tropiTree:an NGS-based EST-SSR resource for 24 tropical tree species

The development of genetic tools for non-model organisms has been hampered by cost, but advances in next-generation sequencing (NGS) have created new opportunities. In ecological research, this raises the prospect for developing molecular markers to simultaneously study important genetic processes such as gene flow in multiple non-model plant species within complex natural and anthropogenic landscapes. Here, we report the use of bar-coded multiplexed paired-end Illumina NGS for the de novo development of expressed sequence tag-derived simple sequence repeat (EST-SSR) markers at low cost for a range of 24 tree species. Each chosen tree species is important in complex tropical agroforestry systems where little is currently known about many genetic processes. An average of more than 5,000 EST-SSRs was identified for each of the 24 sequenced species, whereas prior to analysis 20 of the species had fewer than 100 nucleotide sequence citations. To make results available to potential users in a suitable format, we have developed an open-access, interactive online database, tropiTree (http://bioinf.hutton.ac.uk/tropiTree), which has a range of visualisation and search facilities, and which is a model for the efficient presentation and application of NGS data

Genetic diversity of common guava in Kenya: an underutilized naturalized fruit species

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Cryo‐EM structure of MsbA in saposin‐lipid nanoparticles (Salipro) provides insights into nucleotide coordination

The ATP-binding cassette transporter MsbA is a lipid flippase, translocating lipid A, glycolipids, and lipopolysaccharides from the inner to the outer leaflet of the inner membrane of Gram-negative bacteria. It has been used as a model system for time-resolved structural studies as several MsbA structures in different states and reconstitution systems (detergent/nanodiscs/peptidiscs) are available. However, due to the limited resolution of the available structures, detailed structural information on the bound nucleotides has remained elusive. Here, we have reconstituted MsbA in saposin A–lipoprotein nanoparticles (Salipro) and determined the structure of ADP-vanadate-bound MsbA by single-particle cryo-electron microscopy to 3.5 Å resolution. This procedure has resulted in significantly improved resolution and enabled us to model all side chains and visualise detailed ADP-vanadate interactions in the nucleotide-binding domains. The approach may be applicable to other dynamic membrane proteins

Extending Drill-Down through Semantic Reasoning on Indicator Formulas

Performance indicators are calculated by composition of more basic pieces of information, and/or aggregated along a number of different dimensions. The multidimensional model is not able to take into account the compound nature of an indicator. In this work, we propose a semantic multidimensional model in which indicators are formally described together with the mathematical formulas needed for their computation. By exploiting the formal representation of formulas an extended drill-down operator is defined, which is capable to expand an indicator into its components, enabling a novel mode of data exploration. Effectiveness and efficiency are briefly discussed on a prototype introduced as a proof-of concept

A Suite of Models to Support the Quantitative Assessment of Spread in Pest Risk Analysis

Pest Risk Analyses (PRAs) are conducted worldwide to decide whether and how exotic plant pests should be regulated to prevent invasion. There is an increasing demand for science-based risk mapping in PRA. Spread plays a key role in determining the potential distribution of pests, but there is no suitable spread modelling tool available for pest risk analysts. Existing models are species specific, biologically and technically complex, and data hungry. Here we present a set of four simple and generic spread models that can be parameterised with limited data. Simulations with these models generate maps of the potential expansion of an invasive species at continental scale. The models have one to three biological parameters. They differ in whether they treat spatial processes implicitly or explicitly, and in whether they consider pest density or pest presence/absence only. The four models represent four complementary perspectives on the process of invasion and, because they have different initial conditions, they can be considered as alternative scenarios. All models take into account habitat distribution and climate. We present an application of each of the four models to the western corn rootworm, Diabrotica virgifera virgifera, using historic data on its spread in Europe. Further tests as proof of concept were conducted with a broad range of taxa (insects, nematodes, plants, and plant pathogens). Pest risk analysts, the intended model users, found the model outputs to be generally credible and useful. The estimation of parameters from data requires insights into population dynamics theory, and this requires guidance. If used appropriately, these generic spread models provide a transparent and objective tool for evaluating the potential spread of pests in PRAs. Further work is needed to validate models, build familiarity in the user community and create a database of species parameters to help realize their potential in PRA practice. © 2012 Robinet et al

Collaborative Building of an Ontology of Key Performance Indicators

none4In the present paper we propose a logic model for the representation of Key Performance Indicators (KPIs) that supports the construction of a valid reference model (or KPI ontology) by enabling the integration of definitions proposed by different engineers in a minimal and consistent system. In detail, the contribution of the paper is as follows: (i) we combine the descriptive semantics of KPIs with a logical representation of the formula used to calculate a KPI, allowing to make the algebraic relationships among indicators explicit; (ii) we discuss how this representation enables reasoning over KPI formulas to check equivalence of KPIs and overall consistency of the set of indicators, and present an empirical study on the efficiency of the reasoning; (iii) we present a prototype implementing the approach to collaboratively manage a shared ontology of KPI definitions.noneDiamantini, Claudia; Genga, Laura; Potena, Domenico; Storti, EmanueleDiamantini, Claudia; Genga, Laura; Potena, Domenico; Storti, Emanuel