Predicting metal-binding site residues in low-resolution structural models

The accurate prediction of the biochemical function of a protein is becoming increasingly important, given the unprecedented growth of both structural and sequence databanks. Consequently, computational methods are required to analyse such data in an automated manner to ensure genomes are annotated accurately. Protein structure prediction methods, for example, are capable of generating approximate structural models on a genome-wide scale. However, the detection of functionally important regions in such crude models, as well as structural genomics targets, remains an extremely important problem. The method described in the current study, MetSite, represents a fully automatic approach for the detection of metal-binding residue clusters applicable to protein models of moderate quality. The method involves using sequence profile information in combination with approximate structural data. Several neural network classifiers are shown to be able to distinguish metal sites from non-sites with a mean accuracy of 94.5%. The method was demonstrated to identify metal-binding sites correctly in LiveBench targets where no obvious metal-binding sequence motifs were detectable using InterPro. Accurate detection of metal sites was shown to be feasible for low-resolution predicted structures generated using mGenTHREADER where no side-chain information was available. High-scoring predictions were observed for a recently solved hypothetical protein from Haemophilus influenzae, indicating a putative metal-binding site.

Pressing technique and its effect on the quality of Dhaka cheese

Dhaka cheese is a semihard artisanal variety made mainly from bovine milk, using very simple pressing methods. Experimental cheeses were pressed at gauge pressures up to 31 kPa for 12 h at 24 °C and 70% RH. These cheeses were subsequently examined for their compositional, textural and rheological properties plus their microstructures investigated by confocal laser microscopy. The cheese pressed at 15.6 kPa was found to have the best compositional and structural properties.

Cost effectiveness of mitigation measures for water security and water quality in the River Thames catchment: impacts of changing climate, land use and water scarcity

The catchment of the River Thames, the principal river system in southern England, provides the main water supply for London but is highly vulnerable to changes in climate, land use and population. The river is eutrophic with significant algal blooms with phosphorus assumed to be the primary chemical indicator of ecosystem health. In the Thames Basin, phosphorus is available from point sources such as wastewater treatment plants and from diffuse sources such as agriculture. In order to predict vulnerability to future change, the integrated catchments model for phosphorus (INCA-P) has been applied to the river basin and used to assess the cost-effectiveness of a range of mitigation and adaptation strategies. It is shown that scenarios of future climate and land-use change will exacerbate the water quality problems, but a range of mitigation measures can improve the situation. A cost-effectiveness study has been undertaken to compare the economic benefits of each mitigation measure and to assess the phosphorus reductions achieved. The most effective strategy is to reduce fertilizer use by 20% together with the treatment of effluent to a high standard. Such measures will reduce the instream phosphorus concentrations to close to the EU Water Framework Directive target for the Thames.

Evaluating the potential of high pressure high temperature and thermal processing on volatile compounds, nutritional and structural properties of orange and yellow carrots

The present study compares the impact of thermal and high pressure high temperature(HPHT) processing on volatile profile (via a non-targeted headspace fingerprinting) and structural and nutritional quality parameter (via targeted approaches) of orange and yellow carrot purees. The effect of oil enrichment was also considered. Since oil enrichment affects compounds volatility, the effect of oil was not studied when comparing the volatile fraction. For the targeted part, as yellow carrot purees were shown to contain a very low amount of carotenoids, focus was given to orange carrot purees. The results of the non-targeted approach demonstrated HPHT processing exerts a distinct effect on the volatile fractions compared to thermal processing. In addition, different colored carrot varieties are characterized by distinct headspace fingerprints. From a structural point of view, limited or no difference could be observed between orange carrot purees treated with HPHT or HT processes, both for samples without and with oil. From nutritional point of view, only in samples with oil, significant isomerisation of all-trans-β-carotene occurred due to both processing. Overall, for this type of product and for the selected conditions, HPHT processing seems to have a different impact on the volatile profile but rather similar impact on the structural and nutritional attributes compared to thermal processing.

The EU societal awareness of landscape indicator: a review of its meaning, utility and performance across different scales

There is increasing recognition that agricultural landscapes meet multiple societal needs and demands beyond provision of economic and environmental goods and services. Accordingly, there have been significant calls for the inclusion of societal, amenity and cultural values in agri-environmental landscape indicators to assist policy makers in monitoring the wider impacts of land-based policies. However, capturing the amenity and cultural values that rural agrarian areas provide, by use of such indicators, presents significant challenges. The EU social awareness of landscape indicator represents a new class of generalized social indicator using a top-down methodology to capture the social dimensions of landscape without reference to the specific structural and cultural characteristics of individual landscapes. This paper reviews this indicator in the context of existing agri-environmental indicators and their differing design concepts. Using a stakeholder consultation approach in five case study regions, the potential and limitations of the indicator are evaluated, with a particular focus on its perceived meaning, utility and performance in the context of different user groups and at different geographical scales. This analysis supplements previous EU-wide assessments, through regional scale assessment of the limitations and potentialities of the indicator and the need for further data collection. The evaluation finds that the perceived meaning of the indicator does not vary with scale, but in common with all mapped indicators, the usefulness of the indicator, to different user groups, does change with scale of presentation. This indicator is viewed as most useful when presented at the scale of governance at which end users operate. The relevance of the different sub-components of the indicator are also found to vary across regions.