Impact of land cover changes on the South African climate

The Joint UK Land Environmental Simulator (JULES) was run offline to investigate the sensitivity of land surface type changes over South Africa. Sensitivity tests were made in idealised experiments where the actual land surface cover is replaced by a single homogeneous surface type. The vegetation surface types on which some of the experiments were made are static. Experimental tests were evaluated against the control. The model results show among others that the change of the surface cover results in changes of other variables such as soil moisture, albedo, net radiation and etc. These changes are also visible in the spin up process. The model shows different surfaces spinning up at different cycles. Because JULES is the land surface model of Unified Model, the results could be more physically meaningful if it is coupled to the Unified Model.

Influence of temperature on the motility of Pseudomonas oryzihabitans and control of Globodera rostochiensis

The motility and efficacy of Pseudomonas oryzihabitans as a biocontrol agent against the potato cyst nematode Globodera rostochiensis were studied with respect to temperature. The influence of soil moisture on bacterial movement was also tested. In a closed container trial, P. oryzihabitans significantly reduced invasion of second stage juveniles (J2) of G. rostochiensis in potato roots, its effect being more marked at 25 and 21 degreesC than at 17 degreesC. P. oryzihabitans motility in vitro was optimal at 26 degreesC and inhibited at temperatures below 18 degreesC. In soil, both temperature and matric potential affected bacterial movement. At 16 degreesC its movement and survival were suppressed, but they were unaffected at 25 degreesC. At both temperatures the biocontrol agent moved faster in the wetter (- 0.03 MPa) than in the drier soil (- 0.1 MPa). These results suggest that temperature is a key factor in determining the potential of P. or.yzihabitans as a biocontrol agent. (C) 2003 Elsevier Science Ltd. All rights reserved.

Formulation and delivery of the bacterial antagonist Bacillus subtilis for management of lentil vascular wilt caused by Fusarium oxysporum f. sp lentis

Different formulations of Bacillus subtilis were prepared using standard laboratory protocols. Bacillus subtilis survived in glucose and talc powders at 8.6 and 7.8 log(10) CFU/g, respectively, for 1 year of storage at room temperature compared with 3.5 log(10) CFU/g on a peat formulation. Glasshouse experiments using soil and seed treatments were conducted to test the efficacy of B. subtilis for protecting lentil against the wilt disease caused by Fusariumoxysporum f. sp. lentis. Seed treatments with formulations of B. subtilis on glucose, talc and peat significantly enhanced its biocontrol activity against Fusarium compared with a treatment in which spores were applied directly to seed. The formulations decreased disease severity by reducing colonization of plants by the pathogen, promoting their growth and increased the dry weight of lentil plants. Of these treatments the glucose and talc-based powder formulations were more effective than the peat formulation and the spore application without a carrier. It was shown that the B. subtilis spores applied with glucose were viable for longer than those applied with other carriers. Seed treatment with these formulated spores is an effective delivery system that can provide a conducive environment for B. subtilis to suppress vascular wilt disease on lentil and has the potential for utilization in commercial field application.

The survival advantage of milk and dairy consumption: An overview of evidence from cohort studies of vascular diseases, diabetes and cancer

Objectives: To conduct it detailed evaluation, with meta-analyses, of the published evidence on milk and dairy consumption and the incidence of vascular diseases and diabetes. Also to summarise the evidence on milk and dairy consumption and cancer reported by the World Cancer Research Fund and then to consider the relevance of milk and dairy consumption to survival in the UK, a typical Western community. Finally, published evidence on relationships with whole milk and fat-reduced milks was examined. Methods: Prospective cohort studies of vascular disease and diabetes with baseline data on milk or dairy consumption and a relevant disease outcome were identified by searching MEDLINE, and reference lists in the relevant published reports. Meta-analyses of relationships in these reports were conducted. The likely effect of milk and dairy consumption on survival was then considered, taking into account the results of published overviews of relationships of these foods with cancer. Results: From meta-analysis of 15 studies the relative risk of stroke and/or heart disease in subjects with high milk or dairy consumption was 0.84 (95% CI 0.76, 0,93) and 0.79 (0.75, 0.82) respectively, relative to the risk in those with low consumption. Four studies reported incident diabetes as an outcome, and the relative risk in the Subjects with the highest intake of milk or diary foods was 0.92 (0.86, 0.97). Conclusions: Set against the proportion of total deaths attributable to the life-threatening diseases in the UK, vascular disease, diabetes and cancer, the results of meta-analyses provide evidence of an overall survival advantage from the consumption of milk and dairy foods.

Biodiversity of Collembola in urban soils and the use of Folsomia candida to assess soil 'quality'

The effects of metal contamination on natural populations of Collembola in soils from five sites in the Wolverhampton area ( West Midlands, England) were examined. Analysis revealed that metal concentrations were elevated above background levels at all sites. One location in particular (Ladymoor, a former smelting site) was highly contaminated with Cd, Cu, Pb and Zn at more than 20 times background levels. Biodiversity indices ( Shannon - Weiner, Simpson index, Margalef index, alpha index, species richness, Shaneven ( evenness) and Berger - Parker dominance) were calculated. Of these indices, estimates of species richness and evenness were most effective at highlighting the differences between the Collembola communities. Indeed, the highest number of species were found at the most contaminated site, although the Collembola population also had a comparatively low evenness value, with just two species dominating. The number of individuals per species were allocated into geometric classes and plotted against the cumulative number of species as a percentage. At Ladymoor, there were more geometric classes, and the slope of the line was shallower than at the other four sites. This characteristic is a feature of polluted sites, where a few species are dominant and most species are rare. The Ladymoor soil also had a dominance of Isotomurus palustris, and was the only site in which Ceratophysella denticulata was found. Previous studies have shown that these two species are often found in sites subject to high metal contamination. Survival and reproduction of the "standard'' test springtail, Folsomia candida (Willem), were determined in a 4 week exposure test to soils from all five sites. Mortality was significantly increased in adults and reproduction significantly lower in the Ladymoor soil in comparison to the other four sites. This study has shown that severe metal contamination can be related to the population structure of Collembola in the field, and performance of F. candida ( in soils from such sites) in the laboratory.

Effect of replacing grass silage with maize silage in the diet on bovine milk fatty acid composition

Even though extensive research has examined the role of nutrition on milk fat composition, there is less information on the impact of forages on milk fatty acid (FA) composition. In the current study, the effect of replacing grass silage (GS) with maize silage (MS) as part of a total mixed ration on animal performance and milk FA composition was examined using eight multiparous mid-lactation cows in a replicated 4 X 4 Latin square with 28-day experimental periods. Four treatments comprised the stepwise replacement of GS with MS (0, 160, 334 and 500 g/kg dry matter (DM)) in diets containing a 54:46 forage: concentrate ratio on a DM basis. Replacing GS with MS increased (P < 0.001) the DM intake, milk yield and milk protein content. Incremental replacement of GS with MS in the diet enhanced linearly (P < 0.001) the proportions of 6:0-14:0, decreased (P < 0.01) the 16:0 concentrations, but had no effect on the total milk fat saturated fatty acid content. Inclusion of MS altered the distribution of trans-18:1 isomers and enhanced (P < 0.05) total trans monounsaturated fatty acid and total conjugated linoleic acid content. Milk total n-3 polyunsaturated fatty acid (PUFA) content decreased with higher amounts of MS in the diet and n-6 PUFA concentration increased, leading to an elevated n-6: n-3 PUFA ratio. Despite some beneficial changes associated with the replacement of GS with MS, the overall effects on milk FA composition would not be expected to substantially improve long-term human health. However the role of forages on milk fat composition must also be balanced against the increases in total milk and protein yield on diets containing higher proportions of MS.

Using near infrared reflectance spectroscopy (NIRS) to predict the biological parameters of maize silage

The microbial fermentability, ruminal degradability and digestibility of 48 maize silages were determined using in vitro gas production (GP), in situ degradability and in vitro digestibility procedures. The silages were produced from forage maize harvested throughout the summer of 1998, and represent a wide range of physiological maturities. Large variations among samples were observed for all biological parameters, with the exception of in vitro digestibility and the asymptote of in vitro GP. The potential of near infrared reflectance spectroscopy (NIRS) to predict the biological parameters measured was determined by regression of the biological data against the respective spectral profile. NIRS demonstrated only a moderate ability (R-2 > 0.60-0.80) to predict in vitro digestibility, modelled kinetics of gas production (excluding the asymptote of gas production) and the modelled ruminally soluble dry matter (DM) fraction. Calibration statistics for remaining biological parameters were unacceptably poor (R-2 = 0.60). (C) 2004 Elsevier B.V. All rights reserved.

Features of the Atlantic diet and its healthiness: Theory and evidence from social science

In order to understand diets, why and how they change and can be influenced, it is important to understand how food choices are made. The has been the subject of, considerable study within many of the social science disciplines and the humanities. The paper draws on the theoretical and empirical work of psychologists, sociologists, economists, market researchers, anthropologists, geographers and historians to understand better the forces behind food choice, derive some general empirical messages from the literature, to shed light on food choice in a European context and to address the question of whether there is, or has been, a recognisably Atlantic diet. The paper proceeds to analyse the characteristics of the food consumption patterns in the Atlantic diet countries, examines whether their food consumption patterns are homogenous (i.e. similar across the countries of this group), whether they are specific (i.e. different from the ones in other country groups) and finally evaluates the nutritional composition of the Atlantic diet against the WHO/FAO recommendations for a healthy and wholesome diet.

Developments in the Doha Round and WTO dispute settlement: some implications for EU agricultural policy

Progress in the Doha Round is assessed against the changes to the common agricultural policy (CAP) brought about by the Fischler reforms of 2003-2004, and that proposed for sugar. An elimination of export subsidies could place EU exports of processed foods at a competitive disadvantage because of high sugar and milk prices. Provided the single payment scheme falls within the green box, the likely new limits on domestic support should not be problematic for the post-Fischler CAP. However, an ambitious market access package could open up EU markets and bring pressure for further reform. If there is no Doha agreement, existing provisions will continue to apply, but without the protection of the Peace Clause; and increased litigation is likely. Further CAP reform is to be expected.

Implications for food production, land use and rural development of the European Union's Single Farm Payment: Indications from a survey of farmers' intentions in Germany, Portugal and the UK

The 2003 reform of the European Union's (EU) Common Agricultural Policy introduced a decoupled income support for farmers called the Single Farm Payment (SFP). Concerns were raised about possible future land use and production changes and their impact on rural communities. Here, such concerns are considered against the workings of the SFP in three EU Member States. Various quantitative studies that have determined the likely impact of the SFP within the EU and the study countries are reviewed. We present the results of a farm survey conducted in the study countries in which farmers' responses to a decoupling scenario similar to the SFP were sought. We found that little short-term change was proposed in the three, rather different, study countries with only 30% of the farmers stating that they would alter their mix of farm activities. Furthermore, less than 30% of all respondents in each country would idle any land under decoupling. Of those who would adopt a new activity, the most popular choices were forestry, woodland and non-food crops. (c) 2007 Elsevier Ltd. All rights reserved.

The impact of Solanum elaeagnifolium, an invasive plant in the Mediterranean, on the flower visitation and seed set of the native co-flowering species Glaucium flavum

We examined the effect of the invasive Solanum elaeagnifolium (Solanaceae) on flower visitation patterns and seed set of the co-flowering native Glaucium flavum (Papaveraceae). We observed flowering G. flavum plants in invaded and uninvaded sites and found that G. flavum flowers in uninvaded sites received significantly more total visits. In addition, we hand-pollinated flowers on plants of G. flavum with (i) pure conspecific pollen, (ii) pure S. elaeagnifolium pollen and (iii) three different mixtures of the two types of pollen (containing 25, 50 and 75% invasive pollen). As a control, flowers were left unmanipulated or were permanently bagged. Seed set did not differ significantly between flowers receiving pollen mixtures and pure conspecific pollen. However, in the open pollination treatment, seed set was significantly lower than in the 100% conspecific pollen treatment, which suggests pollen limitation. Bagged flowers had very low seed set. G. flavum was generally resilient against the deposition of S. elaeagnifolium pollen.

Rapid model quality assessment for protein structure predictions using the comparison of multiple models without structural alignments

MOTIVATION: The accurate prediction of the quality of 3D models is a key component of successful protein tertiary structure prediction methods. Currently, clustering or consensus based Model Quality Assessment Programs (MQAPs) are the most accurate methods for predicting 3D model quality; however they are often CPU intensive as they carry out multiple structural alignments in order to compare numerous models. In this study, we describe ModFOLDclustQ - a novel MQAP that compares 3D models of proteins without the need for CPU intensive structural alignments by utilising the Q measure for model comparisons. The ModFOLDclustQ method is benchmarked against the top established methods in terms of both accuracy and speed. In addition, the ModFOLDclustQ scores are combined with those from our older ModFOLDclust method to form a new method, ModFOLDclust2, that aims to provide increased prediction accuracy with negligible computational overhead. RESULTS: The ModFOLDclustQ method is competitive with leading clustering based MQAPs for the prediction of global model quality, yet it is up to 150 times faster than the previous version of the ModFOLDclust method at comparing models of small proteins (<60 residues) and over 5 times faster at comparing models of large proteins (>800 residues). Furthermore, a significant improvement in accuracy can be gained over the previous clustering based MQAPs by combining the scores from ModFOLDclustQ and ModFOLDclust to form the new ModFOLDclust2 method, with little impact on the overall time taken for each prediction. AVAILABILITY: The ModFOLDclustQ and ModFOLDclust2 methods are available to download from: http://www.reading.ac.uk/bioinf/downloads/ CONTACT: l.j.mcguffin@reading.ac.uk.

Field evaluation of systemic inducing resistance chemicals at different growth stages for the control of apple (Venturia inaequalis) and pear (Venturia pirina) scab

Two field trials were conducted using established apple (Malus cv. Golden Delicious) and pear (Pyrus communis 'Williams' Bon Chretien') to assess the efficacy of three commercially available systemic inducing resistance (SIR) products, Messenger (a.i. Harpin protein), Phoenix (a.i. Potassium phosphite) and Rigel (a.i. Salicylic acid derivative) applied at four different growth stages of tree development (bud break, green cluster, 90% petal fall, early fruitlet) against the foliar pathogens Venturia inaequalis and Venturia pirina which cause apple and pear scab respectively. A conventional synthetic fungicide (penconazole) used within the UK for apple and pear scab control was included for comparison. Little efficacy as scab protectants was demonstrated when each SIR product and penconazole was applied at only two growth stages (bud break, green cluster). However when the above compounds were applied at three or more growth stages efficacy as scab protectants was confirmed. The synthetic fungicide penconazole provided greatest protection against apple and pear scab in both the 2006 and 2007 field trials. There was little difference in the magnitude of scab protection conferred by each SIR agent. Results suggest application of at least three sprays during bud break to early fruitlet formation with an appropriate SIR agent may provide a useful addition to existing methods of apple and pear scab management under field conditions. (C) 2009 Published by Elsevier Ltd.

Nuclear magnetic resonance structure of the nucleic acid-binding domain of severe acute respiratory syndrome coronavirus nonstructural protein 3

The nuclear magnetic resonance (NMR) structure of a globular domain of residues 1071 to 1178 within the previously annotated nucleic acid-binding region (NAB) of severe acute respiratory syndrome coronavirus nonstructural protein 3 (nsp3) has been determined, and N- and C-terminally adjoining polypeptide segments of 37 and 25 residues, respectively, have been shown to form flexibly extended linkers to the preceding globular domain and to the following, as yet uncharacterized domain. This extension of the structural coverage of nsp3 was obtained from NMR studies with an nsp3 construct comprising residues 1066 to 1181 [ nsp3(1066-1181)] and the constructs nsp3(1066-1203) and nsp3(1035-1181). A search of the protein structure database indicates that the globular domain of the NAB represents a new fold, with a parallel four-strand beta-sheet holding two alpha-helices of three and four turns that are oriented antiparallel to the beta-strands. Two antiparallel two-strand beta-sheets and two 3(10)-helices are anchored against the surface of this barrel-like molecular core. Chemical shift changes upon the addition of single-stranded RNAs (ssRNAs) identified a group of residues that form a positively charged patch on the protein surface as the binding site responsible for the previously reported affinity for nucleic acids. This binding site is similar to the ssRNA-binding site of the sterile alpha motif domain of the Saccharomyces cerevisiae Vts1p protein, although the two proteins do not share a common globular fold.

Mapping the immune response to the outer domain of a human immunodeficiency virus-1 clade C gp120

The outer domain (OD) of human immunodeficiency virus (HIV)-1 gp120 represents an attractive, if difficult, target for a beneficial immune response to HIV infection. Unlike the entire gp120, the OD is structurally stable and contains the surfaces that interact with both the primary and secondary cellular receptors. The primary strain-specific neutralizing target, the V3 loop, lies within the OD, as do epitopes for two cross-reactive neutralizing monoclonal antibodies (mAbs), b12 and 2G12, and the contact sites for a number of inhibitory lectins. The OD is poorly immunogenic, at least in the context of complete gp120, but purposeful OD immunization can lead to a substantial antibody response. Here, we map the antibody generated following immunization with a clade C OD. In contrast to published data for the clade B OD, the majority of the polyclonal response to the complete clade C OD is to the V3 loop; deletion of the loop substantially reduces immunogenicity. When the loop sequence was substituted for the epitope for 2F5, a well-characterized human cross-neutralizing mAb, a polyclonal response to the epitope was generated. A panel of mAbs against the clade C OD identified two mAbs that reacted with the loop and were neutralizing for clade C but not B isolates. Other mAbs recognized both linear and conformational epitopes in the OD. We conclude that, as for complete gp120, V3 immunodominance is a property of OD immunogens, that the responses can be neutralizing and that it could be exploited for the presentation of other epitopes.