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Seasonal Variation Of Macrolide Resistance Gene Abundances In The South Fork Iowa River Watershed, Elizabeth Luby Rieki, Thomas B. Moorman, Elizabeth L. Douglass, Michelle L. Soupir 2018 Iowa State University

Seasonal Variation Of Macrolide Resistance Gene Abundances In The South Fork Iowa River Watershed, Elizabeth Luby Rieki, Thomas B. Moorman, Elizabeth L. Douglass, Michelle L. Soupir

Agricultural and Biosystems Engineering Publications

The Midwestern United States is dominated by agricultural production with high concentrations of swine, leading to application of swine manure onto lands with artificial subsurface drainage. Previous reports have indicated elevated levels of antibiotic resistance genes (ARGs) in surface water and groundwater around confined animal feeding operations which administer antimicrobials. While previous studies have examined the occurrence of ARGs around confined swine feeding operations, little information is known how their transport from tile-drained fields receiving swine manure application impacts downstream environments. To further our knowledge in this area, water samples were collected from five locations in the agriculturally dominated South ...


Plasma Fibroblast Growth Factor-21 Levels In Patients With Inborn Errors Of Metabolism, Brian Kirmse, Juan Cabrera-Luque, Omar Ayyub, Kristina Cusmano-Ozog, Kimberly A. Chapman, Marshall L. Summar 2017 George Washington University

Plasma Fibroblast Growth Factor-21 Levels In Patients With Inborn Errors Of Metabolism, Brian Kirmse, Juan Cabrera-Luque, Omar Ayyub, Kristina Cusmano-Ozog, Kimberly A. Chapman, Marshall L. Summar

Pediatrics Faculty Publications

Fibroblast growth factor-21 (FGF21) levels are elevated in patients with primary mitochondrial disorders but have not been studied in patients with inborn errors of metabolism (IEM) known to have secondary mitochondrial dysfunction. We measured plasma FGF21 by ELISA in patients with and without IEM. FGF21 levels were higher in patients with IEM compared to without IEM (370 pg/dL vs. 0–65 pg/dL). Further study of FGF21 as a biomarker in IEM is warranted.


Genetic Differentiation In A Sample From Northern Mexico City Detected By Hla System Analysis: Impact In The Study Of Population Immunogenetics, Eva D. Juárez Cortés, Miguel A. Contreras Sieck, Agustín J. Arriaga Perea, Rosa M. Macías Medrano, Anaí Balbuena Jaime, Paola Everardo Martínez, Joaquín Zúñiga, Víctor Acuña Alonzo, Julio Granados, Rodrigo Barquera 2017 Laboratorio de Histocompatibilidad, Banco Central de Sangre, Centro Médico Nacional La Raza, Instituto Mexicano del Seguro Social, Mexico City, Mexico

Genetic Differentiation In A Sample From Northern Mexico City Detected By Hla System Analysis: Impact In The Study Of Population Immunogenetics, Eva D. JuáRez CortéS, Miguel A. Contreras Sieck, AgustíN J. Arriaga Perea, Rosa M. MacíAs Medrano, Anaí Balbuena Jaime, Paola Everardo MartíNez, JoaquíN ZúÑIga, VíCtor AcuñA Alonzo, Julio Granados, Rodrigo Barquera

Human Biology Open Access Pre-Prints

The major histocompatibility complex is directly involved in the immune response and thus the genes coding for its proteins are useful markers for the study of genetic diversity, susceptibility to disease (autoimmunity and infections), transplant medicine, and pharmacogenetics, among others. The polymorphism of the system also allows researchers to use it as a proxy for population genetics analysis, such as genetic admixture and genetic structure. In order to determine the immunogenetic characteristics of a sample from the northern part of Mexico City and to use them to analyze the genetic differentiation from other admixed populations, including those from previous studies ...


Leveraging Multiple Populations Across Time Helps Define Accurate Models Of Human Evolution: A Reanalysis Of The Lactase Persistence Adaptation, Chenling Xu Antelope, Davide Marnetto, Fergal Casey, Emilia Huerta-Sanchez 2017 University of California, Berkeley

Leveraging Multiple Populations Across Time Helps Define Accurate Models Of Human Evolution: A Reanalysis Of The Lactase Persistence Adaptation, Chenling Xu Antelope, Davide Marnetto, Fergal Casey, Emilia Huerta-Sanchez

Human Biology Open Access Pre-Prints

Access to a geographically diverse set of modern human samples from the present time and from ancient remains, combined with archaic hominin samples, provides an unprecedented level of resolution to study both human history and adaptation. The amount and quality of ancient human data continues to improve, and enables tracking the trajectory of genetic variation over time. These data have the potential to help us redefine or generate new hypotheses of how human evolution occurred, and revise previous conjectures. In this review, we argue that leveraging all these data will help us better detail adaptive histories in humans. As a ...


Evolution, Function And Deconstructing Histories: A New Generation Of Anthropological Genetics, Omer Gokcumen 2017 State University of New York at Buffalo

Evolution, Function And Deconstructing Histories: A New Generation Of Anthropological Genetics, Omer Gokcumen

Human Biology Open Access Pre-Prints

Introduction to the Special Issue, mainly based on contributions by the speakers in the 2016 AAAG symposium, “Ancient alleles in modern populations: Ancient structure, introgression, and variation-maintaining adaptive forces.”


Chaco Canyon Dig Unearths Ethical Concerns, Katrina G. Claw, Dorothy Lippert, Jessica Bardill, Anna Cordova, Keolu Fox, Joseph M. Yracheta, Alyssa C. Bader, Deborah A. Bolnick, Ripan S. Malhi, Kimberly TallBear, Nanibaa' A. Garrison 2017 University of Washington

Chaco Canyon Dig Unearths Ethical Concerns, Katrina G. Claw, Dorothy Lippert, Jessica Bardill, Anna Cordova, Keolu Fox, Joseph M. Yracheta, Alyssa C. Bader, Deborah A. Bolnick, Ripan S. Malhi, Kimberly Tallbear, Nanibaa' A. Garrison

Human Biology Open Access Pre-Prints

The field of paleogenomics (the study of ancient genomes) is rapidly advancing with more robust methods of isolating ancient DNA and increasing access to next-generation DNA sequencing technology. As these studies progress, many important ethical issues have emerged that should be considered when ancient Native American remains, whom we refer to as ancestors, are used in research. We highlight a recent article by Kennett et al. (2017), “Archaeogenomic evidence reveals prehistoric matrilineal dynasty,” that brings several ethical issues to light that should be addressed in paleogenomics research (Kennett et al. 2017). The study helps elucidate the matrilineal relationships in ancient ...


Linking Taxonomic Diversity And Trophic Function: A Graph-Based Theoretical Approach, Marcella M. Jurotich, Kaitlyn Dougherty, Barbara Hayford, Sally Clark 2017 Wayne State College

Linking Taxonomic Diversity And Trophic Function: A Graph-Based Theoretical Approach, Marcella M. Jurotich, Kaitlyn Dougherty, Barbara Hayford, Sally Clark

Transactions of the Nebraska Academy of Sciences and Affiliated Societies

The purpose of this study is to develop a novel, visual method in analyzing complex functional trait data in freshwater ecology. We focus on macroinvertebrates in stream ecosystems under a gradient of habitat degradation and employ a combination of taxonomic and functional trait diversity analyses. Then we use graph theory to link changes in functional trait diversity to taxonomic richness and habitat degradation. We test the hypotheses that: 1) taxonomic diversity and trophic functional trait diversity both decrease with increased habitat degradation; 2) loss of taxa leads to a decrease in trophic function as visualized using a bipartite graph; and ...


Reverse-Genetic Analysis Of The Two Biotin-Containing Subunit Genes Of The Heteromeric Acetyl-Coenzyme A Carboxylase In Arabidopsis Indicates A Unidirectional Functional Redundancy, Xu Li, Hilal Ilarslan, Libuse Brachova, Hui-Rong Qian, Ling Li, Ping Che, Eve Syrkin Wurtele, Basil J. Nikolau 2017 Iowa State University

Reverse-Genetic Analysis Of The Two Biotin-Containing Subunit Genes Of The Heteromeric Acetyl-Coenzyme A Carboxylase In Arabidopsis Indicates A Unidirectional Functional Redundancy, Xu Li, Hilal Ilarslan, Libuse Brachova, Hui-Rong Qian, Ling Li, Ping Che, Eve Syrkin Wurtele, Basil J. Nikolau

Eve Wurtele

The heteromeric acetyl-coenzyme A carboxylase catalyzes the first and committed reaction of de novo fatty acid biosynthesis in plastids. This enzyme is composed of four subunits: biotin carboxyl-carrier protein (BCCP), biotin carboxylase, α-carboxyltransferase, and β-carboxyltransferase. With the exception of BCCP, single-copy genes encode these subunits in Arabidopsis (Arabidopsis thaliana). Reverse-genetic approaches were used to individually investigate the physiological significance of the two paralogous BCCP-coding genes, CAC1A (At5g16390, codes for BCCP1) and CAC1B (At5g15530, codes for BCCP2). Transfer DNA insertional alleles that completely eliminate the accumulation of BCCP2 have no perceptible effect on plant growth, development, and fatty acid accumulation. In ...


Genome Wide Co-Expression Among The Starch Debranching Enzyme Genes Atisa1, Atisa2, And Atisa3 In Arabidopsis Thaliana, Ling Li, Hilal Ilarslan, Martha G. James, Alan M. Myers, Eve Syrkin Wurtele 2017 Iowa State University

Genome Wide Co-Expression Among The Starch Debranching Enzyme Genes Atisa1, Atisa2, And Atisa3 In Arabidopsis Thaliana, Ling Li, Hilal Ilarslan, Martha G. James, Alan M. Myers, Eve Syrkin Wurtele

Eve Wurtele

Each of four starch debranching enzymes (DBE) is distinct and highly conserved across the plant kingdom; however, the specific functions of these proteins in carbohydrate metabolism are not well understood. DBEs function in both biosynthesis and degradation of starch, and two have been shown to function as multimers in various quarternary structures that can contain one or more DBE proteins, i.e. ISA1 homomultimers and ISA1/ISA2 heteromultimers. This study characterizes potential functional relationships between the three isoamylase-type DBE proteins (ISA) of Arabidopsis using a comprehensive bioinformatics analysis and promoter fusion approach to determine tissue-, subcellular-, and temporal specificity of ...


Materials And Method For Modifying A Biochemical Component In A Plant, Ling Li, Eve Syrkin Wurtele 2017 Iowa State University

Materials And Method For Modifying A Biochemical Component In A Plant, Ling Li, Eve Syrkin Wurtele

Eve Wurtele

A method of modifying the amount of at least one biochemical component in a plant comprising expressing Qua-Quine Starch (QQS) in the plant, the wild-type of which does not express QQS; a transgenic plant, or part thereof, which comprises and expresses QQS as a transgene and in which the amount of at least one biochemical component is modified; a tissue culture of regenerable cells of the transgenic plant; a vector comprising a nucleotide sequence, which encodes the coding sequence of QQS, operably linked to a non-native promoter, which promotes expression of the nucleotide sequence in a plant, which is other ...


A Pectin Methylesterase Zmpme3 Is Expressed In Gametophyte Factor1-S (Ga1-S) Silks And Maps To That Locus In Maize (Zea Mays L.), Adrienne N. Moran Lauter, Michael G. Muszynski, Ryan D. Huffman, M. Paul Scott 2017 U.S. Department of Agriculture

A Pectin Methylesterase Zmpme3 Is Expressed In Gametophyte Factor1-S (Ga1-S) Silks And Maps To That Locus In Maize (Zea Mays L.), Adrienne N. Moran Lauter, Michael G. Muszynski, Ryan D. Huffman, M. Paul Scott

M. Paul Scott

The ga1 locus of maize confers unilateral cross incompatibility, preventing cross pollination between females carrying the incompatible Ga1-s allele and males not carrying a corresponding compatible allele. To characterize this system at the molecular level, we carried out a transcript profiling experiment in which silks from near isogenic lines carrying the Ga1-sand ga1 alleles were compared. While several differentially expressed genes were identified, only one mapped to the known location of ga1. This gene is a pectin methylesterase (PME), which we designated as ZmPme3, and is present and expressed only in Ga1-s genotypes. While a functional ZmPME3 is ...


Jennifer Maurer Phd Thesis.Pdf, Jennifer Maurer 2017 University of Massachusetts Medical School

Jennifer Maurer Phd Thesis.Pdf, Jennifer Maurer

Jennifer Maurer


Signaling cascades, such as the extracellular signal-regulated kinase (ERK) pathway, play vital roles in early vertebrate development. Signals through these pathways are initiated by a growth factor or hormone, are transduced through a kinase cascade, and result in the expression of specific downstream genes that promote cellular proliferation, growth, or differentiation.Tight regulation of these signals is provided by positive or negative modulators at varying levels in the pathway, and is required for proper development and function. Two members of the dual-specificity phosphatase (Dusp) family, dusp6 and dusp2, are believed to be negative regulators of the ERK pathway and are ...


A Pectin Methylesterase Zmpme3 Is Expressed In Gametophyte Factor1-S (Ga1-S) Silks And Maps To That Locus In Maize (Zea Mays L.), Adrienne N. Moran Lauter, Michael G. Muszynski, Ryan D. Huffman, M. Paul Scott 2017 U.S. Department of Agriculture

A Pectin Methylesterase Zmpme3 Is Expressed In Gametophyte Factor1-S (Ga1-S) Silks And Maps To That Locus In Maize (Zea Mays L.), Adrienne N. Moran Lauter, Michael G. Muszynski, Ryan D. Huffman, M. Paul Scott

Agronomy Publications

The ga1 locus of maize confers unilateral cross incompatibility, preventing cross pollination between females carrying the incompatible Ga1-s allele and males not carrying a corresponding compatible allele. To characterize this system at the molecular level, we carried out a transcript profiling experiment in which silks from near isogenic lines carrying the Ga1-sand ga1 alleles were compared. While several differentially expressed genes were identified, only one mapped to the known location of ga1. This gene is a pectin methylesterase (PME), which we designated as ZmPme3, and is present and expressed only in Ga1-s genotypes. While a functional ZmPME3 is ...


A Systems Level Approach To Temporal Expression Dynamics In Drosophila Reveals Clusters Of Long Term Memory Genes, Julianna Bozler, Balint Z. Kacsoh, Hao Chen, William E. Theurkauf, Zhiping Weng, Giovanni Bosco 2017 Geisel School of Medicine at Dartmouth

A Systems Level Approach To Temporal Expression Dynamics In Drosophila Reveals Clusters Of Long Term Memory Genes, Julianna Bozler, Balint Z. Kacsoh, Hao Chen, William E. Theurkauf, Zhiping Weng, Giovanni Bosco

Program in Bioinformatics and Integrative Biology Publications and Presentations

The ability to integrate experiential information and recall it in the form of memory is observed in a wide range of taxa, and is a hallmark of highly derived nervous systems. Storage of past experiences is critical for adaptive behaviors that anticipate both adverse and positive environmental factors. The process of memory formation and consolidation involve many synchronized biological events including gene transcription, protein modification, and intracellular trafficking: However, many of these molecular mechanisms remain illusive. With Drosophila as a model system we use a nonassociative memory paradigm and a systems level approach to uncover novel transcriptional patterns. RNA sequencing ...


Introgression Makes Waves In Inferred Histories Of Effective Population Size, John Hawks 2017 University of Wisconsin-Madison

Introgression Makes Waves In Inferred Histories Of Effective Population Size, John Hawks

Human Biology Open Access Pre-Prints

Human populations have a complex history of introgression and of changing population size. Human genetic variation has been affected by both these processes, so that inference of past population size depends upon the pattern of gene flow and introgression among past populations. One remarkable aspect of human population history as inferred from genetics is a consistent “wave” of larger effective population size, found in both African and non-African populations, that appears to reflect events prior to the last 100,000 years. Here I carry out a series of simulations to investigate how introgression and gene flow from genetically divergent ancestral ...


Background, Needs And Expectations For Genetic Counseling In Adults With Ehlers-Danlos Syndrome, Pooja Swaroop 2017 Long Island University

Background, Needs And Expectations For Genetic Counseling In Adults With Ehlers-Danlos Syndrome, Pooja Swaroop

Post & Beyond

Ehlers-Danlos Syndrome (EDS) is a heterogeneous group of heritable connective

tissue disorders. Patients with EDS often show a wide range of

clinical manifestations, which most often include joint hypermobility, connective

tissue fragility and skin hyperextensibility. The symptomatology of

individuals with EDS-Hypermobile Type (EDS-HT) is complex and can range

in severity from mild to profound with several studies reporting multisystem

involvement. In addition to the aforementioned symptoms, there

is a significant risk for comorbid psychiatric disorders. Currently, genetics

professionals and genetic counselors act primarily as diagnosticians and

provide tertiary support for the ongoing care, coordination and management

of patients with EDS ...


Prebiotic Rna Network Formation: A Taxonomy Of Molecular Cooperation, Cole Mathis, Sanjay N. Ramprasad, Sara Imari Walker, Niles Lehman 2017 Arizona State University

Prebiotic Rna Network Formation: A Taxonomy Of Molecular Cooperation, Cole Mathis, Sanjay N. Ramprasad, Sara Imari Walker, Niles Lehman

Chemistry Faculty Publications and Presentations

Cooperation is essential for evolution of biological complexity. Recent work has shown game theoretic arguments, commonly used to model biological cooperation, can also illuminate the dynamics of chemical systems. Here we investigate the types of cooperation possible in a real RNA system based on the Azoarcusribozyme, by constructing a taxonomy of possible cooperative groups. We construct a computational model of this system to investigate the features of the real system promoting cooperation. We find triplet interactions among genotypes are intrinsically biased towards cooperation due to the particular distribution of catalytic rate constants measured empirically in the real system. For other ...


A Polyglot Approach To Bioinformatics Data Integration: A Phylogenetic Analysis Of Hiv-1, Steven Reisman, Thomas Hatzopoulos, Konstantin Laufer, George K. Thiruvathukal, Catherine Putonti 2017 Loyola University Chicago

A Polyglot Approach To Bioinformatics Data Integration: A Phylogenetic Analysis Of Hiv-1, Steven Reisman, Thomas Hatzopoulos, Konstantin Laufer, George K. Thiruvathukal, Catherine Putonti

Konstantin Läufer

As sequencing technologies continue to drop in price and increase in throughput, new challenges emerge for the management and accessibility of genomic sequence data. We have developed a pipeline for facilitating the storage, retrieval, and subsequent analysis of molecular data, integrating both sequence and metadata. Taking a polyglot approach involving multiple languages, libraries, and persistence mechanisms, sequence data can be aggregated from publicly available and local repositories. Data are exposed in the form of a RESTful web service, formatted for easy querying, and retrieved for downstream analyses. As a proof of concept, we have developed a resource for annotated HIV-1 ...


A Polyglot Approach To Bioinformatics Data Integration: Phylogenetic Analysis Of Hiv-1, Steven Reisman, Catherine Putonti, George K. Thiruvathukal, Konstantin Läufer 2017 Loyola University Chicago

A Polyglot Approach To Bioinformatics Data Integration: Phylogenetic Analysis Of Hiv-1, Steven Reisman, Catherine Putonti, George K. Thiruvathukal, Konstantin Läufer

Konstantin Läufer

RNA-interference has potential therapeutic use against HIV-1 by targeting highly-functional mRNA sequences that contribute to the virulence of the virus. Empirical work has shown that within cell lines, all of the HIV-1 genes are affected by RNAi-induced gene silencing. While promising, inherent in this treatment is the fact that RNAi sequences must be highly specific. HIV, however, mutates rapidly, leading to the evolution of viral escape mutants. In fact, such strains are under strong selection to include mutations within the targeted region, evading the RNAi therapy and thus increasing the virus’ fitness in the host. Taking a phylogenetic approach, we ...


Genetic Diversity In Hypericum And Aflp Markers For Species-Specific Identification Of H. Perforatum L., Ryan J. Percifield, Jennifer S. Hawkins, Joe-Ann McCoy, Mark P. Widrlechner, Jonathan F. Wendel 2017 Iowa State University

Genetic Diversity In Hypericum And Aflp Markers For Species-Specific Identification Of H. Perforatum L., Ryan J. Percifield, Jennifer S. Hawkins, Joe-Ann Mccoy, Mark P. Widrlechner, Jonathan F. Wendel

Jonathan F. Wendel

One of the top-selling medicinal products worldwide is Hypericum perforatum (St. John's Wort). Despite its cosmopolitan distribution and utilization, little is known regarding the relationship of the bioactive compounds in H. perforatum to the plants from which they are purportedly derived. In this study, amplified fragment length polymorphism (AFLP) analysis of 56 Hypericum accessions, representing 11 species, was conducted to gain a better understanding of diversity within Hypericum species, especially within cultivated accessions of H. perforatum, and to establish a molecular methodology that will provide breeders and regulators with a simple, affordable, and accurate tool with which to identify ...


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