Automatic prediction of functional site regions in low-resolution protein structures

World-wide structural genomics initiatives are rapidly accumulating structures for which limited functional information is available. Additionally, state-of-the art structural prediction programs are now capable of generating at least low resolution structural models of target proteins. Accurate detection and classification of functional sites within both solved and modelled protein structures therefore represents an important challenge. We present a fully automatic site detection method, FuncSite, that uses neural network classifiers to predict the location and type of functionally important sites in protein structures. The method is designed primarily to require only backbone residue positions without the need for specific side-chain atoms to be present. In order to highlight effective site detection in low resolution structural models FuncSite was used to screen model proteins generated using mGenTHREADER on a set of newly released structures. We found effective metal site detection even for moderate quality protein models illustrating the robustness of the method.

Variation in the sensitivity of Callosobruchus (Coleoptera: Bruchidae) acetylcholinesterase to the organophosphate insecticide malaoxon: effect of species, geographical strain and food type

BACKGROUND: Bruchid beetles, Callosobruchus species, are serious pests of economically important grain legumes; their activity in stores is often controlled by use of synthetic insecticides. Esterases are known to be involved in insecticide resistance in insects. However, there is dearth of information on esterase activity in the genus Callosobruchus. In this study we investigated the effect of species, geographical strain and food type on the variation of acetylcholinesterase (AChE) activity and its inhibition by malaoxon (malathion metabolite) using an in vitro spectrophotometric method. RESULT: AChE activity varied significantly among species and strains and also among legume type used for rearing them. Generally irrespective of species, strain or food type, the higher the AChE activity of a population, the higher its inhibition by malaoxon. C. chinensis had the highest AChE activity of the species studied and in the presence of malaoxon it had the lowest remaining AChE activity, while C. rhodesianus retained the highest activity. CONCLUSION: A firsthand knowledge of AChE activity in regional Callosobruchus in line with the prevailing food types should be of utmost importance to grain legume breeders, researchers on plant materials for bruchid control and pesticide manufacturer/applicators for a robust integrated management of these bruchids.

Receptor binding profiles of avian influenza virus hemagglutinin subtypes on human cells as a predictor of pandemic potential

The host adaptation of influenza virus is partly dependent on the sialic acid (SA) isoform bound by the viral hemagglutinin (HA). Avian influenza viruses preferentially bind the α-2,3 SA and human influenza viruses the α-2,6 isoform. Each isoform is predominantly associated with different surface epithelial cell types of the human upper airway. Using recombinant HAs and human tracheal airway epithelial cells in vitro and ex vivo, we show that many avian HA subtypes do not adhere to this canonical view of SA specificity. The propensity of avian viruses to adapt to human receptors may thus be more widespread than previously supposed.

Effects of seed addition on beetle assemblages during the re-creation of species-rich lowland hay meadows

Species-rich lowland hay meadows are of conservation importance for both plants and invertebrates; however, they have declined in area across Europe as a result of conversion to other land uses and management intensification. The re-creation of these grasslands on ex-arable land provides a valuable approach to increasing the extent and conservation value of this threatened habitat. Over a 3-year period a replicated block design was used to test whether introducing seeds promoted the re-creation of both plant and phytophagous beetle assemblages typical of a target hay meadow. Seeds were harvested from local hay meadows, and applied to experimental plots in the form of either green hay or brush harvesting seeds. Green hay spreading achieved the greatest success in re-creating plant and phytophagous beetle assemblages. While re-creation success increased over time for both taxa, for the phytophagous beetles the greatest increase in re-creation success relative to the establishment year also occurred where green hay was applied. We also considered the phytophagous beetles in terms of functional traits that describe host plant specificity, larval feeding location and dispersal. Phytophagous beetle functional trait composition was most similar to the target hay meadow assemblage where some form of seed addition was used, i.e. hay spreading or brush harvested seeds. This study identified the importance of introducing target plant species as a mechanism to promote the re-creation of phytophagous beetle communities. Seed addition methods (e.g. green hay spreading) are crucial to successful hay meadow re-creation.

The prediction of nutrients into estuaries and their subsequent behaviour: application to the Tamar and comparison with the Tweed, U.K.

Some of the techniques used to model nitrogen (N) and phosphorus (P) discharges from a terrestrial catchment to an estuary are discussed and applied to the River Tamar and Tamar Estuary system in Southwest England, U.K. Data are presented for dissolved inorganic nutrient concentrations in the Tamar Estuary and compared with those from the contrasting, low turbidity and rapidly flushed Tweed Estuary in Northeast England. In the Tamar catchment, simulations showed that effluent nitrate loads for typical freshwater flows contributed less than 1% of the total N load. The effect of effluent inputs on ammonium loads was more significant (∼10%). Cattle, sheep and permanent grassland dominated the N catchment export, with diffuse-source N export greatly dominating that due to point sources. Cattle, sheep, permanent grassland and cereal crops generated the greatest rates of diffuse-source P export. This reflected the higher rates of P fertiliser applications to arable land and the susceptibility of bare, arable land to P export in wetter winter months. N and P export to the Tamar Estuary from human sewage was insignificant. Non-conservative behaviour of phosphate was particularly marked in the Tamar Estuary. Silicate concentrations were slightly less than conservative levels, whereas nitrate was essentially conservative. The coastal sea acted as a sink for these terrestrially derived nutrients. A pronounced sag in dissolved oxygen that was associated with strong nitrite and ammonium peaks occurred in the turbidity maximum region of the Tamar Estuary. Nutrient behaviour within the Tweed was very different. The low turbidity and rapid flushing ensured that nutrients there were essentially conservative, so that flushing of nutrients to the coastal zone from the river occurred with little estuarine modification.

Comment on “Multiyear prediction of monthly mean Atlantic meridional overturning circulation at 26.5°N”

Matei et al. (Reports, 6 January 2012, p. 76) claim to show skillful multiyear predictions of the Atlantic Meridional Overturning Circulation (AMOC). However, these claims are not justified, primarily because the predictions of AMOC transport do not outperform simple reference forecasts based on climatological annual cycles. Accordingly, there is no justification for the “confident” prediction of a stable AMOC through 2014.

Prediction of visibility and aerosol within the operational Met Office unified model. I: Model formulation and variational assimilation

The formulation and performance of the Met Office visibility analysis and prediction system are described. The visibility diagnostic within the limited-area Unified Model is a function of humidity and a prognostic aerosol content. The aerosol model includes advection, industrial and general urban sources, plus boundary-layer mixing and removal by rain. The assimilation is a 3-dimensional variational scheme in which the visibility observation operator is a very nonlinear function of humidity, aerosol and temperature. A quality control scheme for visibility data is included. Visibility observations can give rise to humidity increments of significant magnitude compared with the direct impact of humidity observations. We present the results of sensitivity studies which show the contribution of different components of the system to improved skill in visibility forecasts. Visibility assimilation is most important within the first 6-12 hours of the forecast and for visibilities below 1 km, while modelling of aerosol sources and advection is important for slightly higher visibilities (1-5 km) and is still significant at longer forecast times

Numerical prediction of atmospheric blocking-A case study

A series of numerical models have been used to investigate the predictability of atmospheric blocking for an episode selected from FGGE Special Observing Period I. Level II-b FGGE data have been used in the experiment. The blocking took place over the North Atlantic region and is a very characteristic example of high winter blocking. It is found that the very high resolution models developed at ECMWF, in a remarkable way manage to predict the blocking event in great detail, even beyond 1 week. Although models with much less resolution manage to predict the blocking phenomenon as such, the actual evolution differs very much from the observed and consequently the practical value is substantially reduced. Wind observations from the geostationary satellites are shown to have a substantial impact on the forecast beyond 5 days, as well as an extension of the integration domain to the whole globe. Quasi-geostrophic baroclinic models and, even more, barotropic models, are totally inadequate to predict blocking except in its initial phase. The prediction experiment illustrates clearly that efforts which have gone into the improvement of numerical prediction models in the last decades have been worth while.

Numerical prediction of atmospheric blocking - A case study

One of the fundamental questions in dynamical meteorology, and one of the basic objectives of GARP, is to determine the predictability of the atmosphere. In the early planning stage and preparation for GARP a number of theoretical and numerical studies were undertaken, indicating that there existed an inherent unpredictability in the atmosphere which even with the most ideal observing system would limit useful weather forecasting to 2-3 weeks.