The research demonstrates that Three-Dimensional Variable-Density Groundwater Flow models such as the SEAWAT model can be effectively used for design of subsurface drainage systems for controlling salt concentration in the root zone on salt affected irrigated land. The SEAWAT model was used to optimize subsurface drainage design to ensure that the salt concentration of the groundwater at the base of the root zone does not exceed pre determined levels instead of the conventional approach of maintaining the groundwater at a predetermined water table level. The study was carried out on a conceptual uniform homogenous block of irrigated flat field of shallow water table depth of 0.5 m and salt concentration of 7200 mg/l with impermeable layer at 20 m deep and impermeable field boundaries. Using the model, spacings were designed to be used as design criteria for subsurface drainage system to maintain salt concentrations of 6000, 5000 and 4000 mg/l at the base of the root zone and water table depth of 0.8 m from the soil surface. The results showed that over a wide range of irrigation water quality and aquifer hydraulic conductivity the optimum drain spacing using SEAWAT was, depending on irrigation water quality and aquifer hydraulic conductivity, wider by between 3 and 50 % and the amount of drain discharge reduced by 1 and 27 % than would be recommended using conventional design equations. It was concluded that Three-Dimensional Variable-Density Groundwater Flow models are better for designing effective drainage systems than Conventional drain spacing design equations such as Hooghoudt.

The disposal of biosolids poses a major environmental and economic problem. Agricultural use is generally regarded as the best means of disposal. Although the impact on soil ecosystems remains uncertain. Biosolids can improve soil properties by supplying nutrients and increasing organic matter content but there is also a potentially negative impact arising from the introduction of heavy metal contaminants into soils. It is widely acknowledged that the bioavailable fraction, rather than total metal content, is indicative of plant metal uptake and toxicity. The bioavailable metal fraction in turn is dependent on soil properties. Therefore, the overall aim of this work was to determine the bio-geochemical factors that control the dynamics of trace element bioavailability in soils that have been subject to the disposal of sewage sludge for over 100 years. Three main investigations were undertaken. In order to determine the current metal composition of the site and identifying the geochemical factors that control the dynamics of metals bioavailability, thirty -eight fields, from a dedicated sewage sludge disposal site for over 100 years, were sampled for both soil (bulk and rhizosphere) and plant. Special attention was devoted to determining soil properties that govern metal partitioning between different metal pools (i.e. total, isotopically exchangeable, Ca(NO3)2-extractable and free ion activity). In order to identify the best estimate of plant uptake and toxic response, a pot experiment was carried out to compare the effects of Zn on plant growth in soils recently spiked with Zn and soils historically amended with biosolids to identify soil properties that best predict metal uptake and subsequent phytotoxicity. The effect of biosolids on soil microorganisms was assessed. Terminal restriction fragment length polymorphism, a fingerprint molecular technique, in combination with multivariate data analysis were used to relate soil microbial diversity and community structure to metal accumulation and bioavailability. High levels of contamination, exceeding the current limits for the use of biosolids in agriculture, were observed in the studied soils reflecting extensive long-term biosolid application. Enrichment factors in relation to background levels in the area were greater than 5 and followed the trend Cd>Cu>Zn>Pb>Ni. Copper and Cd exhibited extremely high enrichment levels, up to 106 and 151 respectively. Except for Pb, the isotopically exchangeable pool of the studied metals (E-value) was mainly controlled by the total metal content in soil, accounting for more than 90% of the variation in E-values. Lead lability was primarily controlled by the total P, LOI and Fe oxides. Metal labilities expressed as % of total metal content were < 40% for the five studied elements following decreasing order of Cu > Cd > Zn ≈ Ni > Pb. Apart from Pb, all the bioavailability estimates (total, E-values, Ca(NO3)2-extractable and free ion activity) correlated strongly with metal concentration in plant, accounting for more than 70% of the variation in plant concentrations. Ca(NO3)2-extractable provided the best estimate out of the four measures of bioavailability, accounting for 87, 77, 87 and 83% of the variation in plant concentration of Ni, Cu, Zn and Cd respectively. The results of the pot trial showed that 67-90% of the added Zn remained isotopically exchangeable after 3 months of Zn addition, suggesting that rapid adsorption processes take place, followed by a slow aging process that cannot be detected over the period of the experiment (3 months). The speciation of soil solution showed that Zn was present mainly (80% on average) as free ion indicating the low affinity of this metal to complexation by dissolved organic matter. An antagonistic relationship was observed between Zn and Cd suggesting that greater Zn availability suppressed Cd uptake by plant. Although Zn addition increased Cd concentration in the soil solution, Cd transfer factor was simultaneously inversely correlated with Zn concentration in soil solution. The free ion activity model (FIAM), based on the biotic ligand model (BLM), accounted for 94% of the variation Zn concentration in plant. Cadmium appeared to play an important role in competing with Zn for uptake. A simple regression model utilising soil total Zn, soil organic matter and soil pH accounted for 88% of the variation in plant uptake. This indicates the possibility of using soil properties that are measured routinely as input for prediction of plant uptake. The results of the Zn phytotoxicity test indicated that the intensity of the exposure (i.e. free ion activity) was the key quantity in the context of predicting plant toxic response, describing 80% of the variation in the response of barley growth to Zn toxicity. Only labile Zn from the quantity based extraction was able to describe the toxic response explaining only 46% of the variation. The study of the effect of biosolids on soil microorganisms showed that soil total Zn concentration could be adopted as a good indicator of the overall (historical) biosolids loading. A biosolids loading, equivalent to 700 – 1000 mg kg-1 Zn appeared to be optimal for maximum bacterial and fungal diversity. This markedly exceeds the maximum soil Zn concentration of 300 mg kg-1permitted under the current UK Sludge (use in agriculture) Regulations. Redundancy analysis (RDA) suggested that the soil microbial communities had been altered in response to the accumulation of trace metals, especially Zn, Cd, and Cu. Based on the findings of this thesis, it can be concluded that (i) the estimation of metal speciation, both in the solution and solid phase is a key factor in determining the bioavailability and thus, has greater chemical and biological significance than soil total metal content; (ii) the maximum beneficial effect of biosolids on soil microbial diversity occurred at a metal (Zn) concentration well in excess of current regulations governing application of biosolids to agricultural land. This indicates that soil microbial diversity is unlikely to be determining factor for regulatory limits for biosolids disposal to agricultural lands.

Master of Science / Department of Grain Science and Industry / Praveen V. Vadlani / Large quantities of byproducts are generated during the biomass processing, which leads to under-utilization of resources and concomitant waste disposal problem. Typically, these byproducts still contain considerable amounts of high-value compounds that have important industrial applications. However, in current time, most of these byproducts are used for low-value applications, including as boiler fuel. These byproducts are potential sources for many valuable chemicals such as antioxidants, flavors, colorants, preservatives, and biocides. Therefore, the reuse and recycle of these biomass residues is very important for the bioeconomy. By some additional and necessary processing steps, we can transfer those biomass residues from a low-value level to a higher value status and apply the final products to various fields such as food industry, and pharmaceutical industry, etc. Till date, limited research has been reported in the production of important specialty chemicals from biomass residues. This thesis is focused on the solvent extraction and isolation of valuable chemicals from bioprocessing byproducts. While choosing different solvents and techniques, “environmental friendly” green solvents were also evaluated. Also some new techniques, such as thin-layer chromatography plates making and laboratory-made lignin are developed to make the research more economically feasible. Even though conventional extraction method such as solid-liquid extraction was evaluated, we tried to minimize the solvent/biomass ratio and also augmented additional processes to the conventional process to obtain higher yield of compounds of interest (COI). In this research, different biomass resources were evaluated for valuable specialty chemicals. These resources include: lignocellulosic biomass and raw biomass. Lignocellulosic biomass is a sustainable feedstock for the production of biofuels and chemicals. The potential chemicals from the resources were extracted using various organic solvents and analyzed by gas chromatography-mass spectrometry (GC-MS). The results indicated that the selected biomass residues contain relatively higher amounts of three valuable compounds: vanillin, apocynin, and phytol. Different types of organic solvents and extraction techniques were tested to optimize the extraction process. Ultra-sonication was considered as an efficient extraction method and ethanol was chosen as the final solvent. Commercially viable isolation methods such as thin-layer chromatography (TLC) and column chromatography were also studied in this research. A solvent system of hexane, dichloromethane, ethyl acetate, and chloroform with 1:1:1:0.1 v/v ratio gave us a good separation of the COI. Biomass-derived lignin was made in the laboratory to compare with commercially available lignin. The results show that the laboratory-made lignin contains similar bioactive compounds and gives us a good quantity of target compounds. In conclusion, instead of letting the byproducts being discarded or used as low-value applications or become a threat to the environment, the decision to select them as raw materials to produce valuable specialty targeted compounds for industries has been demonstrated in our research. The future research will focus on optimization and scale-up study of the extraction process. In addition, the application and production of bioactive compounds will be further evaluated.

Master of Science / Department of Animal Sciences and Industry / Robert Goodband / In 6 experiments, a total of 1,802 pigs were used to determine: 1) effects of increasing crystalline amino acids in sorghum- or corn-based diets on nursery or finishing pig growth performance; 2) effects of different Zn sources on nursery pig performance; and 3) effects of different corn oil sources on nursery pig performance. In the first set of experiments, corn or sorghum-based diets were supplemented with increasing levels of synthetic amino acids up to the 5[superscript]th limiting amino acid. For nursery pigs, there were no main or interactive effects (P>0.05) of grain source or added amino acids which suggests that balancing up to the fifth limiting amino acid is possible in both sorghum- and corn-based diets with the use of crystalline amino acids without detrimental effects on nursery pig growth performance. For finishing pigs, balancing to the 5[superscript]th limiting AA using NRC (2012) suggested amino acid ratios in corn- or sorghum-based diets resulted in decreased ADG and G:F and pigs fed corn-based diets had greater G:F and IV than those fed sorghum. The second set of studies compared two new zinc sources to a diet containing pharmacological levels of ZnO on nursery pig growth performance. These studies demonstrated that increasing Zn up to 3,000 ppm Zn increased ADG and ADFI. Lower levels of the new zinc sources did not elicit similar growth performance as the high level of ZnO. The third set of studies compared increasing levels of different sources of corn oil to diets containing soy oil. In the first study, an oil source × level interaction was observed (P<0.05) for ADG, G:F and caloric efficiency; however in the second study that compared a different corn oil source there were no interactions observed. Overall, increasing the level of oil from either corn- or soy-oil improved feed efficiency similar to expectations. However, the data suggests that differences in performance can be observed between different corn oil sources derived from different locations. These studies show the benefits of adding either corn or soybean oil in late-phase nursery diets to improve performance, and cost and availability should dictate which source to use.

Master of Science / Grain Science and Industry / Sajid Alavi / The U.S. pet food market was approximately worth $22 billion in 2013. Further growth is predicted at a pace faster than most major human food product categories. More than 60% of pet food products are processed using extrusion, and a significant proportion is produced using baking. However, research is lacking on fundamental process and product differences between extrusion and baking. The current study focuses on this aspect and also in-depth characterization of process and product quality. Three iso-nutritional diets were formulated for dry expanded dog food using 0%, 7% and 15% fresh meat inclusion. Major variations between diets were inclusion rates of mechanically deboned chicken, cereal grains, and poultry fat. Each diet was processed with a single screw extruder using various thermal and/or mechanical energy inputs (obtained by varying pre-conditioner stem injection and/or extruder screw speeds). Diets were also processed by baking using a 30 foot experimental oven at 425°F, although the fresh meat inclusion was at 0%, 10% and 20% levels. Proximate analysis of products was conducted. Products were also characterized for physico-chemical properties such as bulk density, piece density, expansion ratio, degree of gelatinization and textural attributes. As fresh meat inclusion increased (0–15%), expansion ratio (4.1–3.5) decreased irrespective of extrusion treatment. Expansion was not evident in the baked kibbles, and bulk and piece densities were up to 56% higher for baked versus extruded kibbles. Textural analysis of extruded kibbles revealed serrated force-deformation response, typical of cellular products, with peak hardness of 2.9–1.5 kgf. On the other hand, baked products had a ‘smooth’ force-deformation response with higher peak hardness than extruded products (up to 3 kgf). Microbial counts for baked products were higher than extruded products, and rancidity profiles as obtained from gas chromatography also had marked differences. The extrusion process was characterized by detailed mass and energy balance analyses, and compared with baking that lacks mechanical energy input. Results from this study provide a useful bench-mark for dry expanded pet food product quality and commonly used processing technologies.

Nematode infection is one of the major causes of disease in young sheep. Selective breeding of genetically nematode resistant sheep is an alternative method for controlling the nematode infection. This process could be simplified if loci that account for nematode resistance can be identified. MHC is one of the candidates and several studies have confirmed the association between MHC alleles and nematode resistance. The aim of this study is to establish the role of MHC class II genes in nematode resistance in Texel sheep. Thus, it can help endorse the usefulness of the MHC class II genes as a genetic marker of nematode resistance and extend the knowledge of the mechanism of resistance against nematodes. This study has been focused on three main areas; 1) description of MHC class II gene diversity, 2) description of haplotype and linkage disequilibrium pattern at MHC class II genes and 3) the association of MHC class II genes and nematode resistance. Sequence-based typing was applied to characterise MHC class II allelic diversity in 235 Texel lambs. The haplotype and linkage disequilibrium patterns were deduced from pedigree information. Finally, the association between MHC class II haplotypes and nematode resistance (FEC and IgE activity against L3) were investigated using a MIXED model approach. MHC class IIa genes were diverse in Texel, consistent with previous studies reported in sheep. The most polymorphic locus among MHC class IIa genes was DRB1. A total of 21 distinct DR-DQ haplotypes were obtained and strong linkage disequilibrium exhibited between DR-DQ genes. There were also statistically significant associations of specific haplotypes and nematode resistance in this population. The work in this thesis confirms the likely importance of MHC genes in regulating resistance against gastrointestinal nematodes, thus supporting the use of MHC as a genetic marker of nematode resistance in selective breeding. Sequence-based typing system for MHC class IIa has been established in this study.

Master of Science / Department of Agricultural Economics / Jeffery R. Williams / In today’s production agricultural sector, managing risk is essential to insuring the economic well being and sustainability of successful enterprises. Considering the inherent risks present in today’s agricultural arena, risk management has become the central focus of discussions for policy makers and producers alike. Therefore the objective of this research paper is to examine the impact a whole-farm adjusted gross revenue insurance risk management program (AGR-Lite) has on reducing farm income variability using historical farm level data for Southeast Kansas farms. A panel data set of actual farm level income data was compiled to evaluate the impact of AGR-Lite on farm income variability for 219 Southeast Kansas farms. Although actual income tax records were not available annual data over the period 1993 to 2005 from the Kansas Farm Management Association was used to reproduce the essential information a farm manager would need from IRS form 1040 schedule F and inventory records to purchase AGR-Lite (Langemeier, 2003). Income distributions for each farm from 1999 to 2005 were calculated for two strategies; the farm manager did not insure and the manager insured each year using AGR-Lite as a stand-alone product. The AGR-Lite insurance strategy assumed a 75% coverage level and 90% payment rate. The income distributions were compared using three premium scenarios. In general, the results of this study reveal participation in the AGR-Lite program, in most instances, reduced standard deviation, Coefficient of Variation (CV), and Downside Risk (DR). Additionally average minimums and Certainty Equivalents (CE) were increased with the product. The following results reflect application of Actuarially Fair Average Rate for farms with Indemnities (AFARI), which is believed to reflect actual market performance. Additionally the following reflects results using Net Farm Income (NFI). Results reveal that purchasing AGR-Lite reduced standard deviations 7.01%, 11.34%, 0.29%, and 2.53% for total, crop, livestock, and dairy farms assuming AFARI. However beef farms were the lone category to sustain a 0.81% standard deviation increase. Despite reductions in absolute variability, relative risk (CV) increased 18.94%, 17.12%, 53.84%, and 3.19% for total, livestock, beef, and dairy. Crop farms were the only category to generate a CV reduction (9.52%). Under AFARI crop farms generated the largest minimum increase, reducing downside risk, by 69.97%. For total and dairy farm categories average minimums increased 62.93% and 0.60%. The remaining farm categories, livestock and beef, yielded 65.07% and 57.03% reductions to average minimum.

The purpose of this research is to investigate the environmental remediation and energy potential of anaerobic digesters on pig and dairy farms and to demonstrate how incorporating those benefits into a cost-benefit analysis would make biodigester projects more financially feasible. By assigning dollar values to the emissions and water pollution avoided by this technology, I sought to update the traditional cost-benefit analyses (CBAs) to demonstrate that this technology is more widely applicable. The study took place In the Lake Champlain Drainage Basin, USA and the Lake Tai Drainage Basin, China. Dairy and pork production are high density endeavors and produce large quantities of waste which make them ideal candidates for biodigesters. Using standard emissions estimates and gas production rates from past research and from the current Cow Power Program in Vermont, the methane and nitrous oxide emissions averted by adding a biodigester to a particular farm were estimated. Additionally, using past research, the total nitrogen and phosphorous collected by the biodigesters and diverted from becoming classified as non-point source pollution was calculated, valued, and incorporated into a CBA tool. The results from this study show that the incorporation of environmental benefits in a CBA for Green Mountain Dairy increased profitability by 60% and reduced the payback period by two years. Overall, projects that include environmental benefits are 72% more profitable and the payback period is cut in half. Further development of the CBA tool is needed to strengthen results. This study points to the need for more experimental data on the environmental benefits of biodigesters.

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