Genetics and Genomics Commons^™

The Potential Of Epigenetics Research To Transform Conceptions Of Phenotype Development, David S. Moore

Pitzer Faculty Publications and Research

Epigenetics remains an exciting subdiscipline of biology, generating discoveries and insights about development. Because epigenetic phenomena can draw attention to the dynamic, interactional, and probabilistic nature of phenotype development, epigenetics research could hasten the demise of both nature-nurture debates and reductionist, genetically determinist perspectives on phenotype development. However, new data alone will not inevitably transform conceptualizations of phenotype origins, because it remains possible to assimilate epigenetic phenomena into traditional conceptual frameworks; epigenetic discoveries could even strengthen biologically determinist conclusions if traditional conceptualizations are retained. Although epigenetics will not force conceptual transformation, epigenetics research encourages the dismissal of the nature-nurture dichotomy …

Fisheries Management Paper No.283 - Abalone Resource Of Western Australia Harvest Strategy 2106 - 2021, Department Of Fisheries Western Australia

Fisheries Management Papers

Harvest strategies for aquatic resources managed by the Western Australian Department of Fisheries (the Department) are formal documents prepared to support the decision-making processes required to ensure the management of these resources are consistent with the principles of Ecologically Sustainable Development (ESD). The objectives of ESD are reflected in the objects of the Fish Resources Management Act 1994 (FRMA) and Section 9 of the Aquatic Resources Management Act, which will replace the FRMA once proclaimed.

The publication of these strategies is intended to make the decision-making considerations and processes for the management of specified aquatic resources publicly transparent and provide …

Mitochondrial-Dna Phylogenetic Information And The Reconstruction Of Human Population History: The South American Case, María Bárbara Postillone, S. Ivan Perez

Human Biology Open Access Pre-Prints

Objectives: Mitochondrial DNA (mtDNA) sequences are becoming increasingly important in the study of human population history. Here, we explore the differences in the amount of information of different mtDNA regions and their utility for the reconstruction of South American population history.

Material and methods: We analyzed six datasets comprising 259 mtDNA sequences from South America: Complete mtDNA, Coding, Control, hypervariable region I (HVRI), cytochrome b (cytb) plus Control, and cytb plus 12S plus 16S. The amount of information in each dataset was estimated employing several site-by-site and haplotype based statistics, distances among sequences, Neighbor-joining trees, distances among the estimated trees, …

Ptsd, Alcohol Dependence, And Conduct Problems: Distinct Pathways Via Lability And Disinhibition, Jeffrey S. Simons, Raluca M. Simons, Carol O'Brien, Scott F. Stoltenberg, Jessica A. Keith, Jaime A. Hudson

Department of Psychology: Faculty Publications

This study tested the role of affect lability and disinhibition in mediating associations between PTSD symptoms and two forms of alcohol-related problems, dependence syndrome symptoms (e.g., impaired control over consumption) and conduct problems (e.g., assault, risk behaviors). Genotype at the serotonin transporter linked polymorphic region (5-HTTLPR) was hypothesized to moderate associations between traumatic stress and PTSD symptoms. In addition, the study tested whether childhood traumatic stress moderated associations between combat trauma and PTSD symptoms. Participants were 270 OIF/OEF/OND veterans. The hypothesized model was largely supported. Participants with the low expression alleles of 5-HTTLPR (S or L_G) exhibited stronger …

Integrating Genetics And Neuroimaging To Study Subtypes Of Binge Drinkers, Megan E. Cooke

Theses and Dissertations

Risky alcohol use is a major health concern among college students, with 40.1% reporting binge drinking (5 or more drinks in one occasion) and 14.4% reporting heavy drinking (binge drinking on 5 or more occasions) in the past month. Risky alcohol use is thought to be the result of a complex interplay between genes, biological processes, and other phenotypic characteristics. Understanding this complex relationship is further complicated by known phenotypic heterogeneity in the development of alcohol use. Developmental studies have suggested two pathways to risky alcohol use, characterized by externalizing and internalizing characteristics, respectively. However, the underlying biological processes that …

Genetic Polymorphisms Of The Glucocorticoid Receptor And Interleulin-8 Receptor Genes And Their Relationship To Production Traits And Hair Coat Scores In Crossbred Cattle, Avery B. Deaton, Laura Meyer, Jeremy Powell, Charles F. Rosenkrans Jr.

Discovery, The Student Journal of Dale Bumpers College of Agricultural, Food and Life Sciences

Little is understood about how the diversity of genes, specifically the glucocorticoid receptor (GR) and interleukin-8 receptor (CXCR2), are related to reproductive health and how this affects physical traits in cattle. Glucocorticoid receptors have been positively associated with higher milk yields, lactose content, feed intake, and feed conversion rates. Interleukin-8 genes are part of the innate immune response and help with many aspects of female reproductive health, such as protecting the embryo from the maternal immune system during pregnancy. The objective of this research was to identify polymorphisms in the GR and CXCR2 genes and to associate genotypes between the …

Ancient Dna Extraction From Stone Tools, Clare Super

Undergraduate Theses, Professional Papers, and Capstone Artifacts

Proteins and DNA can be trapped in the microcracks on the surface of stone tools, which can then be extracted and analyzed to aid in inferring the use of the tool (Shanks et al. 2001; 2005). This nondestructive method involves the use of sonication to release DNA from the microcracks, then amplification of regions of mitochondrial DNA that are species specific. This technique was applied to stone tools from the Bridge River site in British Columbia by researchers at UMT’s Ancient and Modern Molecular Anthropology labs. Bridge River archaeologists have designated the tools as used in “food processing or tool …

A Systematic Review And Secondary Data Analysis Of The Interactions Between The Serotonin Transporter 5-Httlpr Polymorphism And Environmental And Psychological Factors In Eating Disorders, Vanja Rozenblat, Deborah Ong, Matthew Fuller-Tyszkiewicz, Kirsti Akkermann, David Collier, Rutger C. M. E. Engels, Fernando Fernandez-Aranda, Jaanus Harro, Judith R. Homberg, Andreas Karwautz, Evelyn Kiive, Kelly K. Klump, Sarah E. Racine, Jodie Richardson, Howard Steiger, Scott F. Stoltenberg, Tatjana Van Strien, Gudrun Wagner, Janet Treasure, Isabel Krug

Department of Psychology: Faculty Publications

Objectives: To summarize and synthesize the growing gene × environment (G × E) research investigating the promoter region of the serotonin transporter gene (5-HTTLPR) in the eating disorders (ED) field, and overcome the common limitation of low sample size, by undertaking a systematic review followed by a secondary data meta-analysis of studies identified by the review. Method: A systematic review of articles using PsycINFO, PubMed, and EMBASE was undertaken to identify studies investigating the interaction between 5-HTTLPR and an environmental or psychological factor, with an ED-related outcome variable. Seven studies were identified by the systematic review, with complete data sets …

Dna Methylation Signatures Of Chronic Low-Grade Inflammation Are Associated With Complex Diseases, Symen Ligthart, Carola Marzi, Stella Aslibekyan, Michael M. Mendelson, Karen N. Conneely, Toshiko Tanaka, Elena Colicino, Lindsay L. Waite, Roby Joehanes, Weihua Guan, Jennifer A. Brody, Cathy Elks, Riccardo Marioni, Min A. Jhun, Golareh Agha, Jan Bressler, Cavin K. Ward-Caviness, Brian H. Chen, Tianxiao Huan, Kelly Bakulski, Elias L. Salfati, Whi-Empc Investigators, Giovanni Fiorito, Charge Epigenetics Of Coronary Heart Disease, Simone Wahl, Katharina Schramm, Jin Sha, Dena G. Hernandez, Allan C. Just, Jennifer A. Smith, Donna K. Arnett

Epidemiology and Environmental Health Faculty Publications

Background: Chronic low-grade inflammation reflects a subclinical immune response implicated in the pathogenesis of complex diseases. Identifying genetic loci where DNA methylation is associated with chronic low-grade inflammation may reveal novel pathways or therapeutic targets for inflammation.

Results: We performed a meta-analysis of epigenome-wide association studies (EWAS) of serum C-reactive protein (CRP), which is a sensitive marker of low-grade inflammation, in a large European population (n = 8863) and trans-ethnic replication in African Americans (n = 4111). We found differential methylation at 218 CpG sites to be associated with CRP (P < 1.15 × 10^–7) in the discovery panel …

Relationship Among Genetic And Physiological Biomarkers, And Horse Characteristics, Casey Orr

Graduate Theses and Dissertations

The objective of this study was to evaluate relationships among genetic and physiological biomarkers and phenotypic characteristics in horses. Three breeds (Quarter Horse, Thoroughbreds, Miniatures), and five genes of interest (leptin, ghrelin, cytochrome P450, glucocorticoid receptor, and lactate dehydrogenase) were the basis of the investigation. Genomic DNA was extracted from buffy coat samples of Quarter Horses (n = 21), Thoroughbreds (n = 26), and Miniatures (n = 34). Data were analyzed using MIXED MODEL procedures of SAS, with the main effects of breed and SNP genotype. Horse was the experimental unit, and dependent variables were classified as physical, cell differentials, …

Perseverance: Psychospiritual And Genetic Perspectives, Tony N. Jelsma, Arielle Johnston, Bruce Vermeer

Faculty Work Comprehensive List

Perseverance constitutes a quality that motivates humankind to press onward usually in the face of significant adversity and resistance. Perseverance is also important in the Christian life. The apostle Paul, using athletic training metaphors, frequently urges his readers to persevere in the faith, even describing his own life as a fight and a race (2 Tim.4:7). Yet, certain groups of people seem to possess a greater measure of perseverance than others have. We are therefore led to ask, “Can our ability to persevere be, in God’s providence, at least partly genetically influenced?”

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 …

Breast-Cancer-Specific Mortality In Patients Treated Based On The 21-Gene Assay: A Seer Population-Based Study, Valentina I. Petkov, Dave P. Miller, Nadia Howlader, Nathan Gliner, Will Howe, Nicola Schussler, Kathleen Cronin, Frederick L. Baehner, Rosemary Cress, Dennis Deapen, Sally L. Glaser, Brenda Y. Hernandez, Charles F. Lynch, Lloyd Mueller, Ann G. Schwartz, Stephen M. Schwartz, Antoinette Stroup, Carol Sweeney, Thomas C. Tucker, Kevin C. Ward, Charles Wiggins, Xiao-Cheng Wu, Lynne Penberthy, Steven Shak

Markey Cancer Center Faculty Publications

The 21-gene Recurrence Score assay is validated to predict recurrence risk and chemotherapy benefit in hormone-receptor-positive (HR+) invasive breast cancer. To determine prospective breast-cancer-specific mortality (BCSM) outcomes by baseline Recurrence Score results and clinical covariates, the National Cancer Institute collaborated with Genomic Health and 14 population-based registries in the the Surveillance, Epidemiology, and End Results (SEER) Program to electronically supplement cancer surveillance data with Recurrence Score results. The prespecified primary analysis cohort was 40–84 years of age, and had node-negative, HR+, HER2-negative, nonmetastatic disease diagnosed between January 2004 and December 2011 in the entire SEER population, and Recurrence Score results …

Investigating The Effects Of Copy Number Variants On Reading And Language Performance, Alessandro Gialluisi, Alessia Visconti, Erik G. Willcutt, Shelley D. Smith, Bruce F. Pennington, Mario Falchi, John C. Defries, Richard K. Olson, Clyde Francks, Simon E. Fisher

Psychology: Faculty Scholarship

Background

Reading and language skills have overlapping genetic bases, most of which are still unknown. Part of the missing heritability may be caused by copy number variants (CNVs).

Methods

In a dataset of children recruited for a history of reading disability (RD, also known as dyslexia) or attention deficit hyperactivity disorder (ADHD) and their siblings, we investigated the effects of CNVs on reading and language performance. First, we called CNVs with PennCNV using signal intensity data from Illumina OmniExpress arrays (~723,000 probes). Then, we computed the correlation between measures of CNV genomic burden and the first principal component (PC) score …

Successful Enrichment And Recovery Of Whole Mitochondrial Genomes From Ancient Human Dental Calculus, Andrew T. Ozga, Maria A. Nieves-Colon, Tanvi P. Honap, Krithivasan Sankaranarayanan, Courtney A. Hofman, George R. Milner, Cecil M. Lewis Jr., Anne C. Stone, Christina Warinner

Biology Faculty Articles

Objectives

Archaeological dental calculus is a rich source of host‐associated biomolecules. Importantly, however, dental calculus is more accurately described as a calcified microbial biofilm than a host tissue. As such, concerns regarding destructive analysis of human remains may not apply as strongly to dental calculus, opening the possibility of obtaining human health and ancestry information from dental calculus in cases where destructive analysis of conventional skeletal remains is not permitted. Here we investigate the preservation of human mitochondrial DNA (mtDNA) in archaeological dental calculus and its potential for full mitochondrial genome (mitogenome) reconstruction in maternal lineage ancestry analysis.

Materials and …

Beyond Dna: Epigenetics And Proteomics In Forensic Science, Diane F. Eilerts

Themis: Research Journal of Justice Studies and Forensic Science

The use of genetic evidence in criminal cases is well established and has improved the public opinion and credibility of forensic science. However, several shortcomings associated with current genetic profiling techniques exist. Scientific research aimed at increasing the overall knowledge and understanding of biological factors will lead to the development of methods capable of improving the discriminating power of DNA evidence, overcoming limitations associated with DNA evidence, or complementing current methods of DNA profiling. Increased research in the fields of epigenetics and proteomics are particularly promising and relevant to forensic science. Research suggests that epigenetic biomarkers can be used to …

The Effects Of Chronic Partial Sleep Deprivation And Chronic Voluntary Alcohol Consumption On Δfos B Accumulation, Kristian Ponder

Masters Theses, 2010-2019

The present study explores the relation between sleep restriction and alcohol use and the neural substrates that result from chronic behaviors. Accumulation of the transcription factors ΔFosB is suggested as a possible outcome of chronic behaviors, such as addiction. Sleep is discussed as possible mediating factor in the relationship between ΔFosB and chronic alcohol consumption. There were four experimental groups in this study: Control (C), Sleep Deprivation only (SD), Alcohol Exposure only (AO), and both sleep deprivation and alcohol exposure (B). Levels of ΔFosB accumulation in the Nucleus Accumbens (NAc) revealed a significant main effect of sleep deprivation, but no …

Social And Scientific Implications Of Genetic Testing In The Digital Age, Yaruska A. Ordinola

Senior Honors Projects

From Mendel’s law of inheritance in the 19th century through Watson and Crick’s revolutionary observations of the double helix in the 20th century, genetics has been a fascinating and continuing topic of discussion in the field of science (Collins & McKusick, 2001). Major studies like the Human Genome Project (HGP), initiated in 1990 and completed in 2003, provided a starting point from which scientists could more thoroughly investigate the human condition on a genetic level. Arising from this study, personal genomics is considered a blooming field in genetics- in which rapidly developing technological advances are able to provide easier and …

Genetic Moderators Of Cognitive Decline In The Health And Retirement Study, Shannon K. Runge

USF Tampa Graduate Theses and Dissertations

The current dissertation used a gene x environment (G x E) approach to examine the independent and interactive effects of specific genetic variants and participation in physical and cognitive/social activities (PA and CSA) on cognitive performance in 4,764 participants of the Health and Retirement Study. Using three-wave data, three sets of multi-level growth models were conducted to examine baseline, longitudinal, and interactive effects of genotype (i.e., ApoE, COMT, and BDNF) and CSA/PA on performance across five cognitive measures: immediate, delayed and total word recall, and serial 7s and backwards counting.

At baseline, the ApoE ε4 allele predicted …

The Effects Of Chronic Partial Sleep Deprivation On Alcohol Consumption And Delta Fos B Accumulation, Kristian Ponder

Showcase of Graduate Student Scholarship and Creative Activities

The present study explores the relation between sleep restriction and alcohol use and the neural substrates that result from chronic behaviors, such as transcription factors. Transcription factor activity is suggested as a possible outcome of chronic behaviors, such as addiction. Sleep is discussed as possible mediating factor in the relationship between specific transcription factors and alcohol. Analysis will focus on brain areas related to both sleep and reward.

Reinforcement Learning, Error-Related Negativity, And Genetic Risk For Alzheimer's Disease, Christina Marie Figueroa

Dissertations (1934 -)

Reinforcement learning (RL) has been widely used as a model of animal and human learning and decision-making. The neural networks underlying RL involve many of the same structures primarily affected by Alzheimer’s disease (AD) such as the hippocampus. Yet, RL and non-invasive evaluation of its neural underpinnings have been underutilized as a framework for understanding disease pathology and its pre-clinical states. This study aimed to provide a novel approach for assessing subtle changes in asymptomatic apolipoprotein-E (APOE) carriers and non-carriers. Electroencephalography was collected from forty APOE genotyped older adults (Male n = 11; Mage = 79.30; Meducation = 14.88 years) …

Hpcnmf: A High-Performance Toolbox For Non-Negative Matrix Factorization, Karthik Devarajan, Guoli Wang

COBRA Preprint Series

Non-negative matrix factorization (NMF) is a widely used machine learning algorithm for dimension reduction of large-scale data. It has found successful applications in a variety of fields such as computational biology, neuroscience, natural language processing, information retrieval, image processing and speech recognition. In bioinformatics, for example, it has been used to extract patterns and profiles from genomic and text-mining data as well as in protein sequence and structure analysis. While the scientific performance of NMF is very promising in dealing with high dimensional data sets and complex data structures, its computational cost is high and sometimes could be critical for …

Screening Of Exosomal Micrornas From Colorectal Cancer Cells, Cillian Clancy, Sonja Khan, Claire L. Glynn, Emma Holian, Peter Dockery, Pierce Lalor, James A.L. Brown, Myles Joyce, Michael J. Kerin, Roisin M. Dwyer

Forensic Science Publications

BACKGROUND: Cells release extracellular membrane vesicles including microvesicles known as exosomes. Exosomes contain microRNAs (miRNAs) however the full range within colorectal cancer cell secreted exosomes is unknown. OBJECTIVE: To identify the full range of exosome encapsulated miRNAs secreted from 2 colorectal cancer cell lines and to investigate engineering of exosomes over-expressing miRNAs. METHODS: Exosomes were isolated from HCT-116 and HT-29 cell lines. RNA was extracted from exosomes and microRNA array performed. Cells were engineered to express miR-379 (HCT-116-379) or a non-targeting control (HCT-116-NTC) and functional effects were determined. Exosomes secreted by engineered cells were transferred to recipient cells and the …

Conservation Genetics On The Frontline, Kenneth W. Rand

Graduate Student Theses, Dissertations, & Professional Papers

Conservation genetics stands out as an effective tool for discovering and monitoring rare, endangered or invasive populations of plants and animals. Particularly when compared to traditional search and capture methods, it provides more holistic studies to preserve the disappearing biodiversity of the American West and the world.

Three stories highlight the work done to preserve biodiversity through the use of conservation genetics:

1. Trout Rescue: A new hope for westslope cutthroat in Montana How to save a disappearing westslope cutthroat trout through genetic rescue by adding genetic diversity to ensuring future survival in increasingly warming waters more harm than good. …

Mongolians In The Genetic Landscape Of Central Asia: Exploring The Genetic Relations Among Mongolians And Other World Populations, Jane E. Brissenden, Judith R. Kidd, Baigalmaa Evsanaa, Ariunaa Togtokh, Andrew J. Pakstis, Françoise Friedlaender, Kenneth K. Kidd, Janet M. Roscoe

Human Biology Open Access Pre-Prints

Genetic data on North Central Asian populations are underrepresented in the literature, especially autosomal markers. In the present study we use 812 single nucleotide polymorphisms that are distributed across all the human autosomes and that have been extensively studied at Yale to examine the affinities of two recently collected, samples of populations: rural and cosmopolitan Mongolians from Ulaanbaatar and nomadic, Turkic-speaking Tsaatan from Mongolia near the Siberian border. We compare these two populations to one another and to a global set of populations and discuss their relationships to New World populations. Specifically, we analyze data on 521 autosomal loci (single …

Origins Of An Unmarked Georgia Cemetery Using Ancient Dna Analysis, Andrew T. Ozga, Raúl Y. Tito, Brian M. Kemp, Hugh Matternes, Alexandra Obregon-Tito, Leslie Neal, Cecil M. Lewis, Jr.

Human Biology Open Access Pre-Prints

Determining the origins of those buried within undocumented cemeteries is of incredible importance to historical archaeologists and in many cases, the nearby communities. In the case of Avondale Burial Place, a cemetery in Bibb County, Georgia, in use from 1820 to 1950, all written documentation of those interred within it has been lost. Osteological and archaeological evidence alone could not describe, with confidence, the ancestral origins of the 101 individuals buried there. In the present study, we utilize ancient DNA extraction methods to investigate the origins of Avondale Burial Place through the use of well-preserved skeletal fragments from 20 individuals …

Fisheries Management Paper No 274 - Finfish Resources Of The Peel-Harvey Estuary - Harvest Strategy 2015-2020 (Version 1.0), Department Of Fisheries, Western Australia

Fisheries Management Papers

WEST COAST ESTUARINE MANAGED FISHERY (AREA 2)

Harvest strategies for aquatic resources managed by the Western Australian Department of Fisheries (the Department) are formal documents prepared to support the decision-making processes required to ensure the management of these resources are consistent with the principles of Ecologically Sustainable Development (ESD). The objectives of ESD are reflected in the objects of the Fish Resources Management Act 1994 (FRMA), Section 3, and the draft Aquatic Resources Management Bill 2013 (ARMB), Clause 9, which will replace the FRMA once enacted.

The publication of these strategies is intended to make the decision-making considerations and processes …

Spiritual Exploration In The Prenatal Genetic Counseling Session, Katelynn G. Sagaser

Dissertations and Theses (Open Access)

Religion and spirituality are important components of many individuals’ lives, and spiritual needs may present among persons receiving medical care. Spirituality has been demonstrated to be significant in the coping of women experiencing pregnancy complications (Breen et al. 2006; Price et al. 2007). To characterize the manner in which prenatal genetic counselors might address spiritual issues with their patients, we surveyed 283 patients receiving prenatal genetic counseling using the Brief RCope and a series of questions that examined interest in spiritual exploration. Counselors were concurrently surveyed to identify the spiritual language used within the session and the counselor’s perceived importance …

Fisheries Management Paper No.273 - Blue Swimmer Crab Resource Of The Peel-Harvey Estuary Harvest Strategy, 2015-2020. Version 1.0, Department Of Fisheries, Western Australia

Fisheries Management Papers

Harvest strategies for aquatic resources managed by the Western Australian Department of Fisheries (the Department) are formal documents prepared to support the decision-making processes required to ensure the management of these resources are consistent with the principles of Ecologically Sustainable Development (ESD). The objectives of ESD are reflected in the objects of the Fish Resources Management Act 1994 (FRMA), Section 3, and the draft Aquatic Resources Management Bill 2013 (ARMB), Clause 9, which will replace the FRMA once enacted.

The publication of these strategies is intended to make the decision-making considerations and processes for the management of specified aquatic resources …

Oprm1 Rs1799971 Genotype Predicts Drinking Behavior In Males, But Not Females, Sarah Hughes Berheim, Carmen Ochoa, Grace Sullivan, Scott F. Stoltenberg

UCARE: Research Products

• The prevalence of alcohol disorders costs Americans $223.5 billion yearly due mostly from losses in workplace productivity, as well as health care and criminal justice expenses (CDC, 2016).

• Maximum number of drinks consumed in a 24 hour period is a valid indicator of dangerous drinking behavior and may reflect an increased tolerance for high levels of alcohol (Edenberg, 2016).

• Awareness of factors related to such heavy drinking is important for targeting interventions for dangerous alcohol use.

• Men drink significantly more than women, with about 4.5% of men and 2.5% of women meeting the diagnostic criteria for …