Profillinie 5: Kommunikation, Medien, Technik:

Die Forschungsprofillinie 5 “Kommunikation, Medien, Technik” entstand im Jahr 2005 aus der ursprünglichen Profillinie “Medien, Kommunikation und Informationstechnologien”. Sie zeigt heute eine deutlich stärkere Vernetzung über die verschiedenen Fakultäten hinweg, als das die bisherige Ausrichtung des Profils leisten konnte. Der wesentliche Unterschied zu den anderen Forschungsprofillinien der Technischen Universität Chemnitz besteht darin, dass hier der Mensch als der Nutzer technischer Systeme im Zentrum steht. Dies bedeutet jedoch nicht, dass vor allem sozial-, verhaltens- und kulturwissenschaftlich orientierte Professuren die Forschungsprofillinie tragen. Ganz im Gegenteil ist gerade in diesem Themenbereich eine enge Kooperation von naturwissenschaftlichen und technischen Disziplinen auf der einen Seite und sozialwissenschaftlichen Fächern auf der anderen Seite gefordert

Hard x-ray characterization of a HEFT single-reflection prototype

We have measured the hard X-ray reflectivity and imaging performance from depth graded W/Si multilayer coated mirror segments mounted in a single reflection cylindrical prototype for the hard X-ray telescopes to be flown on the High Energy Focusing Telescope (HEFT) balloon mission. Data have been obtained in the energy range from 18 - 170 keV at the European Synchrotron Radiation Facility and at the Danish Space Research Institute at 8 keV. The modeling of the reflectivity data demonstrate that the multilayer structure can be well described by the intended power law distribution of the bilayer thicknesses optimized for the telescope performance and we find that all the data is consistent with an interfacial width of 4.5 Å. We have also demonstrated that the required 5% uniformity of the coatings is obtained over the mirror surface and we have shown that it is feasible to use similar W/Si coatings for much higher energies than the nominal energy range of HEFT leading the way for designing Gamma-ray telescopes for future astronomical applications. Finally we have demonstrate 35 arcsecond Half Power Diameter imaging performance of the one bounce prototype throughout the energy range of the HEFT telescopes

The MOF-containing NSL complex associates globally with housekeeping genes, but activates only a defined subset

The MOF (males absent on the first)-containing NSL (non-specific lethal) complex binds to a subset of active promoters in Drosophila melanogaster and is thought to contribute to proper gene expression. The determinants that target NSL to specific promoters and the circumstances in which the complex engages in regulating transcription are currently unknown. Here, we show that the NSL complex primarily targets active promoters and in particular housekeeping genes, at which it colocalizes with the chromatin remodeler NURF (nucleosome remodeling factor) and the histone methyltransferase Trithorax. However, only a subset of housekeeping genes associated with NSL are actually activated by it. Our analyses reveal that these NSL-activated promoters are depleted of certain insulator binding proteins and are enriched for the core promoter motif ‘Ohler 5’. Based on these results, it is possible to predict whether the NSL complex is likely to regulate a particular promoter. We conclude that the regulatory capacity of the NSL complex is highly context-dependent. Activation by the NSL complex requires a particular promoter architecture defined by combinations of chromatin regulators and core promoter motifs

ZOOTAXA

www.mapress.com/zootaxa

The RNA workbench: Best practices for RNA and high-throughput sequencing bioinformatics in Galaxy

RNA-based regulation has become a major research topic in molecular biology. The analysis of epigenetic and expression data is therefore incomplete if RNA-based regulation is not taken into account. Thus, it is increasingly important but not yet standard to combine RNA-centric data and analysis tools with other types of experimental data such as RNA-seq or ChIP-seq. Here, we present the RNA workbench, a comprehensive set of analysis tools and consolidated workflows that enable the researcher to combine these two worlds. Based on the Galaxy framework the workbench guarantees simple access, easy extension, flexible adaption to personal and security needs, and sophisticated analyses that are independent of command-line knowledge. Currently, it includes more than 50 bioinformatics tools that are dedicated to different research areas of RNA biology including RNA structure analysis, RNA alignment, RNA annotation, RNA-protein interaction, ribosome profiling, RNA-seq analysis and RNA target prediction. The workbench is developed and maintained by experts in RNA bioinformatics and the Galaxy framework. Together with the growing community evolving around this workbench, we are committed to keep the workbench up-to-date for future standards and needs, providing researchers with a reliable and robust framework for RNA data analysis

A defect of sphingolipid metabolism modifies the properties of normal appearing white matter in multiple sclerosis

Maintaining the appropriate complement and content of lipids in cellular membranes is critical for normal neural function. Accumulating evidence suggests that even subtle perturbations in the lipid content of neurons and myelin can disrupt their function and may contribute to myelin and axonal degradation. In this study, we determined the composition and quantified the content of lipids and sterols in normal appearing white matter (NAWM) and normal appearing grey matter (NAGM) from control and multiple sclerosis brain tissues by electrospray ionization tandem mass spectrometry. Our results suggest that in active-multiple sclerosis, there is a shift in the lipid composition of NAWM and NAGM to a higher phospholipid and lower sphingolipid content. We found that this disturbance in lipid composition was reduced in NAGM but not in NAWM of inactive-multiple sclerosis. The pattern of disturbance in lipid composition suggests a metabolic defect that causes sphingolipids to be shuttled to phospholipid production. Modelling the biophysical consequence of this change in lipid composition of NAWM indicated an increase in the repulsive force between opposing bilayers that could explain decompaction and disruption of myelin structure

Hard x-ray characterization of a HEFT single-reflection prototype

We have measured the hard X-ray reflectivity and imaging performance from depth graded W/Si multilayer coated mirror segments mounted in a single reflection cylindrical prototype for the hard X-ray telescopes to be flown on the High Energy Focusing Telescope (HEFT) balloon mission. Data have been obtained in the energy range from 18 - 170 keV at the European Synchrotron Radiation Facility and at the Danish Space Research Institute at 8 keV. The modeling of the reflectivity data demonstrate that the multilayer structure can be well described by the intended power law distribution of the bilayer thicknesses optimized for the telescope performance and we find that all the data is consistent with an interfacial width of 4.5 Å. We have also demonstrated that the required 5% uniformity of the coatings is obtained over the mirror surface and we have shown that it is feasible to use similar W/Si coatings for much higher energies than the nominal energy range of HEFT leading the way for designing Gamma-ray telescopes for future astronomical applications. Finally we have demonstrate 35 arcsecond Half Power Diameter imaging performance of the one bounce prototype throughout the energy range of the HEFT telescopes

Towards a molecular dynamics consensus view of B-DNA flexibility

We present a systematic study of B-DNA flexibility in aqueous solution using long-scale molecular dynamics simulations with the two more recent versions of nucleic acids force fields (CHARMM27 and parmbsc0) using four long duplexes designed to contain several copies of each individual base pair step. Our study highlights some differences between pambsc0 and CHARMM27 families of simulations, but also extensive agreement in the representation of DNA flexibility. We also performed additional simulations with the older AMBER force fields parm94 and parm99, corrected for non-canonical backbone flips. Taken together, the results allow us to draw for the first time a consensus molecular dynamics picture of B-DNA flexibility

Transcriptional Regulation: Effects of Promoter Proximal Pausing on Speed, Synchrony and Reliability

Recent whole genome polymerase binding assays in the Drosophila embryo have shown that a substantial proportion of uninduced genes have pre-assembled RNA polymerase-II transcription initiation complex (PIC) bound to their promoters. These constitute a subset of promoter proximally paused genes for which mRNA elongation instead of promoter access is regulated. This difference can be described as a rearrangement of the regulatory topology to control the downstream transcriptional process of elongation rather than the upstream transcriptional initiation event. It has been shown experimentally that genes with the former mode of regulation tend to induce faster and more synchronously, and that promoter-proximal pausing is observed mainly in metazoans, in accord with a posited impact on synchrony. However, it has not been shown whether or not it is the change in the regulated step per se that is causal. We investigate this question by proposing and analyzing a continuous-time Markov chain model of PIC assembly regulated at one of two steps: initial polymerase association with DNA, or release from a paused, transcribing state. Our analysis demonstrates that, over a wide range of physical parameters, increased speed and synchrony are functional consequences of elongation control. Further, we make new predictions about the effect of elongation regulation on the consistent control of total transcript number between cells. We also identify which elements in the transcription induction pathway are most sensitive to molecular noise and thus possibly the most evolutionarily constrained. Our methods produce symbolic expressions for quantities of interest with reasonable computational effort and they can be used to explore the interplay between interaction topology and molecular noise in a broader class of biochemical networks. We provide general-purpose code implementing these methods