Academic literature on the topic 'Fields of Research – 300000 Agricultural, Veterinary and Environmental Sciences – 300400 Animal Production'

The experiments described in this thesis investigated nutritional and physiological aspects of antler growth in red deer stags. The initial experiment (Section 3) examined the effects of winter nutrition on subsequent antler casting date and velvet antler weight. Mature stags on two different farm types (hill country, Farm H and irrigated lowland, Farm L) were offered three levels of winter nutrition, two levels of a concentrate supplement (ad libitum pellets and 1/2 ad libitum pellets) and a basal hay ration. On both properties liveweight gains occurred in supplemented groups and liveweight losses in unsupplemented groups. At antler casting there were significant differences in liveweight of approximately 10 kg between fully supplemented and unsupplemented groups. Realimentation of winter liveweight losses subsequently occurred so that by the following rut the effects of winter undernutrition had been eliminated. On Farm H poor winter nutrition (hay only) resulted in a significant delay in casting date (13 days) and lower velvet antler yields (0.24 kg), than in stags offered the ad libitum concentrate ration. Stags on Farm H were 13 kg lighter at commencement of the trial than at Farm L and the differences in treatment effects obtained between farms may have been due to differences in body condition at commencement of the trial. An association was demonstrated between liveweight and date of antler casting, with heavier stags casting earlier than lighter stags. There was no effect of age of stag on casting date. Of the liveweights recorded, liveweight prior to the rut showed the best relationship with casting date, possibly because the seasonal nature of liveweight change meant that a weight recorded at this time gave the best indicator of the true frame size of a stag. Both age and liveweight significantly affected velvet antler weight, with increases of velvet antler weight of 0.26 kg between 3 and 4-year-old stags and of 0.30 kg between 4 and 5-year-old stags at the same liveweight. Within an age group velvet weight increased by 0.12 kg for each 10 kg increase in pre-rut liveweight. The experiments described in Section 4 comprised studies on antler growth and composition. In order to obtain data on antler growth and composition individual antlers were removed sequentially from mature red deer stags between 28 and 112 days after casting of hard antlers. Contralateral antlers were removed after stripping of velvet. Wide variation occurred in antler casting date (53 days) compared to date of velvet stripping (24 days). The duration of the period of antler growth may therefore be governed more by date of casting than by date of velvet stripping. Mean duration of the antler growth period was 164 days. Growth in length of the antler appeared to follow a sigmoid curve. However, between 28 and 112 days after casting, rates of elongation were close to linear. Mean length of hard stripped antlers was 0.71 m and between 28 to 112 days after casting mean rate of antler elongation was 0.62 cm/day. Over this period indivdual antlers increased in fresh weight at a rate of 13.7 g/d, with heaviest weight recorded 112 days after antler casting, at approximately 130% of final hard antler weight. Between 28 and 91 days of growth, volume of blood in the antler increased linearly at a rate of 194 ml/kg. Three phases of mineralization were demonstrated in developing antlers. Tips of growing antlers were cartilaginous and poorly mineralized. A zone of mineralization occurred 5.0 to 7.5 cm behind the antler tip which corresponded histologically to the transition from mineralized cartilage to trabecular bone. The second phase of mineralization occurred through continued accretion of trabecular bone in the antler shaft. The third phase, described as "terminal mineralization" in this study, appeared to be associated with a rapid increase in density of cortical bone in the periphery of the antler shaft. Terminal mineralization (between 91 and 112 days after casting of hard antlers) coincided with the slowing of growth in length, a decrease in relative blood volume in the antler and an increase in levels of plasma testosterone. These events occurred close to the summer solstice. At velvet stripping individual antlers had a mean weight of 1.12 kg and contained 81.1% dry matter (DM). Fat free organic matter (FFOM) and ash concentration in DM were 36.6 and 60.0%, respectively. Peak daily rates of FFOM and ash deposition occurred between 91 days and 112 days after casting, at rates of 1.4% of hard antler FFOM and 1.6% of hard antler ash. For a stag producing 2.24 kg of hard antler mean rates of FFOM and ash deposition over this period were 9.3 and 18.3 g/d, respectively. On a whole antler basis calcium concentration in antler ash remained constant, at around 35%. Therefore peak rate of antler calcium deposition would be 6.4 g/d. In the final experiment (Section 5) mature stags were offered a maintenance ration of greenfeed oats during the period of peak calcium requirement for antler growth and the kinetics of calcium metabolism were examined using a radio-isotope (⁴⁵Ca). Rates of faecal endogenous loss were low and at approximately 6.4 mg/kg BW per were half the estimated requirements of ARC (1980) for sheep and cattle. Availability of calcium from greenfeed oats was low (mean, 37%) and less than 30% of total calcium requirements were derived from the diet. Poorly mineralized skeletal bones indicated that the shortfall in antler calcium was derived from the skeleton. In spite of a severely negative calcium balance stags were capable of maintaining high and apparently normal rates of antler calcium deposition (mean, 44 mg/kg BW per day). Antlers appear to be acting as a sink with calcium being irreversibly deposited in the antler and lost to the animal's body. On the assumption therefore that antler calcium behaves like calcium lost during lactation a kinetic model of calcium metabolism in the stag was developed.

The Kahne rumen sensor (bolus) is a device developed to measure temperature, pressure and pH in non-fistulated animals. This bolus allows real-time monitoring of the rumen environment, which could help preventing health problems such as rumen acidosis in cows. It is less invasive to use boluses compared to other technologies that measure the ruminal pH (e.g. rumenocentesis). Kahne boluses and transceivers are commercially available in the market. Several studies on the relationships between data recorded by the bolus and actual data recorded by independent devices were conducted. The bolus temperature and pressure were compared with actual temperature and pressure under controlled conditions. The pH drift was studied by comparing the difference between bolus and direct measurement over time. The capture of the data was calculated for each bolus in various experiments to examine the factors affecting the data capture rate of the boluses. Animal to animal variation was studied using boluses in a group of cows fed and managed under uniform conditions. An animal experiment involving fistulated cows eating two different diets was performed using boluses to monitor the changes of ruminal pH. There was no apparent interruption to normal animal behaviour as a result of using boluses. Regression relationships between bolus measurements and actual data for both temperature and pressure were developed and used for calibration of bolus data. The pH drift was a problem, as the regression relation between the pH difference and the time for one bolus from one experiment could not represent this bolus on other experiment. The data capture rate on the hourly basis ranged from 0 to 100%, but was usually between 30 to 70%. The data capture rate was affected by many factors and further studies to identify these factors are needed. A study of animal to animal variation suggests that in a comparison of 2 treatments, a minimum 3 cows per group would be required to detect the standard deviation of 0.11 for a pH difference of 5% of the mean (approximately 0.35 pH units). Seventeen cows per group would be required to detect the standard deviation of 0.33 for the same difference. The boluses effectively monitored the ruminal pH change in cows easting two different diets and the profile of change of pH was successfully analysed. Feeding 7.6 kg baleage twice a day cause pH to decrease at 0.009 pH units per minute during feeding, while offering a similar quantity of grass and hay once a day resulted in a decrease of 0.0009 pH units per minute during feeding. The beginning of pH increase was about 1 hour following feeding and continuous during resting and rumination. The level of pH increase did not differ significantly for two diets.. The Kahne devices appear to have advantages compared to other technologies for the measurement of parameters of the rumen environment on a real-time basis. Boluses are especially good at intensively monitoring the temperature, pressure, and pH in the rumen. The major limitations of this technology to be used are the data capture rate and the pH drift. By improving the limitations found in the experiment, the Kahne rumen sensor could become very useful for both scientific research and under commercial conditions for monitoring animal health.

There is an extensive debate on the potential environmental impact of dairy farms and in particular the effect of dairy farms on the nitrogen cycle and the effect that this has on ecosystems. Within New Zealand and in particular in the South Island, the expansion of dairying and the adoption of new dairy systems has led to this becoming an increasingly important issue, locally through its effect on water quality and the environment and nationally and internationally through the production of green house gases. Increases in nitrogen usage at the expense of clover nitrogen fixation, irrigation, stocking rate and the introduction of dairy cows onto light free draining soils previously the preserve of arable or sheep farming has led to concern as to the effect intensive pastoral dairying may have on the nitrogen dynamics of the farm and the environment. This study is designed to assess how changes in grazing management in particular changes in pre-grazing and post-grazing residuals alter the clover/ryegrass balance on the farm and the effect that this has on the farm’s nitrogen dynamics. The effects of qualitative changes in grazing management on pasture composition are well established but little is known of the effect of quantitative changes in pasture management on composition, in particular the effect of grazing residuals. There are a number of detailed models of the physiological processes in the energy and nutrient cycling in plants, animals and the soil. There are a smaller number of whole farm models that through integration and simplification of component models attempt to represent the flux of nutrients though a dairy farm. None of these whole farm models is currently able to model the nitrogen flux through a dairy farm at a sufficient level of resolution to capture differences in pasture composition as these occur spatially, temporally and in response to grazing management. This project sought to better understand the nitrogen dynamics on a dairy farm by constructing and then linking component models – a pasture composition and growth model, a cow model, an excretal return model, a soil model and a water balance model – within a whole farm management schedule. The formal null hypothesis is that the mechanistic, mathematical model constructed for this PhD cannot capture and explain the full range of the changes in soil water content, soil nitrogen status, pasture production and composition and animal production, following the alteration in management of the dairy farm between 2002 and 2004. Individual component models were constructed by the author using the computer software package (Matlab) and validated against data extracted from the literature. The models were then converted into one simulation package using C-sharp as the source code language by Elizabeth Post, Senior Computer Scientist at Lincoln Ventures Ltd, Lincoln, New Zealand and the author. This model was then used to investigate the nitrogen dynamics of a dairy farm: the relationship with pasture composition and whether small changes in pasture residuals make a difference to pasture composition and nitrogen dynamics. Two different simulations were run based on the management practice of Lincoln University Dairy farm (LUDF) over two dairy seasons (2002-03 and 2003-04) and validated against the data recorded on this farm. In 2002-03, 50 cows were over wintered and 580 cows were subsequently milked on 200ha. Post grazing residuals where maintained at 1600-1750KgDM/ha. In 2003-04, 125 cows were overwintered and 635 cows were milked on 200ha with post grazing residuals maintained at 1400KgDm/ha. All models operate on a daily time step. Within the pasture model composition is described by 9 state variables describing different components of the pasture and pasture growth is modelled mechanistically from a calculation of component photosynthesis. A further 9 state variables describe the nitrogen composition of the pasture components. The soil model is a variable two layer, mechanistic representation, parametised for the shallow, stony soils of LUDF. Soil water status is an input for the pasture model while water uptake by the growing plants affects the soil water balance within the soil model. Animal intake and production are modelled mechanistically with model cows described in terms of their age, genetic merit, body weight, breed, pregnancy status, conception date and body condition score. Each cow type produces a different quantity of urinary and faecal excretion which varies with dry matter intake, milk yield and the sodium and potassium status of the pasture. Excretal nitrogen composition is predicted within a separate model which calculates daily nitrogen excretion in faeces, urine and milk. Excretions are deposited randomly over the grazed area and account is taken of overlapping excretions that are created on the same day and overlaps that occur with older excretal patches deposited in previous grazing rounds. Each excretal patch has its own associated pasture, water and soil model reflecting the differences in nitrogen status between patches. Grazing preference is expressed within the model between different classes of excretal patch and between excretal patches and the base pasture and between clover and grass. Supplementary silage is conserved and fed according to the management schedule of LUDF. Cows calve, become pregnant and are dried off within the model according to the relevant records from LUDF. Cows are deemed to arrive on the farm on the day of calving and to leave on the day that drying off is finished (a 5 day procedure within the model), except for those cows that are overwintering which remain on the farm. The soil model has multiple nitrogen/carbon pools and is dynamically linked to all the other models. External nitrogen losses from the system are modelled as volatilisation, leaching and denitrification, with pasture nitrogen uptake from the soil model and fixation by clover from the atmosphere. Both the individual component models and the final assembled composite model were successful in matching the available data in terms of pasture and animal production, pasture composition, soil water balance and nitrogen status and external losses. The model indicates that the low residual, high stocking rate farm returns more excreta to the soil. However, this is countered by a reduction in the amount of dead material returned to the paddock and this reduces the relative size of the pool of nitrogen in the dead organic matter. This produces a relative lack of substrate for the soil microbes which are thus unable to exploit all of the nitrogen in the available pool. Soil ammonium and nitrate pools are also increased from the increase in faecal and urinary return so precipitating an immobilising flux from these larger pools to the smaller pool of nitrogen available to the soil microbes. However, the relative inability of the soil bacteria to fully exploit this means that the production of soil organic live matter and the resulting mineralising flux from the dead organic matter pool through the available pool to the ammonium and nitrate pools is reduced. The larger ammonium and nitrate pools will also be associated with increased external losses from the system as denitrification, leaching and volatilisation are increased. The increase in the clover percentage within the sward in 2003-04 led to greater nitrogen fixation and the model suggests that some of the extra nitrogen is effectively captured by the animals in increased production. However, the reduction in the return of dead matter coupled with an increase in excretal return and the consequent increase in the mineral nitrogen pools within the soil lead to greater losses of nitrogen from the soil.

There is little evidence that the productivity of New Zealand beef herds has improved over time. Data from the NZ Meat and Wool Board’s Economic Service (2006) suggest that the average national calving percentage has declined over the last two decades. During the same period cattle carcass weights have increased but so too has the average cow live-weight which has resulted in increased maintenance costs of the cow herds. It is unclear whether production efficiency in the industry has improved or declined over time. The aim of this research was to develop means of improving productivity in commercial beef herds through practical methods of performance recording. The objectives were firstly to establish current management practices in commercial herds and secondly to develop an objective system for cow selection and culling which would have practical application in commercial herds. Beef management survey Ninety two commercial beef producers with more than 100 breeding cows from the greater Canterbury region of New Zealand were surveyed. Pasture control was the main reason given for owning a beef herd. Size and conformation were the main selection criteria for choosing replacement heifers and bulls. Over 80% of herds retained their own heifers as replacements and >60% mated yearling heifers to first calve at two years of age. Fertility was poor in the surveyed herds. In-calf rates at pregnancy testing averaged 88% for maiden heifers, 92% for rising second calvers and 93% for mixed age (m.a.) cows. There was no significant difference between in-calf rates of maiden heifers mated to first calve at two or three years of age; nor was there any significant difference between the re-breeding success of the two groups. Heifers mated at least one week earlier than m.a. cows, achieved a re-breeding success 4.7% greater (P<.01) than those mated at the same time. Reasons for cows not weaning a calf included wet dry (9.3% of pregnant cows wintered), pregnancy tested not-in-calf (7.4%) and dam death (2.6%). Only 87.9% of pregnant females wintered weaned a calf (89.4% of m.a. cows and 84.9% of heifers). Reasons why cows exited the herds included diagnosed empty (37.2% of all exits), involuntary culls (25.4%), sold wet dry (16.2%), deaths (13.1%) and poor calf production (5.1%). Vaccination was infrequent with clostridial vaccines the most common in m.a. cows (15.2%) and in calves (40.7%); vaccination against Leptospirosis was much less common. Very few of the surveyed farms used any system of performance recording; as a result there was very little performance-based selection or culling practiced. Evaluation of alternative measures of cow productivity Data from four performance recording beef herds were used to compare alternative measures of cow productivity with the industry standard which is calf weaning weight adjusted for sex (SOC) and age of calf and age of dam (AOD), i.e. the “200 day weight.” None of the alternative measures evaluated required knowledge of calving date and all were relatively easily obtainable in extensively managed beef herds. The assessment of cows was based not on their estimated breeding values but instead on their most probable producing ability which, as the sum of all of the permanent, repeatable aspects of the calf-rearing ability of the cow, explains considerably more of the variance of weaning weight than does breeding value alone. SOC and AOD-adjusted marking weight, weaning weight and average daily gain (ADG) between marking and weaning were the traits mostly highly correlated with the 200d wt of calves (r = 0.68, 0.90 and 0.74. respectively). An Extensively- Grazed-Cow-Weaning-Index of these three indicator traits was found to be more highly correlated than any of the individual traits on their own (r = 0.94). Index weights for the three indicator traits were calculated within each herd and then those within-herd index weights were regressed on readily obtainable herd descriptive variables to obtain a regression equation that could predict index weights for any herd. When the model was applied to data from two additional herd years not included in the original model, the EGCW Index was highly correlated with the 200d weights (r>0.90). Performance-based culling of previously unselected commercial beef herds based on the EGCW Index will result in improved productivity due to the moderately high repeatability of calf weaning weight. Objective data from extensively grazed commercial herds will also make possible the use of commercial herd data in genetic evaluations of herd sires.

Organic dairying is growing in popularity in New Zealand and the demand for knowledge is ever increasing. Many more farmers are considering organics as an alternative to their current conventional system. However, limited information is available on organic dairying in a New Zealand pastoral situation particularly in relation to its effect on fertility. The New Zealand dairy industry requires the dairy cow to become pregnant every year at the same time to maximise milk production and utilise the high pasture production in spring. A cow requires 40 to 60 days for uterine involution to occur and for resumption of oestrous cycles. It is critical that the cow becomes pregnant within the six to eight week mating period, however, this can be difficult for late calvers or those cows that had or still have a uterine infection, to undergo uterine involution and be successfully mated. These cows will often not become pregnant and as a consequence be culled for infertility. During the first few weeks postpartum, the bacterial composition of the uterus fluctuates as a result of spontaneous contamination, elimination and recontamination. Most cows are able to eliminate these bacteria, however, 10 to 17% of cows are unable to do this. In these cows, the bacteria persist, cause infection and inflammation, and delay uterine involution. The main objective of this present study was to investigate the effect of different management systems (Organic and Conventional) on productivity and reproduction, particularly the process of uterine involution and its relationship with reproductive outcomes. Uterine involution will be studied through the following measurements: cervical diameter as assessed by measurement per rectum, plasma concentrations of glucocorticoids and bacteriology of the uterus. Lactation characteristics: milk yield, cumulative milk yield, milksolids production and somatic cell count will also be investigated. From the results, it can be concluded that Organic cows have reduced milk yield (P=0.05) and milksolids production (P<0.01) through there were no major differences at peak lactation or in the rate of decline after. However, overall somatic cell count was not affected by management system though the Conventional cows had high somatic cell counts in early lactation (P=0.925). Cervical diameter was affected by the management system with the difference between Organic and Conventional cows almost significant (P=0.06). Cortisol concentrations were significantly higher in Organic cows (0.68 ± 0.08 ng/ml) when compared to Conventional cows (0.95 ± 0.06 ng/ml) (P=0.01). Cortisol concentrations decreased over time postpartum (P<0.01). Additionally Organic cows had a shorter interval from calving to AI (P=0.017). However, none of the other reproductive outcomes were affected by management system. Simple correlations established that reproductive outcomes and bacterial counts, reproductive outcomes and cortisol at Day seven, and cortisol and milk production characteristics, were not independent of each other. Aerobic bacterial counts on Day 28 and the interval from calving to AI were found to be significantly correlated (r= 0.615). Stepwise partial regression analysis, plus analysis of variance calculated on the relationships between uterine involution parameters and reproductive outcomes found multiple weak correlations. It found that cervical diameter, and aerobic and anaerobic bacterial counts on Day 28 were significantly correlated with the interval from calving to first AI (P=0.018). The differences in lactation characteristics are related to the lower pasture production on the organic farmlet reducing the maximal potential milk production and the possibly earlier calving dates of the Conventional cows. The differences in bacterial counts and almost significant difference in cervical diameter may be related to the lower cortisol levels and thus suggest that the Organic cows may be less stressed. As stress suppresses the immune system, it may be possible that the higher bacterial counts are indicitative of a less efficient or slightly weakened immune system which takes longer to eliminate bacteria in the uterus; however this is open to conjecture. The shorter interval from calving to AI suggests that Organic cows may be exhibiting oestrus behaviour earlier postpartum or the Conventional cows are having “silent heats” but this difference is possibly related to human factors. The correlation between parameters of uterine involution and interval from calving to AI, and the lower values for uterine involution parameters in Organic cows suggest the possibility of faster uterine involution and this may result in better fertility in the Organic cows. More research needs to be carried out to further investigate the effect of organic dairying on uterine involution and reproduction outcomes but organic dairying at the very least does not negatively impact on uterine involution and fertility.

Exposure of the fetus to adverse conditions in utero may result in developmental adaptations that alter metabolism and postnatal growth of the offspring. This thesis investigated the effects of dam size and nutrition during pregnancy on growth, metabolic function and lactational and productive performance of the female offspring to two years of age. Four-hundred and fifty heavy (60.8 kg ± 0.18) and 450 light (42.5 kg ± 0.17) dams were randomly allocated to ad libitum or maintenance nutritional regimens from days 21 - 140 of pregnancy, under pastoral grazing conditions. From one week prior to lambing, all dams were fed ad libitum until weaning. After weaning, female progeny were managed and fed under pastoral conditions as one group. Maternal nutrition during pregnancy affected lamb growth to weaning, however, after weaning lamb growth was affected by dam size. Dam size had no effect on glucose metabolism, adrenal function or fat metabolism in 16-month-old female twin offspring. Dam nutrition during pregnancy had a minor effect on glucose metabolism and no effect on adrenal function or lipolysis, however, it did possibly affect gluconeogenesis and/or glycogenolysis, with increased glucose production in ewes born to maintenance-fed dams. Ewes born to dams fed maintenance showed greater milk production, lactose percentage, lactose and crude protein yield. Ewes born to heavy dams showed greater milk production and lactose yield. Dam size had no effect on reproductive performance of the female offspring. Being born to a larger dam showed no advantages over being born to smaller dams, for number of lambs born and weight of lambs at birth and weaning. ‘Grand’dam maintenance nutrition increased lamb birth and weaning weight and lamb growth rates of the ‘grand’offspring. Ewes born to maintenance-fed dams could have an advantage over ewes born to ad libitum-fed dams in physiological stressful situations in life as their liver may be able to supply more glucose to support their growing conceptus and milk production to increase the chances of survival of their offspring. These results indicate that it is possible to programme the offspring by feeding their dams differently during pregnancy under grazing conditions. With a better understanding of how offspring can be programmed through different maternal nutritional regimens, it may be possible to significantly increase the production potential of the New Zealand ewe population.

The nutritional value of faba beans (Vicia faba), Australian sweet lupins (Lupinus angustifolius), white lupins (Lupinus albus) and peas (Pisum sativum) grown in New Zealand for broilers were evaluated in terms of their nutritional characteristics, protein quality (protein efficiency ratio), apparent metabolisable energy, apparent ileal digestibility coefficient of amino acids and the effects on bird performance. The effects of dehulling and extrusion cooking on the nutritive value of legumes were also investigated. The first experiment discussed in Chapter 3 evaluated the effect of cultivars on the nutrient profile and protein quality of chickpeas (Cicer arietinum), Australian sweet lupins, peas and soybeans (Glycine max). With the exception of white lupins, cultivars had no effect on the proximate and fibre composition of grain legumes. Starch was the primary carbohydrate component of chickpeas and peas, whilst non-starch polysaccharides were the major carbohydrates in lupins. The legume proteins were deficient in lysine, methionine, cystine and threonine. No differences were found in protein quality between cultivars of the different grain legume species. The lowest weight gain and protein efficiency ratio, in addition to the highest relative pancreatic weight and mortality rate was found in raw soybeans, suggesting that soybeans contained high a concentration of anti-nutritional factors, such as protease inhibitors. Birds fed chickpeas, lupins and peas had a low mortality rate and relative pancreatic weight, confirming that the level of anti-nutrients in these legume seeds was low. The apparent metabolisable energy and apparent ileal digestibility coefficient of amino acids of faba beans, Australian sweet lupins, white lupins and peas were determined in the second experiment (Chapter 4). Cultivar effect on the apparent metabolisable energy values was observed only for faba beans and white lupins. Faba beans, white lupins and peas had comparable apparent metabolisable energy values, but these values were higher than those of Australian sweet lupins, and lower than that of soybean meal. No cultivar differences were found in the apparent ileal digestibility coefficient of amino acids of grain legumes. The apparent ileal digestibility coefficient of amino acids of both lupin species was found to be comparable to that of soybean meal. The effects of feeding diets containing 200 g/kg faba beans, lupins or peas on the performance, digestive tract development and litter quality of broilers were investigated in the third and fourth trials. In the cage trial (Chapter 5), the results showed that the weight gain of birds fed diets containing grain legumes was similar to that of control diet. Feed intake and feed per gain of birds fed diets containing the majority of grain legume cultivars did not differ from those fed the maize-soy diet. Birds fed diets containing faba beans had more dry and friable excreta compared to other treatment diets. The performance of birds fed diets containing 200 g/kg grain legumes during the 35 d grow-out period, in the floor pen trial (Chapter 6), confirmed the results of the cage trial. In this trial, weight gain and feed per gain of birds fed diets without meat meal were superior to those with meat meal. In cage trials, the modification of some segments of digestive tract development was probably due to the dietary NSP. Whilst in floor pen trial, digestive tract development was not influenced by the inclusion of grain legumes. The effect of methodology of determination (direct vs. difference method) on the apparent ileal digestibility coefficient of amino acids of wheat, maize, Australian sweet lupins, peas and soybean meal for broilers was evaluated in the fifth study (Chapter 7). The influence of methodology on apparent ileal digestibility coefficient of amino acids was found to vary amongst the feed ingredients. In general, the apparent ileal digestibility coefficient of amino acids of test ingredients determined by the difference method was higher than those determined by the direct method, suggesting that the use of the direct method may underestimate the apparent ileal digestibility coefficient of amino acids in low and medium protein ingredients. Data reported in Chapter 8 shows that dehulling increased the apparent metabolisable energy values of faba beans and Australian sweet lupins, but it had no beneficial effect on peas. The increase of apparent metabolisable energy values may be attributed to the decrease in non-starch polysaccharides of these legume seeds after dehulling. The removal of hulls increased the amino acid concentrations, but it had no effect on the apparent ileal digestibility coefficient of most amino acids. These results suggest that dehulling of grain legumes would be nutritionally beneficial and, likely to be economical in view of the improved amino acid concentrations and energy values. The final experiment (Chapter 9) demonstrated that extrusion of peas markedly influenced the content of crude protein, non-starch polysaccharides, starch, and trypsin inhibitors. The soluble non-starch polysaccharides and trypsin inhibitor contents of the majority of extruded pea samples were higher than those of raw peas, but insoluble and total non-starch polysaccharides decreased with extrusion. Extrusion had no effect on the apparent ileal protein digestibility and the apparent metabolisable energy of peas, but it increased ileal starch digestibility.

Animal health surveillance is an important part of animal health care, particularly in countries dependent on livestock for food production and international trade. There are two major issues related to the provision of e®ective surveillance activities. Firstly, for good information to become available, the design and conduct of data collection activ- ities should be carried out following sound statistical principles. In reality, constraints such as imperfect tests and unavoidably-biased sampling strategies hinder straightfor- ward analysis and interpretation of survey results. Risk-based surveillance is used to target high-risk sub-populations to increase e±ciency of disease detection; however, biased datasets are generated. This thesis develops methodologies to design risk-based surveillance systems and al- low statistically valid analysis of the inherently biased data they generate. The ¯rst example describes the development of a method to analyse surveillance data gathered for bovine spongiform encephalopathy (BSE). The data are collected from four dif- ferent surveillance streams of animals tested for BSE, with each stream containing unavoidable biases and limitations. In the BSurvE model, these data are combined with demographic information for each birth cohort to estimate the proportion of each birth cohort infected with BSE. The prevalence of BSE in a national herd can then be estimated using the method of moments, whereby the observed number of infected animals is equated with the expected number. The upper 95% con¯dence limit for the prevalence is estimated both for infected countries and for those where no BSE has previously been detected. A similar approach to that used in BSurvE is then applied to surveillance data for trichinellosis, for which risk-based post-mortem testing is also performed. Negative results from multiple species using di®erent, imperfect tests are combined to give an estimate of the upper 95% con¯dence limit of the national prevalence of trichinellosis in a reference population. This method is used to provide support for freedom from trichinellosis in Great Britain. A di®erent approach to risk-based surveillance is explored as the surveillance strategy for detection of exotic causes of abortion in sheep and goats in New Zealand is examined. Using a geographic information system (GIS) maps of disease risk factors were overlain to produce a risk landscape for the lower North Island. This was used to demonstrate how areas of high- and low-risk of disease occurrence can be identi¯ed and used to guide the design of a risk-based surveillance programme. Secondly, within one surveillance objective there may be many ways in which the available funds or human resources could be distributed. This thesis develops a method to assess BSE surveillance programmes, and provides tools to facilitate BSE detection on the basis of infection risk and to increase the e±ciency of surveillance strategies. A novel approach to allocation of resources is developed, where portfolio theory con- cepts from ¯nance are applied to animal health surveillance. The example of surveil- lance for exotic causes of sheep and goat abortion is expanded upon. Risk of disease occurrence is assessed for a population over di®erent time periods and geographical areas within a country, and portfolio theory used to allocate the number of tests to be carried out within each of these boundaries. This method is shown to be more likely to detect disease in a population when compared to proportional allocation of the available resources. The studies presented here show new approaches that allow better utilisation of imperfect data and more e±cient use of available resources. They allow development of surveillance programmes containing an appropriate balance of scanning and targeted surveillance activities. Application of these methods will enhance the implementation and value of surveillance in animal health.

This thesis is concerned with the application of recently developed epidemiological and statistical tools to inform the optimisation of a national surveillance strategy of considerable importance to human health. The results of a series of epidemiological investigations of surveillance strategies for zoonotic Salmonella are presented. Salmonella are one of the most common and serious zoonotic foodborne pathogenic bacteria globally. These studies were motivated by the increasing focus on the cost-effectiveness of surveillance while maintaining consumer confidence in food supply. Although data from the Danish Salmonella surveillance and control programme has been used in these investigations, the techniques may be readily applied to other surveillance data of similar quality. The first study describes the spatial epidemiological features of Danish Salmonella surveillance and control programme data from 1995 to 2004, using a novel method of spatially adaptive smoothing. The conditional probability of a farm being a case was consistently high in the the south-west of Sonderjylland on the Jutland peninsula, identifying this area for further investigation and targeted surveillance. The identification of clustering of case farms led into the next study, which closely examines one year of data, 2003, for patterns of spatial dependency. K-function analyses provided evidence for aggregation of Salmonella case farms over that of all farms at distances of up to six kilometres. Visual semivariogram analyses of random farm-level effects from a Bayesian logistic regression model (adjusted for herd size) of Salmonella seropositivity, revealed spatial dependency between pairs of farms up to a distance of four kilometres apart. The strength of the spatial dependency was positively associated with slaughter pig farm density. We describe how this might inform the surveillance programme by potentially targeting herds within a four kilometre radius of those with high levels of Salmonella infection. In the third study, farm location details, routinely recorded surveillance information, and industry survey data from 1995 were combined to build a logistic seroprevalence model. This identified wet-feeding and specific pathogen free herd health status as protective factors for Salmonella seropositivity, while purchasing feed was a risk factor. Once adjusting for these covariates, we identified pockets of unexplained risk for Salmonella seropositivity and found spatial dependency at distances of up to six km (95% CI: 2–35 km) between farms. A generalised linear spatial model was fitted to the Jutland data allowing formal estimation of the range of spatial correlation and a measure of the uncertainty about it. There was a large within-farm component to the variance, suggesting that gathering more farm level information would be advantageous if this approach was to be used to target surveillance strategy. The fourth study again considers data from the whole study period, 1995 to 2004. A detailed temporal analysis of the data revealed there was no consistent seasonal pattern and correspondingly no benefit in targeting sampling to particular times of the year. Spatiotemporal analyses suggested a local epidemic of increased seroprevalence occured in west Jutland in late 2000. Lorelogram analyses showed a defined period of statistically significant temporal dependency, suggesting that there is little value in sampling more frequently than every 10 weeks on the average farm. The final study uses findings from the preceding chapters to develop a zero-inflated binomial model which predicts which farms are most at risk of Salmonella, and then preferentially samples these high-risk farms. This type of modelling allows assessment of similarities and differences between factors that affect herd infection status (introduction) and those that affect the seroprevalence in infected herds (persistence and spread). The model suggested that many of the herds where Salmonella was not detected were infected but at a low prevalence. Using cost and sensitivity, we compared the results with those under the standard sampling scheme based on herd size, and the recently introduced risk-based approach. Model based results were less sensitive, but showed significant cost savings. Further model refinements, sampling schemes, and the methods to evaluate their performance are important areas for future work, and should continue to occur in direct consultation with Danish authorities.

This thesis describes two approaches for studying of lipoprotein metabolism in sheep. The first approach involves the assay of lipoprotein lipase (LPL) activity to determine the role of lipoprotein-triacylglycerol fatty acids in fat deposition in sheep. This enzyme is the rate limiting enzyme in the hydrolysis of fatty acids from lipoprotein-triacylglycerol. The second approach was to characterize and quantify in vivo lipoprotein metabolism using iodinated very low density lipoprotein (¹²⁵I-VLDL) and low density lipoprotein (¹³¹I-LDL). Cross-bred lambs were divided into two treatment groups and either weaned early at 5 weeks of age or remained suckling. Lambs were slaughtered at 12 or 23 weeks at which time the body composition and adipose tissue LPL activity were determined. The differences in rearing led to differences in body composition. The suckled lambs were larger and fatter than weaned lambs. The increased fatness in the suckled lambs was associated with increased LPL activity (U/mg protein) in subcutaneous adipose tissue and was reflected in higher LPL activity in post-heparin plasma (PHP) taken 2 days prior to slaughter. The role of insulin in the regulation of LPL activity was investigated by either infusing a subset of the weaned and suckled lambs with insulin for 7 or 18 weeks or using the euglycemic clamp technique to study the effect of short insulin infusions. The long term infusion of insulin had no significant effect on PHP LPL or on adipose tissue LPL (U/g tissue). However, after infusing insulin for 6h at 6.3 mU.kg⁻·⁷⁵.h⁻¹ during the euglycemic clamps, a two fold increase in LPL activity in biopsied subcutaneous adipose tissue was observed. In the second approach, in vivo lipoprotein metabolism was investigated in 4 lambs using apolipoprotein B as a marker. Following the simultaneous injection of ¹²⁵I VLDL and ¹³¹I VLDL, the specific activities of apoB in VLDL, IDL and LDL fractions were determined. ApoB specific activity curves demonstrated that VLDL is metabolised to IDL and subsequently to LDL. The turnover of VLDL-B (3.45mg.d⁻¹.kg⁻¹) and LDL-B (4.8mg.d⁻¹.kg⁻¹) was calculated by fitting the VLDL-¹²⁵I-B and LDL-¹³¹I-B specific activity data to a mono-exponential equation. The metabolism of lipoproteins, inferred from the study of apoB, was shown to be similar in sheep to that reported in other animals although the amount of lipoprotein synthesised was low. A model to describe the kinetics of apoB metabolism in sheep was developed using SAAM. The proposed model features a three pool delipidation chain for VLDL, and subsystems containing two pools for IDL and LDL. IDL may be catabolised to LDL or cleared directly from the plasma. The developed model can now be used to compare the metabolism of lipoproteins in different physiological states and to design new experiments to study lipoprotein metabolism further.