The advent of real time polymerase chain reaction test (qPCR) allows greater diagnostic and research capacity especially beneficial in the field of virology. Infectious bursal disease (IBD) is a well-known viral disease of poultry and occurs world-wide despite widespread use of vaccination. In this thesis study, the real time reverse transcription method (qRT-PCR) was used to address to a range of research questions to provide better understanding and control of IBD in chickens in Australia and world-wide. One experiment was conducted to define the differences between Australian endemic classical and variant infectious bursal disease virus (IBDV) strains by infecting maternal antibody (MAb) free specific pathogen free (SPF) chickens separately with classical strain 06/95 and variant strain 02/95 in isolators. The results revealed that the two IBDV strains did not differ in the degree of bursal atrophy induced, IBDV viral RNA (vRNA) load in bursal and non-bursal lymphoid organs and faecal shedding but variant strain 02/95 induced a greater antibody response to the infection than classical strain 06/95 which was associated with a more rapid decline in IBDV vRNA genome copy number (VCN) in lymphoid organs.

Marek's disease (MD) is an economically important poultry disease, which is successfully controlled by imperfect vaccines. The imperfect vaccines for MD, herpesvirus of turkeys (HVT) and HVT/Gallid herpesvirus 3 (GaHV-3) (bivalent) are likely to have contributed to the observed increase in virulence which has led to sequential failure of these vaccines in some parts of the world. The Gallid herpesvirus 2 (GaHV-2, MDV-1) Rispens CVI988 vaccine, first developed in 1972, has not been affected by this failure and is considered to be the gold standard Marek's disease vaccine, being widely used worldwide to vaccinate long lived layers and breeders. Two experiments were designed to investigate this vaccine and its efficacy in Australia. An experiment in isolators investigated the protection provided by Rispens vaccine against Australian pathogenic GaHV-2 isolates of varying virulence (virulent, vMDV and very virulent vvMDV), and the kinetics of viral genome copy number of Rispens and the pathogenic MDV isolates in single and mixed infections. In the second experiment, a Rispens virus specific qPCR test was used to measure the vaccine take in invasive and non-invasive samples and the long-term viral kinetics of the Rispens virus in the field. Co-infection levels of Rispens and pathogenic GaHV-2 in the field and the possibility of establishment of Rispens virus in unvaccinated broiler flocks were also examined. Experiment one used 236 commercial ISA Brown chickens having maternal antibody directed against Rispens vaccine in 12 isolators. Chicks were vaccinated or not vaccinated with Rispens vaccine at hatch and challenged with vMDV isolate MPF57, vvMDV isolate FT158 at 5 days of age or left unchallenged. Each of the six treatment combinations was replicated in two positive pressure isolators.

An acute paralysis syndrome (APS) of broiler chickens was first reported in 2010 in an Australian chicken meat production region. The APS was characterised by flaccid paralysis of the neck, prostration and eventually death of the affected chicken and elevated flock mortalities from 26 days of age. The purpose of the work presented in this doctoral thesis was to establish causation of the APS, risk factors for it and management strategies for controlling it.

The legislation to ban the use of in-feed antibiotics in the poultry industry in European Union and voluntarily removal of antibiotics in animal feed have led to the emergence of wet litter problems, imbalanced gut microflora and reduced nutrient digestibility due to enteric disorders such as necrotic enteritis. Thus, the performance, health and welfare of broilers are affected and the profitability in the industry compromised. There has been a concerted effort to find alternative strategies to modulate gut microflora, augment the immune response and reduce pathogens through management and nutritional intervention, such as the inclusion of fibre and large particle size in diet, in an attempt to improve health and digestive efficiency of broilers. The current thesis examined a variety of strategies to minimise and tackle the issues that raised after the ban of in-feed antibiotics in the poultry industry. Chapter 1 presents the summary of literature related to fiber and ingredient particle size and their potential roles in poultry nutrition and management. Chapter 2 examined the effect of pelleted wheat straw as a bedding material on broiler performance, gut microflora and welfare in contrast to other litter sources commonly used in the broiler industry. The feed conversion ratio (FCR) of birds reared on pelleted straw was improved compared (P<0.05) to that of birds raised on rice hulls. However, it was observed that the birds reared on wood shavings had higher relative gizzard weight at d 24 compared to those reared on pelleted straw (P<0.05). Further, birds reared on pelleted wheat straw had a lower incidence of foot pad lesions than those on chopped straw and shredded paper on d 24 (P<0.001) and 29 (P<0.01). The study demonstrated the potential benefits to using pelleted wheat straw as a bedding material.

Chapter 1 reviews the literature on Marek's disease relevant to the work carried out in this thesis. Methods for TaqMan® quantitative real-time PCR (qPCR) assays to detect the three serotypes of Marek's disease virus (MDV) are already available, and absolute quantification has been developed for MDV serotype 1 and serotype 3. The development of a method for absolute quantification of Marek's disease virus serotype 2 (MDV2) is described in Chapter 2. Using plasmid DNA, the lower detection limit of the MDV2 assay was determined to be 10 copies of the viral genome. Three independent assay runs showed highly reproducible Ct values and calculated copy numbers, with mean intra- and interassay coefficients of variation of less than 3 % for Ct and 21.5 % for calculated copy number. Absolute quantification of MDV2 was performed successfully on dust samples collected from poultry farms across Australia, material from infectious spleens and feather tips from chickens vaccinated with an avirulent strain of MDV2. Thus, it is now possible to use qPCR assays for absolute quantification of all three serotypes of MDV in a sample. The sequencing of the 'meq' gene of 5 Australian isolatres of MDV1 isolated between 1992 and 2004 which had been pathotyped in an experiment using unvaccinated and HVT-vaccinated specific pathogen free (SPF) chickens is reported in Chapter 3. The sequencing results were compared with a range of MDV1 meq sequences published in GenBank® and associations with virulence examined.

An opportunity exists to infer the physiological and physical state of an animal from changes in their behaviour. As resting, eating, walking and ruminating are the predominant daily activities of ruminant animals, monitoring these behaviours could provide valuable information for monitoring individual animal health and welfare status. Conventional animal monitoring methods have relied on visual observations of animals by human labour. This can only provide information on an animal's behaviour for the period in which they are being observed. Historically, observations could be made for long periods where shepherds were employed to observe their flocks nearly constantly. This is obviously no-longer feasible in the current livestock industry. Recently, with the advent of small, low power accelerometer technology, the ability to remotely monitor animal movement continuously has arisen. This is achieved through the application of on-animal inertia monitoring unit (IMU) sensors. This movement data might potentially lead to continuous behavioural monitoring of livestock. These devices have been developed for higher value livestock such as dairy cattle but little research or development has been directed towards their use in sheep. Previous work has evaluated collar and leg deployments however the sheep industry demands these devices be in an eartag form factor to align with current industry practices. Therefore, this thesis aims to evaluate the potential for using ear-borne accelerometer devices to detect and categorise key behaviours expressed by sheep. Deviation from normal patterns of behaviour may be used as an indicator of changes in individual health status. If behaviour can be categorised using the data collected by these body worn devices and radio telemetry incorporated, animal health could be monitored in near real time allowing early treatment intervention when necessary, ultimately improving on-farm productivity. Scoping work in this thesis identified the difference in acceleration signals between the basic sheep behaviours: grazing, walking and resting, giving potential for discrimination between behaviours with classification algorithms. Subsequently a successful behaviour classification algorithm was developed based on accelerometer data obtained from the ear deployment, yielding activity predictions similar to those obtained through visual observation. To apply this technology to a commercial application, a simulated lameness experiment was designed, where lame walking behaviour was discriminated from sound walking events successfully using the ear and leg modes of deployment. The final experiment investigated the application of ear deployed accelerometer devices to detect behavioural changes associated with increased infection by internal parasites, a disease of extreme economic importance within Australia. Animals with a higher faecal worm egg count were shown to have a lower probability of engaging in longer periods of activity, however this experiment was limited by a very mild level of infection. Overall this thesis demonstrates that sheep behaviour can be classified using an ear-mounted tri-axial accelerometer sensor, the first of its kind to date. It also explored the suitability of using time-series behavioural classification data as an early indicator of health and welfare issues. This work aims to link a previous "research only" technology in sheep, to a commercial application, a stepping stone towards bridging the gap between research and industry adoption.

The attenuated MDV-1 Rispens/CVI988 vaccine is widely used to vaccinate chickens worldwide and is the most effective current vaccine against MD. Two experiments were designed to investigate transmission of the Rispens/CVI988 vaccine virus (Rispens/CVI988) between chickens, the viral kinetics and shedding profile of Rispens/CVI988 and very virulent MDV (vvMDV, isolate 02LAR) in single and mixed infections and the effect of vaccination to challenge interval on the protection provided by Rispens/CVI988 against vvMDV challenge. Experiment 1 used 70 specific pathogen free (SPF) chickens in four climate controlled rooms. In three rooms, 10 chickens were vaccinated with one of the three commercial Rispens/CVI988 vaccines at day old and left in contact with 10 unvaccinated chickens. The fourth room held 10 unvaccinated control birds. As determined by MDV-specific qPCR of weekly room dust, PBL and feather samples the commercially available Rispens/CVI988 vaccine virus strains are shed in significant quantities and transmit effectively to in-contact chickens. Experiment 2 used 600 commercial ISA Brown layers of the same age (day old) in 24 isolators. Chickens were vaccinated with Rispens/CVI988 (3200 pfu) and/or challenged with the 02LAR (400 pfu) on days 0, 5, 10 post hatching providing vaccination to challenge intervals (VCI) of -10, -5, 0, 5, 10 days with the negative values indicating challenge prior to vaccination. As determined by MDV-specific qPCR able to differentiate between the viruses, vaccination with Rispens/CVI988 greatly reduced the viral load of vvMDV in PBL and feather cells but only if birds were vaccinated prior challenge.

The aim of my thesis is to document the cultural history and heritage of the ancient Australian canine, the dingo. An analysis of the complex symbiotic relationship between the dingo and human society for over 4,600 years reveals an animal uniquely positioned as both a human companion and top-order predator - fulfilling important ecosystem services across the Australian mainland, complementary to their role in traditional Aboriginal society. The thesis collates ethnographic, scientific and social representations of the dingo, and interrogates the legacy of 200 years of dingo control across the south-eastern third of the continent. I use a writing technique called a prosopography to explore areas of knowledge about dingoes, and the culture and heritage surrounding them. This involves recording human-animal encounters in the form of the stories of individual animals within a contextual history, revealing themes, patterns, inconsistencies and anomalies in dingo-human history. The listing of the species as endangered on the IUCN Red List (2004) and as a threatened species in the State of Victoria (2008) underscores the importance of critical analysis, revealing processes underlying the construction and dissemination of dingo knowledge that reinforce their cultural and physical marginalization. The study reveals a complex human-dingo history, and strives to present this information in a comprehensible format as a basis for discussion - allowing new insights into the unique history of the dingo's survival at the heart of traditional Aboriginal society and at the limits and borderlands of contemporary environmental management.