access)

Over two decades ago, Dicer was discovered as the primary enzyme responsible for the generation of small RNAs known as the microRNAs (miRNAs) and short interfering RNAs (siRNAs). Spatiotemporal regulation of Dicer-dependent small-RNA biogenesis affects many aspects of biology, including aging, disease progression, fertility, and cancer. Interestingly, a distinct population of Dicer-dependent small RNAs, known as the endogenous siRNAs (endo-siRNAs), are uniquely abundant in the germ cells and gametes, and are critical for normal fertility. Despite their function regulating new life, the mechanisms controlling their biogenesis and subsequent germ cell functions remain poorly defined. Work to parse these mechanisms in …

Capsinoids, Non-Pungent Trpv1 Agonists, Induce A Mild Hypothermia That Provides Short- And Long-Term Neuroprotection After Ischemic Stroke, Alexander Andersohn, Alexander Andersohn

Dissertations and Theses (Open Access)

Therapeutic hypothermia (TH) has demonstrated neuroprotection in instances of cardiac arrest and neonatal hypoxia/ischemia but faces different challenges in application to stroke due to the activation of cold defense mechanisms in conscious patients. This dissertation examines the efficacy and specificity of capsinoids (a purified mixture of capsiate and dihydrocapsiate) to induce a sustained mild hypothermia in conscious mice that is neuroprotective after stroke. Capsinoids function as TRPV1 agonists. However, unlike capsaicin, capsinoids are vulnerable to esterase-mediated breakdown, thus significantly restricting their action to the site of delivery. We showed that capsinoids delivered intraperitoneally (IP) to mice induced a TRPV1-dependent drop …

Functional Analysis Of Ftsa-Mediated Recruitment Of Ftsk In Escherichia Coli, Abbigale Perkins

Dissertations and Theses (Open Access)

Bacterial cytokinesis requires precise coordination between cytoplasmic and periplasmic components of the divisome to ensure that membrane constriction and chromosome segregation occur in synchrony. The actin-like protein FtsA plays a central role in this process by tethering FtsZ to the membrane and recruiting downstream division proteins. Despite its essential function, the mechanisms by which FtsA coordinates divisome activation and the recruitment of late-acting proteins remain incompletely defined. To address this, the role of FtsA in activating septal synthesis and recruiting the DNA translocase FtsK was examined using mutational analysis in Escherichia coli.

The FtsA^{M96E R153D} variant, which has …

Neural Dynamics Supporting Flexible Cognition, Meredith J. Mccarty

Dissertations and Theses (Open Access)

Flexible cognition enables humans to adapt their behavior to changing circumstances by prioritizing relevant information and filtering out distractions. This process is thought to be supported by the integration of ongoing behavioral goals with incoming sensory information, but how this integration is realized in the human brain remains unclear. It is unknown how high-order sensory cortices can balance specialized processing with flexible integration of changing behavioral goals. In the following investigations, we use intracranial EEG (iEEG) recordings in humans to study the neural dynamics of flexible cognition during high-order sensory processing. First, we validated assumptions about the locality of iEEG …

Orthogonal Comparison Of Nuclear And Mitochondrial Clonal Architectures In Hematologic Malignancies, Nehali Shah

Dissertations and Theses (Open Access)

Acute myeloid leukemia (AML) is a hematologic malignancy characterized by accumulation of mutations that disrupt hematopoietic differentiation and promote clonal expansion. Understanding how these mutations arise and evolve is essential for improving diagnosis, prognosis, and treatment stratification. Current methods are limited by either restricted genomic coverage (targeted panels) or low throughput and high cost (in single-cell whole genome sequencing, scWGS). An emerging alternative is the use of mitochondrial DNA (mtDNA) mutations as clonal markers.

This study aims to determine whether mitochondrial-derived clonal architectures correlate with nuclear-derived clonal architectures in AML, thereby evaluating mtDNA as a scalable orthogonal tool for lineage …

A Mixed Methods Study Of The Weather And Climate Science Curriculum Pilot In South Carolina K-12 Schools, 4-H, And Agricultural Education Programs, Emily B. Hood

All Dissertations

Weather and climate science topics in K-12 education are more important now than ever due to extreme weather and climate events happening worldwide. Most U.S. science teachers included climate science in their courses, but they may not have a sufficient background in the topic which can hinder their efforts, or there is no explicit curriculum for the teacher to utilize. Research indicates that there is a need for innovation in the curriculum to help prepare children to become the next generation of leaders and address complex problems, such as issues related to weather and climate science. There are a few …

Horticultural Strategies To Improve Yield And Efficiency For Controlled-Environment Cannabis Production, Michael John Alden

All Dissertations

Controlled-environment cannabis (Cannabis sativa L.) production is a novel horticultural industry due to long-standing federal prohibitions associated with production, distribution, and consumption of this species. Many cannabis production methods are based on legacy knowledge and hypotheses that often contradict standard practices used in the agriculture and floriculture sectors. During this research, several horticultural practices were evaluated, including shoot number manipulation, fertilizer restriction, harvest timing, and photoperiod manipulation. Shoot number manipulation was achieved by repeatedly pinching apical shoots, which reduced reproductive shoot length (cm/shoot) and improved inflorescence:trim ratio, both of which can reduce material cost in production and labor cost …

Breeding For Disease Resistance In Melon And Watermelon, Venkata Rao Ganaparthi

All Dissertations

Watermelon and cantaloupe are two widely consumed cucurbits, but their acreage in the United States reduced by nearly 50% in last two decades. Fusarium wilt caused by a soil borne pathogen Fusarium oxysporum f. sp. niveum(Fon) race 2 is a major limiting factor in watermelon production as it reduces yields by 80%. Grafting watermelon plants onto the root stock of wild, disease-resistant varieties like ‘Carolina Strongback’ is the best strategy to manage Fon race 2. Though effective, this approach increases production costs.

Part of this dissertation focused on finding more sustainable, cost-effective solutions to control Fusarium wilt …