Genetics Commons^™

Population Structure Of A Federally Endangered Plant (Astragalus Jaegerianus Munz, Fabaceae) With Limited Range Using Microsatellites, Sueann Neal

Electronic Theses, Projects, and Dissertations

Studies on population genetics examine the relationship and effects of population structure, migration, gene flow and demographic history, and are therefore important in the conservation of endangered species. Astragalus jaegerianus, a critically federally endangered species found in a geographically restricted range is investigated to determine population structure and genetic variation. Previous research on A. jaegerianus focused on DNA sequence data for cpDNA and nrDNA showed no variation. Further research on A. jaegerianus utilizing AFLP’s on the whole genome indicated substantial gene diversity and population structure consistent with geographically widespread species. AFLP research is a cost-effective process to identify levels …

Bayesian Variable Selection Methods For Genome-Wide Association Studies With Categorical Phenotypes, Benazir Rowe

UNLV Theses, Dissertations, Professional Papers, and Capstones

Genome-wide association studies (GWAS) attempt to find the associations between genetic markers and studied traits (phenotypes). The problem of GWAS is complex and various methods have been developed to approach it. One of such methods is Bayesian variable selection (BVS). We describe the BVS methods in detail and demonstrate the ability of BVS method Posterior Inference via Model Averaging and Subset Selection (piMASS) to improve the power of detecting phenotype-associated genetic loci, potentially leading to new discoveries from existing data without increasing the sample size.

We present several ways to improve and extend the applicability of piMASS for GWAS. The …

Characterization Of Adiposity And Inflammation Genetic Pleiotropy Underlying Cardiovascular Risk Factors In Hispanics., Mohammad Yaser (Anwar)

Electronic Theses and Dissertations

The observed overlap between genetic variants associated with both adiposity and inflammatory markers suggests that changes in both adiposity and inflammation could be partially mediated by common pathways. The pervasive but sparsely characterized “pleiotropic” genetic variants associated with both adiposity and inflammation have been hypothesized to provide insight into the shared biology. This study explored and characterized the genetic pleiotropy underpinning adiposity and inflammation using genetic and phenotypic observations from the Cameron County Hispanic Cohort (CCHC). A total of 3,313 samples and >9 million single nucleotide polymorphisms (SNPs) were examined in this study. Mixed model genome-wide association studies (GWAS) were …

Assessment Of Genetic Diversity In Largetooth Sawfish, Pristis Pristis, Populations Over The 20th Century, Ann Fearing

Master's Theses

The Critically Endangered Largetooth Sawfish, Pristis pristis, experienced global declines in range and abundance over the past century and Australia is now their last stronghold. This research aimed to understand whether these declines have been accompanied by a reduction in levels of genetic diversity. Using P. pristis tissue samples sourced from natural history specimens, three fragments (616-bp, 386-bp, 141-bp) in the mitochondrial DNA (mtDNA) control region were PCR-amplified. At each fragment, significant genetic structure was found in P. pristis overall (Φ_ST=0.946, N=9; 0.813, N=54; 0.771, N=99). The Indo-West Pacific and Atlantic/Eastern Pacific each harbor genetically distinct lineages of …

Genetic And Clinical Determinants Of Racial/Ethnic Differences In Multiple Myeloma Susceptibility And Outcomes Focusing On Hispanics, Alem Belachew

Dissertations and Theses (Open Access)

Multiple Myeloma (MM) constitutes 10% of diagnosed hematologic malignancies in the US, with over 12,000 deaths recorded each year. Race/ethnicity is a well-known MM risk factor, where individuals of African descent have over 2- to 3-fold increased risk of incidence compared to those of European descent. Additionally, Hispanics are diagnosed approximately three years younger than white American counterparts, for unknown reasons. Differences in clinical phenotype are also present for MM patients by ancestry, including varying rates of common initiation mutations such as IgH translocations and TP53 mutation between patients of European and African descent. Studies have begun to interrogate the …

P53 Drives A Transcriptional Program That Elicits A Non-Cell-Autonomous Response And Alters Cell State In Vivo, Sydney Moyer

Dissertations and Theses (Open Access)

Cell stress and DNA damage activate the tumor suppressor p53, triggering transcriptional activation of a myriad of target genes. The molecular, morphological, and physiological consequences of this activation remain poorly understood in vivo. We activated a p53 transcriptional program in mice by deletion of Mdm2, a gene which encodes the major p53 inhibitor. By overlaying tissue-specific RNA-sequencing data from pancreas, small intestine, ovary, kidney, and heart with existing p53 ChIP-sequencing, we identified a large repertoire of tissue-specific p53 genes and a common p53 transcriptional signature of seven genes which included Mdm2 but not p21. Global p53 activation …

The Genome-Wide Roles Of The Lung Lineage Transcription Factor Nkx2-1 In The Regulation Of Opposing Cell Fates In Vivo, Danielle Renae Little

Dissertations and Theses (Open Access)

Lineage transcription factors mark, promote, and maintain multiple distinct cell types originating from a common progenitor. Despite their essential role, how such factors function and bind genome wide to orchestrate the epigenetic changes necessary to form and maintain these identities in vivo is unclear. One lineage transcription factor NK Homeobox 2-1 (NKX2-1) is expressed throughout the lung epithelium during development and was thought to be lost in the extraordinarily thin cell type required for gas exchange– the alveolar type 1 (AT1) cell. Complementing precise genetic knockouts with cell type-specific ChIP-seq, ATAC-seq, and scRNA-seq, our study shows that AT1 and AT2 …

Decoding The Evolutionary Response To Prostate Cancer Therapy Using Plasma Genome Sequencing, Naveen Ramesh

Dissertations and Theses (Open Access)

Investigating genome evolution in response to therapy is difficult in human tissue samples due to the difficulty in accessing metastatic tumor sites and logistical challenges of collecting longitudinal samples. To overcome these issues, we developed an unbiased whole-genome plasma DNA sequencing approach called PEGASUS that concurrently measures genomic copy number and exome mutations from archival cryostored plasma samples. This approach was applied to study longitudinal blood plasma samples from prostate cancer patients. A molecular characterization of archival plasma DNA from 233 patients and genomic profiling of 101 patients identified clinical correlations of aneuploid plasma DNA profiles with poor survival, increased …

Genetic And Mirna Transcriptomic Analysis Of Autoregulation Of Nodulation Signaling In Medicago Truncatula, Diptee Chauligain

All Dissertations

Legumes can source nitrogen from the air through biological nitrogen fixation inside root nodules formed in a symbiosis with rhizobia. A complex root-to-shoot-to-root signaling pathway called Autoregulation of Nodulation (AON) controls the number of nodules formed depending on the plant’s nitrogen requirements. In Medicago truncatula, the MtSUNN receptor complex in the shoot binds to the root-generated AON signals, peptides called MtCLEs, resulting in downregulation of miR2111 expression in the shoot, with the effect of decreased transport of miR2111 to the roots. Decreased miR2111 levels in the roots then cause an increase in transcript levels of the miR2111 targets MtTML1 …

Development And Use Of An Environmental Dna Tool To Monitor Recovery Of The Critically Endangered Smalltooth Sawfish, Pristis Pectinata, In The Northwest Atlantic, Ryan N. Lehman

Master's Theses

The Critically Endangered Smalltooth Sawfish, Pristis pectinata, was once common in the tropical and subtropical waters of the Atlantic Ocean; however, following global declines in range and abundance over the past century, individuals were restricted to the waters of south and southwest Florida (SWFL) by about the 1980’s. Recently, public encounter reports have emerged in historically occupied habitats in United States waters, suggesting individuals are present in, or re-occupying, these areas, although the status of P. pectinata outside of SWFL is not currently well understood. Targeted environmental DNA (eDNA) surveys were chosen to assess the occurrence of P …

Neogene And Quaternary Events Shaped Diversification And Speciation In Bhutanese Rheophilic Fishes Of The Family Nemacheilidae (Cypriniformes) And Sisoridae (Siluriformes), Karma Wangchuk

Graduate Theses and Dissertations

Biogeography of the Himalayan region [to include the Qinghai-Tibetan Plateau (QTP)] evolved over a ~30M year span, catalyzed by the collision of the Indian and Eurasian plates. The resulting uplift produced major ecological and climatic effects, that in turn drove the diversification of biodiversity. As a result, the QTP is designated as a global biodiversity hotspot particularly vulnerable to cumulative climatic effects, including shrinking distributions, declining numbers, and local extinctions. Understanding how the biodiversity within the Himalaya/ QTP was established and maintained is a necessary first step in prioritizing conservation efforts.

Fishes in global montane regions, such as the Himalaya, …

Evaluation Of The Xpert Carba-R Nxg Assay For Detection Of Carbapenemase Genes In A Global Challenge Set Of Pseudomonas Aeruginosa Isolates, Fred C. Tenover, Christian M. Gill, Tomefa E. Asempa, Isabella A. Tickler, Caitlin M. Dela Cruz, David P. Nicolau

Biology Faculty Publications

The growing prevalence and diversity of carbapenemase producers among carbapenem-resistant Pseudomonas aeruginosa (CRPA) isolates warrants an expansion of detection capabilities. The purpose of this study was to evaluate the performance of the commercially available Xpert Carba-R (Carba-R) and the research-use-only Xpert Carba-R NxG (Carba-R NxG) in a global collection of P. aeruginosa. The challenge set included 123 P. aeruginosa clinical isolates from 12 countries. Isolates were previously categorized via PCR or whole-genome sequencing. Carbapenemase classes tested include VIM, IMP, NDM, SPM, KPC, and GES. Non-carbapenemase (non-CP)-harboring isolates were also tested (negative control). Isolates were tested using the Carba-R NxG and …

Quantifying Structure And Variation In Complex Phylogenetic Data, Genevieve Geraldine Mount

LSU Doctoral Dissertations

Identifying the source and structure of variation in nature is crucial to understanding fundamental aspects of evolution. Despite a recent plethora of genetic and morphological data, many interesting questions about the relationships between different groups remain unresolved. My dissertation evaluates three approaches for identifying and quantifying the variation within phylogenetic datasets. Characterizing variation within datasets and across analytical methods gives insight into biologically interesting characters, unusual evolutionary processes, and areas for model improvement.

Network-based community detection approaches offer a powerful tool to describe variation in phylogenetic signal across the genome (i.e., gene tree variation). In Chapter 2, I investigate the …

The Effect Of Fcgammariia Polymorphisms On Dengue Outbreak Severity, Leah Darwin, Richard V. Clarke

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

The Nature Of Genes Expressed Differently After Environmental Drug Exposure, Nicci Siffel

Scholars Week

The Nature of Genes Expressed Differently after Environmental Drug Exposure

N. Siffel, S. Anderson, B. Subedi, D.R. Hammond-Weinberger

Drug use, of prescription or illicit varieties, alter bodily functions in different ways, especially in the nervous system. These drugs are found in sources of drinking water because they are not removed by wastewater treatment facilities. To investigate the effects of these drugs as they appear in mixtures, we exposed groups of zebrafish embryos to cocktails of drugs and screened for genes that were differentially expressed between the experimental and control groups and could thus give more insight into their biological functions. …

Denisovan Dna In Late Pleistocene Sediments From Baishiya Karst Cave On The Tibetan Plateau, Dongju Zhang, Huan Xia, Fahu Chen, Bo Li, Viviane Slon, Ting Cheng, Ruowei Yang, Melinda A. Yang

Biology Faculty Publications

A late Middle Pleistocene mandible from Baishiya Karst Cave (BKC) on the Tibetan Plateau has been inferred to be from a Denisovan, an Asian hominin related to Neanderthals, on the basis of an amino acid substitution in its collagen. Here we describe the stratigraphy, chronology, and mitochondrial DNA extracted from the sediments in BKC. We recover Denisovan mitochondrial DNA from sediments deposited ~100 thousand and ~60 thousand years ago (ka) and possibly as recently as ~45 ka. The long-term occupation of BKC by Denisovans suggests that they may have adapted to life at high altitudes and may have contributed such …

Inheritability Of Ciprofloxacin-Induced Mitochondrial Mutations From Parental To Offspring Generation Using Quantitative Polymerase Chain Reaction, Rose Mccoy

Honors Program: Senior Projects (Public)

In all eukaryotes, mitochondria are known as the powerhouse of the cell (Siekevitz, 1957). In plants, however, their mitochondrial genome is especially strange. Plant mitochondrial genomes are extremely large and contain both linear and circular subgenomic DNA fragments. Plant mitochondrial genomes undergo a significant amount of mutations in the form of rearrangements. However, it is not known how often these rearrangements are inherited by the next generation. It is thought that plant cells that are still dividing have higher rates of DNA repair, such as double-strand break repair, to ensure the quality of that plant lineage. As follows, it is …

Identification And Characterization Of Novel Genes And Genetic Interactions That Influence Iba Metabolism, Vanessica Jawahir

Dissertations

Indole-3-butyric acid (IBA) is an endogenous storage auxin important for maintaining appropriate indole-3-acetic acid (IAA) levels that influences primary root elongation and lateral root development. IBA is metabolized into free IAA in the peroxisome in a multistep process similar to fatty acid β-oxidation. Although many components specific to IBA metabolism and peroxisome function have been identified, our understanding is incomplete. I sought to identify novel components of IBA metabolism or peroxisome function by conducting a forward genetic screen for Arabidopsis thaliana plants with enhanced resistance to IBA. I identified Long chain acyl-CoA synthetase 4 (LACS4) as a novel gene functioning …

Herb-Layer Dynamics In An Old-Growth Forest: Vegetation–Environment Relationships And Response To Invasion-Related Perturbations, Taylor M. Buskey, Margaret E. Maloney, Julia I. Chapman, Ryan W. Mcewan

Biology Faculty Publications

Temperate forests of eastern North America are subject to multiple invasions from non-native species that have the potential to drive long-term dynamics in biodiversity. Garlic mustard (Alliaria petiolata (M. Bieb.) Cavara and Grande) is an invasive plant in many deciduous forests, and management efforts often focus on removing this species to initiate native species restoration. Agrilus planipennis Fairmaire (emerald ash borer; Coleoptera: Buprestidae) is a non-native insect pest that has caused substantial loss of ash trees (Fraxinus spp. L.) in North America. Our goal was to understand how the herbaceous layer in an old-growth forest responded to the removal of …

Genetics Fall 2020 Infographics, Robyn Puffenbarger

Genetics Fall 2020

No abstract provided.