ALBERT

Notes: Abstract The transaction ordering problem of the original PCI 2.1 standard bus specification violates the desired correctness property of maintaining the so called ‘Producer/Consumer’ relationship between writers and readers of data. This violation stems mainly from the so called completion stealing problem, first identified and solved by Corella et al. [4], and supported by a formal paper and pencil argument. In this paper, we develop a flexible graph theory library in PVS for modeling computer bus structures, formalize the PCI 2.1 protocol containing the solution of [4] in it, and mechanically prove the absence of completion stealing. Next, we define the Producer/Consumer property in PVS and sketch its mechanical proof. Noting the complexity of this proof effort (unfinished as yet), we explore a combination of theorem proving and model-checking in which the model used for model-checking is made tractable by exploiting the formal theorems established during theorem-proving as well as several intuitively justified assumptions. The theorem-proving infrastructure we have built for modeling CPU interconnect structures is highly reusable. Our work is one example of a natural division of labor between theorem-proving and model-checking in tackling system-level verification problems under realistic time budgets.

Notes: Abstract Von Hippel-Lindau (VHL) disease is a dominantly inherited familial cancer syndrome characterised by the development of retinal and central nervous system haemangioblastomas, renal cell carcinoma (RCC), phaeochromocytoma and pancreatic tumours. The VHL disease gene maps to chromosome 3p25-p26. To investigate the mechanism of tumourigenesis in VHL disease, we analysed 24 paired blood/tumour DNA samples from 20 VHL patients for allele loss on chromosome 3p and in the region of tumour suppressor genes on chromosomes 5, 11, 13, 17 and 22. Nine out of 24 tumours showed loss of heterozygosity (LOH) at at least one locus on chromosome 3p and in each case the LOH included the region to which the VHL gene has been mapped. Chromosome 3p allele loss was found in four tumour types (RCC, haemangioblastoma, phaeochromocytoma and pancreatic tumour) suggesting a common mechanism of tumourigenesis in all types of tumour in VHL disease. The smallest region of overlap was between D3S1038 and D3S18, a region that corresponds to the target region for the VHL gene from genetic linkage studies. The parental origin of the chromosome 3p25-p26 allele loss could be determined in seven tumours from seven familial cases; in each tumour, the allele lost had been inherited from the unaffected parent. Our results suggest that the VHL disease gene functions as a recessive tumour suppressor gene and that inactivation of both alleles of the VHL gene is the critical event in the pathogenesis of VHL neoplasms. Four VHL tumours showed LOH on other chromosomes (5q21, 13q, 17q) indicating that homozygous VHL gene mutations may be required but may not be sufficient for tumourigenesis in VHL disease.

Notes: Abstract Septoria nodorum blotch is the most important leaf disease of wheat in Western Australia. A potentially useful source of resistance has been identified in an accession of Aegilops tauschii. To study the genetics of resistance of this source a cross was made between the resistant Ae. tauschii accession, RL5271, and a susceptible accession, CPI110889. The resistant parent took significantly longer to develop symptoms, developed significantly fewer lesions and expressed significantly lower levels of disease than the susceptible parent. The F1 mean response for disease severity indicated there was no complete dominance. The F3 families were classified using three approaches. In the first approach the individual F3 plant response was used to classify the F3 families. In the second approach the F3 family means and standard errors were used to classify the F3 families. In the final approach Best Linear Unbiased Predictors of disease score and standard error for each F3 family derived from a REML analysis were used to classify the F3 families. The genotypic ratios generated by each of the approaches suggested that resistance is controlled by a single gene. The effectiveness of the resistance and its simple genetic control in the Ae. tauschii, accession RL5271 may be a useful resistance source for use in a bread wheat breeding program.

Notes: Abstract The Australian and New Zealand Environment and Conservation Council (ANZECC) and the Australian Water Resources Council (AWRC) have developed a National Water Quality Management Strategy which seeks to ensure that the nation's water resources are managed on a sustainable basis. An important element of this strategy are the Australian Water Quality Guidelines which focus on the protection of Australian freshwater and marine ecosystems. Here the aim is to protect biodiversity and maintain the ecological integrity of each marine and freshwater resource. Specific guidelines have been formulated in terms of key indicators of quality, with a single reference value or ranges of reference values provided for guidance. For those indicators where ranges are provided, it is the expectation that State environmental and resource management agencies will undertake local, site-specific investigations of their own systems to define the specific levels to be adopted. For the first time, specific and quantitative biological indicators have been introduced; these are species richness, species composition, primary production, and ecosystem function. As Australia progresses towards broader, more holistic, ecologically-based management of the nation's water resources, the present water quality guidelines must be extended to ecosystem or environmental guidelines, where the maintenance of adequate water quality is seen as only one (albeit important) component. Other considerations must include habitat protection, sediment quality, and stream flow maintenance. This increased emphasis on more ecologically-focused management of Australia's inland and coastal waters will present a number of challenges for the three major groups involved: the community, the managers, and the researchers. These challenges are discussed.

Notes: Abstract Three large plastic enclosures (5 m diam, volume 40 m3) were used to study the effects of copper, manganese and zinc, on the phytoplankton community in Island billabong, a floodplain billabong (waterhole) situated in the Magela Creek in tropical northern Australia. Copper was added to one enclosure, and manganese and zinc to another, to give initial concentrations around ten times the normal wet season values. The enclosures and the billabong were monitored over a ten week period towards the end of the dry season, with the enclosures allowed to stabilise for four weeks before the metals were added. The control enclosure adequately simulated the temperature and pH changes in the billabong. The trends in conductivity, dissolved oxygen and major ion concentrations were similar in the enclosure and the billabong, with the minor differences observed attributed to either epiphytic growth on the enclosure walls (influenced dissolved oxygen, pH and bicarbonate concentration) or ingress of sulphate-rich groundwater into the billabong (influenced sulphate concentration and conductivity). Major differences in both the composition of species and the size of the phytoplankton populations were observed between the three enclosures and between the control enclosure and the billabong. This variability reflects the great natural variability in the phytoplankton communities in tropical lentic systems, and means that enclosures are unlikely to adequately simulate the biological communities in the billabongs. The control enclosure appeared to simulate quite well the longer term changes in total concentration and speciation of the three metals (copper, manganese & zinc) in the billabong. The mean concentrations of copper and zinc were similar in the two systems, although the mean concentration of manganese in the billabong was almost double that in the enclosure, possibly due to ingress of manganese-enriched groundwater. Particulate forms dominated the speciation of copper and manganese. There was considerable short term variation in both total metal concentration and speciation in both the enclosure and the billabong. This variability appears to be a feature of these small tropical waterbodies. The added heavy metals were found to have minimal detrimental effect on the phytoplankton community in each metal-loaded enclosure. The high natural variability in the phytoplankton community in these tropical systems will make it difficult to separate natural changes from those caused by low level contamination from mining operations should this occur. All three metals were rapidly removed from the water column, so that by the end of the six week period, only ca. 5% of each added metal remained in the water column. Association with the particulate matter (phytoplankton, abiotic particulate matter and MnOx in enclosure 2) followed by sedimentation was the major removal pathway. Epiphytes growing on the enclosure walls appeared to have a minor influence (〈10% of the total amount of metal added) on the removal of the added metals. For copper, uptake by phytoplankton followed by sedimentation was the major (65%) removal process. Manganese and zinc, added together, were found to influence each other. The major manganese removal process (60%) was rapid (ca. 3 days) involving bacterial oxidation and sedimentation of the MnOx formed. This material appeared to have little influence on the behaviour of zinc, possibly because other particulate matter competed more effectively for the zinc. A further 30% of the added manganese was removed via initial adsorption to other particulate matter, possibly phytoplankton. Approximately one third of this adsorbed manganese (10% of the total added) appeared to undergo delayed oxidation some 8 days after the initial additions, and the heavier particles settled out more rapidly. This path was responsible for removing the major amount (ca. 60%) of the added zinc. We hypothesis that the sorbed zinc inhibited the bacterial oxidation of the manganese. A further 25% of the zinc was removed in association with a ‘burst’ of phytoplankton activity. The occurrence of bursts in the phytoplankton activity, when populations can increase very substantially and then decrease again, all within the space of a day, appears to be an important mechanism for removing copper and zinc from the water column in these tropical water bodies