Investigating the microstructure of plant leaves in 3D with lab-based X-ray Computed Tomography

Background Leaf cellular architecture plays an important role in setting limits for carbon assimilation and, thus, photosynthetic performance. However, the low density, fine structure, and sensitivity to desiccation of plant tissue has presented challenges to its quantification. Classical methods of tissue fixation and embedding prior to 2D microscopy of sections is both laborious and susceptible to artefacts that can skew the values obtained. Here we report an image analysis pipeline that provides quantitative descriptors of plant leaf intercellular airspace using lab-based X-ray Computed Tomography (microCT). We demonstrate successful visualisation and quantification of differences in leaf intercellular airspace in 3D for a range of species (including both dicots and monocots) and provide a comparison with a standard 2D analysis of leaf sections. Results We used the microCT image pipeline to obtain estimates of leaf porosity and mesophyll exposed surface area (Smes) for three dicot species (Arabidopsis, tomato and pea) and three monocot grasses (barley, oat and rice). The imaging pipeline consisted of (1) a masking operation to remove the background airspace surrounding the leaf, (2) segmentation by an automated threshold in ImageJ and then (3) quantification of the extracted pores using the ImageJ ‘Analyze Particles’ tool. Arabidopsis had the highest porosity and lowest Smes for the dicot species whereas barley had the highest porosity and the highest Smes for the grass species. Comparison of porosity and Smes estimates from 3D microCT analysis and 2D analysis of sections indicates that both methods provide a comparable estimate of porosity but the 2D method may underestimate Smes by almost 50%. A deeper study of porosity revealed similarities and differences in the asymmetric distribution of airspace between the species analysed. Conclusions Our results demonstrate the utility of high resolution imaging of leaf intercellular airspace networks by lab-based microCT and provide quantitative data on descriptors of leaf cellular architecture. They indicate there is a range of porosity and Smes values in different species and that there is not a simple relationship between these parameters, suggesting the importance of cell size, shape and packing in the determination of cellular parameters proposed to influence leaf photosynthetic performance

Genetic algorithms and their application to in silico evolution of genetic regulatory networks

“The original publication is available at www.springerlink.com”. Copyright SpringerA genetic algorithm (GA) is a procedure that mimics processes occurring in Darwinian evolution to solve computational problems. A GA introduces variation through "mutation" and "recombination" in a "population" of possible solutions to a problem, encoded as strings of characters in "genomes," and allows this population to evolve, using selection procedures that favor the gradual enrichment of the gene pool with the genomes of the "fitter" individuals. GAs are particularly suitable for optimization problems in which an effective system design or set of parameter values is sought.In nature, genetic regulatory networks (GRNs) form the basic control layer in the regulation of gene expression levels. GRNs are composed of regulatory interactions between genes and their gene products, and are, inter alia, at the basis of the development of single fertilized cells into fully grown organisms. This paper describes how GAs may be applied to find functional regulatory schemes and parameter values for models that capture the fundamental GRN characteristics. The central ideas behind evolutionary computation and GRN modeling, and the considerations in GA design and use are discussed, and illustrated with an extended example. In this example, a GRN-like controller is sought for a developmental system based on Lewis Wolpert's French flag model for positional specification, in which cells in a growing embryo secrete and detect morphogens to attain a specific spatial pattern of cellular differentiation.Peer reviewe

A retrospective analysis to explore the applicability of fish biomarkers and sediment bioassays along contaminated salinity transects

Biological-effects monitoring in estuarine environments is complex as a result of strong gradients and fluctuations in salinity and other environmental conditions, which may influence contaminant bioavailability and the physiology and metabolism of the organisms. To select the most robust and reliable biological-effect methods for monitoring and assessment programmes, a large-scale field study was conducted in two estuarine transects in the Netherlands. The locations ranged from heavily polluted harbour areas (the ports of Rotterdam and Amsterdam) to cleaner coastal and freshwater sites. Assessment methods used included a variety of biomarkers in flounder (Platichthys flesus) and a range of in vitro (sediment extracts) and in vivo bioassays. Multivariate statistical analysis was applied to investigate correlations and relationships between various biological effects and contaminant levels in flounder liver or sediments. Several biological methods seemed to be too much affected by salinity differences for routine use in estuaries. The most discriminative biomarkers in the study were hepatic metallothionein content and biliary 1-OH pyrene in fish. Mechanism-based in vitro assays DR-CALUX and ER-CALUX applied to sediment extracts for screening of potential toxicity were much more responsive than in vivo bioassays with macro-invertebrates using survival as an endpoin

WS-PGRADE/gUSE Generic DCI Gateway Framework for a Large Variety of User Communities

The WS-PGRADE/gUSE generic DCI gateway framework has been developed to support a large variety of user communities. It provides a generic purpose, workflow-oriented graphical user interface to create and run workflows on various DCIs including clusters, Grids, desktop Grids and clouds. The framework can be used by NGIs to support small user communities who cannot afford to develop their own customized science gateway. The WS- PGRADE/gUSE framework also provides two API interfaces (Application Specific Module API and Remote API) to create application-specific science gateways according to the needs of different user communities. The paper describes in detail the workflow concept of WS-PGRADE, the DCI Bridge service that enables access to most of the popular European DCIs and the Application Specific Module and Remote API concepts to generate application-specific science gateways. © 2012 Springer Science+Business Media Dordrecht