Genetics and Genomics Commons^™

Determining The Impacts Of Environmental Contaminants To Zebra Mussels Using Genetic Biomarkers, Nicklaus James Neureuther

Theses and Dissertations

ABSTRACT

DETERMINING THE IMPACTS OF ENVIRONMENTAL CONTAMINANTS TO ZEBRA MUSSELS USING GENETIC BIOMARKERS

by

Nicklaus James Neureuther

The University of Wisconsin-Milwaukee, 2016

Under the Supervision of Professor Rebecca Klaper, PhD

Persistent legacy contaminants and emerging chemicals of concern continue to be a threat to the function and health in the Great Lakes Areas of Concern (AOCs). While chemical monitoring programs traditionally sample water and sediment, these studies can only provide information of the type and level of contamination within an (AOC). This being said, information on the biological impacts to the biota are needed to measure impairments of chemical exposure, …

Genetic Counseling For Alcohol Use Disorder: Assessment Of Need In Affected And At-Risk Populations, Fayth Michelle Kalb

Theses and Dissertations

Introduction: Alcohol use disorder (AUD) is highly heritable, yet there has been no investigation regarding the possible benefits of genetic counseling for AUD. This study assessed the beliefs individuals with and at risk for AUD have regarding recurrence risk and etiology of AUD, how the presence of the condition in themselves or their family history has affected their lifestyle decisions, and potential benefit from AUD genetic counseling. Methods: An online questionnaire was distributed through social media to support groups for AUD inviting adults 18 years and older with a personal or family history of AUD. Results: Of the 122 individuals …

The Undiagnosed Patient And The Diagnostic Odyssey: Current Genetic Counseling Practices And Perspectives, Amelia Cordell Wardyn

Theses and Dissertations

Patients seen in genetics clinics often endure a diagnostic odyssey in their search for answers for their medical symptoms. This time is not only challenging for patients and their families, but also for the genetic counselors who are trying to help the patients. Previous research has shown that parents of children with undiagnosed medical disorders have specific goals and reasons for wanting to find a diagnosis, and there are many difficulties faced by these parents. Genetic counselors often serve as a prominent figure during the diagnostic odyssey, but little known research has assessed the current practices of and impact that …

Re-Contacting Cancer Genetic Counseling Patients: Expectations Of Patients And Physicians, Zoe Elizabeth Siegel

Theses and Dissertations

The landscape of cancer genetic counseling and testing is rapidly evolving. Genetic testing technology is improving, management guidelines are evolving, and genetic testing options are expanding. These frequent updates to the components of cancer genetics have increased the complexity of managing patient care over time. In particular, this raises questions on the duty to re-contact patients as new information becomes available. This study explored healthcare providers’ duty to re-contact through the interests and expectations of patients, including which circumstances warrant re-contacting, which healthcare provider is responsible for re-contacting the patient, and the preferred method of re-contacting. Physicians’ opinions on whether …

Reflections On The Current State Of Healthcare Transition For Young Adult Women With Turner Syndrome: Strategies For Facilitating Autonomy And Self-Management, Molly Elizabeth Snyder

Theses and Dissertations

The transition to adult-centered healthcare is a critical period for emerging adults, especially those with special healthcare needs (SHCNs). Considering the ongoing medical monitoring necessary for women with Turner syndrome (TS), it is essential that the transition process be comprehensive and well-coordinated. The aims of this study were to invite young women with TS to reflect on their healthcare transition experiences, to explore participants’ perceived control of their medical management, and to identify ways in which genetic counselors can be involved in multidisciplinary healthcare teams. The hypotheses were that young women with TS are motivated to learn more about their …

Unaffected Women’S Decisions To Have Prophylactic Risk-Reducing Mastectomies, Stephanie N. Galloway

Theses and Dissertations

When a woman is at an increased risk of developing breast cancer due to a pathogenic mutation or a significant family history of the disease, she will be faced with choosing from among multiple management options, including risk-reducing mastectomy (RRM). The relative rate of RRM for both diagnosed and unaffected high-risk women has increased in recent years. Previous research has investigated the factors that influence women diagnosed with the disease to undergo RRM, but has not fully addressed how unaffected women make their decisions to choose RRM as an option when they are still healthy. This study was designed to …

Parents’ Understanding Of Sensory Processing In Their Child With Autism Spectrum Disorder, Katelynn M. Anderson

Theses and Dissertations

Purpose: The purpose of this study was to assess the need and desire of parents of children with Autism Spectrum Disorder (ASD) to receive sensory processing disorder (SPD) education. We hoped to identify misconceptions of parents about sensory processing and examined the utility of providing information on SPDs to these parents within the genetic counseling session. Methods: Invitations to participate were sent to support groups in the Southeast United States. A survey tool was used to obtain demographic information. A short presentation was given to clarify the definition of sensory processing, give examples of signs and symptoms of SPDs, and …

Identification Of Xpa And Xpc Gene Mutations In Patients With Xeroderma Pigmentosum, Eman Abdelalim Sidky Rabie

Theses and Dissertations

The human body employs different DNA repair pathways to protect itself against cancers induced by DNA damage. The nucleotide excision repair (NER) pathway comprises different synchronously working DNA repair proteins; two of which are XPA and XPC. Mutations of any of the genes encoding the NER proteins cause an autosomal recessive genetic disorder called Xeroderma Pigmentosum (XP). XP patients present with characteristic dry atrophic freckle-like pigmentation of the skin, photosensitivity and photophobia. Some patients develop neurodegenerative symptoms early in life, including mental retardation. Patients have a 10,000-fold increased risk for UV-induced skin cancers, moreover, a higher risk for ocular, oral …

Applying The Water Governance Framework On Rural Water Development Projects In Guatemala, Muhanad M. Alkharaz

Theses and Dissertations

According to the Organization for Economic Cooperation and Development (OECD), ‘Water crisis is mainly a governance crisis’, (OECD, 2013). Many water experts, as individuals, organizations and even governmental bodies have developed water governance frameworks to overcome water challenges on local, national, and international levels such as Integrated Water Resource Management. In rural areas, especially in developing countries, access to safe drinking water is a daily challenge due to a variety of political, economic, and social constraints. For in-stance, some developing countries have a strong centralized governance system. Due to lack of capacity and resources, central governments are incapable of providing …

Effects Of Drift, Selection And Gene Flow On Immune Genes In Prairie Grouse, Zachary Bateson

Theses and Dissertations

Fragmentation of natural habitats is related to population decline in many species. The resulting small and isolated populations are expected to lose genetic variation at a rapid rate, which reduces the ability to adapt to environmental change. One concern is that small populations are more susceptible to emerging pathogens due to the loss of variation at immune genes. My dissertation examined the relative effects of gene flow, genetic drift and selection on immune genes in prairie-chickens (Tympanuchus cupido), a species that has undergone drastic population declines across their range. In the first chapter, I examined how artificial gene flow through …

Investigating The Roles And Interactions Of Sad-6 Within The Parameters Of Meiotic Silencing By Unpaired Dna ( Msud )., Zachary J. Smith

Theses and Dissertations

Meiotic silencing by unpaired DNA (MSUD) is a process observed in the model organism Neurospora crassa. During this process unpaired DNA between homologous chromosomes is detected and silenced, resulting in the suppression of unpaired genes. The effects of MSUD can be seen using phenotypic markers such as the Roundspore gene and evidence supports the existence of a physical search for unpaired DNA. However, the mechanism for detecting unpaired DNA remains uncertain. Previously, we have shown evidence that a Rad54-like protein, SAD-6 is required for the efficient completion of MSUD and may be necessary for the detection of unpaired DNA. Currently, …

The Role Of E-Cadherin Force In The Maintenance Of Homeostasis In Epithelial Acini, Fnu Vani Narayanan

Theses and Dissertations

Numerous three-dimensional model systems have emerged for emulating the biochemical and physiological states of native tissue. Yet little is known about the effects of mechanical forces on cell behavior in the context of an organized tissue structure in three-dimensional cell-culture. Epithelial cells cultured in a three-dimensional environment comprised of extracellular matrix proteins form spheroids of polarized cells. Cellular responses to mechanical cues, generated from dynamic interactions with the extracellular matrix and neighboring cells, are known to influence cellular behavior to a great extent. Previous studies have shown that tumorigenic progression has been frequently linked to the down regulation of E-cadherin, …

System Genetic Analysis Of Mechanisms Underlying Excessive Alcohol Consumption, Maren L. Smith

Theses and Dissertations

Increased alcohol consumption over time is one of the characteristic symptoms of Alcohol Use Disorder (AUD). The molecular mechanisms underlying this escalation in intake is still the subject of study. However, the mesocortical and mesolimbic dopamine pathways, and the extended amygdala, because of their involvement in reward and reinforcement are believed to play key roles in these behavioral changes. Multiple gene expression studies have shown that alcohol affects the expression of thousands of genes in the brain. The studies discussed in this document use the systems biology technique of co-expression network analysis to attempt to find

patterns within genome-wide expression …

A Mechanistic Study Of An Ipsc Model For Leigh’S Disease Caused By Mtdna Mutataion (8993 T>G), John P. Galdun

Theses and Dissertations

Mitochondrial diseases encompass a broad range of devastating disorders that typically affect tissues with high-energy requirements. These disorders have been difficult to diagnose and research because of the complexity of mitochondrial genetics, and the large variability seen among patient populations. We have devised and carried out a mechanistic study to generate a cell based model for Leigh’s disease caused by mitochondrial DNA mutation 8993 T>G. Leigh’s disease is a multi-organ system disorder that depends heavily on the mutation burden seen within various tissues. Using new reprogramming and sequencing technologies, we were able to show that Leigh’s disease patient fibroblasts …

Genomic Comparisons And Genome Architecture Of Divergent Trypanosoma Species, Katie Bradwell

Theses and Dissertations

Virulent Trypanosoma cruzi, and the non-pathogenic Trypanosoma conorhini and Trypanosoma rangeli are protozoan parasites with divergent lifestyles. T. cruzi and T. rangeli are endemic to Latin America, whereas T. conorhini is tropicopolitan. Reduviid bug vectors spread these parasites to mammalian hosts, within which T. rangeli and T. conorhini replicate extracellularly, while T. cruzi has intracellular stages. Firstly, this work compares the genomes of these parasites to understand their differing phenotypes. Secondly, genome architecture of T. cruzi is examined to address the effect of a complex hybridization history, polycistronic transcription, and genome plasticity on this organism, and study its highly …

Examining Genetic And Environmental Influences On Alcohol Use And Externalizing Behaviors In African American Adolescents, Neeru Goyal

Theses and Dissertations

The aim of this thesis is to expand our understanding of the etiology of alcohol misuse and related disorders in African Americans using genetically informative study designs. Specifically, we take advantage of the candidate-gene approach and polygenic score analysis to extend the literature specific to African American populations. Chapter 2 explores gene x environment (GxE) interactions through the candidate gene approach to explore the relationship between two genes chosen on their potential relevance to stress response and adolescent alcohol use and misuse, among African American youth living in highly impoverished neighborhoods, as moderated by stressful life events. Chapter 3 implements …

A Pipeline For Creation Of Genome-Scale Metabolic Reconstructions, Shaun W. Norris

Theses and Dissertations

The decreasing costs of next generation sequencing technologies and the increasing speeds at which they work have lead to an abundance of 'omic datasets. The need for tools and methods to analyze, annotate, and model these datasets to better understand biological systems is growing. Here we present a novel software pipeline to reconstruct the metabolic model of an organism in silico starting from its genome sequence and a novel compilation of biological databases to better serve the generation of metabolic models. We validate these methods using five Gardnerella vaginalis strains and compare the gene annotation results to NCBI and the …

Independent Origination Of Floral Zygomorphy, A Predicted Adaptive Response To Pollinators: Developmental And Genetic Mechanisms, Ghadeer Bukhari, Wenheng Zhang

Theses and Dissertations

Observations of floral development indicate that floral organ initiation in pentapetalous flowers more commonly results in a medially positioned abaxial petal (MAB) than in a medially positioned adaxial petal (MAD), where the medial plane is defined by the stem and the bract during early floral development. It was proposed that the dominant MAB petal initiation might impose a developmental constraint that leads to the evolution of limited patterns of floral zygomorphy in Asteridae, a family in which the floral zygomorphy develops along the medial plane and results in a central ventral (CV) petal in mature flowers. Here, I investigate whether …

Power Analysis In Applied Linear Regression For Cell Type-Specific Differential Expression Detection, Edmund Glass

Theses and Dissertations

The goal of many human disease-oriented studies is to detect molecular mechanisms different between healthy controls and patients. Yet, commonly used gene expression measurements from any tissues suffer from variability of cell composition. This variability hinders the detection of differentially expressed genes and is often ignored. However, this variability may actually be advantageous, as heterogeneous gene expression measurements coupled with cell counts may provide deeper insights into the gene expression differences on the cell type-specific level. Published computational methods use linear regression to estimate cell type-specific differential expression. Yet, they do not consider many artifacts hidden in high-dimensional gene expression …

Functional Consequences Of Mtdna Methylation On Mitochondrial Transcription Factor Binding And Transcription Initiation, Elliot N. Burton

Theses and Dissertations

The role of cytosine modifications on nuclear transcription has been well characterized, but the function of DNA methylation in the mitochondrial genome has not been determined. Previous studies conducted by the Taylor laboratory have shown overexpression of the mitochondrial isoform of DNMT1 leads to strand-specific changes in gene expression. Here, we show that increased mtDNMT1 expression leads to an increase in the polycistronic transcript encoding the ND1 and Cox1 sequences. In order to understand the mechanistic basis of these changes, we investigated the effects of CpG methylation in the heavy strand promoter on transcription initiation and TFAM binding. Methylation was …

Investigating The Molecular Etiologies Of Sporadic Als (Sals) Using Rna-Sequencing, David G. Brohawn

Theses and Dissertations

ALS is an often lethal disease involving degeneration of motor neurons in the brain and spinal cord. Current treatments only extend life by several months, and novel therapies are needed. We combined RNA-Sequencing, systems biology analyses, and molecular biology assays to elucidate sporadic ALS group-specific differences in postmortem cervical spinal sections (7 sALS and 8 control samples) that may be relevant to disease pathology. >55 million 2X150 RNA-sequencing reads per sample were generated and processed.

In Chapter 2, we used bioinformatics tools to identify nuclear differentially expressed genes (DEGs) between our two groups. Further, we used Weighted Gene Co-Expression Network …

Genome Wide Epigenetic Analyses Of Araptus Attenuatus, A Bark Beetle, Chitra Seshadri

Theses and Dissertations

Phylogeographic studies have relied on surveying neutral genetic variation in natural populations as a way of gaining better insights into the evolutionary processes shaping present day population demography. Recent emphasis on understanding putative adaptive variation have brought to light the role of epigenetic variation in influencing phenotypes and the mechanisms underlying local adaptation. While much is known about how methylation acts at specific loci to influence known phenotypes, there is little information on the spatial genetic structure of genome-wide patterns of methylation and the extent to which it can extend our understanding of both neutral and putatively adaptive processes. This …

Functional Significance Of Mtdna Cytosine Modification Tested By Genome Editing, Jason M. Robinson

Theses and Dissertations

The field of epigenetics is gaining popularity and speed, due in part to its capability to answer lingering questions about the root cause of certain diseases. Epigenetics plays a crucial role in regulation of the cell and cell survival, particularly by cytosine methylation. It remains controversial if DNMT’s which facilitate methylation are present in mammalian mitochondria and what the functional significance they may have on modification of mitochondrial DNA. CRISPR-Cas9 technology enabled genome editing to remove the MTS (mitochondrial targeting sequence) from DNMT1 of HCT116 cells, purposefully minimizing effects on nuclear cytosine methylation, while exclusively impacting mitochondrial modification. Removal of …

The Informational And Emotional Support Needs Of Grandparents Of Children With Pompe Disease, Natasha Lousie Rudy

Theses and Dissertations

The complex roles and experiences of grandparents of children with various diagnoses have been described, but previous studies have not investigated the roles and experiences of grandparents of children with treatable, Mendelian conditions such as Pompe disease. The availability of treatment and heritable nature of Pompe introduce the possibility for unique grandparent roles, experiences and needs. This is a particularly timely investigation given the advent of newborn screening for Pompe. This study aimed to characterize grandparents’ roles and involvement, identify grandparents’ information and emotional support needs, and explore the psychosocial impact felt by grandparents of children with Pompe. An online …

Adducins Are Negative Regulators Of Migration And Invasion Of Normal Lung Epithelial Cells And Lung Cancer Cells, Parth Hitenbhai Amin, Parth Amin

Theses and Dissertations

Cell migration is an important component of many physiological and pathological processes such as tissue and organ morphogenesis during development, wound healing, inflammatory immune response, and tumor metastasis. The actin cytoskeleton is the basic engine driving cell migration. In the present study, we elucidate the role of an important actin interacting proteins, Adducins, in motility of normal lung epithelium and lung cancer cells. Adducins are the family of cytoskeleton protein capping the fast growing end and facilitating the bundling of actin filaments. Adducins are encoded by the three closely related genes namely alpha (ADD1), beta (ADD2) and gamma (ADD3) Adducin. …