Cyclic endoperoxides of β-carotene, potential pro-oxidants, as products of chemical quenching of singlet oxygen

AbstractPhotoprotection by carotenoids is generally considered to be based on the photophysical quenching of triplets and singlet oxygen. There is also accumulating evidence of an alternative, chemical quenching of triplets and singlet oxygen by carotenoids. We report the identification of relatively stable cyclic mono- and diendoperoxides as first products of such an alternative reaction. Nevertheless, these species remain reactive and in the dark cause autooxidation of β-carotene in our model system. Their formation could explain the intriguing pro-oxidant and cytotoxic activity of carotenoids

Masterclasses in Quantenphysik

Im Rahmen des Exzellenzclusters QuantumFrontiers werden Masterclasses konzipiert, die Themen aus den Forschungsbereichen des Clusters vermitteln. Die Zielgruppe sind dabei vor allem Schülerinnen und Schüler der gymnasialen Oberstufe, aber es werden auch Angebote für Lehrkräfte und ausgesuchte (z.B. Wettbewerbs-) Gruppen konzipiert. Die Lernenden sollen durch eine Kombination aus Workshops, eigenständigem Lernen und Experimentieren, Laborführungen und Kontakt zu Wissenschaftlerinnen und Wissenschaftler an ein konkretes Forschungsthema herangeführt werden. An den beiden Clusterstandorten Braunschweig und Hannover werden Kurse zu verschiedenen Themen konzipiert in deren Durchführung auch Forschende der beteiligten Institutionen LUH, PTB und TU BS mit einbezogen werden. Somit verfolgen die Masterclasses nicht nur das Ziel die Schülerinnen und Schüler für Physik zu begeistern, sondern bieten ebenfalls eine wertvolle Lehrerfahrung für (Nachwuchs- ) Wissenschaftlerinnen und Wissenschaftler. Die größte inhaltliche Herausforderung dieses Formats ist die Aufarbeitung aktueller Forschungsthemen – thematisch oft gar nicht oder nur teilweise in den Lehrplänen verankert – auf ein angemessenes fachliches Niveau.

Masterclasses in Quantenphysik

Im Rahmen des Exzellenzclusters QuantumFrontiers werden Masterclasses konzipiert, die Themen aus den Forschungsbereichen des Clusters vermitteln. Die Zielgruppe sind dabei vor allem Schülerinnen und Schüler der gymnasialen Oberstufe, aber es werden auch Angebote für Lehrkräfte und ausgesuchte (z.B. Wettbewerbs-) Gruppen konzipiert. Die Lernenden sollen durch eine Kombination aus Workshops, eigenständigem Lernen und Experimentieren, Laborführungen und Kontakt zu Wissenschaftlerinnen und Wissenschaftler an ein konkretes Forschungsthema herangeführt werden. An den beiden Clusterstandorten Braunschweig und Hannover werden Kurse zu verschiedenen Themen konzipiert in deren Durchführung auch Forschende der beteiligten Institutionen LUH, PTB und TU BS mit einbezogen werden. Somit verfolgen die Masterclasses nicht nur das Ziel die Schülerinnen und Schüler für Physik zu begeistern, sondern bieten ebenfalls eine wertvolle Lehrerfahrung für (Nachwuchs- ) Wissenschaftlerinnen und Wissenschaftler. Die größte inhaltliche Herausforderung dieses Formats ist die Aufarbeitung aktueller Forschungsthemen – thematisch oft gar nicht oder nur teilweise in den Lehrplänen verankert – auf ein angemessenes fachliches Niveau.

Non-Equilibrium Quasiclassical Theory for Josephson Structures

We present a non-equilibrium quasiclassical formalism suitable for studying linear response ac properties of Josephson junctions. The non-equilibrium self-consistency equations are satisfied, to very good accuracy, already in zeroth iteration. We use the formalism to study ac Josephson effect in a ballistic superconducting point contact. The real and imaginary parts of the ac linear conductance are calculated both analytically (at low frequencies) and numerically (at arbitrary frequency). They show strong temperature, frequency, and phase dependence. Many anomalous properties appear near phi = pi. We ascribe them to the presence of zero energy bound states.Comment: 11 pages, 9 figures, Final version to appear in PR

Lysimeter-based full fertilizer 15N balances corroborate direct dinitrogen emission measurements using the 15N gas flow method

The $^{15}$N gas flux ($^{15}$NGF) method allows for direct in situ quantification of dinitrogen (N$_2$) emissions from soils, but a successful cross-comparison with another method is missing. The objectives of this study were to quantify N$_2$ emissions of a wheat rotation using the $^{15}$NGF method, to compare these N$_2$ emissions with those obtained from a lysimeter-based $^{15}$N fertilizer mass balance approach, and to contextualize N$_2$ emissions with $^{15}$N enrichment of N$_2$ in soil air. For four sampling periods, fertilizer-derived N$_2$ losses ($^{15}$NGF method) were similar to unaccounted fertilizer N fates as obtained from the $^{15}$N mass balance approach. Total N$_2$ emissions ($^{15}$NGF method) amounted to 21 ± 3 kg N ha− 1, with 13 ± 2 kg N ha− 1 (7.5% of applied fertilizer N) originating from fertilizer. In comparison, the $^{15}$N mass balance approach overall indicated fertilizer-derived N$_2$ emissions of 11%, equivalent to 18 ± 13 kg N ha− 1. Nitrous oxide (N$_2$O) emissions were small (0.15 ± 0.01 kg N ha− 1 or 0.1% of fertilizer N), resulting in a large mean N$_2$:(N$_2$O + N$_2$) ratio of 0.94 ± 0.06. Due to the applied drip fertigation, ammonia emissions accounted for < 1% of fertilizer-N, while N leaching was negligible. The temporal variability of N$_2$ emissions was well explained by the δ$^{15}$N$_2$ in soil air down to 50 cm depth. We conclude the $^{15}$NGF method provides realistic estimates of field N$_2$ emissions and should be more widely used to better understand soil N$_2$ losses. Moreover, combining soil air δ$^{15}$N$_2$ measurements with diffusion modeling might be an alternative approach for constraining soil N$_2$ emissions

Dynamic Modelling under Uncertainty: The Case of Trypanosoma brucei Energy Metabolism

Kinetic models of metabolism require detailed knowledge of kinetic parameters. However, due to measurement errors or lack of data this knowledge is often uncertain. The model of glycolysis in the parasitic protozoan Trypanosoma brucei is a particularly well analysed example of a quantitative metabolic model, but so far it has been studied with a fixed set of parameters only. Here we evaluate the effect of parameter uncertainty. In order to define probability distributions for each parameter, information about the experimental sources and confidence intervals for all parameters were collected. We created a wiki-based website dedicated to the detailed documentation of this information: the SilicoTryp wiki (http://silicotryp.ibls.gla.ac.uk/wiki/Glycolysis). Using information collected in the wiki, we then assigned probability distributions to all parameters of the model. This allowed us to sample sets of alternative models, accurately representing our degree of uncertainty. Some properties of the model, such as the repartition of the glycolytic flux between the glycerol and pyruvate producing branches, are robust to these uncertainties. However, our analysis also allowed us to identify fragilities of the model leading to the accumulation of 3-phosphoglycerate and/or pyruvate. The analysis of the control coefficients revealed the importance of taking into account the uncertainties about the parameters, as the ranking of the reactions can be greatly affected. This work will now form the basis for a comprehensive Bayesian analysis and extension of the model considering alternative topologies

The Annotation, Mapping, Expression and Network (AMEN) suite of tools for molecular systems biology

<p>Abstract</p> <p>Background</p> <p>High-throughput genome biological experiments yield large and multifaceted datasets that require flexible and user-friendly analysis tools to facilitate their interpretation by life scientists. Many solutions currently exist, but they are often limited to specific steps in the complex process of data management and analysis and some require extensive informatics skills to be installed and run efficiently.</p> <p>Results</p> <p>We developed the Annotation, Mapping, Expression and Network (AMEN) software as a stand-alone, unified suite of tools that enables biological and medical researchers with basic bioinformatics training to manage and explore genome annotation, chromosomal mapping, protein-protein interaction, expression profiling and proteomics data. The current version provides modules for (i) uploading and pre-processing data from microarray expression profiling experiments, (ii) detecting groups of significantly co-expressed genes, and (iii) searching for enrichment of functional annotations within those groups. Moreover, the user interface is designed to simultaneously visualize several types of data such as protein-protein interaction networks in conjunction with expression profiles and cellular co-localization patterns. We have successfully applied the program to interpret expression profiling data from budding yeast, rodents and human.</p> <p>Conclusion</p> <p>AMEN is an innovative solution for molecular systems biological data analysis freely available under the GNU license. The program is available via a website at the Sourceforge portal which includes a user guide with concrete examples, links to external databases and helpful comments to implement additional functionalities. We emphasize that AMEN will continue to be developed and maintained by our laboratory because it has proven to be extremely useful for our genome biological research program.</p

p53 and TAp63 promote keratinocyte proliferation and differentiation in breeding tubercles of the zebrafish

p63 is a multi-isoform member of the p53 family of transcription factors. There is compelling genetic evidence that ΔNp63 isoforms are needed for keratinocyte proliferation and stemness in the developing vertebrate epidermis. However, the role of TAp63 isoforms is not fully understood, and TAp63 knockout mice display normal epidermal development. Here, we show that zebrafish mutants specifically lacking TAp63 isoforms, or p53, display compromised development of breeding tubercles, epidermal appendages which according to our analyses display more advanced stratification and keratinization than regular epidermis, including continuous desquamation and renewal of superficial cells by derivatives of basal keratinocytes. Defects are further enhanced in TAp63/p53 double mutants, pointing to partially redundant roles of the two related factors. Molecular analyses, treatments with chemical inhibitors and epistasis studies further reveal the existence of a linear TAp63/p53->Notch->caspase 3 pathway required both for enhanced proliferation of keratinocytes at the base of the tubercles and their subsequent differentiation in upper layers. Together, these studies identify the zebrafish breeding tubercles as specific epidermal structures sharing crucial features with the cornified mammalian epidermis. In addition, they unravel essential roles of TAp63 and p53 to promote both keratinocyte proliferation and their terminal differentiation by promoting Notch signalling and caspase 3 activity, ensuring formation and proper homeostasis of this self-renewing stratified epithelium