Genetic Analysis Workshop 18: Methods And Strategies For Analyzing Human Sequence And Phenotype Data In Members Of Extended Pedigrees,
2014
Dordt College
Genetic Analysis Workshop 18: Methods And Strategies For Analyzing Human Sequence And Phenotype Data In Members Of Extended Pedigrees, Heike Bickeboller, Julia N. Bailey, Joseph Beyene, Rita M. Cantor, Heather J. Cordell, Robert C. Culverhouse, Corinne D. Engelman, David W. Fardo, Saurabh Ghosh, Inke R. Konig, Justo Lorenzo Bermejo, Phillip E. Melton, Stephanie A. Santorico, Glen A. Satten, Lei Sun, Nathan L. Tintle, Andreas Ziegler, Jean W. Maccluer, Laura Almasy
Faculty Work Comprehensive List
Genetic Analysis Workshop 18 provided a platform for developing and evaluating statistical methods to analyze whole-genome sequence data from a pedigree-based sample. In this article we present an overview of the data sets and the contributions that analyzed these data. The family data, donated by the Type 2 Diabetes Genetic Exploration by Next-Generation Sequencing in Ethnic Samples Consortium, included sequence-level genotypes based on sequencing and imputation, genome-wide association genotypes from prior genotyping arrays, and phenotypes from longitudinal assessments. The contributions from individual research groups were extensively discussed before, during, and after the workshop in theme-based discussion groups before being submitted …
Early Back-To-Africa Migration Into The Horn Of Africa,
2014
Imperial College London
Early Back-To-Africa Migration Into The Horn Of Africa, Jason A. Hodgson, Connie J. Mulligan, Ali Al-Meeri, Ryan L. Raaum
Publications and Research
Genetic studies have identified substantial non-African admixture in the Horn of Africa (HOA). In the most recent genomic studies, this non-African ancestry has been attributed to admixture with Middle Eastern populations during the last few thousand years. However, mitochondrial and Y chromosome data are suggestive of earlier episodes of admixture. To investigate this further, we generated new genome-wide SNP data for a Yemeni population sample and merged these new data with published genome-wide genetic data from the HOA and a broad selection of surrounding populations. We used multidimensional scaling and ADMIXTURE methods in an exploratory data analysis to develop hypotheses …
Holding Back The Genes: Limitations Of Research Into Canine Behavioural Genetics,
2014
University of Sydney
Holding Back The Genes: Limitations Of Research Into Canine Behavioural Genetics, Diane Van Rooy, Elizabeth R. Arnott, Jonathan B. Early, Paul Mcgreevy, Claire M. Wade
Genetics Collection
Canine behaviours that are both desirable and undesirable to owners have a demonstrable genetic component. Some behaviours are breed-specific, such as the livestock guarding by maremmas and flank sucking seen in Dobermanns. While the identification of genes responsible for common canine diseases is rapidly advancing, those genes underlying behaviours remain elusive. The challenges of accurately defining and measuring behavioural phenotypes remain an obstacle, and the use of variable phenotyping methods has prevented meta-analysis of behavioural studies. International standardised testing protocols and terminology in canine behavioural evaluations should facilitate selection against behavioural disorders in the modern dog and optimise breeding success …
A Classification And Characterization Of Two-Locus, Pure, Strict, Epistatic Models For Simulation And Detection,
2014
Dartmouth College
A Classification And Characterization Of Two-Locus, Pure, Strict, Epistatic Models For Simulation And Detection, Ryan J. Urbanowicz, Ambrose L. S. Granizo-Mackenzie, Jeff Kiralis, Jason H Moore
Dartmouth Scholarship
BackgroundThe statistical genetics phenomenon of epistasis is widely acknowledged to confound disease etiology. In order to evaluate strategies for detecting these complex multi-locus disease associations, simulation studies are required. The development of the GAMETES software for the generation of complex genetic models, has provided the means to randomly generate an architecturally diverse population of epistatic models that are both pure and strict, i.e. all n loci, but no fewer, are predictive of phenotype. Previous theoretical work characterizing complex genetic models has yet to examine pure, strict, epistasis which should be the most challenging to detect. This study addresses three goals: …
Human Diversity In Jordan: Polymorphic Alu Insertions In General Jordanian And Bedouin Groups,
2014
Department of Animal Biology-Anthropology, University of Barcelona, Barcelona, Spain
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,
2014
1Center of Biodiversity Studies, Institute of Ecology, Ilia State University, Tbilisi, Georgia
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,
2014
Laboratoire de Génétique Moléculaire Humaine, Département de Recherche Scientifique, Institut Pasteur du Maroc
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%. …
An Asian Origin Of Virulent Aeromonas Hydrophila Responsible For Disease Epidemics In United States-Farmed Catfish,
2014
Auburn University
An Asian Origin Of Virulent Aeromonas Hydrophila Responsible For Disease Epidemics In United States-Farmed Catfish, Mohammad J. Hossain, Dawei Sun, Donald J. Mcgarey, Shannon Wrenn
Faculty Articles
Unlabelled: Since 2009, catfish farming in the southeastern United States has been severely impacted by a highly virulent and clonal population of Aeromonas hydrophila causing motile Aeromonas septicemia (MAS) in catfish. The possible origin of this newly emerged highly virulent A. hydrophila strain is unknown. In this study, we show using whole-genome sequencing and comparative genomics that A. hydrophila isolates from diseased grass carp in China and catfish in the United States have highly similar genomes. Our phylogenomic analyses suggest that U.S. catfish isolates emerged from A. hydrophila populations of Asian origin. Furthermore, we identified an A. hydrophila strain isolated …
Mitochondrial Dna Variability Among Six South-American Amerindian Villages From The Pano Linguistic Group,
2014
Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Brazil
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 …
Obligate Male Death And Sexual Cannibalism In Dark Fishing Spiders,
2014
Macquarie University
Obligate Male Death And Sexual Cannibalism In Dark Fishing Spiders, Steven Schwartz, William E. Wagner, Eileen A. Hebets
Eileen Hebets Publications
Male dark fishing spiders (Dolomedes tenebrosus Araneae, Pisauridae) always die during their first and only copulation, making all males monogynous. Such obligate male death can be adaptive if it facilitates sexual cannibalism, and if sexual cannibalism results in male reproductive benefits, such as an advantage in sperm competition through reduced female remating. We first conducted an experiment to determine the extent to which D. tenebrosus (1) males are cannibalized by females and (2) females engage in remating, both of which are prerequisites for several adaptive hypotheses of male self-sacrifice. We then conducted an experiment to test the hypothesis that …
Ept7 Influences Estrogen Action In The Pituitary Gland And Body
Weight Of Rats,
2014
University of Nebraska-Lincoln
Ept7 Influences Estrogen Action In The Pituitary Gland And Body Weight Of Rats, Scott G. Kurz, Kirsten L. Mcfee, Nyssa Becker Samanas, Maureen Peters Hickman, Quincy A. Eckert, Tiffany L. Walker, Andrea S. Cupp, James D. Shull
Department of Animal Science: Faculty Publications
Estrogens control many aspects of pituitary gland biology, including regulation of lactotroph homeostasis and synthesis and secretion of prolactin. In rat models, these actions are strain specific and heritable, and multiple quantitative trait loci (QTL) have been mapped that impact the responsiveness of the lactotroph to estrogens. One such QTL, Ept7, was mapped to RNO7 in female progeny generated in an intercross between BN rats, in which the lactotroph population is insensitive to estrogens, and ACI rats, which develop lactotroph hyperplasia/adenoma and associated hyperprolactinemia in response to estrogen treatment. The primary objective of this study was to confirm the …
Secretory Iga Is Concentrated In The Outer Layer Of Colonic Mucus Along With Gut Bacteria,
2014
University of Kentucky
Secretory Iga Is Concentrated In The Outer Layer Of Colonic Mucus Along With Gut Bacteria, Eric W. Rogier, Aubrey L. Frantz, Maria E. C. Bruno, Charlotte S. Kaetzel
Microbiology, Immunology, and Molecular Genetics Faculty Publications
Antibodies of the secretory IgA (SIgA) class comprise the first line of antigen-specific immune defense, preventing access of commensal and pathogenic microorganisms and their secreted products into the body proper. In addition to preventing infection, SIgA shapes the composition of the gut microbiome. SIgA is transported across intestinal epithelial cells into gut secretions by the polymeric immunoglobulin receptor (pIgR). The epithelial surface is protected by a thick network of mucus, which is composed of a dense, sterile inner layer and a loose outer layer that is colonized by commensal bacteria. Immunofluorescence microscopy of mouse and human colon tissues demonstrated that …
Questioning The “Melting Pot”: Analysis Of Alu Inserts In Three Population Samples From Uruguay,
2014
Departamento de Antropología Biológica. Facultad de Humanidades y Ciencias de la Educación. Universidad de la República, Uruguay
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, …
Genetic Explanations: Sense And Nonsense,
2014
Washington University in St Louis
Genetic Explanations: Sense And Nonsense, Garland E. Allen
Biology Faculty Research
Book review of Sheldon Krimsky; Jeremy Gruber (Editors). Genetic Explanations: Sense and Nonsense. xi + 368 pp., index. Cambridge, Mass.: Harvard University Press, 2013. $45 (cloth).
The Evolution Of Respiratory O2/No Reductases: An Out-Of-The-Phylogenetic-Box Perspective,
2014
University of Nebraska-Lincoln
The Evolution Of Respiratory O2/No Reductases: An Out-Of-The-Phylogenetic-Box Perspective, Anne-Lise Ducluzeau, Barbara Schoepp-Cothenet, Robert Van Lis, Frauke Baymann, Michael J. Russell, Wilfgang Nitschke
Department of Biochemistry: Faculty Publications
Complex life on our planet crucially depends on strong redox disequilibria afforded by the almost ubiquitous presence of highly oxidizing molecular oxygen. However, the history of O2-levels in the atmosphere is complex and prior to the Great Oxidation Event some 2.3 billion years ago, the amount of O2 in the biosphere is considered to have been extremely low as compared with present-day values. Therefore the evolutionary histories of life and of O2-levels are likely intricately intertwined. The obvious biological proxy for inferring the impact of changing O2-levels on life is the evolutionary history …
Cd21 And Cd24 Co-Expression: A Translational Model Between Mouse And Human,
2014
Loma Linda University
Cd21 And Cd24 Co-Expression: A Translational Model Between Mouse And Human, Abigail Benitez
Loma Linda University Electronic Theses, Dissertations & Projects
Systemic Lupus Erythematosus and Rheumatoid Arthritis are B cell-mediated autoimmune diseases that afflict millions of people worldwide. B cell-targeted therapies for these diseases result in variable clinical outcomes. Thus, a need exists to better understand the dynamics of human B cell production and function. The mouse model has provided a foundation for understanding the mechanisms involved in human B cell development and autoimmune disease. However, differences in mouse and human B cells are not fully understood. Our work shows that the co-expression of CD21 and CD24, determined by 7-color flow cytometry, can be used to demarcate developmental subsets of B …
Computational Analysis Of Gene Expression And Connectivity Patterns In The Convoluted Structures Of Mouse Cerebellum,
2014
Old Dominion University
Computational Analysis Of Gene Expression And Connectivity Patterns In The Convoluted Structures Of Mouse Cerebellum, Tao Zeng
Computer Science Theses & Dissertations
One significant difference between evolved mammalian brains and other species is that mammalian brains exhibit increasingly convoluted structures in the cerebral cortex. Groove and ridge shaped structures named gyri and sulci expand surface area of cerebral cortex, making more functions possible. Prior studies using neuroimaging techniques such as dMRI and DTI have revealed that neural fibers are heavily connected to gyri comparing to those connected to sulci, such macro-scale experiments indicates that gyri are involved in large scale information processing while sulci process information locally. However, molecular and cellar level evidences, namely, gene expression pattern and its resulting neuronal connectivity …
Structural Features Of The Pseudomonas Fluorescens Biofilm Adhesin Lapa Required For Lapg-Dependent Cleavage, Biofilm Formation, And Cell Surface Localization,
2014
Dartmouth College
Structural Features Of The Pseudomonas Fluorescens Biofilm Adhesin Lapa Required For Lapg-Dependent Cleavage, Biofilm Formation, And Cell Surface Localization, Chelsea D. Boyd, T. Jarrod Smith, Sofiane El-Kirat-Chatel, Peter D. Newell, Yves F. Dufrêne, George A. O'Toole
Dartmouth Scholarship
The localization of the LapA protein to the cell surface is a key step required by Pseudomonas fluorescens Pf0-1 to irreversibly attach to a surface and form a biofilm. LapA is a member of a diverse family of predicted bacterial adhesins, and although lacking a high degree of sequence similarity, family members do share common predicted domains. Here, using mutational analysis, we determine the significance of each domain feature of LapA in relation to its export and localization to the cell surface and function in biofilm formation. Our previous work showed that the N terminus of LapA is required for …
Novel Telomere-Anchored Pcr Approach For Studying Sexual Stage Telomeres In Aspergillus Nidulans,
2014
Lake Forest College
Novel Telomere-Anchored Pcr Approach For Studying Sexual Stage Telomeres In Aspergillus Nidulans, Nengding Wang, Saajidha Rizvydeen, Mithaq Vahedi, Daysi M. Vargas Gonzalez, Amanda L. Allred, Dustin Wayne Perry, Peter M. Mirabito, Karen E. Kirk
Biology Faculty Publications
Telomere length varies between germline and somatic cells of the same organism, leading to the hypothesis that telomeres are lengthened during meiosis. However, little is known about the meiotic telomere length in many organisms. In the filamentous fungus Aspergillus nidulans, the telomere lengths in hyphae and asexual spores are invariant. No study using existing techniques has determined the telomere length of the sexual ascospores due to the relatively low abundance of pure meiotic cells in A. nidulans and the small quantity of DNA present. To address this, we developed a simple and sensitive PCR strategy to measure the telomere length …
Genome Sequence And Phenotypic Characterization Of Caulobacter Segnis,
2014
University of South Carolina-Columbia
Genome Sequence And Phenotypic Characterization Of Caulobacter Segnis, Sagar Patel
Senior Theses
Caulobacter segnis is a unique species of Caulobacter in that it is slow growing, found in soil samples, and has other phenotypic differences from the freshwater Caulobacter that it is most closely related to. Initially deemed Mycoplana segnis, it was reclassified after a 16s rRNA analysis and found to be most closely related to the Caulobacter NA1000 branch. Because the annotated sequence available in GenBank contained a large number of pseudogenes (126), we compared the original sequencing data to the GenBank sequence and determined that many of the pseudogenes were due to sequence errors in the Genbank sequence. Consequently, …
