The current research program was designed to evaluate the impact of various dietary and ingredient nutrient profiles and exogenous enzyme inclusion on growth performance and energy utilization in broilers. Experiment one was designed to observe increasing levels of distillers’ dried grains with Solubles (DDGS) and a non-starch polysaccharide degrading enzyme (NSPase) on energy digestibility. Experiment two evaluated the influence nutrient variation in corn and xylanase supplementation on growth performance and nutrient utilization. In experiment one, DDGS concentration was increased from 0 to 15% in 5% increments and included the addition of an NSPase enzyme. Early broiler body weight and FCR was negatively affected with increasing DDGS concentration up to 15%. The decreased growth performance was associated with a decrease in energy and nitrogen utilization as a linear decrease was observed in IDE, INDC, and AMEn. Addition of the NSPase negated many of the negative effects on nutrient utilization as improvements in all digestibility measurements were observed. Interactions were observed with DDGS concentration and NSPase inclusion as the benefit of enzyme inclusion was augmented as DDGS level increase. Experiment two evaluated different corn crops from six geographical locations in the US in an effort to determine the effects of xylanase inclusion and corn nutrient variation on growth performance and nutrient utilization. Significant differences were observed in growth performance, IDE, and AMEn in broilers when fed corn. Corn source impacted early body weights, and FCR throughout the experiment. Energy utilization was also impacted on all measured parameters, following the starter phase (day 17) and at the conclusion of the trial (day 41) by corn source. Xylanase inclusion improved FCR during the finisher phase as well as the cumulative FCR (day 1-41). Digestibility data indicates that corn source impacts the xylanase effectiveness in young broilers, as improvements were not observed in all corn types. Xylanase inclusion, however, did increase IDE and AMEn in all corn sources on day 41 of age. Data from this research program confirm that ingredient nutrient content, through the presence of ingredients with anti-nutritive properties or the incidence of varying nutrient profiles, does impact observed growth performance as related to reduced nutrient digestibility. Additionally, the inclusion of a dietary exogenous enzyme does improve energy and nitrogen digestibility in broilers, ultimately improving growth performance of broilers and improving efficiency.

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In the context of nutrient cycling in soil, plant-mediated mineralisation of carbon (C) and nitrogen (N) is poorly understood. The broad focus of this thesis was to investigate the potential importance of plant-mediated mineralisation (i.e.priming) on C and N mineralisation in soils with contrasting crop productivities. The studies focus on two soils, which had similar chemical and physical properties but contrasting plant productivities relating to their N supply capacity. These soils were used to investigate the potential importance of priming processes in contributing to the contrasting capacities of these soils to supply N for plant growth. 13C and 15N stable isotopes were used to measure specific gross C and N fluxes. Sole C or N and combined C with N treatments were established to disentangle the effect of carbon and nitrogen availability on plant-mediated mineralisation. The addition of labile C increased gross carbon and nitrogen fluxes from native soil organic matter (SOM) but the effect was soil specific. The addition of nitrogen did not affect SOM mineralisation in either soil. The much lower C-to-N ratio of the 'primed' flux compared to the 'basal' flux indicated that the primed flux utilises different OM pools highlighting that primed and basal mineralisation may be distinct processes. The priming response (i.e. positive or negative and associated mechanisms) was different depending on carbon and nitrogen supply to the microbial community. Overall, the studies in this thesis places the microbial community as the focal point of soil N supply. This data strongly supports the concept that the release of labile carbon from plant roots functions as a nutrient acquisition response, increasing mineralisation of SOM. From the data a conceptual model of priming mechanisms, based on nutrient availability to the microbial community, was established. This could be used as the foundation to develop key concepts for sustainable agricultural practice.

Master of Science / Agronomy / Ignacio Ciampitti / P. V. Vara Prasad / Mid-west grain sorghum (Sorghum bicolor (L.) Moench) producers are currently obtaining much lower than attainable yields across varying environments, therefore, closing yield gaps will be important. Yield gaps are the difference between maximum economic attainable yield and current on-farm yields. Maximum economic yield can be achieved through the optimization of utilizing the best genotypes and management practices for the specific site-environment (soil-weather) combination. This research project examines several management factors in order to quantify complex farming interactions for maximizing sorghum yields and studying nutrient partitioning. The factors that were tested include narrow row-spacing (37.5 cm) vs. standard wide row-spacing (76 cm), high (197,600 seeds haˉ¹) and low (98,800 seeds haˉ¹) seeding rates, balanced nutrient management practices including applications of NPKS and micronutrients (Fe and Zn), crop protection with fungicide and insecticide, the use of a plant growth regulator, and the use of precision Ag technology (GreenSeeker for N application). This project was implemented at four sites in Kansas during 2014 (Rossville, Scandia, Ottawa, and Hutchinson) and 2015 (Topeka, Scandia, Ottawa, Ashland Bottoms) growing seasons. Results from both years indicate that irrigation helped to minimize yield variability and boost yield potential across all treatments, though other factors affected the final yield. In 2014, the greatest significant yield difference under irrigation in Rossville, KS (1.32 Mg haˉ¹) was documented between the ‘low-input’ versus the ‘high-input’ treatments. The treatment difference in grain sorghum yields in 2014 was not statistically significant. In 2014, the Ottawa site experienced drought-stress during reproductive stages of plant development, which resulted in low yields and was not influenced by the cropping system approach. In 2015 the treatments were significant, and in Ottawa, narrow row spacing at a lower seeding rate maximized yield for this generally low-yielding environment (<6 Mg haˉ¹) (treatment two at 6.26 vs. treatment ten at 4.89 Mg haˉ¹). Across several sites, including Rossville, Hutchinson, Scandia, Topeka, and Ashland, a similar trend of narrow row spacing promoting greater yields has been documented. Additionally, when water was not limiting sorghum yields (i.e., under irrigation), a balanced nutrient application and optimization of production practices did increase grain sorghum yields (‘high-input’ vs. ‘low-input’; the greatest difference was seen in 2014 in Rossville, 1.2 Mg haˉ¹, and in 2015 in Ashland, 1.98 Mg haˉ¹). In the evaluation of nutrient uptake and partitioning in different plant fractions, there was variability across all site-years which did not always follow the same patterns as the yield, however, the low-input treatment was shown to have significantly lower nutrient uptakes across all the nutrients evaluated (N, P, K, S, Fe, Zn) and across most fractions and sampling times. The objectives of this project were to identify management factors that contributed to high sorghum yields in diverse environments, and to investigate nutrient uptake and partitioning under different environments and crop production practices.

Brazil is the world's sixth largest cocoa producer with 270,000 tonnes of cocoa produced per year. In a world with an increasing demand for chocolate, but with agriculture threatened by climate change, the chocolate industry is worried about a possible shortage of cocoa. Furthermore, growing cocoa is a main cause of deforestation. However, in the state of Bahia, Northeast Brazil, cocoa is grown in traditional agroforests called 'cabrucas' which maintain a forest cover. Cocoa, an understorey crop, is planted under the shade of native Atlantic Forest trees and exotic fruit trees introduced by the farmers. These cabrucas have high conservation value but very low cocoa yield. In my thesis I investigate the factors limiting cocoa yield and how to increase yield in cabrucas. I explore the role of shade trees and the nutrient dynamics in litterfall. Finally, I explore the risk that climate change could represent for cocoa production in the future by looking at the effects of an unexpected drought caused by an El Niño Southern Oscillation (ENSO) event between November 2015 and May 2016. My study is based on data collected in permanent transects in 32 randomly chosen cabruca farms in Barro Preto a municipality of Bahia over a period of three years. I also established littertraps in 10 cocoa farms where I intensively studied nutrient dynamics and cocoa yield per tree over 12 months. My results showed that unproductive trees, low cocoa tree density, high shade cover and high cocoa mortality due to drought were the main factors limiting cocoa yield in cabrucas. Surprisingly, adding fertilisers to the cocoa trees did not increase yield. This suggests that there is no nutrient deficiency in cabrucas. In the farms, I found 69 species of shade trees for an average density of 125 ± 32 trees per hectare. Half of the species of shade trees were Atlantic Forest species of conservation value. The litterfall experiment showed the shade tree species and the quantity of litterfall produced, can affect the number of cocoa pods per tree. In cabrucas, a higher number of cocoa pods was found on cocoa trees under shade trees than under no shade. Finally, I showed that the exceptionally severe ENSO-related drought caused 80% loss in yield and 11% cocoa tree mortality in Barro Preto. Climate models predict an increased frequency of strong ENSO events in the future. Farmers in Bahia are not prepared to face regular drought events. The 2015/16 drought affected the dynamics of cocoa production in Brazil: it accelerated the decrease of extensive wildlife-friendly cocoa production in Bahia whereas it increased the development of cocoa production in intensive low shade plantations in the state of Pará. This suggests that climate change could be a threat to traditional cocoa agroforests in Bahia. Developing wildlife-friendly certification schemes and Payment for Ecosystem Services to internalise the value of forest conservation and to encourage farmers to maintain their shade trees could save cabruca systems from going extinct.

Background: It is well established throughout the literature that regularly engaging in physical activity throughout pregnancy is associated with optimized health outcomes for both the mother and the fetus. The mediators and mechanistic pathways through which these observed exercise-induced outcomes are achieved are largely unknown. This thesis attempts to address this gap in knowledge. Methods: The objective of the first study was to develop an exercise protocol based on the recommendations from the ‘2019 Canadian guideline for physical activity throughout pregnancy’ and to subsequently evaluate the myokine response post-exercise. Pregnant (n=13) and non-pregnant (n=17) women performed a moderate-intensity bout of treadmill walking following which pre- and post-exercise serum for a panel of ten well-characterized myokines was analyzed. The objective of the second study was to evaluate whether acute and/or chronic exercise elicited changes in metrics of placental growth and development – thereby proposing possible mechanisms through which physical activity may be conferring health benefits to the fetus. Serum (pre- and post-exercise) collected from the first study was used to treat placental cell lines to assess the effect of acute exercise on cellular proliferation as well as nutrient transporter (GLUT1, SNAT1, FATP4) expression and localization. Term placental tissue collected from active (n=10) and non-active (n=10) participants in the PLACENTA study were used to evaluate the role of chronic exercise on changes in nutrient transporter (GLUT1, SNAT1, FATP4) expression and localization. Results: Pregnant women from the first study exhibited higher levels of four myokines post- versus pre-exercise: FGF21, EPO, BDNF and IL-15. As for the second study, BeWo cell lines treated with serum collected from pregnant women yielded higher GLUT1 expression compared to non-pregnant serum, independently of exercise. Lastly, FATP4 expression was found to be higher in term placentas of active compared to non-active pregnant women. Conclusion: This thesis identified four myokines that are elevated in the serum of pregnant women following a bout of acute exercise. The role of these myokines in pregnancy remains to be elucidated. Further, chronic and acute exercise are shown to alter expression of key placental macronutrient transporters.

Cystic fibrosis (CF) is a hereditary multi-organ disorder characterized by formation of thick, viscous mucus in the lungs, leading to decreased fluid clearance and significant bacterial colonization. The bacteria form colonies, called biofilms, that are attached to the mucosal surface and produce a protective polymeric matrix. The matrix helps the biofilms form stable structures in the lungs while also protecting the embedded bacterial colonies from the host defense system and antimicrobials. Pseudomonas aeruginosa are opportunistic bacteria that commonly infect CF airways in the biofilm form. Current antibiotic treatment regimens fail to completely eradicate these biofilms, leading to chronic, persistent infections that over time lead to patient death. Therefore, there is a need to investigate antibacterial strategies that would completely eradicate these infections at reasonable doses and improve quality of patients’ lives. In this thesis, two strategies are investigated to better eradicate bacterial colonies – (1) the use of nutrient dispersion compounds for increasing the susceptibility of biofilm bacteria to the co-administered antibiotics, and (2) PEGylation of antimicrobial peptides to increase peptide retention in the lung airways. Clinical strains of P. aeruginosa isolated from lungs of CF patients were used in this research to better mimic the greater robustness of clinical biofilms compared to biofilms of laboratory bacterial strains. Growth curve studies were carried out to characterize the growth patterns of the bacterial strains. Antibiotic susceptibility of the planktonic (free-flowing) bacteria was studied using the minimum inhibitory concentration (MIC) assay. A method to grow and characterize 1-day and 4-day old biofilms in the minimum biofilm eradication concentration (MBEC) assay apparatus was developed and characterized. The MBECs of combination formulations consisting of an antibiotic and a nutrient dispersion compound for different treatment durations were measured against biofilms of the clinical isolates using four commonly used antibiotics, and sodium citrate as the nutrient dispersion compound. The growth curve studies allowed for better understanding of the clinical isolates’ growth rates in vitro, which could play an important role on their susceptibility to antibiotics. All bacterial strains displayed susceptibility to tobramycin sulfate and ciprofloxacin hydrochloride. Uniform bacterial growth was observed for 1-day old biofilms of both clinical isolates across all pegs. Growing 4-day old biofilms using 100% MHB without refreshing the bacterial suspension over 4 days gave uniform biofilm bacterial growth across the pegs. Four-day old biofilms displayed greater biomass than 1-day old biofilms for 2 out of 3 bacterial strains. Combination formulations eradicated 1-day and 4-day old biofilms at lower antibiotic concentrations than the antibiotic alone, with further improvement in eradication after increasing the duration of treatment. Sodium citrate did not enhance the metabolic activity of the biofilm bacteria. The antimicrobial peptide CaLL was conjugated with different MW polyethylene glycol (PEG) molecules using disulfide and maleimide linkages, and the effect of PEGylation on its antibacterial activity against P. aeruginosa laboratory strain PAO1 was evaluated. PEGylation was observed to reduce bacterial growth inhibition by CaLL, with the disulfide-linked CaLL-PEG less efficacious than the maleimide-linked CaLL-PEG. Time-kill assays demonstrated the longer duration of action of PEGylated peptides compared to non-PEGylated peptides, probably due to prevention of enzymatic degradation of the peptide by the PEG molecule. This research will shed light on antibacterial strategies for complete and rapid eradication of bacterial biofilms, thereby reducing development of antibiotic resistance and prevent recurrence of infection, reducing progressive lung damage caused in people with CF, and improve their quality of life.

This book was assembled using the latest information for compiling the nutrient requirements of sheep, goats, cattle and water buffalo. Because of the complexity of the interactions between an animal, its diet, its physiological state, and the environment; the values depicting the nutrient requirements are estimates and not absolutes. These values, however, are considered to be adequate to meet the minimum requirements of healthy animals maintained in a thermoneutral environment. The mean energy and protein values used in the nutrient tables were arrived at from combining values found in the literature and those provided in personal communication with animal nutritionists in many developing countries. In some cases, only two or three observations were found for estimating the values used. Future research in ruminant nutrition should be designed to provide information needed to confirm or modify the values presented here. Feed composition tables representing feeds commonly found in Latin America, Africa, Asia and the Middle East have been included for an easy reference when formulating diets. Units of expression of data in the tables of feed composition and animal nutrient requirements are presented using three systems: Metabolizable energy (ME), net energy (NE); total digestible nutrients (TDN) and Scandinavian feed units (FU). conversion factors from SE to ME, TDN, etc., are presented in Section 1 for those who need this information. Also a list of abbreviations used appear in Appendix 5. A brief discussion showing three methods of calculating rations by hand are presented. Each of these methods permits some consideration for calculating a "least-cost" ration. It is important, however, that the person formulating a diet has a knowledge of the animal's nutrient requirements, an understanding of the digestibility and utilization of feeds and the various combinations required to formulate a diet adequate to supply all the needs of animals. Examples of hand calculated rations appear in Appendix 3. Adulteration of feedstuffs is a common complaint from livestock producers in many developing countries. This problem has been encountered at various times throughout most regions of the world. In section 12, some suggestions are offered as a means to establish quality control regulations and to set standards for all manufactured feedstuffs offered for sale.

Adoption of supplemental irrigation as a practice in Puerto Rico will be slow, Because irrigation is thought to be needed only occasionally, farmers look at it as an uneconomical operation. Even in the agricultural policy, supplemental irrigation is treated lightly, with limited funds allocated for research in this area.

The basic mineral nutritional requirements of Proteaceae are not well understood.They are generally assumed to require low levels of nutrients and be susceptible to nutrient (especially Phosphorus) toxicity.This project aimed to estimate the general nutritional requirements of Proteaceae for optimum growth, with special emphasis on the Phosphorus requirement. Potted plants were grown in soilless growth media with controlled release fertiliser and were watered according to need in a naturally lit greenhouse. The nutrient requirements of Proteaceae were found to vary among species but were not lower than the reported requirements for the Ericaceae, another heath family. The variables of growth media and plant development were found to be important factors affecting the critical Phosphorus concentration and need consideration in the derivation of the Phosphorus requirement of Banksia ericifolia. / Doctor of Philosophy (PhD)