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Full-Text Articles in Life Sciences

Defining A Haplotype Encompassing The Lcorl-Ncapg Locus Associated With Increased Lean Growth In Beef Cattle, Leif E. Majeres May 2024

Defining A Haplotype Encompassing The Lcorl-Ncapg Locus Associated With Increased Lean Growth In Beef Cattle, Leif E. Majeres

Masters Theses

Numerous studies have shown genetic variation at the LCORL-NCAPG locus is strongly associated with growth traits in beef cattle. However, a causative molecular variant has yet to be identified. To define all possible candidate variants, 34 Charolais-sired calves were whole genome sequenced including 17 homozygous for a long-range haplotype associated with increased growth (QQ), and 17 homozygous for potential ancestral haplotypes for this region (qq). The Q haplotype was refined to an 814-kb region between chr6:37,199,897-38,014,080 and contained 218 variants not found in qq individuals. These variants include an insertion in an intron of NCAPG, …


Using Novel Phenotypes To Understand And Predict Fertility In Beef Cows, Cassidy Catrett Aug 2023

Using Novel Phenotypes To Understand And Predict Fertility In Beef Cows, Cassidy Catrett

Masters Theses

Reproduction plays a major role in the production efficiency of livestock species. However, cow-centric reproductive traits are lowly heritable and are not expressed until later in an animal’s lifetime, making phenotypic selection ineffective at generating genetic gain. We can generate genetic progress by focusing selection on the genetic component of reproductive traits using Expected Progeny Differences (EPDs). We used the American Simmental Association’s performance and Total Herd Enrollment data, made up of 533,155 calving records from 303,158 females (132,403 cows and 170,755 heifers), 33,732 of which are genotyped, to develop two continuous and two discrete phenotypes focused on quantifying early …


Mechanisms By Which Xenorhabdus Nematophila Interacts With Hosts Using Integrated -Omics Approaches, Nicholas C. Mucci May 2022

Mechanisms By Which Xenorhabdus Nematophila Interacts With Hosts Using Integrated -Omics Approaches, Nicholas C. Mucci

Doctoral Dissertations

Nearly all organisms exist in proximity to microbes. These microbes perform most of the essential metabolic processes necessary for homeostasis, forming the nearly hidden support system of Earth. Microbial symbiosis, which is defined as the long-term physical association between host and microbes, relies on communication between the microbial community and their host organism. These interactions among higher order organisms (such as animals, plants, and fungi) and their bacteria links metabolic processes between interkingdom consortia. Many questions on microbial behavior within a host remain poorly understood, such as the colonization efficiency among different microbial species, or how environmental context changes their …


3d Genome Architecture Under Stress: A Survey Of Ionizing Radiation, Progeria, And Osmotic Stress, Jacob Tyler Sanders Dec 2020

3d Genome Architecture Under Stress: A Survey Of Ionizing Radiation, Progeria, And Osmotic Stress, Jacob Tyler Sanders

Doctoral Dissertations

The human nucleus contains 2 meters of DNA which is intricately folded into a three-dimensional (3D) structure. It has become increasingly clear that this 3D structure plays an important role in the expression of genes. Proper gene expression is necessary for cellular homeostasis, cell state, and response to environmental/physical perturbations. Faithful repair of damage DNA damage is necessary to prevent genomic aberrations, such as translocations, which may lead to misregulation of gene expression. Hi-C, a sequencing technique that labels proximal chromatin interactions, provides a clearer picture of how the genome is spatially organized within the nucleus. Here, we discuss the …


Assessment Of Genetic And Education Recovery Plan Objectives For The Bog Turtle (Glyptemys Muhlenbergii), Cassie Marie Dresser Aug 2017

Assessment Of Genetic And Education Recovery Plan Objectives For The Bog Turtle (Glyptemys Muhlenbergii), Cassie Marie Dresser

Doctoral Dissertations

Unprecedented declines in biodiversity are threatening the natural world as we know it. Without human intervention, two thousand species listed under the US Endangered Species Act are likely to disappear. Fortunately, these species receive federal protection and increased research effort is needed to create and satisfy the objectives outlined in the mandated Species Recovery Plan. In this dissertation, I address three conservation objectives outlined in the Recovery Plan for North America’s smallest and rarest turtle, the Bog Turtle (Glyptemys muhlenbergii): (1) investigate the potential genetic differentiation in southern portions of the species’ range, (2) investigate the genetic impacts …


Detection, Diversity, And Evolution Of Fungal Nitric Oxide Reductases (P450nor), Steven Adam Higgins Aug 2017

Detection, Diversity, And Evolution Of Fungal Nitric Oxide Reductases (P450nor), Steven Adam Higgins

Doctoral Dissertations

Nitrous oxide (N2O) is a gas responsible for significant ozone layer depletion and contributes to greenhouse effects in Earth’s atmosphere. N2O is primarily generated by denitrification, whereby nitrate (NO3-) or nitrite (NO2-) is converted to gaseous N2O or N2. Teragram quantities of N2O are emitted annually from agricultural soils treated with nitrogenous fertilizers due to the activity of soil microbiota. Although bacteria and fungi harbor genes permitting denitrification, fungi lack NosZ, an enzyme responsible for reducing N2O into inert N2 gas. Historically, scientists have linked fungi …


Systematics, Diversification, And Functional Diversity Of Russulaceae (Russulales), Brian Patrick Looney May 2017

Systematics, Diversification, And Functional Diversity Of Russulaceae (Russulales), Brian Patrick Looney

Doctoral Dissertations

The family Russulaceae is an iconic family of mushroom-forming Basidiomycetes both because of their importance as edible mushrooms in many parts of the world and their species richness in both temperate and tropical forested biomes. While much mycological research has been focused on this group, recent systematic and ecological research has failed to develop a comprehensive or cohesive organization by which to understand the evolutionary relationships, patterns of diversification, or functional importance of the group. Recently, interest in ectomycorrhizal fungi (EmF), of which Russulaceae is a key lineage, has greatly increased due to the recognition of the importance of EmF …


Whole Genome Sequencing As A Tool For Identifying Phenotypic Properties And Underlying Genetic Mechanisms In Staphylococcus Pseudintermedius, Matthew C. Riley Dec 2016

Whole Genome Sequencing As A Tool For Identifying Phenotypic Properties And Underlying Genetic Mechanisms In Staphylococcus Pseudintermedius, Matthew C. Riley

Doctoral Dissertations

Staphylococcus pseudintermedius is a Gram-positive bacterial opportunistic pathogen commonly associated with dermal infections in canines, but capable of causing serious disease in other species. Reports of human infections caused by S. pseudintermedius along with an increase in resistance to multiple antibiotics highlights the importance of this organism. Whole genome sequencing can allow large scale investigation of genetic mechanisms underlying phenotypic properties that contribute to the expansion of successful S. pseudintermedius clonal lineages.

The increase in multidrug and methicillin-resistant S. pseudintermedius (MRSP) may result from horizontal transfer of genetic material between bacterial isolates, yet is thought to be rare in Staphylococci …


Assessment Of Next Generation Sequencing Technologies For De Novo And Hybrid Assemblies Of Challenging Bacterial Genomes, Sagar Mukund Utturkar May 2016

Assessment Of Next Generation Sequencing Technologies For De Novo And Hybrid Assemblies Of Challenging Bacterial Genomes, Sagar Mukund Utturkar

Doctoral Dissertations

In past decade, tremendous progress has been made in DNA sequencing methodologies in terms of throughput, speed, read-lengths, along with a sharp decrease in per base cost. These technologies, commonly referred to as next-generation sequencing (NGS) are complimented by the development of hybrid assembly approaches which can utilize multiple NGS platforms. In the first part of my dissertation I performed systematic evaluations and optimizations of nine de novo and hybrid assembly protocols across four novel microbial genomes. While each had strengths and weaknesses, via optimization using multiple strategies I obtained dramatic improvements in overall assembly size and quality. To select …


Characterization Of Uncultured, Human Oral Microbiota Using A Targeted, Single-Cell Genomics Approach, Alisha Gail Campbell May 2013

Characterization Of Uncultured, Human Oral Microbiota Using A Targeted, Single-Cell Genomics Approach, Alisha Gail Campbell

Doctoral Dissertations

Microbial communities associated with the human oral cavity are complex, and many oral microbes have yet to be cultured. These uncultured community members are of interest ecologically and phylogenetically, and a number of uncultured species have been positively correlated with oral diseases such as periodontitis. Thus, an approach was adapted to selectively separate single cells from mixed populations of oral bacteria and obtain genomic information for uncultured community members. A combination of fluorescent labeling, cell sorting with flow cytometry and multiple displacement amplification was used to obtain sufficient genomic material for whole-genome pyrosequencing.

The first targets were from uncultured oral …