Using the Gini coefficient with BIOLOG substrate utilisation data to provide an alternative quantitative measure for comparing bacterial soil communities

A measure quantifying unequal use of carbon sources, the Gini coefficient (G), has been developed to allow comparisons of the observed functional diversity of bacterial soil communities. This approach was applied to the analysis of substrate utilisation data obtained from using BIOLOG microtiter plates in a study which compared decomposition processes in two contrasting plant substrates in two different soils. The relevance of applying the Gini coefficient as a measure of observed functional diversity, for soil bacterial communities is evaluated against the Shannon index (H) and average well colour development (AWCD), a measure of the total microbial activity. Correlation analysis and analysis of variance of the experimental data show that the Gini coefficient, the Shannon index and AWCD provided similar information when used in isolation. However, analyses based on the Gini coefficient and the Shannon index, when total activity on the microtiter plates was maintained constant (i.e. AWCD as a covariate), indicate that additional information about the distribution of carbon sources being utilised can be obtained. We demonstrate that the Lorenz curve and its measure of inequality, the Gini coefficient, provides not only comparable information to AWCD and the Shannon index but when used together with AWCD encompasses measures of total microbial activity and absorbance inequality across all the carbon sources. This information is especially relevant for comparing the observed functional diversity of soil microbial communities.

Capacity of fatty acid profiles and substrate utilization patterns to describe differences in soil microbial communities associated with increased salinity or alkalinity at three locations in South Australia

Fatty acid methyl ester (FAME) profiles, together with Biolog substrate utilization patterns, were used in conjunction with measurements of other soil chemical and microbiological properties to describe differences in soil microbial communities induced by increased salinity and alkalinity in grass/legume pastures at three sites in SE South Australia. Total ester-linked FAMEs (EL-FAMEs) and phospholipid-linked FAMEs (PL-FAMEs), were also compared for their ability to detect differences between the soil microbial communities. The level of salinity and alkalinity in affected areas of the pastures showed seasonal variation, being greater in summer than in winter. At the time of sampling for the chemical and microbiological measurements (winter) only the affected soil at site 1 was significantly saline. The affected soils at all three sites had lower organic C and total N concentrations than the corresponding non-affected soils. At site 1 microbial biomass, CO 2-C respiration and the rate of cellulose decomposition was also lower in the affected soil compared to the non-affected soil. Biomarker fatty acids present in both the EL- and PL-FAME profiles indicated a lower ratio of fungal to bacterial fatty acids in the saline affected soil at site 1. Analysis of Biolog substrate utilization patterns indicated that the bacterial community in the affected soil at site 1 utilized fewer carbon substrates and had lower functional diversity than the corresponding community in the non-affected soil. In contrast, increased alkalinity, of major importance at sites 2 and 3, had no effect on microbial biomass, the rate of cellulose decomposition or functional diversity but was associated with significant differences in the relative amounts of several fatty acids in the PL-FAME profiles indicative of a shift towards a bacterial dominated community. Despite differences in the number and relative amounts of fatty acids detected, principal component analysis of the EL- and PL-FAME profiles were equally capable of separating the affected and non-affected soils at all three sites. Redundancy analysis of the FAME data showed that organic C, microbial biomass, electrical conductivity and bicarbonate-extractable P were significantly correlated with variation in the EL-FAME profiles, whereas pH, electrical conductivity, NH 4-N, CO 2-C respiration and the microbial quotient were significantly correlated with variation in the PL-FAME profiles. Redundancy analysis of the Biolog data indicated that cation exchange capacity and bicarbonate-extractable K were significantly correlated with the variation in Biolog substrate utilization patterns.

The role of core protest group members in sustaining protest against controversial construction and engineering projects

Community-based protests against major construction and engineering projects are becoming increasingly common as concerns over issues such as corporate social accountability, climate change and corruption become more prominent in the public's mind. Public perceptions of risk associated with these projects can have a contagious effect, which mismanaged can escalate into long-term and sometimes acrimonious protest stand-offs that have negative implications for the community, firms involved and the construction industry as a whole. This paper investigates the role of core group members in sustaining community-based protest against construction and engineering projects. Using a thematic story telling approach which draws on ethnographic method and social contagion theories, it presents an in-depth analysis of a single case study - one of Australia's longest standing community protests against a construction project. It concludes that core group members play a critical role, within anarchic structures which provide a high degree of spontaneity and improvisation, in sustaining movement continuity by building collective identity, mobilising resources and a moving interface which developers find hard to communicate with.

Physisorption-induced electron scattering on the surface of carbon-metal core-shell nanowire arrays for hydrogen sensing

Palladium is sputtered on multi-walled carbon nanotube forests to form carbon-metal core-shell nanowire arrays. These hybrid nanostructures exhibited resistive responses when exposed to hydrogen with an excellent baseline recovery at room temperature. The magnitude of the response is shown to be tuneable by an applied voltage. Unlike the charge-transfer mechanism commonly attributed to Pd nanoparticle-decorated carbon nanotubes, this demonstrates that the hydrogen response mechanism of the multi-walled carbon nanotube-Pd core-shell nanostructure is due to the increase in electron scattering induced by physisorption of hydrogen. These hybrid core-shell nanostructures are promising for gas detection in hydrogen storage applications.

Core-leaf onion-like carbon/MnO2 hybrid nano-urchins for rechargeable lithium-ion batteries

A hybrid nano-urchin structure consisting of spherical onion-like carbon and MnO2 nanosheets is synthesized by a facile and environmentally-friendly hydrothermal method. Lithium-ion batteries incorporating the hybrid nano-urchin anode exhibit reversible lithium storage with superior specific capacity, enhanced rate capability, stable cycling performance, and nearly 100% Coulombic efficiency. These results demonstrate the effectiveness of designing hybrid nano-architectures with uniform and isotropic structure, high loading of electrochemically-active materials, and good conductivity for the dramatic improvement of lithium storage.

Control of core-shell structure and elemental composition of binary quantum dots

The possibility of initial stage control of the elemental composition and core/shell structure of binary SiC quantum dots by optimizing temporal variation of Si and C incoming fluxes and surface temperatures is shown via hybrid numerical simulations. Higher temperatures and influxes encourage the formation of a stoichiometric outer shell over a small carbon-enriched core, whereas lower temperatures result in a larger carbon-enriched core, Si-enriched undershell, and then a stoichiometric SiC outer shell. This approach is generic and is applicable to a broad range of semiconductor materials and nanofabrication techniques. © 2007 American Institute of Physics.

Effect of soil properties on the response of pile to underground explosion

This paper develops and presents a fully coupled non-linear finite element procedure to treat the response of piles to ground shocks induced by underground explosions. The Arbitrary Lagrange Euler coupling formulation with proper state material parameters and equations are used in the study. Pile responses in four different soil types, viz, saturated soil, partially saturated soil and loose and dense dry soils are investigated and the results compared. Numerical results are validated by comparing with those from a standard design manual. Blast wave propagation in soils, horizontal pile deformations and damages in the pile are presented. The pile damage presented through plastic strain diagrams will enable the vulnerability assessment of the piles under the blast scenarios considered. The numerical results indicate that the blast performance of the piles embedded in saturated soil and loose dry soil are more severe than those in piles embedded in partially saturated soil and dense dry soil. Present findings should serve as a benchmark reference for future analysis and design.

Impact of nitrification inhibitor (DMPP) on soil nitrous oxide emissions from an intensive broccoli production system in sub-tropical Australia

Vegetable cropping systems are often characterised by high inputs of nitrogen fertiliser. Elevated emissions of nitrous oxide (N2O) can be expected as a consequence. In order to mitigate N2O emissions from fertilised agricultural fields, the use of nitrification inhibitors, in combination with ammonium based fertilisers, has been promoted. However, no data is currently available on the use of nitrification inhibitors in sub-tropical vegetable systems. A field experiment was conducted to investigate the effect of the nitrification inhibitor 3,4-dimethylpyrazole phosphate (DMPP) on N2O emissions and yield from broccoli production in sub-tropical Australia. Soil N2O fluxes were monitored continuously (3 h sampling frequency) with fully automated, pneumatically operated measuring chambers linked to a sampling control system and a gas chromatograph. Cumulative N2O emissions over the 5 month observation period amounted to 298 g-N/ha, 324 g-N/ha, 411 g-N/ha and 463 g-N/ha in the conventional fertiliser (CONV), the DMPP treatment (DMPP), the DMMP treatment with a 10% reduced fertiliser rate (DMPP-red) and the zero fertiliser (0N), respectively. The temporal variation of N2O fluxes showed only low emissions over the broccoli cropping phase, but significantly elevated emissions were observed in all treatments following broccoli residues being incorporated into the soil. Overall 70–90% of the total emissions occurred in this 5 weeks fallow phase. There was a significant inhibition effect of DMPP on N2O emissions and soil mineral N content over the broccoli cropping phase where the application of DMPP reduced N2O emissions by 75% compared to the standard practice. However, there was no statistical difference between the treatments during the fallow phase or when the whole season was considered. This study shows that DMPP has the potential to reduce N2O emissions from intensive vegetable systems, but also highlights the importance of post-harvest emissions from incorporated vegetable residues. N2O mitigation strategies in vegetable systems need to target these post-harvest emissions and a better evaluation of the effect of nitrification inhibitors over the fallow phase is needed.

Mechanisms of mono- and poly-ubiquitination : ubiquitination specificity depends on compatibility between the E2 catalytic core and amino acid residues proximal to the lysine

Ubiquitination involves the attachment of ubiquitin to lysine residues on substrate proteins or itself, which can result in protein monoubiquitination or polyubiquitination. Ubiquitin attachment to different lysine residues can generate diverse substrate-ubiquitin structures, targeting proteins to different fates. The mechanisms of lysine selection are not well understood. Ubiquitination by the largest group of E3 ligases, the RING-family E3 s, is catalyzed through co-operation between the non-catalytic ubiquitin-ligase (E3) and the ubiquitin-conjugating enzyme (E2), where the RING E3 binds the substrate and the E2 catalyzes ubiquitin transfer. Previous studies suggest that ubiquitination sites are selected by E3-mediated positioning of the lysine toward the E2 active site. Ultimately, at a catalytic level, ubiquitination of lysine residues within the substrate or ubiquitin occurs by nucleophilic attack of the lysine residue on the thioester bond linking the E2 catalytic cysteine to ubiquitin. One of the best studied RING E3/ E2 complexes is the Skp1/Cul1/F box protein complex, SCFCdc4, and its cognate E2, Cdc34, which target the CDK inhibitor Sic1 for K48-linked polyubiquitination, leading to its proteasomal degradation. Our recent studies of this model system demonstrated that residues surrounding Sic1 lysines or lysine 48 in ubiquitin are critical for ubiquitination. This sequence-dependence is linked to evolutionarily conserved key residues in the catalytic region of Cdc34 and can determine if Sic1 is mono- or poly-ubiquitinated. Our studies indicate that amino acid determinants in the Cdc34 catalytic region and their compatibility to those surrounding acceptor lysine residues play important roles in lysine selection. This may represent a general mechanism in directing the mode of ubiquitination in E2 s.

Soil-pile interaction of pile embedded in deep layered marine sediment under seismic excitation

This research provides validated Finite Element techniques to analyse pile foundations under seismic loads. The results show that the capability of the technique to capture the important pile response which includes kinematic and inertial interaction effects, effects of soil stiffness and depth on pile deflection patterns and permanent deformations.