Open Access. Powered by Scholars. Published by Universities.®

Genetic Structures Commons

Open Access. Powered by Scholars. Published by Universities.®

142 Full-Text Articles 624 Authors 25,123 Downloads 47 Institutions

All Articles in Genetic Structures

Faceted Search

142 full-text articles. Page 3 of 6.

Multipoint Genome-Wide Linkage Scan For Nonword Repetition In A Multigenerational Family Further Supports Chromosome 13q As A Locus For Verbal Trait Disorders, D. T. Truong, L. D. Shriberg, S. D. Smith, K. L. Chapman, A. R. Scheer-Cohen, M. M.C. DeMille, A. K. Adams, Alejandro Q. Nato Jr., E. M. Wijsman, J. D. Eicher, J. R. Gruen 2016 Marshall University

Multipoint Genome-Wide Linkage Scan For Nonword Repetition In A Multigenerational Family Further Supports Chromosome 13q As A Locus For Verbal Trait Disorders, D. T. Truong, L. D. Shriberg, S. D. Smith, K. L. Chapman, A. R. Scheer-Cohen, M. M.C. Demille, A. K. Adams, Alejandro Q. Nato Jr., E. M. Wijsman, J. D. Eicher, J. R. Gruen

Biochemistry and Microbiology

Verbal trait disorders encompass a wide range of conditions and are marked by deficits in five domains that impair a person’s ability to communicate: speech, language, reading, spelling, and writing. Nonword repetition is a robust endophenotype for verbal trait disorders that is sensitive to cognitive processes critical to verbal development, including auditory processing, phonological working memory, and motor planning and programming. In the present study, we present a six-generation extended pedigree with a history of verbal trait disorders. Using genome-wide multipoint variance component linkage analysis of nonword repetition, we identified a region spanning chromosome 13q14–q21 with LOD = 4 ...


High-Throughput Allele-Specific Expression Across 250 Environmental Conditions, Gregory A. Moyerbrailean, Allison L. Richards, Daniel Kurtz, Cynthia A. Kalita, Gordon O. Davis, Chris T. Harvey, Adnan Alazizi, Donovan Watza, Yoram Sorokin, Nancy J. Hauff, Xiang Zhou, Xiaoquan Wen, Roger Pique-Regi, Francesca Luca 2016 Wayne State Center for Molecular Medicine and Genetics, Wayne State University

High-Throughput Allele-Specific Expression Across 250 Environmental Conditions, Gregory A. Moyerbrailean, Allison L. Richards, Daniel Kurtz, Cynthia A. Kalita, Gordon O. Davis, Chris T. Harvey, Adnan Alazizi, Donovan Watza, Yoram Sorokin, Nancy J. Hauff, Xiang Zhou, Xiaoquan Wen, Roger Pique-Regi, Francesca Luca

Center for Molecular Medicine and Genetics

Gene-by-environment (GxE) interactions determine common disease risk factors and biomedically relevant complex traits. However, quantifying how the environment modulates genetic effects on human quantitative phenotypes presents unique challenges. Environmental covariates are complex and difficult to measure and control at the organismal level, as found in GWAS and epidemiological studies. An alternative approach focuses on the cellular environment using in vitro treatments as a proxy for the organismal environment. These cellular environments simplify the organism-level environmental exposures to provide a tractable influence on subcellular phenotypes, such as gene expression. Expression quantitative trait loci (eQTL) mapping studies identified GxE interactions in response ...


Comparing Performance Of Non-Tree-Based And Tree-Based Association Mapping Methods, Katherine L. Thompson, David W. Fardo 2016 University of Kentucky

Comparing Performance Of Non-Tree-Based And Tree-Based Association Mapping Methods, Katherine L. Thompson, David W. Fardo

Statistics Faculty Publications

A central goal in the biomedical and biological sciences is to link variation in quantitative traits to locations along the genome (single nucleotide polymorphisms). Sequencing technology has rapidly advanced in recent decades, along with the statistical methodology to analyze genetic data. Two classes of association mapping methods exist: those that account for the evolutionary relatedness among individuals, and those that ignore the evolutionary relationships among individuals. While the former methods more fully use implicit information in the data, the latter methods are more flexible in the types of data they can handle. This study presents a comparison of the 2 ...


The Long Non-Coding Rna Malat1 Regulates Inflammatory Cytokine Production In Chronic Diabetic Complications, Andrew D. Gordon 2016 The University of Western Ontario

The Long Non-Coding Rna Malat1 Regulates Inflammatory Cytokine Production In Chronic Diabetic Complications, Andrew D. Gordon

Electronic Thesis and Dissertation Repository

We examined the role of MALAT1, a highly conserved nuclear lncRNA, in chronic diabetic complications affecting the heart and kidneys, specifically with respect to inflammatory cytokine production. Endothelial cells, exposed to various glucose levels, and MALAT1 knockout mice and controls, with or without streptozotocin-induced diabetes were examined. Endothelial cells cultured with high glucose, and renal and cardiac tissue from diabetic mice showed increased inflammatory cytokine (eg. IL-6, IL1β, TNFα) production along with transient MALAT1 upregulation. This was confirmed by both transcript and protein analyses, and such changes were prevented in the MALAT1 knockout diabetic animals. In the malat1 knockout animals ...


Cellular Pathways In The Repair And Tolerance Of Formaldehyde-Induced Dna Damage, Eleonora Juarez 2016 Oregon Health & Science University

Cellular Pathways In The Repair And Tolerance Of Formaldehyde-Induced Dna Damage, Eleonora Juarez

Scholar Archive

No abstract provided.


Analyzing Mutations Of Spt7 Protein That Disrupt Interaction With Sf3b Subunits, Arryn T. Harris, Peyton J. Spreacker, Rachel Stegeman, Vikki M. Weake, Edwin C. Acosta 2016 Purdue University

Analyzing Mutations Of Spt7 Protein That Disrupt Interaction With Sf3b Subunits, Arryn T. Harris, Peyton J. Spreacker, Rachel Stegeman, Vikki M. Weake, Edwin C. Acosta

The Summer Undergraduate Research Fellowship (SURF) Symposium

Proper transcription, the process of converting DNA to RNA, is crucial for the health and viability of an organism. This process is regulated by many proteins, such as co-transcriptional activators; one being the protein complex known as Spt-Ada-Gcn5-acetyltransferase, or SAGA. While much is known about the roles of SAGA in cell processes, how SAGA’s subunits promote functionality is still unknown. The focus of this study is to analyze the purpose of SAGA’s SF3B subunits. These subunits are also found in the spliceosome, the compound responsible for generating mature RNA. SAGA has no known functions relating to this process ...


Genetic Candidate Variants In Two Multigenerational Families With Childhood Apraxia Of Speech, Peter Beate, Ellen M. Wijsman, Alejandro Q. Nato Jr., University of Washington Center for Mendelian Genomics, Mark M. Matsushita, Kathy L. Chapman, Ian B. Stanaway, John Wolff, Kaori Oda, Virginia B. Gabo, Wendy H. Raskind 2016 Marshall University

Genetic Candidate Variants In Two Multigenerational Families With Childhood Apraxia Of Speech, Peter Beate, Ellen M. Wijsman, Alejandro Q. Nato Jr., University Of Washington Center For Mendelian Genomics, Mark M. Matsushita, Kathy L. Chapman, Ian B. Stanaway, John Wolff, Kaori Oda, Virginia B. Gabo, Wendy H. Raskind

Biochemistry and Microbiology

Childhood apraxia of speech (CAS) is a severe and socially debilitating form of speech sound disorder with suspected genetic involvement, but the genetic etiology is not yet well understood. Very few known or putative causal genes have been identified to date, e.g., FOXP2 and BCL11A. Building a knowledge base of the genetic etiology of CAS will make it possible to identify infants at genetic risk and motivate the development of effective very early intervention programs. We investigated the genetic etiology of CAS in two large multigenerational families with familial CAS. Complementary genomic methods included Markov chain Monte Carlo linkage ...


A Myriad Of Reasons: Incentives For Innovation In Genetic Research And Diagnostics Post-Myriad, Zachary King 2016 North Carolina Central University School of Law

A Myriad Of Reasons: Incentives For Innovation In Genetic Research And Diagnostics Post-Myriad, Zachary King

North Carolina Central University Science & Intellectual Property Law Review

No abstract provided.


Identification Of Potential Drug Targets In Cancer Signaling Pathways Using Stochastic Logical Models, Peican Zhu, Hamidreza Montazeri Aliabadi, Hasan Uludag, Jie Han 2016 Northwestern Polytechnical University

Identification Of Potential Drug Targets In Cancer Signaling Pathways Using Stochastic Logical Models, Peican Zhu, Hamidreza Montazeri Aliabadi, Hasan Uludag, Jie Han

Pharmacy Faculty Articles and Research

The investigation of vulnerable components in a signaling pathway can contribute to development of drug therapy addressing aberrations in that pathway. Here, an original signaling pathway is derived from the published literature on breast cancer models. New stochastic logical models are then developed to analyze the vulnerability of the components in multiple signalling sub-pathways involved in this signaling cascade. The computational results are consistent with the experimental results, where the selected proteins were silenced using specific siRNAs and the viability of the cells were analyzed 72 hours after silencing. The genes elF4E and NFkB are found to have nearly no ...


Comparative Genomic Mapping Of Uncharacterized Canine Retinal Ests To Identify Novel Candidate Genes For Hereditary Retinal Disorders, Barbara Zangerl, Jennifer L. Johnson, Jarek Pillardy, Qi Sun, Catherine André, Francis Galibert, Gregory M. Acland, Gustavo D. Aguirre 2016 University of Pennsylvania

Comparative Genomic Mapping Of Uncharacterized Canine Retinal Ests To Identify Novel Candidate Genes For Hereditary Retinal Disorders, Barbara Zangerl, Jennifer L. Johnson, Jarek Pillardy, Qi Sun, Catherine André, Francis Galibert, Gregory M. Acland, Gustavo D. Aguirre

Gustavo D. Aguirre, VMD, PhD

Purpose: To identify the genomic location of previously uncharacterized canine retina-expressed expressed sequence tags (ESTs), and thus identify potential candidate genes for heritable retinal disorders. Methods: A set of over 500 retinal canine ESTs were mapped onto the canine genome using the RHDF5000–2 radiation hybrid (RH) panel, and the resulting map positions were compared to their respective localization in the CanFam2 assembly of the canine genome sequence. Results: Unique map positions could be assigned for 99% of the mapped clones, of which only 29% showed significant homology to known RefSeq sequences. A comparison between RH map and sequence assembly ...


Cloning And Characterization Of Canine Pax6 And Evaluation As A Candidate Gene In A Canine Model Of Aniridia, Linda S. Hunter, Duska J. Sidjanin, Manuel Villagrasa Hijar, Jennifer L. Johnson, Ewen Kirkness, Gregory M. Acland, Gustavo D. Aguirre 2016 University of Pennsylvania

Cloning And Characterization Of Canine Pax6 And Evaluation As A Candidate Gene In A Canine Model Of Aniridia, Linda S. Hunter, Duska J. Sidjanin, Manuel Villagrasa Hijar, Jennifer L. Johnson, Ewen Kirkness, Gregory M. Acland, Gustavo D. Aguirre

Gustavo D. Aguirre, VMD, PhD

Purpose: Mutations in PAX6 cause human aniridia. The small eye (sey) mouse represents an animal model for aniridia. However, no large animal model currently exists. We cloned and characterized canine PAX6, and evaluated PAX6 for causal associations with inherited aniridia in dogs. Methods: Canine PAX6 was cloned from a canine retinal cDNA library using primers designed from human and mouse PAX6 consensus sequences. An RH3000 radiation hybrid panel was used to localize PAX6 within the canine genome. Genomic DNA was extracted from whole blood of dogs with inherited aniridia, and association testing was performed using markers on CFA18. Fourteen PAX6 ...


Estimating Relationships Between Phenotypes And Subjects Drawn From Admixed Families., Elizabeth M. Blue, Lisa A. Brown, Matthew P. Conomos, Jennifer L. Kirk, Alejandro Q. Nato Jr., Alice B. Popejoy, Jesse Raffa, John Ranola, Ellen M. Wijsman, Timothy Thornton 2016 Marshall University

Estimating Relationships Between Phenotypes And Subjects Drawn From Admixed Families., Elizabeth M. Blue, Lisa A. Brown, Matthew P. Conomos, Jennifer L. Kirk, Alejandro Q. Nato Jr., Alice B. Popejoy, Jesse Raffa, John Ranola, Ellen M. Wijsman, Timothy Thornton

Biochemistry and Microbiology

Background: Estimating relationships among subjects in a sample, within family structures or caused by population substructure, is complicated in admixed populations. Inaccurate allele frequencies can bias both kinship estimates and tests for association between subjects and a phenotype. We analyzed the simulated and real family data from Genetic Analysis Workshop 19, and were aware of the simulation model.

Results: We found that kinship estimation is more accurate when marker data include common variants whose frequencies are less variable across populations. Estimates of heritability and association vary with age for longitudinally measured traits. Accounting for local ancestry identified different true associations ...


Identity-By-Descent Estimation With Population- And Pedigree-Based Imputation In Admixed Family Data, Mohamad Saad, Alejandro Q. Nato Jr., Fiona L. Grimson, Steven M. Lewis, Lisa A. Brown, Elizabeth M. Blue, Timothy A. Thornton, Elizabeth A. Thompson, Ellen M. Wijsman 2016 Marshall University

Identity-By-Descent Estimation With Population- And Pedigree-Based Imputation In Admixed Family Data, Mohamad Saad, Alejandro Q. Nato Jr., Fiona L. Grimson, Steven M. Lewis, Lisa A. Brown, Elizabeth M. Blue, Timothy A. Thornton, Elizabeth A. Thompson, Ellen M. Wijsman

Biochemistry and Microbiology

Background: In the past few years, imputation approaches have been mainly used in population-based designs of genome-wide association studies, although both family- and population-based imputation methods have been proposed. With the recent surge of family-based designs, family-based imputation has become more important. Imputation methods for both designs are based on identity-by-descent (IBD) information. Apart from imputation, the use of IBD information is also common for several types of genetic analysis, including pedigree-based linkage analysis.

Methods: We compared the performance of several family- and population-based imputation methods in large pedigrees provided by Genetic Analysis Workshop 19 (GAW19). We also evaluated the ...


Molecular Genetics Of Ms4a6a And Alzheimer's Disease, Ryan Harpole 2016 University of Kentucky

Molecular Genetics Of Ms4a6a And Alzheimer's Disease, Ryan Harpole

Lewis Honors College Capstone Collection

Increased Alzheimer’s disease (AD) risk has previously been associated with a SNP called rs610932 near the gene MS4A6A. The goal of this experiment was to quantify the expression of two MS4A6A isoforms in the brains of AD and non-AD subjects, particularly as a function of rs610932 genotype. According to an article titled “Alzheimer’s Disease Susceptibility Variants in the MS4A6A Gene are Associated with Altered Levels of MS4A6A Expression in Blood”, MS4A6A has four different isoforms that have been reported to be differentially expressed in the blood of AD subjects compared to non-AD subjects (Petroula et al., 2014). After ...


Il-15 Mediates Mitochondrial Activity Through A Ppar𝛿-Dependent-Ppar𝛼-Independent Mechanism In Skeletal Muscle Cells, Shantaé M. Thornton, James E. Krolopp, Marcia J. Abbott 2016 Chapman University

Il-15 Mediates Mitochondrial Activity Through A Ppar𝛿-Dependent-Ppar𝛼-Independent Mechanism In Skeletal Muscle Cells, Shantaé M. Thornton, James E. Krolopp, Marcia J. Abbott

Health Sciences and Kinesiology Faculty Articles

Molecular mediators of metabolic processes, to increase energy expenditure, have become a focus for therapies of obesity. The discovery of cytokines secreted from the skeletal muscle (SKM), termed “myokines,” has garnered attention due to their positive effects on metabolic processes. Interleukin-15 (IL-15) is a myokine that has numerous positive metabolic effects and is linked to the PPAR family of mitochondrial regulators. Here, we aimed to determine the importance of PPAR𝛼 and/or PPAR𝛿 as targets of IL-15 signaling. C2C12 SKM cells were differentiated for 6 days and treated every other day with IL-15 (100 ng/mL), a PPAR𝛼 inhibitor (GW-6471 ...


Bayesian Integration Of Genetics And Epigenetics Detects Causal Regulatory Snps Underlying Expression Variability, Avinash Das, Michael Morley, Christine S. Moravec, W.H.W. Tang, Hakon Hakonarson, MAGNet Consortium, Kenneth B. Margulies, Thomas P. Cappola, Shane T. Jensen, Sridhar Hannenhalli 2015 University of Pennsylvania

Bayesian Integration Of Genetics And Epigenetics Detects Causal Regulatory Snps Underlying Expression Variability, Avinash Das, Michael Morley, Christine S. Moravec, W.H.W. Tang, Hakon Hakonarson, Magnet Consortium, Kenneth B. Margulies, Thomas P. Cappola, Shane T. Jensen, Sridhar Hannenhalli

Statistics Papers

The standard expression quantitative trait loci (eQTL) detects polymorphisms associated with gene expression without revealing causality. We introduce a coupled Bayesian regression approach—eQTeL, which leverages epigenetic data to estimate regulatory and gene interaction potential, and identifies combination of regulatory single-nucleotide polymorphisms (SNPs) that explain the gene expression variance. On human heart data, eQTeL not only explains a significantly greater proportion of expression variance but also predicts gene expression more accurately than other methods. Based on realistic simulated data, we demonstrate that eQTeL accurately detects causal regulatory SNPs, including those with small effect sizes. Using various functional data, we show ...


An Overview Of Leber’S Hereditary Optic Neuropathy, Matthew R. Dalton 2015 Liberty University

An Overview Of Leber’S Hereditary Optic Neuropathy, Matthew R. Dalton

The Kabod

Typically affecting males ranging from 20 to 24 years of age, Leber’s Hereditary Optic Neuropathy (LHON) is a disorder that is characterized by an acute loss of central vision. Although a heritable disease, LHON does not follow the patterns of classical Mendelian genetics. In fact, one of the most striking characteristics of LHON is that the disease is virtually always inherited maternally. Unlike most genetic disorders that result from a mutation in genomic DNA, LHON is caused by a mutation in the genetic information of mitochondria (mtDNA). Currently there is no treatment for LHON. Despite this, pharmaceutical interventions and ...


Gene Expression Profiles Identify Features Common To Lobular And Ductal Premalignant Breast Lesions, Amy L. Roberts, D. Joseph Jerry, Kelly J. Gauger, Sallie S. Schneider, Giovanna M. Crisi, Grace Makari-Judson, Ashraf Khan, Karl Simin 2015 University of Massachusetts Amherst

Gene Expression Profiles Identify Features Common To Lobular And Ductal Premalignant Breast Lesions, Amy L. Roberts, D. Joseph Jerry, Kelly J. Gauger, Sallie S. Schneider, Giovanna M. Crisi, Grace Makari-Judson, Ashraf Khan, Karl Simin

Grace Makari-Judson MD

Premalignant lesions have been identified in both the ductal and lobular units of the breast epithelium. These lesions have a 4-fold increase in risk of progression to invasive breast cancer, but 80% will remain indolent. This may be due, in part, to the uncertainty of diagnoses as inter-observer reproducibility is poor. When treated with prophylactic hormone therapies blocking the estrogen receptor, up to 40% of women still develop tumors. Therefore the challenge is to develop diagnostic tests that identify the subset of high-risk lesions and provide appropriate prophylactic therapies. We undertook genome-wide expression studies to define sets of genes that ...


Exploration Of Putative Mitochondrial Gene Expression In Crithidia Fasciculata As A Model For Pathogenic Trypanosomes Causing Human Disease, Baylye Boxall, Nadjean Sagesse 2015 Georgia State University

Exploration Of Putative Mitochondrial Gene Expression In Crithidia Fasciculata As A Model For Pathogenic Trypanosomes Causing Human Disease, Baylye Boxall, Nadjean Sagesse

Georgia State Undergraduate Research Conference

No abstract provided.


Comparative Transcriptome Analyses Of Pseudomonas Aeruginosa, Deepak Balasubramanian, Kalai Mathee 2015 Florida International University, Department of Biological Sciences

Comparative Transcriptome Analyses Of Pseudomonas Aeruginosa, Deepak Balasubramanian, Kalai Mathee

Kalai Mathee

One of the hallmarks of bacterial survival is their ability to adapt rapidly to changing environmental conditions. Niche adaptation is a response to the signals received that are relayed, often to regulators that modulate gene expression. In the post-genomic era, DNA microarrays are used to study the dynamics of gene expression on a global scale. Numerous studies have used Pseudomonas aeruginosa--a Gram-negative environmental and opportunistic human pathogenic bacterium--as the model organism in whole-genome transcriptome analysis. This paper reviews the transcriptome studies that have led to immense advances in our understanding of the biology of this intractable human pathogen. Comparative ...


Digital Commons powered by bepress