Genetics and Genomics Commons^™

Self-Reported Oral Health Assessment And Attitudes Toward Oral Health For Adults With Cystic Fibrosis, Ahmed Ali Almuntashiri

Dental Hygiene Theses & Dissertations

Purpose: Cystic fibrosis (CF) is a chronic genetic disorder that an individual has at birth. Cystic fibrosis impacts equally all races, gender and becomes worse over time. The aim of this current study was to evaluate oral health status, interaction with the oral health system, and oral health awareness in adults with cystic fibrosis. Methods: A validated survey consisting of 27 questions was distributed online through cystic fibrosis Facebook pages. Individuals with CF who were 18 years old or older, residing in the U.S. and having English as their primary language were asked to respond to the survey. Independent variables …

Epigenetic Alterations Mediate Ipsc Normalization Of Dna-Repair Expression And Tnr Stability In Huntington's Disease, Peter A. Mollica, Martina Zamponi, John Reid, Deepak Sharma, Alyson E. White, Roy C. Ogle, Robert D. Bruno, Patrick C. Sachs

School of Medical Diagnostics & Translational Sciences Publications

Huntington's disease (HD) is a rare autosomal dominant neurodegenerative disorder caused by a cytosine-adenine-guanine (CAG) trinucleotide repeat (TNR) expansion within the HTT gene. The mechanisms underlying HD-associated cellular dysfunction in pluripotency and neurodevelopment are poorly understood. We had previously identified downregulation of selected DNA repair genes in HD fibroblasts relative to wild-type fibroblasts, as a result of promoter hypermethylation. Here, we tested the hypothesis that hypomethylation during cellular reprogramming to the induced pluripotent stem cell (iPSC) state leads to upregulation of DNA repair genes and stabilization of TNRs in HD cells. We sought to determine how the HD TNR region …

Detecting, Quantifying, And Discriminating The Mechanism Of Mosaic Chromosomal Aneuploidies Using Mad-Seq, Yu Kong, Esther R. Berko, Anthony Marcketta, Shahina B. Maqbool, Claudia A. Simoes-Pires, David F. Kronn, John M. Greally

NYMC Faculty Publications

Current approaches to detect and characterize mosaic chromosomal aneuploidy are limited by sensitivity, efficiency, cost, or the need to culture cells. We describe the mosaic aneuploidy detection by massively parallel sequencing (MAD-seq) capture assay and the MADSEQ analytical approach that allow low (

The Effect Of Sweeteners In Drosophila Melanogaster's Locomotion., Araceli Francisco

The International Student Science Fair 2018

This research aims to measure how much locomotion is affected in Drosophila melanogaster considering the alimentation. The experiment was divided in a control group, a group fed with natural sugar and another fed with artificial sugar. The diets were prepared based on standard laboratory food (SLF) by varying the sugar. Several generations were grown. The locomotion was measured through monitors with infrared lasers which calculated the number of times the fly passed through it. They were accustomed to a day and night cycle and were kept under observation for a period of 13 days. As a result, the group that …

Exploring The Role Of Rna Polymerase Iii Complex Assembly On Ribosomal Dna Silencing In Saccharomyces Cerevisiae, Kyle Thomas Kern

LSU Doctoral Dissertations

The yeast rDNA region is host to a number of transcriptional regulatory elements, which work in conjunction to generate essential RNA subunits of ribosomes, as well as protecting the region from DNA damage. The role of RNA polymerase III complex binding at the 5S gene on rDNA silencing in the NTS2 region was investigated, both by use of a TY1:MET15 reporter insert and a MET15 gene integration at an endogenous SphI site. It was discovered that Pol III complexes do have an effect on reporter expression in the NTS2 region, though the specific effect was different based on the method …

Differential Preservation Of Endogenous Human And Microbial Dna In Dental Calculus And Dentin, Allison E. Mann, Susanna Sabin, Kirsten Ziesemer, Ashild J. Vagene, Hannes Schroeder, Andrew T. Ozga, Krithivasan Sankaranarayanan, Courtney A. Hofman, James A. Fellows Yates, Domingo C. Salazar-Garcia, Bruno Frohlich, Mark Aldenderfer, Menno Hoogland, Christopher Read, George R. Milner, Anne C. Stone, Cecil M. Lewis Jr., Johannes Krause, Corinne Hofman, Kirsten I. Bos, Christina Warinner

Biology Faculty Articles

Dental calculus (calcified dental plaque) is prevalent in archaeological skeletal collections and is a rich source of oral microbiome and host-derived ancient biomolecules. Recently, it has been proposed that dental calculus may provide a more robust environment for DNA preservation than other skeletal remains, but this has not been systematically tested. In this study, shotgun-sequenced data from paired dental calculus and dentin samples from 48 globally distributed individuals are compared using a metagenomic approach. Overall, we find DNA from dental calculus is consistently more abundant and less contaminated than DNA from dentin. The majority of DNA in dental calculus is …

Computational Analysis Of Papionini Evolution Using Alu Insertions, Vallmer Edward Jordan Ii

LSU Doctoral Dissertations

Alu elements are primate specific retrotransposons that have remained active throughout the course of primate evolution. As a result of this sustained mobilization. Alu elements are present in greater copy number in primate genomes than any other transposable element. An average of over one million Alu elements has been identified in every sequenced haplorrhine genome to date. These characteristics qualify Alu elements as ideal characters for studying evolutionary relationship among primates.

The increasing availability of whole genome sequencing data presents novel challenges and opportunities for comparative genomic analyses. Genomic data is now publicly available for most primate species. Such an …

The Effect Of Sweeteners In Drosophila Melanogaster's Locomotion., Araceli Francisco

The International Student Science Fair 2018

This research aims to measure how much locomotion is affected in Drosophila melanogaster considering the alimentation. The experiment was divided in a control group, a group fed with natural sugar and another fed with artificial sugar. The diets were prepared based on standard laboratory food (SLF) by varying the sugar. Several generations were grown. The locomotion was measured through monitors with infrared lasers which calculated the number of times the fly passed through it. They were accustomed to a day and night cycle and were kept under observation for a period of 13 days. As a result, the group that …

The Zinc Transporter Zipt-7.1 Regulates Sperm Activation In Nematodes, Yanmei Zhao, Chieh-Hsiang Tan, Amber Krauchunas, Andrea Scharf, Nicholas Dietrich, Kurt Warnhoff, Zhiheng Yuan, Marina Druzhinina, Sam Guoping Gu, Long Miao, Andrew Singson, Ronald E Ellis, Kerry Kornfeld

Rowan-Virtua School of Osteopathic Medicine Departmental Research

Sperm activation is a fascinating example of cell differentiation, in which immotile spermatids undergo a rapid and dramatic transition to become mature, motile sperm. Because the sperm nucleus is transcriptionally silent, this transition does not involve transcriptional changes. Although Caenorhabditis elegans is a leading model for studies of sperm activation, the mechanisms by which signaling pathways induce this transformation remain poorly characterized. Here we show that a conserved transmembrane zinc transporter, ZIPT-7.1, regulates the induction of sperm activation in Caenorhabditis nematodes. The zipt-7.1 mutant hermaphrodites cannot self-fertilize, and males reproduce poorly, because mutant spermatids are defective in responding to activating …

Completion Of Dna Replication In Escherichia Coli, Brian Michael Wendel

Dissertations and Theses

To maintain genomic integrity, all cells must accurately duplicate their genetic material in order to provide intact and complete copies to each daughter cell following cell division. Successful inheritance of chromosomal information without changing even a single nucleotide requires accurate and robust DNA replication. This requires that cells tightly control replication initiation from the origin(s), processive elongation of the replisome, and the completion of DNA replication by resolving convergent replication forks ensuring that each sequence is duplicated without alteration. Unlike initiation and elongation, the process by which replication forks converge and are resolved into two discrete, inheritable DNA molecules is …

Loss Of Function Of Gene X Protects Against Α-Dicarbonyl Stress Through The Skn-1 Pathway In C. Elegans, Austin Lim

Dissertations, Masters Theses, Capstones, and Culminating Projects

Diabetes mellitus and Parkinson’s Disease (PD) are debilitating diseases that are increasing in prevalence worldwide. One potential cause of these diseases is the accumulation of advanced glycation end products (AGEs), which are macromolecules that cause irreversible damages. AGEs are a diverse group of highly oxidative byproducts produced from α-dicarbonyl compounds (α-dcs), which are highly reactive molecules that bind indiscriminately to protein and DNA and, are regulated by a conserved glyoxalase system (GLO1 and DJ-1) in humans. Utilizing the conserved glyoxalase system, we were able to establish within a C. elegans model that when this glyoxalase system is impaired, …

Population Genetics And Bumble Bee Conservation: Saving Species By Thinking Small, Cady Greenslit

Lawrence University Honors Projects

Pollinators have experienced a severe decline over the last few decades, and this includes bumble bee populations (g. Bombus). Bumble bees are important native pollinators, and here I investigate the health of local populations with molecular tools. The field of conservation genetics has created useful methodology for investigating the health and informing management strategies of threatened populations. This work investigates and describes the applications of population genetics, which uses span across the board. These applications are then brought back into the context of bumble bee conservation, and how they fit into the experimental plan I originally designed. I designed …

Population Structure, Demographic History, And Environmental Niche Of The Sand Fly Disease Vector Lutzomyia Shannoni (Dyar) (Diptera: Psychodidae) In The U.S., Mexico, And Colombia, Matthew E. Wolkoff

Biology Theses

Lutzomyia shannoni (Dyar, 1929) (Diptera: Psychodidae) is the only known sand fly vector of vesicular stomatitis virus, a putative leishmaniasis vector, and also boasts the widest distribution of any sand fly in the New World. Research on Lu. shannoni in Central and South America has revealed genetically divergent subpopulations; however, tentative analysis of Lu. shannoni in the U.S. has failed to detect any significant population structure, even between specimens collected from highly disparate localities.

The present study used four molecular markers to more closely investigate the population structure of Lu. shannoni in the U.S., and assess the species’ relationships with …

Investigating The Role Of Genomic Variation In Susceptibility To Environmental Chemicals Across Populations, Lindsay Adrian Holden

Dissertations and Theses

No two individuals are identical. This is true at the genetic level and at the phenotypic level. One of the traits that varies between populations is toxicant susceptibility: some individuals are sensitive to the effects of environmental chemical exposure, and others are resistant. This body of work aims to address the impact of genomic copy number variants (CNV)--large (>1 Kb) duplications or deletions across the genome--on the toxicant-susceptibility phenotype.

Herein copy number variants were characterized across three commonly used laboratory strains of zebrafish (Danio rerio) and mRNA expression phenotypes were identified in the same strains. It was found that …

The Receptor Protein Tyrosine Phosphatase Clr-1 Is Required For Synaptic Partner Recognition, Aruna Varshney, Kelli Benedetti, Katherine Watters, Raakhee Shankar, David Tatarakis, Doris Coto Villa, Khristina Magallanes, Venia Agenor, William Wung, Fatima Farah, Nebat Ali, Nghi Le, Jacqueline Pyle, Amber Farooqi, Zanett Kieu, Martina Bremer, Miri Vanhoven

Faculty Publications, Biological Sciences

During neural circuit formation, most axons are guided to complex environments, coming into contact with multiple potential synaptic partners. However, it is critical that they recognize specific neurons with which to form synapses. Here, we utilize the split GFP-based marker Neuroligin-1 GFP Reconstitution Across Synaptic Partners (NLG-1 GRASP) to visualize specific synapses in live animals, and a circuit-specific behavioral assay to probe circuit function. We demonstrate that the receptor protein tyrosine phosphatase (RPTP) clr-1 is necessary for synaptic partner recognition (SPR) between the PHB sensory neurons and the AVA interneurons in C. elegans. Mutations in clr-1/RPTP result in …

Characterization Of An N-Terminal Non-Core Domain Of Rag1 Gene Disrupted Syrian Hamster Model Generated By Crispr Cas9, Jinxin Miao, Baoling Ying, Rong Li, Ann E. Tollefson, Jacqueline F. Spencer, William S.M. Wold, Seok-Hwan Song, Il-Keun Kong, Karoly Toth, Yaohe Wang, Zhongde Wang

Animal, Dairy, and Veterinary Science Faculty Publications

The accumulating evidence demonstrates that Syrian hamsters have advantages as models for various diseases. To develop a Syrian hamster (Mesocricetus auratus) model of human immunodeficiency caused by RAG1 gene mutations, we employed the CRISPR/Cas9 system and introduced an 86-nucleotide frameshift deletion in the hamster RAG1 gene encoding part of the N-terminal non-core domain of RAG1. Histological and immunohistochemical analyses demonstrated that these hamsters (referred herein as RAG1-86nt hamsters) had atrophic spleen and thymus, and developed significantly less white pulp and were almost completely devoid of splenic lymphoid follicles. The RAG1-nt86 hamsters had barely detectable CD3+ and CD4+ T cells. The …

Determinants Of Multi-Scale Patterning In Growth Plate Cartilage, Alek Erickson

Theses & Dissertations

ABSTRACT

Functional architectures of complex adaptive systems emerge by dynamic control over properties of individual components. During skeletal development, growth plate cartilage matches bone geometries to body plan requisites by spatiotemporally regulating chondrocyte actions. Bone growth potential is managed by the proximodistal patterning of chondrocyte populations into differentiation zones, while growth vectors are specified by the unique columnar arrangement of clonal groups. Chondrocyte organization at both tissue and cell levels is influenced by a cartilage-wide communication network that relies on zone-specific release and interpretation of paracrine signals. Despite genetic characterization of signaling interactions necessary for cartilage maturation, the regulatory mechanisms …

Landscape Genetics Of Ambystoma Opacum In Mammoth Cave National Park, Haley Austin

Mahurin Honors College Capstone Experience/Thesis Projects

No abstract provided.

Functional Studies Of The E. Coli Proc And A Putative Ortholog Mrub_1345, Maureen Azar, Dr. Lori Scott

Meiothermus ruber Genome Analysis Project

This project is part of the Meiothermus ruber genome analysis project, which uses the bioinformatics tools associated with the Guiding Education through Novel Investigation –Annotation Collaboration Toolkit (GENI-ACT) to predict gene function. We investigated the biological function of Escherichia coli and Meiothermus ruber proC genes using the complementation assay. In this research project, mutants of varying severity to the functional state of the protein were developed. The results showed that two or more amino acid deletions reduced or eliminated ProC function. Amino acid substitutions, on the other hand, were not severe enough to impact ProC function. Double and triple mutants …

Effects Of Mitochondrial Nadp+-Dependent Isocitrate Dehydrogenase Deficiency On Fructose-Induced Obesity In Mice, Allison Michelle Montalbano, Kaleigh Elizabeth Beane

Human Nutrition and Hospitality Management Undergraduate Honors Theses

Obesity prevalence in the United States continues to increase and is associated with health consequences such as type 2 diabetes, hypertension, atherosclerosis, and hyperlipidemia. Among many contributing factors to obesity, fructose may be one of the major reasons as it disrupts the antioxidant system thereby resulting in an accumulation of reactive oxidative species and leading to obese conditions. The enzyme, isocitrate dehydrogenase 2 (IDH2), reduces nicotinamide adenine dinucleotide phosphate from the TCA Cycle, hence might be implicated with not only energy metabolism but also cellular redox homeostasis. Therefore, the hypothesis was that IDH2 deficiency in mice would exacerbate hepatic lipid …

Association Between A Single Nucleotide Polymorphism In Neuregulin-1 And Schizophrenia In Pakistani Patients, Haider Ali Naqvi, Shafqat Huma, Hira Waseem, Kashaf Aqeel Zaidi, Hina Saeed Zuberi, Syed Hani Abidi

Department of Biological & Biomedical Sciences

Objective: To determine the association of single-nucleotide polymorphism8nrg433E1006 in the neuregulin-1 gene associated with schizophrenia.
Methods: This case-control study was conducted at the Fountain House, Lahore, and the psychiatric clinics at the Aga Khan University, Karachi, from 2010 to 2013.The total genomic deoxyribonucleic acid was isolated and single-nucleotide polymorphism8nrg433E1006 was screened by nested polymerase chain reaction followed by sequencing. These sequences, from patients and controls, were aligned with the human neuregulin-1-glial growth factor 2 gene sequence, which served as a reference sequence. The single nucleotide polymorphism genetic algorithm was characterised at position 433 in the neuregulin-1 gene by …

Crispr Gene Editing In The Sea Squirt, Ciona Intestinalis, Evelyn Siler, Steven Irvine

Senior Honors Projects

Genetic manipulation has come a long way in the past ten years alone. Scientists have had access to gene editing techniques for decades, but until recently these methods have proven to be expensive and unpredictable. However, thanks to the development of a new, more efficient genome editing strategy called CRISPR/Cas9, more aggressive progress can now be made in genetics research.

CRISPR is not a machine or a physical tool, but rather it is a system that involves introducing a protein into a cell, along with a DNA segment that will attract the protein to a desired location on the DNA. …

Genetic Testing And A Real World Case Of Lynch Syndrome, Paige Montanaro

Senior Honors Projects

In recent years, advancements in genetic testing methods have revolutionized the medical field by enhancing the ability to identify persons with an inherited predisposition to cancer. According to the American Society for Clinical Oncology, individuals should undergo genetic testing when he or she meets the following criteria: the individual demonstrates familial history that indicates a predisposition to certain cancers, the test can be adequately interpreted, and the results will aid in the diagnosis, treatment, or management of the patient or additional family members at risk. Genetic testing can be done on samples of hair, skin, blood, amniotic fluid, or other …

Regulation Of The Tubulin Homolog Ftsz In Escherichia Coli, Monika S. Buczek

Dissertations, Theses, and Capstone Projects

Escherichia coli is a well-known pathogen, and importantly, a widely used model organism in all fields of biological sciences for cloning, protein purification, and as a model for Gram-negative bacterial species. And yet, researchers do not fully understand how this bacterium replicates and divides. Every year additional division proteins are discovered, which adds complexity to how we understand E. coli undergoes cell division. Due to their specific roles in cytokinesis, some of these proteins may be potential targets for development of antibacterials or bacteriostatics, which are much needed for fighting the current global antibacterial deficit. My thesis work focuses on …

Optimizing Genetic Manipulation Of Methanogens Through Faster Cloning Techniques, Merrisa Jennings

Biological and Agricultural Engineering Undergraduate Honors Theses

Methanogenesis is the biological production of methane. Only anaerobic archaea known as methanogens are capable of such a metabolic feat. They have strict living conditions and substrate sources which determine their rate of metabolism. This is of particular importance from a greenhouse gas reduction perspective or biogas capturing perspective. One of the best ways to optimize methanogen methane production is via genetic manipulation. The current procedures are timely though, therefore a faster cloning processes should be developed. The objective of this study was to optimize a premade genetic transformation kit known as the Gibson Kit. The Gibson Kit was supposed …

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 …

Internal Validation Of Strmix™ – A Multi Laboratory Response To Pcast, Jo-Anne Bright, Rebecca Richards, Maarten Kruijver, Hannah Kelly, Catherine Mcgovern, Alan Magee, Andrew Mcwhorter, Anne Cieko, Brian Peck, Chase Baumgartner, Christina Buettner, Scott Mcwilliams, Claire Mckenna, Colin Gallacher, Ben Mallinder, Darren Wright, Deven Johnson, Dorothy Catella, Eugene Lien, Craig O'Connor, George Duncan, Jason Bundy, Jillian Echard, John Lowe, Joshua Stewart, Kathleen Corrado, Sheila Gentile, Marla Kaplan, Michelle Hassler, Naomi Mcdonald, Paul Hulme, Rachel H. Oefelein, Shawn Montpetit, Melissa Strong, Sarah Noel, Simon Malsom, Steven Myers, Susan Welti, Tamyra Moretti, Teresa Mcmahon, Thomas Grill, Tim Kalafut, Mary Margaret Greer-Ritzheimer, Vickie Beamer, Duncan A. Taylor, John S. Buckleton

Biology Faculty Articles

We report a large compilation of the internal validations of the probabilistic genotyping software STRmix™. Thirty one laboratories contributed data resulting in 2825 mixtures comprising three to six donors and a wide range of multiplex, equipment, mixture proportions and templates. Previously reported trends in the LR were confirmed including less discriminatory LRs occurring both for donors and non-donors at low template (for the donor in question) and at high contributor number. We were unable to isolate an effect of allelic sharing. Any apparent effect appears to be largely confounded with increased contributor number.

The Role Of Merlin And Apicobasal Polarity In Endometrial Development And Homeostasis, Erin Lopez

Dissertations and Theses (Open Access)

Apicobasal polarity and cell adhesion are necessary for the proper formation and organization of epithelial tissues. Merlin couples cell polarity and adhesion through correct localization of the polarity protein Par3 and maturation of apical junctions. Merlin and Par3 are necessary for the development and homeostasis of highly regenerative tissues like the epidermis. The continual repopulation of the endometrium after each menstrual cycle requires a constant reorganization of cell polarity and adhesion. The endometrium consists of a luminal epithelium that postnatally gives rise to the distinct glandular epithelium. Endometrial glands are necessary to secrete nutrients for the pre-implantation embryo. In addition, …

Psychiatric Impact Of Tuberous Sclerosis Complex And Utilization Of Mental Health Treatment, Kate Mowrey

Dissertations and Theses (Open Access)

Tuberous sclerosis complex (TSC) is a multi-system, neurocutaneous disorder with neuropsychiatric features known as TSC-associated neuropsychiatric disorders (TAND). While 90% of individuals with TSC have some TAND features, only 20% receive treatment, leading to a 70% treatment gap. This study evaluated perception of disease severity, presence of anxiety and depression, as well as the utilization and barriers towards mental health services among adults with TSC. Disease severity had a moderate and low-moderate association with anxiety and depression, respectively. Regardless of past utilization, respondents had a positive outlook towards the use of mental health services with the major barrier being cost.

Vascular Injury In Col3a1+/- Mice Model Of Vascular Ehler-Danlos Syndrome, Ping Zhou Ms

Dissertations and Theses (Open Access)

Vascular type of Ehlers-Danlos Syndrome (vEDS) is an inherited cardiovascular disease affecting the middle to large sized arteries, with an incidence rate of 1/5000. vEDS patients also show a significant phenotype of easily bruised skin, indicating aberrant wound healing and injury repair ability. Over 70% of the patients carry a glycine mutation located in their COL3A1 gene, which encodes the propeptide of type III collagen. Mutations in glycine residues lead to a disruption in the assembly and maturation of type III collagen. The goal and significance of the current study was to investigate the potential role of COL3A1 haploinsufficiency …