Life Sciences Commons^™

Systematics And Comparative Genomics Of The Petaluridae (Odonata: Anisoptera), Ethan R. Tolman

Dissertations, Theses, and Capstone Projects

The Anisoptera (Insecta: Odonata), or dragonflies exhibit diverse life histories and diversification patterns, with the family Petaluridae standing out as particularly unique. Comprising only 11 extant species, all of which inhabit increasingly threatened fen habitats, Petaluridae are known for their longevity, which can exceed five years, semi-terrestrial lifestyle, and remarkable physical size, ranking among the largest insects on Earth. Despite the evolutionary peculiarities of this family, no previous genomic studies have investigated the Petaluridae. This work presents two high-quality genome sequences and a targeted enrichment dataset to explore the chromosome architecture of Petaluridae, identifies genomic adaptations associated with their distinctive …

Role Of Integrase-Pp2a Interaction In Human T-Cell Leukemia Virus Type-1 Replication And Pathogenesis, Shayna Turbin

Senior Honors Papers / Undergraduate Theses

Human T-cell leukemia virus type-1 (HTLV-1) is an oncogenic retrovirus that causes multiple disorders, including adult T-cell leukemia and HTLV-1-associated myelopathy/tropical spastic paraparesis. HTLV-1 retroviral integrase binds to the regulatory B’56γ subunit of the host cell Protein Phosphatase 2A (PP2A). Integrase contains a highly conserved LxxIxE motif that is essential for binding, which increases integration efficiency and facilitates HTLV-1 hijack of host cell machinery. We aim to understand how mutations introduced in the highly conserved binding site can affect viral particle production and infectivity. We transfected 729B human lymphoblastoid cells and 293T cells with mutant and wildtype virus. Mutations L213A, …

Dynamic Genomic Evolution Via Active Ltr Transposable Elements In Maize, Taylor Isles

Theses, Dissertations and Culminating Projects

Long terminal repeats (LTR) retrotransposons, found across eukaryotes, are transposable elements which can copy and insert themselves into other loci within a genome. These transposable elements are similar to retroviruses in that they rely on reverse transcriptase to “copy and paste” themselves elsewhere in the genome. From the RNA transcript they are able to use reverse transcriptase to make another DNA copy of themselves. This initially gave them the moniker, selfish genes. However, in the decades after the discovery of reverse transcriptase and LTR retrotransposons, it became known that non-genic DNA could have other functions. LTR retrotransposons are sources of …

Evolution Of Forest Bitis (Macrocerastes) In Africa: Phylogeography, Population Genetics, And Potential As A Model For Batesian Mimicry, Eugene Richard Vaughan

Open Access Theses & Dissertations

The major biogeographical patterns characterizing the diversification of widely distributed species in the African rainforest remain poorly understood because of the low number of well-sampled studies that are focused on this region. I examine the phylogeography and population genetics of two broadly sympatric sister lineages of large African forest vipers (genus Bitis, subgenus Macrocerastes), the rhinoceros viper (B. nasicornis) and the Gaboon vipers (B. gabonica and B. rhinoceros). Despite their close relationship, these two lineages have notably different patterns of divergence in time and space. A time-calibrated phylogeny with sequence data from five genes, and population structure and PCA analyses …

The Modulation Of Lfp Characteristics In The Freely Moving Common Marmoset, William Jm Assis

Electronic Thesis and Dissertation Repository

The hippocampus is a neural structure critical for navigation. Neurons in this region, along with others, create a functional network which generates large-amplitude modulations known as local field potential (LFP) activity. Prior LFP research has predominantly used rodent animal models, however recent studies have shown that frequencies associated with navigation in other mammals do not correlate to those of the rodent. We hypothesized that LFP characteristics in the common marmoset are modulated by the speed and axis of travel of the animal. Two marmosets were placed in a free moving 3-dimensional environment where movement and neurological activity were recorded. Results …

Understanding The Environmental And Genetic Influence On Fluctuating Asymmetry And Developmental Instability In Primates, Ashly N. Romero

Graduate Theses and Dissertations

This dissertation explored the impact of environmental factors on the development and perpetuation of fluctuating asymmetry (FA) and sought to understand the role evolution may play in the FA exhibited in two primate populations: the free-ranging Cayo Santiago rhesus macaques (Macaca mulatta) and the Southwest National Primate Research Center olive baboons (Papio hamadryas anubis). Demographic, ontogenetic, secular, external, and genetic factors were examined. Specifically, this dissertation investigated FA over all ontogenetic stages, across decades, between sexes, in association with ecological catastrophes, and with tooth pathology to try and tease apart factors that may influence FA and developmental instability. This dissertation …

The Evolution Of Transposable Elements As Cis-Regulatory Elements In Mammals, Alan Y. Du

Arts & Sciences Electronic Theses and Dissertations

Transposable elements (TEs) are mobile genetic elements that make up a large proportion of mammalian genomes. Although TEs are highly prevalent genomic sequences, they have been understudied as they were once labeled as “junk DNA.” Despite their initial status as simple genomic parasites, recent studies have implicated TEs as cis-regulatory elements, supplying promoters, enhancers, and boundary elements. Functional testing of regulatory activity, however, remains a significant bottleneck. Nonetheless, due to their repetitive nature, TEs provide a unique model to examine the evolution of cis-regulatory elements, which has traditionally been difficult to study due to lack of homology at the sequence …

Neural Tabula Rasa: Foundations For Realistic Memories And Learning, Patrick R. Perrine

Master's Theses

Understanding how neural systems perform memorization and inductive learning tasks are of key interest in the field of computational neuroscience. Similarly, inductive learning tasks are the focus within the field of machine learning, which has seen rapid growth and innovation utilizing feedforward neural networks. However, there have also been concerns regarding the precipitous nature of such efforts, specifically in the area of deep learning. As a result, we revisit the foundation of the artificial neural network to better incorporate current knowledge of the brain from computational neuroscience. More specifically, a random graph was chosen to model a neural system. This …

Host-Acquired Virus Genes Support An Ancient Antiviral Role Of The Pirna Pathway In Dipterans, Rebecca Christian

Theses and Dissertations

Endogenous viral elements (EVEs) have been recently investigated as a source of transgenerational immune memory. These “viral fossils” are abundant in Aedes mosquitoes and partner with the host’s primary antiviral defense system, the RNA interference (RNAi) pathways. This partnership appears unique to mosquitoes, which encode an expansion of the Piwi endoribonucleases. To interrogate EVE-Piwi partnerships and their role in antiviral defense, I performed a comparative small RNA analysis of two naturally occurring EVE-virus pairs – one in the mosquito Aedes albopictus, and one in the midge Chaoborus americanus. Both express an EVE related to the nucleoprotein of their …

Diversification And Convergence Following The Transition From Saltwater To Freshwater In Stingrays., Autumn D. Magnuson

College of Arts & Sciences Senior Honors Theses

One of the most fundamental questions in biology is why some groups of organisms are more diverse than others. Classic hypotheses for explaining differences in diversity consider distinctions in time, place, resources, and competitors as the staging grounds for differential diversification. Freshwater and saltwater environments have similar levels of diversity despite significant differences in size, so studying transitions between the two systems can provide insights into evolutionary processes. Despite the challenges associated with this transition, stingrays have invaded freshwater habitats multiple times across different continents, making them useful for better understanding these systems. In this study, I evaluated the frequency …

Identification Of Sva-Mediated 3’ And 5’ Transductions In Human Genome Sequences, Emily C. Golba

Honors College Theses

Transposable elements (TEs) are sequences of DNA that can move, or transpose, within a genome. Retrotransposons are TEs that propagate via a “copy and paste” mechanism where the elements are transposed to a new genomic location via an RNA intermediate. Short interspersed element (SINE)-VNTR-Alu elements (SVAs) are non-autonomous retrotransposons that use long interspersed element 1 proteins to mobilize. SVAs are currently active in the human genome and often are characterized by the mobilization of sequences adjacent to the 3’ and 5’ ends of insertions, known as transduction events (TDs). TDs were a focus of this study due to their contribution …

Unveiling The Ancestral Function Of A Neuroendocrine Regulator, Pou-I/Pit1: Insights From Gene Expression Analysis In The Sea Anemone Nematostella Vectensis, Miguel Agostinho Pina Da Silva

Graduate Theses and Dissertations

Cnidaria (i.e., sea anemones, jellyfish, corals) and Bilateria (i.e., vertebrates, sea stars, fruit flies), are sister groups that diverged around 600 million years ago. Despite the long evolutionary time, many cellular differentiation mechanisms, cell types, tissues and behaviors are conserved. Such as neurons, mechanosensory hair cells, feeding behaviors, peristaltic movements, and sleep. Recent advances in genomics, molecular biology and microscopy have fueled an increased interest in understanding cnidarian nervous and neuroendocrine systems. Understanding the developmental mechanisms and the mode of operation of Cnidarian nervous systems helps to reconstruct the ancestral nervous system of the last common ancestor of Cnidaria and …

Environmental Drivers Of Stress In Red Pandas (Ailurus Fulgens) : Behavior And Space Use Changes In Response To Redesigned Naturalistic Enclosures, Alexis Michelle Lawson

Theses, Dissertations and Culminating Projects

Animal welfare encompasses the physical and mental state of an animal, as well as how that animal is cared for. Recently, zoological settings have shifted from strictly housing animals to improving the welfare of the animal such that the goal of captivity is for residents to thrive. This is especially crucial as global wildlife numbers and biodiversity continues to decrease due to anthropogenic impacts such as poaching, mining, habitat destruction, fragmentation. Further confounding this issue is climate change, air pollution, invasive species, ocean acidification, and more. In particular, the red panda (Ailurus fulgens) is an endangered species whose declined 50% …

Systems Dynamics Of The Anterior Cingulate Cortex And Hippocampus In Behavioral Switching, Spatial Working Memory, And Disease, Ryan Wirt

UNLV Theses, Dissertations, Professional Papers, and Capstones

The electrophysiological properties of the hippocampus (HC) and anterior cingulate cortex (ACC) are the central focus of research on learning, memory, and neurological disease. Previous research has shown that HC is essential for forming new memories, spatial navigation, and temporal processing. While the function of ACC, located within the medial prefrontal cortex, remains controversial, it has a role in long-term memory recall, processing pain, monitoring current state, learning, schema updates, and information integrations. Interactions between the ACC and HC occur during social memory, spatial working memory performance, and long-term memory recall. Notably, the HC and ACC are among the first …

Vibroacoustic Response Of The Tympanic Membrane To Hyoid-Borne Sound Generated During Echolocation In Bats, Chelsie Snipes

Electronic Theses and Dissertations

The hyoid apparatus in laryngeally echolocating bats forms a mechanical connection between the larynx and auditory bullae and has been hypothesized to transfer the outgoing echolocation call to the middle ear during echolocation call emission. We used µCT data to build models of the hyoid apparatus and middle ear from six species of bats and used finite element modeling (FEM) to measure the vibroacoustic response of the tympanic membrane due to hyoid-borne sound generated during echolocation. We found that hyoid-borne sound in all six species stimulated the eardrum within a range likely heard by bats. Although there were minor differences …

Applying Unsupervised Multi-Omic Learning To Identify Patterns Of Human Genomic Regulatory Regions With An Emphasis In Characterizing Hervh Loci., Corinne Sexton

UNLV Theses, Dissertations, Professional Papers, and Capstones

With the increase of diverse genomic data types, machine learning provides an opportunity to integrate several omics datasets into one cohesive annotation. In this dissertation, I apply an unsupervised clustering approach to a novel representation of 3D chromosome conformation data and chromatin mark data. Specifically I use this new method to annotate the regulatory function of human endogenous retrovirus H (HERVH). In chapter 1, I propose a synthesized model of HERVH function as an activating lncRNA based on previously published work. As HERVH and transposable elements in general are repetitive due to their methods of retrotransposition, in chapter 2 I …

Molecular Characterization Of The Antiviral Properties Of The Small Herc Family Of Proteins, Ermela Paparisto

Electronic Thesis and Dissertation Repository

Although viruses are obligate intracellular parasites, they have their own evolutionary trajectory, their genomes are in a constant battle to overcome the defenses of the host. This thesis investigates the role of the small HERC family of proteins in the battle against two deadly viruses: Human Immunodeficiency Virus -1 (HIV) and Zaire ebolavirus (EBOV). Although their discovery occurred decades ago, little knowledge is available about the small HERC family, their functions, and modes of interactions with other cellular proteins. In the first chapter, the structural evolution of the small HERC family and related functional changes that have occurred over time …

From Micro To Macro: Examining Potential Microbiome Mediated Influences On Human Growth And Health Outcomes Through Breastfeeding And Antibiotic Exposures, Nicole K. Phillips

Electronic Thesis and Dissertation Repository

Human microbiome research has rapidly developed over the past two decades yet absent from most research is the composition and dynamics of microbiomes within human populations. Given the limitations in longitudinal studies which requires decades of repeated microbe taxonomic testing of a population sample, an alternative option is to examine microbiomes and their influences via proxies using pre-existing health datasets. This research demonstrates preliminary associations between presumed disrupted and supportive microbiomes dynamics proxied by antibiotic and breastmilk exposure respectively. Using health record data across the life span from approximately 500,000 U.K. participants, this research demonstrates variable altered growth and health …

Anteromedial Thalamus Gates The Selection & Stabilization Of Long-Term Memories, Andrew Toader

Student Theses and Dissertations

The hippocampus is necessary for the initial encoding and recent storage of memories. Under the standard model of systems consolidation, it is thought that the memory trace eventually reorganizes from the hippocampus to a distributed cortical network, with the anterior cingulate cortex playing a central role in remote memory retrieval. However, little is known about the mechanisms responsible for coordinating this process. Additionally, the intermediate memory representations in the brain and the circuits that might gate and select memories for permanent storage remain unknown. To facilitate the longitudinal tracking of memory circuits in the brain, we first developed a novel …

The Development Of A New Pertussis Booster Formulation Via The Implementation Of New Adjuvants And Utilization Of Alternate Routes Of Administration, Megan Ashley Dejong

Graduate Theses, Dissertations, and Problem Reports

Pertussis (whooping cough) is a respiratory disease caused by airborne transmission of the Gram-negative bacterium, Bordetella pertussis. Prior to the development of the first pertussis vaccines (whole cell (wP) vaccines), the incidence of pertussis was in the hundreds of thousands of cases per year, which led to the death of many children, as the infection is most severe in younger populations. Thankfully, the wP formulation resulted in a dramatic decrease in the number of annual pertussis cases, nearly eradicating the disease. However, as wP contained the whole B. pertussis bacterium (and its lipooligosaccharide (LOS)), reactogenicity issues became apparent, leading …

Investigating Mirna Regulation Of The Human Apobec3 Enzymes, William Dietrich

All Graduate Theses, Dissertations, and Other Capstone Projects

The human apolipoprotein B mRNA editing enzyme catalytic polypeptide 3 (APOBEC3, A3) are a family of proteins consisting of seven enzymes, A3A, B, C, D, F, G and H, which function as cytosine deaminases. The enzymes’ purpose in the cell is to mutate viral DNA during infection hindering or stopping replication of viruses such as human papillomavirus, herpes simplex virus, and HIV-1. Several of the A3 enzymes have also been implicated in contributing to cancers such as head and neck and breast cancers by mutating cellular genomic DNA, making the ability to control A3 expression an attractive target for cancer …

The Neuroscience Of Art: An Examination Of Uniqueness, Risa Davis

Regis University Student Publications (comprehensive collection)

The field of Neuroaesthetics has an overwhelming potential for helping us to understand the world and human behavior through consideration of both neuroscience and art. Looking at the production of art across human history, it is clear we have evolved with art as every culture has developed some style and desire for art without influence of other peoples. The intriguing and undeniable psychological phenomenon of pareidolia raises the question of why the visual system might be set up in a way that leads to illusions and visual suggestions. The amygdala is also involved as the nuclei’s reaction to perceived or …

Managing Death In Termites, Jizhe Shi

Theses and Dissertations--Entomology

Death of individuals from the same species represents potential risks from disease, predation or competition for animals. Diverse responses associated with death have evolved ranging from simply avoiding or being attracted to the corpses in solitary animals to complicated undertaking behavioral repertoire in eusocial insects. A systematic review in chapter 1 suggested cannibalism is an ancestral and widespread death-related behavior in all non-human animals. Termites are suggested to switch their undertaking behavioral responses from cannibalism to burial based on interactions between chemicals associated with death to balance risks and benefits associated with decomposition. In eusocial animals like termites with caste …

Population Demography, Spatial Ecology, And Habitat Use Of The Florida Box Turtle (Terrapene Bauri) On A Barrier Island, Michael D. Mills

USF Tampa Graduate Theses and Dissertations

Turtles are one the most threatened vertebrate groups in the world due to anthropogenic threats such as habitat loss and overexploitation. In addition to occupying a range that has been vulnerable to major habitat loss, the Florida box turtle (Terrapene bauri) is particularly at risk of overexploitation due to its popularity in the pet trade. Sanibel Island is a barrier island in southwest Florida that has experienced major habitat loss and is the site of a recent poaching event. In response to these threats, studies of both the population demography and spatial ecology were conducted on Sanibel’s Florida box turtle …

Understanding The Role Of Involucrin In Skin Inflammation, Alina Schmidt

Arts & Sciences Electronic Theses and Dissertations

Terminally differentiated keratinocytes are essential for skin barrier function and are surrounded by an involucrin (IVL)-rich cornified envelope. Increased IVL expression in the epidermis is associated with recent positive selection in European populations, yet the functional significance of this finding is unclear. An upstream enhancer of IVL, the 923 enhancer, regulates IVL expression, and the impact of IVL enhancer variants on involucrin expression in modifying the penetrance of filaggrin (FLG) loss-of-function variants associated with atopic dermatitis (AD) has not been explored. I hypothesize involucrin to modulate the environmentally sensitive Vitamin D receptor (Vdr) activity in the epidermis and involucrin enhancer …

The Effects Of Hybridization On Skeletal Morphology In Two Closely Related Populations Of Rhesus Macaques (Macaca Mulatta): A Geometric Morphometric Approach, Cody Zachery Schumacher

Theses and Dissertations

Precise identification and classification techniques are vital for the field of paleoanthropology to ensure that hominin fossilized remains are labeled accurately. The morphology of extinct hominin specimens will typically be compared to extant nonhuman primate species because of how closely related they are phylogenetically. Observable similarities in their morphological variation can be examined to infer which traits may be a result of evolution and this can update our understanding of their evolutionary relationships. The genus Macaca displays a level of morphological variation that is similar to that seen in the genus Homo, therefore macaques can be used as an analogous …

Molecular Evolution And Biogeography Of The New World Eptesicus Bats, Xueling Yi

Theses and Dissertations

Molecular evolution refers to a broad field of studies ranging from microevolution (e.g., population genetics) to macroevolution (e.g., phylogeny), including the bridging field of phylogeography. In natural populations, molecular studies are also combined with biogeography that links biological diversity with geographic distributions to provide a comprehensive understanding of evolutionary processes. The field of molecular evolution has been largely advanced from early exploratory descriptions to statistical tests on biological hypotheses and integrative analyses using sophisticated modeling. However, studies of molecular evolution still face some unresolved questions and challenges, especially in non-model systems. For example, the application of new technology has largely …

Architecture Of Mate Choice Decisions In Enchenopa Treehoppers, Bretta Speck

Theses and Dissertations

Mate selection is one of the most important choices a female can make for herself and her offspring. Variation in mate choice decisions has consequences for the maintenance of and the diversity within a population and the promotion of divergence between populations. Mate choice decisions arise from the interaction of two main components: “mate preferences” (the relative attractiveness of a potential mate) and “choosiness” (the effort put into procuring a preferred mate). My dissertation analyzes the relationship between the components involved in female mate choice decisions in Enchenopa binotata treehoppers. I take a three-pronged approach. First, I investigated how E. …

An Investigation Into The Roles Of Aldose Reductase And Acetate Kinase In The Metabolism Of Entamoeba Histolytica, Matthew B. Angel

All Dissertations

Entamoeba histolytica is an amoebic parasite that infects an estimated 90 million people worldwide and causes approximately 100,000 deaths per year. As the causative agent of amoebic dysentery, this food- and water-borne pathogen represents a significant public health burden worldwide, particularly in areas with poor sanitation. While treatments for amoebiasis exist, they are often limited in their effectiveness. Thus, efforts to better understand the biology and physiology of this organism are vital to the development of novel treatments for this disease.

E. histolytica lacks the enzymes for many common metabolic pathways such as the citric acid cycle and oxidative phosphorylation …

Response And Molecular Control Of Cd8 T Cells During Infection And Cancer, Nicholas K. Preiss Dr.

Dartmouth College Ph.D Dissertations

CD8 T cells are potent immune effector cells capable of vast clonal expansion and clearance of infected or cancerous cells. After control of the pathogenic insult, CD8 T cells develop into quiescent, long-lived memory populations that are poised to mediate rapid protection upon reencounter with cognate antigen. These properties make control of CD8 T cell responses a highly desirable outcome of vaccine strategies and immunotherapy. Therefore, understanding how the effector function and memory differentiation of CD8 T cells are controlled at a molecular level is of great importance. In the context of infection with gammaherpesviruses (γHV), which form a latent …