Life Sciences Commons^™

Peroxiredoxin 6 And Inflammation In Alzheimer's Disease, Jared Ferrell-Penniman

Biological Sciences Theses and Dissertations

Alzheimer’s disease (AD) is known for its debilitating symptoms and poor prognosis. However, despite intense research into neurodegenerative diseases, there are few therapies targeted at the underlying mechanisms of the disease. Oxidative stress (OS) and inflammation are cellular phenomena thought to be key to the progression of the disease. Critically, peroxiredoxin 6 (Prx6), an antioxidant protein with multiple functions, has been identified from mammalian studies as a potential regulator of both OS and inflammation that may have a specific effect on AD. This project seeks to elucidate the role of Prx6 in AD as well as the underlying mechanisms. Drosophila …

Genetic And Biochemical Analysis Of A Conserved, Multi-Gene System Regulation Spore-Associated Proteins In Streptomyces Coelicolor, Joseph Sallmen

Electronic Theses and Dissertations

Streptomyces coelicolor is a Gram positive, filamentous soil dwelling bacterium that exhibits a complex life cycle including the transition from a vegetative mycelium to a sporulating, aerial mycelium. Early genetic studies identified two classes of genes that resulted in developmental blocks, bald and white. The bald (bld) phenotype occurs when colonies cannot produce aerial hyphae. White (whi) colonies exhibit incomplete sporulation and/or loss of production of the concurrently produced grey pigment. While some of the original mutants have been explored, the developmental functions of many of the identified genes are not well understood. Of particular interest …

The Role Of Histone Chaperone Fact Complex In Base Excision Repair Pathway And Its Therapeutic Potential In Colon Cancer And Medulloblastoma, Heyu Song

Theses & Dissertations

Base excision repair (BER) pathway is required for the removal of damaged bases caused by alkylation, oxidation and ring-saturation. Human apurinic/apyrimidinic endonuclease 1 (APE1) plays a central role in BER pathway. Although repair of damaged bases by recombinant APE1 has been well investigated in vitro, how APE1 gains access to damaged bases in the context of chromatin is largely unknown. A prominent member of the histone chaperone family, FACT (Facilitates Chromatin Transcription) is thought to reorganize nucleosomes through the destabilization of multiple intra-nucleosome contacts. FACT complex is composed of two polypeptides identified as SPT16 (Suppressor of Ty 16) and SSRP1 …

Activation And Regulation Of The Alkbh3-Ascc Alkylation Repair Pathway, Josh Brickner

Arts & Sciences Electronic Theses and Dissertations

DNA repair is essential to prevent the cytotoxic or mutagenic effects of various types of DNA lesions. These lesions are sensed by distinct pathways to recruit repair factors specific to type of damage. In particular, the ALKBH family of proteins recognizes and repairs specific alkylated lesions, including 1-methyladenine (m1A) and 3-methylcytosine (m3C). A major outstanding question in the field is how the AlkB homologue ALKBH3 and its associated protein partners are recruited to sites of alkylation damage and how this repair activity is regulated. Understanding the upstream signaling events that mediate recognition and repair of DNA alkylation damage is particularly …

Elucidating Enhancer Function In Epidermal Development And Filaggrin Loss-Of-Function Variants In African American Atopic Dermatitis, Mary Elizabeth Mathyer

Arts & Sciences Electronic Theses and Dissertations

The epidermis is the outermost tissue of the skin and provides the body’s first line of defense against external assaults. The epidermis is primarily composed of keratinocytes that terminally differentiate and rise apically toward the surface to form the semipermeable barrier of the skin. A hallmark of keratinocyte terminal differentiation is the expression of genes from the Epidermal Differentiation Complex (EDC) locus. Many of the EDC protein products contribute to the structural integrity of the skin barrier, evidenced by several gene knockouts such as loricrin, and even genetic variation within gene coding sequences, that modulate the integrity of the skin …

Genomic Contributors To Individual Differences In Reward-Related Neural Activity, Lindsay Jane Michalski

Arts & Sciences Electronic Theses and Dissertations

Aberrant reward-related behavior, including impulsive and risk-taking behaviors, is a common feature of externalizing psychopathology (e.g., attention deficit hyperactivity disorder, antisocial personality disorder, and substance-use disorders). Through imaging studies, these behaviors have been linked to dysregulated reactivity within a diffuse reward-related corticostriatal neural network, including the striatum, frontal regions (namely orbital, ventromedial, and dorsolateral cortices), the insula, and the hippocampus. Because variability in risk-taking behavior and related psychopathology is moderately-to-largely heritable (i.e., with estimates ranging from 40 – 80%), a genetically-informed approach is well-positioned to provide valuable insight into the etiology of reward-related neural and behavioral phenotypes that characterize externalizing …

Physiologic And Pathologic Profiling Of Clonal Variations, Wing Hing Wong

Arts & Sciences Electronic Theses and Dissertations

This thesis sought to provide a better understanding of clonality in various malignant and non-malignant settings using a variety of genomic analytical tools. Clonality is pre-defined as the presence of a mixed population of cells in which each sub-population has distinct somatic mutation profile. It is a common feature in cancers where subpopulations of cells arise as a result of independent, yet continual acquisition of somatic mutations. The clonal architecture of cancers can be used as a diagnostic and prognostic biomarker as well as to monitor disease progression or resolution. Besides cancer, clonal variability and expansion is also implicated in …

A Noncanonical Function Of The Telomerase Rna Component In Human Embryonic Stem Cells, Kirsten Ann Brenner

Arts & Sciences Electronic Theses and Dissertations

Telomeres are stretches of TTAGGG nucleotide repeats located at the ends of linear chromosomes that shorten with progressive cell division and prevent genomic instability at the cost of limiting a cell’s capacity to proliferate. This limitation can be overcome by telomerase, a ribonucleoprotein complex that elongates telomeres via reverse-transcription of the template telomerase RNA component (TERC). Recent studies have reported potential functions of TERC outside of its role in telomere maintenance. These noncanonical functions of TERC are however poorly defined, and the molecular mechanisms and biological relevance behind such functions remain elusive. Here, we generated conditional TERC knock-out human embryonic …

An Evolving Epigenome That Determines Tissue And Cell Specificity, Renee Louise Sears

Arts & Sciences Electronic Theses and Dissertations

Understanding the mechanisms driving phenotypic variation is a major goal of biology that unifies classical genetics with the emerging fields of genomics and epigenomics. Human and mouse share over 90% of genes and global tissue-specific patterns of expression are maintained between the species. Thus, it is hypothesized that gene expression is influenced through distinctive regulation among species in order to account for the unmistakable phenotypic divergence. DNA methylation, histone modifications, open chromatin patterns, transcription factor binding, and other epigenetic factors are all associated with shaping, maintaining, and repressing regulatory regions which in turn coordinate gene expression. It is vital to …

Genetics With Nettie And Friends: An Exploration Of Genetics In Children's Literature, Erin Soule, Madeleine Gray Burland

Honors Projects

Genetics with Nettie and Friends is an exploration of chromosomal disorders and its place within children's literature. The book provides a comprehensive examination the genetic composition of Downs syndrome, Williams Syndrome, and Duchenne muscular dystrophy at a level to increase understanding in children. This paper provides an insight to the development and construction of the children's book that is available for purchase on Barnes and Noble as well as why representation of genetic disorders in children's literature is needed.

Characterization Of Bacterial Communities In Biscayne Bay Through Genomic Analysis, Eric Fortman

HCNSO Student Theses and Dissertations

Biscayne Bay is a shallow oligotrophic estuary in Southeast Florida. Channelization of rivers, and dredging of canals has greatly altered the historical flow of fresh water into the bay. This, coupled with the rise of a sprawling urban & suburban development, has greatly increased the nutrient load in the bay. This study examined the bacterial community at 14 stations throughout Biscayne Bay —6 stations were located at the mouths of canals; 1 upstream-canal station; 6 stations in the center of the bay; and one ocean influenced station, located near the entrance to the bay. One liter, surface water samples were …

Mechanisms And Consequences Of Myb Gene Activation In Salivary Gland Tumors, Candace Frerich

Biomedical Sciences ETDs

Salivary gland adenoid cystic carcinoma (ACC) is an aggressive tumor with a tendency to infiltrate surrounding nerves and metastasize to distant sites. The standard treatment often fails to control local tumor recurrence and distant metastases and no approved targeted therapeutic options exist for these tumors. The goal of our studies was to reveal the molecular mechanisms driving ACC tumor development and novel drug targets to improve patient morbidity and mortality.

We first analyzed clinical and RNA-sequencing (RNA-seq) data for 68 formalin-fixed paraffin-embedded (FFPE) ACC tumor samples and described previously unappreciated molecular heterogeneity that predicts patient outcome. The poor outcome subgroup …

Functional Importance Of Lipin Phosphorylation, Stephanie Elizabeth Hood

Graduate Theses and Dissertations

Highly conserved throughout evolution, lipins are dual functioning proteins found from yeast to humans. Functioning in the cytoplasm as phosphatidate phosphatase enzymes (PAP), lipins produce diacylglycerol that serves as a precursor for neutral fats and membrane phospholipids. Alternatively, nuclear lipins are responsible for the regulation of metabolic genes. Interestingly, both the mammalian lipin 1 paralog and the single Drosophila Lipin ortholog are highly phosphorylated proteins. Target of rapamycin (TOR) has previously been identified as one of the kinases that controls the subcellular localization of both lipin 1 and Drosophila Lipin. However, other serine and threonine kinases are predicted to be …

Estimation Of Genetic Components Related To Infectious Bovine Keratoconjunctivitis Susceptibility In Angus And Angus Derived Cattle Produced In The Southern United States, Eric Oxford

Graduate Theses and Dissertations

The economic impact of infectious bovine keratoconjunctivitis (IBK) has been documented in many parts of the world. Many researchers have observed that prevention of this disease is very difficult given current methodologies. This is primarily due to the multifactorial nature of this disease. The objective of this dissertation was to determine the impact of IBK on calf performance and estimate genetic parameters, heritability and estimated breeding values for IBK susceptibility. Data were analyzed using PROC GLIMMIX of SAS; while genetic parameters were estimated using a linear animal model for both single- and two-traits through MTDFREML. Additional evaluations calculated heritability using …

An Autism-Causing Variant Misregulates Selective Autophagy To Alter Axon Targeting And Behavior, Tyler Buddell

Theses and Dissertations

Neurodevelopmental disorders cause debilitating disruptions to the cellular mechanisms that underlie development of the brain. Unfortunately, the complexities of neurodevelopmental disorders make them difficult to study, and the molecular mechanisms perturbed by these disorders remain elusive. Better understanding of neurodevelopmental mechanisms, and the related genes involved, will likely yield new insight into neurodevelopmental disorders. A gene that has been associated with a number of neurodevelopmental disorders is the calcium voltage-gated channel subunit alpha1 C (CACNA1C) gene. Common and rare variants of the CACNA1C gene have been associated with autism and other neurodevelopmental disorders including schizophrenia, bipolar disorder and ADHD. However, …

A Possible Luxr Solo Type Regulator Of An Antibiotic-Like Compound From The Soil Bacterium Rhodococcus, Katelyn Sellick

Electronic Theses and Dissertations

Rhodococcus, a species of bacteria commonly found in the soil, is an under-explored producer of small bioactive compounds including siderophores, pigments and antibiotics. MTM3W5.2 is a strain of Rhodococcus that was previously discovered to produce an antibiotic-like compound that has inhibitory effects on other Rhodococcus strains, including the veterinary pathogen, R. equi. The biosynthetic gene cluster responsible for production of the antibiotic has been identified, and a small gene, BTZ20_3964 at the start of the operon is believed to be a luxR solo regulator of the gene cluster. The goal of this project was to determine this gene’s …

Chasing The Genetics Of Ascites In Broilers Using Whole Genome Resequencing, Alia Parveen

Graduate Theses and Dissertations

We are using whole genome resequencing to identify chromosomal regions associated with resistance or susceptibility to ascites, a form of pulmonary hypertension syndrome, meat-type chickens. Previous Genome Wide Association Studies (GWAS) based on Single Nucleotide Polymorphisms (SNPs) have identified regions on chromosomes 2, 9 and Z. Despite several GWAS and further genotyping, there are no reliable or potential markers for ascites phenotype. We have completed screening of Copy Number Variations (CNVs) and Single Nucleotide Polymorphisms in ascites resistant and susceptible birds from the relaxed, REL, line derived from a commercial elite broiler line. DNA samples from resistant and susceptible birds …

Investigating Growth Performance And Intestinal Barrier Integrity In Heat-Stressed Modern Broilers And Their Ancestor Jungle Fowl, Travis Tabler

Graduate Theses and Dissertations

Heat stress (HS) has a negative effect on poultry production sustainability due to its adverse consequence on bird welfare, health, growth, and mortality. Although modern broilers have greater gut mass and higher energy use efficiency than unselected birds, they are more vulnerable to HS that induces “leaky gut syndrome,” or increased intestinal permeability. The aim of the current study was to determine the effect of HS on growth performance and gut barrier integrity in three modern broiler lines and their ancestor the Jungle Fowl. Four chicken populations including Giant Jungle Fowl (JF), Athens Canadian Random Bred (ACRB), 1995 Arkansas Random …

A Seascape Genetics Approach To Studying Genetic Differentiation In The Bull Kelp Nereocystis Luetkeana, Lily G. Gierke

Theses and Dissertations

The brown alga Nereocystis luetkeana is a foundation species found from Alaska to California. In the Salish Sea, N. luetkeana is declining, but little is known about its population structure. We explored N. luetkeana 1) allelic dissimilarity and richness using seven microsatellite markers, and 2) tested models of gene flow in the Salish Sea using a hydrodynamic transport model. Our results suggest that the N. luetkeana distribution is comprised of four genetic co-ancestry groups that are geographically coherent, apart from the separation of the Strait of Georgia/Puget Sound by the Strait of Juan de Fuca. Our model supported that environmental …

The Effects Of Foot And Udder Scoring On Cow And Calf Performance, Clayton Lee Mcguire

Graduate Theses and Dissertations

Foot soundness and udder conformation are essential for longevity in beef cattle. The objective of this study was to investigate the effects of foot angle (FA), claw set (CS), teat size (TS) and udder suspension (US) scores on cowherd performance. Data were analyzed for 1,685 observations on Angus-based cows over a four-year period. At weaning FA, CS, TS, and US were evaluated. Scores are based on nine-point scales. A score of one indicates straight pasterns, divergent toes, enlarged bottle shaped teats, and absence of a median suspensory ligament; nine indicates weak pasterns, curled toes, small symmetrical teats, and a tight …

Two Fields, One Pellet: Combining Demographics And Population Genetics Through Non-Invasive Sampling Of Snowshoe Hare Fecal Pellets In Michigan., Genelle Nicole Uhrig

Theses and Dissertations

As climate continues to change at a rapid rate, species are increasingly vulnerable to the resulting environmental changes. This is especially true for species whose fitness is closely linked to climate-associated environmental conditions. One of these vulnerable species is snowshoe hare, Lepus americanus, who depends on the timing and duration of snowfall to provide camouflage when they go through seasonal pelage changes from brown in the summer to white in the winter. Whereas snowshoe hare are stable across the core of their range, populations along the southern range edge are experiencing declines due to climate driven environmental changes that cause …

Exploring Secondary Structure In Bacteriophage Programmed Frameshift Elements, Samuel Okabayashi, Sean Mcclory

HON499 projects

Bacteriophages are viruses that infect bacteria and reproduce using host bacterial components. Part of the bacteriophage reproduction is assembly of the tail complex, which requires two assembly chaperone (TAC) proteins. In many phages the TAC’s are produced from a single gene through a non-canonical process called programmed translational frameshifting (PTF). The SEA-PHAGES program has produced hundreds of TAC genes that are accessible through phagesdb, a database of sequenced and annotated phage genomes. The sequences for the TAC gene were gathered from phagesdb and analyzed using ClustalOmega; a multiple sequence alignment (MSA) tool which revealed several positions where total conservation was …

Molecular Survey Of Helminths Infecting Ground Dwelling Birds In The Grouse Subfamily Tetraoninae, Briana M. Sesmundo

Honors College Theses

Alaskan grouse and ptarmigan (Galliformes) are important avian game species in Alaska. Interestingly, gallids harbor a fairly diverse helminth fauna, particularly cestodes, which may make birds with high parasite loads more susceptible to predation. Unfortunately, there is limited information available on the helminth fauna of Alaskan gallids, and no molecular surveys. The present study aims to develop baseline data on diversity of intestinal and subcutaneous (filariid) helminth infections in galliforms using morphological and molecular (DNA) approaches. These data can then be used to better understand changes in helminth community structure given current environmental volatility. The intestines, cloaca, liver and kidneys …

Immune Gene Diversity And Populations Structure Of Reticulated Flatwoods Salamander (Ambystoma Bishopi), Steven Tyler Williams

LSU Master's Theses

Reticulated flatwoods salamander (Ambystoma bishopi) populations began decreasing dramatically in the late 1900s. Contemporary populations are small, isolated, and may be susceptible to inbreeding and reduced adaptive potential because of low genetic variation. Genetic variation at immune genes is especially important as it influences disease susceptibility and adaptation to emerging infectious pathogens, a central conservation concern for declining amphibians. Connectivity between isolated populations is also vital to maintain genetic diversity and avoid inbreeding. I collected tissue samples from across the extant range of this salamander to examine genetic variation and population structure in: immune genes broadly (immunome), the …

Characterization And Amplification Of Retrotransposable Elements Platy-1 And Alu In The Cebidae Lineage Of Platyrrhine Primates, Jessica Storer

LSU Doctoral Dissertations

Alu mobile elements are much more than “junk DNA”. Inherent properties such as high copy number, small ~300 bp size, and their nearly homoplasy-free nature make these elements particularly useful in resolving primate phylogenies. In addition, shared sequence features and identity with the Alu element allow for discovery of new SINE retrotransposons, such as the Platyrrhine-limited Platy-1 element. Building on previous research of subfamily analysis, the Platy-1 and Alu elements can be used not only to explore the controversial New World monkey (NWM) phylogeny, but also the mode and tempo of their amplification in different primate genera and species.

Chapter …

Rna Interference Of Worker Sterility Genes: Testing Mechanisms Of Reproductive Regulation In Apis Mellifera, Anthony J. Gallo

Electronic Thesis and Dissertation Repository

Social insects such as the honey bee (Apis mellifera) are well known for their reproductive division of labour and eusocial colony systems. Honey bee workers forgo reproduction in favour of being selfless in directing reproductive benefits towards their queen mother. This altruistic tendency is a result of both behavioural and physiological changes under control of the presence of the queen’s mandibular pheromone. The genetic mechanism that underlies this response is, however, not well understood. Here, this study used RNA interference to knock down the expression of single genes (fruitless and ftz-f1) that have been previously identified …

The Role Of Chromatin State Transitions In Modulating Early Phosphate-Deficiency Response Genes In Plants, Maryam Foroozani

LSU Doctoral Dissertations

Phosphorus (P) is an essential plant macronutrient vital to fundamental metabolic processes. Plant-available P is low in most soils, making it a frequent limiter of growth. Declining P reserves for fertilizer production exasperates this agricultural challenge. Plants modulate complex responses to fluctuating P levels via global transcriptional regulatory networks. Although chromatin structure plays a substantial role in controlling gene expression, the chromatin-level mechanisms involved in regulating P homeostasis have not been determined.

In this work, I used chromatin immunoprecipitation (ChIP) combined with next-generation DNA sequencing (ChIP-seq) to map the distribution of H3K4me3 in rice (Oryza sativa L.) during both …

Eugenics In The 21st Century, Jessica Linn Chin

Dissertations, Theses, and Capstone Projects

Eugenics is the science of enhancing the human population through the management of breeding and hereditary traits. This thesis explores the history of eugenics and shows how eugenic practices continue in the 21^st century with advancements in technology and positive eugenic goals that can result in adverse effects on the human body and society. When Sir Francis Galton coined the term eugenics in 1883, he intended to improve British society with the use of positive eugenics. Galton used positive eugenics to encourage people with good mental and physical qualities to produce more children. He avoided negative eugenics, which involved …

Towards A Mathematical Model Of Motility Using Dictyostelium Discoideum: Proteins And Geometric Features That Regulate Bleb-Based Motility, Zully Santiago

Dissertations, Theses, and Capstone Projects

A variety of biological functions depend on actin organization. The organization of actin is tightly regulated by a plethora of extracellular and intracellular signaling, scaffolding, and actin-binding proteins. Dysfunctions in this regulation lead to immune diseases, increased susceptibility to pathogens, neurodegenerative diseases, developmental disorders, and cancer metastasis. A variety of actin-dependent processes, including cell motility, are regulated by several proteins of interest: Paxillin, a scaffolding protein; WASP, an actin nucleating protein; SCAR/WAVE, another WASP family actin nucleating protein; Talin, a cortex-to-membrane binding protein; Myosin II, an F-actin contracting motor protein; and Protein Kinase C, a protein kinase. D. discoideum cells …

Assessing The Role Of Drosophila Melanogaster Neuroligin 3 On Social Spacing And Climbing Behaviour, J. Wesley Robinson

Electronic Thesis and Dissertation Repository

Autism spectrum disorders can be clinically defined in part by impairments of social interactions. Social interactions can be modeled in Drosophila melanogaster with behaviours such as social spacing. Here, I examined the effects of autism-related gene neuroligin 3 on fly social spacing. I hypothesized if neuroligin 3 is mutated or gene expression is targeted for knockdown, then flies will have altered social space in males and females at different ages. Using the social space assay, I found that different mutations to neuroligin 3 change the fly’s behavior, in a mutation and sex-specific manner. Using an antibody against Nlg3, I localized …