Thalamocortical Processing Of Temporal Cues In Sounds, 2018 University of Connecticut
Thalamocortical Processing Of Temporal Cues In Sounds, Kasey Smith
Honors Scholar Theses
The ability of the brain to extract meaningful information from complex sounds is what allows mammals to understand species-specific communication as well as important environmental cues such as the sound of water or of potential predators or prey. The auditory cortex of humans and other mammals contains multiple cortical regions that unique sensitivities to both spectral and temporal sound cues. This discourse will explore three main factors proposed to determine these distinct processing capabilities in regard to temporal sound cues; the distribution of glutamate transporters in the thalamus, the architecture of afferent pathways between the thalamus and auditory cortex, and ...
Genome-Wide Association Study Of Offspring Birth Weight In 86 577 Women Identifies Five Novel Loci And Highlights Maternal Genetic Effects That Are Independent Of Fetal Genetics, 2018 University of Iowa
Genome-Wide Association Study Of Offspring Birth Weight In 86 577 Women Identifies Five Novel Loci And Highlights Maternal Genetic Effects That Are Independent Of Fetal Genetics, Robin N. Beaumont, Nicole M. Warrington, Alana Cavadino, Jessica Tyrrell, Michael Nodzenski, Momoko Horikoshi, Frank Geller, Ronny Myhre, Rebecca C. Richmond, Lavinia Paternoster, Jonathan P. Bradfield, Eskil Kreiner-Møller, Ville Huikari, Sarah Metrustry, Kathryn L. Lunetta, Jodie N. Painter, Jouke-Jan Hottenga, Catherine Allard, Sheila J. Barton, Ana Espinosa, Julie A. Marsh, Catherine Potter, Ge Zhang, Wei Ang, Diane J. Berry, Luigi Bouchard, Shikta Das, Hakon Hakonarson, Jani Heikkinen, Øyvind Helgeland, Berthold Hocher, Albert Hofman, Hazel M. Inskip, Samuel E. Jones, Manolis Kogevinas, Penelope A. Lind, Letizia Marullo, Sarah E. Medland, Anna Murray, Jeffrey C. Murray, Pål R. Njølstad, Ellen A. Nohr, Christoph Reichetzeder, Susan M. Ring, Katherine S. Ruth, Loreto Santa-Marina, Denise M. Scholtens, Sylvain Sebert, Verena Sengpiel, Marcus A. Tuke, Marc Vaudel, Michael N. Weedon, Gonneke Willemsen, Andrew R. Wood, Hanieh Yaghootkar, Louis J. Muglia, Meike Bartels, Caroline L. Relton, Craig E. Pennell, Leda Chatzi, Xavier Estivill, John W. Holloway, Dorret I. Boomsma, Grant W. Montgomery, Joanne M. Murabito, Tim D. Spector, Christine Power, Marjo-Ritta Järvelin, Hans Bisgaard, Struan F A Grant, Thorkild I A Sørensen, Vincent W. Jaddoe, Bo Jacobsson, Mads Melbye, Mark I. Mccarthy, Andrew T. Hattersley, M Geoffery Hayes, Timothy M. Frayling, Marie-France Hivert, Janine F. Felix, Elina Hyppönen, William L. Lowe, David M. Evans, Debbie A. Lawlor, Bjarke Feenstra, Rachel M. Freathy
Stead Family Department of Pediatrics Publications
Genome-wide association studies of birth weight have focused on fetal genetics, whereas relatively little is known about the role of maternal genetic variation. We aimed to identify maternal genetic variants associated with birth weight that could highlight potentially relevant maternal determinants of fetal growth. We meta-analysed data on up to 8.7 million SNPs in up to 86 577 women of European descent from the Early Growth Genetics (EGG) Consortium and the UK Biobank. We used structural equation modelling (SEM) and analyses of mother-child pairs to quantify the separate maternal and fetal genetic effects. Maternal SNPs at 10 loci (MTNR1B ...
A Plasma Telomeric Cell-Free Dna Level In Unaffected Women With Brca1 Or/And Brca2 Mutations: A Pilot Study, Shatovisha Dey, Natascia Marino, Kanokwan Bishop, Paige N. Dahlgren, Aditi Shendre, Anna Maria Storniolo, Chunyan He, Hiromi Tanaka
Internal Medicine Faculty Publications
Plasma cell-free DNA (cfDNA) is a small DNA fragment circulating in the bloodstream originating from both non-tumor- and tumor-derived cells. A previous study showed that a plasma telomeric cfDNA level decreases in sporadic breast cancer patients compared to controls. Tumor suppressor gene products including BRCA1 and BRCA2 (BRCA1&2) play an important role in telomere maintenance. In this study, we hypothesized that the plasma telomeric cfDNA level is associated with the mutation status of BRCA1&2 genes. To test this hypothesis, we performed plasma telomeric cfDNA quantitative PCR (qPCR)-based assays to compare 28 women carriers of the BRCA1&2 ...
Evolution Of Bordetella Pertussis Genome May Play A Role In The Increased Rate Of Whooping Cough Cases In The United States, 2018 James Madison University
Evolution Of Bordetella Pertussis Genome May Play A Role In The Increased Rate Of Whooping Cough Cases In The United States, Kevin Loftus
Senior Honors Projects, 2010-current
Bordetella pertussis is the bacterium responsible for pertussis, a disease commonly referred to as whooping cough. Recently, pertussis has made a resurgence in the U.S. despite high-vaccination coverage. Possible causes of the increased number of pertussis cases include genetic evolution of B. pertussis, increased awareness of the disease, better laboratory diagnostics, and the switch from a whole-cellular (wP) vaccine to an acellular vaccine (aP) in the 1990s. Fortunately, just as B. pertussis is evolving, so is the arsenal of technologies used to understand and combat this pathogenic bacterium. Whole genome sequencing is one technology that helps researchers better understand ...
Foki Vitamin D Receptor Gene Polymorphisms And Metabolic Health In Pregnant Saudi Women, 2018 University of Massachusetts Amherst
Foki Vitamin D Receptor Gene Polymorphisms And Metabolic Health In Pregnant Saudi Women, Maysa Alzaim
Lifestyles have been dynamically changing in the past few years in Saudi Arabia, and the prevalence of non-communicable diseases (NCDs), such as obesity, diabetes, hypertension, high cholesterol, and other cardiovascular diseases (CVD), is notably increasing. In fact, NCDs are affecting a growing number of people in SA, especially women of childbearing age. Vitamin D deficiency has also become pandemic and a major public health concern among the Saudi population despite the abundance of sunlight. The most vulnerable groups are pregnant women and their newborns. Previous studies have correlated low vitamin D status with a higher risk of adverse short- and ...
Validation Of Minimally-Invasive Sample Collection Methods For Measurement Of Telomere Length, 2017 University of Denver
Validation Of Minimally-Invasive Sample Collection Methods For Measurement Of Telomere Length, Stephanie A. Stout, Jue Lin, Natalie Hernandez, Elyssia Poggi Davis, Judith E. Carroll, Laura M. Glynn
Psychology Faculty Articles and Research
Objective: The discovery of telomere length (TL) as a biomarker of cellular aging and correlate of age-related disease has generated a new field of research in the biology of healthy aging. Although the most common method of sample collection for TL is venous blood draw, less-invasive DNA collection methods are becoming more widely used. However, how TL relates across tissues derived from these sample collection methods is poorly understood. The current study is the first to characterize the associations in TL across three sample collection methods: venous whole blood, finger prick dried blood spot and saliva.
Methods: TL was measured ...
Genome-Wide Top2a Dna Cleavage Is Biased Toward Translocated And Highly Transcribed Loci, 2017 University of Pennsylvania
Genome-Wide Top2a Dna Cleavage Is Biased Toward Translocated And Highly Transcribed Loci, Xiang Yu, James W. Davenport, Karen A. Urtishak, Marie L. Carillo, Sager J. Gosai, Christos P. Kolaris, Jo Ann W. Byl, Eric F. Rappaport, Neil Osheroff, Brian D. Gregory, Carolyn A. Felix
Departmental Papers (Biology)
Type II topoisomerases orchestrate proper DNA topology, and they are the targets of anti-cancer drugs that cause treatment-related leukemias with balanced translocations. Here, we develop a high-throughput sequencing technology to define TOP2 cleavage sites at single-base precision, and use the technology to characterize TOP2A cleavage genome-wide in the human K562 leukemia cell line. We find that TOP2A cleavage has functionally conserved local sequence preferences, occurs in cleavage cluster regions (CCRs), and is enriched in introns and lincRNA loci. TOP2A CCRs are biased toward the distal regions of gene bodies, and TOP2 poisons cause a proximal shift in their distribution. We ...
Intratracheal Instillation Of Cerium Oxide Nanoparticles Induces Hepatic Toxicity In Male Sprague-Dawley Rats, Siva Krishna Nalabotu, Madhukar Babu Kolli, William E. Triest, Jane Y. Ma, Nandini Dpk Manne, Anjaiah Katta, Hari S. Addagarla, Kevin M. Rice, Eric R. Blough
Background: Cerium oxide (CeO2) nanoparticles have been posited to have both beneficial and toxic effects on biological systems. Herein, we examine if a single intratracheal instillation of CeO2 nanoparticles is associated with systemic toxicity in male Sprague-Dawley rats. Methods and results: Compared with control animals, CeO2 nanoparticle exposure was associated with increased liver ceria levels, elevations in serum alanine transaminase levels, reduced albumin levels, a diminished sodium-potassium ratio, and decreased serum triglyceride levels (P < 0.05). Consistent with these data, rats exposed to CeO2nanoparticles also exhibited reductions in liver weight (P < 0.05) and dose-dependent hydropic degeneration, hepatocyte enlargement, sinusoidal ...
Mitochondrial Dna Heteroplasmy In Cardiac Tissue From Individuals With And Without Coronary Artery Disease, 2017 Harrisburg University of Science and Technology
Mitochondrial Dna Heteroplasmy In Cardiac Tissue From Individuals With And Without Coronary Artery Disease, Erik Hefti, Javier G. Blanco
Harrisburg University Faculty Works
The cellular environment associated with coronary artery disease (CAD) can lead to mitochondrial DNA (mtDNA) damage. Mitochondrial variants in some copies of mtDNA (heteroplasmy) and mtDNA content are potential genetic biomarkers for CAD-associated disease states. Massively parallel sequencing and qRT-PCR techniques were used to measure heteroplasmic variants and mtDNA content in heart samples from donors with (n = 8) and without (n = 7) documented CAD. Both groups showed increased numbers of heteroplasmic mtDNA variants in the control region (CR) (p < .0010, ANOVA). The donors with CAD displayed a 41.07% increase in heteroplasmic mtDNA variant number in the CR (p = .043), an 87.50% increase in the number of heteroplasmic mtDNA deletions (p = .12), and a 48.76% increase in ... .0010,>
Approaches To Mitochondrial Genome Sequencing Using The Oxford Nanopore Minion Device, 2017 University of North Texas Health Science Center at Fort Worth
Approaches To Mitochondrial Genome Sequencing Using The Oxford Nanopore Minion Device, Kelcie C. Thorson
Theses and Dissertations
Current DNA sequencing methods rely on polymerase chain reaction (PCR) to create sufficient copies of targeted DNA fragments to serve as a library. PCR and subsequent clean-up steps add considerable time and cost to the process and provide opportunity for introduction of amplification errors or contamination. The aim of this study was to develop a reliable method for mitochondrial genome sequencing sans PCR using the Oxford Nanopore MinION. Our hypothesis was that results generated from native DNA sequencing would be concordant to sequencing results generated from PCR-enriched libraries. Error-rates of 1.47% (enriched) and 1.26% (native) were observed when ...
Adaptation Of The Genetic Risk Prediction Model Brcapro For Primary Care Settings, 2017 University of North Texas Health Science Center at Fort Worth
Adaptation Of The Genetic Risk Prediction Model Brcapro For Primary Care Settings, Philamer M. Atienza
Theses and Dissertations
Identifying women at high risks of carrying the breast cancer susceptibility genes is crucial for providing timely surveillance and necessary health management interventions. BRCAPRO is one of the most widely used statistical models for breast cancer risk prediction in genetic counseling. It provides carrier probabilities of BRCA1/2 mutations and calculates the risks of developing breast and ovarian cancers. This calculation requires extensive personal and family history information, which makes it difficult to use in primary care where a wider population could be reached. Thus, we developed a two-stage approach for the genetic risk prediction of BRCA1/2 mutation. In ...
Evidence Of Strain Structure In Plasmodium Falciparum Var Gene Repertoires In Children From Gabon, West Africa, 2017 New York Medical College
Evidence Of Strain Structure In Plasmodium Falciparum Var Gene Repertoires In Children From Gabon, West Africa, K Day, Y Artzy-Randrup, K Tiedje, V Rougeron, Donald S. Chen, T Rask, M Rorick, F Migot-Nabias, P Deloron, A Luty, M Pascual
NYMC Faculty Publications
Existing theory on competition for hosts between pathogen strains has proposed that immune selection can lead to the maintenance of strain structure consisting of discrete, weakly overlapping antigenic repertoires. This prediction of strain theory has conceptual overlap with fundamental ideas in ecology on niche partitioning and limiting similarity between coexisting species in an ecosystem, which oppose the hypothesis of neutral coexistence. For Plasmodium falciparum, strain theory has been specifically proposed in relation to the major surface antigen of the blood stage, known as PfEMP1 and encoded by the multicopy multigene family known as the var genes. Deep sampling of the ...
P33. Design And Evaluation Of An Escherichia Coli Biomarker For Indication Of Ph, 2017 Western University
P33. Design And Evaluation Of An Escherichia Coli Biomarker For Indication Of Ph, Kevin X. Zhou, Luana Langlois, Ashmita Singh, John Prince
Western Research Forum
Measuring pH is one of the most commonly used techniques in both the laboratory as well as the field due to its importance in a multitude of biochemical processes. Traditional methods of measuring pH may be highly developed in accuracy and precision but often involve disruption of the environment. Biological markers offer an alternative that allows for long-term pH monitoring. This innovative approach allows for vast applications such as in the manufacturing, food processing and research industries. Under moderate acidic conditions, the asr (acid shock RNA) gene is highly inducible and has been demonstrated to be crucial for growth at ...
The Dynamic Nature Of Chromatin, 2017 University of Kentucky
The Dynamic Nature Of Chromatin, Caitlyn M. Riedmann
Theses and Dissertations--Molecular and Cellular Biochemistry
Eukaryotic organisms contain their entire genome in the nucleus of their cells. In order to fit within the nucleus, genomic DNA wraps into nucleosomes, the basic, repeating unit of chromatin. Nucleosomes wrap around each other to form higher order chromatin structures. Here we study many factors that affect, or are effected by, chromatin structure including: (1) how low-dose inorganic arsenic (iAs) changes chromatin structures and their relation to global transcription and splicing patterns, and (2) how chromatin architectural proteins (CAPs) bind to and change nucleosome dynamics and DNA target site accessibility.
Despite iAs’s non-mutagenic nature, chronic exposure to low ...
A Study Of Subthreshold Hallucinatory Experiences And Their Relationship To Genetic Liability For Schizophrenia, 2017 University of Colorado Boulder
A Study Of Subthreshold Hallucinatory Experiences And Their Relationship To Genetic Liability For Schizophrenia, Hannah Young
Undergraduate Honors Theses
One of the hallmarks of schizophrenia is the presence of psychosis. However, subthreshold psychotic symptoms characterized by attenuated delusions and hallucinations also occur in healthy individuals from the general population. A body of evidence suggests that this phenomenon represents a continuum of schizophrenia, with severe and attenuated symptoms sharing a common genetic etiology. Hallucinations are one subthreshold psychotic symptom in which a clear continuum has been observed. The aim of this study is to assess if subthreshold hallucinatory experiences and schizophrenia share genetic liability.
3,028 participants were administered the Launay-Slade Hallucination Scale (LSHS), which measures a predisposition ...
Employing The Enzyme Cofactor Function Of Ascorbic Acid To Affect Oncogenic Pathways In Human Melanoma: Modulating Hypoxia Inducible Factor-1Α And Dna Demethylation To Reduce Malignant Potential, 2017 Marshall University
Employing The Enzyme Cofactor Function Of Ascorbic Acid To Affect Oncogenic Pathways In Human Melanoma: Modulating Hypoxia Inducible Factor-1Α And Dna Demethylation To Reduce Malignant Potential, Adam Patrick Fischer
Theses, Dissertations and Capstones
Dioxygenase enzymes such as the HIF hydroxylases (PHD1-3, FIH) and the Ten-eleven translocation (TET1-3) enzymes regulate the activity of the hypoxia inducible factor-1a (HIF1a) transcription factor and the DNA methylation status of cells, respectively. Aberrant accumulation and activation of HIF-1a can allow malignant cells to acquire attributes that promote progression, chemotherapy resistance, and survival, while aberrant hypermethylation of gene promoters can silence the expression of tumor suppressor genes essential to preventing tumorigenesis. Inadequate levels of intracellular ascorbic acid (AA), a necessary cofactor for optimal dioxygenase enzyme function, could potentiate these tumorigenic conditions. In fact, plasma levels of ...
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 ...
A Tale Of Two Species: Evolvability, Genomic Context, And Pathogen Forecasting, 2016 University of New England
A Tale Of Two Species: Evolvability, Genomic Context, And Pathogen Forecasting, Meghan May
Biomedical Sciences Faculty Presentations
Dr. Meghan May gives an overview presentation of her research on evolution of virulence and pathogen prediction. The focus of the presentation is a group of organisms called mycoplasmas, and covered subjects include: Mycoplasma synoviae, Mycoplasma gallisepticum, genomic context, predictive modeling, sequence evolution, and genome reduction.
High-Throughput Allele-Specific Expression Across 250 Environmental Conditions, 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, 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 ...