Single copy nuclear DNA markers characterized for comparative phylogeography in Australian wet tropics rainforest skinks

In order to investigate population history and demography in skinks endemic to the wet tropics of Australia, multiple nuclear DNA markers were sought. The utility of 72 primers (including 63 published intron-spanning 'CATS' primers) was tested.. Seven loci were characterized and shown to be single copy by single-strand conformation polymorphism analysis. Primers to five nuclear loci were developed, four with utility in skinks and three with utility in frogs. These observations extend the available information on intron-spanning primers for amphibians and reptiles.

Mutation scanning analysis of Marteilia sydneyi populations from different geographical locations in eastern Australia

Marteilia sydneyi (Paramyxea) is the causative agent of QX disease in oysters. In spite of the economic impact of this disease, its origin and the precise reason(s) for its apparent spread in Australian waters are not yet known. Given such knowledge gaps, investigating the population genetic structure(s) of M. sydneyi populations could provide insights into the epidemiology and ecology of the parasite and could assist in its prevention and control. In this study, single strand conformation polymorphism (SSCP)-based analysis of a region (195 bp) of the first internal transcribed spacer (ITS-1) of ribosomal DNA was employed to investigate genetic variation within and among five populations of M. sydneyi from oysters from five different locations in eastern Australia. The analysis showed the existence of a genetic variant of M. sydneyi common to the Great Sandy Strait, and the Richmond and Georges Rivers, as distinct from variants at the Pimpama and Clarence Rivers. Together with historical and other information relating to the QX disease outbreaks in eastern Australia, the molecular findings support the proposal that the parasite originated in the Great Sandy Strait and/or Richmond River and then extended southward along the coast. From a technical perspective, the study demonstrated the usefulness of SSCP as a tool to study the population genetics and epidemiology of M. sydneyi. (C) 2003 Elsevier Ltd. All rights reserved.

Binomial leap methods for simulating stochastic chemical kinetics

This paper discusses efficient simulation methods for stochastic chemical kinetics. Based on the tau-leap and midpoint tau-leap methods of Gillespie [D. T. Gillespie, J. Chem. Phys. 115, 1716 (2001)], binomial random variables are used in these leap methods rather than Poisson random variables. The motivation for this approach is to improve the efficiency of the Poisson leap methods by using larger stepsizes. Unlike Poisson random variables whose range of sample values is from zero to infinity, binomial random variables have a finite range of sample values. This probabilistic property has been used to restrict possible reaction numbers and to avoid negative molecular numbers in stochastic simulations when larger stepsize is used. In this approach a binomial random variable is defined for a single reaction channel in order to keep the reaction number of this channel below the numbers of molecules that undergo this reaction channel. A sampling technique is also designed for the total reaction number of a reactant species that undergoes two or more reaction channels. Samples for the total reaction number are not greater than the molecular number of this species. In addition, probability properties of the binomial random variables provide stepsize conditions for restricting reaction numbers in a chosen time interval. These stepsize conditions are important properties of robust leap control strategies. Numerical results indicate that the proposed binomial leap methods can be applied to a wide range of chemical reaction systems with very good accuracy and significant improvement on efficiency over existing approaches. (C) 2004 American Institute of Physics.

DHPLC analysis of patients with nevoid basal cell carcinoma syndrome reveals novel PTCH missense mutations in the serol-sensing domain

Nevoid Basal Cell Carcinoma Syndrome (NBCCS) is an autosomal dominant disorder characterised by multiple basal cell carcinomas, palmar and plantar pitting, odontogenic keratocysts of the jaws and bilamellar calcification of the falx. Mutations in the PTCH gene are responsible for NBCCS but most studies have found mutations in less than half of the cases tested. We used denaturing high performance liquid chromatography (DHPLC) to screen for PTCH mutations in 28 NBCCS cases, most of whom had been previously evaluated by single stranded conformation polymorphism analysis but found to be negative. Protein truncating (n = 10) and missense or indel (n = 4) mutations were found in 14/28 (50%) cases and one additional case carried an unclassified variant, c.2777G>C. Thirteen of the variants were novel. The mutation frequency was similar in inherited and de novo cases. Three of the missense and indel mutations were in the sterol-sensing domain, and one was in the sixth transmembrane domain.

Kinetics of reduction of FeO from slag by graphite and coal chars

The rates of reduction of FeO from iron-saturated FeO-CaO-Al2O3-SiO2 slags by graphite, coke, bituminous coal and anthracitic coal chars at temperatures in the range 1 673-1873 K have been measured using a sessile drop technique. The extents of reaction were determined using EPMA analysis of quenched samples, and on line gas analysis using a quadrupole mass spectrometer. The reaction rates have been shown to be dependent critically on carbon type. For the reaction geometry used in this investigation the reduction rates of graphite and coke are observed to be faster than with coal chars. This unexpected finding is shown to be associated with differences in the dominant chemical and mass transfer mechanisms occurring at the reaction interface. High reaction rates are observed to occur with the formation of liquid Fe-C alloy product and the associated gasification of carbon from the alloy. The rates of reduction by coal chars are determined principally by the chemical reaction at the carbon/gas interface and slag phase mass transfer.

Observations of the reduction of FeO from slag by graphite, coke and coal char

The reduction of FeO from iron-saturated FeO-CaO-Al2O3-SiO2 slags by graphite, coke and coal char at 1 673 K has been investigated using a sessile drop technique. Metallographic analysis of samples quenched from the reaction temperature, and in situ observations of the reaction interface, reveal significant differences in the slag/carbon contact, and in the morphologies of the product iron and its composition; these differences were found to depend on the carbon type used in the reduction. In particular it has been shown that, in the case of graphite and coke, liquid Fe-C droplets were rapidly formed at the slag/C interface. Reactions of the slag with coal chars, in contrast, result predominantly in the formation of solid iron. These observations indicate that the reaction pathways, and hence reaction kinetics, are dependent on carbon type.

Lithium-aluminium casting alloys and their associated metal-mould reactions

Aluminium - lithium alloys are specialist alloys used exclusively by the aerospace industry. They have properties that are favourable to the production of modern military aircraft. The addition of approximately 2.5 percent lithium to aluminium increases the strength characteristics of the new alloys by 10 percent. The same addition has the added advantage of decreasing the density of the resulting alloy by a similar percentage. The disadvantages associated with this alloy are primarily price and castability. The addition of 2.5 weight percent lithium to aluminium results in a price increase of 100% explaining the aerospace exclusivity. The processability of the alloys is restricted to ingot casting and wrought treatment but for complex components precision casting is required. Casting the alloys into sand and investment moulds creates a metal - mould reaction, the consequences of which are intolerable in the production of military hardware. The primary object of this project was to investigate and characterise the reactions occurring between the newly poured metal and surface of the mould and to propose a method of counteracting the metal - mould reaction. The constituents of standard sand and investment moulds were pyrolised with lithium metal in order to simplify the complex in-mould reaction and the products were studied by the solid state techniques of powder X-Ray diffraction and magic angle spinning nuclear magnetic resonance spectroscopy. The results of this study showed that the order of reaction was: Organic reagents> > Silicate reagents> Non silicate reagents Alphaset and Betaset were the two organic binders used to prepare the sand moulds throughout this project. Studies were carried out to characterise these resins in order to determine the factors involved in their reaction with lithium. Analysis revealed that during the curing process the phenolic hydroxide groups are not reacted out and that a redox reaction takes place between these hydroxides and the lithium in the molten alloys. Casting experiments carried out to assess the protection afforded by various hydroxide protecting agents showed that modern effective, protecting chemicals such as bis-trimethyl silyl acetamide and hexamethyldisilazane did not inhibit the metal - mould reaction to a sufficiently high standard and that tri-methylchlorosilane was consistently the best performer. Tri-methyl chlorosilane has a simple functionalizing mechanism compared to other hydroxide protecting reagents and this factor is responsible for its superior inhibiting qualities. Comparative studies of 6Li and 7Li N.M.R. spectra (M.A.S. and `off angle') establish that, for solid state (and even solution) analytical purposes 6Li is the preferred nucleus. 6Li M.A.S.N.M.R. spectra were obtained for thermally treated laponite clay. At temperatures below 800oC both dehydrated and rehydrated samples were considered. The data are consistent with mobility of lithium ions from the trioctahedral clay sites at 600oC. The superior resolution achievable in 6Li M.A.S.N.M.R. is demonstrated in the analysis of a microwave prepared lithium exchanged clay where 6Li spectroscopy revelaed two lithium sites in comparison to 7Li M.A.S.N.M.R. which gave only a single lithium resonance.

A desalination system with efficiency approaching the theoretical limits

The objective of this project is to design a new desalination system with energy efficiency approaching the theoretical thermodynamic limit—even at high recovery ratio. The system uses reverse osmosis (RO) and a batch principle of operation to overcome the problem of concentration factor which prevents continuous-flow RO systems from ever reaching this limit and thus achieving the minimum possible specific energy consumption, SEC. Batch operation comprises a cycle in three phases: pressurisation, purge, and refill. Energy recovery is inherent to the design. Unlike in closed-circuit desalination (CCD), no feedwater is added to the pressure circuit during the pressurisation phase. The batch configuration is compared to standard configurations such as continuous single-stage RO (with energy recovery) and CCD. Theoretical analysis has shown that the new system is able to use 33% less energy than CCD at a recovery ratio of 80%. A prototype has been constructed using readily available parts and tested with feedwater salinities and recovery ratios ranging from 2,000 to 5,000 ppm and 17.2–70.6%, respectively. Results compare very well against the standard configurations. For example, with feedwater containing 5,000 ppm NaCl and recovery ratio of 69%, a hydraulic SEC of 0.31 kWh/m3 was obtained—better than the minimum theoretically possible with a single-stage continuous flow system with energy recovery device.

Practical secure information flow in programming languages

If we classify variables in a program into various security levels, then a secure information flow analysis aims to verify statically that information in a program can flow only in ways consistent with the specified security levels. One well-studied approach is to formulate the rules of the secure information flow analysis as a type system. A major trend of recent research focuses on how to accommodate various sophisticated modern language features. However, this approach often leads to overly complicated and restrictive type systems, making them unfit for practical use. Also, problems essential to practical use, such as type inference and error reporting, have received little attention. This dissertation identified and solved major theoretical and practical hurdles to the application of secure information flow. ^ We adopted a minimalist approach to designing our language to ensure a simple lenient type system. We started out with a small simple imperative language and only added features that we deemed most important for practical use. One language feature we addressed is arrays. Due to the various leaking channels associated with array operations, arrays have received complicated and restrictive typing rules in other secure languages. We presented a novel approach for lenient array operations, which lead to simple and lenient typing of arrays. ^ Type inference is necessary because usually a user is only concerned with the security types for input/output variables of a program and would like to have all types for auxiliary variables inferred automatically. We presented a type inference algorithm B and proved its soundness and completeness. Moreover, algorithm B stays close to the program and the type system and therefore facilitates informative error reporting that is generated in a cascading fashion. Algorithm B and error reporting have been implemented and tested. ^ Lastly, we presented a novel framework for developing applications that ensure user information privacy. In this framework, core computations are defined as code modules that involve input/output data from multiple parties. Incrementally, secure flow policies are refined based on feedback from the type checking/inference. Core computations only interact with code modules from involved parties through well-defined interfaces. All code modules are digitally signed to ensure their authenticity and integrity. ^

Genetic individualization of Cannabis sativa by a short tandem repeat multiplex system

Cannabis sativa is the most frequently used of all illicit drugs in the United States. Cannabis has been used throughout history for its stems in the production of hemp fiber, for its seed for oil and food, and for its buds and leaves as a psychoactive drug. Short tandem repeats (STRs), were chosen as molecular markers because of their distinct advantages over other genetic methods. STRs are co-dominant, can be standardized such that reproducibility between laboratories can be easily achieved, have a high discrimination power and can be multiplexed. ^ In this study, six STR markers previously described for Cannabis were multiplexed into one reaction. The multiplex reaction was able to individualize 98 Cannabis samples (14 hemp and 84 marijuana, authenticated as originating from 33 of the 50 United States) and detect 29 alleles averaging 4.8 alleles per loci. The data did not relate the samples from the same state to each other. This is the first study to report a single reaction six-plex and apply it to the analysis of almost 100 Cannabis samples of known geographic collection site. ^

Measuring the sustainability of a national economy. The application of three measures of sustainability to Ireland

An assessment of the sustainability of the Irish economy has been carried out using three methodologies, enabling comparison and evaluation of the advantages and disadvantages of each, and potential synergies among them. The three measures chosen were economy-wide Material Flow Analysis (MFA), environmentally extended input-output (EE-IO) analysis and the Ecological Footprint (EF). The research aims to assess the sustainability of the Irish economy using these methods and to draw conclusions on their effectiveness in policy making both individually and in combination. A theoretical description discusses the methods and their respective advantages and disadvantages and sets out a rationale for their combined application. The application of the methods in combination has provided insights into measuring the sustainability of a national economy and generated new knowledge on the collective application of these methods. The limitations of the research are acknowledged and opportunities to address these and build on and extend the research are identified. Building on previous research, it is concluded that a complete picture of sustainability cannot be provided by a single method and/or indicator.

Heteroduplex PCR analysis of rearranged immunoglobulin genes for clonality assessment in multiple myeloma.

BACKGROUND AND OBJECTIVE: Molecular analysis by PCR of monoclonally rearranged immunoglobulin (Ig) genes can be used for diagnosis in B-cell lymphoproliferative disorders (LPD), as well as for monitoring minimal residual disease (MRD) after treatment. This technique has the risk of false-positive results due to the "background" amplification of similar rearrangements derived from polyclonal B-cells. This problem can be resolved in advance by additional analyses that discern between polyclonal and monoclonal PCR products, such as the heteroduplex analysis. A second problem is that PCR frequently fails to amplify the junction regions, mainly due to somatic mutations frequently present in mature (post-follicular) B-cell lymphoproliferations. The use of additional targets (e.g. Ig light chain genes) can avoid this problem. DESIGN AND METHODS: We studied the specificity of heteroduplex PCR analysis of several Ig junction regions to detect monoclonal products in samples from 84 MM patients and 24 patients with B cell polyclonal disorders. RESULTS: Using two distinct VH consensus primers (FR3 and FR2) in combination with one JH primer, 79% of the MM displayed monoclonal products. The percentage of positive cases was increased by amplification of the Vlamda-Jlamda junction regions or kappa(de) rearrangements, using two or five pairs of consensus primers, respectively. After including these targets in the heteroduplex PCR analysis, 93% of MM cases displayed monoclonal products. None of the polyclonal samples analyzed resulted in monoclonal products. Dilution experiments showed that monoclonal rearrangements could be detected with a sensitivity of at least 10(-2) in a background with >30% polyclonal B-cells, the sensitivity increasing up to 10(-3) when the polyclonal background was