FunFOLDQA: a quality assessment tool for protein-ligand binding site residue predictions

The estimation of prediction quality is important because without quality measures, it is difficult to determine the usefulness of a prediction. Currently, methods for ligand binding site residue predictions are assessed in the function prediction category of the biennial Critical Assessment of Techniques for Protein Structure Prediction (CASP) experiment, utilizing the Matthews Correlation Coefficient (MCC) and Binding-site Distance Test (BDT) metrics. However, the assessment of ligand binding site predictions using such metrics requires the availability of solved structures with bound ligands. Thus, we have developed a ligand binding site quality assessment tool, FunFOLDQA, which utilizes protein feature analysis to predict ligand binding site quality prior to the experimental solution of the protein structures and their ligand interactions. The FunFOLDQA feature scores were combined using: simple linear combinations, multiple linear regression and a neural network. The neural network produced significantly better results for correlations to both the MCC and BDT scores, according to Kendall’s τ, Spearman’s ρ and Pearson’s r correlation coefficients, when tested on both the CASP8 and CASP9 datasets. The neural network also produced the largest Area Under the Curve score (AUC) when Receiver Operator Characteristic (ROC) analysis was undertaken for the CASP8 dataset. Furthermore, the FunFOLDQA algorithm incorporating the neural network, is shown to add value to FunFOLD, when both methods are employed in combination. This results in a statistically significant improvement over all of the best server methods, the FunFOLD method (6.43%), and one of the top manual groups (FN293) tested on the CASP8 dataset. The FunFOLDQA method was also found to be competitive with the top server methods when tested on the CASP9 dataset. To the best of our knowledge, FunFOLDQA is the first attempt to develop a method that can be used to assess ligand binding site prediction quality, in the absence of experimental data.

Comparison of MODIS broadband albedo over an agricultural site with ground measurements and values derived from Earth observation data at a range of spatial scales

Land surface albedo is dependent on atmospheric state and hence is difficult to validate. Over the UK persistent cloud cover and land cover heterogeneity at moderate (km-scale) spatial resolution can also complicate comparison of field-measured albedo with that derived from instruments such as the Moderate Resolution Imaging Spectrometer (MODIS). A practical method of comparing moderate resolution satellite-derived albedo with ground-based measurements over an agricultural site in the UK is presented. Point measurements of albedo made on the ground are scaled up to the MODIS resolution (1 km) through reflectance data obtained at a range of spatial scales. The point measurements of albedo agreed in magnitude with MODIS values over the test site to within a few per cent, despite problems such as persistent cloud cover and the difficulties of comparing measurements made during different years. Albedo values derived from airborne and field-measured data were generally lower than the corresponding satellite-derived values. This is thought to be due to assumptions made regarding the ratio of direct to diffuse illumination used when calculating albedo from reflectance. Measurements of albedo calculated for specific times fitted closely to the trajectories of temporal albedo derived from both Systeme pour l'Observation de la Terre (SPOT) Vegetation (VGT) and MODIS instruments.

10,000 years in the life of the river Wandle: excavations at the former Vinamul site, Butter Hill, Wallington

Archaeological excavations alongside the river Wandle in Wallington produced evidence of the environmental history and human exploitation of the area. The recovery of a large assemblage of struck flint provided information on the nature of the prehistoric activities represented, while a detailed environmental archaeological programme permitted an examination of both the local sediment successions and thus an opportunity to reconstruct the environmental history of the site. The site revealed a complex sedimentary sequence deposited in riverine conditions, commencing during the early Holocene (from c 10,000 years before present) and continuing through the late Holocene (c last 3000 years). Large flint nodules were washed by the river onto the site where they were procured and worked by Mesolithic and Bronze Age communities. Potentially usable nodules had been tested, and suitable pieces completely reduced, while the majority of useful flakes and blades had been removed for use elsewhere. Small numbers of retouched pieces, such as scrapers and piercers, indicate that domestic activities took place nearby. By the Saxon period the site had begun to stabilise, although it remained marshy and probably peripheral to habitation. Two pits from this period were excavated, one of which contained an antler pick. A small quantity of cereal grain also suggests that cultivated land lay in the vicinity of the site. During the 19th century a mill race was dug across the site, redirecting water from the river Wandle, which resulted in episodic flooding.

Identification of critical residues in the active site of porcine membrane-bound aminopeptidase P

The membrane-bound form of mammalian aminopeptidase P (AP-P; EC 3.4. 11.9) is a mono-zinc-containing enzyme that lacks any of the typical metal binding motifs found in other zinc metalloproteases. To identify residues involved in metal binding and catalysis, sequence and structural information was used to align the sequence of porcine membrane-bound AP-P with other members of the peptidase clan MG, including Escherichia coli AP-P and methionyl aminopeptidases. Residues predicted to be critical for activity were mutated and the resultant proteins were expressed in COS-1 cells. Immunoelectrophoretic blot analysis was used to compare the levels of expression of the mutant proteins, and their ability to hydrolyze bradykinin and Gly-Pro-hydroxyPro was assessed. Asp449, Asp460, His523, Glu554, and Glu568 are predicted to serve as metal ion ligands in the active site, and mutagenesis of these residues resulted in fully glycosylated proteins that were catalytically inactive. Mutation of His429 and His532 also resulted in catalytically inactive proteins, and these residues, by analogy with E. coli AP-P, are likely to play a role in shuttling protons during catalysis. These studies indicate that mammalian membrane-bound AP-P has an active-site configuration similar to that of other members of the peptidase clan MG, which is compatible with either a dual metal ion model or a single metal ion in the active site. The latter model is consistent, however, with the known metal stoichiometry of both the membrane-bound and cytosolic forms of AP-P and with a recently proposed model for methionyl aminopeptidase.

Implementing ‘Site BIM’: a case study of ICT innovation on a large hospital project

Numerous Building Information Modelling (BIM) tools are well established and potentially beneficial in certain uses. However, issues of adoption and implementation persist, particularly for on-site use of BIM tools in the construction phase. We describe an empirical case-study of the implementation of an innovative ‘Site BIM’ system on a major hospital construction project. The main contractor on the project developed BIM-enabled tools to allow site workers using mobile tablet personal computers to access design information and to capture work quality and progress data on-site. Accounts show that ‘Site BIM’, while judged to be successful and actively supporting users, was delivered through an exploratory and emergent development process of informal prototyping. Technical IT skills were adopted into the construction project through personal relationships and arrangements rather than formal processes. Implementation was driven by construction project employees rather than controlled centrally by the corporate IT function.

Identifying time lags in the restoration of grassland butterfly communities: a multi-site assessment

Although grasslands are crucial habitats for European butterflies, large-scale declines in quality and area have devastated many species. Grassland restoration can contribute to the recovery of butterfly populations, although there is a paucity of information on the long-term effects of management. Using eight UK data sets (9-21 years), we investigate changes in restoration success for (1) arable reversion sites, were grassland was established on bare ground using seed mixtures, and (2) grassland enhancement sites, where degraded grasslands are restored by scrub removal followed by the re-instigation of cutting/grazing. We also assessed the importance of individual butterfly traits and ecological characteristics in determining colonisation times. Consistent increases in restoration success over time were seen for arable reversion sites, with the most rapid rates of increase in restoration success seen over the first 10 years. For grasslands enhancement there were no consistent increases in restoration success over time. Butterfly colonisation times were fastest for species with widespread host plants or where host plants established well during restoration. Low mobility butterfly species took longer to colonise. We show that arable reversion is an effective tool for the management of butterfly communities. We suggest that as restoration takes time to achieve, its use as a mitigation tool against future environmental change (i.e. by decreasing isolation in fragmented landscapes) needs to take into account such time lags.

Preferred orientation in an angled intercalation site of a chloro-substituted lambda- [Ru(TAP)2(dppz)]2+ complex bound to d(TCGGCGCCGA)2

The crystal structure of the ruthenium DNA ‘light-switch’ complex -[Ru(TAP)2(11-Cl-dppz)]2+ (TAP = tetraazaphenanthrene, dppz = dipyrido[3,2-a':2',3'-c]phenazine)) bound to the oligonucleotide duplex d(TCGGCGCCGA)2 is reported. The synthesis of the racemic ruthenium complex is described for the first time, and the racemate was used in this study. The crystal structure, at atomic resolution (1.0 Å), shows one ligand as a wedge in the minor groove, resulting in the 51 kinking of the double helix, as with the parent lambda-[Ru(TAP)2(dppz)]2+. Each complex binds to one duplex by intercalation of the dppz ligand and also by semi-intercalation of one of the orthogonal TAP ligands into a second symmetrically equivalent duplex. The 11-Cl substituent binds with the major component (66%) oriented with the 11-chloro substituent on the purine side of the terminal step of the duplex.

Persistence and photochemical decay of springtime total ozone anomalies in the Canadian Middle Atmosphere Model

The persistence and decay of springtime total ozone anomalies over the entire extratropics (midlatitudes plus polar regions) is analysed using results from the Canadian Middle Atmosphere Model (CMAM), a comprehensive chemistry-climate model. As in the observations, interannual anomalies established through winter and spring persist with very high correlation coefficients (above 0.8) through summer until early autumn, while decaying in amplitude as a result of photochemical relaxation in the quiescent summertime stratosphere. The persistence and decay of the ozone anomalies in CMAM agrees extremely well with observations, even in the southern hemisphere when the model is run without heterogeneous chemistry (in which case there is no ozone hole and the seasonal cycle of ozone is quite different from observations). However in a version of CMAM with strong vertical diffusion, the northern hemisphere anomalies decay far too rapidly compared to observations. This shows that ozone anomaly persistence and decay does not depend on how the springtime anomalies are created or on their magnitude, but reflects the transport and photochemical decay in the model. The seasonality of the long-term trends over the entire extratropics is found to be explained by the persistence of the interannual anomalies, as in the observations, demonstrating that summertime ozone trends reflect winter/spring trends rather than any change in summertime ozone chemistry. However this mechanism fails in the northern hemisphere midlatitudes because of the relatively large impact, compared to observations, of the CMAM polar anomalies. As in the southern hemisphere, the influence of polar ozone loss in CMAM increases the midlatitude summertime loss, leading to a relatively weak seasonal dependence of ozone loss in the Northern Hemisphere compared to the observations.

Safe construction through design: perspectives from the site team

How does the work of designers impact on the safety of operatives at the construction site? Safety research and policy emphasize the importance of designing for safe construction, yet the interface between design and construction is poorly understood: accidents have multiple causes making it hard to establish causal links between design choices and safety outcomes. An in-depth case study of a major station project examines how professionals on the construction site perceive and manage the safety challenges of a building design. Analyses reveal understandings that, on the project studied, design has an impact on safety because of: (1) the timing of design work, where the volume of late design changes increased the difficulty of planning safe procedures, e.g. for working at height, lifting heavy items, refurbishing and demolishing old buildings; and (2) inputs from design stakeholders with insufficient practical knowledge of construction and operation required unplanned work-arounds, e.g. to coordinate different sub-systems, provide maintenance access, and manage loads during construction. These findings suggest that safety suffers where projects are under-designed, and that alongside regulation, there is a need for robust management attention to the contractual structures, incentives, processes and tools that enable clients and designers to understand material practices of construction and operation.

Cloud optical and microphysical properties derived from ground-based and satellite sensors over a site in the Yangtze Delta region

Comprehensive surface-based retrievals of cloud optical and microphysical properties were made at Taihu, a highly polluted site in the central Yangtze Delta region, during a research campaign from May 2008 to December 2009. Cloud optical depth (COD), effective radius (Re), and liquid water path (LWP) were retrieved from measurements made with a suite of ground-based and spaceborne instruments, including an Analytical Spectral Devices spectroradiometer, a multi␣lter rotating shadowband radiometer, a multichannel microwave radiometer profiler, and the Moderate Resolution Imaging Spectroradiometer (MODIS) on Terra and Aqua satellites. Retrievals from zenith radiance measurements capture better the temporal variation of cloud properties than do retrievals from hemispherical fluxes. Annual mean LWP, COD, and Re are 115.8 ± 90.8 g/m2, 28.5 ± 19.2, and 6.9 ± 4.2 microns. Over 90% of LWP values are less than 250 g/m2. Most of the COD values (>90%) fall between 5 and 60, and ~80% of Re values are less than 10 microns. Maximum (minimum) values of LWP and Re occur in summer (winter); COD is highest in winter and spring. Raining and nonraining clouds have signi␣cant differences in LWP, COD, and Re. Rainfall frequency is best correlated with LWP, followed by COD and Re. Cloud properties retrieved from multiple ground-based instruments are also compared with those from satellite retrievals. On average, relative to surface retrievals, mean differences of satellite retrievals in cloud LWP, COD, and Re were -33.6 g/m2 (-26.4%), -5.8 (-31.4%), and 2.9 ␣m (29.3%) for 11 MODIS-Terra overpasses and -43.3 g/m2 (-22.3%), -3.0 (-10.0%), and -1.3 ␣m (-12.0%) for 8 MODIS-Aqua overpasses, respectively. These discrepancies indicate that MODIS cloud products still suffer from large uncertainties in this region.

Settlement patterns in the late Mesolithic of western Scotland: the implications of Bayesian analysis of radiocarbon dates and inter-site technological comparisons

The character of settlement patterns within the late Mesolithic communities of north-west Europe is a topic of substantial debate. An important case study concerns the five shell middens on the island of Oronsay, Inner Hebrides, western Scotland. Two conflicting interpretations have been proposed: the evidence from seasonality indicators and stable isotope analysis of human bones has been used to support a model of year-round settlement on this small island; alternatively, the middens have been interpreted as resulting from short-term intermittent visits to Oronsay within a regionally mobile settlement pattern. We contribute to this debate by describing Storakaig, a newly discovered site on the nearby island of Islay, undertaking a Bayesian chronological analysis and providing evidence for technological continuity between Oronsay and sites elsewhere in the region. While this new evidence remains open to alternative interpretation, we suggest that it makes regional mobility rather than year-round settlement on Oronsay a more viable interpretation for the Oronsay middens. Our analysis also confirms the likely overlap of the late Mesolithic with the earliest Neolithic within western Scotland.