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.     

Semi‐dry grasslands along a climatic gradient across Central Europe: Vegetation classification with validation

Question: What is the variation in species composition of Central European semi‐dry grasslands? Can we apply a training‐and‐test validation approach for identifying phytosociological associations which are floristically well defined in a broad geographic comparison; can we separate them from earlier described associations with only a local validity? Location: A 1200 km long transect running along a gradient of increasing continentality from central Germany via Czech Republic, Slovakia, NE Austria, Hungary to NW Romania. Methods: Relevés with > 25% cover of Brachypodium pin‐natum and/or Bromus erectus were geographically selected from a larger database. They were randomly split into two data sets, TRAINING and TEST, each with 422 relevés. Cluster analysis was performed for each data set on scores from significant principal coordinates. Different partitions of the TRAINING data set were validated on the TEST data set, using a new method based on the comparison of % frequencies of species occurrence in clusters. Clusters were characterized by statistically defined groups of diagnostic species and values of climatic variables. Results: Species composition changed along the NW‐SE gradient and valid clusters were geographically well separated. Optimal partition level was at 11 clusters, six being valid: two clusters Germany and the Czech Republic corresponded to the Bromion erecti; two clusters from the Czech Republic and Hungary to the Cirsio‐Brachypodion, and two clusters were transitional between these two alliances. Conclusion: The training‐and‐test validation method used in this paper proved to be efficient for discriminating between robust clusters, which are appropriate candidates for inclusion in the national or regional syntaxonomic overviews, and weak clusters, which are specific to the particular classification of the given data set.     

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.     

Knowledge networks in the age of the Semantic Web

The Web has become the major medium for various communities to share their knowledge. To this end, it provides an optimal environment for knowledge networks. The web offers global connectivity that is virtually instantaneous, and whose resources and documents can easily be indexed for easy searching. In the coupled realms of biomedical research and healthcare, this has become especially important where today many thousands of communities already exist that connect across academia, hospitals and industry. These communities also rely on several forms of knowledge assets, including publications, experimental data, domain-specific vocabularies and policies. Web-based communities will be one of the earlier beneficiaries of the emerging Semantic Web. With the new standards and technologies of the Semantic Web, effective utilization of knowledge networks will expand profoundly, fostering new levels of innovation and knowledge.     

Prescribed fires in Artemisia tridentata ssp. vaseyana steppe have minor and transient effects on vegetation cover and composition

Question: What is the impact of prescribed fires on the cover and composition of vegetation in Artemisia tridentata ssp. vaseyana steppe? Location: United States Department of Agriculture, Agricultural Research Service, United States Sheep Experiment Station, eastern Idaho (44°14′44′’ N, 112°12′47′’ W). Methods: Multiple prescribed fires were lit in 2002 and 2003 in an Artemisia tridentata ssp. vaseyana (mountain big sagebrush) steppe ecosystem that was relatively free of exotic plants. Measurements of cover components and plant species frequencies were taken pre‐ and for 2 to 3 years post‐fire. Results: Cover of forbs and grasses returned to pre‐fire levels after two years. Shrub cover declined from 36 to 6% in the first year post‐fire. Fire reduced the frequencies of three species, A. tridentata ssp. vaseyana, Festuca idahoensis, and Cordylanthus ramosus, of rangeland plants. Frequencies of four plant species, Hesperostipa comata, Polygonum douglasii, Chenopodium fremontii and Chenopodium leptophyllum increased, but only P. douglasii increased for more than a year. Conclusion: This study demonstrates that in an Artemisia tridentata ssp. vaseyana steppe ecosystem without significant non‐native species or anthropogenic disturbances vegetative cover and species composition of the herbaceous community are only minimally altered by fire. The herbaceous component returned to pre‐fire conditions within three years of a fire.     

RiDs db: Repeats in diseases database

The non-coding fraction of the human genome, which is approximately 98%, is mainly constituted by repeats. Transpositions, expansions and deletions of these repeat elements contribute to a number of diseases. None of the available databases consolidates information on both tandem and interspersed repeats with the flexibility of FASTA based homology search with reference to disease genes. Repeats in diseases database (RiDs db) is a web accessible relational database, which aids analysis of repeats associated with Mendelian disorders. It is a repository of disease genes, which can be searched by FASTA program or by limitedor free- text keywords. Unlike other databases, RiDs db contains the sequences of these genes with access to corresponding information on both interspersed and tandem repeats contained within them, on a unified platform. Comparative analysis of novel or patient sequences with the reference sequences in RiDs db using FASTA search will indicate change in structure of repeats, if any, with a particular disorder. This database also provides links to orthologs in model organisms such as zebrafish, mouse and Drosophila. AVAILABILITY: The database is available for free at http://115.111.90.196/ridsdb/index.php.     

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.     

Mixed messages from multiple information sources on invasive species: a case of too much of a good thing?

Aim The increasing number and availability of online databases of alien species beg a question of their comparability given most do not adopt standard criteria in the definition of species status or taxonomic treatment and vary in their comprehensiveness. In this study, we compare the consistency of two major European databases for the regions they have in common. We assess whether they use consistent terminology to classify species status, provide similar taxonomic classification and coverage, deliver comparable estimates of alien richness per country and identify comparable correlates of alien richness. Location Northern Europe. Methods Data on the total number of alien species as well as the number of established alien species were extracted from the online databases DAISIE and NOBANIS for 13 European countries and classified into comparable taxonomic groups. Analyses across countries examined trends in alien species richness, correlations among taxonomic groups and the explanatory power of population density, country area and per capita GDP on alien species richness. Results Alien species richness, intertaxon correlations and the significance of individual drivers of invasion were all strongly database dependent. Differences were more marked for total numbers of aliens than established aliens. Over all taxonomic groups, DAISIE had lower species richness and fewer significant intertaxon correlations but presented a greater number of significant explanatory models of alien species richness. Trends in species richness were not generally correlated between the two databases with human population density being a more important driver in DAISIE while country area had greater explanatory power in NOBANIS. Main conclusions Considerable caution should be applied when collating data from different databases because often their underlying structure and content may differ markedly. For Europe, the analysis indicates that having two contrasting databases is not an ideal basis for implementing invasive species policy and moves should be made soon to establish a central pan‐European database.