Digital Commons Network^™

Distinct And Shared Determinants Of Cardiomyocyte Contractility In Multi-Lineage Competent Ethnically Diverse Human Ipscs, Martin L. Tomov, Zachary T. Olmsted, Haluk Dogan, Eda Gongorurler, Maria Tsompana, Hasan H. Otu, Michael Buck, Eun-Ah Chang, Jose Cibelli, Janet L. Paluh

Department of Electrical and Computer Engineering: Faculty Publications

The realization of personalized medicine through human induced pluripotent stem cell (iPSC) technology can be advanced by transcriptomics, epigenomics, and bioinformatics that inform on genetic pathways directing tissue development and function. When possible, population diversity should be included in new studies as resources become available. Previously we derived replicate iPSC lines of African American, Hispanic-Latino and Asian self-designated ethnically diverse (ED) origins with normal karyotype, verified teratoma formation, pluripotency biomarkers, and tri-lineage in vitro commitment. Here we perform bioinformatics of RNA-Seq and ChIP-seq pluripotency data sets for two replicate Asian and Hispanic-Latino ED-iPSC lines that reveal differences in generation of …

Reproductive Potential Of Spodoptera Eridania (Stoll) (Lepidoptera: Noctuidae) In The Laboratory: Effect Of Multiple Couples And The Size, Alexandre Specht, Débora Goulart Montezano, Daniel Ricardo Sosa-Gómez, Silvana L. Vieira De Paula Moraes, Vânia F. Roque-Specht, Neiva M. Barros

Department of Entomology: Faculty Publications

This study aimed to evaluate the effect of keeping three couples in the same cage, and the size of adults emerged from small, medium-sized and large pupae (278.67 mg; 333.20 mg and 381.58 mg, respectively), on the reproductive potential of Spodoptera eridania (Stoll, 1782) adults, under controlled conditions (25 ± 1 °C, 70% RH and 14 hour photophase). We evaluated the survival, number of copulations, fecundity and fertility of the adult females. The survival of females from these different pupal sizes did not differ statistically, but the survival of males from large pupae was statistically shorter than from small pupae. …

Differential Contribution Of Genomic Regions To Marked Genetic Variation And Prediction Of Quantitative Traits In Broiler Chickens, Rostam Abdollaha- Arpanahi, Gota Morota, Bruno D. Valente, Andreas Kranis, Guilherme J. M. Rosa, Daniel Gianola

Department of Animal Science: Faculty Publications

Background: Genome-wide association studies in humans have found enrichment of trait-associated single nucleotide polymorphisms (SNPs) in coding regions of the genome and depletion of these in intergenic regions. However, a recent release of the ENCyclopedia of DNA elements showed that ~80 % of the human genome has a biochemical function. Similar studies on the chicken genome are lacking, thus assessing the relative contribution of its genic and non-genic regions to variation is relevant for biological studies and genetic improvement of chicken populations. Methods: A dataset including 1351 birds that were genotyped with the 600K Affymetrix platform was used. We partitioned …

Eps Producing Microorganisms From Municipal Wastewater Activated Sludge, Klai Nouha, Yan S, Tyagi Rd, Surampalli Ry

Department of Civil and Environmental Engineering: Faculty Publications

Bacterial exopolysacchrides (EPSs) are produced by many bacteria. Nowadays there is an increasing interest in the isolation and exploitation of these polymers for industrial purposes. In general, biosynthesis of EPS varies from one strain to other strain and it depends on genes and enzymes involved in EPS production and secretion. In this study, EPS producing strains were isolated from municipal wastewater treatment plant and their potential of EPS production was evaluated. The role of EPS in sludge flocculation was also studied. Three types of EPS (LB-EPS (Loosely bound EPS), TB-EPS (Tightly bound EPS) and B-EPS (broth EPS)) were harvested and …

Emergence Of A Potent Multidrug Efflux Pump Variant That Enhances Campylobacter Resistance To Multiple Antibiotics, Hong Yao, Zhangql Shen, Yang Wang, Fengru Deng, Dejun Liu, Gaowa Naren, Lel Dal, Chih-Chia Su, Bing Wang, Shaolin Wang, Congming Wu, Edward W. Yu, Qijing Zhang, Jianzhong Shen

Department of Food Science and Technology: Faculty Publications

Bacterial antibiotic efflux pumps are key players in antibiotic resistance. Although their role in conferring multidrug resistance is well documented, the emergence of “super” efflux pump variants that enhance bacterial resistance to multiple drugs has not been reported. Here, we describe the emergence of a resistance-enhancing variant (named RE-CmeABC) of the predominant efflux pump CmeABC in Campylobacter, a major zoonotic pathogen whose resistance to antibiotics is considered a serious antibiotic resistance threat in the United States. Compared to the previously characterized CmeABC transporters, RECmeABC is much more potent in conferring Campylobacter resistance to antibiotics, which was shown by increased …

The Worm’S Eye View Of Community Ecology, Tavis K. Anderson, Michael V. K. Sukhdeo

United States Department of Agriculture-Agricultural Research Service / University of Nebraska-Lincoln: Faculty Publications

The study of parasites in the context of community level organization, either as parasites embedded within host communities, or as parasite communities themselves, is now quite prevalent in parasitology and ecology today. However, this was not always the case. In terms of publications, there was almost no consideration of parasite interactions at the community level for most of the first half of the last century. Papers in The Journal of Parasitology by Clark Read (1951) and John Holmes (1961) were the defining contributions to the beginning of the field, and the ideas elaborated by these two parasitologists still inspire current …

Conserving California Condors In The 1980s, Noel F.R. Snyder

United States Geological Survey: Staff Publications

By the late 1970s, the California condor (Gymnogyps californianus) was in serious trouble, with probably no more than about 30 birds left in existence, all in a mountainous region just north of Los Angeles that is vegetated mainly in chaparral and grasslands. All estimates of population size and trends offered since the early condor studies by Carl Koford in the 1930s and 1940s indicated a continuing decline toward extinction, and it appeared that few years were left before the species would be gone (see Koford, 1953; Wilbur, 1978). Evidently, the conservation steps that had been taken, including the …

A Computational Study Of The Evolution Of Cretan And Related Scripts, Peter Revesz

School of Computing: Conference and Workshop Papers

Crete was the birthplace of several ancient writings, including the Cretan Hieroglyphs, the Linear A and the Linear B scripts. Out of these three only Linear B is deciphered. The sound values of the Cretan Hieroglyph and the Linear A symbols are unknown and attempts to reconstruct them based on Linear B have not been fruitful. In this paper, we compare the ancient Cretan scripts with four other Mediterranean and Black Sea scripts, namely Phoenician, South Arabic, Greek and Old Hungarian. We provide a computational study of the evolution of the three Cretan and four other scripts. This study encompasses …

Paleoepidemiology Of Intestinal Parasites And Lice In Pre-Columbian South America *, Adauto Araujo, Karl J. Reinhard, Daniela Leles, Luciana Sianto, Alena Iniguez, Martin Fugassa, Berrnardo Arriaza, Nancy Orellana, Luiz Fernando Ferreira

Karl Reinhard Publications

Some human parasites originated in prehominid ancestors in Africa. Nematode species, such as Enterobius vermicularis (pinworm), hookworms and Trichuris trichiura are shared by humans and other close phylogenetic primates (Pan and Gorilla), showing that they infected a common ancestor to this group. When humans migrated from Africa to other continents they carried these parasites wherever climate conditions allowed parasite transmission from host to host. Other parasites, however, were acquired throughout human biological and social evolutive history when new territories were occupied. Paleoparasitology data is a valuable source to recover emergence and disappearance of parasite infections through analysis of archaeological remains. …

A Visual Analysis Of Articulated Motion Complexity Based On Optical Flow And Spatial-Temporal Features, Beau Michael Christ

School of Computing: Dissertations, Theses, and Student Research

The understanding of motion is an important problem in computer vision with applications including crowd-flow analysis, video surveillance, and estimating three-dimensional structure. A less-explored problem is the visual characterization and quantification of motion complexity. An important motion class that is prevalent in living beings is articulated motion (segments connected by joints). At present, no known standardized measure for quantifying the complexity of articulated motion exists. Such a measure could facilitate advanced motion analysis with applications including video indexing, motion comparison, and advanced biological study of visual signals in organisms.

This dissertation presents an in-depth study of the development of several …

Shorebird Migratory Stopover Responses To Local And Regional Change: Habitat Decisions In A Vanishing Landscape, Caitlyn Gillespie

School of Natural Resources: Dissertations, Theses, and Student Research

Understanding the consequences of anthropogenic change for migratory species is challenging because although they have evolved to cope with environmental uncertainty, migrants still rely on predictable relationships within and among habitats to make informed decisions. Calidris shorebirds rely on ephemeral wetlands during northward migration through mid-continental North America, where favorable habitat conditions are annually and regionally unpredictable and increasingly altered by land-use change. During spring 2013 and 2014, we assessed Calidris habitat use in the Rainwater Basin (RWB) and the Prairie Pothole Region (PPR) at both local and landscape scales. Although anthropogenic change has altered the wetland landscape in both …

Mammalian Synthetic Biology: Emerging Medical Applications, Zoltan Kis, Hugo Sant'ann Pereira, Takayuki Homma, Ryan M. Pedrigi, Rob Krams

Department of Mechanical and Materials Engineering: Faculty Publications

In this review, we discuss new emerging medical applications of the rapidly evolving field of mammalian synthetic biology.We start with simple mammalian synthetic biological components and move towards more complex and therapy-oriented gene circuits. A comprehensive list of ON–OFF switches, categorized into transcriptional, post-transcriptional, translational and posttranslational, is presented in the first sections. Subsequently, Boolean logic gates, synthetic mammalian oscillators and toggle switches will be described. Several synthetic gene networks are further reviewed in the medical applications section, including cancer therapy gene circuits, immuno-regulatory networks, among others. The final sections focus on the applicability of synthetic gene networks to drug …

A Comparison Of Two Low-Stakes Methods For Administering A Program-Level Biology Concept Assessment, Brian A. Couch, Jennifer K. Knight

School of Biological Sciences: Faculty Publications

Concept assessments are used commonly in undergraduate science courses to assess student learning and diagnose areas of student difficulty. While most concept assessments align with the content of individual courses or course topics, some concept assessments have been developed for use at the programmatic level to gauge student progress and achievement over a series of courses or an entire major. The broad scope of a program-level assessment, which exceeds the content of any single course, creates several test administration issues, including finding a suitable time for students to take the assessment and adequately incentivizing student participation. These logistical considerations must …

Green And Energy-Efficient Methods For The Production Of Metallic Nanoparticles, Mitra Naghdi, Mehrdad Taheran, Satinder K. Brar, M. Verma, R. Y. Surampalli, J. R. Valero

Department of Civil and Environmental Engineering: Faculty Publications

In the last decade, researchers paid great attention to the concept of “Green Chemistry”, which aims at development of efficient methods for the synthesis of nanoparticles (NPs) in terms of the least possible impact on human life and environment. Generally, several reagents including precursors, reducing agents, stabilizing agents and solvents are used for the production of NPs and in some cases, energy is needed to reach the optimum temperature for reduction. Therefore, to develop a green approach, researchers had the opportunity to investigate eco-friendly reagents and new energy transfer techniques. In order to substitute the harmful reagents with green ones, …

Substrate Stiffness Regulates Primary Hepatocyte Functions†, Vaishaali Natarajan, Eric J. Berglund, Dorothy X. Chen, Srivatsan Kidambi

Department of Chemical and Biomolecular Engineering: Faculty Publications

Liver fibrosis occurs as a consequence of chronic injuries from viral infections, metabolic disorders, and alcohol abuse. Fibrotic liver microenvironment (LME) is characterized by excessive deposition and aberrant turnover of extracellular matrix proteins, which leads to increased tissue stiffness. Liver stiffness acts as a vital cue in the regulation of hepatic responses in both healthy and diseased states; however, the effect of varying stiffness on liver cells is not well understood. There is a critical need to engineer in vitro models that mimic the liver stiffness corresponding to various stages of disease progression in order to elucidate the role of …

Is Anthropogenic Cougar Mortality Compensated By Changes In Natural Mortality In Utah? Insight From Long-Term Studies, Michael L. Wolfe, David N. Koons, David C. Stoner, Patricia Terletzky, Eric M. Gese, David M. Choate, Lise M. Aubry

United States Department of Agriculture Wildlife Services: Staff Publications

Understanding the interplay between exploitation and natural mortality is essential to guiding sustainable conservation of wildlife. Exploitation of carnivores by humans has long been thought to result in compensatory reductions of natural mortality among survivors. If rates of human exploitation exceed natural mortality, however, such actions will ‘add’ to overall mortality and could imperil the sustainability of such actions. We applied competing risk analyses to >/= 16 years of data for heavily harvested and semi-protected cougar populations in Utah to test the additive and compensatory mortality hypotheses, while accounting for parameter uncertainty. We additionally tested for presence of the two …

Is Anthropogenic Cougar Mortality Compensated By Changes In Natural Mortality In Utah? Insight From Long-Term Studies, Michael L. Wolfe, David N. Koons, David C. Stoner, Patricia Terletzky, Eric M. Gese, David M. Choate, Lise M. Aubry

United States Department of Agriculture Wildlife Services: Staff Publications

Understanding the interplay between exploitation and natural mortality is essential to guiding sustainable conservation of wildlife. Exploitation of carnivores by humans has long been thought to result in compensatory reductions of natural mortality among survivors. If rates of human exploitation exceed natural mortality, however, such actions will ‘add’ to overall mortality and could imperil the sustainability of such actions. We applied competing risk analyses to >16 years of data for heavily harvested and semi-protected cougar populations in Utah to test the additive and compensatory mortality hypotheses, while accounting for parameter uncertainty. We additionally tested for presence of the two primary …

Hydrolytically Stable Analogues Of Sugar Phosphates And A Miniaturized In Situ Enzymatic Screen, Xiang Fei

Department of Chemistry: Dissertations, Theses, and Student Research

The glmS riboswitch undergoes self-cleavage upon binding its metabolic product GlcN6P, thereby providing a negative feedback mechanism limiting translation of the glmS protein when GlcN6P is abundant. As a first step toward the development of novel antimicrobials, we have synthesized a series of GlcN6P analogues bearing phosphatase-inert surrogates in place of the natural phosphate ester functionality. The self-cleavage assay identified two such compounds that display significant riboswitch actuator activity; namely those bearing a 6-phosphonomethyl group or a 6-O-malonyl ether. These two analogues exhibit a 22-fold and a 27-fold higher catalytic efficiency, respectively, than does glucosamine. Docking experiments were …

Documentation Of The Black-Footed Ferret, Mustela Nigripes On The Standing Rock Indian Reservation, Mobridge, South Dakota, Michael P. Gutzmer, Jeffrey C. Kelly

Transactions of the Nebraska Academy of Sciences and Affiliated Societies

Since 1991, 19 specific black-footed ferret reintroduction projects have been conducted across 8 States, Canada, and Mexico. All five of the first ferret reintroductions (from 1991 to 1996) continue to be occupied by ferrets. The photographs of October 31 and November 1 are the first unequivocal documentation of black-footed ferrets on the Standing Rock Indian Reservation. Ferrets observed on Standing Rock may be dispersals from the nearby Cheyenne River Sioux Indian Reservation to the south. The nearest re-introduction site for ferrets is approximately 20 miles away, in Whitehorse, South Dakota, and the observation of ferrets on Standing Rock could document …

Use Of Cysteine-Reactive Crosslinkers To Probe Conformational Flexibility Of Human Dj-1 Demonstrates That Glu18 Mutations Are Dimers, Janani Prahlad, David N. Hauser, Nicole M. Milkovic, Mark R. Cookson, Mark A. Wilson

Department of Biochemistry: Faculty Publications

The oxidation of a key cysteine residue (Cys106) in the parkinsonism-associated protein DJ-1 regulates its ability to protect against oxidative stress and mitochondrial damage. Cys106 interacts with a neighboring protonated Glu18 residue, stabilizing the Cys106-SO₂ ⁻ (sulfinic acid) form of DJ-1. To study this important post-translational modification, we previously designed several Glu18 mutations (E18N, E18D, E18Q) that alter the oxidative propensity of Cys106. However, recent results suggest these Glu18 mutations cause loss of DJ-1 dimerization, which would severely compromise the protein’s function. The purpose of this study was to conclusively determine the oligomerization state of these mutants using X-ray …

A Catalog Of Scolytidae And Platypodidae (Coleoptera), Supplement 3 (2000-2010), With Notes On Subfamily And Tribal Reclassifications, Donald E. Bright

Insecta Mundi

A third Supplement to the 1992 Catalog of the Scolytidae and Platypodidae (Coleoptera) of the World (Wood and Bright 1992) is presented. This Supplement updates the taxonomy, distribution, and biology pertaining to these families of Coleoptera from 2000 to the end of 2010. A few 2011 taxonomic references are included in order to make the nomenclature as current as possible. The format of this Supplement differs slightly from the format of the original 1992 Catalog and the two previous Supplements. Only references relating to general biology, systematics and distribution were selected to be included. Tribal arrangement follows the scheme established …

A History Of Sockeye Salmon Research, Karluk River System, Alaska, 1880–2010, Richard Gard, Richard Lee Bottorff

United States Department of Commerce: Staff Publications

One of Alaska’s most famous runs of sockeye salmon, Oncorhynchus nerka, returns each year to spawn in the pristine waters of the Karluk River drainage on Kodiak Island. The sheer magnitude and long duration of the run are remarkable. Within recorded history, this run has, in peak years, exceeded 4,000,000 fish, a wondrous spectacle of nature. This abundance is particularly striking since, physically, the Karluk River is relatively small when compared with other notable salmon-stream systems of Alaska and the Pacific Coast. Such vibrant profusion has riveted human attention for as long as people have occupied Kodiak Island, an …

Identification Of A Fourth Haplotype Of Bactericera Cockerelli (Hemiptera: Triozidae) In The United States, Kylie D. Swisher, Donald C. Henne, James M. Crosslin

United States Department of Agriculture-Agricultural Research Service / University of Nebraska-Lincoln: Faculty Publications

The potato psyllid, Bactericera cockerelli (Sulc) (Hemiptera: Triozidae), is a pest of potato and other solanaceous crops in North and Central America and New Zealand. Previous genotyping studies have demonstrated the presence of three different haplotypes of B. cockerelli in the United States corresponding to three geographical regions: Central,Western, and Northwestern. These studies utilized psyllids collected in the western and central United States between 1998 and 2011. In an effort to further genotype potato psyllids collected in the 2012 growing season, a fourth B. cockerelli haplotype was discovered corresponding to the Southwestern United States geographical region. High-resolution melting analyses identified …

The Emerging Field Of Geogenomics: Constraining Geological Problems With Genetic Data, Paul A. Baker, Sherilyn C. Fritz, Christopher W. Dick, Andrew J. Eckert, Brian K. Horton, Stefano Manzoni, Camila C. Ribas, Carmala N. Garzione, David S. Battisti

Department of Earth and Atmospheric Sciences: Faculty Publications

The development of a genomics-derived discipline within geology is timely, as a result of major advances in acquiring and processing geologically relevant genetic data. This paper articulates the emerging field of “geogenomics,” which involves the use of large-scale genetic data to constrain geological hypotheses. The paper introduces geogenomics and discusses how hypotheses can be ad-dressed through collaboration between geologists and evolutionary biologists. As an example, geogenomic methods are applied to evaluate competing hypotheses regarding the timing of the Andean uplift, the closure of the Isthmus of Panama, the onset of trans-Amazon drainage, and Quaternary climate variation in the Neotropics.

Phosphatase-Inert Glucosamine 6‑Phosphate Mimics Serve As Actuators Of The Glms Riboswitch, Xiang Fei, Thomas Holmes, Julianna Diddle, Lauren Hintz, Dan Delaney, Alex Stock, Danielle Renner, Molly Mcdevitt, David B. Berkowitz, Juliane K. Soukup

David Berkowitz Publications

The glmS riboswitch is unique among generegulating riboswitches and catalytic RNAs. This is because its own metabolite, glucosamine-6-phosphate (GlcN6P), binds to the riboswitch and catalytically participates in the RNA selfcleavage reaction, thereby providing a novel negative feedback mechanism. Given that a number of pathogens harbor the glmS riboswitch, artificial actuators of this potential RNA target are of great interest. Structural/kinetic studies point to the 2- amino and 6-phosphate ester functionalities in GlcN6P as being crucial for this actuation. As a first step toward developing artificial actuators, we have synthesized a series of nine GlcN6P analogs bearing phosphatase-inert surrogates in place …

Structure And Function Of Human Dnaj Homologue Subfamily A Member 1 (Dnaja1) And Its Relationship To Pancreatic Cancer, Jaime L. Stark, Kamiya Mehla, Nina V. Chaika, Thomas B. Acton, Rong Xiao, Pankaj K. Singh, Gaetano T. Montelione, Robert Powers

Robert Powers Publications

Pancreatic cancer has a dismal 5 year survival rate of 5.5% that has not been improved over the past 25 years despite an enormous amount of effort. Thus, there is an urgent need to identify truly novel yet druggable protein targets for drug discovery. The human protein DnaJ homologue subfamily A member 1 (DNAJA1) was previously shown to be downregulated 5- fold in pancreatic cancer cells and has been targeted as a biomarker for pancreatic cancer, but little is known about the specific biological function for DNAJA1 or the other members of the DnaJ family encoded in the human genome. …

Genetic Variability Of Spined Soldier Bugs (Hemiptera: Pentatomidae) Sampled From Distinct Field Sites And Laboratory Colonies In The United States, Fatima Mustafa, Muhammad Ullah, Kathleen M. Kneeland, Thomas A. Coudron, W. Wyatt Hoback, S. R. Skoda, Jaime Molina-Ochoa, John E. Foster

Department of Entomology: Faculty Publications

The spined soldier bug, Podisus maculiventris (Say), is an important biological control agent of agricultural and forest pests; and it preys on eggs and larvae of lepidopteran and coleopteran species. Genetic variability among field samples collected from Michigan, Mississippi, Missouri, Florida and established laboratory colonies was examined using Amplified Fragment Length Polymorphism-Polymerase Chain Reaction (AFLP-PCR). Four AFLP primer pairs generated a total of 340 molecular markers for evaluation. Results from Analysis of Molecular Variance showed that the majority of the genetic variation occurred within populations (individuals from each sample site). Nei’s method indicated reduced genetic diversity in laboratory populations compared …

Alginate Hydrogel As A Three-Dimensional Extracellular Matrix For In Vitro Models Of Development, Catherine Sargus-Patino

Department of Agricultural and Biological Systems Engineering: Dissertations, Theses, and Student Research

Tissue engineering, involving the use of three-dimensional (3-D) scaffolds for cell and tissue culture, is a promising technique for establishing in vitro culture models that mimic in vivo environments. In vitro models present ethical and cost advantages over in vivo models, and allow for controlled, mechanistic studies on factors that regulate normal and abnormal tissue development. Alginate, a linear polysaccharide derived from brown algae, has properties that make it a favorable material as a 3-D extracellular matrix for in vitro cell and tissue models. After demonstrating alginate’s tunable physical and chemical properties with respect to gel formation, stiffness, and cellular …

Dna Barcoding Distinguishes Pest Species Of The Black Fly Genus Cnephia (Diptera: Simuliidae), I. M. Confitti, K. P. Pruess, A. Cywinska, T. O. Powers, D. C. Currie

Department of Entomology: Faculty Publications

Accurate species identification is essential for cost-effective pest control strategies. We tested the utility of COI barcodes for identifying members of the black fly genus Cnephia Enderlein (Diptera: Simuliidae). Our efforts focus on four Nearctic Cnephia species—Cnephia dacotensis (Dyar & Shannon), Cnephia eremities Shewell, Cnephia ornithophilia (Davies, Peterson & Wood), and Cnephia pecuarum (Riley)—the latter two being current or potential targets of biological control programs. We also analyzed one Palearctic species, Cnephia pallipes (Fries). Although Cnephia adults can be identified anatomically to species, control programs target the larval stage, which is difficult or impossible to distinguish morphologically. By using …

Ecology Of Musk Thistle (Carduus Nutans) Seed Germination For Grasslands Of Temperate Climates, Chengchou Han, Stephen L. Young

West Central Research and Extension Center, North Platte

Musk thistle is an invasive weed that is widely distributed throughout much of North America, including grasslands in temperate climates of the midwest USA. A series of laboratory and greenhouse experiments were conducted to determine the effect of various environmental factors on germination of musk thistle seeds. In temperature-fluctuation experiments, seed germination was greater than 65% in both alternating (30/20 C) and constant (20 or 25 C) temperature regimes with an 8-h day but less (33%) in warmer regimes (35/20 C). Germination of musk thistle seeds was 37% in alternating temperature regimes of 30/20 C in total darkness, but less …