| 1. |
- Brouns, Stan J. J., et al.
(författare)
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Identification of the missing links in prokaryotic pentose oxidation pathways : evidence for enzyme recruitment
- 2006
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Ingår i: Journal of Biological Chemistry. - 0021-9258 .- 1083-351X. ; 281:37, s. 27378-27388
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Tidskriftsartikel (refereegranskat)abstract
- The pentose metabolism of Archaea is largely unknown. Here, we have employed an integrated genomics approach including DNA microarray and proteomics analyses to elucidate the catabolic pathway for D-arabinose in Sulfolobus solfataricus. During growth on this sugar, a small set of genes appeared to be differentially expressed compared with growth on D-glucose. These genes were heterologously overexpressed in Escherichia coli, and the recombinant proteins were purified and biochemically studied. This showed that D-arabinose is oxidized to 2-oxoglutarate by the consecutive action of a number of previously uncharacterized enzymes, including a D-arabinose dehydrogenase, a D-arabinonate dehydratase, a novel 2-keto-3-deoxy-D-arabinonate dehydratase, and a 2,5-dioxopentanoate dehydrogenase. Promoter analysis of these genes revealed a palindromic sequence upstream of the TATA box, which is likely to be involved in their concerted transcriptional control. Integration of the obtained biochemical data with genomic context analysis strongly suggests the occurrence of pentose oxidation pathways in both Archaea and Bacteria, and predicts the involvement of additional enzyme components. Moreover, it revealed striking genetic similarities between the catabolic pathways for pentoses, hexaric acids, and hydroxyproline degradation, which support the theory of metabolic pathway genesis by enzyme recruitment.
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| 2. |
- Van Oost, G., et al.
(författare)
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Turbulent transport reduction by E x B velocity shear during edge plasma biasing : recent experimental results
- 2003
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Ingår i: Plasma Physics and Controlled Fusion. - 0741-3335 .- 1361-6587. ; 45:5, s. 621-643
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Tidskriftsartikel (refereegranskat)abstract
- Experiments in the tokamaks TEXTOR, CASTOR, T-10 and ISTTOK, as well as in the reversed field pinch RFX have provided new and complementary evidence on the physics of the universal mechanism of E x B velocity shear stabilization of turbulence, concomitant transport barrier formation and radial conductivity by using various edge biasing techniques. In TEXTOR the causality between transport reduction and induced electric fields in the edge has been for the first time clearly demonstrated. The high electric field gradients have been identified as the cause for the quenching of turbulent cells. A quantitative analysis of the measured transport reduction is in good agreement with theoretical predictions. The scaling of plasma turbulence suppression with velocity shear has been established, revealing the density-potential cross-phase as a key element. Reduction in poloidal electric field, temperature, and density fluctuations across the shear layer lead to a reduction of the anomalous conducted and convected heat fluxes resulting in an energy transport barrier that is measured directly. In CASTOR the biasing electrode is placed at the separatrix in a non-intrusive configuration which has demonstrated strongly sheared electric fields and consequent improvement of the global particle confinement, as predicted by theory. The impact of sheared E x B flow on edge turbulent structures has been measured directly using a comprehensive set of electrostatic probe arrays as well as emissive probes. Measurements with a full poloidal Langmuir probe array have revealed quasi-coherent electrostatic waves in the SOL with a dominant mode number equal to the edge safety factor. In T-10 edge biasing is clearly improving the global performance of ECR heated discharges. Reflectometry and heavy ion beam probe measurements show the existence of a narrow plasma layer with strong suppression of turbulence. On ISTTOK, the influence of alternating positive and negative electrode and (non-intrusive) limiter biasing has been compared. Electrode biasing is found to be more efficient in modifying the radial electric field E, and confinement, limiter biasing acting mainly on the SOL. In the RFX reversed field pinch it has been demonstrated that also in RFPs biasing can increase the local E x B velocity shear in the edge region, and hence substantially reduce the local turbulence driven particle flux mainly due to a change in the relative phase between potential and density fluctuations.
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| 3. |
- Ettema, Thijs J G, et al.
(författare)
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Molecular characterization of a conserved archaeal copper resistance (cop) gene cluster and its copper-responsive regulator in Sulfolobus solfataricus P2.
- 2006
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Ingår i: Microbiology. - : Microbiology Society. - 1350-0872 .- 1465-2080. ; 152:Pt 7, s. 1969-79
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Tidskriftsartikel (refereegranskat)abstract
- Using a comparative genomics approach, a copper resistance gene cluster has been identified in multiple archaeal genomes. The cop cluster is predicted to encode a metallochaperone (CopM), a P-type copper-exporting ATPase (CopA) and a novel, archaea-specific transcriptional regulator (CopT) which might control the expression of the cop genes. Sequence analysis revealed that CopT has an N-terminal DNA-binding helix-turn-helix domain and a C-terminal TRASH domain; TRASH is a novel domain which has recently been proposed to be uniquely involved in metal-binding in sensors, transporters and trafficking proteins in prokaryotes. The present study describes the molecular characterization of the cop gene cluster in the thermoacidophilic crenarchaeon Sulfolobus solfataricus. The polycistronic copMA transcript was found to accumulate in response to growth-inhibiting copper concentrations, whereas copT transcript abundance appeared to be constitutive. DNA-binding assays revealed that CopT binds to the copMA promoter at multiple sites, both upstream and downstream of the predicted TATA-BRE site. Copper was found to specifically modulate the affinity of DNA binding by CopT. This study describes a copper-responsive operon in archaea, a new family of archaeal DNA-binding proteins, and supports the idea that this domain plays a prominent role in the archaeal copper response. A model is proposed for copper-responsive transcriptional regulation of the copMA gene cluster.
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| 4. |
- Legradi, J. B., et al.
(författare)
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An ecotoxicological view on neurotoxicity assessment
- 2018
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Ingår i: Environmental Sciences Europe. - : Springer. - 2190-4707 .- 2190-4715. ; 30
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Forskningsöversikt (refereegranskat)abstract
- The numbers of potential neurotoxicants in the environment are raising and pose a great risk for humans and the environment. Currently neurotoxicity assessment is mostly performed to predict and prevent harm to human populations. Despite all the efforts invested in the last years in developing novel in vitro or in silico test systems, in vivo tests with rodents are still the only accepted test for neurotoxicity risk assessment in Europe. Despite an increasing number of reports of species showing altered behaviour, neurotoxicity assessment for species in the environment is not required and therefore mostly not performed. Considering the increasing numbers of environmental contaminants with potential neurotoxic potential, eco-neurotoxicity should be also considered in risk assessment. In order to do so novel test systems are needed that can cope with species differences within ecosystems. In the field, online-biomonitoring systems using behavioural information could be used to detect neurotoxic effects and effect-directed analyses could be applied to identify the neurotoxicants causing the effect. Additionally, toxic pressure calculations in combination with mixture modelling could use environmental chemical monitoring data to predict adverse effects and prioritize pollutants for laboratory testing. Cheminformatics based on computational toxicological data from in vitro and in vivo studies could help to identify potential neurotoxicants. An array of in vitro assays covering different modes of action could be applied to screen compounds for neurotoxicity. The selection of in vitro assays could be guided by AOPs relevant for eco-neurotoxicity. In order to be able to perform risk assessment for eco-neurotoxicity, methods need to focus on the most sensitive species in an ecosystem. A test battery using species from different trophic levels might be the best approach. To implement eco-neurotoxicity assessment into European risk assessment, cheminformatics and in vitro screening tests could be used as first approach to identify eco-neurotoxic pollutants. In a second step, a small species test battery could be applied to assess the risks of ecosystems.
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| 5. |
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| 6. |
- Blombach, Fabian, et al.
(författare)
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Archaeal MBF1 binds to 30S and 70S ribosomes via its helix-turn-helix domain
- 2014
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Ingår i: Biochemical Journal. - 0264-6021 .- 1470-8728. ; 462, s. 373-384
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Tidskriftsartikel (refereegranskat)abstract
- MBF1 (multi-protein bridging factor 1) is a protein containing a conserved HTH (helix-turn-helix) domain in both eukaryotes and archaea. Eukaryotic MBF1 has been reported to function as a transcriptional co-activator that physically bridges transcription regulators with the core transcription initiation machinery of RNA polymerase II. In addition, MBF1 has been found to be associated with polyadenylated mRNA in yeast as well as in mammalian cells. aMBF1 (archaeal MBF1) is very well conserved among most archaeal lineages; however, its function has so far remained elusive. To address this, we have conducted a molecular characterization of this aMBF1. Affinity purification of interacting proteins indicates that aMBF1 binds to ribosomal subunits. On sucrose density gradients, aMBF1 co-fractionates with free 30S ribosomal subunits as well as with 70S ribosomes engaged in translation. Binding of aMBF1 to ribosomes does not inhibit translation. Using NMR spectroscopy, we show that aMBF1 contains a long intrinsically disordered linker connecting the predicted N-terminal zinc-ribbon domain with the C-terminal HTH domain. The HTH domain, which is conserved in all archaeal and eukaryotic MBF1 homologues, is directly involved in the association of aMBF1 with ribosomes. The disordered linker of the ribosome-bound aMBF1 provides the N-terminal domain with high flexibility in the aMBF1 ribosome complex. Overall, our findings suggest a role for aMBF1 in the archaeal translation process.
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| 7. |
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| 8. |
- Ettema, Thijs J. G., et al.
(författare)
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The non-phosphorylating glyceraldehyde-3-phosphate dehydrogenase (GAPN) of Sulfolobus solfataricus : a key-enzyme of the semi-phosphorylative branch of the Entner-Doudoroff pathway
- 2008
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Ingår i: Extremophiles. - : Springer Science and Business Media LLC. - 1431-0651 .- 1433-4909. ; 12:1, s. 75-88
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Tidskriftsartikel (refereegranskat)abstract
- Archaea utilize a branched modification of the classical Entner-Doudoroff (ED) pathway for sugar degradation. The semi-phosphorylative branch merges at the level of glyceraldehyde 3-phosphate (GAP) with the lower common shunt of the Emden-Meyerhof-Parnas pathway. In Sulfolobus solfataricus two different GAP converting enzymes-classical phosphorylating GAP dehydrogenase (GAPDH) and the non-phosphorylating GAPDH (GAPN)-were identified. In Sulfolobales the GAPN encoding gene is found adjacent to the ED gene cluster suggesting a function in the regulation of the semi-phosphorylative ED branch. The biochemical characterization of the recombinant GAPN of S. solfataricus revealed that-like the well-characterized GAPN from Thermoproteus tenax-the enzyme of S. solfataricus exhibits allosteric properties. However, both enzymes show some unexpected differences in co-substrate specificity as well as regulatory fine-tuning, which seem to reflect an adaptation to the different lifestyles of both organisms. Phylogenetic analyses and database searches in Archaea indicated a preferred distribution of GAPN (and/or GAP oxidoreductase) in hyperthermophilic Archaea supporting the previously suggested role of GAPN in metabolic thermoadaptation. This work suggests an important role of GAPN in the regulation of carbon degradation via modifications of the EMP and the branched ED pathway in hyperthermophilic Archaea.
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| 9. |
- Fortuna, E., et al.
(författare)
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Properties of co-deposited layers on graphite high heat flux components at the TEXTOR tokamak
- 2007
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Ingår i: Journal of Nuclear Materials. - : Elsevier. - 0022-3115 .- 1873-4820. ; 367:B, s. 1507-1511
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Tidskriftsartikel (refereegranskat)abstract
- The objective of this work was to examine the structure, composition and properties of co-deposited films from the TEXTOR tokamak. Hydrogenated films formed on the toroidal belt pump limiter (ALT-II), and on the ICRF antenna grill were studied using a set of material analysis techniques. Plasma edge diagnostics were used to assess the parameters influencing the film formation during discharges auxiliary heated by ICRF. The essential results are summarized as follows: (i) the distribution of plasma impurities co-deposited in the films is non-uniform and (ii) the surface topography, crystallographic structure, fuel retention and composition (i.e., content of re-deposited plasma impurities) of the films show significant diversity depending on the location where they were formed. These differences are associated with the local geometry, the tokamak operation scenarios and the resulting plasma edge properties.
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| 10. |
- Tendler, Michael, et al.
(författare)
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Models for transitions into regimes with enhanced confinement
- 2002
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Ingår i: Comments on modern physics. - 1560-5892. ; 2:6, s. C203-C214
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Tidskriftsartikel (refereegranskat)abstract
- The model based upon the concept of E x B flow velocity shear suppression is explained. It is asserted that there are models enabling to understand the physics involved in L-H transitions. The issue is more whether one wishes to employ the theoretical results available in order to interpret the reality.
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