Master of Science / Department of Grain Science and Industry / Cassandra Jones / In two experiments, conditioning time and temperature of swine feed were altered to determine effects of starch, vitamin retention, and swine growth performance. A third experiment evaluated methodologies for estimating gelatinized starch in swine feed. Across all experiments, diet formulation was constant. In Exp. 1, treatments were arranged in a 2 × 3 factorial design plus a control, including 2 conditioning temperatures (77 vs. 88°C) and 3 conditioner retention times (15, 30, and 60 s). A mash diet was added for a total of 7 treatments. Total starch was affected by conditioning temperature (P = 0.04) but not time (P = 0.50). Similar results were observed for gelatinized starch (P = 0.005 and 0.65, respectively). Sample location also affected total starch (P = 0.0002) and gelatinized starch (P = 0.0001), with the greatest increase in gelatinization occurring between conditioned mash and hot pellets. Conditioning alone did not influence gelatinization as evidenced by similar values between cold and hot mash (P > 0.05). Neither conditioning temperature nor time affected vitamin concentrations (P > 0.50). A portion of these treatments were then fed to 180 nursery pigs (PIC 327 × 1050; initially 12.6kg) in an 18-d study. Treatments included: 1) non-processed mash (negative control); 2) pelleted diet conditioned for 30 s (positive control); 3) pelleted diet conditioned for 15 s and reground; 4) pelleted diet conditioned for 30 s and reground, and 5) pelleted diet conditioned for 60 s and reground. Observed growth performance differences appear to be due to feed form, not conditioning time. Average daily gain and G:F did not differ (P > 0.12) between treatments, but ADFI was decreased (P = 0.03) as expected for pigs fed the positive control pelleted diet compared to all other diets. There were no differences (P > 0.05) in any growth performance variables amongst the three conditioning temperatures. In Exp. 3, it was determined that the method developed by Mason et al. (1982) was the best indicator of gelatinization in livestock feed. In summary, feed form, but not conditioning time affected gelatinized starch and swine growth performance.

Doctor of Philosophy / Department of Biological & Agricultural Engineering / Donghai Wang / Grain sorghum is the second major starch-rich raw material (after corn) for bioethanol production in the United States. Most sorghum feedstock for bioethanol production is normal non-tannin sorghum. Waxy sorghum and tannin sorghum are rarely used due to lack of scientific information about waxy sorghum fermentation performance and the way to increase fermentation efficiency of tannin sorghum. The main objectives of this study were to investigate the fermentation performance of waxy sorghum and to improve fermentation efficiency of tannin sorghum using techniques such as germination and ozonation treatments. The ethanol fermentation performance on both waxy sorghum and tannin sorghum were evaluated using a dry grind ethanol fermentation procedure. Fermentation efficiencies of tested waxy sorghum varieties ranged from 86 to 93%, which was higher than normal (non-waxy) sorghum varieties. The advantages of using waxy sorghums for ethanol production include less energy consumption, higher starch and protein digestibility, shorter fermentation time, and less residual starch in distillers dried grains with solubles (DDGS). Results from germination study showed germination significantly increased fermentation efficiency of tannin sorghum. The laboratory results were further confirmed by those from five field-sprouted grain sorghum samples. Significantly increased free amino nitrogen (FAN) contents in sprouted sorghum samples accelerated the ethanol fermentation process. Results from both laboratory-germinated and fieldsprouted samples demonstrated that germination not only increased fermentation efficiency (higher than 90%) but also reduced fermentation time by about 50%, which could result in energy saving and increased production capacity without additional investment. The excellent performance of sprouted sorghums may provide farmers a new market for field-sprouted sorghum (poor quality as food or feed) in a bad year. A previous study showed ozone had a strong connection to degradation of lignin macromolecules. The hypothesis was that ozone treatment may also reduce tannin activity and increase fermentation efficiency of tannin sorghum. Results showed that the ethanol production performance (ethanol yield, fermentation efficiency, and fermentation kinetics) of the ozone-treated, tannin sorghum flours was significantly improved compared with the untreated control. The other effects of ozonation on sorghum flour include pH value decrease, discoloration, and inactivation of tannin. In summary, these studies showed sorghum, no matter it was waxy, field-sprouted, or tannin sorghum, can be an excellent feedstock for ethanol production.

Master of Agribusiness / Department of Agricultural Economics / Michael Langemeier / This thesis examines flour moisture control and how this control can be an effective tool for cost minimization in a flour mill. Specifically, this thesis discusses the economic rationale behind the value of moisture control, the variables associated with moisture control, options for controlling those variables, the current control strategies, the decision process used to examine moisture control options, analysis of the solution, and implementation of optimal control strategies. In the area of optimal control strategies, two outcomes were generated in the thesis. The first outcome involved collecting data and developing a better understanding of the factors impacting flour moistures. The second outcome was to create a spreadsheet tool for use in the flour mill that would allow operators to determine an optimal water set point that would bring about a desired flour moisture taking into consideration the variables effecting flour moisture and their status at a given time. Both outcomes have been met and are outlined in detail in the thesis. It is understood that the conclusions of this thesis do not represent an end to the flour moisture control challenge and that more research is needed in order to implement further control measures. Work that remains to be done in order to achieve even better moisture control is also outlined in this thesis.

Master of Science / Department of Grain Science and Industry / Xuzhi Susan Sun / Large amount of fiberboard are used for packaging applications every year, which generate a large amount of solid wastes causing environmental pollution if these packaging materials are not recycled. Also, a large amount of wood are needed for making fiberboard, which is limited resource in the earth. Reducing the weight of fiberboard and recycling the fiberboard materials are two methods to save quantities of wood fiber in fiberboard manufacture, which benefit the environment and economy. Besides, most adhesives used for producing the fiberboard contain environmental hazardous chemicals. It is necessary to develop new technology to produce cellulosic fiberboards with environmental friendly bio-based adhesives. The soybean is an agricultural product, and its resource is abundant. Soybean protein is a bio- material that offers an alternative to the existing synthetic adhesives to reduce petroleum dependence of the U.S. energy strategy. The newly developed soy-based adhesive is also competitive in cost. Material cost based on food-grade soybean protein is around 20 cents/Lb. The cost of commercial PF resin is about 14 ~ 17 cents/Lb. Price of hot-melt adhesive for fiberboard is around $6/Lb. In this study, soybean protein was modified with sodium dodecyl sulfate as an adhesive for two bio-based fiberboards products, medium density fiberboard by dry processing and light weight cardboard by wet processing. The mechanical and water soaking properties of these cellulosic fiberboards were stronger than or as same as commercial solid fiberboard. This research suggests that these cellulosic fiberboards with modified soybean protein based adhesive have great potential as alternative to current commercial fiberboard.

Master of Science / Department of Animal Sciences and Industry / John A. Unruh / Forty-eight Brahman-cross male calves were fed to 26 mo of age and used to determine carcass cutability and meat quality characteristics of four muscles from intact bulls and steers castrated at 3, 7, or 12 mo of age grown under tropical pasture conditions. Longissimus lumborum (LL), Psoas major (PM), Gluteus medius (GM), and Semitendinosus (ST) steaks were aged for 2, 7, 14, or 28 d for Warner Bratzler shear force (WBSF) analysis. Live weight, carcass traits, and total subprimal yields were not affected by male sex condition. For PM, GM, and ST steaks, WBSF values were similar for steaks from intact bulls and steers castrated at all ages. For both PM and GM muscles, steaks aged for 28 d had the lowest (most tender) WBSF values and steaks aged for 2 d had the highest WBSF values. For the ST, WBSF values were highest for steaks aged 2 d. A treatment × aging interaction was detected for LL WBSF values. At 14 d of aging, LL steaks from steers castrated at 3 mo tended to have lower WBSF values than those from intact bulls. At 28 d of aging, steaks from steers had lower WBSF values than steaks from intact bulls and steaks from steers castrated at 3 mo tended to have lower WBSF values than steaks from steers castrated at 12 mo. For LL steaks from steers castrated at 3, 7 or12 mo, WBSF values linearly decreased with increased days of aging. Although all sensory panel data collected were not statistically different, LL steaks from steers castrated at 3 mo tended to have higher (more tender) scores for overall tenderness than steaks from intact bull. This study indicates that castration at 3 mo would be the recommended production practice as it provided the greatest improvement of LL tenderness over intact bulls with no differences in carcass traits or subprimal yields. The degree of improvement in tenderness due to aging is muscle dependent.

The mechanisms behind how a transcription factor elicits a given phenotype can be complex. The aim of the research presented herein was to provide experimental evidence to characterise the upstream and downstream regulation of the Arabidopsis thaliana R2R3-MYB transcription factor, AtMYB61. To address these aims, three separate experiments were undertaken. First, three direct downstream target genes of AtMYB61 were predicted based on a two-stage complete transcriptome analysis, using publicly available microarray datasets in combination with a custom microarray dataset comparing the transcriptomes of WT, atmyb61 and 35S::MYB61 plants. These candidate target genes encode the following proteins: a KNOTTED1-like transcription factor, a caffeoyl-CoA 3-O-methyltransferase and a pectin-methylesterase. AtMYB61 bound the 5’ non-coding regulatory regions of these target genes, as determined by electrophoretic mobility shift assay. Second, the preferred DNA-binding sites of recombinant AtMYB61 protein were assessed with a cyclic amplification and selection of targets (CASTing) assay. Key interactions between amino acids in the AtMYB61 DNA-binding site and nucleotides in the preferred DNA targets were predicted by molecular modeling. While recombinant AtMYB61 was sufficient to drive gene expression from CASTing-identified target DNA sequences in yeast, it did so in a manner that was not entirely consistent with predicted DNA-binding affinities determined by a nitrocellulose filter binding assay. Finally, the molecular components that function upstream to modulate AtMYB61 expression were determined. AtMYB61 was determined to be de-repressed by sucrose in a mechanism involving its second intron. An over-represented motif was conserved within the second intron of Brassicaceae AtMYB61 homologues and this motif functioned as a binding target for a putative sugar-mediated repressor, as determined by EMSA. Putative AtMYB61 repressor proteins that bound this motif in the absence of sucrose were affinity purified and characterised using LC-MS/MS, and the proteins identified based on their MS fingerprints.

The mechanisms behind how a transcription factor elicits a given phenotype can be complex. The aim of the research presented herein was to provide experimental evidence to characterise the upstream and downstream regulation of the Arabidopsis thaliana R2R3-MYB transcription factor, AtMYB61. To address these aims, three separate experiments were undertaken. First, three direct downstream target genes of AtMYB61 were predicted based on a two-stage complete transcriptome analysis, using publicly available microarray datasets in combination with a custom microarray dataset comparing the transcriptomes of WT, atmyb61 and 35S::MYB61 plants. These candidate target genes encode the following proteins: a KNOTTED1-like transcription factor, a caffeoyl-CoA 3-O-methyltransferase and a pectin-methylesterase. AtMYB61 bound the 5’ non-coding regulatory regions of these target genes, as determined by electrophoretic mobility shift assay. Second, the preferred DNA-binding sites of recombinant AtMYB61 protein were assessed with a cyclic amplification and selection of targets (CASTing) assay. Key interactions between amino acids in the AtMYB61 DNA-binding site and nucleotides in the preferred DNA targets were predicted by molecular modeling. While recombinant AtMYB61 was sufficient to drive gene expression from CASTing-identified target DNA sequences in yeast, it did so in a manner that was not entirely consistent with predicted DNA-binding affinities determined by a nitrocellulose filter binding assay. Finally, the molecular components that function upstream to modulate AtMYB61 expression were determined. AtMYB61 was determined to be de-repressed by sucrose in a mechanism involving its second intron. An over-represented motif was conserved within the second intron of Brassicaceae AtMYB61 homologues and this motif functioned as a binding target for a putative sugar-mediated repressor, as determined by EMSA. Putative AtMYB61 repressor proteins that bound this motif in the absence of sucrose were affinity purified and characterised using LC-MS/MS, and the proteins identified based on their MS fingerprints.

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.