Genetics Commons^™

Genetic Structure Of Ixodes Scapularis Say 1821 (Acari: Ixodidae), The Blacklegged Tick, By Microsatellite Analysis, John Ludwig

College of Graduate Studies: Theses & Dissertations

The blacklegged tick, Ixodes scapularis (Acari: Ixodidae) is the subject of intense research due to its economic importance from being a vector of several diseases. Previous studies have examined its taxonomic status and more recently, its genetic structure. This study embarked upon resolving the questions surrounding the genetic structuring of the tick, by using different molecular markers. Molecular data were first phylogenetically analyzed by using four different mitochondrial and nuclear markers (12SrDNA n=483, Dloop n=432, ITS2 n=156, Actin n=117). A Bayesian tree was inferred from the concatenated mitochondrial dataset, whereas nuclear gene markers were found to be uninformative. Nine microsatellites …

The Genetic Ancestry Of African Americans, Latinos, And European Americans Across The United States, Katarzyna Bryc, Eric Y. Durand, J. Michael Macpherson, David Reich, Joanna Mountain

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Over the past 500 years, North America has been the site of ongoing mixing of Native Americans, European settlers, and Africans (brought largely by the trans-Atlantic slave trade), shaping the early history of what became the United States. We studied the genetic ancestry of 5,269 self-described African Americans, 8,663 Latinos, and 148,789 European Americans who are 23andMe customers and show that the legacy of these historical interactions is visible in the genetic ancestry of present-day Americans. We document pervasive mixed ancestry and asymmetrical male and female ancestry contributions in all groups studied. We show that regional ancestry differences reflect historical …

Influence Of Landscape On Gene Differentiation In The American Pika (Ochotona Princeps) Within The Interstate 90 Snoqualmie Pass Corridor, Craig P. Fergus

All Master's Theses

Understanding the impact of different landscape features on the movement of genes among populations can be helpful in managing wildlife populations. Our study used GIS tools to compare genetic connectivity among 13 American pika (Ochotona princeps) habitat patches across an approximately 77 square km area adjacent to Interstate 90 near Snoqualmie Pass, WA. Tissue samples were collected from 85 individuals and genotyped at six microsatellite loci to determine genetic differentiation among each pair of patches. A variety of models estimating the influence of landscape factors on gene flow were then used to find “resistance scores” between each pair …

Carnivore Diet Identification Through Scat And Genetic Analysis In Namibia, Africa, Alicia J. Walsh

Honors Theses and Capstones

Worldwide the cheetah population is declining making them Africa’s most endangered large cat. Namibia, Africa currently has the largest population of cheetahs in the world. During the summer of 2014, I did scat analysis of carnivores on the property of the Cheetah Conservation Fund (CCF) in Namibia in order to better understand the predators that compete with the cheetah and how the ecosystem works as a whole. I worked at CCF for nine weeks to analyze the diets of carnivores in the area through genetic and scat analysis. Analyzing carnivore feces would ultimately identify the diet of various carnivores in …

Fungicide Resistance Genetics Of Apple Scab Fungus Venturia Inaequalis, Alexis Lt Reddel

Honors Theses and Capstones

Apple scab, caused by the ascomycete fungus Venturia inaequalis, is considered the most devastating disease on domestic apple crops. Apples are the most important cultivated crop in temperate regions and the United States produced about 4.6 million tons of apples in 2010. Traditional methods to control fungal plant diseases like apple scab are based on the use of chemical compounds that may produce serious negative effects, mainly related with environmental pollution and the development of fungicide resistance. Identifying genes and mechanisms of fungicide resistance in V. inaequalis is imperative to developing new and more effective defenses against the spread …

Directed Evolution Of Genetic Regulatory Elements Using Crispr/Cas Genome Engineering, Candice J. Coppola

Summer Community of Scholars Posters (RCEU and HCR Combined Programs)

No abstract provided.

Impacts Of Climate, Geography And White-Nose Syndrome Mortality On The Population Genetic Structure And Variation Of Myotis Lucifugus In The Eastern United States, Shannon Marie Dodge Morgan

Legacy Theses & Dissertations (2009 - 2024)

A myriad of biotic and abiotic factors contribute to the fluctuations in geographic range and size of animal populations. In the Nearctic, bat species have experienced drastic historic changes in available habitat due to Pleistocene glaciations, and are recently imperiled by the introduction of a novel fungal pathogen, Pseudogymnoascus destructans within the last decade. Myotis lucifugus in particular has lost 90-95% of the population in the eastern US due to the fungal disease White-Nose Syndrome (WNS). A population decline of this magnitude will likely result in a loss of allelic diversity as a result of a genetic bottleneck. My study …

A Genetic Epidemiologic Investigation Of Breast Cancer Susceptibility, Cristy Ellen Stagnar

Legacy Theses & Dissertations (2009 - 2024)

Introduction

Genome-Scale Analyses Of Transcription And Transcriptional Regulation In Bacteria, Devon Marie Fitzgerald

Legacy Theses & Dissertations (2009 - 2024)

The textbook model of bacterial transcription regulation posits that promoters occur immediately upstream of genes and that transcription factors (TFs) modulate transcription through promoter-proximal binding. However, the recent application of unbiased genome-wide approaches, such as ChIP-seq and RNA-seq, has revealed a much more complex picture, including TF binding and transcription initiation occurring in unexpected locations. This dissertation describes the use of deep sequencing-based approaches to evaluate the genome-wide binding of transcription-related proteins and identify locations of transcription initiation. I have assessed the genome-wide binding of three Escherichia coli TFs and an alternative σ factor. Additionally, I have analyzed genome-wide patterns …

Foraminiferal Beta 2-Tubulin And Microtubule To Helical Filament Transition In Reticulomyxa Filosa, Ingrid Ann Hahn

Legacy Theses & Dissertations (2009 - 2024)

Foraminifera have unusually fast dynamic movements resulting in the reorganization of the microtubule cytoskeleton (Travis and Bowser, 1988; Travis et al., 1983). We are interested in using Reticulomyxa filosa as a model to investigate the mechanisms and factors that regulate such fast microtubule assembly/disassembly rates (Chen and Schliwa 1990; Travis and Bowser, 1991; Welnhofer and Travis, 1996). Compared to conventional microtubule assembly and disassembly models, foraminifera tubulin can exist in another assembly state termed helical filaments. A novel form of tubulin, β2, in foraminifera is likely critical to these unusual microtubule properties. This thesis investigates Reticulomyxa filosa, a freshwater foraminifera …

Evolution Of New Duplicate Genes In Arabidopsis Thaliana, Nicholas Curtis Marowsky

Wayne State University Theses

Abstract

Gene duplication is one of the major mechanisms by which organisms expand their genomes. The material added to the genome can then be acted upon by mutation and natural selection to increase the fitness of the species. By studying these duplicate sequences we can understand the process by which species evolve new functional genes. In a previous paper we identified 100 new duplicate genes through a genome wide comparison between A. thaliana and related species. We selected three of these new duplicate genes and investigated more closely their sequence and expression divergence from their parental gene. The three new …

An Assessment Of The Role Of Roads In Population Demography And Genetic Structuring In Two Species Of Lizards In The Northern Chihuahuan Desert, Kevin Floyd

Open Access Theses & Dissertations

Roads can fragment habitat and increase mortality rates of wildlife, potentially reducing population sizes and gene flow, which in turn can reduce genetic diversity through genetic drift. Although negative road impacts have been found in a variety of taxa, not all species are impacted. For instance, species that move less and rarely encounter roads and those that avoid the roads are predicted to not be negatively affected. Yet tests of these predictions are uncommon, especially for reptiles and particularly lizards. Side-blotched lizards (Uta stansburiana) are small sit-and-wait predators, while the larger marbled whiptails (Aspidoscelis marmorata) are active foragers. Their responses …

Developing Microbial Biomarkers To Non-Invasively Assess Health In Wild Elk (Cervus Canadensis) Populations, Samuel B. Pannoni

Undergraduate Theses, Professional Papers, and Capstone Artifacts

The composition of the intestinal bacterial community (intestinal microbiome) of mammals is associated with changes in diet, stress, disease and physical condition of the animal. The relationship between health and the microbiome has been extensively demonstrated in studies of humans and mice; this provides strong support for its potential utility in wildlife. When managing elk (Cervus canadensis), federal and state agencies currently must rely on invasive sampling and coarse demographic data on which to base their decisions. By developing microbiome-based biomarkers that vary as a function of elk body condition and disease (i.e. microbial biomarkers), we hope to …

Postmitotic Expression Of Sod1g93a Gene Affects The Identity Of Myogenic Cells And Inhibits Myoblasts Differentiation, M. Martini, G. Dobrowolny, M. Aucello, Antonio Musaro

Research outputs 2014 to 2021

To determine the role of mutant SOD1 gene (SOD1G93A) on muscle cell differentiation, we derived C2C12 muscle cell lines carrying a stably transfected SOD1G93A gene under the control of a myosin light chain (MLC) promoter-enhancer cassette. Expression of MLC/SOD1G93A in C2C12 cells resulted in dramatic inhibition of myoblast differentiation. Transfected SOD1G93A gene expression in postmitotic skeletal myocytes downregulated the expression of relevant markers of committed and differentiated myoblasts such as MyoD, Myogenin, MRF4, and the muscle specific miRNA expression. The inhibitory effects of SOD1G93A gene on myogenic program perturbed Akt/p70 and MAPK signaling pathways which promote differentiation cascade. Of note, …

Erratum To: Hclp46 Increases Smad3 Protein Stability Via Inhibiting Its Ubiquitin-Proteasomal Degradation, Yingying Xing, Qiaoyun Chu, Run Feng, Wei Wang, Lixin Lu

Research outputs 2014 to 2021

No abstract provided.

Chromosomal Rearrangements Directly Cause Underdominant F1 Pollen Sterility In Mimulus Lewisii-M. Cardinalis Hybrids, Angela M. Stathos

Graduate Student Theses, Dissertations, & Professional Papers

Chromosomal rearrangements can contribute to the evolution of postzygotic reproductive isolation directly, by disrupting meiosis in F₁ hybrids, or indirectly, by suppressing recombination among genic incompatibilities. Because direct effects of rearrangements on fertility imply fitness costs during their spread, understanding the mechanism of F₁ hybrid sterility is integral to reconstructing the role(s) of rearrangements in speciation. In hybrids between monkeyflowers Mimulus cardinalis and M. lewisii, rearrangements contain all quantitative trait loci (QTLs) for both premating barriers and pollen sterility, suggesting that they may have facilitated speciation in this model system. I used artificial chromosome doubling and …

Phenotypic Characterization Of Pnpase Knockdown In C. Elegans, Laura A. Lambert

Theses and Dissertations

The multifunctional exoribonuclease protein PNPase is implicated as a potential target for cancer therapy as well as causing mitochondrial disorders in humans, but there has yet to be a whole animal knockdown model created. In this study, C. elegans was used to investigate the effect of knocking down pnpt-1, the gene that encodes PNPase. It was discovered that pnpt-1 knockdown significantly extends lifespan via an increase in superoxide production similar to other known mitochondrial lifespan extension pathways. Additionally, mitochondrial networks, size and respiration are affected indication of other mitochondrial dysfunction..

PNPase is also known to transport small RNAs into the …

Investigation Into The Specification Of Nurf Recruitment To The Genome, Marissa Mack

Theses and Dissertations

The nucleosome remodeling factor (NURF) is a mutli-protein complex that plays a role in the regulation of gene expression through its ability to remodel nucleosomes. The largest subunit of this complex, Bptf (Bromodomain PHD Finger Transcription Factor) is important for many cellular processes as a transcriptional regulator and improper function results in disease or malignancy. To further understand the genome-wide recruitment of the NURF complex, the interaction partner for the N-terminal PHD finger domain of Bptf was investigated through pull down assays followed by mass spectrometry. It was determined that this domain does not recognize histones; instead it recognizes a …

Global Analysis Of Gene Expression And Projection Target Correlations In The Mouse Brain, Ahmed Fakhry, Tao Zeng, Hanchuan Peng, Shuiwang Ji

Computer Science Faculty Publications

Recent studies have shown that projection targets in the mouse neocortex are correlated with their gene expression patterns. However, a brain-wide quantitative analysis of the relationship between voxel genetic composition and their projection targets is lacking to date. Here we extended those studies to perform a global, integrative analysis of gene expression and projection target correlations in the mouse brain. By using the Allen Brain Atlas data, we analyzed the relationship between gene expression and projection targets. We first visualized and clustered the two data sets separately and showed that they both exhibit strong spatial autocorrelation. Building upon this initial …

The Mechanisms Of Α-Amanitin Resistance In The Fruit Fly Drosophila Melanogaster, Chelsea L. Mitchell

Dissertations, Master's Theses and Master's Reports

Insect pesticide resistance has become a costly problem in the US. To make things more problematic, resistance to one pesticide is often associated with cross-resistance to other toxins, including pesticides that have not yet even been developed. In this study, we investigated a possible type of cross-resistance in the model fruit fly Drosophila melanogaster, some stocks of which are resistant to the very potent mushroom toxin α-amanitin. Because α-amanitin is solely produced by mushrooms, and because D. melanogaster does not feed on mushrooms in nature, the fruit flies should not be resistant to this toxin. In order to understand …

Sperm Dna Oxidative Damage And Dna Adducts, Hueiwang Anna Jeng, Chih-Hong Pan, Mu-Rong Chao, Wen-Yi Lin

Community & Environmental Health Faculty Publications

The objective of this study was to investigate DNA damage and adducts in sperm from coke oven workers who have been exposed to polycyclic aromatic hydrocarbons. A longitudinal study was conducted with repeated measurements during spermatogenesis. Coke-oven workers (n =112) from a coke-oven plant served the PAH-exposed group, while administrators and security personnel (n=67) served the control. Routine semen parameters (concentration, motility, vitality, and morphology) were analyzed simultaneously; the assessment of sperm DNA integrity endpoints included DNA fragmentation, bulky DNA adducts, and 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-oxo-dGuo). The degree of sperm DNA fragmentation was measured using the terminal deoxynucleotidyl transferase-mediated dUTP nick end-labeling …

Drosophila Cyclin J And The Somatic Pirna Pathway Cooperate To Regulate Germline Stem Cells, Paul Michael Albosta

Wayne State University Dissertations

Cyclin J (CycJ) is a highly conserved cyclin that is uniquely expressed specifically in ovaries in Drosophila. Deletion of the genomic region containing CycJ and adjacent genes resulted in a genetic interaction with neighboring piRNA pathway gene, armitage (armi). Here I assessed oogenesis in CycJ null in the presence or absence of mutations in armi or other piRNA pathway genes. Although CycJ null flies had decreased egg laying and hatching rates, ovaries appeared normal indicating that CycJ is dispensable for oogenesis under normal conditions. Further double mutant analysis of CycJ and neighbor armi, as well as two other piRNA pathway …

The Role Of Crebh In Hepatic Energy Regulation Under Metabolic Stress, Roberto Mendez

Wayne State University Dissertations

Lipid metabolism is tightly regulated by nuclear receptors, transcription factors, and cellular enzymes in response to nutritional, hormonal, and stress signals. Hepatocyte specific, cyclic AMP responsive element-binding protein (CREBH) is a transcription factor that is preferentially expressed in the liver and localized in the endoplasmic reticulum (ER) membrane. CREBH is known to be activated by ER stress, inflammatory stimuli, and metabolic signals to regulate hepatic acute-phase response, lipid metabolism, and glucose metabolism. In my thesis research, I have characterized the roles and mechanisms of CREBH in these functions, as well as the overall phenotype of CrebH-null mice. I demonstrated that …

Crebh, A Novel Liver Clock Keeper For Energy Metabolism, Ze Zheng

Wayne State University Dissertations

Circadian rhythms play crucial roles in orchestrating diverse physiological processes that are critical for health and disease. Cyclic AMP responsive element binding protein 3-like 3 (CREB3L3, also known as CREBH) is a liver-enriched, endoplasmic reticulum (ER)-tethered transcription factor known to regulate hepatic acute-phase response and energy homeostasis under stress conditions. Here, we demonstrate that CREBH is regulated by the circadian clock and functions as a diurnal regulator of hepatic lipid and glucose metabolism. CREBH is required to maintain circadian profiles of blood triglycerides, fatty acids, and glucose as well as hepatic glycogen storage. CREBH rhythmically regulates expression levels and amplitudes …

Functional Analysis Of A Highly Conserved Cyclin, Cyclin Y, In Drosophila Melanogaster, Nermin Gerges

Wayne State University Dissertations

Cyclin Y is a highly conserved member of the Cyclin superfamily of proteins. In Drosophila the Cyclin Y gene (CycY) is required for progression through several stages of development but the specific pathways that Cyclin Y belongs to and that account for its requirement are not known. Studies in human and Drosophila cell lines have shown that membrane-localized Cyclin Y is required for phosphorylation of the wingless/Wnt co-receptor, arrow/LRP6, and for full activation of the canonical wingless/Wnt pathway. CycY null Drosophila, however, do not phenocopy loss-of-function mutations in canonical wingless pathway genes, suggesting that Cyclin Y may have additional roles …

Using Large Snp Datasets To Understand The Genetic Mechanisms Of Complex Traits In Arabidopsis Thaliana, Elisabeth S. Harrison

Open Access Theses

Arabidopsis thaliana, as a model species, has been widely genotyped and sequenced. Many studies have been done to understand the kinship and population structure of the species. This data and information is beneficial for understanding the genetic mechanisms of complex traits. In this thesis, we first used genotyped data for 5,967 accessions to study the occurrence of tetraploidy in the species. We found that tetraploidy is a transient character state, and the species is a diploid species. Secondly, we used 211K and 1.6M SNPs for 440 accessions to run genome-wide analyses (GWA) for four traits: glufosinate tolerance, hybrid incompatibilities, seed …

Expression, Purification, And Activity Of Peptidyl-Trna Hydrolase 1 Of Rickettsia Rickettsii, Jessica Osler

Summer Community of Scholars Posters (RCEU and HCR Combined Programs)

No abstract provided.

A Meta-Analysis Of Association Between One-Carbon Metabolism Gene Polymorphisms And Risk Of Prostate Cancer, Mahmood Tazari

Walden Dissertations and Doctoral Studies

Prostate cancer is the most common cancer among men. The purpose of this quantitative, meta-analysis study was to examine one-carbon metabolism gene polymorphisms in a group of genes to determine their association with prostate cancer risk. The genetic epidemiology theory provided the framework for the study. The data collected were from published articles. From over 2,800 individual studies, 20 articles were retained for results and data abstraction, following the title, abstract screen, and full text screening in the second phase. The data were analyzed by a meta-analysis statistical method, combining the results from selected studies to estimate the overall association. …

The Role Of Tfec In Zebrafish Neural Crest Cell And Rpe Development., Samantha A. Spencer

Theses and Dissertations

Zebrafish (Danio rerio) show a unique pigmentation pattern comprised of three pigment cell types: melanophores, iridophores and xanthophores. Other pigmented cells include the retinal pigmented epithelium (rpe) which absorbs excess light in the eye and maintain the extracellular environment around the photoreceptors. While previous mutations in mitfa showed a role in regulating trunk melanophores, the rpe was not affected. TALENs and CRISPR-Cas9 systems were used to generate mutant zebrafish for tfec, a transcription factor expressed in both neural crest and rpe. Embryos with tfec mutations showed a loss of iridophore pigmentation, and delays in the pigmentation of …

Functional Characterization Of Rai1 In Zebrafish, Joshua S. Beach

Theses and Dissertations

Smith-Magenis Syndrome (SMS; OMIM #182290) is a multiple congenital abnormality and intellectual disability (ID) disorder caused by either an interstitial deletion of the 17p11.2 region containing the retinoic acid induced-1 (RAI1) gene or a mutation of the RAI1 gene. Individuals diagnosed with SMS typically present characteristics such as ID, self-injurious behavior, sleep disturbance, ocular and otolaryngological abnormalities, craniofacial and skeletal abnormalities, neurological and behavioral abnormalities, as well as other systemic defects and manifestations. Previous work by Vyas in 2009 showed temporal expression of rai1 in zebrafish embryos as early as 9 hpf. We hypothesize that there is maternal …