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Practical And Predictive Bioinformatics Methods For The Identification Of Potentially Cross-Reactive Protein Matches, Richard E. Goodman

Department of Food Science and Technology: Faculty Publications

A bioinformatics comparison of proteins introduced into food crops through genetic engineering provides a mechanism to identify those proteins that may present an increased risk of allergic reactions for individuals with existing allergies. The goal is to identify proteins that are known to be allergens or are so similar to an allergen that they may induce allergic cross-reactions. Three comparative approaches have traditionally been used, or considered for safety evaluations. One identifies any short (6–8) amino acid segment of the protein that exactly matches a known allergen sequence. The second is an overall primary sequence comparison using Basic Local Alignment …

Biotinylation Of K8 And K12 Co-Occurs With Acetylation And Mono-Methylation In Human Histone H4, Yap Ching Chew, Ashraf S. Raza, Gautam Sarath, Janos Zempleni

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

Histones H1, H2A, H2B, H3, and H4 are proteins that are critical for folding of DNA into chromatin. Posttranslational acetylation, methylation, and biotinylation of histones participate in gene silencing, mitotic condensation of chromatin, and the cellular response to DNA damage. Various modifications of histones are known to interact ("cross-talk") in chromatin-remodeling events; interactions may be synergistic or antagonistic. Here, we sought to identify biotinylation sites in human histone H4 by using mass spectrometry (MS/MS), and we sought to determine whether biotinylation co-exists with acetylation and methylation in the same H4 molecule. Nuclear histones from human lymphoid (Jurkat) cells were digested …

Survey Of Phytophagous Insects And Foliar Pathogens In China For A Biocontrol Perspective On Kudzu, Pueraria Montana Var. Lobata (Willd.) Maesen And S. Almeida (Fabaceae), Jiang-Hua Sun, Zhu-Dong Liu, Kerry O. Britton, Ping Cai, David Orr, Judith Hough-Goldstein

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

A three-year survey of kudzu foliage, seed, stems, and roots for associated phytophagous insects was conducted to establish basic information about the insect communities that kudzu harbors in China and to assess the abundance, diversity and damage caused by these insects. Diseases of kudzu were also surveyed in southern China. A total of 116 phytophagous insect species in 31 families and 5 orders were collected from kudzu in China, in six feeding guilds: foliage, sap, stem, terminal, seed and root feeders. The impact of foliage feeders varied from site to site and year to year, and over the course of …

Remote Sensing Techniques To Assess Active Fire Characteristics And Post-Fire Effects, Leigh B. Lentile, Zachary A. Holden, Alistair M.S. Smith, Michael J. Falkowski, Andrew T. Hudak, Penelope Morgan, Sarah A. Lewis, Paul E. Gessler, Nate C. Benson

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

Space and airborne sensors have been used to map area burned, assess characteristics of active fires, and characterize post-fire ecological effects. Confusion about fire intensity, fire severity, burn severity, and related terms can result in the potential misuse of the inferred information by land managers and remote sensing practitioners who require unambiguous remote sensing products for fire management. The objective of the present paper is to provide a comprehensive review of current and potential remote sensing methods used to assess fire behavior and effects and ecological responses to fire. We clarify the terminology to facilitate development and interpretation of comprehensible …

Biological Opinion On The Operation Of The Missouri River Main Stem System, Missouri River Bank Stabilization And Navigation Project, And Operation Of The Kansas River Reservoir System

United States Army Corps of Engineers, Omaha District

The U.S. Army Corps of Engineers (Corps) prepares an annual report for interested parties in accordance with the reporting requirements of the “Biological Opinion (BiOp) on the Operation of the Missouri River Main Stem System, Operation and Maintenance of the Missouri River Bank Stabilization and Navigation Project (BSNP), and Operation of the Kansas River Reservoir System” prepared by the U.S. Fish and Wildlife Service (Service) dated November 30, 2000 and the Amendment, thereto, dated December 16, 2003.

This annual report documents the Corps threatened and endangered species conservation activities to comply with the provisions of the 2000 BiOp and the …

Molecular Effects Of Nicarbazin On Avian Reproduction, C. A. Yoder, J. K. Graham, L. A. Miller

United States Department of Agriculture Wildlife Services: Staff Publications

Nicarbazin (NCZ) is an anticoccidial drug routinely used in the poultry industry that can negatively affect reproduction by reducing egg production, egg weight, and egg hatchability. The molecular mechanisms by which NCZ affects reproduction are unknown. Lipoprotein lipase, vitellogenin, transglutaminase, and calcium are all involved in egg formation and embryogenesis. Therefore, in vitro assays were used to evaluate 4 potential mechanisms of action of NCZ on egg formation and embryogenesis. First, a lipoprotein lipase assay was conducted to determine if NCZ increases lipoprotein lipase activity. Second, vitellogenin phosphorylation was evaluated to determine if NCZ acts as a vitellogenin phosphatase. Third, …

Anthropogenic Drivers Of Ecosystem Change: An Overview, Gerald C. Nelson, Elena Bennett, Asmeret A. Berhe, Kenneth G. Cassman, Ruth Defries, Thomas Dietz, Achim R. Dobermann, Andrew Dobson, Anthony Janetos, Marc Levy, Diana Marco, Nebojsa Nakicenovic, Brian O'Neill, Richard Norgaard, Gerhard Petschel-Held, Dennis Ojima, Prabhu Pingali, Robert Watson, Monika Zurek

Department of Agronomy and Horticulture: Faculty Publications

This paper provides an overview of what the Millennium Ecosystem Assessment (MA) calls “indirect and direct drivers” of change in ecosystem services at a global level. The MA definition of a driver is any natural or human-induced factor that directly or indirectly causes a change in an ecosystem. A direct driver unequivocally influences ecosystem processes. An indirect driver operates more diffusely by altering one or more direct drivers. Global driving forces are categorized as demographic, economic, sociopolitical, cultural and religious, scientific and technological, and physical and biological. Drivers in all categories other than physical and biological are considered indirect. Important …

Ethylene Could Influence Ferric Reductase, Iron Transporter, And H+-Atpase Gene Expression By Affecting Fer (Or Fer-Like) Gene Activity, Carlos Lucera, Brian M. Waters, Francisco Javier Romera, María José García, María Morales, Esteban Alcántara, Rafael Pérez-Vicente

Department of Agronomy and Horticulture: Faculty Publications

In previous works, it has been shown, by using ethylene inhibitors and precursors, that ethylene could participate in the regulation of the enhanced ferric reductase activity of Fe-deficient Strategy I plants. However, it was not known whether ethylene regulates the ferric reductase gene expression or other aspects related to this activity. This paper is a study of the effects of ethylene inhibitors and precursors on the expression of the genes encoding the ferric reductases and iron transporters of Arabidopsis thaliana (FRO2 and IRT1) and Lycopersicon esculentum (= Solanum lycopersicum) (FRO1 and IRT1) plants. The effects …

Land Application Of Manure For Beneficial Reuse, L. M. Risse, M. L. Cabrera, A. J. Franzluebbers, J. W. Gaskin, John E. Gilley, R. Killorn, D. E. Radcliffe, W. E. Tollner, H. Zhang

Department of Agricultural and Biological Systems Engineering: Faculty Publications

The concentration of animal production systems has increased efficiency and improved overall economic return for animal producers. This concentration, along with the advent of commercial fertilizers, has led to a change in the way animal producers view manure. Manure, once valued as a resource by farmers, is now treated as a waste. Air and water quality concerns that arise primarily from the under-utilization or inefficient use of manure contribute to these changing views. However, when properly used, manure is a resource and should be regulated as such. In the United States, the USDA/EPA Unified National Strategy for Animal Feeding Operations …

Social Play In Kakapo (Strigops Habroptilus) With Comparisons To Kea (Nestor Notabilis) And Kaka (Nestor Meridionalis), Judy Diamond, Daryl Eason, Clio Reid, Alan B. Bond

Papers in Behavior in Biological Sciences

The play behavior of the critically endangered kakapo (Strigops habroptilus; Aves: Psittaciformes: Psittacidae) is here compared to that of its closest relatives, the kea (Nestor notabilis) and the kaka (Nestor meridionalis). Contrasting kakapos, which are relatively solitary, with the more social Nestor parrots provides an attractive test of the relative contributions of phylogeny and sociality to the evolution of play. Overlapping cluster analysis of play sequences using a hypergeometric similarity metric indicated that kakapo play is generally less complex, lacking the intensity, duration, structure, and reciprocity of play in the Nestor parrots. Kakapos have …

Microsatellite Genotyping To Distinguish Colonies And Intraspecies Genetic Variation In The Eastern Subterranean Termite, Reticulitermes Flavipes (Isoptera: Rhinotermitidae), Timothy J. Husen, Shripat T. Kamble, Julie M. Stone

Department of Biochemistry: Faculty Publications

Microsatellite markers and fingerprinting techniques have demonstrated great potential for assessing colony affiliation in Reticulitermes species. This study utilized microsatellite allele fingerprints and examined variation at eight micro satellite loci within five different R. flavipes collection sites in each of Lancaster and Madison counties in Nebraska. In the termite populations from Lancaster County, five of the eight microsatellite loci (Rf 1-3, Rf 3-1, Rf 5-1 0, Rf 6-1, and Rf 24-2) provided informative genotypic variability allowing colony distinction. DNA sequence data at locus Rf24-2 also provided conclusive evidence that populations sampled were distinct colonies. Five micro satellite loci (Rf 3-1, …

Wing Dimorphism In Aphids, Christian Braendle, Gregory K. Davis, Jennifer A. Brisson, David L. Stern

School of Biological Sciences: Faculty Publications

Many species of insects display dispersing and nondispersing morphs. Among these, aphids are one of the best examples of taxa that have evolved specialized morphs for dispersal versus reproduction. The dispersing morphs typically possess a full set of wings as well as a sensory and reproductive physiology that is adapted to flight and reproducing in a new location. In contrast, the nondispersing morphs are wingless and show adaptations to maximize fecundity. In this review, we provide an overview of the major features of the aphid wing dimorphism. We first provide a description of the dimorphism and an overview of its …

The Pea Aphid, Acyrthosiphon Pisum: An Emerging Genomic Model System For Ecological, Developmental, And Evolutionary Studies, Jennifer A. Brisson, David L. Stern

School of Biological Sciences: Faculty Publications

Aphids display an abundance of adaptations that are not easily studied in existing model systems. Here we review the biology of a new genomic model system, the pea aphid, Acyrthosiphon pisum. We then discuss several phenomena that are particularly accessible to study in the pea aphid: the developmental genetic basis of polyphenisms, aphid–bacterial symbioses, the genetics of adaptation and mechanisms of virus transmission. The pea aphid can be maintained in the laboratory and natural populations can be studied in the field. These properties allow controlled experiments to be performed on problems of direct relevance to natural aphid populations. Combined …

The Developmental And Molecular Basis Of Allometry In Drosophila, Alexander W. Shingleton, Jennifer A. Brisson, David L. Stern

School of Biological Sciences: Faculty Publications

Allometry is the scaling relationship between the size of an organism and the size of its constituent parts. Despite its obvious developmental and evolutionary importance, very little is known of the mechanisms that regulate allometries. Here, we look at one particular type of allometry—that created by rearing Drosophila under different nutritional conditions. Drosophila larvae that are fed increasingly suboptimal diets eclose into increasingly small adults with increasingly small body parts. Surprisingly, however, the male genitals remain approximately the same size under a range of nutritional conditions. The genitals therefore maintain a different allometric relationship with the body than other structures. …

Optimal Time Allocation In Parasitic Wasps Searching For Hosts And Food, Brigitte Tenhumberg, Gitta Siekmann, Michael A. Keller

School of Biological Sciences: Faculty Publications

Many species of parasitic wasp feed on sugar sources such as nectar and honeydew in order to replenish their energy reserves and so extend their life expectancy, which is often correlated with higher reproductive success. Recent research suggests that carbohydrates are also a key component in flight fuel in such insects. The importance of sugar in fuelling locomotion suggests location of sugar-rich food may be more important in parasitoid foraging behavior than has previously been assumed. If sugar sources and hosts are separated in space, parasitoids have to allocate their time between sugar-searching and host-searching. Using a stochastic dynamic programming …

Microorganisms Pumping Iron: Anaerobic Microbial Iron Oxidation And Reduction, Karrie A. Weber, Laurie A. Achenbach, John D. Coates

School of Biological Sciences: Faculty Publications

Iron (Fe) has long been a recognized physiological requirement for life, yet for many microorganisms that persist in water, soils and sediments, its role extends well beyond that of a nutritional necessity. Fe(II) can function as an electron source for iron-oxidizing microorganisms under both oxic and anoxic conditions and Fe(III) can function as a terminal electron acceptor under anoxic conditions for iron-reducing microorganisms. Given that iron is the fourth most abundant element in the Earth’s crust, iron redox reactions have the potential to support substantial microbial populations in soil and sedimentary environments. As such, biological iron apportionment has been described …

Superoxide Dismutase Activities In Long-Lived Drosophila Melanogaster Females: Chico1 Genotypes And Dietary Dilution, Hadise Kabil, Linda Partridge, Lawrence G. Harshman

Lawrence G. Harshman Publications

Superoxide dismutase (SOD) activities were determined for dietary dilution conditions that extend the life span of Drosophila melanogaster. The hypothesis motivating this research was that elevated SOD activity is associated with increased life span resulting from flies being held on a restricted diet. SOD activities were also measured for chico¹ which is a mutation in the insulin receptor substrate protein gene associated with life span extension. This allowed us to confirm the results of (Clancy et al. 2001) and extend the results by measuring CuZn SOD and Mn SOD activities in addition to the previously determined overall SOD activity. …

Negative Impact Of Noise On The Principal Component Analysis Of Nmr Data, Steven M. Halouska, Robert Powers

Department of Chemistry: Faculty Publications

Principal component analysis (PCA) is routinely applied to the study of NMR based metabolomic data. PCA is used to simplify the examination of complex metabolite mixtures obtained from biological samples that may be composed of hundreds or thousands of chemical components. PCA is primarily used to identify relative changes in the concentration of metabolites to identify trends or characteristics within the NMR data that permits discrimination between various samples that differ in their source or treatment. A common concern with PCA of NMR data is the potential over emphasis of small changes in high concentration metabolites that would over-shadow signifi …

Glucocorticoid Hormone Levels Increase With Group Size And Parasite Load In Cliff Swallows, Samrrah A. Raouf, Linda C. Smith, Mary Bomberger Brown, John C. Wingfield, Charles R. Brown

School of Biological Sciences: Faculty Publications

Animals often cope with adverse events by releasing glucocorticoid hormones, which in turn promote increased energy assimilation. In captive animals, crowding also leads to increased glucocorticoid activity, probably because of increased levels of social competition. We investigated how group size and ectoparasite infestations affected endogenous levels of the glucocorticoid hormone, corticosterone, in colonial cliff swallows, Petrochelidon pyrrhonota, in southwestern Nebraska, USA. Parasites were removed from some colonies by fumigating nests. Baseline levels of corticosterone in breeding adults varied significantly with whether parasites were present, colony size (measured by total number of active nests at a site), and nesting stage. …

A Coprological View Of Ancestral Pueblo Cannibalism Debate Over A Single Fecal Fossil Offers A Cautionary Tale Of The Interplay Between Science And Culture, Karl J. Reinhard

Karl Reinhard Publications

As the object of my scientific study, I’ve chosen coprolites. It’s not a common choice, but to a paleonutritionist and archaeoparasitologist, a coprolite—a sample of ancient feces preserved by mineralization or simple drying—is a scientific bonanza. Analysis of coprolites can shed light on both the nutrition of and parasites found in prehistoric cultures. Dietary reconstructions from the analysis of coprolites can inform us about, for example, the origins of modern Native American diabetes. With regard to parasitology, coprolites hold information about the ancient emergence and spread of human infectious disease. Most sensational, however, is the recent role of coprolite analysis …

Abundance And Distribution Of Selected Elements In Soils, Stream Sediments, And Selected Forage Plants From Desert Tortoise Habitats In The Mojave And Colorado Deserts, Usa, M. A. Chaffee, K. H. Berry

United States Geological Survey: Staff Publications

A baseline and background chemical survey was conducted in southeastern California, USA, to identify potential sources of toxicants in natural and anthropogenically-altered habitats of the threatened desert tortoise (Gopherus agassizii). Soil, stream sediment, and plant samples were collected from six tortoise habitat study areas in the Mojave and Colorado deserts and analysed for up to 66 different elements. The chemical analyses provided new information on the abundances and distributions of selected elements in this region. Soil, stream-sediment, and plant analyses showed distinct variations in bulk chemistries from locality to locality. Variations were, in general, consistent with the many …

Landscape Context Mediates Influence Of Local Food Abundance On Wetland Use By Wintering Shorebirds In An Agricultural Valley, Oriane W. Taft, Susan M. Haig

United States Geological Survey: Staff Publications

While it is widely understood that local abundance of benthic invertebrates can greatly influence the distribution and abundance of wetland birds, no studies have examined if wetland landscape context can mediate this relationship. We studied the influence of wetland food abundance and landscape context on use of agricultural wetlands by wintering dunlin (Calidris alpina) and killdeer (Charadrius vociferus) in the Willamette Valley of Oregon, USA, over two winters (1999–2000, 2000–2001) of differing rainfall and subsequent habitat distribution. We monitored bird use (frequency of occurrence and abundance) at a sample of wetlands differing in local food abundance …

Environmental Contaminants In Fish And Their Associated Risk To Piscivorous Wildlife In The Yukon River Basin, Alaska, Jo Ellen Hinck, Christopher J. Schmitt, Kathy R. Echols, Tom W. May, Carl E. Orazio, Donald E. Tillitt

United States Geological Survey: Staff Publications

Organochlorine chemical residues and elemental contaminants were measured in northern pike (Esox lucius), longnose sucker (Catostomus catostomus), and burbot (Lota lota) from 10 sites in the Yukon River Basin (YRB) during 2002. Contaminant concentrations were compared to historical YRB data and to toxicity thresholds for fish and piscivorous wildlife from the scientific literature. A risk analysis was conducted to screen for potential hazards to piscivorous wildlife for contaminants that exceeded literature-based toxicity thresholds. Concentrations of total DDT (sum of p,p¢-homologs; 1.09–13.6 ng/g), total chlordane (0.67–7.5 ng/g), dieldrin (<0.16–0.6 ng/g), toxaphene (<11–34 ng/g), total PCBs (<20– 87 ng/g), TCDD-EQ (<1.7 pg/g), arsenic (0.03–1.95 lg/g), cadmium (<0.02–0.12 lg/g), copper (0.41–1.49 lg/g), and lead (<0.21–0.27 lg/g) did not exceed toxicity thresholds for growth and reproduction in YRB fish. Concentrations of mercury (0.08–0.65 lg/g), selenium (0.23–0.85 lg/g), and zinc (11–56 lg/g) exceeded toxicity thresholds in one or more samples and were included in the risk analysis for piscivorous wildlife. No effect hazard concentrations (NEHCs) and low effect hazard concentrations (LEHCs), derived from literaturebased toxicity reference values and avian and mammalian life history parameters, were calculated for mercury, selenium, and zinc. Mercury concentrations in YRB fish exceeded the NEHCs for all bird and small mammal models, which indicated that mercury concentrations in fish may represent a risk to piscivorous wildlife throughout the YRB. Low risk to piscivorous wildlife was associated with selenium and zinc concentrations in YRB fish. Selenium and zinc concentrations exceeded the NEHCs and LEHCs for only the small bird model. These results indicate that mercury should continue to be monitored and assessed in Alaskan fish and wildlife.

Dinsdale Family Luncheon, John Owens

John Owens: Speeches and Appearances

Today we celebrate and honor the 2006 recipients of the Dinsdale Family Faculty Awards, made possible by the generosity of the Dinsdale family.

Aglec Advisory Council Meeting, John Owens

John Owens: Speeches and Appearances

Thank you for inviting me to be with you today to discuss one of my favorite topics - education and the terrifically talented young people who come to study with us in the College of Agricultural Sciences and Natural Resources, or CASNR, in the Institute of Agriculture and Natural Resources here at the University of Nebraska-Lincoln.

Nebraska Hall Of Agricultural Achievement Dinner, John Owens

John Owens: Speeches and Appearances

It is my pleasure to be with you tonight celebrating the accomplishments of these wonderful and worthy new additions to the Nebraska Hall of Agricultural Achievement. I'm delighted to have this opportunity to help recognize these individuals so deserving of their honors. What a pleasure to say, “well done and thank you” to people who make such significant contributions to the world, who live their lives meaningfully in the way they choose to put their talents and energies to work.

Omtvedt Innovation Award Presented To Marilyn Fox, John Owens

John Owens: Speeches and Appearances

It is such a pleasure to honor innovation and strength in the Institute of Agriculture and Natural Resources today through this 2006 Omtvedt Innovation Award. This award is made possible because of the generosity of Leone and the late Neal Harlan, great friends of the Institute of Agriculture and Natural Resources. The Harlans had the vision and the foresight to realize the importance of recognizing and supporting outstanding and innovative work in the Institute, and honored Irv Omtvedt on his retirement as Vice Chancellor of the Institute with a generous gift of funds to support the Omtvedt Innovation Awards. These …

Tannerella Forsythia, A Periodontal Pathogen Entering The Genomic Era, Anne C. R. Tanner, Jacques Izard

Department of Food Science and Technology: Faculty Publications

Several questions need to be addressed to evaluate whether Tannerella forsythia is to be considered a periodontal pathogen. T. forsythia has been detected in periodontal health and disease, so could it be a pathogen? The species was not detected in many studies despite finding other putative pathogens, so could it be important in pathogenicity? The challenges of working with T. forsythia include its fastidious and anaerobic growth requirements for cultural detection. Thus, studies associating T. forsythia with periodontal and other oral infections have used noncultural approaches (immunoassays and DNA-based assays) in addition to cultural approaches. We feel …

Nutrient Uptake Of Maize Affected By Nitrogen And Potassium Fertility In A Humid Subtropical Environment, H. Arnold Bruns, M. Wayne Ebelhar

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

Nitrogen (N) and potassium (K) fertility management of maize (Zea mays L.) in the humid subtropical Mississippi Delta may differ from a temperate climate because of its use in rotation with cotton (Gossypium hirsutum L.), soil temperatures rarely falling to 0 °C, and heavy winter rains that facilitate nutrient losses. An experiment to determine the [N] (concentration = [ ]), phosphorus [P], [K], calcium [Ca], magnesium [Mg], iron [Fe], manganese [Mn], zinc [Zn], and copper [Cu] and their total contents plant^-1 of maize grown in rotation with cotton, using N fertility levels of (134, 179, 224, 269, …

International Shipping Of Fumonisins From Maize Extracts On C18 Sorbent, R. T. Riley, O. A. Torres, E. Palencia

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

Fumonisins are mycotoxins found in maize. In developing countries, the resources required for analysis are often lacking, and the shipping of maize between countries can be difficult since the importation of plant materials requires permits/ inspection to prevent the entry of pests that frequently infest maize. A simple, safe and legal method for shipping maize extracts to the USA was needed to conduct a survey of fumonisins in Central America. The objective was to develop a method for isolating and shipping maize extracts for fumonisin analysis so as to facilitate a survey of fumonisin exposure. The results indicate that fumonisins …