Biology Commons^™

Effect Of Osmolytes On The Interplay Of Water Protein And Dna In Ecori Dna Recognition Using Molecular Dynamics Simulations, Aathithya D

Theses and Dissertations

EcoRI is a type II restriction endonuclease that has been widely used as a model system to study protein-DNA interaction owing to its high degree of specificity. This enzyme does not recognize even a single basepair change in its recognition sequence, (GAATTC)2, under normal conditions. However, in the presence of osmolytes, such as glycerol and DMSO, the specificity of EcoRI is slightly relaxed and recognizes sequences that differ from its cognate sequence in the first basepair position. This relaxed specificity has been attributed to the dehydration of the EcoRI-DNA which presumably results in tighter complex formation and subsequent catalysis. However, …

Transcription Fidelity In The Face Of Oxidative Damage, Eastilan Gyiwah Appiah

Theses and Dissertations

It is very important that the process of transcription is correctly carried out in the cell for the faithful expression of the genetic code. However, should mistakes happen, they can result in transcription errors which interfere with the protein-making machinery of the cell. This will result in accumulation of proteins and dysfunctional proteins that have the potential of causing diseases like Alzheimer’s. Oxidative damage caused by hydrogen peroxide is known to cause transcription errors in organisms like yeast. It is therefore important to investigate the extent to which hydrogen peroxide can damage cells.

Assessment Of Floral Resources From Three Tamaulipan Thornscrub Communities Of The Lower Rio Grande Valley, Gracie Makenna Granados

Theses and Dissertations

The Tamaulipan thornscrub is a transition zone between the neotropics and the temperate regions, harboring high biodiversity. This habitat supports a diverse insect community, including many pollinators of native and cultivated plants in Texas and northeastern Mexico. This ecosystem has been extensively degraded and lost; only 5% of its original cover remains north of the Rio Grande. Restoration of the Tamaulipan thornscrub has been ongoing for over three decades, but the important roles of pollinators in the success of such efforts and the functioning of the restored ecosystem have rarely been considered in restoration efforts. The purpose of this study …

Opa1-Mediated Mitochondrial Dynamics In Myogenic Differentiation Of C2c12 Myoblasts, Daniel Eloy Bazan

Theses and Dissertations

Mitochondria play a pivotal role in metabolic energy production, cellular signaling, and apoptosis. To carry out these key cellular roles, mitochondria dynamically balance their organization through opposing including fusion and fission processes. The balance between mitochondrial fusion and fission is regulated by key proteins such as OPA1 (optic atrophy 1) and OMA1 (overlapping activity with metalloprotease). More recently, mitochondria have been increasingly revealed to play key roles in cellular differentiation, where metabolic demands are reprogrammed. This study aims to elucidate the specific roles of OPA1 and OMA1 in the differentiation of C2C12 myoblast cells into myotubes.

Our data demonstrates that …

Phenotypic Plasticity In Response To Abiotic Factors In Silverleaf Nightshade (Solanum Elaeagnifolium), And The Effectiveness Of North American Lacebug (Gargaphia Arizonica Drake And Calvo) As A Biocontrol, Marco Andre Silguero

Theses and Dissertations

Silverleaf nightshade (Solanum elaeagnifolium) is a widespread invasive weed in South Texas and other arid regions, where it reduces crop productivity, competes with native vegetation, and resists conventional control methods. Its ability to thrive across different environments is linked to phenotypic plasticity, allowing it to adjust growth and physiology in response to light and water availability. In this thesis, I examine the role of plasticity in S. elaeagnifolium under field conditions and evaluate the potential of the North American lacebug (Gargaphia arizonica) as a biological control agent. Field observations were used to measure plant traits such as height, stem thickness, …

Selenium Nanoparticles Synthesized By Pulsed Laser Ablation In Liquids For Antimicrobial Applications, Tina Hesabizadeh

Theses and Dissertations

This study aimed to synthesize selenium nanoparticles (Se NPs) by Pulsed Laser Ablation in Liquids (PLAL) and investigate their antibacterial and biological effects, particularly their impact on cell viability and related biological responses. Spherical amorphous Se NPs were produced by irradiating a selenium target using a combination of bottom- and top-ablation protocols. After autoclaving, the amorphous Se NPs were converted into trigonal Se NPs. Se NPs were characterized by using Scanning Electron Microscopy (SEM), Transmission Electron Microscopy (TEM), and Fourier Transform Infrared Spectroscopy (FTIR). The biological effects of Se NPs were quantitatively assessed through evaluations of cell viability and associated …

Transformation With Genes To Improve Lipid Production And Barcoding To Identify Unknown Algal Species, Michelle T. Rada

Theses and Dissertations

With the rising demand for alternative fuels, algal-based biofuels are a promising, sustainable source that meets commercial interest while producing lower greenhouse gas emissions compared to fossil fuels. This thesis explored two studies, evaluating microalgae for their future potential in lipid yield for biofuel production.

The first study involved developing a cost-efficient electroporation protocol that allowed for the genetic transformation of Chlamydomonas reinhardtii using the pChlamy_4 vector, which supports future cloning of genes to enhance lipid production. Parameters affecting DNA uptake and integration into algal genomes were studied: the effect of cell density, the settings of the electroporation device, and …

Circannual And Kinship Cues Shape Reproduction And Epigenetic Aging In Peromyscus, Kim Tuyen Huynh Dam

Theses and Dissertations

Evolutionary success is defined by the ability of a species to adapt and survive across many generations. This success is not determined by any single attribute but rather includes the entrenched, complex system that could be associated with biological rhythms, reproductive strategies, and regulations of epigenetic and genetic components. By using closed Peromyscus colonies as a model and by coupling mathematical modeling, analyses of breeding records, epigenetic studies, and in vitro and in vivo experiments, this dissertation aims to discover how Peromyscus adjusts to the internal and external pressures to ensure their survival and preserve evolutionary fitness in controlled environments. …

Exploring The Ancestry And Mutational Signatures Of Free-Breeding Dogs From Chernobyl And The Galápagos Islands, Gabriella Jean Spatola

Theses and Dissertations

Two free-breeding dog populations, one in Chernobyl, Ukraine, and the other on the Galápagos Islands, Ecuador, exist on opposite sides of the globe, yet both hold unique scientific potential to further our understanding of free-breeding dog population dynamics and evolutionary processes related to their environments. In the following studies, blood samples from more than 400 individual Chernobyl dogs were collected and their genomes were analyzed alongside over 1500 purebred and 200 global free-breeding dogs, describing genetic relationships and the extent of admixture with purebred migrants. Importantly, the sampled Chernobyl dogs had long-term exposures to ionizing radiation because of the 1986 …

Hybrid Penstemon Flowers: Colors, Pigments, And Detectability & Experimental Teaching: Evaluating The Impact Of Active Learning, Josh Thomas Edward Stevens

Theses and Dissertations

Shifts to different primary pollinators are often accompanied by changes in suites of floral traits. Understanding how and why these floral adaptations evolve is a central goal in evolutionary biology. Within the genus Penstemon, the transition from bee-pollinated to hummingbird-pollinated flowers is a common evolutionary pattern. These pollinator shifts have caused several closely related species to exhibit distinct pollination syndromes. One example of this evolutionary phenomenon can be seen within the sister species P. eatonii (hummingbird-pollinated) and P. laevis (bee-pollinated). These two species form several hybrid zones, in which hybrid individuals exhibit colors resembling both parental species, along with a …

Investigating The Threshold Of Opa1-Mediated Mitochondrial Fusion In Shsy5y Cells, Jorge Alberto Elizondo

Theses and Dissertations

Mitochondrial dynamics occurring under stress-induced conditions in SHSY5Y neuroblastoma cells provide insight into the OPA1-mediated mitochondrial fusion threshold in cells of varying energetic demands. Mitochondria are dynamic structures that are continuously balancing fusion and fission, depending on cellular needs. The ability to fuse and divide relies on the maintenance of the mitochondrial transmembrane potential. Stress-induced conditions in SHSY5Y cells were induced via utilization of carbonyl cyanide m-chlorophenylhydrazone (CCCP), a protonophore that disrupts the transmembrane potential. OMA1 protein reacts to the loss of transmembrane potential and subsequently cleaves the fusion-active isoforms of OPA1, L-OPA1. This causes an accumulation of S-OPA1, the …

Investigating The Immunomodulatory Effects Of Cdk8/19 Inhibitor Senexin631 In A Her2-Positive Breast Cancer Model, Stephen O'Rourke

Theses and Dissertations

HER2-positive (HER2⁺) breast cancer is aggressive and often develops resistance to anti-HER2 therapies. CDK8 and CDK19, transcription-associated cyclin-dependent kinases (tCDKs) in the Mediator complex, are dysregulated in HER2⁺ breast cancer, correlate with poor survival, and support transcriptional escape driving therapeutic resistance. Previous studies Previous studies in immune-deficient models demonstrated that CDK8/19 inhibition (CDK8/19i) reduces pro-tumor macrophages (M2Φs), but its role in immune-competent tumors and innate immune–mediated tumor control remains unclear. Since HER2⁺ tumors are often immunogenic and anti-HER2 therapies rely on innate immune activation, reprogramming immunosuppressive M2Φ toward an M1Φ-like phenotype could enhance antitumor immunity. We hypothesized that CDK8/19i modulates …

Contributions Of Citizen Science Data To Butterflies Of The Lower Rio Grande Valley, Akane Jazmyn Benitez

Theses and Dissertations

Citizen science-provided insect data inherently exhibits variability in accuracy. In the Lower Rio Grande Valley (LRGV), butterfly occurrence reporting is predominantly reliant on citizen science contributions. My research compared fieldwork conducted monthly over a year to occurrence records submitted by visitors at the National Butterfly Center and in Mission, Hidalgo County, Texas. I hypothesized that butterfly occurrences at the Center would be maximized during the fall and minimized during winter and summer months. My research findings revealed that butterfly taxa richness is contingent upon the following factors: 1) the impact of citizen science submitting reports, and 2) monthly butterfly activity …

Exploring Soft Polymeric Nanoparticles For Targeted Biomolecule Delivery In Plant Cells, Mohammad Rashid

Theses and Dissertations

Safe and efficient agricultural practices require innovative technologies. Nanotechnology offers promising solutions for advancing plant agriculture by enabling the targeted delivery of biomolecules such as agrochemicals and nucleic acids. This study focuses on developing a safe nanotechnological approach for delivering molecules of interest into plant cells. We investigated the ability of four types of polymeric nanoparticles such as Polyethylene glycol N, Nʹ-dibutylethylenediamine (PEG-DB), Polyethylene glycol 2-pyrrolidin-1-yl-ethyl-amine (PEG-PY), Polyethyleneimine (PEI), Arabinoxylan (AX)+, and Zein+ to form conjugates with plasmid DNA (pDNA). Our findings confirm that plant-derived cationic nanopolymers, AX+ and Zein+, effectively bind negatively charged pDNA (pGFPGUSPlus) carrying a GFP reporter …

Assessing Illegal Take Of Sea Turtle In Bocas Del Toro, Panamanian Caribbean, Daniela Carolina Rojas-Cañizales

Theses and Dissertations

In Bocas del Toro, Panama, sea turtles were exploited for generations to supply local, national, and international markets. Today, sea turtle species are globally protected by different laws, and Panama is no exception. However, the use of sea turtles in Bocas del Toro and local perceptions regarding the consumption of these reptiles are unknown. Accordingly, during May of 2024, I conducted twenty-five semi-structured interviews with key informants selected by targeted and snowball sampling. Sea turtle consumption persists, and there is a clandestine network to sell turtle meat and derived products in Bocas del Toro. This study provides the first assessment …

Ecology And Management Of Alligatorweed (Alternanthera Philoxeroides) And An Associated Thrips Biological Control Agent (Amynothrips Andersoni), Samuel Alec Schmid

Theses and Dissertations

Alligatorweed (Alternanthera philoxeroides), native to South America, is a highly invasive aquatic macrophyte that is globally distributed and particularly problematic in the southeastern United States. In the United States, alligatorweed management has a long history, particularly of chemical and biological control. Alligatorweed management saw early success with a South American flea beetle (Agasicles hygrophila), but this agent’s utility has waned. Despite the long history of alligatorweed invasion, several important research questions remain, and the research in this dissertation seeks to answer some of these questions. This research focuses on multiple and diverse aspects of alligatorweed biology, ecology, and management: (1) …

Quantification Of Blue Carbon Within The Marine Animal Forest On The Rio Grande Valley Artificial Reef, Michelle Kathryn King

Theses and Dissertations

The protection and enhancement of coastal ecosystems provides a number of benefits such as heightened biodiversity, increased fisheries, and enhanced carbon capture (Yeemin et al., 2024). The study of blue carbon ecosystems has expanded rapidly in the last two decades since the term was coined in 2009 (Lovelock & Duarte, 2019). The most well-known blue carbon ecosystems include vegetation-dominated ecosystems such as seagrass meadows, salt marshes, and mangrove forests (Howard et. al., 2014). Prior studies have overlooked Marine Animal Forests (MAF) ability to capture carbon, until recent studies on soft coral (Coppari et al., 2019) and sponge (Rix et al., …

A Comparative Study Of Urban And Natural Nesting Gray Hawks In The Lower Rio Grande Valley Of South Texas, Evan Farese

Theses and Dissertations

Urbanization can negatively impact birds of prey, which occupy higher trophic levels. The Gray Hawk (Buteo plagiatus) is a neotropical raptor inhabiting the Lower Rio Grande Valley (LRGV) of Texas, where it is threatened. The species’ ecology has been little studied and it is unclear how urbanization may affect population viability. I studied Gray Hawk reproductive success, diet, and thermal ecology at nests in urban and natural habitats in the LRGV. Camera trap data showed adults at urban nests delivered mostly avian prey, while mammalian prey was most frequently brought to natural nests. Data from temperature loggers showed …

A Study To Identify The Causal Rare Genetic Variants In Primary Open And Closed Angle Glaucoma, Pseudoexfoliation Syndrome, And Associated Glaucoma, Suganya K

Theses and Dissertations

BACKGROUND: Glaucoma is the second most common cause of blindness globally typically diagnosed with a triad of clinical symptoms of increased intraocular pressure (IOP) with associated optic disc, optic nerve head (ONH) changes, and visual field defects. Genetic and environmental factors are some of the strong aetiology factors for glaucoma and identification of these factors has a potential implication in the management of the disease and its outcome. There is a paradigm shift towards understanding the genetics of glaucoma, wherein the variants in the nuclear, mitochondrial genome and other regulatory regions are being identified as contributing risk factors.

METHODOLOGY AND …

Molecular Mechanisms Of Niemann-Pick Type C: Investigating Gene Expression, Lipid Metabolism, And Mitochondrial Dysfunction In Fibroblasts, Sarah Kim

Theses and Dissertations

Niemann-Pick Disease Type C (NPC) is a progressive lysosomal storage disorder characterized by the accumulation of lipids, particularly cholesterol, within cells, leading to severe neurological manifestations and developmental issues. This study employs RNA-seq to compare gene expression profiles between fibroblasts derived from a healthy individual and a patient with the NPC1 mutation. A total of 12,978 genes were analyzed, revealing 191 differentially expressed genes. Functional enrichment analysis disclosed significant associations with biological processes related to development, lipid metabolism, embryonic organ development, vascularization, and neuroinflammation. Additionally, the connection between mitochondrial function and lysosomal impairment was explored, revealing that NPC1 mutant fibroblasts …

Evolution Of Chitinases In Amphibians: A Multi-Faceted Group Of Enzymes With Dual Function In Digestion And At The Forefront Against Fungal Infections, Devashri Narayan

Theses and Dissertations

Chitinases are essential enzymes found in living organisms such as amphibians, and they ensure that amphibians survive in their varied ecosystems. They are crucial in the digestion and immunity of most organisms, including plants and animals. Chitinases’ diversity of functions is a testament to their evolutionary adaptability. The primary function of chitinases is the breakdown of chitin, a complex polymer of saccharides often found in the exoskeleton of insects and the walls of fungi. Amphibians that feed on insects make use of chitinases to hydrolyze chitin into simpler sugars that can be easily absorbed to extract the necessary nutrients from …

Aligning Exons, Introns, And Flanking Regions Of Cyc And Cuc Genes In Lonicera (Caprifoliaceae), Mark Mordukhay

Theses and Dissertations

The genus Lonicera (Caprifoliaceae) exhibits great diversity in floral symmetry, petal fusion, and organ arrangement, making it an ideal system for exploring the genetic basis of morphological evolution. We focus here on the roles of CYC and CUC gene families, (CYC2A, CYC2B, CYC3A, CYC3B, CUC2A, and CUC2B) and their potential contributions in shaping floral symmetry and organ fusion. The data set included nucleotide sequences from over 90 Lonicera species, extracted from samples collected from natural habitats or herbaria and then sequenced. A custom bioinformatics pipeline was developed in R using Bioconductor packages to automate BLAST searches, filter results, scan for …

Propelling Whole-Cell Biosensor Creation By Leveraging Gene Fusion To Assemble Synthetic Functional Transcription Factors For The Detection Of Biomarkers, Samuel J. Verzino

Theses and Dissertations

Biosensors are analytical devices that leverage biological modules for the detection of molecules of interest. As customizable tools designed to aid in a wide array of diagnostics, these instruments are rapidly advancing the field of synthetic biology. While varied in their construction and purpose, biosensors are ultimately concerned with converting a physicochemical stimulus into a detectable signal. Among the many existing variants, whole-cell biosensors (WCBs) stand out due to their versatility and engineering potential. WCBs are a type of biosensor in which a physiologically active cell sustains an array of biomolecular elements - receptors, transporters, regulators, etc. - capable of …

Diversification Of Avifauna In The Darién Highland Region: Ecological Niche Modeling, Phylogeography And Morphology To Explore Speciation In The Montane Species Myadestes Coloratus, Chlorospingus Tacarcunae And Margarornis Bellulus., Jorge L. Garzon Vasquez Mrs

Theses and Dissertations

Montane regions in the Neotropics are hotspots of endemism and biodiversity, yet their species are especially vulnerable to the impacts of climate change and geographic isolation. This thesis investigates the evolutionary and ecological dynamics of three bird species endemic to the Darién Highlands of eastern Panama: Myadestes coloratus, Chlorospingus tacarcunae, and Margarornis bellulus. Through an integrative approach combining ecological niche modeling, morphometric analysis, and genomic data from ultraconserved elements (UCEs) and mitochondrial DNA, the study explores the historical biogeography, current distribution patterns, population structure, and phenotypic differentiation of these montane taxa. Ecological niche models revealed that suitable habitat …

Physiological Responses And Plant Trait Interactions With Coastal Dune And Swale Development, Emily C. Riffe

Theses and Dissertations

Vegetation is crucial to coastal ecosystems experiencing climate change and storm-induced disturbance. Plant species interact with the physical environment and are considered “ecosystem engineers.” Sand dunes and barrier islands are at the forefront of climate change impacts as they are barriers that protect landward habitat and communities. Nature based solutions are utilized to protect infrastructure on developed coastlines. Understanding how dominant plant species interact with and alter the physical environment enhances our understanding of the mechanisms of change and consequences to the system. The goal of this research was to quantify physiological and functional trait differences in dominant species found …

The Comparative Effects Of A Thermal Gradient On The Age And Growth Characteristics Of Largemouth Bass (Micropterus Nigricans), And Atlantic Cod (Gadus Morhua), Whitney Hall

Theses and Dissertations

Thermal gradients impact fishes differently, due to variations in ecological niches and physiological adaptations. I assessed the effects of temperature on Largemouth Bass (Micropterus nigricans) and Atlantic Cod (Gadus morhua) using data from peer-reviewed journals, state records, and fisheries agencies. For Largemouth Bass, I analyzed the relationships between air temperature (MAT_min°C, MAT24hr°C, and MAT_max°C), and growth parameters including maximum length and weight, growth rate (K), longevity, and total length-at-ages 3, 5, and 8 years (TLAge_3,5,8), using least squares regression. Significant correlations were found between all temperature and growth metrics. Positive correlations were found between …

Caspases Protect Against Hyperglycemia Induced Necroptosis-Like Cell Death In Brain Endothelial Cells, Aleena S. Mathew

Theses and Dissertations

Acute diabetes characterized by high spikes in blood glucose levels in association with severe hyperglycemia can lead to an increased risk of ischemic stroke in the brain. To better understand high blood glucose levels, hyperglycemia, in the brain we explored its effects on endothelial cells. Endothelial cells line the inner walls of blood vessels and are directly impacted in hyperglycemia. Brain endothelial cells are a major component of the blood brain barrier (BBB) which tightly regulates the brain’s microenvironment. The type of cell death such as apoptosis, caspase dependent, or necroptosis, caspase independent, can exacerbate diabetes associated complications. There is …

Involvement Of Integrated Stress Response In Primary And Secondary Dystonia, Tricia Aleena Dulice Simon

Theses and Dissertations

ABSTRACT Dystonia is the third most common movement disorder in the United States of America , the first two being essential tremor and Parkinson’s disease. Gaining mechanistic knowledge about pathobiology of dystonia is essential for development of effective therapies. As the only therapies currently available are invasive procedures such as deep brain stimulation (DBS) or frequent botulinum toxin injections, it is critical to understand the underlying molecular mechanisms leading to dystonia. A maladaptive integrated stress response (ISR) involving dysregulation of the eukaryotic translation initiation factor  (eIF2) mediated signaling is observed in DYT-PRKRA patient cells. Mutations in PRKRA gene, which …

Examining The Distribution And Predictability Of Population Dynamics Across Geographic Space, Cleber Ten Caten

Theses and Dissertations

Populations occupy different regions of the geographic space and may experience distinct conditions over time that can cause fluctuations in their number of individuals. Environmental conditions, dispersal events, and resource availability are some of the factors that influence populations. A central goal in ecology has been to develop generalizations about how these factors that affect population dynamics are structured in geographic space. However, limited knowledge about where species occur and a lack of long-term surveys of populations has hindered the development, and validation, of such generalizations. In this dissertation, I use a combination of observational data, simulations, and experimental approaches …

Isolating Confounding Abiotic And Biotic Effects On The Phenotype On Physa Acuta Snails, Ashley M. Bauer

Theses and Dissertations

Organisms match their phenotypes to prevailing environmental conditions leading to habitat specific polymorphisms. Polymorphisms arise from genetic divergence, phenotypic plasticity, or a combination of both processes. I examined the presence of habitat-specific polymorphism in Physa acuta snails collected from three streams and their corresponding downstream reservoir. In lotic systems shells were rotund with larger apertures, while those from lentic systems were more elongate with smaller apertures. In a reciprocal transplant lab experiment that crossed flow regime and crayfish predator cues, I tested for the underlying mechanisms responsible for the observed phenotypic differences. I found no evidence for plasticity in relation …