Showing papers by "Cooperative Research Centre published in 2011"

Biochar reduces the bioavailability and phytotoxicity of heavy metals

Abstract: Biochar has attracted research interest due to its ability to increase the soil carbon pool and improve crop productivity. The objective of this study was to evaluate the metal immobilizing impact of chicken manure- and green waste-derived biochars, and their effectiveness in promoting plant growth. The immobilization and phytoavailability of Cd, Cu and Pb was examined using naturally contaminated shooting range and spiked soils. Biochar samples prepared from chicken manure and green waste were used as soil amendments. Application of biochar significantly reduced NH4NO3 extractable Cd, Cu and Pb concentrations of soils, indicating the immobilization of these metals. Chicken manure-derived biochar increased plant dry biomass by 353 and 572% for shoot and root, respectively with 1% of biochar addition. This might be attributed to reduced toxicity of metals and increased availability of nutrients such as P and K. Both biochars significantly reduced Cd, Cu and Pb accumulation by Indian mustard (Brassica juncea), and the reduction increased with increasing amount of biochar application except Cu concentration. Metal sequential fractionation data indicated that biochar treatments substantially modified the partitioning of Cd, Cu and Pb from the easily exchangeable phase to less bioavailable organic bound fraction. The results clearly showed that biochar application was effective in metal immobilization, thereby reducing the bioavailability and phytotoxicity of heavy metals.

Removal of methyl orange from aqueous solution using bentonite-supported nanoscale zero-valent iron

Abstract: Zero-valent iron (ZVI) nanoparticles tend to agglomerate, resulting in a significant loss in reactivity. To address this issue, synthesized bentonite-supported nanoscale zero-valent iron (B-nZVI) was used to remove azo dye methyl orange (MO) in aqueous solution. Batch experiments show that various parameters, such as pH, initial concentration of MO, dosage, and temperature, were affected by the removal of MO. Scanning electron microscopy (SEM) confirmed that B-nZVI increased their reactivity and a decrease occurred in the aggregation of iron nanoparticles for the presence of bentonite (B). Using B-nZVI, 79.46% of MO was removed, whereas only 40.03% when using nZVI after reacting for 10 min with an initial MO concentration of 100 mg/L (pH = 6.5). Furthermore, after B-nZVI reacted to MO, XRD indicated that iron oxides were formed. FTIR showed that no new bands appeared, and UV–vis demonstrated that the absorption peak of MO was degraded. Kinetics studies showed that the degradation of MO fitted well to the pseudo first-order model. A degradation mechanism is proposed, including the following: oxidation of iron, adsorption of MO to B-nZVI, formation of Fe(II)–dye complex, and cleavage of azo bond. Finally, the removal rate of MO from actual wastewater was 99.75% when utilizing B-nZVI.

Decrease in rate of myopia progression with a contact lens designed to reduce relative peripheral hyperopia: one-year results.

Abstract: PURPOSE. To determine whether a novel optical treatment using contact lenses to reduce relative peripheral hyperopia can slow the rate of progress of myopia. METHODS. Chinese children, aged 7 to 14 years, with baseline myopia from sphere 0.75 to 3.50 D and cylinder 1.00 D, were fitted with novel contact lenses (n 45) and followed up for 12 months, and their progress was compared with that of a group (n 40) matched for age, sex, refractive error, axial length, and parental myopia wearing normal, single-vision, spherocylindrical spectacles. RESULTS. On adjusting for parental myopia, sex, age, baseline spherical equivalent (SphE) values, and compliance, the estimated progression in SphE at 12 months was 34% less, at 0.57 D, with the novel contact lenses (95% confidence interval [CI], 0.45 0.69 D) than at 0.86 D, with spectacle lenses (95% CI, 0.74 to 0.99 D). For an average baseline age of 11.2 years, baseline SphE of 2.10 D, a baseline axial length of 24.6 mm, and 320 days of compliant lens wear, the estimated increase in axial length (AL) was 33% less at 0.27 mm (95% CI, 0.22‐0.32 mm) than at 0.40 mm (95% CI, 0.35‐0.45 mm) for the contact lens and spectacle lens groups, respectively. CONCLUSIONS. The 12-month data support the hypothesis that reducing peripheral hyperopia can alter central refractive development and reduce the rate of progress of myopia. (chictr.org number, chiCTR-TRC-00000029 or chiCTRTRC-00000032.) (Invest Ophthalmol Vis Sci. 2011;52: 9362‐9367) DOI:10.1167/iovs.11-7260 I n addition to the cost, inconvenience, and complications associated with traditional optical and surgical correction strategies, myopia is associated with ocular complications that can lead to permanent vision loss. Excessive axial elongation in high myopia increases the risk for cataract, glaucoma, chorioretinal degeneration, and idiopathic retinal detachment 1‐3

The NAL-NL2 prescription procedure

Abstract: NAL-NL2 is the second generation of prescription procedures from The National Acoustic Laboratories (NAL) for fitting wide dynamic range compression (WDRC) instruments. Like its predecessor NALNL1 (Dillon, 1999), NAL-NL2 aims at making speech intelligible and overall loudness comfortable. This aim is mainly driven by a belief that these factors are most important for hearing aid users, but is also driven by the fact that less information is available about how to adjust gain to optimise other parameters that affect prescription such as localisation, tonal quality, detection of environmental sounds, and naturalness. In both formulas, the objective is achieved by combining a speech intelligibility model and a loudness model in an adaptive computer- controlled optimisation process. Adjustments have further been made to the theoretical component of NAL-NL2 that are directed by empirical data collected during the past decade with NAL-NL1. In this paper, the data underlying NAL-NL2 and the derivation procedure are presented, and the main differences from NAL-NL1 are outlined.

Climate change and diseases of food crops

Abstract: Despite complex regional patterns of projected climate change, significant decreases in food crop yields have been predicted using the ‘worst case’ CO2 emission scenario (A1FI) of the Intergovernmental Panel on Climate Change. Overall, climate change is predicted to have a progressively negative effect on the yield of food crops, particularly in the absence of efforts to mitigate global CO2 emissions. As with all species, plant pathogens will have varying responses to climate change. Whilst the life cycle of some pathogens will be limited by increasing temperatures, e.g. Puccinia striiformis f.sp. tritici, other climatic factors such as increasing atmospheric CO2, may provide more favourable conditions for pathogens such as Fusarium pseudograminearum. Based on published literature and unpublished work in progress, we have reviewed the qualitative effects of climate change on pathogens that cause disease of four major food crops: wheat, rice, soybean and potato. The limited data show that the influence will be positive, negative or neutral, depending on the host–pathogen interaction. Quantitative analysis of climate change on pathogens of these crops is largely lacking, either from field or laboratory studies or from modelling-based assessments. Systematic quantitative analysis of these effects will be necessary in developing future disease management plans, such as plant breeding, altered planting schedules, chemical and biological control methods and increased monitoring for new disease threats.

Prescribed burning: how can it work to conserve the things we value?

Abstract: Prescribed burning is a commonly applied management tool, and there has been considerable debate over the efficacy of its application. We review data relating to the effectiveness of prescribed burning in Australia. Specifically, we address two questions: (1) to what extent can fuel reduction burning reduce the risk of loss of human life and economic assets posed from wildfires? (2) To what extent can prescribed burning be used to reduce the risk of biodiversity loss? Data suggest that prescribed burning can achieve a reduction in the extent of wildfires; however, at such levels, the result is an overall increase in the total area of the landscape burnt. Simulation modelling indicates that fuel reduction has less influence than weather on the extent of unplanned fire. The need to incorporate ecological values into prescribed burning programmes is becoming increasingly important. Insufficient data are available to determine if existing programs have been successful. There are numerous factors that prevent the implementation of better prescribed burning practices; most relate to a lack of clearly defined, measurable objectives. An adaptive risk management framework combined with enhanced partnerships between scientists and fire-management agencies is necessary to ensure that ecological and fuel reduction objectives are achieved.

Use and understanding of organic amendments in Australian agriculture: a review

Abstract: A wide range of organic amendments (OA) is currently available to Australian farmers. These products have numerous agronomic applications, including the supply of plant nutrients, control of pests and diseases, and in management of soil health. Several of these products are also used in contaminated and degraded land remediation. The most commonly identifiable groups of OA in Australia are composts, compost teas, vermicasts, humic substances, meat, blood and bone meal, fish hydrolysates, seaweed extracts, bio-inoculants, biodynamic products, and biochars. Many of these OA contain nutrients within organic molecular structures; these nutrients are usually not immediately available to plants and must first be mineralised. Mineralisation often occurs as OA are consumed by microbes, thereby stimulating soil microbial activity. The application of OA such as bio-inoculants, humic substances, and seaweed extracts can potentially stimulate crop growth and development through the actions of plant growth-promoting hormones, including cytokinins, auxins, and gibberellins. Yet despite these apparent benefits, the widespread adoption of OA in Australia has been limited, due in part to the high application rates required to produce agronomic benefits, a lack of consistency in the composition of some products, a poor public perception of their utility, and a lack of unbiased scientific research into the agricultural potential of these products.

Observed decreases in oxygen content of the global ocean

Abstract: Comparing the high-quality oxygen climatology from the World Ocean Circulation Experiment to earlier data we reveal near-global decreases in oxygen levels in the upper ocean between the 1970s and the 1990s. This globally averaged oxygen decrease is −0.93 ± 0.23 mmol l−1, which is equivalent to annual oxygen losses of −0.55 ± 0.13 × 1014 mol yr−1 (100–1000 m). The strongest decreases in oxygen occur in the mid-latitudes of both hemispheres, near regions where there is strong water renewal and exchange between the ocean interior and surface waters. Approximately 15% of global oxygen decrease can be explained by a warmer mixed-layer reducing the capacity of water to store oxygen, while the remainder is consistent with an overall decrease in the exchange between surface waters and the ocean interior. Here we suggest that this reduction in water mass renewal rates on a global scale is a consequence of increased stratification caused by warmer surface waters. These observations support climate model simulations of oxygen change under global warming scenarios.

Modelling horses for novel climate courses: insights from projecting potential distributions of native and alien Australian acacias with correlative and mechanistic models

Abstract: Aim Investigate the relative abilities of different bioclimatic models and data sets to project species ranges in novel environments utilizing the natural experiment in biogeography provided by Australian Acacia species. Location Australia, South Africa. Methods We built bioclimatic models for Acacia cyclops and Acacia pycnantha using two discriminatory correlative models (MaxEnt and Boosted Regression Trees) and a mechanistic niche model (CLIMEX). We fitted models using two training data sets: native-range data only (‘restricted’) and all available global data excluding South Africa (‘full’). We compared the ability of these techniques to project suitable climate for independent records of the species in South Africa. In addition, we assessed the global potential distributions of the species to projected climate change. Results All model projections assessed against their training data, the South African data and globally were statistically significant. In South Africa and globally, the additional information contained in the full data set generally improved model sensitivity, but at the expense of increased modelled prevalence, particularly in extrapolation areas for the correlative models. All models projected some climatically suitable areas in South Africa not currently occupied by the species. At the global scale, widespread and biologically unrealistic projections by the correlative models were explained by open-ended response curves, a problem which was not always addressed by broader background climate space or by the extra information in the full data set. In contrast, the global projections for CLIMEX were more conservative. Projections into 2070 indicated a polewards shift in climate suitability and a decrease in model interpolation area. Main conclusions Our results highlight the importance of carefully interpreting model projections in novel climates, particularly for correlative models. Much work is required to ensure bioclimatic models performed in a robust and ecologically plausible manner in novel climates. We explore reasons for variations between models and suggest methods and techniques for future improvements.

The ecology of Bactrocera tryoni (Diptera: Tephritidae): what do we know to assist pest management?

Abstract: The distribution, systematics and ecology of Bactrocera tryoni, the Queensland fruit fly, are reviewed. Bactrocera tryoni is a member of the B. tryoni complex of species, which currently includes four named species, viz. B. tryoni ssp., B. neohumeralis, B. melas and B. aquilonis. The species status of B. melas and B. aquilonis is unclear (they may be junior synonyms of B. tryoni) and their validity, or otherwise, needs to be confirmed as a matter of urgency. While Queensland fruit fly is regarded as a tropical species, it cannot be assumed that its distribution will spread further south under climate change scenarios. Increasing aridity and hot dry summers, as well as more complex, indirect interactions resulting from elevated CO2, make predicting the future distribution and abundance of B. tryoni difficult. The ecology of B. tryoni is reviewed with respect to current control approaches (with the exception of sterile insect technique (SIT) which is covered in a companion paper). We conclude that there are major gaps in the knowledge required to implement most noninsecticide-based management approaches. Priority areas for future research include host–plant interactions, protein and cue-lure foraging and use, spatial dynamics, development of new monitoring tools, investigating the use of natural enemies and better integration of fruit flies into general horticultural IPM systems.

Different models of genetic variation and their effect on genomic evaluation

Abstract: The theory of genomic selection is based on the prediction of the effects of quantitative trait loci (QTL) in linkage disequilibrium (LD) with markers. However, there is increasing evidence that genomic selection also relies on "relationships" between individuals to accurately predict genetic values. Therefore, a better understanding of what genomic selection actually predicts is relevant so that appropriate methods of analysis are used in genomic evaluations. Simulation was used to compare the performance of estimates of breeding values based on pedigree relationships (Best Linear Unbiased Prediction, BLUP), genomic relationships (gBLUP), and based on a Bayesian variable selection model (Bayes B) to estimate breeding values under a range of different underlying models of genetic variation. The effects of different marker densities and varying animal relationships were also examined. This study shows that genomic selection methods can predict a proportion of the additive genetic value when genetic variation is controlled by common quantitative trait loci (QTL model), rare loci (rare variant model), all loci (infinitesimal model) and a random association (a polygenic model). The Bayes B method was able to estimate breeding values more accurately than gBLUP under the QTL and rare variant models, for the alternative marker densities and reference populations. The Bayes B and gBLUP methods had similar accuracies under the infinitesimal model. Our results suggest that Bayes B is superior to gBLUP to estimate breeding values from genomic data. The underlying model of genetic variation greatly affects the predictive ability of genomic selection methods, and the superiority of Bayes B over gBLUP is highly dependent on the presence of large QTL effects. The use of SNP sequence data will outperform the less dense marker panels. However, the size and distribution of QTL effects and the size of reference populations still greatly influence the effectiveness of using sequence data for genomic prediction.

A dynamic early East Antarctic Ice Sheet suggested by ice-covered fjord landscapes

Abstract: The East Antarctic ice sheet has played a fundamental part in modulating climate and sea level during the past 30 million years. Understanding its history is crucial to evaluating its future behaviour and response to global warming. Airborne ice-penetrating radar studies now reveal a fjord-like landscape beneath several kilometres of ice in the East Antarctic Aurora subglacial basin. The data confirm, and provide a new constraint on, the magnitude and dynamics of the oscillations of the East Antarctic ice sheet during the late Cenozoic, which had previously been supported only by marine cores. The first Cenozoic ice sheets initiated in Antarctica from the Gamburtsev Subglacial Mountains1 and other highlands as a result of rapid global cooling ∼34 million years ago2. In the subsequent 20 million years, at a time of declining atmospheric carbon dioxide concentrations2 and an evolving Antarctic circumpolar current2, sedimentary sequence interpretation3 and numerical modelling4 suggest that cyclical periods of ice-sheet expansion to the continental margin, followed by retreat to the subglacial highlands, occurred up to thirty times. These fluctuations were paced by orbital changes and were a major influence on global sea levels5. Ice-sheet models show that the nature of such oscillations is critically dependent on the pattern and extent of Antarctic topographic lowlands. Here we show that the basal topography of the Aurora Subglacial Basin of East Antarctica, at present overlain by 2–4.5 km of ice, is characterized by a series of well-defined topographic channels within a mountain block landscape. The identification of this fjord landscape, based on new data from ice-penetrating radar, provides an improved understanding of the topography of the Aurora Subglacial Basin and its surroundings, and reveals a complex surface sculpted by a succession of ice-sheet configurations substantially different from today’s. At different stages during its fluctuations, the edge of the East Antarctic Ice Sheet lay pinned along the margins of the Aurora Subglacial Basin, the upland boundaries of which are currently above sea level and the deepest parts of which are more than 1 km below sea level. Although the timing of the channel incision remains uncertain, our results suggest that the fjord landscape was carved by at least two iceflow regimes of different scales and directions, each of which would have over-deepened existing topographic depressions, reversing valley floor slopes.

Climate change and its implications for Australia's freshwater fish

Abstract: Freshwater environments and their fishes are particularly vulnerable to climate change because the persistence and quality of aquatic habitat depend heavily on climatic and hydrologic regimes. In Australia, projections indicate that the rate and magnitude of climate change will vary across the continent. We review the likely effects of these changes on Australian freshwater fishes across geographic regions encompassing a diversity of habitats and climatic variability. Commonalities in the predicted implications of climate change on fish included habitat loss and fragmentation, surpassing of physiological tolerances and spread of alien species. Existing anthropogenic stressors in more developed regions are likely to compound these impacts because of the already reduced resilience of fish assemblages. Many Australian freshwater fish species are adapted to variable or unpredictable flow conditions and, in some cases, this evolutionary history may confer resistance or resilience to the impacts of climate change. However, the rate and magnitude of projected change will outpace the adaptive capacities of many species. Climate change therefore seriously threatens the persistence of many of Australia’s freshwater fish species, especially of those with limited ranges or specific habitat requirements, or of those that are already occurring close to physiological tolerance limits. Human responses to climate change should be proactive and focus on maintaining population resilience through the protection of habitat, mitigation of current anthropogenic stressors, adequate planning and provisioning of environmental flows and the consideration of more interventionist options such as managed translocations.

Mechanisms of Phosphine Toxicity

Abstract: Fumigation with phosphine gas is by far the most widely used treatment for the protection of stored grain against insect pests. The development of high-level resistance in insects now threatens its continued use. As there is no suitable chemical to replace phosphine, it is essential to understand the mechanisms of phosphine toxicity to increase the effectiveness of resistance management. Because phosphine is such a simple molecule (PH3), the chemistry of phosphorus is central to its toxicity. The elements above and below phosphorus in the periodic table are nitrogen (N) and arsenic (As), which also produce toxic hydrides, namely, NH3 and AsH3. The three hydrides cause related symptoms and similar changes to cellular and organismal physiology, including disruption of the sympathetic nervous system, suppressed energy metabolism and toxic changes to the redox state of the cell. We propose that these three effects are interdependent contributors to phosphine toxicity.

Genome-wide association studies for feedlot and growth traits in cattle.

Abstract: A genome wide-association study for production traits in cattle was carried out using genotype data from the 10K Affymetrix (Santa Clara, CA) and the 50K Illumina (San Diego, CA) SNP chips. The results for residual feed intake (RFI), BW, and hip height in 3 beef breed types (Bos indicus, Bos taurus, and B. indicus × B. taurus), and for stature in dairy cattle, are presented. The aims were to discover SNP associated with all traits studied, but especially RFI, and further to test the consistency of SNP effects across different cattle populations and breed types. The data were analyzed within data sets and within breed types by using a mixed model and fitting 1 SNP at a time. In each case, the number of significant SNP was more than expected by chance alone. A total of 75 SNP from the reference population with 50K chip data were significant (P < 0.001) for RFI, with a false discovery rate of 68%. These 75 SNP were mapped on 24 different BTA. Of the 75 SNP, the 9 most significant SNP were detected on BTA 3, 5, 7, and 8, with P ≤ 6.0 × 10(-5). In a population of Angus cattle divergently selected for high and low RFI and 10K chip data, 111 SNP were significantly (P < 0.001) associated with RFI, with a false discovery rate of 7%. Approximately 103 of these SNP were therefore likely to represent true positives. Because of the small number of SNP common to both the 10K and 50K SNP chips, only 27 SNP were significantly (P < 0.05) associated with RFI in the 2 populations. However, other chromosome regions were found that contained SNP significantly associated with RFI in both data sets, although no SNP within the region showed a consistent effect on RFI. The SNP effects were consistent between data sets only when estimated within the same breed type.

A combined long-range phasing and long haplotype imputation method to impute phase for SNP genotypes.

Abstract: Background Knowing the phase of marker genotype data can be useful in genome-wide association studies, because it makes it possible to use analysis frameworks that account for identity by descent or parent of origin of alleles and it can lead to a large increase in data quantities via genotype or sequence imputation. Long-range phasing and haplotype library imputation constitute a fast and accurate method to impute phase for SNP data.