Using Pooled Data For Genomic Prediction In A Bivariate
Framework With Missing Data,
2022
University of Nebraska-Lincoln
Using Pooled Data For Genomic Prediction In A Bivariate Framework With Missing Data, Johnna L. Baller, Stephen D. Kachman, Larry A. Kuehn, Matthew L. Spangler
Department of Animal Science: Faculty Publications
Pooling samples to derive group genotypes can enable the economically efficient use of commercial animals within genetic evaluations. To test a multivariate framework for genetic evaluations using pooled data, simulation was used to mimic a beef cattle population including two moderately heritable traits with varying genetic correlations, genotypes and pedigree data. There were 15 generations (n = 32,000; random selection and mating), and the last generation was subjected to genotyping through pooling. Missing records were induced in two ways: (a) sequential culling and (b) random missing records. Gaps in genotyping were also explored whereby genotyping occurred through generation 13 …
Gene Drives And The Consequences Of Over-Suppression,
2022
Virginia Commonwealth University
Gene Drives And The Consequences Of Over-Suppression, Cole Butler
Biology and Medicine Through Mathematics Conference
No abstract provided.
Elevated Substitution Rates Among Wolbachia-Infected Mosquito Species Results In Apparent Phylogenetic Discordance.,
2022
Georgia Gwinnett College
Elevated Substitution Rates Among Wolbachia-Infected Mosquito Species Results In Apparent Phylogenetic Discordance., James E. Russell, Michael Saum, Rebekah Williams
Georgia Journal of Science
As one of the most widely distributed bacterial cytoplasmic symbionts on earth, Wolbachia pipientis Hertig serves as a model organism for the understanding of host-symbiont interactions. Many mosquito species are infected with Wolbachia strains that induce a form of reproductive manipulation called cytoplasmic incompatibility, in which infected females gain a reproductive advantage over uninfected females in mixed infection populations. The selective advantage of cytoplasmic incompatibility often results in a population sweep of Wolbachia and co-transmitted mitochondrial genomes. Mitochondrial evolution and phylogenetic inferences drawn from mitochondrial gene sequences are thus potentially compromised by reproductive manipulating symbionts, like Wolbachia. Our initial …
Du Undergraduate Showcase: Research, Scholarship, And Creative Works: Abstracts,
2022
University of Denver
Du Undergraduate Showcase: Research, Scholarship, And Creative Works: Abstracts, Emma Aggeler, Elena Arroway, Daisy T. Booker, Justin Bravo, Kyle Bucholtz, Megan Burnham, Nicole Choi, Spencer Cockerell, Rosie Contino, Jackson Garske, Kaitlyn Glover, Caroline Hamilton, Haley Hartmann, Madalyne Heiken, Colin Holter, Leah Huzjak, Alyssa Jeng, Cole Jernigan, Chad Kashiwa, Adelaide Kerenick, Emily King, Abigail Langeberg, Maddie Leake, Meredith Lemons, Alec Mackay, Greer Mckinley, Ori Miller, Guy Milliman, Katherine Miromonti, Audrey Mitchell, Lauren Moak, Megan Morrell, Gelella Nebiyu, Zdenek Otruba, Toni V. Panzera, Kassidy Patarino, Sneha Patil, Alexandra Penney, Kevin Persky, Caitlin Pham, Gabriela Recinos, Mary Ringgenberg, Chase Routt, Olivia Schneider, Roman Shrestha, Arlo Simmerman, Alec Smith, Tessa Smith, Nhi-Lac Thai, Kyle Thurmann, Casey Tindall, Amelia Trembath, Maria Trubetskaya, Zachary Vangelisti, Peter Vo, Abby Walker, David Winter, Grayden Wolfe, Leah York
DU Undergraduate Research Journal Archive
Abstracts from the DU Undergraduate Showcase.
The Effect Of The Oncometabolite Fumarate In The Response To Dna Damage: An Analysis Of The Role Of Fumarate In The Response Of Cells A2780 To Dna Damage Induced By Cisplatin,
2022
University of Denver
The Effect Of The Oncometabolite Fumarate In The Response To Dna Damage: An Analysis Of The Role Of Fumarate In The Response Of Cells A2780 To Dna Damage Induced By Cisplatin, Gillian Luczyk, Luisa María Sierra, Enol Álvarez González
DU Undergraduate Research Journal Archive
Previous research has been conducted on the effect of oncometabolites on DNA damage repair; however, these studies have traditionally focused on the response to damage caused by DNA double-strand breaks, whereas this study involves cisplatin-induced damage that creates DNA cross-links. This study reports on the effect of the oncometabolite fumarate on the response of A2780 cells to DNA damage produced by cisplatin. Three assays were used to complete this study: comet assay, cell cycle assay and apoptosis assay. The comet assay revealed that fumarate influenced the response of cells to DNA damage and, at a lower 1mM concentration, appeared to …
Investigation Into The Genetic Basis Of Capsaicin Production In Peppers Using Next Generation Rna Sequencing And Synthetic Biology Approaches,
2022
Rowan University
Investigation Into The Genetic Basis Of Capsaicin Production In Peppers Using Next Generation Rna Sequencing And Synthetic Biology Approaches, Ryan Patrick Calhoun
Theses and Dissertations
Capsaicin, a molecule synthesized by plants in the Capsicum genus, is popular for its ability to produce a sensation of burning in any tissue it encounters. The synthesis of capsaicin molecules is achieved through the capsaicin biosynthesis pathway. In this dual study, our goal was to insert two crucial genes, pun1 and pAMT, into a strain of Saccharomyces cerevisiae to allow capsaicin synthesis and perform Illumina RNA sequencing on seven pepper species of increasing pungency to identify other key or novel genes needed or related to capsaicin synthesis. We implemented a golden gate cloning strategy to insert our genes of …
The Nature Of Phenotypes: Provoking And Measuring The Dynamic Processes Of Swarm Expansion, Predation, And Antibiotic Resistance In Myxococcus Xanthus,
2022
Syracuse University
The Nature Of Phenotypes: Provoking And Measuring The Dynamic Processes Of Swarm Expansion, Predation, And Antibiotic Resistance In Myxococcus Xanthus, Linnea Judith Ritchie
Dissertations - ALL
The question of how genotype affects phenotype has fascinated and puzzled scientists for generations. Regardless of organism, the correlation between observation and underlying condition is necessary for scientists to understand the world around us. Myxococcus xanthus, a fascinating organism with a large genome (7,314 genes), is known for complex social behaviors and is an excellent model system for the study of this relationship. Upon starvation, M. xanthus cells condense into large multicellular aggregates to await renewed nutrient availability. M. xanthus cells swarm together on surfaces as a predatory biofilm, lysing and killing prey as a singular unit. During predation, swarms …
Evaluating Threats To The Water Quality Of Little Buffalo Creek And Sarver Run Through Water Quality Analysis And Backpack Electrofishing Surveys,
2022
Duquesne University
Evaluating Threats To The Water Quality Of Little Buffalo Creek And Sarver Run Through Water Quality Analysis And Backpack Electrofishing Surveys, Riley Williams
Electronic Theses and Dissertations
Currently, 64.8% and 52.2% of Little Buffalo Creek and Sarver Run stream kilometers are impaired, respectively. Impairment sources to Little Buffalo Creek include agriculture, riparian deforestation, on-site wastewater, and urban runoff. Impairment sources to Sarver Run are unknown. Our goal was to understand sources of impairment through water quality analysis and fish surveys. Water samples were collected monthly and analyzed for cation and anion concentrations. Mass ratio analysis comparing Br/SO4 and Mg/Li, Ca/Mg and Ca/Sr, Mg/Na and SO4/Cl, and SO4/Cl and Mg/Li suggests that mine drainage and conventional oil and gas may be impacting water …
Analysis Of Water Quality And Fish Communities Of Crooked Creek, Tributary To The Allegheny River In Southwestern Pennsylvania,
2022
Duquesne University
Analysis Of Water Quality And Fish Communities Of Crooked Creek, Tributary To The Allegheny River In Southwestern Pennsylvania, Katherine Stupar
Electronic Theses and Dissertations
Crooked Creek is a tributary of the Allegheny River with a drainage area of 292 square miles. It has been historically affected by mine drainage pollution. Extensive cleanup and monitoring efforts by the Commonwealth of Pennsylvania and the U.S. Army Corps of Engineers (USACE) have taken place over the last four decades. Unconventional oil extraction, or fracking, presents an emerging threat to the water quality of this stream and the health of its fish communities. Here we perform an analysis of the Crooked Creek watershed utilizing backpack electrofishing, eDNA metabarcoding, and various methods of water quality analysis. Seven sites on …
A Review Of Current Methods In Avian Dietary Analysis And Their Integrated Application To Characterize The Trophic Niche Of Louisiana Waterthrush (Parkesia Motacilla).,
2022
Duquesne University
A Review Of Current Methods In Avian Dietary Analysis And Their Integrated Application To Characterize The Trophic Niche Of Louisiana Waterthrush (Parkesia Motacilla)., Brandon Hoenig
Electronic Theses and Dissertations
Characterizing a species’ dietary composition presents an avenue to understand many facets of its ecological niche and can provide essential information for the species’ long-term conservation. To date, the vast majority of diet studies have relied on direct identification of prey during foraging observations or from diet samples to characterize the dietary habits of birds. However, advancements in laboratory-based approaches have revolutionized the field of trophic ecology by allowing researchers to indirectly infer dietary habits with higher resolution across greater time scales. Here, I apply two of these laboratory-based techniques, namely DNA metabarcoding and stable isotope analysis, to characterize the …
Identification Of Pneumococcal Membrane Proteins Involved In Colonization/Biofilm Formation And Cognate Host Cellular Receptors,
2022
Mississippi State University
Identification Of Pneumococcal Membrane Proteins Involved In Colonization/Biofilm Formation And Cognate Host Cellular Receptors, Yoonsung Hu
Theses and Dissertations
Colonization is prerequisite for infection and transmission of Streptococcus pneumoniae, or pneumococcus. Currently available pneumococcal conjugate and pneumococcal polysaccharide vaccines can provide protection against a limited number of capsular serotypes. Implementation of vaccines has decreased the frequency of invasive pneumococcal disease and their colonization rates, but only in a serotype-dependent manner. This has led to serotype replacement in pneumococcal ecology and increased invasive disease caused by non-vaccine serotypes. Development of conserved protein-based vaccine that can provide protection against all pneumococcal serotypes is needed. Numerous surface proteins are conserved in all serotypes, and some are known to be involved in …
Investigation Of Dna Variability And Phylogenetic Relationships Of Perlesta (Plecoptera: Perlidae) In Mississippi,
2022
University of Southern Mississippi
Investigation Of Dna Variability And Phylogenetic Relationships Of Perlesta (Plecoptera: Perlidae) In Mississippi, James C. Valentine, Mac H. Alford
Master's Theses
The genus Perlesta Banks, 1906 (Plecoptera: Perlidae) consists of 35 species, 33 native to the United States and Canada and two native to China. For over a century these small, brown stonefly adults and freckled yellow nymphs have gone by the name of the type species of the genus, Perlesta placida, but taxonomic work in the genus since 1989 has resulted in the recognition of additional species. These species were mostly recognized and described using morphological characteristics, but two areas that are lacking include (1) linking nymphs to adults and (2) phylogenetic analysis of all species occurring in Mississippi …
Reassessment Of Species Boundaries And Phylogenetic Relationships In The Desmodium Ciliare Complex (Fabaceae) Using Morphological And Dna Data,
2022
The University of Southern Mississippi
Reassessment Of Species Boundaries And Phylogenetic Relationships In The Desmodium Ciliare Complex (Fabaceae) Using Morphological And Dna Data, Joshua Wilkinson
Master's Theses
Desmodium (Beggar's ticks) is a generally weedy genus of approximately 280 species in the angiosperm family Fabaceae (Subfamily Papilionoideae, Tribe Desmodieae) characterized by indehiscent loments constricted into segments. Within the Southeastern U.S., the Desmodium ciliare group is one of two Desmodium species complexes that have been historically difficult, with much argument about the limits of species and the role of hybridization. There are three commonly recognized species within the D. ciliare group, D. ciliare (Muhl. ex Willd.) DC., Desmodium marilandicum (L.) DC., and D. obtusum (Muhl. ex Willd.) DC., with two supposed hybrids in addition to the …
Characterization Of A Helicobacter Pylori Small Rna By Rt-Pcr,
2022
Eastern Washington University
Characterization Of A Helicobacter Pylori Small Rna By Rt-Pcr, Roxanne Mcpeck, Andrea Castillo
2022 Symposium
Helicobacter pylori, a bacterial gastric pathogen infecting approximately 50% of the human population, produces gastritis, ulcers, and gastric cancers. Colonizing the inhospitable and fluctuating environment in the stomach requires tight genetic control. However, H. pylori lacks many genetic regulatory elements present in other bacteria to control gene expression. Instead, over 200 small RNAs (sRNAs; noncoding RNAs shorter than 300 nucleotides) have been found in this bacterium, but few have been fully characterized. Of those, many are antisense to virulence genes. Characterizing these sRNAs is important in understanding the mechanisms of molecular genetics and potentially supporting medical management of this …
Genetic Structure Of Urban White-Tailed Deer In West Michigan,
2022
Grand Valley State University
Genetic Structure Of Urban White-Tailed Deer In West Michigan, Jacob David Brand
Masters Theses
In urban areas, green spaces are used by humans and wildlife. The proximity between them can lead to both positive and negative interactions, which can make managing urban wildlife difficult. Managers are challenged due to conflicts between wildlife population sizes that can be naturally supported versus those that are socially tolerable. White-tailed deer (Odocoileus virginianus) thrive in urban environments because their habitat requirements are met within green spaces and backyard vegetation. Matrilineal groups of urban white-tailed deer live within the same areas, at times forming high densities that can lead to the spread of diseases or environmental pests, including hemlock …
Heterogeneity Of Gene Expression In Peanut-Allergic Cells May Be Related To Differing Cell Subpopulations,
2022
Seattle Pacific University
Heterogeneity Of Gene Expression In Peanut-Allergic Cells May Be Related To Differing Cell Subpopulations, Sophia R. Tekorius
Honors Projects
Peanut allergies can have severe and life-threatening complications. By understanding the biology of individuals struggling with this disease, better treatments can be developed. This project explores the possibility of two phenotypically distinct cell types within CD154+ cell types in patients with peanut allergy. Previous studies show that there is a Th2 cell subpopulation associated with allergies, and within effector CD4+ memory populations two distinct phenotypes have been found. This project expands upon this research at the genetic level and through bioinformatic analyses, including the production of heatmaps, the project has found evidence for differing gene expression in two cell subpopulations. …
Invasion Of The Northeastern United States By The Southern Pine Beetle, Dendroctonus Frontalis, And The Impacts On Signatures Of Isolation By Distance Assessed Using Mitochondrial Dna,
2022
University of Mississippi
Invasion Of The Northeastern United States By The Southern Pine Beetle, Dendroctonus Frontalis, And The Impacts On Signatures Of Isolation By Distance Assessed Using Mitochondrial Dna, Lora Grace Holman
Honors Theses
The southern pine beetle (SPB) is a small, black beetle that parasitizes pine trees across the United States and Central America. Recently it has been recognized that the range of SPB is not limited to the southern United States, but rather extends northward across the eastern United States, which raises concerns for pine trees that have never encountered the pest before. Using mitochondrial DNA sequences from a section of the cytochrome oxidase I gene and four different measures of genetic distance compared to geographic distance, we tested for evidence of isolation by distance (IBD) among sampled SPB to see whether …
Developing A Novel Place Preference Assay To Compare Drosophila Species Over Time,
2022
University of Mississippi
Developing A Novel Place Preference Assay To Compare Drosophila Species Over Time, Martha M. Brinson
Honors Theses
Across phylogeny, integration of external factors, memory, and internal states of the organism dictate organismal behavior and mechanisms. The underlying genetic components can affect these behaviors such as in genomic changes arising from speciation. In this thesis, a new place preference assay was evaluated in the analysis and investigation of two species of Drosophila flies (D. melanogaster and D. simulans) to measure similarities and differences and their attraction to two different food substrates. Sleep and circadian measurements were also recorded during experimentation. The Drosophila Activity Monitor 5M (DAM5M) System and Sleep Circadian Analysis MATLAB Program (SCAMP) analysis were …
Extracellular Mechanotransduction In Marfan Syndrome: An Equivalence Principle,
2022
University of Nebraska Medical Center
Extracellular Mechanotransduction In Marfan Syndrome: An Equivalence Principle, Stephen Haller
Theses & Dissertations
Biological tissues continuously experience mechanical stress and have evolved sophisticated mechanisms to sense mechanical stimuli. While traditional viewpoints regard cells as the ultimate sensors and processors of mechanical information, compounding evidence demonstrates that extracellular matrix, the structural component of tissues, also exhibits evolved molecular responses to force. This led us to propose a new paradigm termed extracellular mechanotransduction, in which matrix orchestrates a complementary form of force integration distinct from traditional cellular and extracellular viewpoints. We thus propose that force-sensitive signaling mechanisms evolved within the extracellular space to help cells maintain mechanical homeostasis in tissues. In this dissertation, we apply …
A Genetic Evaluation Of The Impacts Of Dams On Sauger Movement Patterns In The Arkansas River,
2022
Arkansas Tech University
A Genetic Evaluation Of The Impacts Of Dams On Sauger Movement Patterns In The Arkansas River, Emily R. Jonagan
ATU Theses and Dissertations 2021 - Present
Decreased habitat connectivity as a result of damming can lead to genetic isolation in fish communities, especially in highly migratory species. Sauger Sander canadensis is a migratory freshwater species native to the Arkansas River. Sauger are highly sought after by anglers during their annual spawning migration in late winter. In order to investigate the impacts Arkansas River dams on Sauger populations, fin clips were collected in the winters of 2019, 2020, and 2021 below eight dams in the McClellan-Kerr Arkansas River Navigational System (MKARNS). Fin clips were also collected from two reservoirs in Kansas to serve as distinct reference populations. …
