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Articles 1 - 17 of 17
Full-Text Articles in Molecular Genetics
Identification Of Genomic, Proteomic, And Metabolomic Signatures Associated With Pulmonary Hypertension Syndrome In Broilers, Duaa Almansaf
Identification Of Genomic, Proteomic, And Metabolomic Signatures Associated With Pulmonary Hypertension Syndrome In Broilers, Duaa Almansaf
Graduate Theses and Dissertations
The present dissertation contains a collection of studies that examine the genomic, proteomic, and metabolomic association to pulmonary hypertension or ascites phenotype in fast-growing broilers. Pulmonary hypertension is a multifactorial metabolic disease influenced by physiological, environmental, and nutritional factors. It is characterized by a number of structural changes including, thrombosis and adverse pulmonary vascular remodeling. Thus, the atrial pressure is increased, and the right ventricle becomes hypertrophied, resulting in heart failure and the death of the bird. Pulmonary hypertension or ascites is a global problem that has negatively impacted the economy. The increased mortality rate of broilers (25%) is estimated …
Characterization Of Genetic Pathways Involved In Resistance To A Novel Antifungal Peptide, Kayla L. Haberman
Characterization Of Genetic Pathways Involved In Resistance To A Novel Antifungal Peptide, Kayla L. Haberman
Graduate Theses and Dissertations
Antibiotic resistance is increasing prevalence, particularly in Candida glabrata. This opportunistic pathogen is closely phylogenetically related to Saccharomyces cerevisiae; however, its characterization is limited. C. glabrata is only second to Candida albicans as a fungal pathogen in immunocompromised patients. Commonly resistant to azoles, the most common fungal therapy, it has become costly and challenging to treat. A histatin 5 derived antifungal peptide, KM29, has a high degree of efficacy in Candida species and S. cerevisiae. The objective of this work is to advance our understanding of the mechanism of action of KM29 against C. glabrata. Previous work in the lab …
Validation Of Whole Genome Resequencing For Mapping The Genetics Of Ascites In Broilers And Viral Susceptibility In Layers, Katherine Pepper Lee
Validation Of Whole Genome Resequencing For Mapping The Genetics Of Ascites In Broilers And Viral Susceptibility In Layers, Katherine Pepper Lee
Graduate Theses and Dissertations
This dissertation focused on the efficacy and validity of whole genome resequencing (WGR) for fine mapping genetic determinants of particular traits in a given organism. Previously, our research group used WGR to identify haplotype blocks of single nucleotide polymorphisms associated with ascites resistance with some as strong candidates for use in marker-assisted selection (MAS). Chapter 2 discusses the completion of a MAS project through evaluation of ascites incidence as well as production traits of economic value to poultry producers. Thus, the MAS project also covered viability of this methodology in the industry. The MAS significantly reduced ascites incidence in broilers …
Impact Of Genetic Variation And Timescale On Diatom Salinity Stress Response, Kala M. Downey
Impact Of Genetic Variation And Timescale On Diatom Salinity Stress Response, Kala M. Downey
Graduate Theses and Dissertations
Natural environments are dynamic, and organisms must sense and respond to changing conditions. One common way organisms deal with stressful environments is through gene expression changes, allowing for stress acclimation and resistance which occurs over varying time spans in different species. The recent evolutionary history of populations could greatly influence their ability to respond successfully. An evolutionary history in disturbed or fluctuating conditions could promote increased resistance or a more rapid response to these environmental stressors. To understand the impact of genotypic variation and timescales on response and acclimation to salinity changes, we have been exploiting the abilities of euryhaline …
The Role Of Ccaat Binding Factor In The Regulation Of Catalase Gene Expression In Candida Albicans, Zahra Al-Rumaih
The Role Of Ccaat Binding Factor In The Regulation Of Catalase Gene Expression In Candida Albicans, Zahra Al-Rumaih
Graduate Theses and Dissertations
Candida albicans is a fungal opportunistic human pathogen. Its infections range from surficial infections like skin rash to fatal systemic infections. Filamentation growth mode is associated with C. albicans virulence because it helps penetration of the host’s epithelial cells. The CCAAT-binding factor (CBF) is a conserved heterooligomeric transcription factor found in 30% of eukaryotes genes. In C. albicans it is composed of 4 major subunits, including Hap2, Hap3, Hap4, and Hap5. Hap2 and Hap5 are essential for DNA binding and function. Hap4 has 3 homologous subunits: Hap41 and Hap42 are putative subunits of CBP. Hap43 is the only Hap4 subunit …
Development Of A Long-Read Sequencing Protocol To Assess The Precision And Efficacy Of Gene Editing For Duchenne Muscular Dystrophy, Landon Andrew Burcham
Development Of A Long-Read Sequencing Protocol To Assess The Precision And Efficacy Of Gene Editing For Duchenne Muscular Dystrophy, Landon Andrew Burcham
Graduate Theses and Dissertations
This work establishes a method for assessing on-target precision due to CRISPR-Cas9 gene editing, especially within the context of exon skipping therapy for Duchenne Muscular Dystrophy. The proposed method utilizes an Oxford nanopore long-read sequencing approach to sequence amplified regions of DNA that have been edited using CRISPR-Cas9. NIH3T3 and C2C12 cell lines were treated with a dual-guide CRISPR-Cas9 system, that targets and deletes exon 23 from the DMD gene in mouse samples. Deletion PCR revealed deletion of exon 23 in both DNA and cDNA samples. Additionally, sequencing using Oxford Nanopore revealed targeted exon 23 deletion as the most prevalent …
Genome-Wide Analyses Of Genomic Variation Regulating Differential Stress Responses In Japanese Quail, Steven Anthony Shumaker
Genome-Wide Analyses Of Genomic Variation Regulating Differential Stress Responses In Japanese Quail, Steven Anthony Shumaker
Graduate Theses and Dissertations
As consumer demands for poultry grow, producers work to improve bird productivity in both meat and egg production. This endeavor is multifaceted, as many different factors play a part in influencing the productivity of birds, including environmental conditions, overall health, and genetic potential. One aspect controlled for in all aspects of poultry production optimization is stress management. Mitigation of stress is of primary concern to producers, as improper stress management can have many deleterious effects on chickens. Stress management requires an understanding of poultry stress responses and their physiological mechanisms, which can be more deeply understood through genomic analysis. Chapter …
Liver Transcriptomic Analysis After Short- And Long-Term Feeding Of Soy Protein Isolate And Its Ability To Reduce Liver Steatosis In Obese Zucker Rats, Melisa Kozaczek
Liver Transcriptomic Analysis After Short- And Long-Term Feeding Of Soy Protein Isolate And Its Ability To Reduce Liver Steatosis In Obese Zucker Rats, Melisa Kozaczek
Graduate Theses and Dissertations
According to the Centers for Disease Control and Prevention (CDC) the prevalence of obesity in adults in the United States during 2017-2018 was a 42.4%, a high number considering all the risks factors associated with this disorder, such as cardiovascular disease, insulin resistance, diabetes type 2, and fatty liver disease, among others. Fatty liver disease is the accumulation of lipids in the liver that can account for more than 5 to 10% of the liver’s weight. There are two types of fatty liver disease, alcoholic fatty liver disease (AFLD), and non-alcoholic fatty liver disease (NAFLD). AFLD is the detrimental accumulation …
Chasing The Genetics Of Ascites In Broilers Using Whole Genome Resequencing, Alia Parveen
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 …
Unravelling The Layers Of Cell Wall Synthesis And Function In Rice, Ritu Mihani
Unravelling The Layers Of Cell Wall Synthesis And Function In Rice, Ritu Mihani
Graduate Theses and Dissertations
The plant cell wall is of critical importance to plant growth and survival, functioning in maintaining structural integrity, supporting cell expansion, and acting as the first line of defense in response to biotic and abiotic stresses. The major components of the cell wall are cellulose, hemicelluloses, lignin, and pectin. Recent focus on the transcriptional machinery regulating cell wall biosynthesis in plants has revealed many key transcription factors responsible for orchestrating cell wall deposition. However, many of these TFs act redundantly and work coherently with a suite of TFs to activate the cell wall biosynthetic machinery. Heterologous expression of TFs is …
Phylogeny And Evolutionary Genomics Of Non-Photosynthetic Diatoms, Anastasiia Onyshchenko
Phylogeny And Evolutionary Genomics Of Non-Photosynthetic Diatoms, Anastasiia Onyshchenko
Graduate Theses and Dissertations
Diatoms are prolific photosynthesizers responsible for some 20% of global primary production. In real terms, the oxygen in one of every five breaths traces back to photosynthesis by marine diatoms. Among the tens of thousands of diatom species, a small handful of colorless diatom species in the genus Nitzschia have lost photosynthesis altogether and rely exclusively on extracellular organic carbon for growth. I used DNA sequence data to reconstruct the phylogeny of this group, and found that nonphotosynthetic diatoms are monophyletic, indicating that photosynthesis was lost just one time over the course of some 200 million years of diatom evolution. …
Involvement Of The Ino80 Complex In Chromosome Segregation, Jesus Moreno
Involvement Of The Ino80 Complex In Chromosome Segregation, Jesus Moreno
Graduate Theses and Dissertations
Chromatin remodeling complexes are multi-protein complexes that regulate the dynamics of the nucleosomes in the genome. The INO80 chromatin remodeling complex participates in varied biological processes such as: transcription, DNA repair, DNA replication and chromosome integrity. It catalyzes the eviction of the H2A.Z variant histone as well as whole nucleosome eviction. This complex is comprised of 15 subunits and the contribution of each to chromosome segregations remains unknown. To evaluate the contribution of each subunit to chromosome segregation, we tested deletion mutants of the non-essential subunits for DNA content and benomyl sensitivity. Also, we assessed members of the SWR1 and …
A Genetic Analysis Of Nuclear Functions Of The Lipin Protein In Drosophila Melanogaster, Xeniya Rudolf
A Genetic Analysis Of Nuclear Functions Of The Lipin Protein In Drosophila Melanogaster, Xeniya Rudolf
Graduate Theses and Dissertations
Lipins are a family of proteins that have critical functions in the control of fat storage and energy homeostasis. Biochemically, lipins have two functions. They provide an enzymatic activity (phosphatidate phosphatase or PAP activity) in the glycerol-3 phosphate pathway that leads to the production of storage fats (triacylglycerols). In addition, they play a role in the regulation of genes in the cell nucleus as transcriptional co-regulators. The PAP activity of lipins has been widely studied in a number of organisms. However, the transcriptional co-regulator function is not as well described in the literature. The transcriptional function of lipins depends on …
Genetic Determinants Of Salmonella And Campylobacter Required For In Vitro Fitness, Rabindra Kumar Mandal
Genetic Determinants Of Salmonella And Campylobacter Required For In Vitro Fitness, Rabindra Kumar Mandal
Graduate Theses and Dissertations
Non-typhoidal Salmonella (NTS) and Campylobacter play a major role in foodborne illness caused by the consumption of food contaminated by pathogens worldwide. A comprehensive understanding of the genetic factors that increase the survival fitness of these foodborne pathogens will effectively help us formulate mitigation strategies without affecting the nutrition ecology. The objective of this study was to identify the genetic determinants of Salmonella and Campylobacter that are required for fitness under various in vitro conditions. For the purpose, we used a high throughput Transposon sequencing (Tn-seq) that utilizes next generation sequencing (NGS) to screen hundreds of thousands of mutants simultaneously. …
A Phylogenetic Analysis Of Dictyostelium Purpureum Based On Nuclear Rdna Sequences, Mahmoud Suliman
A Phylogenetic Analysis Of Dictyostelium Purpureum Based On Nuclear Rdna Sequences, Mahmoud Suliman
Graduate Theses and Dissertations
Dictyostelids (cellular slime molds) are eukaryotic microorganisms that have both unicellular and multicellular stages during their life cycle. In this study, a molecular phylogenetic analysis was conducted for isolates of one species (Dictyostelium purpureum) based DNA sequences of the ITS, 5.8S and SSU regions of nuclear rDNA. Moreover, a detailed morphological study was carried out using images obtained with both dissecting and compound microscopes. Mating experiments were carried out to assess macrocysts formation between each pair of isolates. The constructed molecular phylogenetic trees indicate that (1) D. purpureum isolates are more closely related to each other than to other species …
Genetic Structure Of The Copperhead (Viperidae: Agkistrodon Contortrix Mokasen) At Its Most Northern Distribution, Brenna Aaren Levine
Genetic Structure Of The Copperhead (Viperidae: Agkistrodon Contortrix Mokasen) At Its Most Northern Distribution, Brenna Aaren Levine
Graduate Theses and Dissertations
The focus of molecular studies in North American pitvipers has been on species that warrant conservation concern, such as Timber (Crotalus horridus) and Massasauga rattlesnakes (Sistrurus catenatus). Scant effort has been directed towards the molecular ecology of the Copperhead (Agkistrodon contortrix), other than to evaluate male reproduction in a laboratory setting and phylogenetic history. Thus, employing DNA-based molecular techniques to study the natural history of A. contortrix will broaden our knowledge of molecular ecology in North American pitvipers, and particularly in a non-threatened species that can serve as a surrogate for threatened and endangered …
The Role Of Centromeric Chromatin And Kinetochore-Associated Factors In Chromosome Segregation, Wesley Williamson
The Role Of Centromeric Chromatin And Kinetochore-Associated Factors In Chromosome Segregation, Wesley Williamson
Graduate Theses and Dissertations
Previous work in our lab has identified a point mutation in HTA1, one of the genes encoding histone H2A, which causes an increase-in-ploidy phenotype in Saccharomyces cerevisiae. This histone mutant strain was used to carry out a transposon insertion screen to identify suppressors of the increase-in-ploidy phenotype. This screen identified all three subunits of the Hda histone deacetylase complex, HDA1, HDA2, and HDA3. This study aims to elucidate the function of the Hda complex in chromosome segregation by exploring interactions among the members of the complex, as well as interactions between Hda complex and kinetochore components. …