Assembly rules for protein networks derived from phylogenetic-statistical analysis of whole genomes

Background: We report an analysis of a protein network of functionally linked proteins, identified from a phylogenetic statistical analysis of complete eukaryotic genomes. Phylogenetic methods identify pairs of proteins that co-evolve on a phylogenetic tree, and have been shown to have a high probability of correctly identifying known functional links. Results: The eukaryotic correlated evolution network we derive displays the familiar power law scaling of connectivity. We introduce the use of explicit phylogenetic methods to reconstruct the ancestral presence or absence of proteins at the interior nodes of a phylogeny of eukaryote species. We find that the connectivity distribution of proteins at the point they arise on the tree and join the network follows a power law, as does the connectivity distribution of proteins at the time they are lost from the network. Proteins resident in the network acquire connections over time, but we find no evidence that 'preferential attachment' - the phenomenon of newly acquired connections in the network being more likely to be made to proteins with large numbers of connections - influences the network structure. We derive a 'variable rate of attachment' model in which proteins vary in their propensity to form network interactions independently of how many connections they have or of the total number of connections in the network, and show how this model can produce apparent power-law scaling without preferential attachment. Conclusion: A few simple rules can explain the topological structure and evolutionary changes to protein-interaction networks: most change is concentrated in satellite proteins of low connectivity and small phenotypic effect, and proteins differ in their propensity to form attachments. Given these rules of assembly, power law scaled networks naturally emerge from simple principles of selection, yielding protein interaction networks that retain a high-degree of robustness on short time scales and evolvability on longer evolutionary time scales.

The rodent species of the Ifugao Rice Terraces, Philippines - Target or non-target species for management?

We investigated the species diversity and habitat use of rodents in the Ifugao Rice Terraces (IRT), Luzon, Philippines, as a first step in their assessment either as pest species of rice or as potential non-target species of rodent control practice. Trapping was carried out in caneland and forest habitats adjacent to rice cropland using trap lines of 10 - 15 cage-traps. Four trapping rounds, each consisting of 5 nights trapping, were replicated at two sites during the months of May and June. A diverse rodent fauna was recorded, including the non-native pest species, Rattus tanezumi, and the native species, Rattus everetti and Chrotomys mindorensis. Results from trapping and spool-and-line tracking suggested that these native species do not contribute to rice damage and that several may actually be beneficial in the ricefield ecosystem as vermivores that feed on invertebrate pests. Control should therefore be directed at the pest species, R. tanezumi, minimising non-target effects on the non-pest rodent species.

Predicting functional gene links from phylogenetic-statistical analyses of whole genomes

An important element of the developing field of proteomics is to understand protein-protein interactions and other functional links amongst genes. Across-species correlation methods for detecting functional links work on the premise that functionally linked proteins will tend to show a common pattern of presence and absence across a range of genomes. We describe a maximum likelihood statistical model for predicting functional gene linkages. The method detects independent instances of the correlated gain or loss of pairs of proteins on phylogenetic trees, reducing the high rates of false positives observed in conventional across-species methods that do not explicitly incorporate a phylogeny. We show, in a dataset of 10,551 protein pairs, that the phylogenetic method improves by up to 35% on across-species analyses at identifying known functionally linked proteins. The method shows that protein pairs with at least two to three correlated events of gain or loss are almost certainly functionally linked. Contingent evolution, in which one gene's presence or absence depends upon the presence of another, can also be detected phylogenetically, and may identify genes whose functional significance depends upon its interaction with other genes. Incorporating phylogenetic information improves the prediction of functional linkages. The improvement derives from having a lower rate of false positives and from detecting trends that across-species analyses miss. Phylogenetic methods can easily be incorporated into the screening of large-scale bioinformatics datasets to identify sets of protein links and to characterise gene networks.

Studies on the effects of oxadiargyl on direct-seeded rice and Echinochloa crus-galli under drained and flooded conditions

Dose–response experiments were conducted in glasshouse pot experiments to investigate the selectivity of oxadiargyl, a recently introduced herbicide, in direct-seeded rice under both aerobic and anaerobic conditions. Crop sensitivity to oxadiargyl was comparatively greater for wet-seeded (anaerobic) than for dry-seeded rice (aerobic). Likewise, greater efficacy against Echinochloa crus-galli (L.) was also observed under anaerobic conditions. These results indicate greater activity of oxadiargyl under anaerobic conditions, but that application pre-sowing with subsequent flooding would reduce selectivity in wet-seeded rice. The results are discussed in relation to rice production in Mediterranean agriculture.

The role of polyphenolic compounds in the diet as inhibitors of platelet function

Platelets play a substantial role in cardiovascular disease, and for many years there has been a search for dietary components that are able to inhibit platelet function and therefore decrease the risk of cardiovascular disease. Platelets can be inhibited by alcohol, dietary fats and some antioxidants, including a group of compounds, the polyphenols, found in fruits and vegetables. A number of these compounds have been shown to inhibit platelet function both in vitro and in vivo. In the present study the effects of the hydroxycinnamates and the flavonoid quercetin on platelet activation and cell signalling in vitro were investigated. The hydroxycinnamates inhibited platelet function, although not at levels that can be achieved in human plasma by dietary intervention. However, quercetin inhibited platelet aggregation at levels lower than those previously reported. Quercetin was also found to inhibit intracellular Ca mobilisation and whole-cell tyrosine protein phosphorylation in platelets, which are both processes essential for platelet activation. The effect of polyphenols on platelet aggregation in vivo was also investigated. Twenty subjects followed a low-polyphenol diet for 3 d before and also during supplementation. All subjects were supplemented with a polyphenol-rich meal every lunchtime for 5 d. Platelet aggregation and plasma flavonols were measured at baseline and after 5 d of dietary supplementation. Total plasma flavonoids increased significantly after the dietary intervention period (P = 0.001). However, no significant changes in ex vivo platelet aggregation were observed. Further investigation of the effects of individual polyphenolic compounds on platelet function, both in vitro and in vivo, is required in order to elucidate their role in the relationship between diet and the risk of cardiovascular disease.

Vision 2020 - A whole life-cycle information management system for built environments

A whole life-cycle information management vision is proposed, the organizational requirements for the realization of the scenario is investigated. Preliminary interviews with construction professionals are reported. Discontinuities at information transfer throughout life-cycle of built environments are resulting from lack of coordination and multiple data collection/storage practices. A more coherent history of these activities can improve the work practices of various teams by augmenting decision making processes and creating organizational learning opportunities. Therefore, there is a need for unifying these fragmented bits of data to create a meaningful, semantically rich and standardized information repository for built environment. The proposed vision utilizes embedded technologies and distributed building information models. Two diverse construction project types (large one-off design, small repetitive design) are investigated for the applicability of the vision. A functional prototype software/hardware system for demonstrating the practical use of this vision is developed and discussed. Plans for case-studies for validating the proposed model at a large PFI hospital and housing association projects are discussed.

Reliability in the whole life cycle of building systems

Purpose – The purpose of this research is to show that reliability analysis and its implementation will lead to an improved whole life performance of the building systems, and hence their life cycle costs (LCC). Design/methodology/approach – This paper analyses reliability impacts on the whole life cycle of building systems, and reviews the up-to-date approaches adopted in UK construction, based on questionnaires designed to investigate the use of reliability within the industry. Findings – Approaches to reliability design and maintainability design have been introduced from the operating environment level, system structural level and component level, and a scheduled maintenance logic tree is modified based on the model developed by Pride. Different stages of the whole life cycle of building services systems, reliability-associated factors should be considered to ensure the system's whole life performance. It is suggested that data analysis should be applied in reliability design, maintainability design, and maintenance policy development. Originality/value – The paper presents important factors in different stages of the whole life cycle of the systems, and reliability and maintainability design approaches which can be helpful for building services system designers. The survey from the questionnaires provides the designers with understanding of key impacting factors.