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

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

A capture approach for supercoiled plasmid DNA using a triplex-forming oligonucleotide

This is the final version of the article. Available from the publisher via the DOI in this record.Proteins that recognize and bind specific sites in DNA are essential for regulation of numerous biological functions. Such proteins often require a negative supercoiled DNA topology to function correctly. In current research, short linear DNA is often used to study DNA-protein interactions. Although linear DNA can easily be modified, for capture on a surface, its relaxed topology does not accurately resemble the natural situation in which DNA is generally negatively supercoiled. Moreover, specific binding sequences are flanked by large stretches of non-target sequence in vivo. Here, we present a straightforward method for capturing negatively supercoiled plasmid DNA on a streptavidin surface. It relies on the formation of a temporary parallel triplex, using a triple helix forming oligonucleotide containing locked nucleic acid nucleotides. All materials required for this method are commercially available. Lac repressor binding to its operator was used as model system. Although the dissociation constants for both the linear and plasmid-based operator are in the range of 4 nM, the association and dissociation rates of Lac repressor binding to the plasmid-based operator are ~18 times slower than on a linear fragment. This difference underscores the importance of using a physiologically relevant DNA topology for studying DNA-protein interactions.Netherlands Organisation for Scientific Research and the Netherlands Institute for Space Research [ALW-GO-PL/ 08-08]; NWO Vidi grant [864.11.005 to S.J.J.B.]. Funding for open access charge: Microbiology department/ Wageningen UR library

Error estimates for solid-state density-functional theory predictions: an overview by means of the ground-state elemental crystals

Predictions of observable properties by density-functional theory calculations (DFT) are used increasingly often in experimental condensed-matter physics and materials engineering as data. These predictions are used to analyze recent measurements, or to plan future experiments. Increasingly more experimental scientists in these fields therefore face the natural question: what is the expected error for such an ab initio prediction? Information and experience about this question is scattered over two decades of literature. The present review aims to summarize and quantify this implicit knowledge. This leads to a practical protocol that allows any scientist - experimental or theoretical - to determine justifiable error estimates for many basic property predictions, without having to perform additional DFT calculations. A central role is played by a large and diverse test set of crystalline solids, containing all ground-state elemental crystals (except most lanthanides). For several properties of each crystal, the difference between DFT results and experimental values is assessed. We discuss trends in these deviations and review explanations suggested in the literature. A prerequisite for such an error analysis is that different implementations of the same first-principles formalism provide the same predictions. Therefore, the reproducibility of predictions across several mainstream methods and codes is discussed too. A quality factor Delta expresses the spread in predictions from two distinct DFT implementations by a single number. To compare the PAW method to the highly accurate APW+lo approach, a code assessment of VASP and GPAW with respect to WIEN2k yields Delta values of 1.9 and 3.3 meV/atom, respectively. These differences are an order of magnitude smaller than the typical difference with experiment, and therefore predictions by APW+lo and PAW are for practical purposes identical.Comment: 27 pages, 20 figures, supplementary material available (v5 contains updated supplementary material

Measurement of the ability of science students to recognize business opportunities

This paper describes the development of an instrument measuring students’ ability to recognize business opportunities. Recognition of business opportunities where others do not is one of the basic qualities of entrepreneurs, and therefore needs attention in entrepreneurship education. However, only a few studies have been published on how to teach students to recognize business opportunities. Since the recognition of business opportunities is a context specific form of creativity in entrepreneurship, creativity theories, models, techniques, and instruments can be used in education aiming at the acquisition of competencies for opportunity recognition. Based on existing models on measuring creativity and opportunity recognition the Perception of Opportunity Recognition Ability (PORA) questionnaire has been constructed. Reliability analysis was used to check the internal consistency of the scales. Two PORA-scales proved to be reliable: Divergent Thinking and Self-Efficacy. Correlation analysis was used to explore the relationships between the PORA-scales. There was a strong, positive correlation between the scale Self-Efficacy and three other scales: Divergent Thinking, Problem Solving Style and Handling Extrinsic Restraints. For validation the outcomes of the PORA-test have been compared with the results of the Entrepreneurial Attitude Orientation test. The results are supported by findings reported in literature

Opportunity recognition in entrepreneurship education, design principles on fostering competent entrepreneurs in the science domain

This paper is part of a research project focusing on educational design principles that should help students with a background in Science to become competent with respect to opportunity recognition in business. The recognition of business opportunities is one of the basic competencies of entrepreneurs, and therefore needs attention in entrepreneurship education. Based on existing models, theories and prior experiences we developed and implemented several design principles in a course for students in a Master of Science and Business at Utrecht University. The evaluation and analysis of the learning process and the learning outcomes showed the merits of the principles on intrinsic motivation, avoiding environmental constraints, using prior knowledge and stimulating idea generation in the teaching of opportunity recognition

High resolution effect-directed analysis of steroid hormone (ant)agonists in surface and wastewater quality monitoring

Monitoring of chemical water quality is extremely challenging due to the large variety of compounds and the presence of biologically active compounds with unknown chemical identity. Previously, we developed a high resolution Effect-Directed Analysis (EDA) platform that combines liquid chromatography with high resolution mass spectrometry and parallel bioassay detection. In this study, the platform is combined with CALUX bioassays for (anti)androgenic, estrogenic and glucocorticoid activities, and the performance of the platform is evaluated. It appeared to render very repeatable results, with high recoveries of spiked compounds and high consistency between the mass spectrometric and bioassay results. Application of the platform to wastewater treatment plant effluent and surface water samples led to the identification of several compounds contributing to the measured activities. Eventually, a workflow is proposed for the application of the platform in a routine monitoring context. The workflow divides the platform into four phases, of which one to all can be performed depending on the research question and the results obtained. This allows one to make a balance between the effort put into the platform and the certainty and depth by which active compounds will be identified. The EDA platform is a valuable tool to identify unknown bioactive compounds, both in an academic setting as in the context of legislative, governmental or routine monitoring