Food web models are one tool used by resource managers to evaluate changes in trophic interactions in response to changes in biotic and abiotic drivers in an ecosystem. Food web modeling provides a range of potential outcomes for managers to consider, to use in fisheries management. However, it is well known that food web models require large amounts of disparate data, which can amplify uncertainties in model output. Previous studies have leveraged stable isotope data to compare the trophodynamics between modeled trophic levels and in situ data. Here, we provide a new framework to aid users in evaluating the level of agreement between trophic levels generated from food web models and from stable isotope data using a Bayesian statistical approach. Using a previously developed food web model from coastal Louisiana as a case study, this paper presents an updated framework to use stable isotope analysis as a validation method for food web models. The validation process included Spearman-rank correlation analyses in addition to developing and using the first open-source food web model validation visualization tool, EcoTuneR, this webtool provides a more accessible way visualize the Bayesian derived trophic level probability curves with the food web model trophic levels. Reported correlation between the stable isotope trophic levels and the food web model trophic levels were comparable to previous studies (functional group Spearman-rank correlation, R=0.56, n=47, p > 0.001 | niche-aggregated R=0.77, n=17, p > 0.001 | age-aggregated R=0.53, n=34, p > 0.001). Results of the Bayesian model showed that 47% of the food web model species functional groups fell within the 95% credibility intervals of the Bayesian derived stable isotope trophic levels. Acknowledging that all modeling studies have limitations, this case study provides a framework and a new tool for researchers to better consider uncertainties in data and the inherent variability in coastal ecosystems.

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The frequency, duration, and co-occurrence of several environmental stressors are increasing globally. Multiple stressors may have compounding or interactive effects on animals, resulting in either additive or non-additive costs, but animals may mitigate these costs through various strategies of resource conservation or shifts in resource allocation. Thus, through two related factorial experiments, I measured a range of traits—from those related to life history and behavior to underlying physiology— to investigate the nature of costs (additive, non-additive, or neither additive nor non-additive), cost-mitigating strategies (resource conservation or allocation), and life-history strategy related to multiple stressors. First, I leveraged life-history strategy differences in the sand field cricket, Gryllus firmus, to investigate the individual and interactive effects of food and water limitation on fitness-related traits. Gryllus crickets exhibit a wing dimorphism mediating two distinct life-history strategies—long-winged crickets invest into flight capability while short-winged crickets do not. My results indicate that traits vary in their sensitivity to environmental stressors and stressor-stressor interactions (e.g., flight muscle). I only found support for non-additive costs or single-stressor costs of water and food limitation to fitness-related traits. Water availability had a larger effect on traits than food availability, affected more traits than food availability (wing dimorphism), and mediated the effects of food availability. Second, I investigated the role of life-history strategy in cost-mitigating strategies and further examined the costs (additive or non-additive) of multiple stressors to fitness-related traits, physiology, and behavior. I used the variable field cricket, Gryllus lineaticeps, to examine the costs of a simulated heat wave and water limitation. These stressors resulted primarily in single-stressor or non-additive costs to important traits (e.g., survival, final body mass, and total water content), extensive shifts in resource allocation priorities (e.g., reduced prioritization of body mass), and a limited capacity to conserve resources (heat wave reduced energy use only when water was available). Further, life-history strategy influenced the emergency life history stage (ELHS) because wing morphology and stressor(s) interacted to influence gonad and body mass, boldness behavior, and immunocompetence. Together, these two studies demonstrate that water availability and life-history strategy should be incorporated into future studies integrating important conceptual frameworks of stress (multiple-stressor framework and ELHS) across a suite of traits—from survival and life history to behavior and physiology.

Thesis (MPhil (Animal Sciences))--University of Stellenbosch, 2006. / ENGLISH ABSTRACT: A trial was done to determine if there are any differences in the growth performance of finisher pigs in the old conventional type of housing with disease infected pigs, pigs in multi unit housing that were also disease infected and high health pigs in multi unit type of housing. The high health pigs gave the best results when factors like A.D.I., A.D.G., F.C.R., margin over feed cost and carcass weight are compared with the results of the other two treatments. The difference in achievement between the disease infected pigs and the high health pigs were not the same for all the production factors but it was still in favour of the high health pigs. The trial results show just how dynamic pig production has become. From the results it is very clear that there is not any place anymore for the old conventional type of housing in any modern piggery. The time has also come for every pig farmer to look at and evaluate the health status of his piggery and to consider changing over to a high health herd. From a production as well as an economic viewpoint it makes good sense.

Master of Science / Department of Animal Sciences and Industry / Christopher Reinhardt / Crossbred bull calves at high risk for morbidity (n = 190; BW = 159 ± 68 kg) were received at a commercial stocker operation to evaluate the effects of meloxicam administered at the time of castration on performance and health through d 30 post-arrival. Calves were assigned randomly to receive either a whey-powder placebo (CON), 0.5 mg/kg BW meloxicam (LOW), or 1.0 mg/kg BW meloxicam (HIGH) administered orally. Calves were vaccinated, knife-castrated, and received experimental treatments on d 0. Meloxicam had no effect on ADG (P ≥ 0.63), morbidity (P = 0.66), or mortality (P = 0.62). A second study was conducted using crossbred calves from the southeastern US and Mexico (n = 472; BW = 227 ± 45 kg) to evaluate effects of an injectable trace-mineral solution administered at time of arrival at a commercial stocker operation on animal performance, health, and serum concentrations of Cu, Mn, Se, and Zn on d 0 and d 45. Calves were assigned randomly to receive saline (CON; 1.0 mL/45 kg BW) or injectable trace mineral (ITM; 1.0 mL/45 kg BW) on d 0. Average daily gain from d 0 to d 42, overall ADG from d 0 to d 139, mortality, and morbidity were not different (P ≥ 0.31) between treatments. Calves originating from the Southeastern US had greater (P < 0.01) overall ADG from d 0 to 139. There were no source effects (P ≥ 0.21) on initial serum mineral concentrations for Mn or Zn; however, cattle originating in Mexico had lesser serum Cu (P < 0.01) and cattle originating in the Southeastern US tended to have lesser serum Se (P = 0.06). On d 45, there were no treatment differences (P ≥ 0.20) in serum concentrations of Cu, Mn, or Zn but cattle that received ITM tended (P = 0.09) to have elevated serum Se concentrations compared to those that received CON.

<p> The purpose of this dissertation was to examine the influence of environmental variability on the distribution of prey, and the influence of prey spatial structure and habitat variability may have on the distributions of bottlenose dolphins (<i>Tursiops truncatus</i>). Additionally I examined how sociological differences (behavior type and the changes in a foraging behavior specific to Cedar Key Florida) influences the relative roles of bottlenose dolphins within the population. </p><p> The Gowans et al. scheme assumes that small groups form small communities and that foraging groups are small and rare as there are few foraging benefits to promote grouping. Using network analysis, I found that foraging occurs in small groups or alone, but there were preferential associations between individuals in Overall, Socialize, and Travel networks. </p><p> I examined driver-barrier foraging behavior over several field seasons to assess the prediction that there are few foraging benefits to promote grouping. The driver dolphin does have greater catch success than the barrier dolphins regardless of group size. There is also evidence that barrier dolphins may have a role in increasing foraging efficiency by decreasing the number of incomplete bouts. Both the driver and barrier dolphins do better in larger groups when incomplete bouts are factored in. Therefore there are some foraging benefits that can promote grouping. </p><p> In bottlenose dolphin foraging research, it is often assumed that habitat use is related to prey availability, though this is rarely directly tested. From my collaborative work using a database collected by the Florida Fish and Wildlife Commission&rsquo;s Fisheries-Independent Monitoring (FIM) program, I evaluated the abundance of potential prey and their relationship to habitat and other biological and physical variables. I used MULTISPATI, which uses principal components analysis to partition and display patterns of spatial variation. The results show that there are correlations between fish-site scores and environmental variables. Spatial analysis of fish produced clear results, however neither PCA nor MULTISPATI could explain dolphin distribution. This is likely because the spatial scales are not the same grain for the comparisons; dolphins are highly mobile large marine predators (the scale is fine grained), and their prey are significantly smaller and habitat-specific (the scale is coarser).</p>

Cooling systems used to reduce heat stress in dairy operations require high energy, water usage, or both. Steady increases in electricity costs and reduction of water availability and an increase in water usage regulations require evaluation of passive cooling systems to cool cows and reduce use of water and electricity. A series of experiments were conducted to evaluate the use of heat exchangers buried as components in a conductive system for cooling cows. In the first experiment six cows were housed in environmentally controlled rooms with tiestall beds, which were equipped with a heat exchanger and filled with 25 cm of either sand or dried manure. Beds were connected to supply and return lines and individually controlled. Two beds (one per each kind of bedding material) constituted a control group (water off), and the other 4 (2 sand and 2 dried manure) used water at 7°C passing through the heat exchangers (water on). The experiment was divided in 2 periods of 40 d, and each period involved 3 repetitions of 3 different climates (hot and dry, thermo neutral, and hot and humid). Each cow was randomly assigned to a different treatment after each repetition was over. Sand bedding remained cooler than dried manure bedding in all environments and at all levels of cooling (water on or off). Results from this experiment demonstrated that bed temperatures were lower and heat flux higher during the bed treatment with sand and water on. We also detected a reduction in core body temperatures, respiration rates, rectal temperatures, and skin temperatures of those cows during the sand and water on treatment. Feed intake and milk yield numerically increased during the bed treatment with sand and water on for all climates. No major changes were observed in the lying time of cows or the composition of the milk produced. The efficiency of conductive cooling as a heat abatement technique in dairy production is highly correlated with the distance between the cooling system and the skin of the cow and the type of bedding material used. A second experiment was conducted to identify possible improvements in the utilization of conductive cooling for cooling cows. Heat exchangers buried 12.7 cm below the surface as components in a conductive system ware evaluated in this study. Six cows were housed in environmentally controlled rooms with tie-stall beds, which were equipped with a heat exchanger and filled with 12.7 cm of either sand or dried manure. Beds were connected to supply and return lines and individually controlled. Two beds (one per bedding material type) constituted a control group (water OFF), and the other four (two sand and two dried manure) used water at 7°C passing through the heat exchangers (water ON). The experiment was divided into two periods of 40 days and each period involved three repetitions of three different climates hot dry (HD), thermo neutral(TN) and hot humid (HH). Each cow was randomly assigned to a different treatment after each repetition was over. The sand and water on treatment was the most efficient treatment under heat stress conditions (humid or dry heat). Cows in stalls with the sand and water on treatment demonstrated lower rectal temperatures, respiration rates, skin surface temperatures and core body temperatures compared to the other three treatments. Additionally, the sand and water on treatment increased milk yield and resting time of cows under heat stress. Also, the sand and water on treatment had the lowest bed surface temperatures and highest heat exchange compared to the other treatments. From these two experiments we confirm that heat exchangers are a viable heat abatement technique that could reduce the heat load of heat stressed cows; however, this system should be paired with additional cooling systems (e.g. fans and or misters) to most efficiently reduce the negative effects of heat stress on dairy production. Additionally, Sand was superior to dried manure as a bedding material in combination with heat exchangers. To make further recommendations of the use of heat exchangers in commercial dairy farm, a third study was developed. Based on the data obtained in the previous experiments, a comprehensive energy balance was developed to fully understand conductive cooling in two different environments (HD and HH), two bedding materials (sand and dried manure) and two depths between cows and the heat exchangers (25 vs. 12.5 cm). The energy balance estimates indicated that sand is the most efficient bedding material when utilized as bedding material with conductive cooling in both hot dry and hot humid environments. In the hot-dry environment there was an increase in the conductive heat exchanged with the reduction in bedding depth to 12.5 cm, however this did not result in a reduction in the heat storage of cows. In the hot-humid environment when heat exchangers were placed 12.5 cm from the top of the bed there was an increase in both the conductive heat loss and heat storage of cows when compared to 25 cm. Additionally, results demonstrated that the efficiency of heat exchangers as measured by heat flux was improved when heat exchangers were at a depth of 12.5 cm. The sensibility analysis indicated that a reduction in the depth and/or an increase in the thermal conductivity of both bedding materials would maximize conductive heat exchange. These results should be utilized as recommendations for the utilization of heat exchangers and conductive cooling in commercial dairy farms. Evaporative cooling is widely used in dairy farms located in arid environments. Even though, these cooling systems have been shown to effectively reduce the heat stress of lactating dairy cows, a growing shortage of water and rising cost of electricity compromise its future usage. An experiment was developed to compare two evaporative cooling systems, their interaction with lactating dairy cows and their usage of natural resources. The efficacy of 2 evaporative cooling systems (Korral Kool, KK, Korral Kool Inc., Mesa, AZ; FlipFan dairy system, FF, Schaefer Ventilation Equipment LLC, Sauk Rapids, MN) was estimated utilizing 400 multiparous Holstein dairy cows randomly assigned to 1 of 4 cooled California-style shade pens (2 shade pens per cooling system). Each shaded pen contained 100 cows (days in milk = 58 ± 39, milk production = 56 ± 18 kg/d, and lactation = 3 ± 1). Production data (milk yield and reproductive performance) were collected during 3 months (June–August, 2013) and physiological responses (core body temperature, respiration rates, surface temperatures, and resting time) were measured in June and July to estimate responses of cows to the 2 different cooling systems. Water and electricity consumption were recorded for each system. Cows in the KK system displayed slightly lower respiration rates in the month of June and lower surface temperatures in June and July. However, no differences were observed in the core body temperature of cows, resting time, feed intake, milk yield, services/cow, and conception rate between systems. The FF system used less water and electricity during this study. In conclusion, both cooling systems (KK and FF) were effective in mitigating the negative effects of heat stress on cows housed in arid environments, whereas the FF system consumed less water and electricity and did not require use of curtains on the shade structure. Results of this research indicate that effective use of conductive cooling in combination with efficient evaporative cooling systems offer opportunities to reduce both water and electricity consumption on dairy farms under both hot dry and hot humid environments.

An estrus synchronization trial was conducted to determine the efficacy of adding an injection of gonadotropin releasing hormone (GnRH) at initiation of the controlled intravaginal drug releasing device (CIDR®) progesterone synchronization protocol in heifers. Nulliparous (n=121) beef heifers were randomly assigned to one of two treatment groups. All heifers received a CIDR® implant at the initiation of the breeding season. Half of the heifers (Select Synch) received an injection of GnRH. Heifers in the Select Synch treatment group had a lower numerical response (76.7% versus 88.3%) to treatment (detected in heat) and an overall lower artificial conception rate (46.0% versus 53.3%), but no statistical difference was detected. Days to conception and artificial insemination conception rates for both groups were similar for all heifers inseminated. Three hundred multiparous Hereford, crossbred and composite beef cows were assigned to one of two breeding groups (Early and Late) based on calving date and randomly assigned to receive an injection of GnRH at the time of CIDR® insertion (Select Synch). The addition of GnRH did not impact the percentage of cows detected in estrus or days to conception. Conception rates were not affected by the addition of GnRH (Select Synch), however cows in the early breeding group were more likely to become pregnant (58% versus 45%) by artificial insemination (P<0.02). An experiment evaluated the efficacy of the CIDR® protocol to synchronize estrus in Arizona Holstein dairy cows (n=696). Cows assigned to the CIDR® protocol (n=337) received a CIDR® insert at the end of the voluntary waiting period (55 days). CIDR®s were removed and an injection of prostaglandin was administered seven days after insertion. There was no difference due to CIDR® treatment in number of services per conception or first service conception rate. CIDR® treatment reduced days to first service, days open at first service, and days open (P<0.02). Warm season had a deleterious effect on number of services, days to first service, first service conception rate and days open (P<0.0001). In summary, estrus synchronization improved postpartum reproductive performance; however, thermal stress continues to be a major barrier to reproductive efficiency.

My dissertation hypothesis is that bovine trophoblast cells express cell-surface and secreted non-classical major histocompatibility complex class I (MHC-Ib) proteins which inhibit NK cells and other leukocytes by binding to inhibitory receptors (e.g., LILRB1, LILRB2, KIR2DL4, and/or CD94/NKG2A). Extremely polymorphic and ubiquitously expressed classical MHC class I (MHC-Ia) proteins, which present foreign antigenic peptides to CD8+ T lymphocytes, are involved in acceptance or rejection of tissue grafts. Non-classical MHC class I (MHC-Ib) glycoproteins, such as Human Leukocyte Antigen-G (HLA-G) and murine Qa-2, are important modulators of the maternal immune system during pregnancy. MHC-Ib proteins are: (a) oligomorphic or monomorphic, (b) expressed in specific tissues under specific condtions, and (c) produced as surface and/or soluble isoforms due to alternative splicing. Third trimester-bovine trophoblast cells express both MHC-Ia and MHC-Ib proteins. The MHC-Ib proteins expressed by trophoblast cells during the third trimester of pregnancy are encoded by four bovine leukocyte antigen (BoLA) loci: BoLA-NC1, BoLA-NC2, BoLA-NC3, and BoLA-NC4. Two MHC-Ia (N*01701 and N*01802) and three MHC-Ib (NC1*00501, NC3*00101 and NC4*00201) proteins showed cell-surface expression in transfection studies performed in murine P815 and human K562 cells. Two additional isoforms, NC1*00401 and NC2*00102, were not detected on the surface of these cells. Nevertheless, both class Ia proteins, N*01701 and N*01802, and five class Ib proteins, NC1*00401, NC1*00501, NC2*00102, NC3*00101, and NC4*00201, were detected in crude cell lysates on Western blots. Precipitation of proteins from culture supernatants showed that cell-surface MHC-Ia (N*01701 and N*01802) and MHC-Ib proteins (NC1*00501, NC3*00101, and NC4*00201) are shed from the surface of these cells into the media. The mechanism of shedding of these proteins is, however, not known. Monoclonal antibodies W6/32, IL-A88, H1A, H6A, H11A, H58A, and PT-85A recognized surface MHC-I isoforms with varying affinity. We were able to develop a sandwich enzyme-linked immunosorbent assay (ELISA) using either H1A or IL-A88 antibody as the capture antibody and the W6/32 antibody for detection. We produced monoclonal antibodies against cattle NC1*00501 and NC3*00101 proteins. One monoclonal antibody generated against BoLA-NC3*00101 was highly specific. Unfortunately, due to failure to clone the NC3*00101- hybridoma, we no longer have an infinite source of this monoclonal antibody for NC3*00101. We eluted peptides from NC3*00101-transfected MHC-null K562 cells and identified peptides using liquid chromatography-mass spectrum (LC-MS) analysis. Analysis of peptide binding data using the SAS Proc mixed statistical program, suggested that the peptide EVTNQLVVL is a potential peptide ligand, which can be used to make tetramers for enumeration of antigen-specific leukocytes.