Genetics Commons^™

Structure And Evolution Of Lizard Immunity Genes, Trent Santonastaso

LSU New Orleans Theses and Dissertations

One of the most important gene families to play a role in adaptive immunity is the major histocompatibility complex (MHC). MHC class II loci are considered to be the most variable loci in the vertebrate genome, and studies have shown that this variability can be maintained through complex co-evolutionary dynamics between host and parasite. Despite the rich body of research into the MHC, there is comparatively little understanding of its genomic architecture in reptiles. Similarly, loci associated with innate immunity have received little attention in reptiles compared to other vertebrates. In the first chapter, we investigated the structure and organization …

Identification Of Trim24 Domain Essentiality In Primary Trim24coe Carcinosarcoma Cell Lines, Cem Dede

Dissertations and Theses (Open Access)

Regulation of transcriptional control is a critical feature for organismal development and survival. Because of its effects on chromatin-controlled expression, disruptions of this delicately tuned mechanism are an important factor in development of tumorigenesis. Therefore, there is a growing interest in targeting these control mechanisms for their potential therapeutic values.

Our lab previously discovered the epigenetic regulator function of Tripartite motif protein 24 (TRIM24) through its H3K4me0 and H3K23ac dual histone signature reader function, its negative regulatory effect on the p53 tumor suppressor, in addition to its shown oncogenic driving capacity on immortalized mammary epithelial cells when overexpressed. Although TRIM24 …

Artificial Intron Technology To Generate Conditional Knock-Out Mice, Amber N. Thomas-Gordon

Dissertations and Theses (Open Access)

Genetic engineering has been re-shaped by the invention of new tools in modern biotechnology in a way that offers precision and efficiency in modifying the genome at a single nucleotide level and/or allowing precise control of gene expression. Such gene manipulation brings about significant findings and revelations in comprehending more about embryonic development, cellular and physiological functions, and disease pathology. Current methods used to produce conditional knockouts have limitations on conditional allele placement and modification varies among genes in different organisms. Thus, a system for generating conditional alleles with fidelity remains a challenge. My goal was to examine an approach …

Wild Mice With Different Social Network Sizes Vary In Brain Gene Expression, Patricia C. Lopes, Barbara König

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Background

Appropriate social interactions influence animal fitness by impacting several processes, such as mating, territory defense, and offspring care. Many studies shedding light on the neurobiological underpinnings of social behavior have focused on nonapeptides (vasopressin, oxytocin, and homologues) and on sexual or parent-offspring interactions. Furthermore, animals have been studied under artificial laboratory conditions, where the consequences of behavioral responses may not be as critical as when expressed under natural environments, therefore obscuring certain physiological responses. We used automated recording of social interactions of wild house mice outside of the breeding season to detect individuals at both tails of a distribution …

Cancer Genetic Counselors’ Perceptions Of Nutritional Recommendations, Breann Reinsch

KGI Theses and Dissertations

Objective: The purpose of this research study is to understand the perspectives of genetic counselors who work with patients in the cancer setting and explore if nutrition is a consideration when counseling patients.

Background: Evidence on the influence of nutrition on cancer risk is increasing with retrospective cohort studies. The American Cancer Society states that smoking, body mass index (BMI), poor nutrition, and excess alcohol consumption are directly linked to cancer occurrences, therefore some cancers may be preventable through lifestyle changes (American Cancer Society, 2016). In cancer genetic counseling sessions, patients are often inquiring about nutritional recommendations. A majority of …

Identification Of Clinically-Relevant Sequence Variants Within The Human Reference Genome, Lisa A. Lansdon

Research Days

No abstract provided.

Use Of Embark Database And An Active Learning Protocol In A High School Classroom, Landon Goodreau

Honors Theses

With advances in technology, personal genome sequencing has become more affordable than ever before. With this wealth of genetic information come new individualized approaches to medicine and pharmacology, along with moral, legal, and ethical issues to carefully consider. Yet studies suggest that most members of the general public do not have the genetic literacy required to understand the implications of genomic data. It is important that today’s students are able to grasp concepts relating to their own genome to make informed medical decisions in the future. Here I describe an active learning-based activity designed to enhance high school students’ understanding …

Genetic Studies Of Wildlife, Brittaney L. Buchanan

School of Natural Resources: Dissertations, Theses, and Student Research

Genetic techniques are being more frequently used to understand the biology and management of wildlife species. The wild turkey is one species of genetic interest because the correct identification of individuals to the subspecies level is difficult using traditional methods. Currently phenotypic differences in plumage, especially the upper tail coverts, are used to assign individuals to subspecies. To hunters wanting to complete a “grand slam,” identification of birds’ subspecies is important. This study focuses on the five extant subspecies: Eastern (M. g. silvestris), Osceola (M. g. osceola), Rio Grande (M. g. intermedia), Merriam’s ( …

Evolutionary Ecology Of Host-Parasite Relationships: Role Of Host Ecology, Phylogeny, And Demographics In Shaping Parasite Evolution, Erika Taylor Gendron

Biology ETDs

Host-parasite systems exist across complex and ecologically heterogeneous landscapes, and may occur across taxonomically and ecologically disparate host species. Under these conditions, mechanisms underlying microevolutionary processes (i.e. gene flow, genetic drift) are not always clear, and may be mediated by numerous co-occurring factors specific to individual hosts. Host traits such as host immunology, demographics, phylogeny and ecology may act in concert to shape host-parasite relationships, and ultimately evolutionary processes. The research described herein used phylogeographic, phylogenomic, and population genetic methods to further understanding of how host traits impact the evolutionary ecology of trematode systems, using avian schistosomes (Digenea: Schistosomatidae) as …

Terms Of Service: The Use And Protection Of Genomic Information By Companies, Databases, And Law Enforcement, Sophia Kallas

Honors Program: Senior Projects (Public)

Private genomic companies have become a popular trend in the last two decades by providing customers with information regarding their ancestry and health risks. However, the profiles received from these companies can also be uploaded to public databases for various purposes, including locating other family members. Both testing companies and public databases have private interests, and both are at risk of law enforcement intervention for the purpose of forensic familial searching. There is little federal legislation protecting the privacy of an individual’s genetic profile. Consequently, it has been up to federal agencies, state laws, and judicial precedents to prevent the …

The Role Of Mitochondrial Pyruvate Carrier 1 (Mpc1) In Heart Failure And Its Implications For Cardiac Recovery, Obadiah Issachar Kirk

Mahurin Honors College Capstone Experience/Thesis Projects

Heart failure (HF) is a complex syndrome with high mortality rates around the world. HF also has diverse etiology as many things contribute such as hypertension, obesity, coronary artery disease, inflammation, and cardiac arrhythmias. Studies have shown that unloading of a failing heart with a left ventricular assist device (LVAD) can lead to cardiac recovery in a subpopulation of individuals with advanced HF. RNA-sequencing and protein expression analysis of myocardial tissue from HF patients who underwent the LVAD implant and heart transplant indicated that subpopulation of HF patients who responded to LVAD unloading had significantly lower levels of mitochondrial pyruvate …

Novel Strategies To Overcome Carboplatin Resistance In Triple Negative Breast Cancer Using Patient Derived Xenografts, Mohammad A. Al Zubi

Theses and Dissertations

Triple-negative breast cancer (TNBC) patients have a poor prognosis and rely on chemotherapeutic treatment as standard of care. Often, they develop chemotherapy resistance, which leaves them without more therapeutic options, like targeted therapy. New models have been developed to test targeted inhibitors in human tumors, and they are known as patient-derived xenografts (PDX). These tumors are obtained from patients, then established and maintained in mice where they areused for tumor studies. In this work, we characterized 14 PDXs for their primary tumor growth rate and investigated metastatic propensity using spontaneous and experiment metastasis models. We utilized RNA-sequencing to characterize contributions …

The Host Gatekeeper: Using The Flagellar Pathway To Understand Symbiont Host Adaptation, Adam R. Pollio

Graduate Theses, Dissertations, and Problem Reports (ETD)

The acquisition of microbial partners is a strategy used by a diverse group of arthropods to overcome ecological barriers that might normally make certain niches uninhabitable. The unique phylogenetic opportunities attainable from the natural experiment of the Sodalis-allied clade allow for better understanding of how molecular structures evolve through time. Here, we focus on the evolution of the flagellar synthesis pathway, due to its complexity and ability to diverge in response to ecological pressures. We used this molecular pathway and natural experiment to show that normal evolutionary outcomes associated with symbiosis (i.e., genome reduction) do not explain the predicted conservation …

The Exploration Of Nanotoxicological Copper And Interspecific Saccharomyces Hybrids, Matthew Joseph Winans Phd

Graduate Theses, Dissertations, and Problem Reports (ETD)

Nanotechnology takes advantage of cellular biology’s natural nanoscale operations by interacting with biomolecules differently than soluble or bulk materials, often altering normal cellular processes such as metabolism or growth. To gain a better understanding of how copper nanoparticles hybridized on cellulose fibers called carboxymethyl cellulose (CMC) affected growth of Saccharomyces cerevisiae, the mechanisms of toxicity were explored. Multiple methodologies covering genetics, proteomics, metallomics, and metabolomics were used during this investigation. The work that lead to this dissertation discovered that these cellulosic copper nanoparticles had a unique toxicity compared to copper. Further investigation suggested a possible ionic or molecular mimicry …

Current Dog Breeding Practices Impacts On Health And Preservation Of Purebred Dogs, Bridget E. Baker

Honors Theses and Capstones

No abstract provided.

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 …

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 …

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 …

The Impact Of Heterogeneity In A Global Knowledge Commons: Implications For Governance Of The Dna Barcode Commons, Janis Geary, Trish Reay, Tania M. Bubela

Office of the Provost

The extent of actor heterogeneity is known to influence the outcomes in natural resource commons, and scholars have recently begun addressed the impact of heterogeneity on knowledge commons creation and sustainability. There is increasing evidence to challenge the dominant theory that heterogeneity is uniformly disadvantageous, but little is known about heterogeneity in knowledge commons. Here, we analyse heterogeneity as it applies to rules for governing a knowledge commons – the DNA barcode commons. DNA barcodes are short, standardized gene regions that can be used to inexpensively identify unknown specimens, and proponents have led international efforts to make DNA barcodes a …

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 …

Investigating The Role Of Cd109 In Pancreatic Ductal Adenocarcinoma, Mennatallah Shaheen

Dissertations and Theses (Open Access)

Pancreatic Ductal Adenocarcinoma (PDAC) is the 3rd leading cause of cancer death in the US. We performed loss of function genomic screening on a cohort of four patient derived PDAC cell populations and our data shows a cell surface receptor CD109 to be a common vulnerability, the biologic role of which in PDAC is yet unstudied and largely unknown. We hypothesized that CD109 expression provides PDAC cells with a survival advantage, and promotes cancer progression through activation of downstream signaling. We believe therefore that targeting CD109 could improve PDAC patients’ survival. Here we report that CD109 plays a role in …

Mixing It Up: The Impact Of Episodic Introgression On The Evolution Of High-Latitude Mesocarnivores, Jocelyn P. Colella

Biology ETDs

At high latitudes, climatic oscillations have triggered repeated episodes of organismal divergence by geographically isolating populations. For terrestrial species, extended isolation in glacial refugia – ice-free regions that enable terrestrial species persistence through glacial maxima – is hypothesized to stimulate allopatric divergence. Alternatively, upon glacial recession, divergent populations expanded from independent glacial refugia and often contacted other diverging populations. In the absence of reproductive isolating mechanisms, this biogeographic process may trigger hybridization and ultimately, gene flow between divergent taxa. My dissertation research aims to understand how these episodic periods of isolation and contact have impacted the evolution of high latitude …

Mapping A New Disease Resistance Locus In An F1 Progeny Derived From Two Grape Wild Relatives, Gaurab Bhattarai

Graduate Theses/Dissertations

Linkage maps and quantitative trait loci (QTL) analysis have become essential tools for the positional cloning of agronomically important genes and for marker-assisted breeding. In this study, two North American grape species, Vitis rupestris and Vitis riparia, and their 294 F₁ progeny were used to construct parental linkage maps and to perform QTL analysis for downy mildew resistance. Single nucleotide polymorphism (SNP) discovery was accomplished using genotyping-by-sequencing (GBS) and resulted in 348,888 SNPs. Of these, 11,063 informative SNP markers (3.17% of the original SNP dataset) were derived after filtering for various quality parameters and missing data. A two-way …

Clinical Utility Of Exon Deletion/Duplication Microarray Testing - A Children’S Mercy Kansas City Two-Year Experience, Binu Porath

Research Days

No abstract provided.

A Discrepancy Between The Human Reference Genome (Grch37) And Transcriptome (Refseq) Results In The Incorrect Annotation Of A Clinically-Relevant Sequence Variant In Recql4, Lisa A. Lansdon

Research Days

No abstract provided.

Co-Occurrence Of Manganese Oxidase Genes Indicates Lateral Transfer Between Classes Of Proteobacteria, Jacob Olichney

Student Scholar Showcase

Pseudomonas putida GB-1 is a model organism for the study of manganese oxidation in bacteria, however, the frequency of co-localization of multiple known and suspected manganese oxidizing proteins, as well as their occurrence between species, is unknown. Eight different genes isolated from known manganese oxidizing bacteria (MnxG, MopA, McoA, PputGB1_2552, PputGB1_2553, MoxA, MofA, and Bacillus MnxG) were tested individually using BioPython and BLAST (Basic Local Alignment Search Tool) on multiple genomic databases. BLAST searches had an expect value cutoff of 1e-50, limiting gene homologs to those with high sequence similarity. The abundance of homologous genes across classes of proteobacteria point …

Plant Mitochondrial Genome Evolution And Structure Has Been Shaped By Double-Strand Break Repair And Recombination, Emily Wynn

School of Biological Sciences: Dissertations, Theses, and Student Research

Plant mitochondrial genomes are large but contain a small number of genes. These genes have very low mutation rates, but genomes rearrange and expand at significant rates. We propose that much of the apparent complexity of plant mitochondrial genomes can be explained by the interactions of double-strand break repair, recombination, and selection. One possible explanation for the disparity between the low mutation rates of genes and the high divergence of non-genes is that synonymous mutations in genes are not truly neutral. In some species, rps14 has been duplicated in the nucleus, allowing the mitochondrial copy to become a pseudogene. By …

Unified Methods For Feature Selection In Large-Scale Genomic Studies With Censored Survival Outcomes, Lauren Spirko-Burns, Karthik Devarajan

COBRA Preprint Series

One of the major goals in large-scale genomic studies is to identify genes with a prognostic impact on time-to-event outcomes which provide insight into the disease's process. With rapid developments in high-throughput genomic technologies in the past two decades, the scientific community is able to monitor the expression levels of tens of thousands of genes and proteins resulting in enormous data sets where the number of genomic features is far greater than the number of subjects. Methods based on univariate Cox regression are often used to select genomic features related to survival outcome; however, the Cox model assumes proportional hazards …

Supervised Dimension Reduction For Large-Scale "Omics" Data With Censored Survival Outcomes Under Possible Non-Proportional Hazards, Lauren Spirko-Burns, Karthik Devarajan

COBRA Preprint Series

The past two decades have witnessed significant advances in high-throughput ``omics" technologies such as genomics, proteomics, metabolomics, transcriptomics and radiomics. These technologies have enabled simultaneous measurement of the expression levels of tens of thousands of features from individual patient samples and have generated enormous amounts of data that require analysis and interpretation. One specific area of interest has been in studying the relationship between these features and patient outcomes, such as overall and recurrence-free survival, with the goal of developing a predictive ``omics" profile. Large-scale studies often suffer from the presence of a large fraction of censored observations and potential …