Validating and improving elastic network models with molecular dynamics simulations

Elastic network models (ENMs) are a class of simple models intended to represent the collective motions of proteins. In contrast to all‐atom molecular dynamics simulations, the low computational investment required to use an ENM makes them ideal for speculative hypothesis‐testing situations. Historically, ENMs have been validated via comparison to crystallographic B‐factors, but this comparison is relatively low‐resolution and only tests the predictions of relative flexibility. In this work, we systematically validate and optimize a number of ENM‐type models by quantitatively comparing their predictions to microsecond‐scale all‐atom simulations of three different G protein coupled receptors. We show that, despite their apparent simplicity, well‐optimized ENMs perform remarkably well, reproducing the protein fluctuations with an accuracy comparable to what one would expect from all‐atom simulations run for several hundred nanoseconds. Proteins 2010. © 2010 Wiley‐Liss, Inc.     

Prenatal data impacts common bottlenose dolphin (Tursiops truncatus) growth parameters estimated by length‐at‐age curves

Compilation of marine mammal demographic data is central to management efforts. However, marine mammal length‐at‐age growth curves demonstrate limitations. Physiological growth parameters of terrestrial mammals are typically estimated using curvilinear models fit to size‐at‐age data along a time series from conception to senescence. The difficulty of collecting and aging prenatal cetaceans is addressed here, and growth parameters of common bottlenose dolphins (Tursiops truncatus) along coastal Texas were estimated using length‐at‐age information from a broader scope of age classes, including late‐term fetuses. A Gompertz growth curve fit to pre‐ and postnatal data underestimated size parameters, but demonstrated similar growth rate constants (k) to an exclusively postnatal model. However, when growth parameters were broken out, the absolute growth rate (G) and rate of growth decay (g) decreased (0.44 from 0.27 and 0.55 from 0.39, respectively), which underscores the importance of reporting k in its expanded form (G/g). Although the Gompertz fits most age classes well, it cannot explain growth in all age classes. We argue that a novel sigmoidal model would be more useful for inference.     

Craniometric variation of some Mediterranean and Atlantic populations of Stenella coeruleoalba (Mammalia,Delphinidae): A three‐dimensional geometric morphometric analysis

The variability of cranial features of Atlantic and Mediterranean samples of Stenella coeruleoalba was examined using a three‐dimensional geometric morphometric approach. Data were collected on 79 skulls from the upper and middle Mediterranean Sea, the Atlantic French coasts, and Scotland. Three‐dimensional x, y, and z coordinates of 27 landmarks were recorded on each left half skull using a Microscribe 3‐D digitizer. All configurations were rotated, centered, and scaled, and residuals from the mean configuration were analyzed through multivariate analyses of variance. Mahalanobis distances among populations were used to evaluate phenetic relationships. Consensus configurations were compared to visualize shape differences among samples. Analyses revealed significant differences among populations, a clear distinction of the Scottish coasts dolphins from the other samples, and a closer relationship of the dolphins from the French coasts to the Mediterranean populations than to the Scottish one. Shape differences are mainly concentrated in the rostral and in the occipital regions of the skull. Phylogenetic and adaptive factors were invoked as possible causes of the variation patterns.     

Extended Producer Responsibility in Thailand

Waste electrical and electronic equipment (WEEE) sheds light on the dimmer side of production and consumption patterns in modern societies. The rapid increase in its quantity and complexity contribute to the challenges it poses to solid waste management systems. Several members of the Organisation for Economic Co‐operation and Development (OECD) have relied on the principle of extended producer responsibility (EPR) to tackle the issue, with varying degrees of success. Several non‐OECD countries, including Thailand, are now developing WEEE programs and are looking for lessons from these first movers. This case study aims to provide an understanding both of this context and of the EPR program for WEEE proposed for Thailand. It finds that EPR mechanisms in general, and the proposed buy‐back system financed by product fees in Thailand in particular, have a strong potential to consolidate WEEE collection for the formal recycling sector by offering end users monetary incentives. On the negative side, this is an expensive combination of policy instruments, and the institutional design of the governmental fund is rigid. The policy proposal also contains no mechanism for product redesign—one of the objectives in the national WEEE strategy. This article suggests that the effectiveness of the policy might benefit from more flexibility at the compliance scheme level, in order to lessen the monopoly of the governmental fund, as well as the introduction of differentiated fees to promote environmentally friendly products.     

Patterns of early succession on bare peat in a Swiss mire after a bog burst

Questions: How does plant diversity (species richness, species abundance and rate of change) evolve in early succession on bare peat? Does succession converge towards one equilibrium stage or end up in several stages? Is there a regular pattern in succession velocity? Location: A mire in the calcareous Jura Mountains of northwest Switzerland. Method: Twenty‐one 1‐m² permanent plots on bare peat were used to monitor temporal stages over a 21‐year period (1988 to 2008) in a Swiss mire where a slide occurred in 1987. Species diversity and life forms were analysed based on Shannon's equitability index and cover. We used classification and metric ordination techniques to investigate patterns of successional rates and trends. The high temporal resolution of the survey allowed the pattern of succession velocity to be analysed. Results: Species richness increased continuously over the 21 years of succession. The highest cover throughout the study period was the life form sedge. Time trajectories of the 21 plots revealed three alternative pathways towards intermediate equilibrium stages in the first years, still not converging in the later stages. Changes in succession velocity reached a first maximum about 6 years after the slide had occurred and a second maximum 12 years later.     

Colours of domestication

During the last decade, coat colouration in mammals has been investigated in numerous studies. Most of these studies addressing the genetics of coat colouration were on domesticated animals. In contrast to their wild ancestors, domesticated species are often characterized by a huge allelic variability of coat‐colour‐associated genes. This variability results from artificial selection accepting negative pleiotropic effects linked with certain coat‐colour variants. Recent studies demonstrate that this selection for coat‐colour phenotypes started at the beginning of domestication. Although to date more than 300 genetic loci and more than 150 identified coat‐colour‐associated genes have been discovered, which influence pigmentation in various ways, the genetic pathways influencing coat colouration are still only poorly described. On the one hand, similar coat colourations observed in different species can be the product of a few conserved genes. On the other hand, different genes can be responsible for highly similar coat colourations in different individuals of a species or in different species. Therefore, any phenotypic classification of coat colouration blurs underlying differences in the genetic basis of colour variants. In this review we focus on (i) the underlying causes that have resulted in the observed increase of colour variation in domesticated animals compared to their wild ancestors, and (ii) the current state of knowledge with regard to the molecular mechanisms of colouration, with a special emphasis on when and where the different coat‐colour‐associated genes act.     

Single Nanostructure Electrochemical Devices for Studying Electronic Properties and Structural Changes in Lithiated Si Nanowires

Nanostructured Si is a promising anode material for the next generation of Li‐ion batteries, but few studies have focused on the electrical properties of the Li‐Si alloy phase, which are important for determining power capabilities and ensuring sufficient electrical conduction in the electrode structure. Here, we demonstrate an electrochemical device framework suitable for testing the electrical properties of single Si nanowires (NWs) at different lithiation states and correlating these properties with structural changes via transmission electron microscopy (TEM). We find that single Si NWs usually exhibit Ohmic I–V response in the lithiated state, with conductivities two to three orders of magnitude higher than in the delithiated state. After a number of sequential lithiation/delithiation cycles, the single NWs show similar conductivity after each lithiation step but show large variations in conductivity in the delithiated state. Finally, devices with groups of NWs in physical contact were fabricated, and structural changes in the NWs were observed after lithiation to investigate how the electrical resistance of NW junctions and the NWs themselves affect the lithiation behavior. The results suggest that electrical resistance of NW junctions can limit lithiation. Overall, this study shows the importance of investigating the electronic properties of individual components of a battery electrode (single nanostructures in this case) along with studying the nature of interactions within a collection of these component structures.     

Single Material Solar Cells: the Next Frontier for Organic Photovoltaics?

An overview of various approaches for the realization of single‐material organic solar cells (SMOCs) is presented. Fullerene‐conjugated systems dyads, di‐block copolymers, and self‐organized donor‐acceptor molecules all represent different possible approaches towards SMOCs. Although each of them presents specific advantages and poses specific problems of design and synthesis, these different routes have witnessed significant progress in the past few years and SMOCs with efficiencies in the range of 1.50% have been realized. These performances are already higher than those of bi‐component bulk heterojunction solar cells some ten years ago, demonstrating that SMOCs can represent a credible approach towards efficient and simple organic solar cells. Possible directions for future research are discussed with the aim of stimulating further research on this exciting topic.