Life Cycle Inventories of Metals and Methodological Aspects of Inventorying Material Resources in ecoinvent (7 pp)

Goal, Scope and Background The ecoinvent database provides harmonised generic life cycle inventories for metal production and processing. They can be used as background data for different LCA applications. The goal of this paper is to provide an overview of the metals inventoried in ecoinvent. Beside, some methodological background information is given. The focus lies on a new methodology developed to inventorying joint resources. The implementation is shown in a case study of the production of primary copper on a global average. The respective process is assessed with Eco-indicator 99 (H,A) to identify dominant impacts within the production chain.Methods In ecoinvent, a coupled production is inventoried in multi output unit processes. For database calculation, an allocation by economic revenue is applied. Elementary flows for resources, especially joint resources, include information on type and quality of the resources.Results and Conclusion With the presented method, the extraction of resources can be valuated based on the cost of restoration or the change in the future impact due to the extraction of a specific resource. The case study indicates, for copper / molybdenum production, that the mineral extraction is of minor importance compared to the metallurgical step according to the LCIA results. Air emissions of heavy metals are identified as main impacts. Also, the resource depletion shows a notable impact. The environmental impacts of metals from sulphidic ores, however, are underestimated by neglecting emissions from tailings for lack of reliable data.Recommendation and Perspective Impact assessment methods will have to be updated to account for different grades of ore. The ecoinvent database should be enlarged by more inventories of technically important metals and alloys, e.g. by gold, silver, solders, etc. for the electronics industry and by specific steel and aluminium alloys. Reliable composition data of sulphidic tailings and transfer coefficients for their disposal considering Acidic Rock Drainage (ARD) are to be developed as well.     

A database for medicinal plants used in treatment of asthma

The knowledge of most plants used in the treatment of asthma, the plant part which is effective in treatment is confined to very few persons who are engaged in folklore medicine. However, this form of medicine is not very popular. Therefore, it is of considerable interest to ethno-botanical community to understand the plants and the parts used for treatment. Here, we describe AsthmaPlantBase, a database containing information of medicinal plants for treatment of asthma.

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A barcode of life database for the Cephalopoda? Considerations and concerns

The concept of a Barcode of Life Database (BoLD) for the Class Cephalopoda (Phylum Mollusca) was introduced at the Cephalopod International Advisory Council (CIAC) symposium in Hobart, Australia, February 2006. This suggestion was met with significant interest, concern and debate. This review attempts to describe the concept of the BoLD initiative and to outline considerations and concerns specific to a cephalopod BoLD. Jan M. Strugnell and Annie R. Lindgren contributed equally to this work.     

Application of the secondary structure model of rRNA for phylogeny: D2-D3 expansion segments of the LSU gene of plant-parasitic nematodes from the family Hoplolaimidae Filipjev, 1934

Knowledge of rRNA structure is increasingly important to assist phylogenetic analysis through reconstructing optimal alignment, utilizing molecule features as an additional source of data and refining appropriate models of evolution of the molecule. We describe a procedure of optimization for alignment and a new coding method for nucleotide sequence data using secondary structure models of the D2 and D3 expansion fragments of the LSU-rRNA gene reconstructed for fifteen nematode species of the agriculturally important and diverse family Hoplolaimidae, order Tylenchida. Using secondary structure information we converted the original sequence data into twenty-eight symbol codes and submitted the transformed data to maximum parsimony analysis. We also applied the original sequence data set for Bayesian inference. This used the doublet model with sixteen states of nucleotide doublets for the stem region and the standard model of DNA substitution with four nucleotide states for loops and bulges. By this approach, we demonstrate that using structural information for phylogenetic analyses led to trees with lower resolved relationships between clades and likely eliminated some artefactual support for misinterpreted relationships, such as paraphyly of Helicotylenchus or Rotylenchus. This study as well as future phylogenetic analyses is herein supported by the development of an on-line database, NEMrRNA, for rRNA molecules in a structural format for nematodes. We also have developed a new computer program, RNAstat, for calculation of nucleotide statistics designed and proposed for phylogenetic studies.     

Local motions in a benchmark of allosteric proteins

Allosteric proteins have been studied extensively in the last 40 years, but so far, no systematic analysis of conformational changes between allosteric structures has been carried out. Here, we compile a set of 51 pairs of known inactive and active allosteric protein structures from the Protein Data Bank. We calculate local conformational differences between the two structures of each protein using simple metrics, such as backbone and side-chain Cartesian displacement, and torsion angle change and rearrangement in residue-residue contacts. Thresholds for each metric arise from distributions of motions in two control sets of pairs of protein structures in the same biochemical state. Statistical analysis of motions in allosteric proteins quantifies the magnitude of allosteric effects and reveals simple structural principles about allostery. For example, allosteric proteins exhibit substantial conformational changes comprising about 20% of the residues. In addition, motions in allosteric proteins show strong bias toward weakly constrained regions such as loops and the protein surface. Correlation functions show that motions communicate through protein structures over distances averaging 10-20 residues in sequence space and 10-20 A in Cartesian space. Comparison of motions in the allosteric set and a set of 21 nonallosteric ligand-binding proteins shows that nonallosteric proteins also exhibit bias of motion toward weakly constrained regions and local correlation of motion. However, allosteric proteins exhibit twice as much percent motion on average as nonallosteric proteins with ligand-induced motion. These observations may guide efforts to design flexibility and allostery into proteins.     

Scratchpads 2.0: a Virtual Research Environment supporting scholarly collaboration, communication and data publication in biodiversity science

The Scratchpad Virtual Research Environment (http://scratchpads.eu/) is a flexible system for people to create their own research networks supporting natural history science. Here we describe Version 2 of the system characterised by the move to Drupal 7 as the Scratchpad core development framework and timed to coincide with the fifth year of the project's operation in late January 2012. The development of Scratchpad 2 reflects a combination of technical enhancements that make the project more sustainable, combined with new features intended to make the system more functional and easier to use. A roadmap outlining strategic plans for development of the Scratchpad project over the next two years concludes this article.