Function of the hydration layer around an antifreeze protein revealed by atomistic molecular dynamics simulations

Atomistic molecular dynamics simulations are used to investigate the mechanism by which the antifreeze protein from the spruce budworm, Choristoneura fumiferana, binds to ice. Comparison of structural and dynamic properties of the water around the three faces of the triangular prism-shaped protein in aqueous solution reveals that at low temperature the water structure is ordered and the dynamics slowed down around the ice-binding face of the protein, with a disordering effect observed around the other two faces. These results suggest a dual role for the solvation water around the protein. The preconfigured solvation shell around the ice-binding face is involved in the initial recognition and binding of the antifreeze protein to ice by lowering the barrier for binding and consolidation of the protein:ice interaction surface. Thus, the antifreeze protein can bind to the molecularly rough ice surface by becoming actively involved in the formation of its own binding site. Also, the disruption of water structure around the rest of the protein helps prevent the adsorbed protein becoming covered by further ice growth.

X-ray scattering study of the effect of hydration on the cross-beta structure of amyloid fibrils

We have investigated the effect of sample hydration on the wide-angle X-ray scattering patterns of amyloid fibrils from two different sources, hen egg white lysozyme (HEWL) and an 11-residue peptide taken from the sequence of transthyretin (TTR105-115). Both samples show an inter-strand reflection at 4.7 Å and an inter-sheet reflection which occurs at 8.8 and 10 Å for TTR105-115 and HEWL fibrils, respectively. The positions, widths, and relative intensities of these reflections are conserved in patterns obtained from dried stalks and hydrated samples over a range of fibril concentrations. In 2D scattering patterns obtained from flow-aligned hydrated samples, the inter-strand and inter-sheet reflections showed, respectively, axial and equatorial alignment relative to the fibril axis, characteristic of the cross-β structure. Our results show that the cross-β structure of the fibrils is not a product of the dehydrating conditions typically employed to produce aligned samples, but is conserved in individual fibrils in hydrated samples under dilute conditions comparable to those associated with other biophysical and spectroscopic techniques. This suggests a structure consisting of a stack of two or more sheets whose interfaces are inaccessible to bulk water.

Critical stages of the brewing process for changes in antioxidant activity and levels of phenolic compounds in ale

Samples were taken at each stage of brewing (malt, milling, mashing, wort separation, hop addition, boiling, whirlpool, dilution, fermentation, warm rest, chill-lagering, beer filtration, carbonation and bottling, pasteurization, and storage). The level of antioxidant activity of unfractionated, low-molecular-mass (LMM) and high-molecular-mass (HMM) fractions was measured by the 2,2'-azinobis(3-ethylbenzothiazoline-6-sulfortic acid) radical cation (ABTS(.+)) and ferric-reducing antioxidant power (FRAP) procedures. Polyphenol levels were assessed by HPLC. The LMM fraction (<5 kDa) was responsible for similar to80% of the level of antioxidant activity of the unfractionated malt and beer samples. In the unfractionated samples, significant decreases (P < 0.001) in antioxidant activity levels were observed after milling and beer filtration, with the decrease after beer filtration being accompanied by a significant decrease (P > 0.001) in catechin and ferulic acid levels. Increases in antioxidant activity levels were observed after mashing, boiling, fermentation, chill-lagering, and pasteurization, in line with previous studies on lager. Additionally, increases in the level of antioxidant activity occurred after wort separation and carbonation and bottling and were accompanied by increases in levels of most monitored polyphenols. Data from the ABTS(.-) and FRAP assays indicated that the compounds contributing to the levels of antioxidant activity responded differently in the two procedures. Levels of ferulic, vanillic, and chlorogenic acids and catechin accounted for 45-61% of the variation in antioxidant activity levels.

Validation of the social communication questionnaire in a population cohort of children with autism spectrum disorders

Objective: To examine the properties of the Social Communication Questionnaire (SCQ) in a population cohort of children with autism spectrum disorders (ASDs) and in the general population, Method: SCQ data were collected from three samples: the Special Needs and Autism Project (SNAP) cohort of 9- to 10-year-old children with special educational needs with and without ASD and two similar but separate age groups of children from the general population (n = 411 and n = 247). Diagnostic assessments were completed on a stratified subsample (n = 255) of the special educational needs group. A sample-weighting procedure enabled us to estimate characteristics of the SCQ in the total ASD population. Diagnostic status of cases in the general population samples were extracted from child health records. Results: The SCQ showed strong discrimination between ASD and non-ASD cases (sensitivity 0.88, specificity 0.72) and between autism and nonautism cases (sensitivity 0.90, specificity 0.86). Findings were not affected by child IQ or parental education. In the general population samples between 4% and 5% of children scored above the ASD cutoff including 1.5% who scored above the autism cutoff. Although many of these high-scoring children had an ASD diagnosis, almost all (similar to 90%) of them had a diagnosed neurodevelopmental disorder. Conclusions: This study confirms the utility of the SCQ as a,first-level screen for ASD in at-risk samples of school-age children.

Predictability of the western North Pacific summer climate demonstrated by the coupled models of ENSEMBLES

The Asian monsoon system, including the western North Pacific (WNP), East Asian, and Indian monsoons, dominates the climate of the Asia-Indian Ocean-Pacific region, and plays a significant role in the global hydrological and energy cycles. The prediction of monsoons and associated climate features is a major challenge in seasonal time scale climate forecast. In this study, a comprehensive assessment of the interannual predictability of the WNP summer climate has been performed using the 1-month lead retrospective forecasts (hindcasts) of five state-of-the-art coupled models from ENSEMBLES for the period of 1960–2005. Spatial distribution of the temporal correlation coefficients shows that the interannual variation of precipitation is well predicted around the Maritime Continent and east of the Philippines. The high skills for the lower-tropospheric circulation and sea surface temperature (SST) spread over almost the whole WNP. These results indicate that the models in general successfully predict the interannual variation of the WNP summer climate. Two typical indices, the WNP summer precipitation index and the WNP lower-tropospheric circulation index (WNPMI), have been used to quantify the forecast skill. The correlation coefficient between five models’ multi-model ensemble (MME) mean prediction and observations for the WNP summer precipitation index reaches 0.66 during 1979–2005 while it is 0.68 for the WNPMI during 1960–2005. The WNPMI-regressed anomalies of lower-tropospheric winds, SSTs and precipitation are similar between observations and MME. Further analysis suggests that prediction reliability of the WNP summer climate mainly arises from the atmosphere–ocean interaction over the tropical Indian and the tropical Pacific Ocean, implying that continuing improvement in the representation of the air–sea interaction over these regions in CGCMs is a key for long-lead seasonal forecast over the WNP and East Asia. On the other hand, the prediction of the WNP summer climate anomalies exhibits a remarkable spread resulted from uncertainty in initial conditions. The summer anomalies related to the prediction spread, including the lower-tropospheric circulation, SST and precipitation anomalies, show a Pacific-Japan or East Asia-Pacific pattern in the meridional direction over the WNP. Our further investigations suggest that the WNPMI prediction spread arises mainly from the internal dynamics in air–sea interaction over the WNP and Indian Ocean, since the local relationships among the anomalous SST, circulation, and precipitation associated with the spread are similar to those associated with the interannual variation of the WNPMI in both observations and MME. However, the magnitudes of these anomalies related to the spread are weaker, ranging from one third to a half of those anomalies associated with the interannual variation of the WNPMI in MME over the tropical Indian Ocean and subtropical WNP. These results further support that the improvement in the representation of the air–sea interaction over the tropical Indian Ocean and subtropical WNP in CGCMs is a key for reducing the prediction spread and for improving the long-lead seasonal forecast over the WNP and East Asia.

Collaboration of the weather and climate communities to advance subseasonal-to-seasonal prediction

The World Weather Research Programme (WWRP) and the World Climate Research Programme (WCRP) have identified collaborations and scientific priorities to accelerate advances in analysis and prediction at subseasonal-to-seasonal time scales, which include i) advancing knowledge of mesoscale–planetary-scale interactions and their prediction; ii) developing high-resolution global–regional climate simulations, with advanced representation of physical processes, to improve the predictive skill of subseasonal and seasonal variability of high-impact events, such as seasonal droughts and floods, blocking, and tropical and extratropical cyclones; iii) contributing to the improvement of data assimilation methods for monitoring and predicting used in coupled ocean–atmosphere–land and Earth system models; and iv) developing and transferring diagnostic and prognostic information tailored to socioeconomic decision making. The document puts forward specific underpinning research, linkage, and requirements necessary to achieve the goals of the proposed collaboration.

Flow-dependent predictability of the North Atlantic Jet

The North Atlantic eddy-driven jet is a major component of the large-scale flow in the northern hemisphere. Here we present evidence from reanalysis and ensemble forecast data for systematic flow-dependent predictability of the jet during northern hemisphere winter (DJF). It is found that when the jet is weakened or split it is both less persistent and less predictable. The lack of predictability manifests itself as the onset of an anomalously large instantaneous rate of spread of ensemble forecast members as the jet becomes weakened. This suggests that as the jet weakens or splits it enters into a state more sensitive to small differences between ensemble forecast members, rather like the sensitive region between the wings of the Lorenz attractor.

Local and average structure in zinc cyanide: towards an understanding of the atomistic origin of negative thermal expansion

Neutron diffraction at 11.4 and 295 K and solid-state 67Zn NMR are used to determine both the local and average structures in the disordered, negative thermal expansion (NTE) material, Zn(CN)2. Solid-state NMR not only confirms that there is head-to-tail disorder of the C≡N groups present in the solid, but yields information about the relative abundances of the different Zn(CN)4-n(NC)n tetrahedral species, which do not follow a simple binomial distribution. The Zn(CN)4 and Zn(NC)4 species occur with much lower probabilities than are predicted by binomial theory, supporting the conclusion that they are of higher energy than the other local arrangements. The lowest energy arrangement is Zn(CN)2(NC)2. The use of total neutron diffraction at 11.4 K, with analysis of both the Bragg diffraction and the derived total correlation function, yields the first experimental determination of the individual Zn−N and Zn−C bond lengths as 1.969(2) and 2.030(2) Å, respectively. The very small difference in bond lengths, of ~0.06 Å, means that it is impossible to obtain these bond lengths using Bragg diffraction in isolation. Total neutron diffraction also provides information on both the average and local atomic displacements responsible for NTE in Zn(CN)2. The principal motions giving rise to NTE are shown to be those in which the carbon and nitrogen atoms within individual Zn−C≡N−Zn linkages are displaced to the same side of the Zn···Zn axis. Displacements of the carbon and nitrogen atoms to opposite sides of the Zn···Zn axis, suggested previously in X-ray studies as being responsible for NTE behavior, in fact make negligible contribution at temperatures up to 295 K.

Mid-Holocene climates of the Americas: a dynamical response to changed seasonality

Simulations of the climatic response to mid-Holocene (6 ka BP) orbital forcing with two coupled ocean–atmosphere models (FOAM and CSM) show enhancement of monsoonal precipitation in parts of the American Southwest, Central America and northernmost South America during Northern Hemisphere summer. The enhanced onshore flow that brings precipitation into Central America is caused by a northward displacement of the inter-tropical convergence zone, driven by cooling of the equatorial and warming of the northern subtropical and mid-latitude ocean. Ocean feedbacks also enhance precipitation over the American Southwest, although the increase in monsoon precipitation there is largely driven by increases in land-surface temperature. The northward shift in the equatorial precipitation band that causes enhanced precipitation in Central America and the American Southwest has a negative feedback effect on monsoonal precipitation in northern South America. The simulations demonstrate that mid-Holocene aridity in the mid-continent of North America is dynamically linked to the orbitally induced enhancement of the summer monsoon in the American Southwest, with a spatial structure (wet in the Southwest and dry in the mid-continent) similar to that found in strong monsoon years today. Changes in winter precipitation along the west coast of North America, in Central America and along the Gulf Coast, caused by southward-displacement of the westerly storm tracks, indicate that changes in the Northern Hemisphere winter monsoon also play a role in regional climate changes during the mid-Holocene. Although the simulations with FOAM and CSM differ in detail, the general mechanisms and patterns are common to both. The model results thus provide a coherent dynamical explanation for regional patterns of increased or decreased aridity shown by vegetation, lake status and aeolian data from the Americas

Key conclusions of the first international urban land surface model comparison project

he first international urban land surface model comparison was designed to identify three aspects of the urban surface-atmosphere interactions: (1) the dominant physical processes, (2) the level of complexity required to model these, and 3) the parameter requirements for such a model. Offline simulations from 32 land surface schemes, with varying complexity, contributed to the comparison. Model results were analysed within a framework of physical classifications and over four stages. The results show that the following are important urban processes; (i) multiple reflections of shortwave radiation within street canyons, (ii) reduction in the amount of visible sky from within the canyon, which impacts on the net long-wave radiation, iii) the contrast in surface temperatures between building roofs and street canyons, and (iv) evaporation from vegetation. Models that use an appropriate bulk albedo based on multiple solar reflections, represent building roof surfaces separately from street canyons and include a representation of vegetation demonstrate more skill, but require parameter information on the albedo, height of the buildings relative to the width of the streets (height to width ratio), the fraction of building roofs compared to street canyons from a plan view (plan area fraction) and the fraction of the surface that is vegetated. These results, whilst based on a single site and less than 18 months of data, have implications for the future design of urban land surface models, the data that need to be measured in urban observational campaigns, and what needs to be included in initiatives for regional and global parameter databases.