Biology Commons^™

Patterns Of Molecular Evolution Driving Reproductive And Genomic Processes In Sauropsids, Taylor Green

Theses and Dissertations

Sexual reproduction is an important driver of genetic diversity and speciation through such forces as selection, mutation, and drift. Sauropsids are an appropriate clade to study shared molecular drivers of sexual and genomic evolution due to their genome architecture, sex determination mechanism (SDM) plasticity, and large syntenous genomic regions. Using comparative phylogenetic methods, I identify predictable patterns of selection in meiotic recombination genes and clade-specific drivers of recombination rate evolution. Then, leveraging whole genome sequencing, I demonstrate that American alligator genomes are characterized by an ancient loss of genetic diversity driven by drift and historic inbreeding. I also generate a …

From Miocene Origins To Ecological Diversification: Unraveling Evolutionary Dynamics Of North American Asters (Symphyotrichum), Sushil Dahal

Theses and Dissertations

Symphyotrichum, a plant genus traditionally treated within the genus Aster L., comprises >100 species of annual or perennial plants in the Compositae family Asteraceae. One of the most diverse genera in the southeastern US flora, the genus extends across the Americas, the Caribbean as well as eastern Eurasia. Despite its presence across the major American biomes and with distinctive floristic characteristics, several question regarding Symphyotrichum remains obscure. This research project focuses on exploring diverse aspects of Symphyotrichum systematics, biogeography and evolution. I tested three main hypotheses: (1a) Symphyotrichum originated ancestrally across Mexico and eastern North America in the Miocene ( …

Assessing Biotic And Abiotic Drivers Of Hybridization And Species Delimitation In A Highly Reticulate Syngameon, Nicholas John Engle-Wrye

Theses and Dissertations

Hybridization, or the flow of genetic materials between varieties or species, shapes evolution by generating novel genotypes, altering allele frequencies, and driving diversification. Yet, the rate at which hybridization occurs is heterogeneous across the tree of life and the ecological and evolutionary factors that govern its occurrence remain poorly understood. This dissertation examines how conserved biotic and abiotic niches influence hybridization and uses integrative methods to delimit species boundaries within Heuchera (Saxifragaceae), a genus notable for widespread interspecific gene flow and cryptic morphological diversity. Results reveal that hybridization is most frequent where pre- and postzygotic barriers are weak, as with …

Reproductive Genetics Of Caenorhabditis Nematodes, Dharani U. Matharage

Theses and Dissertations

Variation in reproductive traits and genome evolution reflects the interaction between selection, environment, and life-history. In the genus Caenorhabditis, recombination rate and sperm size exhibit a striking variation between strains and species. Here, Iintegrate three projects investigating recombination rate variation and recombination plasticity in C. elegans and sperm size divergence across Caenorhabditis species. First, I quantify recombination rates in two genetically distinct strains, N2 and CB4856, with different levels of laboratory adaptation using fluorescent markers spanning across gene-rich and gene-poor regions of the chromosome IV. I identify significant differences in recombination rate between the two strains within both gene-rich and …

Genetic Screen For Regulators Of Pol4, A Dna Repair Polymerase In Saccharomyces Cerevisiae, Pasang Dolma Sherpa

Theses and Dissertations

In Saccharomyces cerevisiae, DNA polymerase 4 (POL4) is the beta repair polymerase, the product of the POL4 gene, and is involved in base excision repair (BER) and microhomology-mediated end joining (MMEJ). Despite its involvement in these repair pathways and its conservation across eukaryotes, deletion of POL4 shows no detectable phenotype under standard laboratory conditions. I hypothesized that unknown genes act as backup systems, providing redundant activities that allow pol4Δ cells to survive. To test this, a genetic screen for mutants showing synthetic lethality with pol4Δ was implemented. I constructed a strain lacking the POL4 gene and carrying …

Optimizing Citriculture In South Texas With Endemic Hlb, Ruth Lilia Galan

Theses and Dissertations

The Texas citrus industry has a long history of resilience, rebounding from environmental and economic disasters. Over the last decade it has endured several hurricanes, freezes, pests and diseases. Huanglongbing (HLB), a graft-transmissible disease caused by Gram-negative bacterium Candidatus Liberibacter asiaticus which is vectored by the Asian citrus psyllid (ACP) (Diaphorina citri Kuwayama), is an endemic citrus disease posing serious threat to the long-term viability of the industry. Rapid production of high quality nursery trees and effective protection of young citrus transplants from HLB are critical for long term sustainability of citriculture in this region. Studies were performed to improve …

The Effect Of Drought On Avian Migratory Patterns And Stopover Through Texas And Louisiana, Ian Becker

Theses and Dissertations

Extreme weather events pose a massive threat for native ecosystems. As precipitation and temperature patterns are altered due to climate change, drought may become an incredibly severe event on the landscape. Drought directly impacts resources that migratory birds need during stopover en route to breeding and non-breeding grounds. Here, I quantify the impacts of drought on migration through Texas and Louisiana using 26 years of weather surveillance radar data. To understand how drought interacts with the local environment to impact migration, I tested 4 hypotheses displaying drought’s ability to impact migrants in conjunction with climatic and habitat level characteristics. Fall …

Developing A Qpcr Method For Evaluating Parasitoid Wasps As A Potential Means Of Control Of The Southern Cattle Fever Tick Rhipicephalus (Boophilus) Microplus In South Texas, Abbey Abalos

Theses and Dissertations

Ixodiphagus spp. wasps are natural enemies of ticks that have been reported to cause mortality in multiple tick species. Parasitoid wasps may represent a potential biocontrol alternative to traditional chemical tick control methods, which are challenged by non-target toxicity and the development of pesticide resistance in species of concern such as Rhipicephalus microplus, a pest of livestock that causes billions of dollars in loss to the livestock industry worldwide. Rhipicephalus sanguineus s.l. is a congeneric species of R. microplus, and parasitism of R. sanguineus by Ixodiphagus sp. in areas of co-occurrence has been observed. It is unknown if R. microplus …

The Impact Of Nutrition On Insecticide Resistance And Gene Expression In Aedes Aegypti, Esmeralda Guadalupe Rosas

Theses and Dissertations

The development of insecticide resistance in Aedes aegypti, a major vector of dengue and Zika viruses, threatens vector control efforts, particularly in endemic regions such as South Texas. Insecticides remain widely used; however, their overuse has accelerated metabolic resistance mediated by cytochrome P450 enzymes. Environmental factors such as larval nutrition may influence mosquito physiology and resistance-associated gene expression, yet this relationship remains poorly understood. This study examines how larval nutritional conditions affect the expression of cytochrome P450 genes linked to pyrethroid resistance in Aedes aegypti. Larvae were reared under five dietary treatments differing in lipid and protein ratios, and adults …

Investigating The Ability Of Foxo1 To Maintain Stem Cells, Stella Aime Rios

Theses and Dissertations

Forkhead box O (Foxo) transcription factors are key regulators of stem cell identity and tumor aggressiveness. Prior work from our group and others demonstrates that Foxo factors maintain stem-like states across diverse biological systems; however, the mechanisms by which Foxo1 suppresses differentiation remain poorly defined.

Using C2C12 myoblasts as a model, we investigated whether Foxo1 preserves stem-like programs through regulation of the nuclear pore protein Nup210. RNA interference was used to generate Foxo1 knockdown cells, followed by qRT-PCR, RNA-sequencing, and fluorescence microscopy. Transcriptomic analysis revealed widespread gene expression changes involving metabolic, mitochondrial, and transcriptional pathways. Notably, Nup210 expression was significantly …

Studies On The Contribution Of Osh6 To The Functions Of Late Endosomes, William King

Theses and Dissertations

The late endosome (LE) is a hub organelle connecting endocytic, biosynthetic, exocytotic, and autophagic vesicle traffic pathways. Malfunctions of LEs are associated with multiple age dependent diseases such as Parkinson’s disease (PD). Despite this significance, how cells refurbish lipids and proteins to LEs to maintain their sustained activities are not clear. Previous studies in the model organism budding yeast show that up-regulation of a lipid transporter Osh6 (PERG6-OSH6) accumulates phosphatidylinositol-4-phosphate (PI4P) on the trans-Golgi network. It also promotes vacuole fusion and maintains the robustness of vacuoles in aged cells. Since LEs are the organelle between the TGN and vacuoles in …

Utilizing A Genetically Diverse Species To Investigate Gene-Drug Interactions And Drug Efficacy, Jerry Nawongbay Gbarlea

Theses and Dissertations

Gene-drug interactions are fundamental to understanding variability in drug response and therapeutic efficacy. In this project, we leverage the natural genetic divergence between ecotype morphs of the blind Mexican cavefish (Astyanax mexicanus) to investigate differential responses to neuroactive compounds—specifically, the convulsant pentylenetetrazol (PTZ) and the anxiolytic Buspirone Hydrochloride. Astyanax Mexicanus is a tetra species consisting of both surface-dwelling (ancestral) and cave-dwelling (mutant) populations that have highly variable genetic backgrounds. Independently evolved populations of cavefish exhibit a suite of convergent traits that can be functionally interrogated to discover new genetic functions and interactions. These attributes make A. mexicanus an ideal model …

The Yeast Checkpoint Kinase Mec1p Functions In Transcription Termination By Facilitating Recruitment Of Pcf11p And Regulating The Torpedo Exonuclease Rat1p, Riddhi Patel

Theses and Dissertations

My dissertation includes two projects, centered on transcription regulation by checkpoint kinases of the DNA damage response (DDR). The first project focused on the role of checkpoint kinase Mec1p in transcription termination and regulation of the torpedo exonuclease Rat1p. Termination, closely linked with pre-mRNA 3’ processing, dissociates RNA polymerase II (RNAPII) from DNA and releases the nascent RNA transcript. Efficient termination is required for maintaining a pool of RNAPII that is available for re-entry into new transcription cycle. Previous results showed that inactivation of Mec1p in the absence of exogenous genotoxic stress downregulates the efficiency of transcription termination. This study …

Sex In Plants: Birth, Death, And Trying To Survive In Changing Climates, Elena M. Meyer

Theses and Dissertations

Plant mating systems are key determinants of fitness. Angiosperms exhibit a wide variety of reproductive strategies, including self-fertilization (or selfing), outcrossing, and mixed mating. It has been estimated that up to 43% of plant species are capable of selfing, and selfing has been hypothesized to provide reproductive assurance where opportunities for mating may be limited, such as in marginal environments. However, questions regarding the overall distribution of selfing rates across angiosperms, the maintenance of mixed mating in the face of inbreeding depression, and the impact of self-fertilization on diversification rates remain incompletely resolved. Here, we explore the dynamics of self-fertilization …

Building A Cell Specific System For In Vivo Rna Imaging Of The Endogenous Actin Gene In C. Elegans, Jasmine A. Huerta Canete

Theses and Dissertations

Messenger RNA (mRNA) plays a crucial role in protein synthesis and cellular processes, important for the development of cells such as neurons. When dysregulation occurs, it can lead to outcomes such as aberrant translation, causing neurodegenerative conditions to arise. Unfortunately, the localization of mRNA in an in vivo cell specific manner is still not understood. To address this, we decided to develop a cell-specific system to image RNA in vivo, within the organism known as C. elegans with a focus on the actin gene. The Actin gene encodes for an important cytoskeleton protein expressed ubiquitously, vital for the cell …

The Effect Of Sex On The Signal Transmission Of Duetting Bay Wrens, Rachel C. Schinzler

Theses and Dissertations

During communication, senders send signals for their benefit to elicit a behavioral response from a receiver. Acoustic signals are efficient for long-distance signaling; however, they are influenced by environmental features, such as foliage density, humidity, temperature, and time of day. Individuals can overcome these challenges by using signals with a trajectory of peak frequency, frequencies, volumes, and timing best suited to signal transmission in their environment. Signal transmission has been studied at the species level; however, not much is known about sex differences within the same species. Duetting species provide a useful system for examining sex-specific challenges in transmission, as …

Targeting Pancreatic Cancer With Rapamycin-Loaded Gold Nanoparticles Conjugated To Egf Peptide: Studies On Cytotoxicity And Uptake Mechanisms Aided By Proteomic Analysis, Adeolu Oluremi

Theses and Dissertations

Pancreatic cancer remains one of the most lethal malignancies, with a five-year survival rate below 5%. While rapamycin (Rap) has demonstrated therapeutic potential, its clinical utility is hampered by systemic toxicity. To address this limitation, this study developed a targeted nanocarrier system using gold nanospheres (AuNPs) functionalized with the Epidermal Growth Factor Receptor (EGFR) peptide GE11 for the specific delivery of Rap to pancreatic cancer cells. It is to note that pancreatic cancer overexpresses EGFR. The AuNP–GE11–Rap conjugates were successfully synthesized and characterized using physico-chemical techniques, which confirmed peptide conjugation and drug loading. In vitro studies using PANC-1 cells demonstrated …

Rab32c Mediates Osmoregulation And Calcium Homeoastasis In Dictyostelium Discoideum, Ashley Esparza

Theses and Dissertations

Vesicular trafficking is a fundamental process essential to cell viability and dictates roles in both cellular and tissue function in multicellular organisms. To further understand various vesicular trafficking processes, our lab focuses on the moderators of these processes, Rab GTPases, using the model organism Dictyostelium discoideum. This dissertation focuses explicitly on the uncharacterized protein Rab32C, a homolog of human Rab32. While several Rab family members have been well defined, the functionality of Rab32C remains poorly understood. This project investigated both the subcellular localization and functional role of Rab32C with biochemical, imaging, and molecular assays. Results from this study provide evidence …

Genomics Insights Into The Biogeography And Evolution Of Galapagos Iguanas Using Radseq And Wgseq Techniques, Cecilia Paradiso

Theses and Dissertations

The Galápagos archipelago is known for its unique endemic fauna shaped by isolation and geological dynamism. This thesis explores the evolutionary history of Galápagos iguanas, a monophyletic group comprising the marine iguana (Amblyrhynchus cristatus) and three land iguanas: Conolophus marthae, C. pallidus, and C. subcristatus. These species differ in distribu- tion, population size, and conservation status, with C. marthae classified as Critically Endan- gered due to its restricted range and small population. The main goal of this thesis is to fill knowledge gaps concerning the evolutionary trajectories, demographic histories, and genetic var- iability of Galápagos iguanas. The first chapter reconstructs …

Spatiotemporal Ecology Of Mycobacterium Ulcerans And Mycolactone Functions In French Guiana And Southeastern United States Aquatic Environments, Magdalene Dogbe

Theses and Dissertations

Mycobacterium ulcerans, the causative agent of Buruli ulcer, produces mycolactone, a polyketide toxin traditionally studied for its role in human pathogenesis. This dissertation presents a comprehensive spatiotemporal analysis of M. ulcerans and mycolactone producing mycobacteria (MPM) ecology in the Americas and also reveals mycolactone's role in the environment as a microbial community regulator. Through comparative studies in French Guiana (endemic) and the southeastern United States (non-endemic), combined with experimental microcosm investigations, this research contributes to environmental pathogen ecology understanding. Environmental surveillance across 2,226 samples from French Guiana revealed complete MPM restriction to freshwater environments, with zero detections from 1,226 coastal …

Pfos And Lung Injury: A Review Of Human And Experimental Evidence, Farzana Hakim

Theses and Dissertations

Human epidemiological research has shown the adverse health consequences of long-term accumulation of per- and polyfluoroalkyl substances (PFAS) in human tissue. Specifically, this review will examine the relationship between PFAS exposure, impaired immune system functioning, and an elevated risk of respiratory disease using both human and experimental data. Research on human populations indicates that children exposed to PFAS have lower levels of antibodies to vaccines; those children prenatally exposed to PFAS are more susceptible to upper respiratory infections; and that adult humans have a higher incidence of chronic obstructive pulmonary disease (COPD). Additionally, experimental studies demonstrate that PFOS and PFOA …

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 …

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% …

Testing Microscopic Approaches For Cementochronology In The 21st Century Identified Skeletal Collection, Portugal, Amando Luis Montalvo Jr.

Theses and Dissertations

Age-at-death estimation is a key component to the creation of a biological profile in forensic anthropology. Acellular extrinsic fiber cementum annulations have been shown to correlate with chronological age. Cementochronology examines this correlation through the sum of the alternating translucent bands and opaque annuli, and the age of eruption of a tooth. While several microscopy techniques have been used, there is no consensus on the most optimal. This study will assess the reliability, precision and accuracy of three microscopy techniques: Brightfield (BF), Phase Contrast (PC) and Differential Interference Contrast (DIC). PC was the most reliable (rTEM= 10.4%), the most precise …

Adipokines Mediate Fat-To-Ovary Communication To Regulate Oogenesis, Adipocyte Size, And Lipid Storage In Drosophila Melanogaster, Chad Herbert Simmons

Theses and Dissertations

Humans have complex signaling pathways that allow them to store and expend energy based on nutritional quality and availability. Inter-organ signaling is used to communicate nutrient availability between organs based on nutritional needs and the rate of cellular division. Our main overarching question is to investigate how fat-derived signals affect adipocyte morphology and the maintenance of stem cells in the ovary. While signaling pathways, like insulin and mTOR, and some adipokines that are involved in inter-organ nutrient sensing have been identified, the exact nutrient reliant mechanisms of stem cell maintenance are not completely understood. Using Drosophila melanogaster as a model, …

Unveiling Caulocovert: Conserved Phage And Gene Transfer Agent In Caulobacter, Talia Neco

Theses and Dissertations

Bacteriophage play an important role in bacterial evolution, population control, and horizontal gene transfer within microbial ecosystems. This study focuses on the discovery and characterization of Caulocovert, an active bacteriophage identified in multiple Caulobacter strains. Using genome annotation tools such as Artemis and Mauve, we identified multiple key phage genes, including the major capsid protein, head-tail connector, portal protein, and major tail protein. These phage genes are present in CB13 and several other strains, such as C. vibriodies CB15 and CB2, C. segnis CBR1, Caulobacter sp. FWC26, and the distantly related Caulobacter sp. D5 strain. The location of these genes …

Multiscale Modelling Of Eg5: Structural Insights Into Microtubule Interactions, Atp Hydrolysis, And Allosteric Inhibition Mechanisms, Soundarya Priya Alexandar Ms

Theses and Dissertations

The mitotic kinesin EG5 is essential for spindle bipolarity and accurate chromosome segregation during cell division, making it a validated anti-cancer target. Unlike conventional microtubule-targeting agents, EG5 inhibitors offer mitosis-specific action, reducing neurotoxicity. Although inhibitors targeting EG5’s allosteric site-I have been extensively studied, mechanistic insights into inhibition at site-II, and their combined effects, remain underexplored. This thesis systematically investigates the structural and dynamic mechanisms underlying EG5 function and its inhibition using an integrative computational approach.

Conformational analysis, coarse-grained dynamics, all-atom molecular dynamics simulations, and protein network analysis were performed on EG5 motor domain structures and EG5-microtubule complexes. Results show that …

Ground-Based Modeling Of Deep-Space Risks To The Spleen And Intestine In Mice, Edith Nathalie Pineda Sotomayor

Theses and Dissertations

Deep-space missions, such as those planned for the cis-lunar space and Mars, pose unique challenges to astronaut health due to prolonged microgravity (MG) exposure and low-dose chronic irradiation (CIR). Understanding the impact of these stressors on secondary lymphoid tissues, such as the spleen and intestine, is crucial for ensuring crewmembers' well-being, given the impracticality of conducting this research with human samples. Using a ground-based facility, we exposed C57BL/6 female and male mice to CIR (1.74 Gy at a dose rate of 0.0029 Gy/h) and/or simulated MG (SMG) via hind limb unloading (HLU) for one month. Spleen and intestinal tissues were …

Exposure To Zinc Oxide Nanoparticles Reveals A Death Resistance Mechanism In Dictyostelium Discoideum, Zoya Nadeem Faruqui

Theses and Dissertations

Zinc oxide nanoparticles (ZnO NPs) are very versatile due to their multifunctional properties including unique physicochemical and antimicrobial characteristics. They are widely utilized across various fields such as biomedical, industrial fields, environmental remediation, and agriculture. Therefore, their cytotoxic effects on biological systems necessitate a deeper understanding of the cellular responses to nanoparticle exposure. This project primarily investigates the impact of ZnO NPs on the model organism Dictyostelium discoideum AX4 (social amoeba) which has not been examined before unlike a vast variety of organisms in the literature. The cytotoxic effects of ZnO NPs on Dictyostelium discoideum AX4 cells are compared with …

3d Bioprinting On Electrospun Nanofibrous Scaffolds To Fabricate Myocardial Patches, Muthu Parkkavi S

Theses and Dissertations

Tissue-engineered three-dimensional (3D) myocardial patches offer superior and innovative treatment strategy for myocardial infarction (MI). Among the various scaffold fabrication techniques, electrospinning and 3D bioprinting have received great attention due to their ability to recreate native cardiac tissue mimetic characteristics. Despite several advantages, electrospun nanofibers have limitations in cell delivery due to random cell seeding, while bioprinting faces challenges in creating hydrogel constructs with ideal mechanical properties capable of supporting cardiac contraction/relaxation cycle. Hence in this work, hybrid myocardial patches were developed by converging electrospinning and bioprinting techniques.

Electrospinning of PLCL:PEOz (B73, 7:3 blend of poly-L-lactide-co-ε-caprolactone (PLCL) and polyethyl oxazoline …