Thesis (M.V.Sc.)--University of Melbourne, Dept. of Veterinary Science, 2009. / Typescript. Includes bibliographical references.

Thanks to the affordability of DNA sequencing, hundreds of thousands of individuals with rare disorders are undergoing whole-genome sequencing in an effort to reveal novel disease aetiologies, increase our understanding of biological processes and improve patient care. However, the power to discover the genetic causes of many unexplained rare diseases is hindered by a paucity of cases with a shared molecular aetiology. This thesis presents research into statistical and computational methods for determining the genetic causes of rare diseases. Methods described herein treat important aspects of the nature of rare diseases, including genetic and phenotypic heterogeneity, phenotypes involving multiple organ systems, Mendelian modes of inheritance and the incorporation of complex prior information such as model organism phenotypes and evolutionary conservation. The complex nature of rare disease phenotypes and the need to aggregate patient data across many centres has led to the adoption of the Human Phenotype Ontology (HPO) as a means of coding patient phenotypes. The HPO provides a standardised vocabulary and captures relationships between disease features. I developed a suite of software packages dubbed 'ontologyX' in order to simplify analysis and visualisation of such ontologically encoded data, and enable them to be incorporated into complex analysis methods. An important aspect of the analysis of ontological data is quantifying the semantic similarity between ontologically annotated entities, which is implemented in the ontologyX software. We employed this functionality in a phenotypic similarity regression framework, 'SimReg', which models the relationship between ontologically encoded patient phenotypes of individuals and rare variation in a given genomic locus. It does so by evaluating support for a model under which the probability that a person carries rare alleles in a locus depends on the similarity between the person's ontologically encoded phenotype and a latent characteristic phenotype which can be inferred from data. A probability of association is computed by comparison of the two models, allowing prioritisation of candidate loci for involvement in disease with respect to a heterogeneous collection of disease phenotypes. SimReg includes a sophisticated treatment of HPO-coded phenotypic data but dichotomises the genetic data at a locus. Therefore, we developed an additional method, 'BeviMed', standing for Bayesian Evaluation of Variant Involvement in Mendelian Disease, which evaluates the evidence of association between allele configurations across rare variants within a genomic locus and a case/control label. It is capable of inferring the probability of association, and conditional on association, the probability of each mode of inheritance and probability of involvement of each variant. Inference is performed through a Bayesian comparison of multiple models: under a baseline model disease risk is independent of allele configuration at the given rare variant sites and under an alternate model disease risk depends on the configuration of alleles, a latent partition of variants into pathogenic and non-pathogenic groups and a mode of inheritance. The method can be used to analyse a dataset comprising thousands of individuals genotyped at hundreds of rare variant sites in a fraction of a second, making it much faster than competing methods and facilitating genome-wide application.

The work presented includes over thirty peer reviewed published manuscripts based on studies undertaken during my surgical career. As Principal Investigator, I led the study conception/design/data acquisition/analysis/interpretation and was involved with writing the final drafts of all manuscripts prior to their formal submission to high impact factor peer-reviewed specialist journals. The thesis is divided into subsections reflecting my development and different interests within surgery. The subsections start with my learning basic research principles, moving onto clinical problem solving in general surgical dilemmas, followed by a collection of papers in my subspecialty of vascular surgery. The work culminates with a group of papers focused on aneurysmal disease, specifically, abdominal aortic aneurysms (AAA), the clinical impact of which has had a bearing on the introduction of a National AAA Screening Program in Wales in 2013. I conclude these sections with a collection of papers that reflect my long term commitment to surgical training both at regional level (as Secretary and Deputy Chairman to the Higher Surgical Training Committee and Chairman of the Basic Surgical Training Committee) and national level including my involvement with the Four Royal Colleges of Surgeons for the Intercollegiate Examinations in General Surgery. This examination is undertaken at completion of junior surgical training and used to confirm a doctor's competence for safe independent practice as a consultant. In conclusion, over forty years of academic research during my career as a vascular surgeon has provided unique insight into the pathophysiology, treatment and ultimately prevention of artherosclerotic disease. These findings have improved health policies in Wales and significantly reduced patient morbidity and mortality.

M.Sc. (Nematology) / Please refer to full text to view abstract

M.Tech. (Chiropractic) / Please refer to full text to view abstract

Magister Scientiae - MSc / There have been many cases reported of amphibian populations declining. These are often due to anthropogenic factors such as habitat destruction and pollution. However, some eclines have not had an obvious cause and many of these have been investigated and found to be due to pathogenic disease. Batrachochytrium dendrobatidis is a recently described pathogen of frogs. The population declines that have been associated with chytridiomycosis have occurred in relatively undisturbed areas such as national parks. The declines tend to occur at higher altitudes or in colder climates. This is thought to be because of the frog immune system being slower at lower temperatures. This project gives an overview of chytrid infection in the Western Cape and at a small number of sites in the Northern Cape and Eastern Cape. / South Africa

The focus of the present study was on the investigation of the effects of an intervention strategy on an industrial task in situ and a simulation of the same task within a laboratory setting. The task of offloading crates from a truck at a local business was simulated in a laboratory setting for rigorous analysis. The effect of an ergonomically sound intervention on selected physical, physiological and perceptual variables was evaluated in a test - retest experimental set-up using 28 young, healthy male students. Each of the two experimental conditions lasted for 16 minutes. In the pre-intervention task subjects were required to transfer the crates from one point to another by sliding them along the floor. During the execution of the post-intervention task responses to reductions in the stacking height and modifications of the working method were evaluated. Results obtained for spinal kinematics during the simulated industrial task indicated a high biomechanical risk, due to large ranges of motion, high velocities and accelerations in the sagittal and transverse planes. The heavy workload of the task was also evident in elevated physiological responses (HR, RF, VT, VE, VO2, RQ, EE) and perceptual ratings (RPE, Body Discomfort). Assessment of the intervention strategy revealed that the ‘high risk’ industrial task was reduced to ‘moderate acceptable’, with measurements of spinal kinematics, physiological and perceptual variables being significantly reduced. An in situ re-assessment of the workers’ responses to the intervention also elicited reductions in heart rates and perceptual ratings compared to the original task.

Five virus isolates RS 2, RS 25, RS 26, RS 28 and RS 29, were transmitted by juice-inoculation technique from sour and sweet cherry trees to cucumber. Four isolates were obtained from trees growing in the Kootenay cherry district of British Columbia. Another one was isolated from a tree growing in the coastal area of this province. Viruses known to occur in the source trees are Necrotic Ring Spot Virus, Sour Cherry Yellows Virus, Twisted Leaf Virus and Little Cherry Virus. The relationship and the complexity of the virus isolates was studied with herbaceous hosts, using a mechanical transmission technique. Pincherry (Prunus pennsylvanica L.) was inoculated by the same technique as a means for provisional identification of the virus isolates. The cucumber syndrome of isolate RS 25 was very mild, that of isolate RS 2 mild, that of isolate RS 29 was of medium severity and those of isolates RS 26 and RS 28 were very severe. Inoculates RS 2 and RS 29 varied greatly in symptom expression on cucumber, whereas the symptom expression of the other isolates was less variable. Isolate RS 29 was characterized by symptomless systemic infection of Nemesia sp.. var. Triumph. Isolates RS 26 and RS 28 both infected Petunia hybr., var. Blue Bee, without expressing symptoms, whereas the other isolates did not infect this species. Other host species too carried the isolates without expressing symptoms, whereas symptoms were produced on cucurbit hosts. Isolates RS 2, RS 26, RS 28 and RS 29 appeared to consist of more than one virus. Strains of a virus P occur in all isolates and isolate RS 25 itself is also a strain of this virus. All five strains of virus P express similar very mild symptoms on cucumber, whereas a characteristic severe savoying type of symptom is produced on squash (var. Table Queen). Species susceptible to virus P are cucumber, pincherry, squash, sweet pea, tobacco (under conditions of long day) and other species. Lathyrus odoratus L. and Lens culinaris Medic. are species useful in separating virus P from the other viruses occurring in isolates RS 2, RS 26, RS 28 and RS 29. It is possible that virus P is related to cucumber-mosaic virus as suggested by symptoms on squash and tobacco. In previous work by other investigators a strain of cucumber-mosaic virus was also isolated from Prunus hosts. On pincherry (P. pennsylvanica L.) isolate RS 28 caused acute symptoms of necrosis and shothole. The plants recovered but symptoms of mottling were systemic. Necrotic Ring Spot Virus caused similar symptoms on Prunus hosts and this virus and Sour Cherry Yellows Virus was present in the original source tree. The other isolates in pincherry all caused similar symptoms of mottling on the young leaves. A few necrotic lesions were produced also. On reisolation from pincherry virus P was obtained in case of isolates RS 2, RS 26 and RS 29. No virus was reisolated in the case of isolate RS 25. The complete parent isolate was reisolated in case of isolate RS 28. The results with pincherry suggest that virus P is responsible for the mild symptoms whereas virus P in conjunction with an additional virus as in isolate RS 28 incites the severe shock symptoms. The identification of the viruses present in the isolates can be carried out by scion inoculation of a set of suitable Prunus indicator hosts. / Land and Food Systems, Faculty of / Graduate

Ramets of 14 clones of western black cottonwood Populus trichocarpa Torr. & Gray collected from the interior and coast of British Columbia were tested in the nursery for their growth performance after infection by the leaf rust Melampsora occidentalis Jacks. Linear relationships were demonstrated between various growth parameters (total dry weight, stem dry weight, root dry weight, volume, diameter and height) and disease severity rated as diseased leaf-weeks divided by total leaf-weeks. Losses due to rust infection included reduced total dry weight and volume growth in the year of heavy disease, the death of severely infected ramets during the following winter and reduced initial volume increment in the following growing season. The percentage reduction in yield (total dry weight) was greater than the cumulative percent leaf area infected, suggesting that the rust infected leaf parts act as sinks for photosynthate. The normal pattern of photosynthate allocation was altered in favour of the top growth of ramets. Ratios of stem/root dry weight increased rapidly as disease level increased. A threshold infection level, below which no loss occurred, was not detected in this pathosystem. Significant variation in rust resistance of black cottonwood clones was detected both within and between the two geographic areas. Clones from the coast or warm, moist areas were, on average, more resistant than clones from the interior or cold, dry climates. The phenomenon of induced resistance was not detected at either the local or the systemic levels in black cottonwood challenged by the rust. Variation in rust tolerance among black cottonwood clones was demonstrated. Rust tolerance was defined as the slope of the relationship between yield of ramets (expressed as a proportion of controls) and disease severity (expressed as the proportion of the total number of leaf-weeks infected). A negative correlation between rust tolerance and rust resistance was found. In the collection of clones tested, the positive effect of disease resistance on the growth of cottonwood clones was partially counterbalanced by the negative effect of reduced tolerance on the growth. The importance of this relationship in both natural and artificial selection of superior trees against disease is indicated. / Forestry, Faculty of / Graduate

Polyclonal antisera produced against spores, soluble protein and the whole mycelium fractions of Didymella lycopersici reacted with the homologous and heterologous antigens. The most sensitive antiserum was that raised against the whole mycelium, the soluble protein and the spore, in decreasing order of sensitivity. Using the antiserum raised against the whole mycelium it was possible to detect D. lycopersici on diseased plants and infested seeds. Cross reactivity was observed between the antisera produced to D. lycopersici and D. applanata, D. bryoniae and other tomato fungal pathogens including Fusarium spp. and B. cinerea. ELISA was most sensitive and reliable compared to double immunodiffusion, and latex tests. No reactions were obtained using the latex agglutination procedure and no antiserum detected spores in double diffusion tests. Protein profiles on SDS-PAGE revealed that the total number of protein bands decreased with increased age of cultures of D. lycopersici incubated in liquid media. Western blots probed with the antiserum raised against the whole mycelium showed that protein bands from extracts of both D. lycopersici and D. applanata were antigenic. / Land and Food Systems, Faculty of / Graduate