The MOLDY short-range molecular dynamics package

We describe a parallelised version of the MOLDY molecular dynamics program. This Fortran code is aimed at systems which may be described by short-range potentials and specifically those which may be addressed with the embedded atom method. This includes a wide range of transition metals and alloys. MOLDY provides a range of options in terms of the molecular dynamics ensemble used and the boundary conditions which may be applied. A number of standard potentials are provided, and the modular structure of the code allows new potentials to be added easily. The code is parallelised using OpenMP and can therefore be run on shared memory systems, including modern multicore processors. Particular attention is paid to the updates required in the main force loop, where synchronisation is often required in OpenMP implementations of molecular dynamics. We examine the performance of the parallel code in detail and give some examples of applications to realistic problems, including the dynamic compression of copper and carbon migration in an iron-carbon alloy

Crop-livestock integration provides opportunities to mitigate environmental trade-offs in transitioning smallholder agricultural systems of the Greater Mekong Subregion

CONTEXT: The Greater Mekong Subregion has been undergoing rapid agricultural transformation over the last decades, as traditional diverse subsistence-oriented agriculture is evolving towards intensified commercial production systems. Negative environmental impacts often include deforestation, nutrient pollution, and greenhouse gas (GHG) emissions. OBJECTIVE: This study aims to explore the potential of crop-livestock integration to mitigate trade-offs between economic and environmental impacts of smallholder farming systems at different stages of agricultural transition and degrees of agricultural diversity across the Greater Mekong Subregion. METHODS: We chose a ‘middle ground’ between detailed modeling of few, representative farming systems and modeling of large household populations. 24 low and high diversity farms were selected in Laos (Xieng Khouang province), Cambodia (Ratanakiri province) and Vietnam (Central Highlands) from a survey dataset of 1300 households. These farming systems were simulated with the whole-farm bio-economic and multi-objective optimization model FarmDESIGN, calculating operating profit, GHG emissions and nitrogen (N) balance. Two optimizations (‘business as usual’ vs. ‘crop-livestock integration’) were performed, generating ‘solution spaces’ or alternative configurations aiming to maximize profitability, keep farm N balanced and minimize GHG emissions. RESULTS AND CONCLUSIONS: Agricultural systems across the sites differed in their production orientation and management practices, representing various stages of agricultural transition. Nitrogen balances varied between sites, being negative in Ratanakiri (average 20.5 kg N ha 1 y 1) and Xieng Khouang ( 36.5 kg N ha 1 y 1) and positive in the Central Highlands (73 kg N ha 1 y 1). Negative balances point to unsustainable mining of nutrients due to sale of cash crops without sufficient inputs, and positive balances to the risk of environmental contamination. Total GHG emissions ranged from 0.52–8.12 t CO2e ha 1 and were not significantly impacted by stage of agricultural transformation or agricultural diversity. GHG sources in Ratanakiri and Xieng Khouang were determined by crop residue burning while in Central Highlands fertilizer and livestock were main emitters. High diversity farms obtained higher operating profits (10,379 USD y 1) than low diversity farms (4584 USD y 1). Crop-livestock integration, a combination of measures including introduction of improved forages grasses, manure recycling and residue feeding, and reduction of residue burning, resulted in larger ‘solution spaces’, thus providing farmers with more options to mitigate agro-environmental trade-offs. SIGNIFICANCE: These findings underline the potential of crop-livestock integration to support sustainable intensification pathways in the Greater Mekong region. Public and private investment in further research and extension is needed to develop and scale context-specific crop-livestock integration practices

Edar/Eda interactions regulate enamel knot formation in tooth morphogenesis.

tabby and downless mutant mice have apparently identical defects in teeth, hair and sweat glands. Recently, genes responsible for these spontaneous mutations have been identified. downless (Dl) encodes Edar, a novel member of the tumour necrosis factor (TNF) receptor family, containing the characteristic extracellular cysteine rich fold, a single transmembrane region and a death homology domain close to the C terminus. tabby (Ta) encodes ectodysplasin-A (Eda) a type II membrane protein of the TNF ligand family containing an internal collagen-like domain. As predicted by the similarity in adult mutant phenotype and the structure of the proteins, we demonstrate that Eda and Edar specifically interact in vitro. We have compared the expression pattern of Dl and Ta in mouse development, taking the tooth as our model system, and find that they are not expressed in adjacent cells as would have been expected. Teeth develop by a well recorded series of epithelial-mesenchymal interactions, similar to those in hair follicle and sweat gland development, the structures found to be defective in tabby and downless mice. We have analysed the downless mutant teeth in detail, and have traced the defect in cusp morphology back to initial defects in the structure of the tooth enamel knot at E13. Significantly, the defect is distinct from that of the tabby mutant. In the tabby mutant, there is a recognisable but small enamel knot, whereas in the downless mutant the knot is absent, but enamel knot cells are organised into a different shape, the enamel rope, showing altered expression of signalling factors (Shh, Fgf4, Bmp4 and Wnt10b). By adding a soluble form of Edar to tooth germs, we were able to mimic the tabby enamel knot phenotype, demonstrating the involvement of endogenous Eda in tooth development. We could not, however, reproduce the downless phenotype, suggesting the existence of yet another ligand or receptor, or of ligand-independent activation mechanisms for Edar. Changes in the structure of the enamel knot signalling centre in downless tooth germs provide functional data directly linking the enamel knot with tooth cusp morphogenesis. We also show that the Lef1 pathway, thought to be involved in these mutants, functions independently in a parallel pathway

New yeast expression platforms based on methylotrophic Hansenula polymorpha and Pichia pastoris and on dimorphic Arxula adeninivorans and Yarrowia lipolytica – A comparison

Yeasts combine the ease of genetic manipulation and fermentation of a microbial organism with the capability to secrete and to modify proteins according to a general eukaryotic scheme. Yeasts thus provide attractive platforms for the production of recombinant proteins. Here, four important species are presented and compared: the methylotrophic Hansenula polymorpha and Pichia pastoris, distinguished by an increasingly large track record as industrial platforms, and the dimorphic species Arxula adeninivorans and Yarrrowia lipolytica, not yet established as industrial platforms, but demonstrating promising technological potential, as discussed in this article.