Digital Commons Network^™

Skeletal Muscle Mitochondrial Capacity And Insulin Resistance In Type 2 Diabetes, Sudip Bajpeyi, Magdalena Pasarica, Cedric Moro, Kevin Conley, Sharon Jubrias, Olga Sereda, David H. Burk, Zhengyu Zhang, Alok Gupta, Lise Kjems, Steven R. Smith

Faculty Publications

Objective: The objective of this study was to determine the role of maximum mitochondrial capacity on the variation in insulin sensitivity within a population of patients with type 2 diabetes mellitus (T2DM). Research Design and Methods: Fifty-eight participants enrolled in a cross-sectional design: eight active controls [maximum aerobic capacity (VO2max) . 40 ml/kg . min], 17 healthy sedentary controlswithout a family history (FH-) and seven with a family history (FH+) of diabetes, four obese participants, and 21 patients with T2DM. Mitochondrial capacity was measured noninvasively using 31P magnetic resonance spectroscopy of the vastus lateralis. Maximal ATP synthetic rate (ATPmax) was …

Visual Cues Are Relevant In Behavioral Control Measures For Cosmopolites Sordidus (Coleoptera: Curculionidae), Gadi V.P. Reddy, A. Raman

Faculty Publications

Trap designs for banana root borer, Cosmopolites sordidus (Germar) (Coleoptera: Curculionidae), have been done essentially on the understanding that C. sordidus rely primarily on chemical cues. Our present results indicate that these borers also rely on visual cues. Previous studies have demonstrated that among the eight differently colored traps tested in the field, brown traps were the most effective compared with the performances of yellow, red, gray, blue, black, white, and green traps; mahogany-brown was more effective than other shades of brown. In the current study, efficiency of ground traps with different colors was evaluated in the laboratory for the …

The Role Of Symmetry In The Regulation Of Bacterial Carboxyltransferase, Grover L. Waldrop

Faculty Publications

Carboxyltransferase is one component of the multifunctional enzyme acetyl-CoA carboxylase which catalyzes the first committed step in fatty acid biosynthesis. Carboxyltransferase is an α2β2 heterotetramer and possesses two distinct but integrated functions. One function catalyzes the transfer of carbon dioxide from biotin to acetyl-CoA, whereas the other involves binding to the mRNA encoding both subunits. When carboxyltransferase binds to the mRNA both enzymatic activity and translation of the mRNA are inhibited. However, the substrate acetyl-CoA competes with mRNA for binding. Thus, mRNA binding by carboxyltransferase provides an effective mechanism for regulating enzymatic activity and gene expression. This conceptual review takes …

Direct And Indirect Roles For Values In Science, Kevin Elliott

Faculty Publications

Although many philosophers have employed the distinction between "direct" and "indirect" roles for values in science, I argue that it merits further clarification. The distinction can be formulated in several ways: as a logical point, as a distinction between epistemic attitudes, or as a clarification of different consequences associated with accepting scientific claims. Moreover, it can serve either as part of a normative ideal or as a tool for policing how values influence science. While various formulations of the distinction may (with further clarification) contribute to a normative ideal, they have limited effectiveness for regulating how values influence science.

The Proteogenomic Mapping Tool, William S. Sanders, Nan Wang, Susan M. Bridges, Brandon M. Malone, Yoginder S. Dandass, Fiona M. Mccarthy, Bindu Nanduri, Mark L. Lawrence, Shane C. Burgess

Faculty Publications

Background: High-throughput mass spectrometry (MS) proteomics data is increasingly being used to complement traditional structural genome annotation methods. To keep pace with the high speed of experimental data generation and to aid in structural genome annotation, experimentally observed peptides need to be mapped back to their source genome location quickly and exactly. Previously, the tools to do this have been limited to custom scripts designed by individual research groups to analyze their own data, are generally not widely available, and do not scale well with large eukaryotic genomes.

Results: The Proteogenomic Mapping Tool includes a Java implementation of …

Non-Esterified Fatty Acids Generate Distinct Low-Molecular Weight Amyloid-Β (Aβ42) Oligomers Along Pathway Different From Fibril Formation, Amit Kumar, Rebekah L. Bullard, Pritesh Patel, Lea C. Paslay, Dipti Singh, Ewa A. Bienkiewicz, Sarah E. Morgan, Vijayaraghavan Rangachari

Faculty Publications

Amyloid-beta (A beta) peptide aggregation is known to play a central role in the etiology of Alzheimer's disease (AD). Among various aggregates, low-molecular weight soluble oligomers of A beta are increasingly believed to be the primary neurotoxic agents responsible for memory impairment. Anionic interfaces are known to influence the A beta aggregation process significantly. Here, we report the effects of interfaces formed by medium-chain (C9-C12), saturated non-esterified fatty acids (NEFAs) on A beta 42 aggregation. NEFAs uniquely affected A beta 42 aggregation rates that depended on both the ratio of A beta:NEFA as well the critical micelle concentration (CMC) of …

Perceived Threat Mediates The Relationship Between Psychosis Proneness And Aggressive Behavior, Jennifer Renee Fanning, Mitchell Eric Berman, Richard Mohn, Michael Mccloskey

Faculty Publications

Psychotic symptoms are associated with aggressive tendencies, but this relationship is both complex and imperfect. In contrast to psychotic disorders, little is known about aggressive behavior and sub-clinical psychotic symptoms (e.g., "psychosis proneness"), which are relatively common in the general population. Threat/control-override (TCO), which is the propensity to overestimate the likelihood that an outside agent will (1) inflict harm (threat) or (2) control one's behaviors (control-override), has been associated with aggression in both psychiatric and community samples. The purpose of this study was to determine if psychosis proneness is related to aggression, and if one or both aspects of TCO …

Soil Carbon And Material Fluxes Across The Eroding Alaska Beaufort Sea Coastline, Chien-Lu Ping, Gary J. Michaelson, Laodong Guo, M. Torre Jorgensen, Mikhail Z. Kanevskiy, Yuri L. Shur, Fugen Dou, Jingjing Liang

Faculty Publications

Carbon, nitrogen, and material fluxes were quantified at 48 sampling locations along the 1957 km coastline of the Beaufort Sea, Alaska. Landform characteristics, soil stratigraphy, cryogenic features, and ice contents were determined for each site. Erosion rates for the sites were quantified using satellite images and aerial photos, and the rates averaged across the coastline increased from 0.6 m yr^-1 during circa 1950-1980 to 1.2 m yr^-1 during circa 1980-2000. Soils were highly cryoturbated, and organic carbon (OC) stores ranged from 13 to 162 kg OC m^-2 in banks above sea level and averaged 63 kg OC …

Morphological Convergence During Pregnancy Among Predator And Nonpredator Populations Of The Livebearing Fish Brachyrhaphis Rhabdophora (Teleostei: Poeciliidae), Jeff S. Wesner, Eric J. Billman, Adam Meier, Mark C. Belk

Faculty Publications

Predation can drive morphological divergence in prey populations, although examples of divergent selection are typically limited to nonreproductive individuals. In livebearing females, shape often changes drastically during pregnancy, reducing speed and mobility and enhancing susceptibility to predation. In the present study, we document morphological divergence among populations of nonreproductive female livebearing fish (Brachyrhaphis rhabdophora) in predator and nonpredator environments. We then test the hypothesis that shape differences among nonreproductive females are maintained among reproductive females between predator and nonpredator environments. Nonreproductive females in predator environments had larger caudal regions and more fusiform bodies than females in nonpredator environments; …

Cuban Landscapes: Heritage, Memory, And Place, Mark M. Miller

Faculty Publications

No abstract provided.

Climate-Related Hydrological Regimes And Their Effects On Abundance Of Juvenile Blue Crabs (Callinectes Sapidus) In The Northcentral Gulf Of Mexico, Guillermo Sanchez-Rubio, Harriet M. Perry, Patricia M. Biesiot, Donald R. Johnson, Romuald N. Lipcius

Faculty Publications

The abundance of juvenile blue crabs (Callinectes sapidus) in the northcentral Gulf of Mexico was investigated in response to climate-related hydrological regimes. Two distinct periods of blue crab abundance (1, 1973-94 and 2, 1997-2005) were associated with two opposite climate-related hydrological regimes. Period 1 was characterized by high numbers of crabs, whereas period 2 was characterized by low numbers of crabs. The cold phase of the Atlantic Multidecadal Oscillation (AMO) and high north-south wind momentum were associated with period 1. Hydrological conditions associated with phases of the AMO and North Atlantic Oscillation (NAO) in conjunction with the north-south …

No Place For Children: Addressing Urban Blight And Its Impact On Children Through Child Protection Law, Domestic Relations Law, And "Adult-Only" Residential Zoning, James G. Dwyer

Faculty Publications

No abstract provided.

Heat Expands All Things: The Proliferation Of Greenhouse Gas Regulation Under The Obama Administration, Jonathan H. Adler

Faculty Publications

Although Congress did not put climate change legislation on President Obama’s desk, the Obama Administration still moved ahead with various regulatory measures to control GHG [greenhouse gas] emissions. Using authority under the Clean Air Act and other existing environmental statutes, the Environmental Protection Agency (EPA) and other agencies have been expanding existing regulatory programs to cover GHG emissions and address climate change concerns. Several measures are already in place and others are in the regulatory pipeline, although citizen suit litigation could produce still more.

The extension of federal regulatory authority to control GHG emissions under existing statutory frameworks is a …

Environmental Harms, Use Conflicts, And Neutral Baselines In Environmental Law, Todd S. Aagaard

Faculty Publications

Accounts of environmental law that rely on concepts of environmental harm and environmental protection oversimplify the tremendous variety of uses of environmental resources and the often complex relationships among those uses. Such approaches are analytically unclear and, more importantly, insert hidden normativity into putatively descriptive claims. Instead of thinking about environmental law in terms of preventing environmental harm, environmental problems can be understood more specifically and more meaningfully as disputes over conflicting uses of environmental resources. This Article proposes a use-conflict framework as a means of acquiring a deeper understanding of environmental problems and lawmaking without favoring any particular normative …

Nuclear Versus Mitochondrial Dna: Evidence For Hybridization In Colobine Monkeys, Christian Roos, Dietmar Zinner, Laura S. Kubatko, Christiane Schwarz, Mouyu Yang, Dirk Meyer, Stephen D. Nash, Jinchuan Xing, Mark A. Batzer, Markus Brameier, Fabian H. Leendertz, Thomas Ziegler, Dyah Perwitasari-Farajallah, Tilo Nadler, Lutz Walter, Martin Osterholz

Faculty Publications

Background: Colobine monkeys constitute a diverse group of primates with major radiations in Africa and Asia. However, phylogenetic relationships among genera are under debate, and recent molecular studies with incomplete taxon-sampling revealed discordant gene trees. To solve the evolutionary history of colobine genera and to determine causes for possible gene tree incongruences, we combined presence/absence analysis of mobile elements with autosomal, X chromosomal, Y chromosomal and mitochondrial sequence data from all recognized colobine genera. Results: Gene tree topologies and divergence age estimates derived from different markers were similar, but differed in placing Piliocolobus/Procolobus and langur genera among colobines. Although insufficient …

Electrospinning Fabrication, Structural And Mechanical Characterization Of Rod-Like Virus-Based Composite Nanofibers, Laying Wu, Jianfeng Zang, L. Andrew Lee, Zhongwei Niu, Gary C. Horvatha, Vaughn Braxtona, Arief C. Wibowo, Michael A. Bruckman, Soumitra Ghoshroy, Hans-Conrad Zur Loye, Xiaodong Li, Qian Wang

Faculty Publications

Tobacco mosaic virus (TMV) was electrospun with polyvinyl alcohol (PVA) into continuous TMV–PVA composite nanofibers to form a biodegradable nonwoven fibrous mat as an extracellular matrix (ECM) mimetic. Morphological characterizations by electron microscopyshowed that the addition of varying amounts of TMV resulted in homogeneous nanofibers without phase separation and did not change the diameter of the composite nanofibers. The orientation of TMV in as-spun fibers could be readily controlled and post-processing of the nonwoven TMV–PVA mat significantly improved its water resistance. In addition, tensile tests were performed on individual nanofibers, which revealed that the TMV–PVA composite nanofibers achieved a comparable …

Predicting Phenotypic Severity Of Uncertain Gene Variants In The Ret Proto-Oncogene, David K. Crockett, Stephen R. Piccolo, Perry G. Ridge, Rebecca L. Margraf, Elaine Lyon, Marc S. Williams, Joyce A. Mitchell

Faculty Publications

Although reported gene variants in the RET oncogene have been directly associated with multiple endocrine neoplasia type 2 and hereditary medullary thyroid carcinoma, other mutations are classified as variants of uncertain significance (VUS) until the associated clinical phenotype is made clear. Currently, some 46 non-synonymous VUS entries exist in curated archives. In the absence of a gold standard method for predicting phenotype outcomes, this follow up study applies feature selected amino acid physical and chemical properties feeding a Bayes classifier to predict disease association of uncertain gene variants into categories of benign and pathogenic. Algorithm performance and VUS predictions were …

Stem Cell Factor And Granulocyte Colony-Stimulating Factor Reduce Β-Amyloid Deposits In The Brains Of App/Ps1 Transgenic Mice, Bin Li, Maria E. Gonzalez-Toledo, Chun Shu Piao, Allen Gu, Roger E. Kelley, Li Ru Zhao

Faculty Publications

Introduction. Alzheimer's disease (AD) is widely recognized as a serious public health problem and heavy financial burden. Currently, there is no treatment that can delay or stop the progressive brain damage in AD. Recently, we demonstrated that stem cell factor (SCF) in combination with granulocyte colony-stimulating factor (G-CSF) (SCF+G-CSF) has therapeutic effects on chronic stroke. The purpose of the present study is to determine whether SCF+G-CSF can reduce the burden of β-amyloid deposits in a mouse model of AD. Methods. APP/PS1 transgenic mice were used as the model of AD. To track bone marrow-derived cells in the brain, the bone …

Expression And Localization Of Clc Chloride Transport Proteins In The Avian Retina, Emily Mcmains, Vijai Krishnan, Sujitha Prasad, Evanna Gleason

Faculty Publications

Members of the ubiquitously expressed CLC protein family of chloride channels and transporters play important roles in regulating cellular chloride and pH. The CLCs that function as Cl-/H+ antiporters, ClCs 3-7, are essential in particular for the acidification of endosomal compartments and protein degradation. These proteins are broadly expressed in the nervous system, and mutations that disrupt their expression are responsible for several human genetic diseases. Furthermore, knock-out of ClC3 and ClC7 in the mouse result in the degeneration of the hippocampus and the retina. Despite this evidence of their importance in retinal function, the expression patterns of different CLC …

Across Bacterial Phyla, Distantly-Related Genomes With Similar Genomic Gc Content Have Similar Patterns Of Amino Acid Usage, John Lightfield, Noah R. Fram, Bert Ely

Faculty Publications

The GC content of bacterial genomes ranges from 16% to 75% and wide ranges of genomic GC content are observed within many bacterial phyla, including both Gram negative and Gram positive phyla. Thus, divergent genomic GC content has evolved repeatedly in widely separated bacterial taxa. Since genomic GC content influences codon usage, we examined codon usage patterns and predicted protein amino acid content as a function of genomic GC content within eight different phyla or classes of bacteria. We found that similar patterns of codon usage and protein amino acid content have evolved independently in all eight groups of bacteria. …

Genomic Library Screens For Genes Involved In N-Butanol Tolerance In Escherichia Coli, Luis Reyes, Maria Almario, Katy Kao

Faculty Publications

Backgroundn-Butanol is a promising emerging biofuel, and recent metabolic engineering efforts have demonstrated the use of several microbial hosts for its production. However, most organisms have very low tolerance to n-butanol (up to 2% (v/v)), limiting the economic viability of this biofuel. The rational engineering of more robust n-butanol production hosts relies upon understanding the mechanisms involved in tolerance. However, the existing knowledge of genes involved in n-butanol tolerance is limited. The goal of this study is therefore to identify E. coli genes that are involved in n-butanol tolerance.Methodology/Principal FindingsUsing a genomic library enrichment strategy, we identified approximately 270 genes …

Marr Homologs With Urate-Binding Signature, Inoka C. Perera, Anne Grove

Faculty Publications

Bacteria that associate with living hosts require intricate mechanisms to detect and respond to host defenses. Part of the early host defense against invading bacteria is the production of reactive oxygen species, and xanthine oxidase is one of the main producers of such agents. The end-product of the enzymatic activity of xanthine oxidase, urate, was previously shown to be the natural ligand for Deinococcus radiodurans-encoded HucR and it was shown to attenuate DNA binding by Agrobacterium tumefaciens-encoded PecS and Burkholderia thailandensis-encoded MftR, all members of the multiple antibiotic resistance regulator (MarR) family. We here show that residues involved in binding …

The Utility Of Geometrical And Chemical Restraint Information Extracted From Predicted Ligand-Binding Sites In Protein Structure Refinement, Michal Brylinski, Seung Yup Lee, Hongyi Zhou, Jeffrey Skolnick

Faculty Publications

Exhaustive exploration of molecular interactions at the level of complete proteomes requires efficient and reliable computational approaches to protein function inference. Ligand docking and ranking techniques show considerable promise in their ability to quantify the interactions between proteins and small molecules. Despite the advances in the development of docking approaches and scoring functions, the genome-wide application of many ligand docking/screening algorithms is limited by the quality of the binding sites in theoretical receptor models constructed by protein structure prediction. In this study, we describe a new template-based method for the local refinement of ligand-binding regions in protein models using remotely …

Findsite-Metal: Integrating Evolutionary Information And Machine Learning For Structure-Based Metal-Binding Site Prediction At The Proteome Level, Michal Brylinski, Jeffrey Skolnick

Faculty Publications

The rapid accumulation of gene sequences, many of which are hypothetical proteins with unknown function, has stimulated the development of accurate computational tools for protein function prediction with evolution/structure-based approaches showing considerable promise. In this article, we present FINDSITE-metal, a new threading-based method designed specifically to detect metal-binding sites in modeled protein structures. Comprehensive benchmarks using different quality protein structures show that weakly homologous protein models provide sufficient structural information for quite accurate annotation by FINDSITE-metal. Combining structure/evolutionary information with machine learning results in highly accurate metal-binding annotations; for protein models constructed by TASSER, whose average Cα RMSD from the …

Generation Of Trophoblast Stem Cells From Rabbit Embryonic Stem Cells With Bmp4, Tao Tan, Xianghui Tang, Jing Zhang, Yuyu Niu, Hongwei Chen, Bin Li, Qiang Wei, Weizhi Ji

Faculty Publications

Trophoblast stem (TS) cells are ideal models to investigate trophectoderm differentiation and placental development. Herein, we describe the derivation of rabbit trophoblast stem cells from embryonic stem (ES) cells. Rabbit ES cells generated in our laboratory were induced to differentiate in the presence of BMP4 and TS-like cell colonies were isolated and expanded. These cells expressed the molecular markers of mouse TS cells, were able to invade, give rise to derivatives of TS cells, and chimerize placental tissues when injected into blastocysts. The rabbit TS-like cells maintained self-renewal in culture medium with serum but without growth factors or feeder cells, …

Adjustment For Local Ancestry In Genetic Association Analysis Of Admixed Populations, Xuexia Wang, Xiaofeng Zhu, Huaizhen Qin, Richard S. Cooper, Warren J. Ewens, Chun Li, Mingyao Li

Faculty Publications

Motivation: Admixed populations offer a unique opportunity for mapping diseases that have large disease allele frequency differences between ancestral populations. However, association analysis in such populations is challenging because population stratification may lead to association with loci unlinked to the disease locus. Methods and results: We show that local ancestry at a test single nucleotide polymorphism (SNP) may confound with the association signal and ignoring it can lead to spurious association. We demonstrate theoretically that adjustment for local ancestry at the test SNP is sufficient to remove the spurious association regardless of the mechanism of population stratification, whether due to …

Quantitative Environmental Benchmarking In A Hydrologically Driven Hawaiian Coastal System, Paul Bienfang, Suzanne De Felice, Edward A. Laws

Faculty Publications

The spatial and temporal variability of water quality within aquatic habitats in the Kaloko-Honokohau National Historical Park was examined over a 2-year period to quantitatively establish water quality benchmarks against which future data might be compared to test for evidence of anthropogenic impacts. Throughput of lowsalinity, high-nutrient groundwater and mixing with high-salinity, low-nutrient seawater caused significant temporal and spatial water quality variability in wells, anchialine pools, and fishponds within the study area. Variable mixing of seawater and freshwater was shown to be the primary determinant of changes in nutrient concentrations in these aquatic habitats, although leaching of basaltic rocks (Si) …

Circadian Rhythm Of Cortisol And Neighborhood Characteristics In A Population-Based Sample: The Multi-Ethnic Study Of Atherosclerosis, D. Phuong Do, Ana V. Diez Roux, Anjum Hajat, Amy Auchincloss, Sharon Merkin, Nalini Ranjit, Steven Shea, Teresa Seeman

Faculty Publications

Although stress is often hypothesized to contribute to the effects of neighborhoods on health, very few studies have investigated associations of neighborhood characteristics with stress biomarkers. This study helps address the gap in the literature by examining whether neighborhood characteristics are associated with cortisol profiles. Analyses were based on data from the Multi-Ethnic Study of Atherosclerosis Stress study which collected multiple measures of salivary cortisol over three days on a population based sample of approximately 800 adults. Multilevel models with splines were used to examine associations of cortisol with neighborhood poverty, violence, disorder, and social cohesion. Neighborhood violence was significantly …

Students Studying Students: An Assessment Of Using Undergraduate Student Researchers In An Ethnographic Study Of Library Use, Allyson Washburn, Sheila C. Bibb

Faculty Publications

This paper reports on the use of undergraduate students enrolled in an Applied Anthropology course as researcher for a library use study at Brigham Young University's (BYU) Harold B. Lee Library (HBLL). This is a common practice at BYU, but has not been reported extensively in the literature. The study was carried out by the authors with the assistance of undergraduate students, the students being the researchers and was conducted in order that the HBLL could determine student ideas for reconfiguring some newly opened space in the Periodicals room. Using students assisted the library as well as met a curricular …

Evidence For Mesenchymal-Epithelial Transition Associated With Mouse Hepatic Stem Cell Differentiation, Bin Li, Yun Wen Zheng, Yuuki Sano, Hideki Taniguchi

Faculty Publications

Mesenchymal-epithelial transition events are related to embryonic development, tissue construction, and wound healing. Stem cells are involved in all of these processes, at least in part. However, the direct evidence of mesenchymal-epithelial transition associated with stem cells is unclear. To determine whether mesenchymal-epithelial transition occurs in liver development and/or the differentiation process of hepatic stem cells in vitro, we analyzed a variety of murine liver tissues from embryonic day 11.5 to adults and the colonies derived from hepatic stem/progenitor cells isolated with flow cytometry. The results of gene expression, immunohistochemistry and Western blot showed that as liver develops, the expression …