Genetics Commons^™

Genetic Architecture Of Gene Expression Traits Across Diverse Populations, Lauren S. Mogil, Angela Andaleon, Alexa Badalamenti, Scott P. Dickinson, Xiuqing Guo, Jerome I. Rotter, W. C. Johnson, Hae Kyung Im, Yongmei Liu, Heather E. Wheeler

Bioinformatics Faculty Publications

For many complex traits, gene regulation is likely to play a crucial mechanistic role. How the genetic architectures of complex traits vary between populations and subsequent effects on genetic prediction are not well understood, in part due to the historical paucity of GWAS in populations of non-European ancestry. We used data from the MESA (Multi-Ethnic Study of Atherosclerosis) cohort to characterize the genetic architecture of gene expression within and between diverse populations. Genotype and monocyte gene expression were available in individuals with African American (AFA, n = 233), Hispanic (HIS, n = 352), and European (CAU, n = 578) ancestry. …

The Transcriptome Of The Bermuda Fireworm Odontosyllis Enopla (Annelida: Syllidae): A Unique Luciferase Gene Family And Putative Epitoky-Related Genes, Mercer R. Brugler, M. Teresa Aguado, Michael Tessler, Mark Siddall

Publications and Research

The Bermuda fireworm Odontosyllis enopla exhibits an extremely tight circalunar circadian behavior that results in an impressive bioluminescent mating swarm, thought to be due to a conventional luciferase-mediated oxidation of a light-emitting luciferin. In addition, the four eyes become hypertrophied and heavily pigmented, and the nephridial system is modified to store and release gametes and associated secretions. In an effort to elucidate transcripts related to bioluminescence, circadian or circalunar periodicity, as well as epitoky-related changes of the eyes and nephridial system, we examined the transcriptomic profile of three female O. enopladuring a bioluminescent swarm in Ferry Reach, Bermuda. …

First Record Of The Genus Leptodactylus (Anura: Leptodactylidae) In Cuba: Leptodactylus Fragilis, A Biological Invasion?, Tomás M. Rodríguez-Cabrera, L. Yusnaviel García-Padrón, Andrés R. Acosta Galvis, Rafael O. De Sá, Roberto Alonso Bosch

Biology Faculty Publications

The Neotropical genus Leptodactylus is currently represented by three species in the West Indies (Leptodactylus albilabris, Leptodactylus fallax and Leptodactylus validus). Based on morphological, acoustic and molecular evidence, we document the presence of a fourth species in the Caribbean region, Leptodactylus fragilis (Brocchi, 1877). The species was found at two localities in western Cuba, and molecular data suggest a northern South American origin, possibly Venezuela, for these populations. We discuss the potential invasive status of L. fragilis, based on its known distribution, relative abundance, behaviour and possible impacts on native species of Cuban amphibians.

The Effect Of Maoa And Stress Sensitivity On Crime And Delinquency: A Replication Study, Christa C. Christ, Joseph A. Schwartz, Scott F. Stoltenberg, Jonathan R. Brauer, Jukka Savolainen

Department of Psychology: Faculty Publications

Across several meta-analyses, MAOA-uVNTR genotype has been associated with an increased risk for antisocial behavior among males who experienced early life adversity. Subsequently, early life stress and genetic susceptibility may have long-term effects on stress sensitivity later in life. In support of this assumption, a recent study found evidence, in two independent samples, for a three-way interaction effect (cG × E × E) such that proximate stress was found to moderate the interactive effect of MAOA-uVNTR and distal stress on crime and delinquency among males. In light of recent developments in cG × E research, we attempted to …

Displacement Of The Transcription Factor B Reader Domain During Transcription Initiation, Stefan Dexl, Robert Reichelt, Katharina Kraatz, Sarah Schulz, Dina Grohmann, Michael S. Bartlett, Michael Thomm

Biology Faculty Publications and Presentations

Transcription initiation by archaeal RNA polymerase (RNAP) and eukaryotic RNAP II requires the general transcription factor (TF) B/ IIB. Structural analyses of eukaryotic transcription initiation complexes locate the B-reader domain of TFIIB in close proximity to the active site of RNAP II. Here, we present the first crosslinking mapping data that describe the dynamic transitions of an archaeal TFB to provide evidence for structural rearrangements within the transcription complex during transition from initiation to early elongation phase of transcription. Using a highly specific UV-inducible crosslinking system based on the unnatural amino acid para-benzoyl-phenylalanine allowed us to analyze contacts of …

Genomic And Transcriptomic Landscape Of Colorectal Premalignancy, Kyle Chang

Dissertations and Theses (Open Access)

Colorectal cancer (CRC) is the third most commonly diagnosed cancer among men and women in the United States, with 3 to 5 percent of the cases diagnosed in the background of a hereditary form of the disease. Biologically, CRC is divided into two groups: microsatellite instable (MSI) and chromosomally unstable (CIN). Genomic and transcriptomic characterization of CRC has emerged from large-scale studies in recent years due to the advancement of next-generation sequencing technologies. These studies have identified key genes and pathways altered in CRC and provided insights to the discovery of therapeutic targets. Despite the wealth of knowledge acquired in …

Mechanism Of Incorporation And Repair Of Uracil At Highly Transcribed Genes In Saccharomyces Cerevisiae, Norah Auma Owiti

Dissertations and Theses (Open Access)

Recombination and mutagenesis are elevated by high levels of transcription. The correlation between transcription and genome instability is largely explained by the topological and structural changes in DNA and the associated physical obstacles generated by the transcription machinery. However, such explanation does not directly account for the unique types of mutations originating from the non-canonical residues such as uracil, which are also elevated at highly transcribed regions. Apurinic/Apyrimic or Abasic (AP) sites derived from uracil excision, accumulate at a higher rate in actively transcribed regions of the genome in S. cerevisiae and are primarily repaired by base excision repair (BER) …

Omics Approaches To Uncover Germline And Somatic Variation Underlying Inherited Sarcomagenesis, Justin Wong

Dissertations and Theses (Open Access)

Sarcomas are rare mesenchymal tumors, making up 15% of all childhood and 1% of all adult tumors. They account for a disproportionate share of mortality in young adults, and if left untreated, are highly likely to metastasize. However, sarcoma etiology is poorly understood, and having numerous histological subtypes has complicated elucidation. To better understand factors underlying sarcomagenesis, we leveraged two rare inherited cancer predisposition syndromes, Li-Fraumeni Syndrome (LFS), and LFS-like (LFSL), both with a high incidence of sarcomas. LFS is caused by mutations in the tumor suppressor gene TP53 (p53), but has variable and incomplete penetrance, suggesting additional acquired …

Investigation Of Bacterial Taxa As Biomarkers Of Fescue Toxicosis And Heat Stress In Grazing Beef Cows, Sarah Katherine Chewning

Graduate Theses and Dissertations

Fescue toxicosis in grazing beef cattle is caused by consumption of Ergot alkaloids associated with tall fescue (toxic fescue) and is responsible for substantial economic loss to the U.S. beef industry. Cattle consuming toxic fescue suffer adverse physiological responses, such as: hyperthermia, increased respiration rate (RR), poor reproduction and growth performance. Other adverse responses to fescue toxins include the retention of a winter hair coat and vasoconstriction in the extremities, which can lead to tissue necrosis. Identifying cattle with reduced susceptibility to fescue toxins would allow for efficient use of fescue pastures; thus, the objectives of this thesis was to: …

Impact Of Suburban Landscape Features On Gene Flow Of The Model Invasive Grass, Brachypodium Sylvaticum, Tina Marie Arredondo

Dissertations and Theses

Rapid range expansion of newly invasive species provides a unique opportunity for studying patterns of dispersal and gene flow. In this thesis, I examined the effect of landscape features on gene flow in the invasive grass Brachypodium sylvaticum at the edge of its expanding range. I used genome-wide Single Nucleotide Polymorphism (SNP) surveys of individuals from 22 locations in the Clackamas Watershed in the Portland, Oregon metropolitan region to assess genetic diversity and structure, to identify putative source populations, and to conduct landscape genetic analyses. Resistance surfaces were created for each landscape feature, using ResistanceGA to optimize resistance parameters. My …

Comparative Genetic And Genomic Analysis Of The Novel Fusellovirus Sulfolobus Spindle-Shaped Virus 10, David Andrew Goodman

Dissertations and Theses

Viruses that infect thermophilic Archaea are unique in both their structure and genetic makeup. The lemon-shaped fuselloviruses - which infect members of the order Sulfolobales, growing optimally at 80º C and pH 3 - are some of the most ubiquitous and best studied viruses of the thermoacidophilic Archaea. They provide a malleable and useful genetic tool for probing into the functions of their host, as well as the host responses to infection. Nonetheless, much about these viruses remains to be learned to further understand their morphological, genetic, and life cycle characteristics.

In order to investigate these aspects of these …

Development Of A Rapid Diagnostic Assay For The Colorimetric Detection Of Bacterial And Viral Pathogens Using Loop-Mediated Isothermal Amplification Coupled With A Peptide Nucleic Acid And Gold Nanoparticle Reporter System, William Brown

All NMU Master's Theses

Detection of pathogenic agents remains pivotal to the control and prevention of infectious disease. While diagnostic methods continue to break barriers, the need for accurate, sensitive, and rapid methods persists. Current methods for pathogen detection, including culture, immunochemical, or molecular-based techniques, are subject to significant limitations that restrict their clinical utility. Point-of-care (POC) tests have received attention for the diagnostic screening of infectious disease, with benefits of simplicity, affordability, and convenience. This study describes the development of a novel loop-mediated isothermal amplification (LAMP) reaction followed by a peptide nucleic acid (PNA) probe and gold nanoparticle (AuNP) detection system that results …

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 (

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 …

Arthropod Transcriptional Activator Protein-1 (Ap-1) Aids Tick-Rickettsial Pathogen Survival In The Cold, Supreet Khanal, Vikas Taank, John F. Anderson, Hameeda Sultana, Girish Neelakanta

Biological Sciences Faculty Publications

Ixodes scapularis ticks transmit several pathogens to humans including rickettsial bacterium, Anaplasma phagocytophilum. Here, we report that A. phagocytophilum uses tick transcriptional activator protein-1 (AP-1) as a molecular switch in the regulation of arthropod antifreeze gene, iafgp. RNAi-mediated silencing of ap-1 expression significantly affected iafgp gene expression and A. phagocytophilum burden in ticks upon acquisition from the murine host. Gel shift assays provide evidence that both the bacterium and AP-1 influences iafgp promoter and expression. The luciferase assays revealed that a region of approximately 700 bp upstream of the antifreeze gene is sufficient for AP-1 binding to promote …

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 …

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 …