Divergent roles of CprK paralogues from Desulfitobacterium hafniense in activating gene expression

Gene duplication and horizontal gene transfer play an important role in the evolution of prokaryotic genomes. We have investigated the role of three CprK paralogues from the cAMP receptor protein-fumarate and nitrate reduction regulator (CRP-FNR) family of transcriptional regulators that are encoded in the genome of Desulfitobacterium hafniense DCB-2 and possibly regulate expression of genes involved in the energy-conserving terminal reduction of organohalides (halorespiration). The results from in vivo and in vitro promoter probe assays show that two regulators (CprK1 and CprK2) have an at least partially overlapping effector specificity, with preference for ortho-chlorophenols, while meta-chlorophenols proved to be effectors for CprK4. The presence of a potential transposase-encoding gene in the vicinity of the cprK genes indicates that their redundancy is probably caused by mobile genetic elements. The CprK paralogues activated transcription from promoters containing a 14 bp inverted repeat (dehalobox) that closely resembles the FNR-box. We found a strong negative correlation between the rate of transcriptional activation and the number of nuclecitide changes from the optimal dehalobox sequence (TTAAT-N-4-ATTAA). Transcription was initiated by CprK4 from a promoter that is situated upstream of a gene encoding a methyl-accepting chemotaxis protein. This might be the first indication of taxis of an anaerobic bacterium to halogenated aromatic compounds

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

Contribution to fusion research from IAEA coordinated research projects and joint experiments

The paper presents objectives and activities of IAEA Coordinated Research Projects 'Conceptual development of steady-state compact fusion neutron sources' and 'Utilisation of a network of small magnetic confinement fusion devices for mainstream fusion research'. The background and main projects of the CRP on FNS are described in detail, as this is a new activity at IAEA. Recent activities of the second CRP, which continues activities of previous CRPs, are overviewed

Extremofiele micro-organismen: some like it hot

Een duik nemen in de Noordzee op nieuwjaarsdag vinden we behoorlijk stoer. De Russen doen er een schepje bovenop door het begin van de winter te vieren met een duik in ijswater van nul graden. Dat valt best wel mee, zeker wanneer je dit afwisselt met een bezoek aan de sauna met een luchttemperatuur van 90 graden. Hiermee hebben we de extremen die we als mens kunnen trotseren echter wel gehad. Wat te denken van een duik in kokend water, zwemmen in een zwembad gevuld met azijn of ammonia, of kokend zwavelzuur? Wat voor ons onmogelijk is, is voor veel micro-organismen de normaalste zaak van de werel

Trace models of concurrent valuation algebras

This paper introduces Concurrent Valuation Algebras (CVAs), extending ordered valuation algebras (OVAs) by incorporating two combine operators representing parallel and sequential products that adhere to a weak exchange law. CVAs present significant theoretical and practical advantages for specifying and modelling concurrent and distributed systems. As a presheaf on a space of domains, a CVA facilitates localised specifications, promoting modularity, compositionality, and the capability to represent large and complex systems. Moreover, CVAs facilitate lattice-based refinement reasoning, and are compatible with standard methodologies such as Hoare and Rely-Guarantee logics. We demonstrate the flexibility of CVAs through three trace models that represent distinct paradigms of concurrent/distributed computing, and interrelate them via morphisms. We also discuss the potential for importing a powerful local computation framework from valuation algebras for the model checking of concurrent and distributed systems.Comment: 25 page

Are Medieval Mya arenaria (Mollusca; Bivalvia) in the Netherlands also clams before Columbus?

During the Pleistocene, the coastal marine bivalve mollusc Mya arenaria became extinct in northwest Europe. The species remained present in North America. Datings of Mya shells found in northern Denmark and the southern Baltic Sea suggest that repopulation of northwest European coasts already occurred before Columbus' discovery of America (1492), possibly facilitated by Viking (Norse) settlers at Greenland and northeast North America. In this paper we report on findings of M. arenaria at five locations in the coastal landscape of the Netherlands: polders reclaimed from the Wadden Sea and the former estuaries of Oer-IJ and Old Rhine. The shells from four of these locations also date before 1492 AD

Fidelity in Archaeal Information Processing

A key element during the flow of genetic information in living systems is fidelity. The accuracy of DNA replication influences the genome size as well as the rate of genome evolution. The large amount of energy invested in gene expression implies that fidelity plays a major role in fitness. On the other hand, an increase in fidelity generally coincides with a decrease in velocity. Hence, an important determinant of the evolution of life has been the establishment of a delicate balance between fidelity and variability. This paper reviews the current knowledge on quality control in archaeal information processing. While the majority of these processes are homologous in Archaea, Bacteria, and Eukaryotes, examples are provided of nonorthologous factors and processes operating in the archaeal domain. In some instances, evidence for the existence of certain fidelity mechanisms has been provided, but the factors involved still remain to be identified