Biology Commons^™

Increasing Bacterial Tolerance And Metabolism Of The Biofuel, N-Butanol Using Community-Level Evolution And Functional Genomics, Kayley T. You Mak

Biology ETDs

Bioremediation capability should be developed along with biofuel technology to mitigate the potential damage of future spills. Biobutanol is being developed since n-butanol is more energy dense and less volatile than ethanol. A bottleneck for industrial production of biobutanol is its toxicity; most microbes cannot survive ~1.5% v/v. Thus, microbial bioremediation of n-butanol would need microbes that can both tolerate and metabolize butanol. We used ecological and evolutionary biology approaches to find bacteria that could tolerate and metabolize butanol. Ecological community-level assays followed by 16S amplicon sequencing were completed to identify butanol-tolerant artificial bacterial communities. Secondly, we looked for bacteria …

Maturation Of An Off-Channel Habitat Concept To Conserve Native Fishes In The Lower Colorado River, Paul C. Marsh, Thomas E. Dowling, Thomas F. Turner, Megan J. Osborne, Brian R. Kesner

Monographs of the Western North American Naturalist

Two endemic, “large river” fishes of the Colorado River basin of western North America, bonytail Gila elegans and razorback sucker Xyrauchen texanus, are among several critically endangered species in the system. Wild populations of bonytail are gone, and there are no self-sustaining populations of razorback sucker anywhere; reproduction occurs but recruitment does not. Both species have been under intensive management in the Lower Colorado River since the 1980s. Today, with the single exception of Lake Mead, remaining populations are composed entirely of repatriated individuals that depend on stocking for their continued existence. In 2003, a conceptual off-channel habitat (OCH) …

Energetic Cost Of Biosynthesis Is A Missing Link Between Growth And Longevity In Mammals, Chen Hou

Biological Sciences Faculty Research & Creative Works

The Comparative Studies of Aging Have Established a Negative Correlation between Gompertz Postnatal Growth Constant and Maximum Lifespan Across Mammalian Species, But the Underlying Physiological Mechanism Remains Unclear. This Study Shows that the Gompertz Growth Constant Can Be Decomposed into Two Energetic Components, Mass-Specific Metabolic Rate and the Energetic Cost of Biosynthesis, and that after Controlling the Former as a Confounder, the Negative Correlation between Growth Constant and Lifespan Still Exists Due to a 100-Fold Variation in the Latter, Revealing that the Energetic Cost of Biosynthesis is a Link between Growth and Longevity in Mammals. Previously, the Energetic Cost of …

Intraguild Competition Is More Severe In Obligate Mutualisms Than In Facultative Mutualisms, Thomas Johnson

Theses - ALL

Mutualism, or the beneficial interaction of species, is an important and widespread interaction type in nature. Mutualist species exchange goods or services that benefit the species involved. These benefits can include protection from predators, parasites, and disease, dispersal of individuals, offspring, or gametes, and provisioning of various nutrients. Well-known mutualisms include the pollination of flowering plants by insects, birds, and other animals and the interaction between clownfish and sea anemones. Many mutualistic associations are less visible than these examples, as organisms often form beneficial relationships with microorganisms, like the many beneficial bacteria that live in the human gut, or the …

Investigating Vocal Development In Humpback Whales: Caller Identification, Acoustic And Movement Behavior, And Comparisons Across Age, Julia Marie Zeh

Dissertations - ALL

Studying variation in individual behavior can elucidate drivers related to factors like age, social context, and the environment. Differences in behavior with age are a product of survival needs and developmental differences as animals physiologically mature and modify their behaviors in response to experience. Learning is of particular interest across taxa because it is fundamental to the development of complex behaviors, from problem-solving to social hierarchies to animal songs and human language. Humpback whales (Megaptera noveaeangliae) exhibit a variety of complex and culturally transmitted behaviors across their range, including a diverse acoustic repertoire. Despite decades of research on adult behavior, …

Transcriptional And Environmental Regulation Of A Putative Xylan Biosynthesis Gene, Ptrparvus2 In Poplar, Dan Wang

Dissertations - ALL

Secondary cell wall (SCW) biosynthesis plays a crucial role in plant development and biomass production, with implications for various industries, including biofuels and forestry. Understanding the regulatory mechanisms governing SCW formation is essential for manipulating plant cell wall composition and properties to improve biomass yield and quality. In this study, we investigated the regulatory mechanisms controlling SCW biosynthesis in poplar, focusing on the transcriptional regulation of PtrPARVUS2, a putative gene involved in SCW formation. The regulatory mechanisms governing SCW biosynthesis in poplar were investigated, with a focus on the transcriptional regulation of PtrPARVUS2. Bioinformatic analysis of the PtrPARVUS2 promoter revealed …

The Tissue-Specific Role Of Smn-1 In C. Elegans, Lindsey Philips

Biological Sciences Theses and Dissertations

Spinal muscular atrophy (SMA) is an autosomal recessive disease that results from mutations in the Survival Motor Neuron (SMN-1) gene. Although SMN is a ubiquitously expressed protein that acts as an RNA-binding protein (RBP), SMA is characterized by the selective degeneration of motor neurons of the lower spinal cord. Despite a clear understanding of the genetic causes underlying SMA, the mechanisms associated with low SMN levels to disease pathogenesis remains unclear. Here, we investigate the role SMN-1 has in different tissues to begin understanding possible mechanisms. This project has three aims that has guided our experiments. The first aim is …

Screen For Beneficial Genetic And Chemical Modifiers In Drosophila Models Of Als And Traumatic Brain Injury, Will Bonderer

Biological Sciences Theses and Dissertations

The underlying molecular processes of aberrant protein expression in neurodegeneration are intricate and multifaceted, with ribosome-associated quality control (RQC) emerging as a promising avenue of exploration. Ribosome-associated quality control is integral to cellular function. Its evolutionarily conserved pathway encompasses a network of mechanisms designed to ensure the fidelity of protein synthesis, folding, and degradation within the cells of all eukaryotes. The ribosome, central to protein synthesis, plays a pivotal role in this quality control network, and its malfunction can lead to the accumulation of misfolded or aberrant proteins. In the context of neurodegenerative disorders, this dysfunction can have dire consequences. …

Effects Of Vdac 1 And 2 N-Terminal Peptides On Bax Conformation Assessed By Blue Native Gel Electrophoresis, Allison G. Dupree

Honors Theses

Members of the Bcl-2 family are responsible for regulating the intrinsic pathway of apoptosis through Bcl-2 homology 3 (BH3) domain interactions of pro- and anti-apoptotic members. Apoptosis occurs when BH3-only pro-death members overwhelm the pro-survival ones, leading to oligomerization of the multi-BH domain pro-death protein Bax to signal death by releasing cytochrome c from mitochondria into the cytoplasm. This process is essential for proper embryonic tissue development as well as maintenance of mature tissues. While BH3-only proteins such as Bim and Bid bind to and activate Bax through their BH3 domains, other regulators of this mitochondrial permeabilizer may exist. Two …

Variability In Large Mammal Activity Patterns When Visiting Water In New Mexico, Juan E. Camacho

Biology ETDs

Studying activity patterns of animals can provide vital information about how different species react to environmental changes, yet camera trap studies typically neglect the temporal aspect of the data. Using a 10-year camera trap dataset on Sevilleta National Wildlife Refuge, NM, we explored daily activity patterns when visiting water of five large mammal species. The species of study were mule deer, pronghorn, elk, oryx, and coyote. All species showed significant variability in activity patterns from site to site across the refuge. Within a site, differences in activity across years and seasons were less pronounced. Mule deer and coyote showed very …

Spawning Ecology And Spawning Site Fidelity Of Alligator Gar, Atractosteus Spatula, In The Fourche Lafave River: Implications For River-Floodplain Management And Alligator Gar Conservation, S. Reid Adams, Thomas E. Inebnit, Lindsey C. Lewis, Christopher J. Naus, Edward Kluender, Geoffry G. Spooner

Southeastern Fishes Council Proceedings

We studied the spawning ecology of Alligator Gar, Atractosteus spatula, in the Fourche LaFave River (FLR) of Arkansas to better understand their reproductive ecology and spawning resource requirements. Evidence of spawning was only observed in floodplain tributary habitats, particularly the small, adventitious headwater stream West Fork Mill Creek (WFMC). A mid-May to mid-June spawning season was observed for Alligator Gar in the FLR that corresponded with rising water levels (mostly due to backflooding from the Arkansas River) and increased water temperatures (> 20°C). Direct spawning observations at WFMC were made on 17 June 2007, 15 June 2008, 23 May …

Influence Of Sex And Habitat Structure On Morphology, Predation, And Survival Of Sceloporus Consobrinus, In Central Arkansas, Anju Ghimirey

ATU Theses and Dissertations 2021 - Present

Lizards are useful in determining links between habitat use, morphology, and performance since they occupy many structurally distinct habitats. Prairie lizards (Sceloporus consobrinus) inhabit three distinct habitat types in Central Arkansas: rocky, forested, and intermediate or mixed habitats. Though geographically close, these habitats have fundamentally different microclimates, substrates, predators, and prey availabilities for lizards. My objectives here are to assess the impact of those structurally different habitats on body temperature, morphology, and predation on prairie lizards. I captured 117 individuals in 2022 and compared those lizards with 809 captures from 2016-2017. The cloacal temperature did not differ among habitats yet …

Omani Camels From A Cultural And Genomics Perspective, Al Muatasim Al Zadjali

Electronic Theses and Dissertations

The Dromedarian camel, Camelus dromedarius, is native to the Arabian Peninsula, including the Sultanate of Oman. These camels are used for food, milk, as well as show and racing competitions. Despite their economic and cultural importance research on camels in Oman is limited. The goal of this study was to examine their genomic variation, relationship with camels in other parts of the Arabian Peninsula, and to determine if selective breeding has led to the establishment of distinct breeds in Oman. Information was compiled from multiple sources to produce a comprehensive review on the breeding, management, economic and cultural use, …

New Insights Into T Lymphocyte-Mediated Immunity To Toxoplasma Gondii, Claire Marie Doherty

Biology ETDs

With nearly a third of the global population infected with the protozoan, Toxoplasma gondii, this parasite sits at a unique, immune-mediated interface of health and disease. In healthy individuals, Toxoplasma results in a chronic yet asymptomatic infection of the central nervous system. This quiescent infection is the result of parasite exploitation of host immune barriers, yet Toxoplasma can quickly become an opportunistic pathogen when immunity is disrupted by illness or immunosuppressive therapies. During the HIV-AIDS pandemic, it was observed that once latent Toxoplasma infections became the cause of severe, even fatal, disease in the absence of an intact T …

Characterization Of A Novel Metalloid Reductase Outer Membrane Porin Rara From Sulfurospirillum Barnesii Ses-3, Narthana Jeganathar Kanmanii

Electronic Theses and Dissertations

Sulfurospirillum barnesii SES-3 is a gram-negative epsilon proteobacterium that grows anaerobically by coupling the oxidation of lactate to the reduction of arsenate. Previous work on metal and metalloid metabolism in S. barnesii had identified a redox active protein, designated RarA that when provided an artificial electron donor (i.e., reduced methyl viologen, FMN, or NADH), could reduce a variety of substrates, including arsenate, selenate, selenite, nitrite, and even phosphate. The enzyme’s inferred amino acid sequence showed weak similarity (30%) to outer membrane porins with homologs found in only certain species of Sulfurospirillum. Further, the enzyme did not contain cysteine residues …

Comparative Functional And Computational Analyses Of Primate Seminal Proteins: Insights Into Sexual Selection And Hiv/Siv, Emine Feride Kahveci

Electronic Theses and Dissertations

Male reproductive protein-coding genes are among the most rapidly evolving genes across many animal taxa, commonly attributed to sexual selection; however, pathogen defense mechanisms might also be contributing factors. This study aimed to both computationally and experimentally investigate the selective pressures responsible for the rapid evolution of seminal proteins. In the first part, the research focused on sexual selection in the form of post-copulatory sperm competition as a driving force behind the evolution of kallikrein related peptidase 3 (KLK3), also known as prostate-specific antigen (PSA), a key prostatic seminal protein. KLK3 is responsible for the liquefaction of semen coagulum through …

Patterns And Potential Mechanisms Of Phenotypic Changes In Urban Small Mammals, Leslie Lopez

Master's Theses

Urbanization is an example of human induced rapid environmental change that can have wide-reaching ecological effects, including habitat destruction, fragmentation, and alteration of local climates. Effects of urbanization have been shown to impact wildlife, as disturbances resulting from urbanization can create novel environments and selective pressures that could lead to changes in morphology, physiology, or both. Small mammals such as rodents are an ecologically important set of wildlife species because they are a key prey item for several predators, hold strong influence over plants as a primary consumer, and some species carry and transmit major human and animal diseases. Previous …

Unraveling The Paradox Of The 'Great Speciators': Evolutionary Dynamics Of A Geographic Radiation Of Island Kingfishers (Todiramphus), Jenna Merle Mccullough

Biology ETDs

The paradox of the ‘Great Speciators’ describes a biogeographic pattern in which geographically widespread lineages have strong overwater dispersal capabilities, yet exhibit genetic and phenotypic divergence between islands, suggesting limited dispersal and cessation of gene flow. In my dissertation, I leveraged whole genomes and two comprehensive trait datasets of dispersal ability and plumage coloration of all described diversity within Todiramphus kingfishers, a rapid radiation of largely island endemic ‘Great Speciators.’ Chapter 1 reveals that whole genome datasets do not outright solve the evolutionary relationships of this clade and that widespread incomplete lineage sorting (ILS) and gene flow are sources of …

Removal Of Phenol From Oilfield Produced Water Using Non-Conventional Adsorbent Medium By An Eco-Friendly Approach, Salem Jawad Alhamd, Mohammed Nsaif Abbas, Hassan Jameel Jawad Al-Fatlawy, Thekra Atta Ibrahim, Zaid Nsaif Abbas

Karbala International Journal of Modern Science

Petroleum extraction generates substantial quantities of produced water, a challenge compounded by water scarcity in oil-producing regions, notably the Middle East. Leveraging produced water effectively, adhering to environmental standards, can offer a viable solution to the issue of water scarcity. This study explores the potential of mandarin peels as an available, cost-effective adsorbent for treating synthetic aqueous solution simulated to oil-field produced water, specifically targeting phenol, a dangerous pollutant. Employing a batch-mode adsorption unit, six operational factors—phenol concentration, acidity, agitation speed, contact time, adsorbent dose, and temperature—were investigated. Results revealed an inverse relationship between phenol removal and pH, concentration, and …

Novel Bioinformatics Tools For Biomarker Discovery In Prostate Cancer, Jace Webster

Arts & Sciences Graduate Student Theses and Dissertations

Prostate cancer (PCa) accounts for 29% of all expected cancer diagnoses in men in 2024, but patients presenting with different disease stages can have significantly different outcomes. Patients with indolent PCa may experience little to no impact on their quality of life and have a 5-year survival as high as 98%, but progression to aggressive disease causes 5-year survival to plummet to 30%. Patients with the most lethal form of the disease, metastatic castration-resistant PCa (mCRPC), have a median survival of only 5.5 months if they become resistant to treatment. Due to this clinical heterogeneity, it is critical to quickly …

Characterizing The Expression Of The Sphingosine 1-Phosphate Pathway In Injury And Post-Traumatic Fibrosis, Nicole Cubbage

Masters Theses, 2020-current

Following injury, tissue repair allows for the restoration of the architecture and function of the injured tissue, while tissue replacement is characterized by severely damaged or non-regenerable tissue that is repaired by the laying down of extensive connective tissue, also known as fibrosis. The fibrotic process should be arrested at its early stage to have the greatest impact on preventing or reversing associate sequelae and promoting the regeneration of normal tissue. Sphingosine 1-phosphate (S1P), a metabolic product of cell membrane sphingolipids, has emerged as a pathway that may be involved in fibrosis. Most of S1P’s actions are mediated through the …

Assessing Structural Variation In And Out Of The Classroom: Characterizing Structural Variation Within Campanula Americana And Effects Of Long Read Sequencing On Students Learning, Tyler Gandee

Masters Theses, 2020-current

Cytonuclear incompatibilities are proposed to be one of the first genetic barriers to arise during speciation, so understanding the underlying evolutionary forces that contribute to cytonuclear incompatibilities is important. Many studies have looked at SNP level variation in the plastid genome and its relationship with cytonuclear incompatibility, but no studies have examined structural variation and its relationship to cytonuclear incompatibility, particularly at the early stages of speciation, i.e. within species. Campanula americana is a great system for this because it exhibits cytonuclear incompatibility and the family in which it is found, the Campanulaceae, exhibits rapidly evolving plastid genomes, including …

Dynamics Of Skin-Based Gene Expression In Red-Sided Garter Snakes (Thamnophis Sirtalis Parietalis): Sex And Seasonal Influences, Emily C. Plant

Masters Theses, 2020-current

The skin is the key organ regulating the animal-environment interface and is particularly sensitive to the abiotic factors of temperate environments, such as extreme cold and aridity during winter. Previous research found that, in the skin, temperate birds and reptiles upregulate expression of lipid synthesis genes to prevent tissue freezing and evaporative water loss in winter. My study species, the red-sided garter snake (Thamnophis sirtalis parietalis), has seasonally variable skin lipid composition, and females produce a modified set of these lipids that function as a sex pheromone. The pheromone is maximally produced in the spring breeding season following …

The Ecology And Genetic Diversity Of Buckleya Distichophylla (Santalaceae), Montana Hill

Masters Theses, 2020-current

Piratebush (Buckleya distichophylla) is a native, rare, shrub found along the Blue Ridge mountains in North Carolina, Virginia, and Tennessee. Research on its ecology and genetic diversity is limited due to its rarity; only one population on Poor Mountain has been studied extensively in the past. To determine if there are ecological differences between populations of B. distichophylla, research on sex distribution, floral visitors, individual length, leaf area, and amount of light that reached each specimen were conducted and then compared between a population located on Dragon’s Tooth Trail and a population on Poor Mountain, both located …

The Effects Of Tree Shelters On Tree Seedling Growth, Microclimate, And Seedling Chlorophyll Fluorescence: Two-Year Results, Christina Henriksen

Masters Theses, 2020-current

Continuous land development practices such as property development and large-scale agriculture impact watersheds when excessive nutrients from surface runoff enter streams, and over time, cause a decline in water quality. As these sources of pollution are diffuse, mitigation of nutrient loading can become quite difficult and costly to stakeholders such as farmers. To reduce the effects of nutrient loading into local streams and rivers, riparian forest restoration has long been the focus of many stakeholders wishing to improve water quality in landscapes which have been heavily degraded for agricultural use. There are many methods of riparian forest restoration, however, the …

Greening The Edge: Investigating Riparian Buffer Restorations In A Pastoral Setting And Their Effects On Soil Carbon And Microbial Community Composition., Seth Mccullough

Masters Theses, 2020-current

Riparian buffer restoration represents a critical strategy for enhancing ecosystem health and resilience in agricultural landscapes. This study investigates the effects of riparian buffer restoration on soil properties, microbial communities, and carbon dynamics in Rockingham County, VA. Through a comprehensive field study, we assessed the physicochemical properties of soil, microbial biomass, community composition, and soil carbon storage in restored and unrestored riparian buffers. Our findings reveal significant improvements in soil physical properties in restored buffers, including increased soil moisture (p < 0.05) and decreased bulk density (p < 0.01), indicating enhanced soil structure and water retention capacity. While no significant differences were detected in soil pH or cation exchange capacity, restored buffers exhibited higher soil carbon stocks (p < 0.05) and carbon-to-nitrogen ratios, suggesting potential differences in nutrient cycling processes and organic matter decomposition rates. Moreover, restored buffers showed increased microbial biomass (p < 0.01), potentially driven by improved habitat conditions and shifts towards a fungal-dominated microbial community.

Although no significant differences were found in overall microbial community composition between restored and unrestored sites, specific shifts in bacterial …

Vascular Electrophysiology And Pathogenic Consequences Of Cardiovascular Katp Channel Mutations, Alex Hanson

Arts & Sciences Graduate Student Theses and Dissertations

The complex cardiovascular disorder Cantú Syndrome (CS) arises from gain-of-function (GoF) mutations in either KCNJ8 or ABCC9, the genes encoding the Kir6.1 and SUR2 subunits of cardiovascular ATP-sensitive potassium (KATP) channels, respectively. CS involves an array of cardiovascular pathologies, including cardiac hypertrophy and hypercontractility, low systemic vascular resistance, and excessively compliant, dilated, and tortuous vessels. Together, the latter features exemplify the hypomyotonic and hyperelastic components of CS vasculopathy. It was recently established that CS vasculopathy drives the associated cardiac pathologies, which are observed even in the absence of cardiac KATP GoF. In this thesis, I carried out experiments to determine …

Inducible Crispr-Targeted ‘Knockdown’ Of Human Gut Bacteroides In Mice Reveals Glycan Utilization Strategies, Zachary Beller

Arts & Sciences Graduate Student Theses and Dissertations

Learning how members of the human gut microbiota compete and cooperate for dietary nutrients, such as fiber-associated glycans, should help facilitate development of more precise nutritional recommendations for improving health. To model how bacteria prioritize the utilization of different fiber glycans in the mammalian gut, germ-free mice were colonized with a 13-member consortium of cultured, genome-sequenced human bacterial strains, including seven Bacteroides species. Animals were fed a Western diet supplemented with pea fiber. Once the consortium had time to assemble, an inducible CRISPR-based system was used to deplete the absolute abundance of Bacteroides thetaiotaomicron or B. cellulosilyticus by 10- to …

Examining The Role Of Rgs2 In The Maintenance Of Diapause After Anoxic Stress In Embryos Of The Annual Killifish Austrofundulus Limnaeus, Patrick Clouser

Student Research Symposium

Austrofundulus limnaeus live in ephemeral ponds of Venezuela. They have evolved a unique life history that includes embryonic diapause, a period of developmental dormancy, metabolic arrest, and reduced protein synthesis. Diapausing embryos are resistant to environmental stress and survive months without oxygen (anoxia). A. limnaeus’ anoxia tolerance is an important survival mechanism as they can be buried in anoxic soil during development. Analysis of RNAseq data from diapausing A. limnaeus embryos show significant down-regulation of RGS2 transcripts in anoxic embryos. RGS2 regulates G-protein receptor signaling by inhibiting associated G_a-proteins and can inhibit protein synthesis. I hypothesis that …

Dragon Pseudoscorpions Shed Light On Ancient Climate History In The Pacific Northwest, Joshua W. Hootman

Student Research Symposium

Pseudoscorpions are an ancient and diverse group of understudied arachnids, and there is much to be learned about their relationships to each other. Pseudoscorpions are one of many leaf-litter dwelling and low dispersing invertebrates that inhabit the forests of the Pacific Northwest. Previous phylogeographic studies of Pacific Northwest taxa have shed light on some of the climatic and geologic events that have shaped the area's flora and fauna. One purpose of this study is to determine if there is similar genetic structuring within the pseudoscorpion populations present in the study area, or if there is even more structure likely influenced …