Digital Commons Network^™

A Comprehensive Review Of Duchenne Muscular Dystrophy: Genetics, Clinical Presentation, Diagnosis, And Treatment, Kylie A. Limback, William D. Jacobus, Amber Wiggins-Mcdaniel, Ramon E. Newman, Robert A. White

Faculty Publications

Duchenne Muscular Dystrophy (DMD) is a genetic disorder involving progressive muscle deterioration leading to loss of mobility, cardiomyopathy, and respiratory complications leading to an early death by the fourth decade of life. Males are affected more often as DMD results from a mutation in the dystrophin gene residing on the X chromosome. The DMD genetic mutation results in a complete functional lack of dystrophin, which culminates as an inadequate connection between the intracellular actin filaments and the extracellular skeleton of muscle. Boys affected by DMD clinically present with muscle weakness before age five, are often wheelchair-bound by age 12, and …

Author Correction: Identifying Genetic Factors That Contribute To The Increased Risk Of Congenital Heart Defects In Infants With Down Syndrome, Cristina E. Trevino, Aaron M. Holleman, Holly Corbitt, Cheryl L. Maslen, Tracie C. Rosser, David J. Cutler, H. Richard Johnston, Benjamin L. Rambo-Martin, Jai Oberoi, Kenneth J. Dooley, George T. Capone, Roger H. Reeves, Heather J. Cordell, Bernard D. Keavney, A. J. Agopian, Elizabeth Goldmuntz, Peter J. Gruber, James O'Brien, Douglas Bittel, Lalita Wadhwa, Clifford L. Cua, Ivan P. Moskowitz, Jennifer G. Mulle, Michael P. Epstein, Stephanie L. Sherman, Michael E. Zwick

Faculty Publications

No abstract provided.

Identifying Genetic Factors That Contribute To The Increased Risk Of Congenital Heart Defects In Infants With Down Syndrome, Cristina E. Trevino, Aaron M. Holleman, Holly Corbitt, Cheryl L. Maslen, Tracie C. Rosser, David J. Cutler, H. Richard Johnston, Benjamin L. Rambo-Martin, Jai Oberoi, Kenneth J. Dooley, George T. Capone, Roger H. Reeves, Heather J. Cordell, Bernard D. Keavney, A. J. Agopian, Elizabeth Goldmuntz, Peter J. Gruber, James O'Brien, Douglas Bittel, Lalita Wadhwa, Clifford L. Cua, Ivan P. Moskowitz, Jennifer G. Mulle, Michael P. Epstein, Stephanie L. Sherman, Michael E. Zwick

Faculty Publications

Atrioventricular septal defects (AVSD) are a severe congenital heart defect present in individuals with Down syndrome (DS) at a > 2000-fold increased prevalence compared to the general population. This study aimed to identify risk-associated genes and pathways and to examine a potential polygenic contribution to AVSD in DS. We analyzed a total cohort of 702 individuals with DS with or without AVSD, with genomic data from whole exome sequencing, whole genome sequencing, and/or array-based imputation. We utilized sequence kernel association testing and polygenic risk score (PRS) methods to examine rare and common variants. Our findings suggest that the Notch pathway, particularly …

Impact Of Model Violations On The Inference Of Species Boundaries Under The Multispecies Coalescent, Anthony J. Barley, Jeremy M. Brown, Robert C. Thomson

Faculty Publications

© 2017 The Author(s). The use of genetic data for identifying species-level lineages across the tree of life has received increasing attention in the field of systematics over the past decade. The multispecies coalescent model provides a framework for understanding the process of lineage divergence and has become widely adopted for delimiting species. However, because these studies lack an explicit assessment of model fit, in many cases, the accuracy of the inferred species boundaries are unknown. This is concerning given the large amount of empirical data and theory that highlight the complexity of the speciation process. Here, we seek to …

Developmental Markers Of Genetic Liability To Autism In Parents: A Longitudinal, Multigenerational Study, Molly Losh, Gary E. Martin, Michelle Lee, Jessica Klusek, John Sideris, Sheila Barron, Thomas Wassink

Faculty Publications

Genetic liability to autism spectrum disorder (ASD) can be expressed in unaffected relatives through subclinical, genetically meaningful traits, or endophenotypes. This study aimed to identify developmental endophenotypes in parents of individuals with ASD by examining parents' childhood academic development over the school-age period. A cohort of 139 parents of individuals with ASD were studied, along with their children with ASD and 28 controls. Parents' childhood records in the domains of language, reading, and math were studied from grades K-12. Results indicated that relatively lower performance and slower development of skills (particularly language related skills), and an uneven rate of development …

Backfolding Of Wormlike Chains Confined In Nanochannels, Abhiram Muralidhar, Douglas R. Tree, Kevin D. Dorfman

Faculty Publications

Using pruned-enriched Rosenbluth method (PERM) simulations of a discrete wormlike chain model, we provide compelling evidence in support of Odijk’s prediction of two distinct Odijk regimes for a long wormlike chain confined in a nanochannel. In both cases, the chain of persistence length lp is renormalized into a series of deflection segments of characteristic length D2/3lp1/3, where D is the channel size. In the first (classic) Odijk regime, these deflection segments are linearly ordered. In the second Odijk regime, thin, long wormlike chains can backfold at a length scale quantified by the global persistence length. We …

Genseq: An Updated Nomenclature And Ranking For Genetic Sequences From Type And Non-Type Sources, Prosanta Chakrabarty, Melanie Warren, Lawrence M. Page, Carole C. Baldwin

Faculty Publications

An improved and expanded nomenclature for genetic sequences is introduced that corresponds with a ranking of the reliability of the taxonomic identification of the source specimens. This nomenclature is an advancement of the "Genetypes" naming system, which some have been reluctant to adopt because of the use of the "type" suffix in the terminology. In the new nomenclature, genetic sequences are labeled "genseq," followed by a reliability ranking (e.g., 1 if the sequence is from a primary type), followed by the name of the genes from which the sequences were derived (e.g., genseq-1 16S, COI). The numbered suffix provides an …

Is Dna A Good Model Polymer?, Douglas R. Tree, Abhiram Muralidhar, Patrick S. Doyle, Kevin D. Dorfman

Faculty Publications

The details surrounding the crossover from wormlike-specific to universal polymeric behavior has been the subject of debate and confusion even for the simple case of a dilute, unconfined wormlike chain. We have directly computed the polymer size, form factor, free energy, and Kirkwood diffusivity for unconfined wormlike chains as a function of molecular weight, focusing on persistence lengths and effective widths that represent single-stranded and double-stranded DNA in a high ionic strength buffer. To do so, we use a chain-growth Monte Carlo algorithm, the pruned-enriched Rosenbluth method (PERM), which allows us to estimate equilibrium and near-equilibrium dynamic properties of wormlike …

Beyond Gel Electrophoresis: Microfluidic Separations, Fluorescence Burst Analysis, And Dna Stretching, Kevin D. Dorfman, Scott B. King, Daniel W. Olson, Joel D. P. Thomas, Douglas R. Tree

Faculty Publications

This review addresses methods for obtaining sequence information directly from unamplified genomic length DNA. Our generic starting point is a large piece of DNA that contains many thousands of base pairs (kilobase pairs, kbp) or even millions of base pairs (megabase pairs, Mbp). We would like to determine the genomic distance between two repeats of a given sequence, indicated by the red dots on the coiled DNA molecule in Figure 1. Let us consider the case where these sequences are restriction sites, which can be selectively cut using proteins known as restriction enzymes. For decades, gel electrophoresis served as the …

Incorporating Case Studies Into An Undergraduate Genetics Course, Marlene Murray

Faculty Publications

Genetics is considered one of the most challenging courses in the biology curricula at both the secondary and post secondary levels. Case based teaching has been shown to improve student perception and performance outcomes in both non-science and science courses. Thus in an effort to improve outcomes, case studies were integrated into an undergraduate genetics course as a supplement to lecture and replacement to recitation. Student perception and performance when case studies were used was compared to two previous years before the incorporation of case studies. Student course evaluations, pre and post surveys of student knowledge, and exam scores indicated …

Simulation Of Dna Extension In Nanochannels, Yanwei Wang, Douglas R. Tree, Kevin D. Dorfman

Faculty Publications

We have used a realistic model for double-stranded DNA and Monte Carlo simulations to compute the extension (mean span) of a DNA molecule confined in a nanochannel over the full range of confinement in a high ionic strength buffer. The simulation data for square nanochannels resolve the apparent contradiction between prior simulation studies and the predictions from Flory theory, demonstrating the existence of two transition regimes between weak confinement (the de Gennes regime) and strong confinement (the Odijk regime). The simulation data for rectangular nanochannels support the use of the geometric mean for mapping data obtained in rectangular channels onto …

2c Dna Content Values In Amaranthus (Amaranthaceae) [Abstract], Donald B. Pratt, Shalini N. Jhangiani, Robert J. Wiggers

Faculty Publications

No abstract provided.

Development And Characterization Of Microsatellite Markers For The Grain Amaranths [Abstract], Melanie A. Mallory, Rozaura V. Hall, Andrea R. Mcnabb, Donald B. Pratt, Eric N. Jellen, Peter J. Maughan

Faculty Publications

No abstract provided.

Fpga Acceleration Of Gene Rearrangement Analysis, Jason D. Bakos

Faculty Publications

In this paper we present our work toward FPGA acceleration of phylogenetic reconstruction, a type of analysis that is commonly performed in the fields of systematic biology and comparative genomics. In our initial study, we have targeted a specific application that reconstructs maximum-parsimony (MP) phylogenies for gene-rearrangement data. Like other prevalent applications in computational biology, this application relies on a control-dependent, memory-intensive, and non-arithmetic combinatorial optimization algorithm. To achieve hardware acceleration, we developed an FPGA core design that implements the application's primary bottleneck computation. Because our core is lightweight, we are able to synthesize multiple cores on a single FPGA. …

Fine-Scale Genetic Structure And Social Organization In Female White-Tailed Deer, Christopher E. Comer, John Kilgo, Gino D'Angelo, Travis Glenn, Karl Miller

Faculty Publications

Social behavior of white-tailed deer (Odocoileus virginianus) can have important management implications.

The formation of matrilineal social groups among female deer has been documented and management strategies have been proposed based on this well-developed social structure. Using radiocollared (n = 17) and hunter or vehicle- killed (n = 21) does, we examined spatial and genetic structure in white-tailed deer on a 7,000-ha portion of the

Savannah River Site in the upper Coastal Plain of South Carolina, USA. We used 14 microsatellite DNA loci to calculate pairwise relatedness among individual deer and to assign doe pairs to …

Genetic Enhancement: Plan Now To Act Later, Maxwell J. Mehlman

Faculty Publications

No abstract provided.

Fashionable Genetic Explanations In The Courtroom: Litigating Personal Injuries Based On Genetic Risk, Jennifer Wriggins

Faculty Publications

New developments in molecular genetics hold much promise for society. Gene therapy research is underway with the aim of helping to fight, and perhaps even eliminate some diseases. DNA data can be used as evidence to help free innocent people and put guilty ones in jail. Agricultural biotechnology can make crops and pesticides more productive. And cloning may offer exciting potential. There is little doubt that further· developments in the areas of genetics and biotechnology will change our lives in unanticipated ways.

Despite the potential benefits to society, there exist valid and serious I concerns about the potential for misuse …

Genetic Testing, Genetic Medicine, And Managed Care, Mark A. Rothstein, Sharona Hoffman

Faculty Publications

As modern human genetics moves from the research setting to the clinical setting, it will encounter the managed care system. Issues of cost, access, and quality of care will affect the availability and nature of genetic testing, genetic counseling, and genetic therapies. This articles explores such issues as professional education, coverage of genetic services, privacy and confidentiality, and liability. It concludes with a series of recommendations for the practice of genetic medicine in the age of managed care.

The Law Of Above Averages: Leveling The New Genetic Enhancement Playing Field, Maxwell J. Mehlman

Faculty Publications

In this article, I will explore some of the legal implications of this emerging technology-the technology of genetic enhancement. Specifically, I will discuss how the law might respond to two related consequences: an increase in social inequality, and the

The Human Genome Project And The Courts: Gene Therapy And Beyond, Maxwell J. Mehlman

Faculty Publications

No abstract provided.

How Will We Regulate Genetic Enhancement, Maxwell J. Mehlman

Faculty Publications

Genetic enhancement technologies present difficult and novel regulatory issues, including the problem of measuring and comparing risks and benefits and dealing with the impact of these technologies on social values. This Article describes and evaluates the potential approaches that may be taken to regulate these technologies. The author concludes that a variety of approaches will be necessary, involving self-regulation, government restrictions on access and use, licensing, and a national lottery.