Modeling Gene Expression With Differential Equations,
2020
Arcadia University
Modeling Gene Expression With Differential Equations, Madison Kuduk
Capstone Showcase
Gene expression is the process by which the information stored in DNA is convertedinto a functional gene product, such as protein. The two main functions that makeup the process of gene expression are transcription and translation. Transcriptionand translation are controlled by the number of mRNA and protein in the cell. Geneexpression can be represented as a system of first order differential equations for the rateof change of mRNA and proteins. These equations involve transcription, translation,degradation and feedback loops. In this paper, I investigate a system of first orderdifferential equations to model gene expression proposed by Hunt, Laplace, Miller andPham in …
The Host Gatekeeper: Using The Flagellar Pathway To Understand Symbiont Host Adaptation,
2020
West Virginia University
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 Role Of Genotype In Saccharomyces Cerevisiae Resistance To 4-Methylcyclohexanemethanol,
2020
West Virginia University
The Role Of Genotype In Saccharomyces Cerevisiae Resistance To 4-Methylcyclohexanemethanol, Michael C. Ayers
Graduate Theses, Dissertations, and Problem Reports (ETD)
The chemical 4-methylcyclohexanemethanol (MCHM) spilled in the Elk River near Charleston, WV in January 2014, impacting the drinking water of 300,000 residents. Initial studies on MCHM following the spill attempted to characterize its toxicological effects in animals, but largely ignored characterization of its effects on cellular pathways and metabolism. In this study, I used this chemical as a novel stressor for the model eukaryote S. cerevisiae to explore the relationship of genotype and stress phenotypes. Initial exploration characterized the stress phenotype of MCHM in yeast through growth assays, cell cycle analysis, and transcriptomic data. MCHM exposure caused cells to arrest …
The Morphological, Physiological, And Genetic Underpinnings Of Intraspecific Salinity Tolerance In Sorghum Bicolor,
2020
West Virginia University
The Morphological, Physiological, And Genetic Underpinnings Of Intraspecific Salinity Tolerance In Sorghum Bicolor, Ashley N. Henderson
Graduate Theses, Dissertations, and Problem Reports (ETD)
Decreases in land quality and quantity threaten the efficient production of agriculturally and economically pivotal crops. Such reductions in arable lands are a consequence of population growth and urbanization, and often result in the introduction of various abiotic stresses. The most common abiotic stressors include water limitation (drought), water logging (over watering), poor water quality (salinity), and extreme temperatures (cold, frost, heat). Each of these stressors negatively impact plant growth, development, and yield. Soil salinity, specifically, is a considerable constraint affecting lands used in agriculture. Salts in the soil rise both naturally and through anthropogenic factors making the abundance a …
The Pseudomonas Aeruginosa Interactome: Insights Into Srna-Mediated Regulatory Networks,
2020
Virginia Commonwealth University
The Pseudomonas Aeruginosa Interactome: Insights Into Srna-Mediated Regulatory Networks, Christine M. Van Duyn
Theses and Dissertations
Pseudomonas aeruginosa is a Gram-negative bacterium found in various environmental niches including soil, water, hospital environments, and within a broad range of hosts. It is well known for its metabolic versatility and intrinsic and acquired resistance to a variety of antimicrobial agents. Moreover, this bacterium has a remarkable ability to adapt and survive in suboptimal environments by altering its transcriptional profile in response to nutrient deprivation, changes in temperature and pH, osmotic stress, the presence of reactive oxygen species (ROS), and exposure to antibiotics and host defenses. P. aeruginosa colonizes individuals with compromised immune systems and severe burn injuries and …
The Functional Importance Of Methyl Cpg Binding Domain Proteins 2 And 3 In Regulating Fetal Hemoglobin Expression In Human Adult Erythroid Cells,
2020
Virginia Commonwealth University
The Functional Importance Of Methyl Cpg Binding Domain Proteins 2 And 3 In Regulating Fetal Hemoglobin Expression In Human Adult Erythroid Cells, Alexander Azzo
Theses and Dissertations
Humans undergo two developmental switches in the predominantly expressed β-like globin chain during embryogenesis and fetal development. The first switch from embryonic (ε) to fetal (γ) occurs around week 5 of embryonic development, while the second switch from fetal to adult (β) globin occurs shortly after birth. By adulthood, fetal hemoglobin represents only 1-2% of total hemoglobin in the blood. As sufficiently elevated levels of fetal hemoglobin are beneficial for improving clinical outcomes in sickle cell disease and β-thalassemia, the mechanisms that enforce silencing of fetal hemoglobin expression postnatally are of great clinical significance. The methyl-CpG binding domain protein MBD2 …
Interspecific Gene Flow Potentiates Adaptive Evolution In A Hybrid Zone Formed Between Pinus Strobiformis And Pinus Flexilis,
2020
Virginia Commonwealth University
Interspecific Gene Flow Potentiates Adaptive Evolution In A Hybrid Zone Formed Between Pinus Strobiformis And Pinus Flexilis, Mitra Menon
Theses and Dissertations
Species range margins are often characterised by high degrees of habitat fragmentation resulting in low genetic diversity and higher gene flow from populations at the core of the species range. Interspecific gene flow from a closely related species with abutting range margins can increase standing genetic diversity and generate novel allelic combinations thereby alleviating limits to adaptive evolution in range margin populations. Hybridization driven interspecific gene flow has played a key role in the demographic history of several conifer due to their life history characteristics such as weak crossability barriers and long generation times. Nevertheless, demonstrating whether introgression is adaptive …
Comprehensive Analysis Of Human Subtelomeres By Whole Genome Mapping,
2020
Old Dominion University
Comprehensive Analysis Of Human Subtelomeres By Whole Genome Mapping, Eleanor Young, Heba Z. Abid, Pui-Yan Kwok, Harold Riethman, Ming Xiao
School of Medical Diagnostics & Translational Sciences Publications
Detailed comprehensive knowledge of the structures of individual long-range telomere-terminal haplotypes are needed to understand their impact on telomere function, and to delineate the population structure and evolution of subtelomere regions. However, the abundance of large evolutionarily recent segmental duplications and high levels of large structural variations have complicated both the mapping and sequence characterization of human subtelomere regions. Here, we use high throughput optical mapping of large single DNA molecules in nanochannel arrays for 154 human genomes from 26 populations to present a comprehensive look at human subtelomere structure and variation. The results catalog many novel long-range subtelomere haplotypes …
Role Of Clic4 And The Synaptic Transcriptome In The Behavioral And Molecular Neurobiology Of Ethanol,
2020
Virginia Commonwealth University
Role Of Clic4 And The Synaptic Transcriptome In The Behavioral And Molecular Neurobiology Of Ethanol, Rory M. Weston
Theses and Dissertations
Alcohol use disorder (AUD) is a prevalent neuropsychiatric disease with profound health, social, and economic consequences. With an estimated 50% heritability, identifying genes that engender risk and contribute to the underlying neurobiological mechanisms represents an important first step in developing effective treatments. Gene expression studies are an important source of candidate genes for studying AUD, providing windows into the molecular machinery engaged by the brain in response to ethanol. Published studies have identified chloride intracellular channel 4 (Clic4) as an ethanol-regulated gene in brain capable of modulating sensitivity to sedation in multiple species. The functions of Clic4 are …
The Exploration Of Nanotoxicological Copper And Interspecific Saccharomyces Hybrids,
2020
West Virginia University
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 …
Evolutionary Genomics Of Dynamic Sex Chromosomes In The Salicaceae,
2020
West Virginia University
Evolutionary Genomics Of Dynamic Sex Chromosomes In The Salicaceae, Ran Zhou
Graduate Theses, Dissertations, and Problem Reports (ETD)
Identifying the sex-determination region (SDR) and other genomic features of sex chromosomes are of great importance in the studies of the evolution of sex. However, the process of accurately identifying the size and location of the SDR is often difficult, even when a genomic sequence is available. This usually is hindered by large repetitive elements and a lack of recombination in the SDR. In this thesis, I assemble sex chromosomes with whole genomic sequencing data, identify SDRs and explore their genomic features in two sister species from the Salicaceae family. I also develop an interpretation of the lability of the …
A Genomic Investigation Of The Stomach Phenotype In Teleosts,
2020
Wilfrid Laurier University
A Genomic Investigation Of The Stomach Phenotype In Teleosts, Louis Pfeifer
Theses and Dissertations (Comprehensive)
The stomach, which is physiologically defined in vertebrates by its function in acid-peptic digestion, has been lost independently multiple times during the evolution of the teleost fishes. The function of the stomach is facilitated by the proton pump H+/K+-ATPase, which acidifies the stomach, and pepsinogens, which are converted to proteolytic pepsins in this acidic environment. It is well documented that in agastric (stomachless) fish, the genes what code for the expression of this proton pump (atp4a and atp4b) and the pepsinogens (pga, pgb, pgf, pgc and cym,) are absent from the genome …
Current Dog Breeding Practices Impacts On Health And Preservation Of Purebred Dogs,
2020
University of New Hampshire, Durham
Current Dog Breeding Practices Impacts On Health And Preservation Of Purebred Dogs, Bridget E. Baker
Honors Theses and Capstones
No abstract provided.
Molecular Insights Into Major Peripheral T-Cell Lymphoma Entities With Advances In A Representative Model System,
2019
University of Nebraska Medical Center
Molecular Insights Into Major Peripheral T-Cell Lymphoma Entities With Advances In A Representative Model System, Tayla B. Heavican
Theses & Dissertations
Peripheral T-cell lymphoma (PTCL) is a group of complex clinicopathological entities associated with an aggressive clinical course. Angioimmunoblastic T-cell lymphoma (AITL) and PTCL-not otherwise specified (PTCL-NOS) are the two most frequent categories accounting for more than 50% of PTCLs. Gene expression profiling (GEP) defined molecular signatures for AITL and delineated biological and prognostic subgroups within PTCL-NOS (PTCL-GATA3 and PTCL-TBX21). Genomic copy number analysis and targeted sequencing revealed unique genomic abnormalities and oncogenic pathways, indicating distinct oncogenic evolution. PTCL-GATA3 exhibited higher genomic complexity characterized by frequent loss or mutation of tumor suppressor genes targeting the CDKN2A/B-TP53 axis and PTEN-PI3K pathways. …
A Transcriptomic Exploration Of Hawaiian Drosophilid Development And Evolution,
2019
University of New Orleans
A Transcriptomic Exploration Of Hawaiian Drosophilid Development And Evolution, Madeline M. Chenevert
LSU New Orleans Theses and Dissertations
One in four known species of fruit flies inhabit the Hawaiian Islands. From a small number of colonizing flies, a wide range of species evolved, some of which managed to reverse-colonize other continental environments. In order to explore the developmental pathways, which separate the Hawaiian Drosophila proper and the Scaptomyza group that contains reverse-colonized species, the transcriptomes of two better-known species in each group, Scaptomyza anomala and Drosophila grimshawi, were analyzed to find changes in gene expression between the two groups. This study describes a novel transcriptome for S. anomala studies as well as unusual changes in gene expression …
Characterization Of Bacterial Communities In Biscayne Bay Through Genomic Analysis,
2019
Nova Southeastern University
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 …
Genetic Diversity Of Blue Wildebeest (Connochaetes Taurinus) In The Liuwa Plain Of Zambia,
2019
Northern Michigan University
Genetic Diversity Of Blue Wildebeest (Connochaetes Taurinus) In The Liuwa Plain Of Zambia, Stephanie J. Szarmach
All NMU Master's Theses
Advances in DNA sequencing are enabling researchers to identify and genotype large sets of single nucleotide polymorphisms (SNPs) in non-model organisms to answer questions concerning ecology, evolution, and conservation. Analysis of SNP allele frequencies can provide insight into the amount of genetic diversity present in a population, connectivity between populations, and historical demographic changes. The blue wildebeest (Connochaetes taurinus) plays an important ecological role in many African savanna ecosystems, but little is known about the level of genetic diversity within most populations or the amount of gene flow that occurs between populations. In particular, the wildebeest in the …
Chasing The Genetics Of Ascites In Broilers Using Whole Genome Resequencing,
2019
University of Arkansas, Fayetteville
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 …
Vines In The Neotropics: Phylogenomics, Biogeography And Systematics In Passion Flowers (Passiflora Subgenus Decaloba Section Decaloba),
2019
University of Missouri-St. Louis
Vines In The Neotropics: Phylogenomics, Biogeography And Systematics In Passion Flowers (Passiflora Subgenus Decaloba Section Decaloba), Serena Acha
Dissertations
With 600 species, Passiflora is a large, morphologically complex and broadly distributed genus in Passifloraceae that represents a major challenge to scientists interested in understanding the evolutionary history of tropical vines. Passiflora has been divided into subgenera, super sections and sections. One of the most enigmatic and species-rich (~120 spp.) groups in Passiflora is section Decaloba, which occurs in the Neotropics and is particularly diverse in Andean montane forests. In this study, we used phylogenomic and population genomic approaches to investigate the evolutionary history, biologeography, species boundaries, and taxonomy of Passiflora section Decaloba. We sampled herbarium specimens, extracted …
Multi-Ancestry Sleep-By-Snp Interaction Analysis In 126,926 Individuals Reveals Lipid Loci Stratified By Sleep Duration,
2019
Leiden University, The Netherlands
Multi-Ancestry Sleep-By-Snp Interaction Analysis In 126,926 Individuals Reveals Lipid Loci Stratified By Sleep Duration, Raymond Noordam, Maxime M. Bos, Heming Wang, Thomas W. Winkler, Amy R. Bentley, Tuomas O. Kilpeläinen, Paul S. De Vries, Yun Ju Sung, Karen Schwander, Brian E. Cade, Alisa Manning, Hugues Aschard, Michael R. Brown, Han Chen, Nora Franceschini, Solomon K. Musani, Melissa Richard, Dina Vojinovic, Stella Aslibekyan, Traci M. Bartz, Donna K. Arnett
Epidemiology and Environmental Health Faculty Publications
Both short and long sleep are associated with an adverse lipid profile, likely through different biological pathways. To elucidate the biology of sleep-associated adverse lipid profile, we conduct multi-ancestry genome-wide sleep-SNP interaction analyses on three lipid traits (HDL-c, LDL-c and triglycerides). In the total study sample (discovery + replication) of 126,926 individuals from 5 different ancestry groups, when considering either long or short total sleep time interactions in joint analyses, we identify 49 previously unreported lipid loci, and 10 additional previously unreported lipid loci in a restricted sample of European-ancestry cohorts. In addition, we identify new gene-sleep interactions for known …
