Analysis of water patterns in protein kinase binding sites

Deregulation of protein kinases is associated with numerous diseases, making them important targets for drug discovery. The majority of drugs target the catalytic site of these proteins, but due to the high level of similarity within the ATP binding sites of protein kinases, it is often difficult to achieve the required pharmacological selectivity. In this study, we describe the identification and subsequent analysis of water patterns in the ATP binding sites of 171 protein kinase structures, comprising 19 different kinases from various branches of the kinome, and demonstrate that structurally similar binding sites often have significantly different water patterns. We show that the observed variations in water patterns of different, but structurally similar kinases can be exploited in the structure-based design of potent and selective kinase inhibitors.     

The recombinase IntA is required for excision of esp-containing ICEEfm1 in Enterococcus faecium

Comparative genome analysis of Enterococcus faecium recently revealed that a genomic island containing the esp gene, referred to as the esp-containing pathogenicity island (esp PAI), can be transferred by conjugation and contains a partial Tn916-like element and an integrase gene, intA. Here, we characterize the role of intA in the excision of the esp PAI. An intA insertion-deletion mutant in E. faecium E1162 (E1162ΔintA) was constructed and in trans complemented with wild-type intA (E1162ΔintA::pEF30). Circular intermediates (CI) of excised esp PAI were determined using inverse PCR analysis on purified chromosomal DNA from strains E1162, E1162Δesp, E1162ΔintA, and E1162ΔintA::pEF30. In E1162 and E1162Δesp, CI of the esp PAI were detected. No CI were detected in E1162ΔintA, while in the complemented strain E1162ΔintA::pEF30 CI formation was restored, indicating that intA is essential for excision and subsequent mobilization of the esp-containing genomic island in E. faecium. Based on the fact that this island can be mobilized and is self-transmissible, we propose to change the name of the esp PAI to ICEEfm1.     

The spatial scaling of habitat selection by African elephants

1. Understanding and accurately predicting the spatial patterns of habitat use by organisms is important for ecological research, biodiversity conservation and ecosystem management. However, this understanding is complicated by the effects of spatial scale, because the scale of analysis affects the quantification of species-environment relationships. 2. We therefore assessed the influence of environmental context (i.e. the characteristics of the landscape surrounding a site), varied over a large range of scales (i.e. ambit radii around focal sites), on the analysis and prediction of habitat selection by African elephants in Kruger National Park, South Africa. 3. We focused on the spatial scaling of the elephants' response to their main resources, forage and water, and found that the quantification of habitat selection strongly depended on the scales at which environmental context was considered. Moreover, the inclusion of environmental context at characteristic scales (i.e. those at which habitat selectivity was maximized) increased the predictive capacity of habitat suitability models. 4. The elephants responded to their environment in a scale-dependent and perhaps hierarchical manner, with forage characteristics driving habitat selection at coarse spatial scales, and surface water at fine spatial scales. 5. Furthermore, the elephants exhibited sexual habitat segregation, mainly in relation to vegetation characteristics. Male elephants preferred areas with high tree cover and low herbaceous biomass, whereas this pattern was reversed for female elephants. 6. We show that the spatial distribution of elephants can be better understood and predicted when scale-dependent species-environment relationships are explicitly considered. This demonstrates the importance of considering the influence of spatial scale on the analysis of spatial patterning in ecological phenomena.     

Contrast in chloride exclusion between two grapevine genotypes and its variation in their hybrid progeny

Potted grapevines of 140 Ruggeri (Vitis berlandieri × Vitis rupestris), a good Cl(-) excluder, and K 51-40 (Vitis champinii × Vitis riparia 'Gloire'), a poor Cl(-) excluder, and of a family obtained by crossing the two genotypes, were used to examine the inheritance of Cl(-) exclusion. Rooted leaves were then used to further investigate the mechanism for Cl(-) exclusion in 140 Ruggeri. In both a potting mix trial (plants watered with 50 mM Cl(-)) and a solution culture trial (plants grown in 25 mM Cl(-)), the variation in Cl(-) accumulation was continuous, indicating multiple rather than single gene control for Cl(-) exclusion between hybrids within the family. Upper limits of 42% and 35% of the phenotypic variation in Cl(-) concentration could be attributed to heritable sources in the potting mix and solution culture trials, respectively. Chloride transport in roots of rooted leaves of both genotypes appeared to be via the symplastic pathway, since addition of 8-hydroxy-1,3,6-pyrenetrisulphonic acid (PTS), an apoplastic tracer, revealed no obvious PTS fluorescence in the laminae of either genotype, despite significant accumulation of Cl(-) in laminae of K 51-40 during the PTS uptake period. There was no significant difference in either unidirectional (36)Cl(-) flux (10 min) or (36)Cl(-) uptake (3 h) into roots of rooted leaves exposed to 5, 10, or 25 mM Cl(-). However, the percentage of (36)Cl(-) transported to the lamina (3 h) was significantly lower in 140 Ruggeri than in K 51-40, supporting reduced Cl(-) loading into xylem and implicating the root stele in the Cl(-) exclusion mechanism.     

Synthesis and evaluation of novel macrocyclic antifungal peptides

Echinocandins are a novel class of macrocyclic antifungal peptides that act by inhibiting the β-(1,3)-D-glucan synthase complex, which is not present in mammalian cells. Due to the large number of hydroxyl groups present in these complex macrocyclic lipopeptides, most structure-activity relationship studies have relied upon semisynthetic derivatives. In order to probe the influence of the cyclic peptide backbone on the antifungal activity we developed a successful strategy for the synthesis of novel echinocandins analogues by on-resin ring closing metathesis or disulfide formation. The specific minimum inhibitory activity of each mimic was determined against Candida albicans. Our results indicate that ring size is an important factor for antifungal activity.     

Microsatellite repeat instability and neurological disease

Over 20 unstable microsatellite repeats have been identified as the cause of neurological disease in humans. The repeat nucleotide sequences, their location within the genes, the ranges of normal and disease‐causing repeat length and the clinical outcomes differ. Unstable repeats can be located in the coding or the non‐coding region of a gene. Different pathogenic mechanisms that are hypothesised to underlie the diseases are discussed. Evidence is given both from studies in simple model systems and from studies on human material and in animal models. Since somatic instability might affect the clinical outcome, this is briefly touched on. Available data and theories on the timing and mechanisms of the repeat instability itself are discussed, along with factors that have been observed to affect instability. Finally, the question of why the often harmful unstable repeats have been maintained throughout evolution is addressed.     

Modeling Basic Industries in the Australian Stocks and Flows Framework

The Australian stocks and flows framework (ASFF) is a tool for establishing a coherent historical picture of the Australian physical economy and for testing long-term future scenarios (up to 2050 or even 2100). These scenarios can be used to investigate the long-term physical consequences of current and future choices affecting the physical dimensions of sustainability. In this article we describe the methodology for and construction of a key component of ASFF: a dynamic physical input-output model of material flows in the basic industries.
The materials model in ASFF describes physical flows and their transformation by industrial processes. The model's structure permits scenario analysis of long-term technological change by permitting time-varying input-output coefficients and vintage models of capital stocks. As a consequence, the model contains a large number of parameters, which can be left at default settings or adjusted as the modeler sees fit, in order to simulate the widest possible range of physically realizable scenarios. The materials model is built using a methodology that integrates bottom-up process analysis with top-down statistics on material and energy flows. We present some examples showing how the materials model has been implemented to model Australian heavy industries. Several possibilities for further developing the materials model are also described.