Challenges in Data Intensive Analysis at Scientific Experimental User Facilities

Today's scientific challenges such as routes to a sustainable energy future, materials by design or biological and chemical environmental remediation methods, are complex problems that require the integration of a wide range of complementary expertise to be addressed successfully. Experimental and computational science research methods can hereby offer fundamental insights for their solution. Experimental facilities in particular can contribute through a large variety of investigative methods, which can span length scales from millions of kilometers (radar) to the sub-nucleus (LHC). These methods are used to probe structure, properties, and function of objects from single elements to whole communities. Hereby direct imaging techniques are a powerful means to develop an atomistic understanding of scientific issues. For example, the identification ofmechanisms associated with chemical, material, and biological transformations requires the direct observation of the reactions to build up an understanding of the atom-by-atom structural and chemical changes. Computational science can aid the planning of such experiments, correlate results, explain or predict the phenomena as they would be observed and thus aid their interpretation. Furthermore computational science can be essential for the investigation of phenomena that are difficult to observe due to their scale, reaction time or extreme conditions. Combining experimental and computational techniques provides scientists with the ability to research structures and processes at various levels of theory, e.g. providing molecular 'movies' of complex reactions that show bond breaking and reforming in natural time scales, along with the intermediate states to understand the mechanisms that govern the chemical transformations. This chapter will discuss the critical data intensive analysis challenges faced by the experimental science community at large scale and laboratory based facilities. The chapter will highlight current solutions and lay out perspectives for the future, such as methods to achieve real time analysis capabilities and the challenges and opportunities of data integration across experimental scales, levels of theory, and varying techniques

Development and geometry of isotropic and directional shrinkage crack patterns

We have studied shrinkage crack patterns which form when a thin layer of an alumina/water slurry dries. Both isotropic and directional drying were studied. The dynamics of the pattern formation process and the geometric properties of the isotropic crack patterns are similar to what is expected from recent models, assuming weak disorder. There is some evidence for a gradual increase in disorder as the drying layer become thinner, but no sudden transition, in contrast to what has been seen in previous experiments. The morphology of the crack patterns is influenced by drying gradients and front propagation effects, with sharp gradients having a strong orienting and ordering effect.Comment: 8 pages, 11 figures, 8 in jpg format, 3 in postscript. See also http://mobydick.physics.utoronto.ca/mud.htm

Geothermal direct use engineering and design guidebook

The Geothermal Direct Use Engineering and Design Guidebook is designed to be a comprehensive, thoroughly practical reference guide for engineers and designers of direct heat projects. These projects could include the conversion of geothermal energy into space heating cooling of buildings, district heating, greenhouse heating, aquaculture and industrial processing. The Guidebook is directed at understanding the nature of geothermal resources and the exploration of these resources, fluid sampling techniques, drilling, and completion of geothermal wells through well testing, and reservoir evaluation. It presents information useful to engineers on the specification of equipment including well pumps, piping, heat exchangers, space heating equipment, heat pumps and absorption refrigeration. A compilation of current information about greenhouse, aquaculture and industrial applications is included together with a discussion of engineering cost analysis, regulation requirements, and environmental considerations. The purpose of the Guidebook is to provide an integrated view for the development of direct use projects for which there is a very potential in the United States

Cten Is Targeted by Kras Signalling to Regulate Cell Motility in the Colon and Pancreas

CTEN/TNS4 is an oncogene in colorectal cancer (CRC) which enhances cell motility although the mechanism of Cten regulation is unknown. We found an association between high Cten expression and KRAS/BRAF mutation in a series of CRC cell lines (p = 0.03) and hypothesised that Kras may regulate Cten. To test this, Kras was knocked-down (using small interfering (si)RNA) in CRC cell lines SW620 and DLD1 (high Cten expressors and mutant for KRAS). In each cell line, Kras knockdown was mirrored by down-regulation of Cten Since Kras signals through Braf, we tested the effect of Kras knockdown in CRC cell line Colo205 (which shows high Cten expression and is mutant for BRAF but wild type for KRAS). Cten levels were unaffected by Kras knockdown whilst Braf knockdown resulted in reduced Cten expression suggesting that Kras signals via Braf to regulate Cten. Quantification of Cten mRNA and protein analysis following proteasome inhibition suggested that regulation was of Cten transcription. Kras knockdown inhibited cell motility. To test whether this could be mediated through Cten, SW620 cells were co-transfected with Kras specific siRNAs and a Cten expression vector. Restoring Cten expression was able to restore cell motility despite Kras knockdown (transwell migration and wounding assay, p<0.001 for both). Since KRAS is mutated in many cancers, we investigated whether this relationship could be demonstrated in other tumour models. The experiments were repeated in the pancreatic cancer cell lines Colo357 & PSN-1(both high Cten expressors and mutant for KRAS). In both cell lines, Kras was shown to regulate Cten and forced expression of Cten was able to rescue loss of cell motility following Kras knockdown in PSN-1 (transwell migration assay, p<0.001). We conclude that, in the colon and pancreas, Cten is a downstream target of Kras and may be a mechanism through which Kras regulates of cell motility

Photosynthetic electron flow affects H2O2 signaling by inactivation of catalase in Chlamydomonas reinhardtii

A specific signaling role for H2O2 in Chlamydomonas reinhardtii was demonstrated by the definition of a promoter that specifically responded to this ROS. Expression of a nuclear-encoded reporter gene driven by this promoter was shown to depend not only on the level of exogenously added H2O2 but also on light. In the dark, the induction of the reporter gene by H2O2 was much lower than in the light. This lower induction was correlated with an accelerated disappearance of H2O2 from the culture medium in the dark. Due to a light-induced reduction in catalase activity, H2O2 levels in the light remained higher. Photosynthetic electron transport mediated the light-controlled down-regulation of the catalase activity since it was prevented by 3-(3′4′-dichlorophenyl)-1,1-dimethylurea (DCMU), an inhibitor of photosystem II. In the presence of light and DCMU, expression of the reporter gene was low while the addition of aminotriazole, a catalase inhibitor, led to a higher induction of the reporter gene by H2O2 in the dark. The role of photosynthetic electron transport and thioredoxin in this regulation was investigated by using mutants deficient in photosynthetic electron flow and by studying the correlation between NADP-malate dehydrogenase and catalase activities. It is proposed that, contrary to expectations, a controlled down-regulation of catalase activity occurs upon a shift of cells from dark to light. This down-regulation apparently is necessary to maintain a certain level of H2O2 required to activate H2O2-dependent signaling pathways

Fracture Patterns Induced by Desiccation in a Thin Layer

We study a theoretical model of mud cracks, that is, the fracture patterns resulting from the contraction with drying in a thin layer of a mixture of granules and water. In this model, we consider the slip on the bottom of this layer and the relaxation of the elastic field that represents deformation of the layer. Analysis of the one-dimensional model gives results for the crack size that are consistent with experiments. We propose an analytical method of estimation for the growth velocity of a simple straight crack to explain the very slow propagation observed in actual experiments. Numerical simulations reveal the dependence of qualitative nature of the formation of crack patterns on material properties.Comment: 37 pages,18 figures,REVTEX,submitted to Rhys.Rev.

Enhancement of carotenoids biosynthesis in Chlamydomonas reinhardtii by nuclear transformation using a phytoene synthase gene isolated from Chlorella zofingiensis

The isolation and characterization of the phytoene synthase gene from the green microalga Chlorella zofingiensis (CzPSY), involved in the first step of the carotenoids biosynthetic pathway, have been performed. CzPSY gene encodes a polypeptide of 420 amino acids. A single copy of CzPSY has been found in C. zofingiensis by Southern blot analysis. Heterologous genetic complementation in Escherichia coli showed the ability of the predicted protein to catalyze the condensation of two molecules of geranylgeranyl pyrophosphate (GGPP) to form phytoene. Phylogenetic analysis has shown that the deduced protein forms a cluster with the rest of the phytoene synthases (PSY) of the chlorophycean microalgae studied, being very closely related to PSY of plants. This new isolated gene has been adequately inserted in a vector and expressed in Chlamydomonas reinhardtii. The overexpression of CzPSY in C. reinhardtii, by nuclear transformation, has led to an increase in the corresponding CzPSY transcript level as well as in the content of the carotenoids violaxanthin and lutein which were 2.0- and 2.2-fold higher than in untransformed cells. This is an example of manipulation of the carotenogenic pathway in eukaryotic microalgae, which can open up the possibility of enhancing the productivity of commercial carotenoids by molecular engineering