Doctor of Philosophy / Animal Sciences and Industry / Joel M. DeRouchey / Eight experiments using a total of 2,964 finishing pigs and 2,947 feed, phytase, or premix samples were used to determine the effects of: 1) wheat source, particle size and feed form on finishing pig performance; 2) feed form feeding strategies; 3) fine generation from pellets during feed manufacturing and delivery, and 4) thermal stability and shelf life of phytase products. Exp. 1 and 2 evaluated wheat sources, particle size, and diet form for finishing pigs. Fine gound hard red winter wheat fed in meal form improved G:F and nutrient digestibility, whereas wheat ground from ~700 to 250 µ in pelleted diets did not influence growth or carcass traits. Feeding hard red winter wheat improved ADG and ADFI compared with feeding soft white winter wheat. In Exp. 3, pellet feeding regimens were used to evaluate finishing pig performance and stomach morphology. Feeding pelleted diets improved G:F but increased stomach ulceration and pig removals; however, rotating pellets and meal diets provided an intermediate G:F response with fewer stomach ulcers and pig removals. Experiments 4 to 6 investigated fines formation during pelleted feed manufacturing and delivery. Pellet quality worsened as pellets were transported through the feed mill post pelleting and during delivery. Unloading speed or feed line location had little effect on pellet quality. There were significant differences between the fines and pellet nutrient profiles as noted by the increased concentration of ADF, crude fiber, Ca, ether extract, and starch in the fines and decreased CP and P when compared to pellets. In Exp. 7 and 8, the thermal stability and shelf life of 4 commercial phytase products was determined. Increasing conditioning temperatures decreased phytase stability regardless of product. Phytase activity was affected by storage duration, temperature, product form, and phytase source. Pure products stored between 15 and 22˚C were the most stable and premixes were affected by longer storage times and higher temperatures.

Doctor of Philosophy / Department of Animal Sciences and Industry / Terry Houser / One experiment was conducted to determine the collagen and adipocyte characteristics in pork belly fat with different iodine values (IV) and if these factors contribute to belly firmness. An additional two experiments were conducted to create an objective method to score bacon distortion during cooking and to determine how IV and cooking method contribute to bacon distortion. Experiment 1 sorted pork bellies (n=72) into three IV categories: High 76.5 g/100g, Intermediate 70.5 g/100g, and Low 64.9 g/100g. Belly characteristics and firmness were measured before processing into bacon. After processing, 3 bacon slices were selected from the belly and analyzed for histochemistry and collagen analysis. No differences were observed between belly characteristics, while High IV bellies showed softer bellies. Adipocyte characteristics remained unchanged between IV groups. High IV bellies showed greater amounts of collagen. Experiment 2 cooked bacon slices (n=585) on three different appliances (griddle, microwave, and oven) and scored the resulting distortion using a subjective scale. Raw and cooked bacon characteristics were measured to determine which response variables contributing to distortion. Bacon slices were removed from 6 different locations within each belly sampled. Two distortion measurements were created to objectively describe distortion response (crest frequency and bacon distortion index. Subjective distortion scores, crest frequency, bacon distortion index, and raw and cooked bacon characteristics were shown to change between locations of the belly. Accuracy of predictive equations developed to predict distortion scores were low. Experiment 3 evaluated how IV interacts with cooking methodology to influence cooking characteristics, fat quality and distortion of bacon. Bacon slices (n=300) were organized into two IV categories, Low (61.52 to 65.54 g/100g) and High (78.83 to 85.34 g/100g) and cooked using three different appliances (oven, microwave, and griddle). Bacon from the Low IV group had the greatest amount of fat. Cooking bacon on a griddle showed the greatest distortion scores, while the oven produced bacon with the lowest distortion scores. Bacon with higher IV produced bacon with increased distortion scores. Bacon from the High IV group showed smaller cooked dimensions than the Low IV bacon. Neither cooking method nor IV level affected the cooked fatty acid composition.

Master of Science / Department of Animal Sciences and Industry / James S. Drouillard / Hops β-acid extract was fed to 80 heifers (389 ± 23.6 kg initial BW) to assess impact on feedlot performance and ruminal fermentation. Heifers were randomly assigned to individual pens and fed once daily for 147 d. Treatments were a control (no additive); 33 mg monensin (Elanco Animal Health, Greenfield, IN)/kg diet DM; and 10, 25, 50 mg β-acid extract of hops (DSM Nutritional Products, France)/kg diet DM. Ruminal fluid was collected on d 44 and 86 by rumenocentesis for analyses of VFA, lactate, and NH[subscript]3 concentrations. Cattle were harvested at a commercial abattoir on d 147. Hops β-acids decreased propionate (P = 0.01) concentrations and increased caproate (P = 0.05), A:P (P = 0.04), and ammonia concentrations (P = 0.03) compared to monensin. Growth performance of heifers fed β-acid or monensin was not different than that of heifers fed the control diet. Additionally, two in vitro studies were conducted to evaluate effects of hops β-acid extract on starch fermentation by mixed microbial populations from the bovine rumen. In trial 1, 2 treatments were assigned in triplicate to fermentation bottle, fitted with Ankom[superscript]RF1 Gas Production System modules (Ankom[superscript]RF Technology, Macedon, NY) using starch as substrate (Difco Soluble Starch; Dickinson and Company, Sparks, MD) and either 0 or 33 mg hops β-acid extract (10.99% active hops beadlet; DSM Nutritional Products, France)/kg substrate. Gas production was measured over 30 h. Terminal pH, IVDMD, and VFA and lactate were measured after 30 h of fermentation. Gas production increased in response to β-acid (P ≤ 0.05). Terminal pH, IVDMD, VFA, and lactate were unaffected by addition of β-acid extract (P ≤ 0.05). In trial 2, pH, VFA concentrations, and IVDMD were measured at 6-h intervals during a 30-h incubation period using 36 fermentation tubes. There was no effect of hops β-acid on in vitro fermentation (P > 0.05). In conclusion, under the conditions of these experiments, hops β- acid extracts hops had little impact on feedlot performance, though there are indications of an impact on ruminal fermentation.

Master of Science / Department of Animal Sciences and Industry / Teresa Douthit / Joann Kouba / Gonadotropin-releasing hormone (GnRH-I), as well as its receptor, GnRHR-I, once thought to be localized solely to the hypothalamus and anterior pituitary, have since been detected in the testis of numerous mammals. Another isoform of GnRH, GnRH-II, has been isolated from the testis of numerous mammals and binds a specific receptor, GnRHR-II. Our objective was to establish whether GnRH-I and GnRH-II, along with their specific receptors, are produced and present in the equine testis. Testicular tissue was collected from colts < 2 yr (n = 5) and stallions ≥ 2 yr (n = 10) of age during routine castrations. Total RNA extracted from testicular tissue was reverse transcribed and cDNA was subjected to conventional PCR using gene specific primers for GnRH-I, GnRHR-I, GnRH-II, and GnRHR-II. Protein was extracted and subjected to dot blot and Western blot using antibodies directed against GnRH-I, GnRH-II, GnRHR-I, or GnRHR-II. Transcripts for both ligands and receptors were detected in all testes. Product identity was confirmed by sequencing, which also clarified that unusual band sizes were the result of alternative splicing of GnRHR-II, and the retention of an intron in the GnRH-II mRNA was discovered. Prepro-GnRH-I and prepro-GnRH-II protein was detected in all stallion testes via dot blot technique. On Western blots, testicular samples from colts (n = 4) had 3-fold greater GnRHR-I levels compared to stallions (n = 7; P < 0.022). Conversely, there was a tendency for GnRHR-II protein to be greater in tissue collected from stallions compared to colts (P < 0.0756). Finally semen was collected from mature stallions (9 to 18 yr; n = 4) and purified using a discontinuous gradient. By utilizing immunocytochemistry, GnRHR-II was localized to the connecting piece of mature stallion spermatozoa. This is the first report identifying GnRH-I and -II and their receptors in the equine testis and GnRHR-II on mature stallion spermatozoa. These decapeptide hormones may act via autocrine and/or paracrine signaling to affect steroidogenesis and spermatogenesis in the stallion testis.

Master of Science / Department of Animal Sciences and Industry / Christopher D. Reinhardt / Angus steers (n = 17,919) fed at a single feedlot in southwestern Kansas between 1997 and 2007 were used to evaluate the effects of various demographic and phenotypic characteristics (season of arrival, geographic origin, health status, rate of gain, quality grade, and yield grade) on feedlot health, performance, and carcass traits. Cattle were not commingled and were predominantly preconditioned and backgrounded prior to shipment to the feedlot. Season of arrival was categorized as winter (December, January, and February), spring (March, April, and May), summer (June, July, and August), or fall (September, October, and November). Regions were: SC = Texas, Oklahoma, and New Mexico; C = Colorado and Kansas; NC = Montana, Nebraska, and Wyoming; and SE = Georgia, Mississippi, South Carolina, Tennessee, Virginia, and West Virginia. Steers that originated in SC had the poorest ADG (P < 0.01) and those originating in C had the greatest ADG, HCW, and quality grade (P < 0.01). Steers that arrived during fall had the lowest ADG and those arriving during the summer had the greatest morbidity (P < 0.01). Morbidity decreased and performance increased with increasing initial BW; quality grade was only minimally related to arrival BW in steers which were not treated for disease. After accounting for yield grade differences, the association between morbidity and carcass quality and between quality grade and heavier final BW and HCW were diminished, although ungraded cattle had lower ADG, final BW, and HCW (P < 0.01). Increasing yield grade from 1 and 2 to yield grade 3 increased percentage Choice by 12.1 points (P < 0.01); there was no additional gain in quality grade moving to yield grade 4 and 5. More rapidly gaining steers were heavier and fatter at marketing; this translated to greater quality grade in all but steers with initial BW > 375 kg. Performance was very similar among cattle which graded Prime, Choice, and Select, suggesting that producers do not need to choose between performance and quality grade; instead, much of the difference in quality grade can be explained by differences in yield grade.

Doctor of Philosophy / Department of Biology / Brett K. Sandercock / Samantha Wisely / Anthropogenic activities and climate change have dramatically altered landscapes worldwide. The ability of species to cope and adapt to ongoing changes is likely a function of their behavior, movements, and sensitivity to fragmentation. Greater Prairie-Chickens (GPC) are a lek mating grouse native to the Great Plains Landscape Conservation Cooperative (GPLCC), for which inbreeding depression and anthropogenic avoidance are a concern. The goals of my dissertation were to: 1) identify genetic correlates of male performance which may influence population viability under current land use practices, 2) identify GPC habitat characteristics and delineate areas of critical GPC habitat necessary for GPC conservation, and 3) identify the relative importance of distance and habitat quality for maintaining genetic connectivity among spatially structured populations. First, I found male reproductive success and survival to be positively associated with genetic diversity. Using multistate modeling in Program Mark, male survival across the observed range of variation in number of alleles (15-22) increased more than fourfold from 0.17 to 0.77. Second, I found 35-40% of Kansas, and 1.5 % (11,000 Km squared) of the GPLCC, were considered high-quality lek habitats. Top performing logistic models predicting lek presence (wi=0.95) included strong effects of grassland cover and avoidance of anthropogenic disturbance. When this model was applied to putative future landscapes based on climate change and current land use trends over a 70-year period, I found a 27-40% reduction in habitat area and a 137 Km southeast shift in habitat distribution. Under equilibrium conditions we expect isolation by distance (IBD) to explain the distribution of genetic diversity. However, if the landscape restricts dispersal, then we might observe isolation by resistance (IBR). I used model selection procedures to choose among competing IBR or IBD models to explain the distribution of genetic diversity among GPC populations across Kansas and the GPLCC. IBD was never supported (R-square<0.02, P>0.09). The best models for Kansas (R2=0.69, P<0.02) and for the GPLCC (R-square=0.46, P<0.02) indicated that human-mediated landscape changes have influenced landscape permeability for dispersal. The integration of behavioral, landscape, and genetic data provided new insights on prairie-chicken ecology, and is a powerful approach for developing conservation strategies for sensitive species.

Master of Science / Department of Agricultural Economics / Kevin C. Dhuyvetter / The 2008 National Stocker Survey defines the backgrounding/stocking of cattle as ―operations where calves are grown after weaning and/or preconditioning but before the feedlot. This includes calves purchased for this purpose as well as those retained by cow-calf producers post-weaning, but before marketing or retention through the feedlot. Backgrounding offers many benefits to farmers including, but not limited to, adding value to their feedstuffs—hay, grain, etc.—by feeding it to their cattle and potentially spreading risk by increasing marketing time or engaging in contracts with feedlots. However, producers also take on increased costs as it takes more time to wean, bunk-train, vaccinate, etc. compared to other operations in the cattle industry. This thesis attempts to analyze two studies using the 2008 National Stocker Survey. The first is how producer and operation characteristics—producer age, type of operation, income derived from backgrounding—relate to why producers find variables such as cattle prices, animal health management, marketing practices, and nutrition important. The second is how producer and operation characteristics relate to producers that use futures market contracts and options on futures. Binary and ordered logit models were used to find the statistical significance of the aforementioned studies.Since this survey was specifically designed to profile the stocking/backgrounding industry, some of the estimated models did not add a lot of value beyond the summary statistics for the various dependent variables. That is, the ordered logit models did not identify any strong relationships given that almost all of the producers that responded to these questions found feeder cattle prices, animal health management, marketing practices, and nutrition very important, which can be seen by analyzing the summary statistics. In addition, the binary logit models that were used for the futures market contract and options on futures models, found that the best way to pinpoint producers using either futures contracts or options was if producers were already using risk management strategies. Therefore, the survey’s purpose of profiling the stocker industry may be its best use.

Master of Science / Department of Clinical Sciences / Michael D. Apley / One hundred ninety four steers, bulls, and heifers weighing 182-318 kg were purchased at an Arkansas sale barn and shipped 12 hours to a northern Kansas feedlot. There was no previous history of treatment and the cattle had been delivered to the sale barn within the 24 hour period prior to the sale. The objectives of the study were to evaluate (1) bacterial pathogen isolates in different locations in the respiratory tract, (2) pathogen load in clinically ill and clinically normal calves, and (3) compare histological damage that may be a result of clinical disease. Fifteen calves were identified with signs of acute bovine respiratory disease (BRD) based on clinical score and a minimum rectal temperature of 40° C. An additional 5 calves with no clinical signs and rectal temperatures < 40° C were selected as controls. Cattle were humanely euthanized following recording of antemortem clinical observations. At postmortem, samples for microbiologic and histologic (hematoxylin and eosin stain) analysis were collected from grossly normal and/or consolidated tissue in each lung lobe. Samples were also collected from the tonsils and trachea. Quantification of the BRD pathogens per gram were determined for each positive site and then converted to total counts for each animal. Total colony forming units (CFU) of pathogens in the entire lung for cattle with identified pathogens ranged from 2x10[superscript]7 – 2x10[superscript]8 CFU for Pasturella multocida and 9x10[superscript]6 – 9x10[superscript]8 CFU for Mannheimmia haemolytica. Total visual estimated percent consolidation ranged from 0.0% to 45.0% of the total lung. Isolated pathogens from the upper and lower respiratory tract were compared and showed to have no significant agreement. Histology scores of 0-4 were assigned to the tissue samples and compared to the quantified BRD pathogens to test a possible association between the pathologic process and the total agents in that tissue sample. A significant difference in bacterial counts between histology scores of zero or 1 and a histology score of 4 was observed.

Doctor of Philosophy / Department of Animal Sciences and Industry / Jim L. Nelssen / Eleven-thousand one-hundred eighty-five pigs were used in 11 experiments to determine effects of birth-weight, feeder design, and dietary astaxanthin (AX) and ractopamine HCl (RAC) on growth, carcass, and pork quality characteristics of pigs. Also, data from 27 experiments were used in meta-analyses to improve prediction of pork fat iodine value (IV). In Exp. 1, increased birth-weight resulted in greater (quadratic, P < 0.05) pre-weaning survivability, ADG, final BW, and likelihood of achieving full-value market at 181-d of age. In Exp. 2, 3, 4, 6, 7, and 8, pigs using the wet-dry feeder (WD) had greater (P < 0.05) ADG, ADFI, and final BW than those using the conventional dry feeder (CD). Pigs using WD had poorer (P < 0.05) G:F in Exp. 3 and 4, and increased (P < 0.05) HCW and backfat depth in Exp. 3, 4, 6, and 7, compared to pigs fed using CD. In Exp. 5, pigs using WD from 19 to 38 kg had decreased (P < 0.02) ADFI and better G:F than pigs using CD. Increased feeder opening of WD increased (P < 0.05) ADG, ADFI, and final BW in Exp. 5, 6, and 7; as well as HCW and backfat depth in Exp. 6 and 7. Reducing WD opening at 28- and 56-d in Exp. 7 decreased (P < 0.05) ADG, ADFI, and backfat depth. Different openings of CD had little effect on performance in Exp. 5 and 6. In Exp. 8, changing water-source of WD to a separate location during late-finishing reduced (P < 0.05) overall ADG, ADFI, and final BW. Limited responses to AX were observed in Exp. 9, 10, and 11, but ADG, G:F, final BW, HCW, and fat-free lean were improved (P < 0.05) for pigs fed RAC in Exp. 10 and 11. Total color change during retail display of LM chops for gilts and pigs fed RAC was reduced (P < 0.05) in Exp. 10 and 11, indicating their color shelf-life improved. In the meta-analyses, models using dietary PUFA with ADG, BW, or backfat depth improved the fat IV prediction from R2 = 0.45 to R2 = 0.90.

Master of Science / Department of Animal Sciences and Industry / Michael D. Tokach / A total of 5,212 nursery pigs were used in 11 experiments to evaluate amino acids in nursery pig diets. Experiments 1 and 2 were conducted to determine whether the Lys level fed during one phase of the nursery influenced the response to Lys during subsequent phases. Experiment 1 tested a wide range of dietary Lys in 2 phases and reported that pigs fed high Lys during each period had increased growth performance; however, compensatory growth occurred for the pigs previously fed low Lys diets, resulting in no impact on overall ADG or final BW. Experiment 2 tested a narrow range of dietary Lys in 3 phases and found that marginally deficient diets can be fed in the early nursery phases without influencing final BW or the response to Lys levels in subsequent phases. Both experiments demonstrate that the low dietary Lys levels used in each can be fed in the early nursery phases with no negative impact on overall nursery growth rate provided that adequate levels are fed thereafter. Experiments 3 to 6 were conducted to determine the standardized ileal digestible (SID) Lys requirement of nursery pigs from 7- to 14-kg. Data from all experiments were combined and break-point and quadratic broken-line analysis was used to determine the estimated SID Lys requirement. The SID Lys requirement for optimal growth was at least 1.30% for ADG and 1.37% for G:F, or at least 3.86 and 4.19 g SID Lys/Mcal ME, respectively. Experiments 7 to 11 were conducted to evaluate the effect of replacing specialty protein sources with crystalline AA and AA requirements for 7- to 12-kg pigs. Experiment 7 demonstrated that crystalline AA can be used to replace fish meal in diets with no negative effects on growth performance. Experiment 8 demonstrated that L-Trp, L-Val, and a source of non-essential AA were needed in low-CP, AA-fortified nursery diets to achieve maximum growth performance, whereas the addition of L-Ile was not required. Experiment 9 indicated that feeding greater than 7.35% total Lys:CP decreased growth performance and Exp. 10 indicated that a SID Val:Lys ratio of 65% was sufficient for optimal growth of early nursery pigs. Implementing the results from the previous experiments, Exp. 11 determined that crystalline AA in nursery pigs diets can replace high amounts of fish meal, meat and bone meal, and poultry meal when balanced for minimum AA ratios and maximum Lys:CP with no negative effect on growth performance.