Digital Commons Network^™

Overexpression Of Galnac-Transferase Galnac-T3 Promotes Pancreatic Cancer Cell Growth, Keisuke Taniuchi, Ronald Cerny, Aki Tanouchi, Kimitoshi Kohno, Norihiro Kotani, Koichi Honke, Toshiji Saibara, Michael A. Hollingsworth

Ronald Cerny Publications

O-linked glycans of secreted and membrane bound proteins play an important role in the pathogenesis of pancreatic cancer by modulating immune responses, inflammation, and tumorigenesis. A critical aspect of O-glycosylation, the position at which proteins are glycosylated with N-acetyl-galactosamine on serine and threonine residues, is regulated by the substrate specificity of UDP-GalNAc: polypeptide N-acetylgalactosaminyl-transferases (GalNAc-Ts). Thus, GalNAc-Ts regulate the first committed step in O-glycosylated protein biosynthesis, determine sites of O-glycosylation on proteins, and are important for understanding normal and carcinoma-associated O-glycosylation. We have found that one of these enzymes, GalNAc-T3, is overexpressed in …

Identification And Characterization Of The Anti-Methicillin-Resistant Staphylococcus Aureus Wap-8294a2 Biosynthetic Gene Cluster From Lysobacter Enzymogenes Oh11, Wei Zhang, Yaoyao Li, Guoliang Qian, Yan Wang, Haotong Chen, Yue-Zhong Li, Fengquan Liu, Yuemao Shen, Liangcheng Du

Department of Chemistry: Faculty Publications

Lysobactor enzymogenes strain OH11 is an emerging biological control agent of fungal and bacterial diseases. We recently completed its genome sequence and found it contains a large number of gene clusters putatively responsible for the biosynthesis of nonribosomal peptides and polyketides, including the previously identified antifungal dihydromaltophilin (HSAF). One of the gene clusters contains two huge open reading frames, together encoding 12 modules of nonribosomal peptide synthetases (NRPS). Gene disruption of one of the NRPS led to the disappearance of a metabolite produced in the wild type and the elimination of its antibacterial activity. The metabolite and antibacterial activity were …

Characterizing Rna Dynamics At Atomic Resolution Using Solution-State Nmr Spectroscopy, Jameson R. Bothe, Evgenia N. Nikolova, Catherine D. Eichhorn, Jeetender Chugh, Alexandar L. Hansen, Hashim M. Al-Hashimi

Department of Chemistry: Faculty Publications

Many recently discovered non-coding RNAs do not fold into a single native conformation, but rather, sample many different conformations along their free energy landscape to carry out their biological function. Unprecedented insights into the RNA dynamic structure landscape are provided by solution-state NMR techniques that measure the structural, kinetic, and thermodynamic characteristics of motions spanning picosecond to second timescales at atomic resolution. From these studies a basic description of the RNA dynamic structure landscape is emerging, bringing new insights into how RNA structures change to carry out their function as well as applications in RNA-targeted drug discovery and RNA bioengineering.

Energy And Climate Implications For Agricultural Nutrient Use Efficiency, Adam J. Liska, Richard K. Perrin

Adam Liska Papers

Energy and climate change are beginning to dominate the global political agenda and will drive policy formation that will shape the future of agriculture. Energy issues threaten national security and economic stability, as well as access to low-cost nutrient inputs for agriculture. Climate change has the potential to cause serious disruption to agricultural productivity. Paradoxically, nutrient use in agriculture to increase crop yields has the potential to negatively impact climate. This chapter will discuss recent and future energy and climate trends, the relationships between agricultural nutrient use efficiency and biofuels, and how global land limitations will shape agriculture in the …

Effect Of Distillers Grains Moisture And Inclusion Level In Livestock Diets On Greenhouse Gas Emissions In The Corn-Ethanol-Livestock Life Cycle, Virgil R. Bremer, Andrea K. Watson, Adam J. Liska, Galen Erickson, Kenneth Cassman, Kathryn J. Hanford, Terry Klopfenstein

Adam Liska Papers

A model was previously developed (Biofuel Energy Systems Simulator; www. bess.unl.edu) to predict greenhouse gas (GHG) emissions and net energy yield when ethanol is produced from corn. The model also predicts feedlot cattle, dairy cattle, and swine performance and feed replacement value of ethanol coproducts. Updated equations that predict performance of feedlot cattle fed 0 to 40% of dietary DM as corn wet (WDGS), modified (MDGS), or dry (DDGS) distillers grains plus solubles replacing dry-rolled and high-moisture corn were developed and incorporated into the model. Equations were derived from pen-level performance for 20 finishing studies evaluating WDGS, 4 evaluating MDGS, …

Chromatographic Analysis Of Drug Interactions In The Serum Proteome, David S. Hage, Jeanethe A. Anguizola, Abby J. Jackson, Ryan Matsuda, Efthimia Papastavros, Erika Pfaunmiller, Zenghan Tong, John Vargas-Badilla, Michelle J. Yoo, Xiwei Zheng

David Hage Publications

The binding of drugs with serum proteins and binding agents such as human serum albumin, a1-acid glycoprotein, and lipoproteins is an important process in determining the activity and fate of many pharmaceuticals in the body. A variety of techniques have been used to study drug interactions with serum proteins, but there is still a need for faster or better methods for such work. High-performance liquid chromatography (HPLC) is one tool that has been utilized in many formats for these types of measurements. Advantages of using HPLC for this application include its speed and precision, its ability to be automated, its …

Bioanalysis Young Investigator Award – Sponsored By Waters- Michelle J. Yoo, David S. Hage

David Hage Publications

Supervisor’s supporting comments

have always been impressed with Michelle’s ability to conduct research in an independent and yet highly effective manner. Part of her research in my group has examined the use of affinity columns to examine drug–protein binding with serum proteins, such as human serum albumin. This work is extremely important to the fields of pharmaceutical chemistry and clinical chemistry in providing the data needed for the development of new drugs or in the optimization of treatments for patients with new, or existing, drugs. Another topic that Michelle has examined in her research is the use of new supports …

3-Alkoxy-1,2-Dioxolanes: Synthesis And Evaluation As Potential Antimalarial Agents, Charles E. Schiaffo, Matthias Rottman, Sergio Wittlin, Patrick Dussault

Patrick Dussault Publications

A number of 3-alkoxy-1,2-dioxolanes exhibit promising levels of antimalarial activity against Plasmodium falciparum. A new route to the 1,2-dioxolane core is reported based on tandem peroxidation/cyclization of enones.

Integral Projection Model Of Insect Herbivore Effects On Cirsium Altissimum Populations Along Productivity Gradients, Karen E. Rose, F. Leland Russell, Svata M. Louda

School of Biological Sciences: Faculty Publications

Prediction of the role of native insect herbivores in the population growth and spatial distribution of native plants within the environment remains limited. We developed an integral projection model (IPM) to explore the effect of native insect herbivores on the population dynamics and distribution of the native plant Cirsium altissimum (tall thistle), in two different productivity zones in tallgrass prairie in Nebraska USA. Model parameters were extracted from two field experiments: a seed addition experiment that demonstrated seed limitation by insect herbivores on adult recruitment and an insect herbivory exclusion experiment that demonstrated significant herbivore impacts on both rosette performance …

Characterization Of A Dipartite Iron Uptake System From Uropathogenic Escherichia Coli Strain, Doreen Koch, Anson C. K. Chan, Michael E.P. Murphy, Hauke Lilie, Gregor Grass, Dietrich H. Nies

School of Biological Sciences: Faculty Publications

In the uropathogenic Escherichia coli strain F11, in silico genome analysis revealed the dicistronic iron uptake operon fetMP, which is under iron-regulated control mediated by the Fur regulator. The expression of fetMP in a mutant strain lacking known iron uptake systems improved growth under iron depletion and increased cellular iron accumulation. FetM is a member of the iron/lead transporter superfamily and is essential for iron uptake by the Fet system. FetP is a periplasmic protein that enhanced iron uptake by FetM. Recombinant FetP bound Cu(II) and the iron analog Mn(II) at distinct sites. The crystal structure of the …

Crystallization Of Chlorella Deoxyuridine Triphosphatase, Laura Badalucco, Ishwari Poudel, Mamoru Yamanishi, Chandrasekhar Natarajan, Hideaki Moriyama

School of Biological Sciences: Faculty Publications

Deoxyuridine triphosphatase (dUTPase) is a ubiquitous enzyme that has been widely studied owing to its function and evolutionary significance. The gene coding for the dUTPase from the Chlorella alga was codon-optimized and synthesized. The synthetic gene was expressed in Escherichia coli and recombinant core Chlorella dUTPase (chdUTPase) was purified. Crystallization of chdUTPase was performed by the repetitive hanging-drop vapor-diffusion method at 298 K with ammonium sulfate as the precipitant. In the presence of 2'-deoxyuridine-5'-[(α,β)-imido]triphosphate and magnesium, the enzyme produced die-shaped hexagonal R3 crystals with unit-cell parameters a = b = 66.9, c = 93.6 A, ƴ = 120°. X-ray diffraction …

Interferon Regulatory Factor 4 (Irf-4) Targets Irf-5 To Regulate Epstein-Barr Virus Transformation, Dongsheng Xu, Florencia Meyer, Erica Ehlers, Laura Blasnitz, Luwen Zhang

School of Biological Sciences: Faculty Publications

The cellular interferon regulatory factor-4 (IRF-4), which is a member of IRF family, is involved in the development of multiple myeloma and Epstein-Barr virus (EBV)-mediated transformation of B lymphocytes. However, the molecular mechanism of IRF-4 in cellular transformation is unknown. We have found that knockdown of IRF-4 leads to high expression of IRF-5, a pro-apoptotic member in the IRF family. Overexpression of IRF-4 represses IRF-5 expression. Reduction of IRF-4 leads to growth inhibition, and the restoration of IRF-4 by exogenous plasmids correlates with the growth recovery and reduces IRF-5 expression. In addition, IRF-4 negatively regulates IRF-5 promoter reporter activities and …

Fus Transgenic Rats Develop The Phenotypes Of Amyotrophic Lateral Sclerosis And Frontotemporal Lobar Degeneration, Cao Huang, Hongxia Zhou, Jianbin Tong, Han Chen, Yong-Jian Liu, Dian Wang, Xiaotao Wei, Xugang Xia

Nebraska Center for Biotechnology: Faculty and Staff Publications

Fused in Sarcoma (FUS) proteinopathy is a feature of frontotemporal lobar dementia (FTLD), and mutation of the fus gene segregates with FTLD and amyotrophic lateral sclerosis (ALS). To study the consequences of mutation in the fus gene, we created transgenic rats expressing the human fus gene with or without mutation. Overexpression of a mutant (R521C substitution), but not normal, human FUS induced progressive paralysis resembling ALS. Mutant FUS transgenic rats developed progressive paralysis secondary to degeneration of motor axons and displayed a substantial loss of neurons in the cortex and hippocampus. This neuronal loss was accompanied by ubiquitin aggregation and …

Comparative Manufacture And Cell-Based Delivery Of Antiretroviral Nanoformulations, Shantanu Balkundi, Ari S. Nowacek, Ram S. Veerubhotla, Han Chen, Andrea Martinez-Skinner, Upal Roy, R. Lee Mosley, Georgette Kanmogne, Xinming Liu, Alexander V. Kabanov, Tatiana Bronich, Joellyn Mcmillan, Howard E. Gendelman

Nebraska Center for Biotechnology: Faculty and Staff Publications

Nanoformulations of crystalline indinavir, ritonavir, atazanavir, and efavirenz were manufactured by wet milling, homogenization or sonication with a variety of excipients. The chemical, biological, immune, virological, and toxicological properties of these formulations were compared using an established monocyte-derived macrophage scoring indicator system. Measurements of drug uptake, retention, release, and antiretroviral activity demonstrated differences amongst preparation methods. Interestingly, for drug cell targeting and antiretroviral responses the most significant difference among the particles was the drug itself. We posit that the choice of drug and formulation composition may ultimately affect clinical utility.

Aphids: A Model For Polyphenism And Epigenetics, Dayalan G. Srinivasan, Jennifer A. Brisson

School of Biological Sciences: Faculty Publications

Environmental conditions can alter the form, function, and behavior of organisms over short and long timescales, and even over generations. Aphid females respond to specific environmental cues by transmitting signals that have the effect of altering the development of their offspring. These epigenetic phenomena have positioned aphids as a model for the study of phenotypic plasticity. The molecular basis for this epigenetic inheritance in aphids and how this type of inheritance system could have evolved are still unanswered questions. With the availability of the pea aphid genome sequence, new genomics technologies, and ongoing genomics projects in aphids, these questions can …

Where Have All The Plant Foods Gone? The Search For Refined Dietary Reconstruction From Chinchorro Mummies, Karl J. Reinhard, Sara Le-Roy-Toren, Bernardo Arriaza

Karl Reinhard Publications

The Chinchorro cemeteries of northern Chile are the first graveyards of the Andes (Arriaza 1995, Schiappacasse & Niemeyer 1984). The excavation and analysis of Chinchorro mummies reveals the 'true character of the people'. The burials themselves are optimal for preservation of corpses, burial furniture, and aspects of ceremonies associated with the dead. The analysis of corporeal remains gradually clarifies the details of daily activities and status. Therefore, we feel that a holistic approach to mummy studies provides enormously fruitful paths to understanding the character of the ancient Chinchorro society.

Paleoepidemiology Of Intestinal Parasites And Lice In Pre-Columbian South America, Adauto Araujo, Karl Reinhard, Daniela Leles, Luciana Sianto, Alena M. Iñiguez, Martin Fugassa, Bernardo Arriaza, Nancy Orellana, Luis 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 …

Orbitofrontal Cortex Provides Cross-Modal Valuation Of Self-Generated Stimuli, William A. Cunningham, Ingrid J. Haas, Ashley S. Waggoner

Department of Political Science: Faculty Publications

Prior research has shown that the orbitofrontal cortex (OFC) plays an important role in the representation of the evaluation of stimuli, regardless of stimulus modality. Based on these findings, researchers have proposed that the OFC serves a common currency function, allowing for the direct comparison of different types of perceptual stimuli (e.g. food, drink, money). The present study was designed to extend this research and investigate whether these same regions of OFC that have been identified in previous research are involved in evaluating imagined stimuli. Specifically, we asked participants to draw on prior attitudinal knowledge to generate internal representations of …

Body Mass Estimation In Amphicyonid Carnivoran Mammals: A Multiple Regression Approach From The Skull And Skeleton, Borja Figueirido, Juan Antonio Perez-Claros, Robert Hunt, Paul Palmqvist

University of Nebraska State Museum: Mammalogy Papers

The body masses of sixteen species of amphicyonids (Mammalia, Carnivora, Amphicyonidae) from the New and Old World were estimated on the basis of 86 osteological variables measured from the craniodental (N = 44) and postcranial (N = 42) skeleton of living species of Canidae and Ursidae. Given the absence of complete and well preserved skeletons of amphicyonids in the fossil record, multiple regression functions were derived separately from measurements taken from the mandible, the cranium and the major limb bones. The accuracy of the regression functions was evaluated using the percentage prediction error and the percentage standard error …

Evaluation Of The Modis Lai Product Using Independent Lidar-Derived Lai: A Case Study In Mixed Conifer Forest, Jennifer L.R. Jensen, Karen S. Humes, Andrew T. Hudak, Lee A. Vierling, Eric Delmelle

United States Department of Agriculture, Forest Service / University of Nebraska-Lincoln: Faculty Publications

This study presents an alternative assessment of the MODIS LAI product for a 58,000 ha evergreen needleleaf forest located in the western Rocky Mountain range in northern Idaho by using lidar data to model (R²=0.86, RMSE=0.76) and map LAI at higher resolution across a large number of MODIS pixels in their entirety. Moderate resolution (30 m) lidar-based LAI estimates were aggregated to the resolution of the 1-km MODIS LAI product and compared to temporally-coincident MODIS retrievals. Differences in the MODIS and lidar-derived values of LAI were grouped and analyzed by several different factors, including MODIS retrieval algorithm, sun/sensor …

Socio-Economic Impacts Of Climate Change On Rural United States, Pankaj Lal, Janaki R. R. Alavalapati, Evan D. Mercer

United States Department of Agriculture, Forest Service / University of Nebraska-Lincoln: Faculty Publications

Directly or indirectly, positively or negatively, climate change will affect all sectors and regions of the United States. The impacts, however, will not be homogenous across regions, sectors, population groups or time. The literature specifically related to how climate change will affect rural communities, their resilience, and adaptive capacity in the United States (U.S.) is scarce. This article bridges this knowledge gap through an extensive review of the current state of knowledge to make inferences about the rural communities vulnerability to climate change based on Intergovernmental Panel on Climate Change (IPCC) scenarios. Our analysis shows that rural communities tend to …

A Perspective On Thirty Years Of The Webb, Pearman And Leuning Density Corrections, Xuhui Lee, William J. Massman

United States Department of Agriculture, Forest Service / University of Nebraska-Lincoln: Faculty Publications

The density correction theory of Webb et al. (1980, Q J Roy Meteorol Soc 106: 85–100, hereafter WPL) is a principle underpinning the experimental investigation of surface fluxes of energy and masses in the atmospheric boundary layer. It has a long-lasting influence in boundary-layer meteorology and micrometeorology, and the year 2010 marks the 30th anniversary of the publication of the WPL theory. We provide here a critique of the theory and review the research it has spurred over the last 30 years. In the authors’ opinion, the assumption of zero air source at the surface is a fundamental novelty that …

Invasive Sweetclover (Melilotus Alba) Impacts Native Seedling Recruitment Along Floodplains Of Interior Alaska, Blaine T. Spellman, Tricia L. Wurtz

United States Department of Agriculture, Forest Service / University of Nebraska-Lincoln: Faculty Publications

Sweetclover (Melilotus alba) is a nonnative legume that has formed dense and extensive patches along several rivers in Alaska. Our research objective was to determine if sweetclover impacts recruitment of native seedlings in floodplain habitats. To determine if sweetclover impacted recruitment, we conducted a removal experiment along two rivers in interior Alaska. When compared to areas where sweetclover was removed, areas with sweetclover had approximately 50% greater mortality of native seedlings, 25% less recruiting species, and a significant reduction in the quantity of light available to seedlings on floodplain surfaces. To determine if sweetclover shading was a mechanism …

Engineering A Future For Amphibians Under Climate Change, Luke P. Shoo, Deanna H. Olson, Sarah K. Mcmenamin, Kris A. Murray, Monique Van Sluys, Maureen A. Donnelly, Danial Stratford, Juhani Terhivuo, Andres Merino-Viteri, Sarah M. Herbert, Phillip J. Bishop, Paul Stephen Corn, Liz Dovey, Richard A. Griffiths, Katrin Lowe, Michael Mahony, Hamish Mccallum, Jonathan D. Shuker, Clay Simpkins, Lee F. Skerrat, Stephen E. Williams, Jean-Marc Hero

United States Department of Agriculture, Forest Service / University of Nebraska-Lincoln: Faculty Publications

1. Altered global climates in the 21st century pose serious threats for biological systems and practical actions are needed to mount a response for species at risk.

2. We identify management actions from across the world and from diverse disciplines that are applicable to minimizing loss of amphibian biodiversity under climate change. Actions were grouped under three thematic areas of intervention: (i) installation of microclimate and microhabitat refuges; (ii) enhancement and restoration of breeding sites; and (iii) manipulation of hydroperiod or water levels at breeding sites.

3. Synthesis and applications. There are currently few meaningful management actions that will …

A Habitat Overlap Analysis Derived From Maxent For Tamarisk And The South-Western Willow Flycatcher, Patricia York, Paul Evangelista, Sunil Kumar, James Graham, Curtis Flather, Thomas Stohlgren

United States Department of Agriculture, Forest Service / University of Nebraska-Lincoln: Faculty Publications

Biologic control of the introduced and invasive, woody plant tamarisk (Tamarix spp, saltcedar) in south-western states is controversial because it affects habitat of the federally endangered South-western Willow Flycatcher (Empidonax traillii extimus). These songbirds sometimes nest in tamarisk where floodplain-level invasion replaces native habitats. Biologic control, with the saltcedar leaf beetle (Diorhabda elongate), began along the Virgin River, Utah, in 2006, enhancing the need for comprehensive understanding of the tamarisk-flycatcher relationship. We used maximum entropy (Maxent) modeling to separately quantify the current extent of dense tamarisk habitat (>50% cover) and the potential extent of …

A Qualitative And Quantitative Analysis Of Risk Perception And Treatment Options As Related To Wildfires In The Usda Fs Region 3 National Forests, Ingrid M. Martin, Wade E. Martin, Carol B. Raish

United States Department of Agriculture, Forest Service / University of Nebraska-Lincoln: Faculty Publications

As the incidence of devastating fires rises, managing the risk posed by these fires has become critical. This report provides important information to examine the ways that different groups or disaster subcultures develop the mentalities or perceived realities that affect their views and responses concerning risk and disaster preparedness. Fire risk beliefs and attitudes of individuals and groups from four geographic areas in the Southwest (U.S. Department of Agriculture, Forest Service, Region 3, Arizona and New Mexico) surrounding the Kaibab, Tonto, Santa Fe, and Lincoln National Forests are presented. Using both quantitative and qualitative methods, we collected information from three …

Carrying Capacity For Species Richness As A Context For Conservation: A Case Study Of North American Breeding Birds, Andrew J. Hansen, Linda Bowers Phillips, Curtis H. Flather, Jim Robinson-Cox

United States Department of Agriculture, Forest Service / University of Nebraska-Lincoln: Faculty Publications

Aim To demonstrate that the concept of carrying capacity for species richness (S_K) is highly relevant to the conservation of biodiversity, and to estimate the spatial pattern of S_K for native landbirds as a basis for conservation planning.

Location North America.

Methods We evaluated the leading hypotheses on biophysical factors affecting species richness for Breeding Bird Survey routes from areas with little influence of human activities.We then derived a best model based on information theory, and used this model to extrapolate SK across North America based on the biophysical predictor variables. The predictor variables included the …

Waiting For Grapes: Expectancy And Delayed Gratification In Bonobos, Jeffrey R. Stevens, Alexandra G. Rosati, Sarah R. Heilbronner, Nelly Mühlhoff

Department of Psychology: Faculty Publications

Responses to delayed rewards vary widely across individuals and have important implications for personality and temperament. Animals may avoid delayed rewards because the future is uncertain. Therefore, expectations about receiving a future reward should influence the response to delayed payoffs. Here, we offered bonobos (Pan paniscus) a delayed gratification task in which food accumulated over time. Once subjects chose to consume the reward, food stopped accumulating. We tested their willingness to wait with a reliable and an unreliable experimenter to vary the subjects’ expectations that they would receive the food. Subjects waited less often with the unreliable experimenter …

Cognitive-Behavioral Therapy For Immigrants Presenting With Social Anxiety Disorder: Two Case Studies, Brandon J. Weiss, J. Suzanne Singh, Debra Anne Hope

Department of Psychology: Faculty Publications

Cognitive-behavioral therapy (CBT) for the treatment of social anxiety disorder (SAD) has demonstrated efficacy in numerous randomized trials. However, few studies specifically examine the applicability of such treatment for ethnic minority clients. Thus, the purpose of this article is to present two case studies examining the utility of individualized CBT for SAD with two clients who immigrated to the United States, one from Central America and one from China, for whom English was not the primary language. Both clients demonstrated improvement on a semistructured interview and self-report measures. Necessary adaptations were modest, suggesting that therapy could be conducted in a …

The Importance Of Fatherhood To U.S. Married And Cohabiting Men, Veronica Tichenor, Julia Mcquillan, Arthur L. Greil, Raleigh Contreras, Karina M. Shreffler

Department of Sociology: Faculty Publications

Using a non-hierarchical approach to identity theory, we construct a scale to analyze the characteristics associated with the importance of fatherhood in a national sample of male partners (N = 932) of U.S. women of reproductive age, including fathers and non-fathers. OLS multiple regression shows that economic situation is not associated with importance of fatherhood, but valuing career success, higher education, higher religiosity and non-egalitarian gender attitudes (compared to egalitarian) are associated with higher importance of fatherhood scores. Leisure, age, fertility problems, and non-egalitarian gender attitudes are associated with importance of fatherhood scores differently for fathers and non-fathers. Although fathers …