Formation of convective cells in the scrape-off layer of the CASTOR tokamak

Understanding of the scrape-off layer (SOL) physics in tokamaks requires diagnostics with sufficient temporal and spatial resolution. This contribution describes results of experiments performed in the SOL of the CASTOR tokamak (R=40 cm, a = 6 cm) by means of a ring of 124 Langmuir probes surrounding the whole poloidal cross section. The individual probes measure either the ion saturation current of the floating potential with the spatial resolution up to 3 mm. Experiments are performed in a particular magnetic configuration, characterized by a long parallel connection length in the SOL, L_par ~q2piR. We report on measurements in discharges, where the edge electric field is modified by inserting a biased electrode into the edge plasma. In particular, a complex picture is observed, if the biased electrode is located inside the SOL. The poloidal distribution of the floating potential appears to be strongly non-uniform at biasing. The peaks of potential are observed at particular poloidal angles. This is interpreted as formation of a biased flux tube, which emanates from the electrode along the magnetic field lines and snakes q times around the torus. The resulting electric field in the SOL is 2-dimensional, having the radial as well as the poloidal component. It is demonstrated that the poloidal electric field E_pol convects the edge plasma radially due to the E_pol x B_T drift either inward or outward depending on its sign. The convective particle flux is by two orders of magnitude larger than the fluctuation-induced one and consequently dominates.Comment: 12th International Congress on Plasma Physics, 25-29 October 2004, Nice (France

Modeling of COMPASS tokamak divertor liquid metal experiments

Two small liquid metal targets based on the capillary porous structure were exposed to the divertor plasma of the tokamak COMPASS. The first target was wetted by pure lithium and the second one by a lithium-tin alloy, both releasing mainly lithium atoms (sputtering and evaporation) when exposed to plasma. Due to poorly conductive target material and steep surface inclination (implying the surface-perpendicular plasma heat flux 12-17 MW/m(2)) for 0.1-0.2 s, the LiSn target has reached 900 degrees C under ELMy H-mode. A model of heat conduction is developed and serves to evaluate the lithium sputtering and evaporation and, thus, the surface cooling by the released lithium and consequent radiative shielding. In these conditions, cooling of the surface by the latent heat of vapor did not exceed 1 MW/m(2). About 10(19) lithium atoms were evaporated (comparable to the COMPASS 1 m(3) plasma deuterium content), local Li pressure exceeded the deuterium plasma pressure. Since the radiating Li vapor cloud spreads over a sphere much larger than the hot spot, its cooling effect is negligible (0.2 MW/m(2)). We also predict zero lithium prompt redeposition, consistent with our observation.

Structural basis for CRISPR RNA-guided DNA recognition by Cascade

The CRISPR (clustered regularly interspaced short palindromic repeats) immune system in prokaryotes uses small guide RNAs to neutralize invading viruses and plasmids. In Escherichia coli, immunity depends on a ribonucleoprotein complex called Cascade. Here we present the composition and low-resolution structure of Cascade and show how it recognizes double-stranded DNA (dsDNA) targets in a sequence-specific manner. Cascade is a 405-kDa complex comprising five functionally essential CRISPR-associated (Cas) proteins (CasA1B2C6D1E1) and a 61-nucleotide CRISPR RNA (crRNA) with 5′-hydroxyl and 2′,3′-cyclic phosphate termini. The crRNA guides Cascade to dsDNA target sequences by forming base pairs with the complementary DNA strand while displacing the noncomplementary strand to form an R-loop. Cascade recognizes target DNA without consuming ATP, which suggests that continuous invader DNA surveillance takes place without energy investment. The structure of Cascade shows an unusual seahorse shape that undergoes conformational changes when it binds target DNA.

Overview of power exhaust experiments in the COMPASS divertor with liquid metals

Power handling experiments with a special liquid metal divertor module based on the capillary porous system technology were performed in the tokamak COMPASS. The performance of two metals (Li and LiSn alloy) were tested for the first time in a divertor under ELMy H-mode conditions. No damage of the capillary mesh and a good exhaust capability were observed for both metals in two separate experiments with up to 12 MW/m(2) of deposited perpendicular, inter-ELM steady-state heat flux and with ELMs of relative energy similar to 3% and a local peak energy fluence at the module similar to 15 kJ.m(-2). No droplets were directly ejected from the mesh top surface and for the LiSn experiment, no contamination of the core and SOL plasmas by Sn was observed. The elemental depth profile analysis of 14 stainless-steel samples located around the vacuum vessel for each experiment provides information about the migration of evaporated/redeposited liquid elements

Taming of the shrewd: novel eukaryotic genes from RNA viruses

Genomes of several yeast species contain integrated DNA copies of complete genomes or individual genes of non-retroviral double-strand RNA viruses as reported in a recent BMC Biology article by Taylor and Bruenn. The integrated virus-specific sequences are at least partially expressed and seem to evolve under pressure of purifying selection, indicating that these are functional genes. Together with similar reports on integrated copies of some animal RNA viruses, these results suggest that integration of DNA copies of non-reverse-transcribing RNA viruses might be much more common than previously thought. The integrated copies could contribute to acquired immunity to the respective viruses

Complex Risks from Old Urban Waste Landfills: Sustainability Perspective from Iasi, Romania

Landfills continue to represent the most frequent managerial practice for municipal solid wastes and an increasing and complex problem globally. In certain countries, a transition to an open society and free market is superimposed on the transition to sustainability, resulting in even higher complexity of management. This paper proposes an approach for problem-structuring of landfills in complex transitions: sustainability or unsustainability of a management approach is determined by a set of sustainability filters that are defined by sets of indicators and prioritized according the systemic concept of sustainability, which says that economy is embedded in society, which is embedded in nature. The writers exercise this approach with an old landfill in Iasi, Romania, and conclude for unsustainability, because the ecological sustainability filter is not successfully passed. Social and economic sustainability filters are also discussed in relation with the ecological sustainability indicators. The described approach allows a coherent, transdisciplinary synthesis of knowledge scattered across various disciplines, a pervasive problem in landfill management. The case study helps distinguish between generally true and context-dependent aspects.Peer reviewe

Pathogen-induced activation of disease-suppressive functions in the endophytic root microbiome

Microorganisms living inside plants can promote plant growth and health, but their genomic and functional diversity remain largely elusive. Here, metagenomics and network inference show that fungal infection of plant roots enriched for Chitinophagaceae and Flavobacteriaceae in the root endosphere and for chitinase genes and various unknown biosynthetic gene clusters encoding the production of nonribosomal peptide synthetases (NRPSs) and polyketide synthases (PKSs). After strain-level genome reconstruction, a consortium of Chitinophaga and Flavobacterium was designed that consistently suppressed fungal root disease. Site-directed mutagenesis then revealed that a previously unidentified NRPS-PKS gene cluster from Flavobacterium was essential for disease suppression by the endophytic consortium. Our results highlight that endophytic root microbiomes harbor a wealth of as yet unknown functional traits that, in concert, can protect the plant inside out.Microbial Biotechnolog

Construction and analysis of a modular model of caspase activation in apoptosis

<p>Abstract</p> <p>Background</p> <p>A key physiological mechanism employed by multicellular organisms is apoptosis, or programmed cell death. Apoptosis is triggered by the activation of caspases in response to both extracellular (extrinsic) and intracellular (intrinsic) signals. The extrinsic and intrinsic pathways are characterized by the formation of the death-inducing signaling complex (DISC) and the apoptosome, respectively; both the DISC and the apoptosome are oligomers with complex formation dynamics. Additionally, the extrinsic and intrinsic pathways are coupled through the mitochondrial apoptosis-induced channel via the Bcl-2 family of proteins.</p> <p>Results</p> <p>A model of caspase activation is constructed and analyzed. The apoptosis signaling network is simplified through modularization methodologies and equilibrium abstractions for three functional modules. The mathematical model is composed of a system of ordinary differential equations which is numerically solved. Multiple linear regression analysis investigates the role of each module and reduced models are constructed to identify key contributions of the extrinsic and intrinsic pathways in triggering apoptosis for different cell lines.</p> <p>Conclusion</p> <p>Through linear regression techniques, we identified the feedbacks, dissociation of complexes, and negative regulators as the key components in apoptosis. The analysis and reduced models for our model formulation reveal that the chosen cell lines predominately exhibit strong extrinsic caspase, typical of type I cell, behavior. Furthermore, under the simplified model framework, the selected cells lines exhibit different modes by which caspase activation may occur. Finally the proposed modularized model of apoptosis may generalize behavior for additional cells and tissues, specifically identifying and predicting components responsible for the transition from type I to type II cell behavior.</p