Genetics Commons^™

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 …

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 …

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) …

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 …

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 …

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 …

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

Biology Faculty Articles

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 used ancient DNA extraction methods in well-preserved skeletal fragments from 20 individuals buried in Avondale Burial Place to investigate the origins of the …

Hemochromatosis: Niche Construction And The Genetic Domino Effect In The European Neolithic, John M. Mccullough, Kathleen M. Heath, Alexis M. Smith

Human Biology Open Access Pre-Prints

Hereditary hemochromatosis (HH) is caused by a potentially lethal recessive gene (HFE, C282Y allele) that increases iron absorption and reaches polymorphic levels in Northern European populations. Because persons carrying the allele absorb iron more readily than non-carriers, it has often been suggested HFE is an adaptation to anemia. We hypothesize positive selection for HFE began during or after the European Neolithic with the adoption of an iron-deficient high grain and dairying diet and consequent anemia, a finding confirmed in Neolithic and later European skeletons. HFE frequency compared with rate of lactase persistence in Eurasia yields a positive linear …

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

All Master's Theses

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

Fisheries Management Paper No.266 - Exmouth Gulf Prawn Managed Fishery Bycatch Action Plan 2014-2019. Version 1.0, Department Of Fisheries, Western Australia

Fisheries Management Papers

Bycatch is described as the part of the catch which is returned to the sea (usually referred to as non-retained or discarded) either because it has no commercial value or because legislative requirements preclude it being retained. Thus, this Bycatch Action Plan (BAP) includes unmarketable finfish and invertebrate species, along with endangered, threatened and protected (ETP) species, such as marine mammals, reptiles and some elasmobranchs.

It is Government policy to minimise bycatch in all commercial fisheries. This BAP details a program of actions to address bycatch issues in the Exmouth Gulf Prawn Managed Fishery (EGPMF), in accordance with the EGPMF …

Associated Behavioral, Genetic, And Gene Expression Variation With Alternative Life History Tactics In Salmonid Fishes, Ashley Chin-Baarstad

Open Access Dissertations

Individual differences in behavior can have potential fitness consequences and often reflect underlying genetic variation. My research focuses on three objectives related to individual level variation: 1) evaluating the innate behavioral variation within and between individuals, families, and progeny of different life-history types across time; 2) testing for differences in gene expression within the brain associated with this behavioral variation; and 3) using genetic polymorphisms to test for associations with ecotype, as well as population structure, in polymorphic populations. First, we evaluated the variation in a suite of ecologically relevant behaviors across time in juvenile progeny produced from crosses within …

Genetic Genealogy: What Every Librarian Should Know, Rosemary L. Meszaros, Katherine Pennavaria

DLPS Faculty Publications

The past few years television, podcasts, and blogs across the Internet promoted the role of DNA testing in genealogy. But what do you really get, and is it worth the price? We discuss the logistics of DNA testing as it relates to genealogy and take a hard look at the legal issues involved in genealogy’s hottest topic.

Hla Class Ii Alleles In The Otomi Population Of The Mezquital Valley. A Genetic Approach To The History Of Interethnic Migrations In The Mexican Central Plateau, Ana Itzel Juárez-Martín, Blanca Zoila González-Sobrino, Ángel Eduardo Camarena Olvera, Ramcés Falfán-Valencia

Human Biology Open Access Pre-Prints

From a historic and genetic point of view, the Otomi of the Mezquital Valley are a frontier people that have played an important role in the making of the population dynamics of the Mexican Central Plateau. Due to their antiquity in the area, the Otomi may be bearers of ancient genetic variability, shared mainly today with other groups belonging to the Otomanguean linguistic family and with the Nahua.

This study analyzes the HLA class II allele frequencies reported in Mexican indigenous populations, in order to provide an intra-regional level historical perspective of the genetic relationships between the Otomi of the …

Human Diversity In Jordan: Polymorphic Alu Insertions In General Jordanian And Bedouin Groups, Daniela Zanetti, May Sadiq, Robert Carreras-Torres, Omar Khabour, Almuthanna Alkaraki, Esther Esteban, Marc Via, Pedro Moral

Human Biology Open Access Pre-Prints

Jordan, located in the Levant region, is a crucial area to investigate human migration between Africa and Eurasia. Even thought, the genetic history of Jordanians is far to be clarified including the origin of the Bedouins today resident in Jordan. Here, we provide new genetic data on autosomal independent markers in two Jordanian population samples (Bedouins and general population) in order to approach the genetic diversity inside this country and to give new information about the genetic position of these populations in the frame of the Mediterranean and Middle East area. The analyzed markers are 18 Alu polymorphic insertions characterized …

Human Paternal Lineages, Languages And Environment In The Caucasus, David Tarkhnishvili, Alexander Gavashelishvili, Marine Murtskhvaladze, Mariam Gabelaia, Gigi Tevzadze

Human Biology Open Access Pre-Prints

Publications that describe the human Y-DNA haplogroup composition in different ethnic or linguistic groups and geographic regions provide no explicit explanation of the distribution of human paternal lineages in relation to specific ecological conditions. Our research attempts to address this topic for the Caucasus – a geographic region that encompasses a relatively small area but harbors high linguistic, ethnic, and Y-DNA haplogroup diversity. 224 men that identified themselves as ethnic Georgian were genotyped for Y-chromosome 23 STR markers and assigned to their geographic places of origin. The genotyped data were supplemented with the published data on the haplogroup composition and …

Phylogeography Of E1b1b1b-M81 Haplogroup And Analysis Of Its Subclades In Morocco, Ahmed Reguig, Nourdin Harich, Abdelhamid Barakat, Hassan Rouba

Human Biology Open Access Pre-Prints

In this work, we have analyzed a total of 295 unrelated Berber-speaking men from the northern, center and southern of Morocco, in order to characterize frequency of E1b1b1b-M81 haplogroup and to refine the phylogeny of its subclades: E1b1b1b1-M107, E1b1b1b2-M183 and E1b1b1b2a-M165. For this purpose, we have typed four biallelic polymorphisms: M81, M107, M183 and M165. As results, a large majority of the Berber-speaking male lineages belong to the Y chromosomal E1b1b1b-M81 haplogroup. The frequency ranged from 79.1 to 98.5% in all localities sampled. Then, the E1b1b1b2-M183 was the most dominant subclade in our samples, which ranged from 65.1% to 83.1%. …

Mitochondrial Dna Variability Among Six South-American Amerindian Villages From The Pano Linguistic Group, Celso T. Mendes-Junior, Aguinaldo L. Simoes

Human Biology Open Access Pre-Prints

Although scattered throughout a large geographic area, the members of the Pano linguistic group present strong ethnic, linguistic and cultural homogeneity, a feature that causes them to be considered as components of a same “Pano” tribe. Nevertheless, the genetic homogeneity between Pano villages has not been examined before. To study the genetic structure of the Pano linguistic group, four major Native American mitochondrial DNA (mtDNA) founder haplogroups were analyzed in 77 Amerindians from six villages of four Pano tribes (Katukina, Kaxináwa, Marúbo, and Yaminawa) located in the Brazilian Amazon. The central position of these tribes in the continent makes them …

Questioning The “Melting Pot”: Analysis Of Alu Inserts In Three Population Samples From Uruguay, Pedro C. Hidalgo, Patricia Mut, Elizabeth Ackermann, Gonzalo Figueiro, Monica Sans

Human Biology Open Access Pre-Prints

The way that immigrants integrate to recipient societies has been discussed for decades, mainly from the perspective of the social sciences. Uruguay, as other American countries, received different waves of European immigrants, although the details of the process of assimilation, when occurred, are unclear. In this paper, we use genetic markers to understand the process experienced by the Basques, one of the major migration waves that populated Uruguay, and its relation to other immigrants as well as to Native American and African descendants. For this purpose, we analyze the allele frequencies of ten ALU loci (A25, ACE, APOA1, B65, F13B, …

Science Fiction And The Myth Of Trajectory Evolution, Jocelyn D. Pickreign

The Macalester Review

Stephen Jay Gould first proposed the idea of “iconographies of progress.” Today, one of the most prominent forms of progress iconography is the science fiction story. Science fiction as a genre frequently portrays evolution as a linear trajectory of increasing complexity, and in doing so, furthers a worldview that is not unlike the pre-Darwin understanding of human beings as both the center and the pinnacle of the natural world.

Effects Of Ergot Alkaloids And Bovine Bodily Fluids On Cytochrome P450 Activity, Nicholas Scott Ezell

Graduate Theses and Dissertations

This thesis evaluates the Promega^TM P450-Glo assay (Promega^TM V9800) as a tool for quantifying ergot alkaloid concentration. Current techniques used for detection of ergot alkaloids are slow and expensive, do not detect all ergot alkaloids, or are not effective on bovine bodily fluids. The first study was conducted to determine effects of commercial ergot alkaloids (n = 6; 0 - 400 μM) on the Promega^TM P450-Glo assay. Cytochrome P450 (CYP450) activity in assay had a differential response to each ergot alkaloid and concentration. As concentrations of ergotamine, dihydroergotamine, ergocornine, and ergocryptine increased CYP450 activity was inhibited (P …

Afraid To Help: Social Anxiety Partially Mediates The Association Between 5-Httlpr Triallelic Genotype And Prosocial Behavior, Scott F. Stoltenberg, Christa C. Christ, Gustavo Carlo

Department of Psychology: Faculty Publications

There is growing evidence that the serotonin system influences prosocial behavior. We examined whether anxiety mediated the association between variation in the serotonin transporter gene regulatory region (5-HTTLPR) and prosocial behavior. We collected self-reported tendencies to avoid certain situations and history of helping others using standard instruments and buccal cells for standard 5-HTTLPR genotyping from 398 undergraduate students. Triallelic 5-HTTLPR genotype was significantly associated with prosocial behavior and the effect was partially mediated by social anxiety, such that those carrying the S′ allele reported higher levels of social avoidance and lower rates of helping others. These results are consistent with …

Protective Effects Of The Alcohol Dehydrogenase-Adh1b Allele, Neil Dodge

Wayne State University Theses

Alcohol dehydrogenase is a critical enzyme in the metabolism of alcohol. Expression of three alleles at the ADH1B locus results in enzymes that differ in turnover rate and affinity for alcohol. The ADH1B*3 allele, which appears to be unique to African Americans, is associated with more rapid alcohol metabolism than the more prevalent ADH1B*1 allele. It has been previously demonstrated that the presence of at least one maternal ADH1B*3 allele confers a protective effect against alcohol teratogenicity in African American infants and children. This study was conducted to determine whether the presence of the ADH1B*3 allele in the mother or …

Genetic Diversity Of North American Captive-Born Gorillas (Gorilla Gorilla Gorilla), Noah D. Simmons, Ronald S. Wagner, Joseph G. Lorenz

All Faculty Scholarship for the College of the Sciences

Western lowland gorillas (Gorilla gorilla gorilla) are designated as critically endangered and wild populations are dramatically declining as a result of habitat destruction, fragmentation, diseases (e.g., Ebola) and the illegal bushmeat trade. As wild populations continue to decline, the genetic management of the North American captive western lowland gorilla population will be an important component of the long‐term conservation of the species. We genotyped 26 individuals from the North American captive gorilla collection at 11 autosomal microsatellite loci in order to compare levels of genetic diversity to wild populations, investigate genetic signatures of a population bottleneck and identify …

Genetic Analysis Of Putative Familial Relationships In A Captive Chimpanzee (Pan Troglodytes) Population, Renato Robledo, Joseph G. Lorenz, Jeanne Beck, James Else, Patrick Bender

Anthropology and Museum Studies Faculty Scholarship

Twelve autosomal dinucleotide repeat loci were analyzed in chimpanzees genomes by DNA amplification using primers designed for analysis of human loci. The markers span the entire length of human chromosomes 21 and 22. Nine markers were polymorphic in chimpanzee as well, with a somewhat comparable level of polymorphism and allele size range. Even in the presence of very limited information and in spite of missing samples, it was possible to reconstruct a complex pedigree and to provide molecular data that corroborate family relationships that were deduced from cage history and behavioral data. The conclusions were further supported by mitochondrial DNA …

Impulsiveness Mediates The Association Between Gabra2 Snps And Lifetime Alcohol Problems, S. Villafuerte, V. Strumba, S. F. Stoltenberg, R. A. Zucker, M. Burmeister

Department of Psychology: Faculty Publications

Genetic variants in GABRA2 have previously been shown to be associated with alcohol measures, electroencephalography (EEG) β waves and impulsiveness-related traits. Impulsiveness is a behavioral risk factor for alcohol and other substance abuse. Here, we tested association between 11 variants in GABRA2 with NEO-impulsiveness and problem drinking. Our sample of 295 unrelated adult subjects was from a community of families with at least one male with DSM-IV alcohol use diagnosis, and from a socioeconomically comparable control group. Ten GABRA2 SNPs (single-nucleotide polymorphisms) were associated with the NEO-impulsiveness (P < 0.03). The alleles associated with higher impulsiveness correspond to the minor alleles identified in previous alcohol dependence studies. All ten SNPs are in linkage disequilibrium (LD) with each other and represent one effect on impulsiveness. Four SNPs and the corresponding haplotype from intron 3 to intron 4 were also associated with Lifetime Alcohol Problems Score (LAPS, P < 0.03) (not corrected for multiple testing). Impulsiveness partially mediates (22.6% average) this relation between GABRA2 and LAPS. Our results suggest that GABRA2 variation in …

Serotonin System Gene Polymorphisms Are Associated With Impulsivity In A Context Dependent Manner, Scott F. Stoltenberg, Christa C. Christ, Krista B. Highland

Department of Psychology: Faculty Publications

Impulsivity is a risk factor for adverse outcomes and characterizes several psychiatric disorders and risk for suicide. There is strong evidence that genetic variation influences individual differences in impulsivity, but the details are not yet understood. There is growing interest in better understanding the context dependency of genetic effects that is reflected in studies examining gender specificity, gene × environment interaction and epistasis (gene-gene interaction). In a cross-sectional study we examined whether polymorphisms in six serotonin system candidate genes and the experience of early life trauma (age 0–12) were associated with individual differences in impulsivity in a nonclinical sample of …