Research Repository

    Vegetation patterns in the northern jarrah forest of Western Australia in relation to dieback history and the current distribution of Phytophthora cinnamomi

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    Dieback, largely attributed to the fungal plant pathogen Phytophthora cinnamomi, is characterized in the northern jarrah forest by multiple deaths of many plant species, including the dominant, Eucalyptus marginata (jarrah), a species of great commercial importance. The wide host range of the pathogen has major implications for the biodiversity of the ecosystem. The first records of dieback in the jarrah forest were made in the 1920s.\ud \ud Despite the magnitude and long history of the impact in the jarrah forest, little is known about the vegetation changes that result from dieback. In this dissertation, I develop a model of vegetation change related to dieback by examining the vegetation of a range of dieback sites and relating the patterns identified to the current distribution of P. cinnamomi. The study is the first explicit investigation of floristic and structural patterns on dieback sites in the jarrah forest.\ud \ud Substantial floristic differences were found between dieback and unaffected vegetation. The patterns are strongly correlated with the age of the original dieback event. There was little difference, however, in the mean number of species I quadrat between dieback and unaffected vegetation. The time since the inception of dieback was estimated using aerial photography. The oldest dieback sites located had been affected prior to 1951. Of the species found less frequently on these old dieback sites, 64% had not previously been associated with P. cinnamomi infection. Some of these were assessed for their susceptibility in glasshouse pathogenicity tests. New records of susceptibility were made at the species, genus and family levels. Several species regarded as being highly susceptible to infection by P. cinnamomi were found as frequently on old dieback sites as in unaffected vegetation. Many of the species found more frequently on dieback sites were probably present at the time of the initial dieback event. Others, mostly annuals, may have been introduced from nearby vegetation types with open canopies, such as granite outcrops. If plant invasions have occurred following dieback, the small differences in species richness between dieback and unaffected vegetation may hide a great reduction in species richness due to dieback.\ud \ud Structural changes following dieback may have a profound effect on some species regardless of their susceptibility to infection. A spatial association with trees on dieback sites was demonstrated for a range of species. The apparent reliance of some understorey species on tree cover is discussed in relation to current theories of patch dynamics.\ud \ud Two methods were used to isolate P. cinnamomi from dieback sites. In situ Banksia grandis baits were more effective at detecting P. cinnamomi than ex situ baited soils, especially when P. cinnamomi was apparently rare.\ud \ud P. cinnamomi was frequently isolated from creek edges with a long history of dieback and from active dieback fronts but was rarely found on sloping dieback sites affected prior to 1980. It is not clear if the P. cinnamomi present on pre-1951 dieback sites has persisted there since the initial dieback event or been re-introduced from active dieback fronts upslope.\ud \ud Very few highly susceptible species appear to be totally eliminated by the pathogen at the time of the initial dieback event. The mass deaths at that time are followed by a period of recolonization of susceptible species with highly germinable seed. The survival of the new cohort of these species is a function of the time taken to produce another crop of seed.\ud \ud Susceptible species may persist on the pre-1951 dieback sites because of highly germinable seed, young reproductive age, copious seed production and animal dispersal. The rarity of P. cinnamomi on these sites must greatly contribute to their persistence.\ud \ud Pathogenicity testing in excised stems indicated that resistance to the movement of P. cinnamomi in plant tissue develops in jarrah populations on many dieback sites, although it is unlikely to be integral to regeneration. Evidence of resistance in other spec1es investigated could not be found.\ud \ud The key elements in the model of vegetation change developed in the thesis are (i) the on-going occurrence of P. cinnamomi on dieback sites, (ii) the susceptibility of plant species to infection by P. cinflamomi, (iii) the sensitivity of plant species to structural changes, (iv) the proportion of a plant population killed, (v) the capacity of plant species for rapid recruitment after dieback, (vi) the time taken for plant species from germination to reproduction, and (vii) the capacity of plant species to invade. Stochastic factors such as fire, logging, climatic perturbations, and diseases caused by other pathogens, cannot be quantified and easily incorporated into the model.\ud \ud Predictions are made about the future vegetation of dieback sites, contingent on intervention by forest managers. An epidemic - recovery cycle, involving concomitant fluctuations in pathogen and host populations, has been hypothesized by some authors for sites affected by P. cinnamomi. There is evidence of such a cycle on a small scale. On a larger scale, epidemics on dieback sites in the jarrah forest may be isolated in space and time.\ud \ud The importance of long-term ecological studies of jarrah forest vegetation to our understanding of natural forest processes and the effects of dieback is stressed

    3D model databases and tools

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    Contamination of Australian newborn calf carcasses at slaughter with Clostridium difficile

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    In North America and Europe, reports of a genetic overlap between toxigenic strains of Clostridium difficile isolated from humans, livestock and retail meat suggest that food-borne transmission may be occurring. We investigated the prevalence, concentration and genetic diversity of C. difficile on the carcasses (n = 300) and in the faeces (n = 30) of neonatal veal calves at three abattoirs in Australia in 2013. Selective culture (both direct and enrichment) was performed, and all isolates were characterized by PCR for the toxin genes tcdA, tcdB and cdtA/B and by PCR ribotyping. Prevalence of C. difficile was 25.3% (76/300) on carcasses and 60.0% (18/30) in faeces. Multiple PCR ribotypes (RT) were detected, with four binary toxin-positive RTs accounting for 70.3% (71/101) of isolates; 127 (A+, B+, CDT+, 32.7%), 288 (A-, B-, CDT+, 28.7%), 033 (A-, B-, CDT+, 6.9%) and 126 (A+, B+, CDT+, 2.0%). Viable counts of a subset of samples revealed detectable numbers of C. difficile in 66.7% (10/15) of faecal samples (range 2.0 × 103 to 2.3 × 106 CFU/mL, median count 2.5 × 104 CFU/mL) and in 16.7% (25/150) of carcase samples (range 3 to 33 CFU/cm2, median count 7 CFU/cm2). These data further confirm that Australian neonatal veal calf carcasses are contaminated with potentially significant strains of C. difficile at slaughter

    Mechanisms of hypervirulent Clostridium difficile ribotype 027 displacement of endemic strains: an epidemiological model

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    Following rapid, global clonal dominance of hypervirulent ribotypes, Clostridium difficile now constitutes the primary infectious cause of nosocomial diarrhoea. Evidence indicates at least three possible mechanisms of hypervirulence that facilitates the successful invasion of these atypical strains: 1) increased infectiousness relative to endemic strains; 2) increased symptomatic disease rate relative to endemic strains; and 3) an ability to outcompete endemic strains in the host's gut. Stochastic simulations of an infection transmission model demonstrate clear differences between the invasion potentials of C. difficile strains utilising the alternative hypervirulence mechanisms, and provide new evidence that favours certain mechanisms (1 and 2) more than others (3). Additionally, simulations illustrate that direct competition between strains (inside the host's gut) is not a prerequisite for the sudden switching that has been observed in prevailing ribotypes; previously dominant C. difficile strains can be excluded by hypervirulent ribotypes through indirect (exploitative) competition

    Binaphthyl-1,2,3-triazole peptidomimetics with activity against Clostridium difficile and other pathogenic bacteria

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    Clostridium difficile (C. difficile) is a problematic Gram positive bacterial pathogen causing moderate to severe gastrointestinal infections. Based on a lead binaphthyl-tripeptide dicationic antimicrobial, novel mono-, di- and tri-peptidomimetic analogues targeting C. difficile were designed and synthesized incorporating one, two or three d-configured cationic amino acid residues, with a common 1,2,3-triazole ester isostere at the C-terminus. Copper- and ruthenium-click chemistry facilitated the generation of a 46 compound library for in vitro bioactivity assays, with structure-activity trends over the largest compound subset revealing a clear advantage to triazole-substitution with a linear or branched hydrophobic group. The most active compounds were dicationic-dipeptides where the triazole was substituted with a 4- or 5-cyclohexylmethyl or 4,5-diphenyl moiety, providing MICs of 4 μg mL-1 against three human isolates of C. difficile. Further biological screening revealed significant antimicrobial activity for several compounds against other common bacterial pathogens, both Gram positive and negative, including S. aureus (MICs ≥2 μg mL-1), S. pneumoniae (MICs ≥1 μg mL-1), E. coli (MICs ≥4 μg mL-1), A. baumannii (MICs ≥4 μg mL-1) and vancomycin-resistant E. faecalis (MICs ≥4 μg mL-1)

    Molecular epidemiology of Clostridium difficile infection in a large teaching hospital in Thailand

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    Clostridium difficile infection (CDI) is a leading cause of healthcare-associated morbidity and mortality worldwide. In Thailand, CDI exhibits low recurrence and mortality and its molecular epidemiology is unknown. CDI surveillance was conducted in a tertiary facility (Siriraj Hospital, Bangkok). A total of 53 toxigenic C. difficile strains from Thai patients were analyzed by multi-locus sequence typing (MLST), PCR ribotyping, and pulse-field gel electrophoresis (PFGE). The mean age of the cohort was 64 years and 62.3% were female; 37.7% of patients were exposed to > two antibiotics prior to a diagnosis of CDI, with beta-lactams the most commonly used drug (56.3%). Metronidazole was used most commonly (77.5%; success rate 83.9%), and non-responders were treated with vancomycin (success rate 100%). None of the isolates carried binary toxin genes. Most isolates (98.2-100%) were susceptible to metronidazole, vancomycin, tigecycline and daptomycin. There were 11 sequence types (STs), 13 ribotypes (RTs) and four PFGE types. Six previously identified STs (ST12, ST13, ST14, ST33, ST41 and ST45) and five novel STs unique to Thailand (ST66, ST67, ST68, ST69 and ST70) were identified. PCR RTs UK 017 (ST45) (45.3%) and UK 014/020 (ST33) (24.5%) were the most common. High concordance was observed between the MLST and ribotyping results (p<0.001). C. difficile isolates from Thai patients were highly susceptible to standard antimicrobial agents. In conclusion, the five STs indicate the high genetic diversity and unique polymorphisms in Thailand. Moreover, the emergence of antimicrobial resistance to vancomycin warranted continuous surveillance to prevent further spread of the toxigenic C. difficile isolates

    Evaluation of the BD Max Cdiff assay for the detection of toxigenic Clostridium difficile in human stool specimens

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    The Becton Dickinson (BD) PCR-based GeneOhm Cdiff assay has demonstrated a high sensitivity and specificity for detecting Clostridium difficile. Recently, the BD Max platform, using the same principles as BD GeneOhm, has become available in Australia. This study aimed to investigate the sensitivity and specificity of BD Max Cdiff assay for the detection of toxigenic C. difficile in an Australian setting. Between December 2013 and January 2014, 406 stool specimens from 349 patients were analysed with the BD Max Cdiff assay. Direct and enrichment toxigenic culture were performed on bioMérieux ChromID C. difficile agar as a reference method. isolates from specimens with discrepant results were further analysed with an in-house PCR to detect the presence of toxin genes. The overall prevalence of toxigenic C. difficile was 7.2%. Concordance between the BD Max assay and enrichment culture was 98.5%. The sensitivity, specificity, positive predictive value and negative predictive value for the BD Max Cdiff assay were 95.5%, 99.0%, 87.5% and 99.7%, respectively, when compared to direct culture, and 91.7%, 99.0%, 88.0% and 99.4%, respectively, when compared to enrichment culture. The new BD Max Cdiff assay appeared to be an excellent platform for rapid and accurate detection of toxigenic C. difficile

    A demo of iR2s software: Interactive oriental ink painting tool

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    In recent years, painterly rendering techniques have achieved remarkable success for simulating water color, oil and oriental ink paintings

    Liveweight gains and carcass composition of buffalo (Bubalus bubalis) steers on four feeding regimes

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    Twenty buffalo steers were divided into four groups of five and were lot-fed for 86-287 days on nutritional regimes that varied from roughage to high-grain concentrate, and liveweight gains and carcass composition were determined. Mean daily liveweight gains were 0.74 kg (fed on three-quarters pellets + one-quarter hay), 0.67 kg (all pellets), 0.64 kg (three-quarters hay + one-quarter pellets) and 0.56 kg (all hay). Feeding regime had little effect on carcass composition. The proportions of muscle, bone, fat and connective tissue did not vary significantly among the four nutritional groups. The carcass composition of the buffalo steers did not differ greatly from that of a group of buffalo bulls previously dissected by the authors, the major difference being that the steers had significantly more fat (16.0%) than the bulls (10.6%). It was concluded that the carcass composition of the buffalo is relatively resistant to extremes of diet and to castration, and that the species does not show a propensity to fatten under 30 months of age

    Muscle weight distribution in four breeds of cattle with reference to individual muscles, anatomical groups and wholesale cuts

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    One side of each of 51 carcasses of Hereford, Angus, Friesian and Charolais cross-bred steers was dissected and the weights of individual muscles and total carcass muscle were obtained. The percentage distribution of total carcass muscle weight in muscles and in standard groups of muscles was determined. In addition, the percentage distribution of total carcass muscle weight in wholesale cuts was determined from the weights of whole and part muscles specified as comprising the respective cuts. Minor breed differences only were found in muscle weight distribution among muscles, groups of muscles and wholesale cuts. Similarity of muscle weight distribution in the different types of carcasses studied shows that carcass shape is not associated with differences in the distribution of muscle weight in wholesale cuts
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