Detection of human respiratory syncytial virus in respiratory samples by LightCycler reverse transcriptase PCR

Laboratory diagnosis of human respiratory syncytial virus (hRSV) infections has traditionally been performed by virus isolation in cell culture and the direct fluorescent-antibody assay (DFA). Reverse transcriptase PCR (RT-PCR) is now recognized as a sensitive and specific alternative for detection of hRSV in respiratory samples. Using the LightCycler instrument, we developed a rapid RT-PCR assay for the detection of hRSV (the LC-RT-PCR) with a pair of hybridization probes that target the hRSV L gene. In the present study, 190 nasopharyngeal aspirate samples from patients with clinically recognized respiratory tract infections were examined for hRSV. The results were then compared to the results obtained with a testing algorithm that combined DFA and a culture-augmented DFA (CA-DFA) assay developed in our laboratory. hRSV was detected in 77 (41%) specimens by LC-RT-PCR and in 75 (39%) specimens by the combination of DFA and CA-DFA. All specimens that were positive by the DFA and CA-DFA testing algorithm were positive by the LC-RT-PCR. The presence of hRSV RNA in the two additional LC-RT-PCR-positive specimens was confirmed by a conventional RT-PCR method that targets the hRSV N gene. The sensitivity of LC-RT-PCR was 50 PFU/ml; and this, together with its high specificity and rapid turnaround time, makes the LC-RT-PCR suitable for the detection of hRSV in clinical specimens.

A real-time PCR assay for the detection of Neisseria gonorrhoeae by LightCycler

The detection of Neisseria gonorrhoeae by the polymerase chain reaction (PCR) is now recognized as a sensitive and specific method of diagnosing infection by the organism. In this Study 152 urine specimens were examined for N. gonorrhoeae by a real-time PCR method using the LightCycler platform and results were compared to an in-house PCR assay using an ELISA-based detection method. N. gonorrhoeae DNA was detected in 29 (19%) specimens by LightCycler PCR (LC-PCR) and in 31 (20%) specimens by the in house PCR method. The LightCycler assay proved to be specific and 94% sensitive when compared to the in house PCR method. These features combined with the rapid turn-around time for results makes the LC-PCR particularly suitable for the detection of N. gonorrhoeae in a routine clinical laboratory. (C) 2002 Elsevier Science Inc. All rights reserved.

Reasoning about real-time repetitions: terminating and nonterminating

It is common for a real-time system to contain a nonterminating process monitoring an input and controlling an output. Hence, a real-time program development method needs to support nonterminating repetitions. In this paper we develop a general proof rule for reasoning about possibly nonterminating repetitions. The rule makes use of a Floyd-Hoare-style loop invariant that is maintained by each iteration of the repetition, a Jones-style relation between the pre- and post-states on each iteration, and a deadline specifying an upper bound on the starting time of each iteration. The general rule is proved correct with respect to a predicative semantics. In the case of a terminating repetition the rule reduces to the standard rule extended to handle real time. Other special cases include repetitions whose bodies are guaranteed to terminate, nonterminating repetitions with the constant true as a guard, and repetitions whose termination is guaranteed by the inclusion of a fixed deadline. (C) 2002 Elsevier Science B.V. All rights reserved.

[18O]-Oxygen incorporation reveals novel pathways in spiroacetal biosynthesis by Bactrocera cacuminata and B. cucumis

The origins of the oxygen atoms in 1,7-dioxaspiro[5.5]undecane (1) and hydroxyspiroacetal (2) from Bactrocera cacuminata, and in 2,8-dimethyl-1,7-dioxaspiro[5.5]undecane (3) and hydroxyspiroacetal (4) from B. cucumis, have been investigated by incorporation studies from both [18O2]-dioxygen and [18O]-water. Combined GC-MS examination and high-field NMR analysis have demonstrated that all oxygen atoms in 1 and 2 from B. cacuminata are dioxygen derived, but in contrast, the spiroacetals 3 and 4 from B. cucumis incorporate one ring oxygen from water and one ring oxygen (and the hydroxyl oxygen in 4) from [18O2]-dioxygen. These results reveal not only the generality of monoxygenase mediation of spiroacetal formation in Bactrocera sp., but also an unexpected complexity in their biosynthesis. A general paradigm accommodating these and other observations is presented.

Bis(diethylenetriamine)mercury(II) bis(thiocyanate)

Mercury(II) in the title compound, [Hg(C4H13N3)2](SCN)2, is six-coordinated with two diethylenetriamine (dien) ligands in a sym-facial configuration. The complex cation has a twofold axis of symmetry, and the secondary amine groups are in trans positions.

N-15 natural abundance of fossil peat reflects the influence of animal-derived nitrogen on vegetation

delta(15)N signatures of fossil peat were used to interpret past ecosystem processes on tectonically active subantarctic Macquarie Island. By comparing past vegetation reconstructed from the fossil record with present-day vegetation analogues, our evidence strongly suggests that changes in the delta(15)N signatures of fossil peat at this location reflect mainly past changes in the proportion of plant nitrogen derived from animal sources. Associated with uplift above sea level over the past 8,500 years, fossil records in two peat deposits on the island chronicle a change from coastal vegetation with fur and elephant seal disturbance to the existing inland herbfield. Coupled with this change are synchronous changes in the delta(15)N signatures of peat layers. At two sites N-15-enriched peat delta(15)N signatures of up to +17parts per thousand were associated with a high abundance of pollen of the nitrophile Callitriche antarctica (Callitrichaceae). At one site fossil seal hair was also associated with enriched peat delta(15)N. Less N-15 enriched delta(15)N signatures (e.g. -1.9parts per thousand to +3.9parts per thousand) were measured in peat layers which lacked animal associated C. antarctica and Acaena spp. Interpretation of a third peat profile indicates continual occupation of a ridge site by burrowing petrels for most of the Holocene. We suggest that N-15 signatures of fossil peat remained relatively stable with time once deposited, providing a significant new tool for interpreting the palaeoecology.

Can the nitrogenous composition of xylem sap be used to assess salinity stress in Casuarina glauca?

It is predicted that dryland salinity will affect up to 17 Mha of the Australian landscape by 2050, and therefore, monitoring the health of tree plantings and remnant native vegetation in saline areas is increasingly important. Casuarina glauca Sieber ex Spreng. has considerable salinity tolerance and is commonly planted in areas with a shallow, saline water table. To evaluate the potential of using the nitrogenous composition of xylem sap to assess salinity stress in C. glauca, the responses of trees grown with various soil salinities in a greenhouse were compared with those of trees growing in field plots with different water table depths and groundwater salinities. In the greenhouse, increasing soil salinity led to increased allocation of nitrogen (N) to proline and arginine in both stem and root xylem sap, with coincident decreases in citrulline and asparagine. Although the field plots were ranked as increasingly saline-based on ground water salinity and depth-only the allocation of N to citrulline differed significantly between the field plots. Within each plot, temporal variation in the composition of the xylem sap was related to rainfall, rainfall infiltration and soil salinity. Periods of low rainfall and infiltration and higher soil salinity corresponded with increased allocation of N to proline and arginine in the xylem sap. The allocation of N to citrulline and asparagine increased following rainfall events where rain was calculated to have infiltrated sufficiently to decrease soil salinity. The relationship between nitrogenous composition of the xylem sap of C. glauca and soil salinity indicates that the analysis of xylem sap is an effective method for assessing changes in salinity stress in trees at a particular site over time. However, the composition of the xylem sap proved less useful as a comparative index of salinity stress in trees growing at different sites.

Impact of point source pollution on nitrogen isotope signatures (delta N-15) of vegetation in SE Brazil

This study presents novel evidence that N-15 natural abundance can be used as a robust indicator to detect pollutant nitrogen in natural plant communities. Vegetation from the heavily polluted industrial area of Cubatao in Sao Paulo State, SE Brazil, was strongly N-15 depleted compared to plants at remote sites. Historic herbarium samples from Cubatao were significantly less N-15 depleted than extant plants, indicating that N-15 depletion of vegetation is associated with present-day nitrogen pollution in Cubatao. The heavy load of nitrogenous atmospheric pollutants in Cubatao provides a nitrogen source for plants, and strongly N-15 depleted air NH3 is likely to contribute to plant and soil N-15 depletion. Epiphytic plants from Cubatao were extremely N-15 depleted (average -10.9parts per thousand) contrasting with epiphytes at remote sites (averages -1.0parts per thousand and -3.0parts per thousand). Nitrogen isotope composition of vegetation provides a tool to determine input of pollutant nitrogen into plant communities. The strong isotopic change of epiphytes suggests that epiphytes are particularly sensitive biomonitors for atmospheric pollutant nitrogen.

Site-Directed Mutagenesis of Dimethyl Sulfoxide Reductase from Rhodobacter capsulatus: Characterization of a Y114 → F Mutant

A system for expressing site-directed mutants of the molybdenum enzyme dimethyl sulfoxide reductase from Rhodobacter capsulatus in the natural host was constructed. This system was used to Generate and express dimethyl sulfoxide reductase with a Y114F mutation. The Y114F mutant had an increased k(cat) and increased K-m toward both dimethyl sulfoxide and trimethylamine N-oxide compared to the native enzyme, and the value of k(cat)/K-m was lower for both substrates in the mutant enzyme. The Y114F mutant, as isolated, was able to oxidize dimethyl sulfide with phenazine ethosulfate as the electron acceptor but with a lower k(cat) than that of the native enzyme. The pH optimum of dimethyl sulfide: acceptor oxidoreductase activity in the Y114F mutant was shown to be shifted by +1 pH unit compared to the native enzyme. The Y114F mutant did not form a pink complex with dimethyl sulfide, which is characteristic of the native enzyme. The mutant enzyme showed a large increase in the K-d for DMS. Direct electrochemistry showed that the Mo(V)/Mo(IV) couple was unaffected by the Y114F mutant, but the midpoint potential of the Mo(VI)/Mo(V) couple was raised by about 50 mV. These data confirm that the Y114 residue plays a critical role in oxidation-reduction processes at the molybdenum active site and in oxygen atom transfer associated with sulfoxide reduction.

Eating 'Green': Motivations behind organic food consumption in Australia

Central to the development of green lifestyles is the consumption of foods that by dint of their status as chemical-free, locally produced and/or free of genetically modified ingredients, reduce the environmental impact of food provision. Yet there are many other factors, such as health concerns, that may also encourage the consumption of 'green' foods. This paper explores the ways in which Australian consumers construct organic food-a sector of the food industry that is currently growing at between 20 and 50 percent per annum but is struggling to keep up with rising consumer demand. In order to examine the significance of 'green' signifiers in the consumption practices of Australian consumers a series of focus group interviews and a national consumer survey were conducted. These examined both those characteristics of food that were valued in general, and those meanings that were associated with organic food in particular. In very general terms, analysis reveals that while consumers believed organic foods to be healthy and environmentally sound-both of which were considered desirable-these characteristics were subsumed by an overarching concern with convenience. This does not mean that consumers did not hold genuinely positive environmental attitudes. Rather, it reflects a range of contradictory beliefs and practices that appeared to derive from the discursive conflict between conventional and organic food industries over environmental, health and safety claims. The paper concludes by identifying the barriers and opportunities for expanding the organic industry in Australia in the context of the ways organics is constructed by consumers.

N-15 natural abundance studies in Australian commercial sugarcane

The measurement of natural N-15 abundance is a well-established technique for the identification and quantification of biological N-2 fixation in plants. Associative N-2 fixing bacteria have been isolated from sugarcane and reported to contribute potentially significant amounts of N to plant growth and development. It has not been established whether Australian commercial sugarcane receives significant input from biological N-2 fixation, even though high populations of N-2 fixing bacteria have been isolated from Australian commercial sugarcane fields and plants. In this study, delta(15)N measurements were used as a primary measure to identify whether Australian commercial sugarcane was obtaining significant inputs of N via biological N-2 fixation. Quantification of N input, via biological N-2 fixation, was not possible since suitable non-N-2 fixing reference plants were not present in commercial cane fields. The survey of Australian commercially grown sugarcane crops showed the majority had positive leaf delta(15)N values (73% >3.00parts per thousand, 63% of which were

A refinement calculus for logic programs

Existing refinement calculi provide frameworks for the stepwise development of imperative programs from specifications. This paper presents a refinement calculus for deriving logic programs. The calculus contains a wide-spectrum logic programming language, including executable constructs such as sequential conjunction, disjunction, and existential quantification, as well as specification constructs such as general predicates, assumptions and universal quantification. A declarative semantics is defined for this wide-spectrum language based on executions. Executions are partial functions from states to states, where a state is represented as a set of bindings. The semantics is used to define the meaning of programs and specifications, including parameters and recursion. To complete the calculus, a notion of correctness-preserving refinement over programs in the wide-spectrum language is defined and refinement laws for developing programs are introduced. The refinement calculus is illustrated using example derivations and prototype tool support is discussed.