Digital Commons Network^™

A Nano Particle Vector Comprised Of Poly Lactic-Co-Glycolic Acid And Monophosphoryl Lipid A And Recombinant Mycobacterium Avium Subsp Paratuberculosis Peptides Stimulate A Pro-Immune Profile In Bovine Macrophages, C.D. Souza, John Bannantine, W.C. Brown, M.G. Norton, W.C. Davis, J.K. Hwang, P. Ziaei, Gaber S. Abdellrazeq, M.V. Eren, J.R. Deringer, E. Laws, M.C.D. Cardieri

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

Aims: We evaluated the potential of a nanoparticle (NP) delivery system to improve methods of delivery of candidate peptide-based vaccines for Paratuberculosis in cattle.

Methods and Results: Peptides derived from Mycobacterium avium subsp. paratuberculosis (Map), and the pro-inflammatory monophosphoryl lipid A (MPLA) were incorporated in polymeric NPs based on poly (D,L-lactide-co- glycolide) (PLGA). The PLGA/MPLA NPs carriers were incubated with macrophages to examine their effects on survival and function. PLGA/MPLA NPs, with and without Map antigens, are efficiently phagocytized by macrophages with no evidence of toxicity. PLGA/MPLA NP formulations did not alter the level of expression of MHC I or …

Identification Of Sero-Reactive Antigens For The Early Diagnosis Of Johne’S Disease In Cattle, Lingling Li, J. P. Bannantine, Joseph Campo, Arlo Randall, Yrjo T. Grohn, Robab Katani, Megan Schilling, Jessica Radzio-Basu, Vivek Kapur

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

Mycobacterium avium subsp. paratuberculosis (MAP) is the causative agent of Johne’s disease (JD), a chronic intestinal inflammatory disease of cattle and other ruminants. JD has a high herd prevalence and causes serious animal health problems and significant economic loss in domesticated ruminants throughout the world. Since serological detection of MAP infected animals during the early stages of infection remains challenging due to the low sensitivity of extant assays, we screened 180 well-characterized serum samples using a whole proteome microarray from Mycobacterium tuberculosis (MTB), a close relative of MAP. Based on extensive testing of serum and milk samples, fecal culture and …

Cell Wall Peptidolipids Of Mycobacterium Avium: From Genetic Prediction To Exact Structure Of A Nonribosomal Peptide, John Bannantine, Giles Etienne, Francoise Laval, Judith R. Stabel, Anne Lemassu, Mamadou Daffe, Darrell O. Bayles, Christelle Ganneau, Frederic Bonhomme, Maxime Branger, Thierry Cochard, Sylvie Bay, Franck Biet

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

Mycobacteria have a complex cell wall structure that includes many lipids; however, even within a single subspecies of Mycobacterium avium these lipids can differ. Total lipids from an M. avium subsp. paratuberculosis (Map) ovine strain (S-type) contained no identifiable glycopeptidolipids or lipopentapeptide (L5P), yet both lipids are present in other M. avium subspecies. We determined the genetic and phenotypic basis for this difference using sequence analysis as well as biochemical and physico-chemical approaches. This strategy showed that a nonribosomal peptide synthase, encoded by mps1, contains three amino acid specifying modules in ovine strains, compared to five modules in bovine strains …

Strategies For Evading Blackbird Damage, George M. Linz, Page E. Klug

United States Department of Agriculture Wildlife Services: Staff Publications

Foraging blackbird flocks have great mobility as they search for food that is plentiful, is easily accessed, and has a high nutritional value. Ripening corn, rice, and sunflower fit those criteria, as does seeded rice. The birds will move from field to field to find the ideal combination of energy spent to discover food versus the energy value of the food (Pyke et al. 1977). An extraordinary effort is often needed to actively move the birds from a foraging location with a high positive value (e.g., close to roost and early ripening sunflower) versus a location with a I~w value …

Automating The Milking Process Within A Grass-Based System, John Shortall

Theses

The successful integration of automatic milking (AM) and grazing has resulted in AM becoming a feasible alternative to conventional milking (CM) in pasture-based systems. The objective of this thesis was to establish (i) the social, environmental and economic effects of adopting AM technology and (ii) the factors affecting cow traffic, which once the AM is adopted, can also impact on the sustainability of AM. A theme across this thesis is the examination of AM in the context of a seasonal pasture-based milk production system. Electricity and water meters were installed on seven AM fanns. Milking and livestock/^miscellaneous processes were the …

Meat For Missoula: Educating Our Youth On Sustainable Meat Production Practices, Amelia R G Liberatore

Undergraduate Theses, Professional Papers, and Capstone Artifacts

In autumn 2016, a controversy arose when a student group, Advocates for Animals, took up a campaign against three meat pigs at the PEAS Farm due to strong views about animal consumption. Pigs serve as a central piece of food source education to hundreds of Missoula children who visit the farm every year. Unfortunately, the controversy overshadowed the educational purpose of exposing children to sustainable meat production practices. Moreover, access to the PEAS Farm and good food education is not available to all local children. I wondered whether education was accessible elsewhere. Unfortunately, child-appropriate, culturally relevant food literature is scarce. …

Goldfields Nullarbor Rangelands Biosecurity Association Inc. Activity Report 2016/17, Goldfields Nullarbor Rangelands Biosecurity Association Inc.

Recognised Biosecurity Group Annual Reports

The Goldfields Nullarbor Rangelands Biosecurity Association Inc. (GNRBA) is unique in rangeland management across Western Australia. It has a huge area to service and is working hard to provide a top class service to ratepayers. It is now well recognised as being a leader in the RBG’s in WA. The GNRBA Inc formally became operational on 1st July 2011. At this time it took over the APB Zone 9 operations.

Kimberley Rangelands Biosecurity Association Invasive Species Activity Report 2016/17, Kimberley Rangelands Biosecurity Association

Recognised Biosecurity Group Annual Reports

The Kimberley Rangelands Biosecurity Association (KRBA) has an annual Large Feral Herbivore culling program that includes feral donkeys, horses and camels with other animals such as water buffalo and pigs targeted when located. The program focusses primarily on donkeys, using the radio telemetry technique with horses and camels culled opportunistically during tracking. Currently there are 135 active collars throughout the region.

Meekatharra Rangelands Biosecurity Association Inc. Annual Report 2016/17, Meekatharra Rangelands Biosecurity Association Inc.

Recognised Biosecurity Group Annual Reports

The Meekatharra Rangelands Biosecurity Association Inc (MRBA) is an industry body with a membership of all pastoralists in the Shires of Yalgoo, Mount Magnet, Cue and Meekatharra. The Association has been established under the Biosecurity and Agriculture Management Act 2007 with a charter to manage and control declared pests, both animal and plant.

Pilbara Regional Biosecurity Group Inc. Annual Report 2016/17, Pilbara Regional Biosecurity Group Inc.

Recognised Biosecurity Group Annual Reports

The Pilbara RBG is a not for profit association formed under the Associations Incorporation Act 2015, providing declared pest control programs for land managers, particularly in the pastoral zone. The associations’ primary purpose is the control of declared pests using funding from Declared Pest Rates paid by landholders on pastoral stations. These Declared Pest Rates funds are matched dollar for dollar by the WA Government to reflect the public benefit of controlling declared pest animals and weeds. The association is formally recognised by the Hon Minister for Agriculture and Food as a recognised biosecurity group (RBG).

Closing Abandoned Livestock Lagoons Effectively To Utilize Nutrients And Avoid Environmental Problems, Leslie J. Johnson, Charles Shapiro, Amy Schmidt

Nebraska Cooperative Extension: Faculty and Staff Publications

In Nebraska alone, nearly 400 earthen manure storage structures are in operation; approximately four dozen requests to cease operation of permitted lagoons were received by the Nebraska Department of Environmental Quality in the prior decade with many more non-permitted storage structures being in need of proper closure. Abandoned livestock lagoons, earthen manure storage basins, and other manure storages (e.g. concrete pits) need to be decommissioned in a manner that controls potential environmental risk and makes economical use of accumulated nutrients. Currently, limited guidance is available to support lagoon closure planning and implementation and few professionals who support livestock producers have …

Influence Of Olfactory And Visual Cover On Nest Site Selection And Nest Success For Grassland-Nesting Birds, Dillon T. Fogarty, Dwayne Elmore, Samuel D. Fuhlendorf, Scott R. Loss

Department of Agronomy and Horticulture: Faculty Publications

Habitat selection by animals is influenced by and mitigates the effects of predation and environmental extremes. For birds, nest site selection is crucial to offspring production because nests are exposed to extreme weather and predation pressure. Predators that forage using olfaction often dominate nest predator communities; therefore, factors that influence olfactory detection (e.g., airflow and weather variables, including turbulence and moisture) should influence nest site selection and survival. However, few studies have assessed the importance of olfactory cover for habitat selection and survival. We assessed whether ground-nesting birds select nest sites based on visual and/or olfactory cover. Additionally, we assessed …

Genome-Guided Phylo-Transcriptomic Methods And The Nuclear Phylogentic Tree Of The Paniceae Grasses, Jacob D. Washburn, James C. Schnable, Gavin C. Conant, Thomas P. Brutnell, Ying Shao, Yang Zhang, Martha Ludwig, Gerrit Davidse, J. Chris Pires

Department of Agronomy and Horticulture: Faculty Publications

The past few years have witnessed a paradigm shift in molecular systematics from phylogenetic methods (using one or a few genes) to those that can be described as phylogenomics (phylogenetic inference with entire genomes). One approach that has recently emerged is phylo-transcriptomics (transcriptome-based phylogenetic inference). As in any phylogenetics experiment, accurate orthology inference is critical to phylo-transcriptomics. To date, most analyses have inferred orthology based either on pure sequence similarity or using gene-tree approaches. The use of conserved genome synteny in orthology detection has been relatively under-employed in phylogenetics, mainly due to the cost of sequencing genomes. While current trends …

Dissecting The Genetic Basis Of Local Adaptation In Soybean, Nonoy B. Bandillo, Justin E. Anderson, Michael B. Kantar, Robert M. Stupar, James E. Specht, George L. Graef, Aaron J. Lorenz

Department of Agronomy and Horticulture: Faculty Publications

Soybean (Glycine max) is the most widely grown oilseed in the world and is an important source of protein for both humans and livestock. Soybean is widely adapted to both temperate and tropical regions, but a changing climate demands a better understanding of adaptation to specific environmental conditions. Here, we explore genetic variation in a collection of 3,012 georeferenced, locally adapted landraces from a broad geographical range to help elucidate the genetic basis of local adaptation. We used geographic origin, environmental data and dense genome-wide SNP data to perform an environmental association analysis and discover loci displaying steep …

Comparison Of Organic And Integrated Nutrient Management Strategies For Reducing Soil N2O Emissions, Rebecca F. Graham, Samuel E. Wortman, Cameron M. Pittelkow

Department of Agronomy and Horticulture: Faculty Publications

To prevent nutrient limitations to crop growth, nitrogen is often applied in agricultural systems in the form of organic inputs (e.g., crop residues, manure, compost, etc.) or inorganic fertilizer. Inorganic nitrogen fertilizer has large environmental and economic costs, particularly for low-input smallholder farming systems. The concept of combining organic, inorganic, and biological nutrient sources through Integrated Nutrient Management (INM) is increasingly promoted as a means of improving nutrient use efficiency by matching soil nutrient availability with crop demand. While the majority of previous research on INM has focused on soil quality and yield, potential climate change impacts have rarely been …

Supplemental Material For: Multi-Site Evaluation Of Apex For Water Quality: Ii. Regional Parameterization, Nathan O. Nelson, Claire Baffaut, John A. Lory, G.M.M.M. Anomaa Senaviratne, Ammar B. Bhandari, Ranjith P. Udawatta, Daniel W. Sweeney, Matt J. Helmers, Mike W. Van Liew, Antonio P. Mallarino, Charles S. Wortmann

Department of Agronomy and Horticulture: Faculty Publications

Model performance was assessed using Nash-Sutcliffe model efficiency (NSE), coefficient of determination (r²), and percent bias (PBIAS) as defined by Moriasi et al. (2007 and 2015). Threshold values indicating acceptable model performance based on these statistics are dependent on the spatial and temporal scales of the data, water quality constituents of interest, and the modeling objectives (Moriasi et al., 2015). Although some standard values have been suggested (Moriasi et al., 2007 and 2015), considerable variability exist in the published literature. For instance Ramanarayan et al. (1997) considered r² >0.5 and NSE >0.40 as satisfactory for simulation of …

Author Correction: Genome-Guided Phylo-Transcriptomic Methods And The Nuclear Phylogenetic Tree Of The Paniceae Grasses, Jacob D. Washburn, James C. Schnable, Gavin C. Conant, Thomas P. Brutnell, Ying Shao, Yang Zhang, Martha Ludwig, Gerrit Davidse, J. Chris Pires

Department of Agronomy and Horticulture: Faculty Publications

The original version of this Article contained an error in the title of the paper, where the word “Phylogenetic” was incorrectly given as “Phylogentic”. This has now been corrected in the PDF and HTML versions of the Article, and in the accompanying Supplementary Information file.

The Impact Of Continuous Living Cover On Soil Hydrologic Properties: A Meta-Analysis, Andrea D. Basche, Marcia Delonge

Department of Agronomy and Horticulture: Faculty Publications

Increased rainfall variability due to climate change threatens the efficacy of critical soil ecosystem services. One strategy to negate effects of too much or not enough rainfall is to improve soil water properties. Practices that offer “continuous living cover” can enhance soil water storage and other soil hydrologic properties relative to annual crop systems, but to what extent such benefits can accrue, under different conditions, remains under-quantified. To address these uncertainties, we conducted a meta-analysis that included 27 studies representing 93 paired observations measuring two soil hydrologic properties: porosity and the water retained at field capacity. All experiments compared the …

Genotyping-By-Sequencing Derived High-Density Linkage Map And Its Application To Qtl Mapping Of Flag Leaf Traits In Bread Wheat, Waseem Hussain, P. Stephen Baenziger, Vikas Belamkar, Mary J. Guttieri, Jorge P. Venegas, Amanda Easterly, Ahmed Sallam, Jesse Poland

Department of Agronomy and Horticulture: Faculty Publications

Winter wheat parents ‘Harry’ (drought tolerant) and ‘Wesley’ (drought susceptible) were used to develop a recombinant inbred population with future goals of identifying genomic regions associated with drought tolerance. To precisely map genomic regions, high-density linkage maps are a prerequisite. In this study genotyping-by-sequencing (GBS) was used to construct the high-density linkage map. The map contained 3,641 markers distributed on 21 chromosomes and spanned 1,959 cM with an average distance of 1.8 cM between markers. The constructed linkage map revealed strong collinearity in marker order across 21 chromosomes with POPSEQ-v2.0, which was based on a high-density linkage map. The reliability …

Genetic Characterization Of The Soybean Nested Association Mapping Population, Qijian Song, Long Yan, Charles Quigley, Brandon D. Jordan, Edward Fickus, Steve Schroeder, Bao-Hua Song, Yong-Qiang Charles An, David Hyten, Randall L. Nelson, Katy Rainey, William D. Beavis, Jim Specht, Brian Diers, Perry Cregan

Department of Agronomy and Horticulture: Faculty Publications

A set of nested association mapping (NAM) families was developed by crossing 40 diverse soybean [Glycine max (L.) Merr.] genotypes to the common cultivar. The 41 parents were deeply sequenced for SNP discovery. Based on the polymorphism of the single-nucleotide polymorphisms (SNPs) and other selection criteria, a set of SNPs was selected to be included in the SoyNAM6K BeadChip for genotyping the parents and 5600 RILs from the 40 families. Analysis of the SNP profiles of the RILs showed a low average recombination rate. We constructed genetic linkage maps for each family and a composite linkage map based on …

High-Throughput Profiling And Analysis Of Plant Responses Over Time To Abiotic Stress, Kira M. Veley, Jeffrey C. Berry, Sarah J. Fentress, Daniel P. Schachtman, Ivan Baxter, Rebecca Bart

Department of Agronomy and Horticulture: Faculty Publications

Sorghum (Sorghum bicolor (L.) Moench) is a rapidly growing, high-biomass crop prized for abiotic stress tolerance. However, measuring genotype-by-environment (G x E) interactions remains a progress bottleneck. We subjected a panel of 30 genetically diverse sorghum genotypes to a spectrum of nitrogen deprivation and measured responses using high-throughput phenotyping technology followed by ionomic profiling. Responses were quantified using shape (16 measurable outputs), color (hue and intensity), and ionome (18 elements). We measured the speed at which specific genotypes respond to environmental conditions, in terms of both biomass and color changes, and identified individual genotypes that perform most favorably. With this …

The Future Of Blackbird Management Research, Page E. Klug

United States Department of Agriculture Wildlife Services: Staff Publications

Human society values birds for their intrinsic and aesthetic value as well as the ecosystem services they provide as pollinators, consumers of pests, and distributors of nutrients and seeds (Wenny et al. 2011). At the same time, conflict between birds and humans is an age-old phenomenon that has persisted as society has transformed and the scale of agriculture has expanded (Conover 2002). Managing conflict between birds and agriculture is challenging for many reasons. Foremost, the need to consider both human welfare and conservation of protected bird species is paramount, with nonlethal management methods preferred to lethal measures from societal, economical, …

Genotype × Environment × Management: Implications For Selection To Heat Stress Tolerance And Nitrogen Use Efficiency In Soft Red Winter Wheat, Kathleen Russell

Theses and Dissertations--Plant and Soil Sciences

The complex interaction of genetics, environment and management in determination of crop yields can interfere with selection progress in breeding programs. Specifically, the impact on selection for nitrogen use efficiency (NUE) in wheat (Triticum aestivum L.) under changing climatic conditions can be confounded by these interactions. Temperature increases for the southeastern United States are projected to range from 1-3°C by 2050 with nighttime temperatures increasing more rapidly than day temperatures. High temperatures are known to affect crop development and breeding for tolerance to heat stress is difficult to achieve in field environments. We utilized a multi-environment trial to assess …

Identification Of Novel Seroreactive Antigens In Johne’S Disease Cattle By Using The Mycobacterium Tuberculosis Protein Array, John Bannantine, Joseph J. Campo, Lingling Li, Arlo Randall, Jozelyn Pablo, Craig A. Praul, Juan Antonio Raygoza Garay, Judith R. Stabel, Vivek Kapur

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

Johne’s disease, a chronic gastrointestinal inflammatory disease caused by Mycobacterium avium subspecies paratuberculosis, is endemic in dairy cattle and other ruminants worldwide and remains a challenge to diagnose using traditional serological methods. Given the close phylogenetic relationship between M. aviumsubsp. paratuberculosis and the human pathogen Mycobacterium tuberculosis, here, we applied a whole-proteome M. tuberculosis protein array to identify seroreactive and diagnostic M. avium subsp. paratuberculosis antigens. A genome-scale pairwise analysis of amino acid identity levels between orthologous proteins in M. avium subsp. paratuberculosis and M. tuberculosis showed an average of 62% identity, with more than half the orthologous proteins sharing …

Comparative Water Quality And Channel Catfish Production In Earthen Ponds And A Biofloc Technology Production System, Bartholomew W. Green, Matthew E. Mcentire

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

This 210-day study compared variation in water quality and fish growth for channel catfish (Ictalurus punctatus; 47 g/fish) stocked in earthen ponds (1.5 fish/m², 14,820/ha) and in a biofloc technology (BFT) production system with high-density polyethylene-lined rectangular tanks (12.6 fish/m², 126,000/ha). Feed input and culture environment affected water-quality dynamics. In ponds, phytoplankton uptake predominated and little nitrification occurred, whereas in the BFT system phytoplankton uptake and nitrification maintained low ammonia-nitrogen concentrations. Size classes of fish were skewed toward the larger market sizes in ponds and toward smaller market sizes in the BFT system. Mean …

Restoring And Sustaining Smallholder Kappaphycus Alvarezii Farming Post-Typhoon Haiyan/Yolanda In Molocaboc, Central Philippines, David C. Fenlon

Dissertations, Master's Theses and Master's Reports

The farming of marine seaweed has the potential to provide both nutritional and financial resources to developing communities such as the Molocaboc Islands in the Philippines. To foster this mariculture development approximately $1,000 USD in grant funds received from the US-Philippines Society was used to purchase materials needed to replace seaweed production infrastructure lost to Typhoon Haiyan (known as Super Typhoon Yolanda in the Philippines). The goal was to restore and expand smallholder farming of the seaweed Kappaphycus alvarezii (locally known as ‘guso’ in the Visayan dialect) in the Molocaboc Islands, thereby increasing harvest yields as compared to those …

Soil Erosion Risk Factors And The Impacts Of Diversification On Organic Strawberry Farms Along California’S Central Coast, Kay Sterner

Pomona Senior Theses

Soil erosion is a major issue that threatens to undermine our current system of agriculture. Due to the fact that this system is in turn the number one cause of erosion, agricultural practices in the United States need to be rethought. This study explores how traditional ideas of erosion risks are related to observed erosion on organic strawberry farms along California’s Central Coast. In addition, diversified farming systems are addressed as a possible solution for the current unsustainability of our farming practices. The data from this research suggest that diversity of crops on farms could be linked to less soil …

Defense And Prosecuting Attorney Perceptions Of Facility Dogs In The Courtroom, Kristy Melissa Donaldson

Walden Dissertations and Doctoral Studies

Attorneys must obtain evidence for purporting their position on a court case. Many factors are considered when working with witness testimony such as age, development, narrative recall, and retraumatization. Research has detailed the hardship of obtaining evidence during witness testimony and the importance of support systems to help with the process. Existing research illustrates the stressors caused by the court processes, witness fear, and difficulty for attorneys to ascertain testimony. Therapeutic animals have been well researched and shown to have an important support role in many professions and situations. Additionally, much has been written regarding the use of varying types …

Cultivating Ecological Literacy And Rethinking Our Connections To Nature, Sean Fretwell

College of Graduate Studies: Theses & Dissertations

In this dissertation I explore the complex, often contested, relationships between humankind and nature. I consider the changing state of these relationships as they are influenced by factors rooted in science, technology, and economics. I also examine these relationships as they relate to human activities with agriculture. Considering the present state of environmental crisis and the abundance of evidence indicating the deleterious activities of humankind as primary causes for the many global calamities, I argue for revising industrially-driven ideologies; particularly those driven by the economic paradigm of capitalism and self-interest. Additionally, I submit that a return to kinship with nature …

Effect Of Concrete Slats, Three Mat Types And Out-Wintering Pads On Performance And Welfare Of Finishing Beef Steers, Bernadette Earley, John Mcnamara, Stephen Jerrams, Edward G. O’Riordan

Articles

The objective was to investigate the effect of placing mats on concrete slatted floors on performance, behaviour, hoof condition, dirt scores, physiological and immunological variables of beef steers, and to compare responses with animals on out-wintering pads. Continental crossbred beef steers [n = 360; mean (±SD) initial live weight 539 kg (42.2)] were blocked by breed and live weight and randomly assigned to one of five treatments; (1) Concrete slats alone, (2) Mat 1 (Natural Rubber structure) (Durapak Rubber Products), (3) Mat 2 (Natural rubber structure) (EasyFix), (4) Mat 3 (modified ethylene vinyl acetate (EVA) foam structure) and (5) Out-wintering …