Innate immunity and metabolism in the bovine ovarian follicle

Postpartum uterine disease in dairy cows is associated with reduced fertility. One of the first and most prevalent bacteria associated with uterine disease is Escherichia coli. The bacterial endotoxin, lipopolysaccharide (LPS), accumulates in the ovarian follicular fluid of animals with uterine disease. The granulosa cells of the ovarian follicle respond to LPS by secreting pro-inflammatory cytokines, such as interleukin (IL)-1a, IL-1b and IL-8, and oocyte health is perturbed. Dairy cows also experience metabolic energy stress in the postpartum period, which is associated with an increased risk of developing uterine disease and ovarian dysfunction. This thesis explored the crosstalk between innate immunity and metabolic energy stress in bovine granulosa cells and cumulus-oocyte complex. Firstly, we found that glycolysis, AMP-activated protein kinase and the mechanistic target of rapamycin, regulate the innate immune responses to LPS in granulosa cells isolated from bovine ovarian follicles. Activation of AMP-activated protein kinase decreased the LPS-induced secretion of IL-1a, IL-1b, and IL8, and was associated with shortened duration of ERK1/2 and JNK phosphorylation. Next, we found that decreasing the availability of cholesterol or inhibiting cholesterol biosynthesis using short-interfering RNA impaired the LPS-induced secretion of IL-1a and IL-1b by granulosa cells. Furthermore, metabolic energy stress or inhibiting cholesterol biosynthesis in the bovine cumulus-oocyte complex modulated the innate immune responses to LPS, and perturbed meiotic progression during in vitro maturation. Finally, we explored an in vivo model of uterine disease in heifers, using RNAseq to investigate alterations to the transcriptome of the reproductive tract. We found that uterine disease altered the transcriptome of the endometrium, oviduct, granulosa cells and oocyte, several months after bacterial infusion; these changes were most evident in the granulosa cells and oocyte of the ovarian follicle. The findings from this thesis imply that there is crosstalk between innate immunity and metabolism in the bovine ovarian follicle

Named entity extraction for speech

Named entity extraction is a field that has generated much interest over recent years with the explosion of the World Wide Web and the necessity for accurate information retrieval. Named entity extraction, the task of finding specific entities within documents, has proven of great benefit for numerous information extraction and information retrieval tasks.As well as multiple language evaluations, named entity extraction has been investigated on a variety of media forms with varying success. In general, these media forms have all been based upon standard text and assumed that any variation from standard text constitutes noise.We investigate how it is possible to find named entities in speech data.. Where others have focussed on applying named entity extraction techniques to transcriptions of speech, we investigate a method for finding the named entities direct from the word lattices associated with the speech signal. The results show that it is possible to improve named entity recognition at the expense of word error rate (WER) in contrast to the general view that F -score is directly proportional to WER.We use a. Hidden Markov Model {HMM) style approach to the task of named entity extraction and show how it is possible to utilise a HMM to find named entities within speech lattices. We further investigate how it is possible to improve results by considering an alternative derivation of the joint probability of words and entities than is traditionally used. This new derivation is particularly appropriate to speech lattices as no presumptions are made about the sequence of words.The HMM style approach that we use requires using a number of language models in parallel. We have developed a system for discriminately retraining these language models based upon the results of the output, and we show how it is possible to improve named entity recognition by iterations over both training data and development data. We also consider how part-of-speech (POS) can be used within word lattices. We devise a method of labelling a word lattice with POS tags and adapt the model to make use of these POS tags when producing the best path through the lattice. The resulting path provides the most likely sequence of words, entities and POS tags and we show how this new path is better than the previous path which ignored the POS tags

The cell biology of basal cell carcinoma. relationship to histology and clinical outcome.

Basal cell carcinomas presents with extremely diverse clinical and histological appearances and behaviour. Currently there is little understanding of the biological processes that determine these variations. In an attempt to understand these differences, this thesis evaluated some aspects of the cell biology of BCC both a prospective series and in archival specimens. A variety of measurements were assessed in combination with patient factors (age, presentation etc.) and medical factors (type and adequacy of treatment). The cell kinetics of BCC was studied in vivo following administration of bromodeoxyuridine, which was analysed by flow cytometry. The growth fraction (Ki-67 immunohistochemistry) and the contribution of cell loss to the overall tumour kinetics were studied by evaluating apoptosis (morphologically) and the bcl-2, bax and p53 protein expression, using immunohistochemistry, in both the prospective and archival specimens (including non recurrent, recurrent and horrifying BCCs). It was apparent that BCCs are highly proliferative tumours with a median Ts of 7.6 hours (range 5.0-14-6), Tpot 2.8 days (range 4.0-18.3 days), LI 14%, and Gf 32%. Cell production rates were related to the histological growth pattern with infiltrative and morpheic tumours having a higher Gf than the nodular tumours (p<0.01) and a shorter Tc and Tpot. Cell proliferation was not related to differentiation status. The median apoptotic index was 1% (range l%-5%) and in the absence of apoptotic rate measurements, it was difficult to equate the contribution of apoptosis to the paradox of the slow clinical growth of BCCs. However, the concept of a high apoptotic rate was not supported by bcl-2 and bax protein expression. 88% of BCCs expressed bcl-2 and 23% expressed bax. The relationship between p53 expression and apoptosis was unclear since there was no correlation of p53 with bax, bcl-2 or apoptosis. The apoptotic parameters displayed some relationship to the histological growth patterns. The infiltrative and morpheic tumours exhibited the least apoptosis and least bcl-2 expression (p=0.02), but p53 did not correlate with tumour histology. The contribution of biological factors in determining outcome (the development of recurrence or a horrifying tumour) in BCC are limited because patient factors (late presentation) and treatment factors are dominant. Incomplete excision was associated with recurrence and the development of a horrifying tumour when compared to non recurrent tumours (p<0.01). Primary radiotherapy was also associated with the development of a horrifying tumour (p<0.01). A novel treatment modality, the optomechanically flash scanned carbon dioxide laser, was evaluated to assess its ability to completely ablate BCCs. Complete ablation was associated with ablation depth (p<0.01) and tumour type (p=0.01). Superficial BCCs were most suitable for this modality but required lasering to the middle dermis or deeper for complete eradication. Identification of problem BCCs at an early stage still requires further research but this thesis highlights the need for further improvement in surgical treatment

Keynote address

The requirements for a conference on turbomachinery aerodynamics and hydrodynamics are examined. The subject range of the conference is identified as basic fluid mechanics, propulsion aspects of the field, and design applications to turbomachines using gases and liquids. Background information is provided on the field of hydrodynamic and aerodynamic applications. The investigation of boundary layer theory and acoustics in the area of unsteady fluid mechanics is reported. The remaining challenge to synthesize the disciplines into the design of process of turbomachinery is explained

Field-applied fungicides and postharvest treatments to control asparagus diseases posing biosecurity threats to New Zealand

Collaborative research between New Zealand and Australia has investigated field-applied fungicides and postharvest treatments for control of asparagus rust (caused by Puccinia asparagi) and phomopsis stem blight of asparagus (caused by Phomopsis asparagi) in Queensland. In a 2004 field trial, the fungicides difenoconazole and propiconazole reduced the incidence of asparagus rust. In a 2005 field trial, four fungicides (carbendazim, chlorothalonil, iprodione and propiconazole) reduced the severity of phomopsis stem blight. Postharvest disinfection with sodium hypochlorite or with calcium hypochlorite at 150 ppm was highly effective at reducing Pu. asparagi and Ph. asparagi spore germination on water agar. Integrated disease management based on field and postharvest methods are suggested to reduce the risk of importation of the diseases to New Zealand. Similar methods could be used for controlling these diseases if they establish

Control of bacterial spot in stone fruit orchards

This project has successfully identified new ways of managing one of the most devastating diseases of stonefruit crops, bacterial spot. Bacterial spot (caused by Xanthomonas arboricola pv. pruni, or Xap) is the most devastating bacterial disease currently affecting Australian stonefruit crops. It has been estimated that bacterial spot affects more than one third of all stonefruit growers in Australia in wet spring/summer seasons, with fruit losses of up to 70% in highly susceptible varieties. This disease significantly reduces the numbers of saleable fruit, and if left untreated can cause long term effects such as reduced tree vigour (leading to poor fruit set and quality), branch loss and tree death in plums. The extent of the problem is so severe that some varieties are unviable for commercial production without a method of bacterial spot control

Management of Alternaria leaf and fruit spot in apples

Fungicide trials in New South Wales and Queensland have revealed that different Alternaria species are responsible for Alternaria-like leaf and fruit symptoms in each state. This has resulted in slightly different fungicide spray programs being most effective in each state. We found that more than one species of Alternaria can cause symptoms on apple leaves and fruit in Australian orchards. Further, Alternaria is a common, widespread fungus in Australian apple orchards, with species similar to those causing production losses in Queensland and New South Wales detected in all major production areas in Australia

Alternaria Fruit Spot: New Directions

This project determined the identity of causal pathogens, epidemiology and disease cycle of Alternaria leaf blotch and fruit spot in Australian apples and provided a management strategy for both diseases for inclusion in the integrated fruit production manual