Non-Coding RNAs in Neural Networks, REST-Assured

In the nervous system, several key steps in cellular complexity and development are regulated by non-coding RNAs (ncRNAs) and the repressor element-1 silencing transcription factor/neuron-restrictive silencing factor (REST/NRSF). REST recruits gene regulatory complexes to regulatory sequences, among them the repressor element-1/neuron-restrictive silencer element, and mediates developmental stage-specific gene expression or repression, chromatin (re-)organization or silencing for protein-coding genes as well as for several ncRNAs like microRNAs, short interfering RNAs or long ncRNAs. NcRNAs are far from being just transcriptional noise and are involved in chromatin accessibility, transcription and post-transcriptional processing, trafficking, or RNA editing. REST and its cofactor CoREST are both highly regulated through various ncRNAs. The importance of the correct regulation within the ncRNA network, the ncRNAome, is demonstrated when it comes to a deregulation of REST and/or ncRNAs associated with molecular pathophysiology underlying diverse disorders including neurodegenerative diseases or brain tumors

InP-quantum dots in Al0.20Ga0.80InP with different barrier configurations

Systematic ensemble photoluminescence studies have been performed on type-I InP-quantum dots in Al0.20Ga0.80InP barriers, emitting at approximately 1.85 eV at 5 K. The influence of different barrier configurations as well as the incorporation of additional tunnel barriers on the optical properties has been investigated. The confinement energy between the dot barrier and the surrounding barrier layers, which is the sum of the band discontinuities for the valence and the conduction bands, was chosen to be approximately 190 meV by using Al0.50Ga0.50InP. In combination with 2 nm thick AlInP tunnel barriers, the internal quantum efficiency of these barrier configurations can be increased by up to a factor of 20 at elevated temperatures with respect to quantum dots without such layers.Comment: physica status solidi (c) (Proceedings of QD 2008

Crystal structure of THEP1 from the hyperthermophile Aquifex aeolicus: a variation of the RecA fold

RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are.Abstract Background aaTHEP1, the gene product of aq_1292 from Aquifex aeolicus, shows sequence homology to proteins from most thermophiles, hyperthermophiles, and higher organisms such as man, mouse, and fly. In contrast, there are almost no homologous proteins in mesophilic unicellular microorganisms. aaTHEP1 is a thermophilic enzyme exhibiting both ATPase and GTPase activity in vitro. Although annotated as a nucleotide kinase, such an activity could not be confirmed for aaTHEP1 experimentally and the in vivo function of aaTHEP1 is still unknown. Results Here we report the crystal structure of selenomethionine substituted nucleotide-free aaTHEP1 at 1.4 Å resolution using a multiple anomalous dispersion phasing protocol. The protein is composed of a single domain that belongs to the family of 3-layer (α/β/α)-structures consisting of nine central strands flanked by six helices. The closest structural homologue as determined by DALI is the RecA family. In contrast to the latter proteins, aaTHEP1 possesses an extension of the β-sheet consisting of four additional β-strands. Conclusion We conclude that the structure of aaTHEP1 represents a variation of the RecA fold. Although the catalytic function of aaTHEP1 remains unclear, structural details indicate that it does not belong to the group of GTPases, kinases or adenosyltransferases. A mainly positive electrostatic surface indicates that aaTHEP1 might be a DNA/RNA modifying enzyme. The resolved structure of aaTHEP1 can serve as paradigm for the complete THEP1 family.Published versio

Signals Involved in Regulation of Hepatitis C Virus RNA Genome Translation and Replication

Hepatitis C Virus (HCV) preferentially replicates in the human liver and frequently causes chronic infection, often leading to cirrhosis and liver cancer. HCV is an enveloped virus classified in the genus Hepacivirus in the family Flaviviridae and has a single-stranded RNA genome of positive orientation. The HCV RNA genome is translated and replicated in the cytoplasm. Translation is controlled by the Internal Ribosome Entry Site (IRES) in the 5´untranslated region (5´UTR), while also downstream elements like the cis-replication element (CRE) in the coding region and the 3´UTR are involved in translation regulation. The cis-elements controlling replication of the viral RNA genome are located mainly in the 5´- and 3´-UTRs at the genome ends but also in the protein coding region, and in part these signals overlap with the signals controlling RNA translation. Many long-range RNA-RNA interactions (LRIs) are predicted between different regions of the HCV RNA genome, and several such LRIs are actually involved in HCV translation and replication regulation. A number of RNA cis-elements recruit cellular RNA-binding proteins that are involved in the regulation of HCV translation and replication. In addition, the liver-specific microRNA-122 (miR-122) binds to two target sites at the 5´end of the viral RNA genome as well as to at least three additional target sites in the coding region and the 3´UTR. It is involved in the regulation of HCV RNA stability, translation and replication, thereby largely contributing to the hepatotropism of HCV. However, we are still far from completely understanding all interactions that regulate HCV RNA genome translation, stability, replication and encapsidation. In particular, many conclusions on the function of cis-elements in HCV replication have been obtained using full-length HCV genomes or near-full-length replicon systems. These include both genome ends, making it difficult to decide if a cis-element in question acts on HCV replication when physically present in the plus strand genome or in the minus strand antigenome. Therefore, it may be required to use reduced systems that selectively focus on the analysis of HCV minus strand initiation and/or plus strand initiation

Generation and functional analysis of an octameric C3d construct to act as a molecular adjuvant in vaccine design

This thesis investigated two separate theoretical advancements for vaccine design: (1) present antigen in a self-forming natural C4b binding protein-based octameric array (to engage multiple adjacent B-cell receptors or BCR) and (2) combined with fusion to a molecular adjuvant C3d or C3dg, to cross-link C3d-receptor (complement receptor 2 (CR2) CD21). Initially, yellow fluorescent protein test antigen was evaluated, but only to monitor intracellular and extracellular protein levels for a range of C3 forms: C3dg (smallest covalently bound CR1/factor I processed form of activated C3) or C3d (non-complement enzyme processed C3), as well as consequence of mutating the internal thioester bond (C988S, 'C3dsg7 C3ds) that may confound recombinant production of C3dg/C3d fragments. The test antigen was then switched to hen egg lysozyme (HEL), with the hope that spider-like HEL octamer arrays would be expressed with the C3dg/C3d fused proteins at the outermost reach. Mutating the thioester bond increased expression for both C3 forms, and C3dsg-fusion octamers expressed at the highest levels, although C3ds had the highest binding for human CR2. Receptor binding was considered more important for vaccine function, leading to the prototype vaccine, hC3ds-HEL-Oct. Further dissection of the CR2-C3d interaction utilised cell-based assays and surface plasmon resonance (SPR) analysis, using dimeric immunoglobulin Fc-fusion recombinant forms of human C3d, C3dg and murine C3d. All C3dg/C3d Fc proteins bound strongly, although cross-species murine C3d Fc binding to human CR2 was 2-3 times higher than human counterparts. In vivo production of total immunoglobulin G (IgG) and IgM levels was measured, following injection of hC3ds-HEL-Oct, either as DNA or purified protein, and showed successful initiation of a HEL-specific immune response. Data suggested that CpG sequences may have a detrimental impact on vaccine function. These results highlight the power and flexibility of the octamer approach as well as C3d and their applications in vivo and in vitro

"What's (the) Matter?", A Show on Elementary Particle Physics with 28 Demonstration Experiments

We present the screenplay of a physics show on particle physics, by the Physikshow of Bonn University. The show is addressed at non-physicists aged 14+ and communicates basic concepts of elementary particle physics including the discovery of the Higgs boson in an entertaining fashion. It is also demonstrates a successful outreach activity heavily relying on the university physics students. This paper is addressed at anybody interested in particle physics and/or show physics. This paper is also addressed at fellow physicists working in outreach, maybe the experiments and our choice of simple explanations will be helpful. Furthermore, we are very interested in related activities elsewhere, in particular also demonstration experiments relevant to particle physics, as often little of this work is published. Our show involves 28 live demonstration experiments. These are presented in an extensive appendix, including photos and technical details. The show is set up as a quest, where 2 students from Bonn with the aid of a caretaker travel back in time to understand the fundamental nature of matter. They visit Rutherford and Geiger in Manchester around 1911, who recount their famous experiment on the nucleus and show how particle detectors work. They travel forward in time to meet Lawrence at Berkeley around 1950, teaching them about the how and why of accelerators. Next, they visit Wu at DESY, Hamburg, around 1980, who explains the strong force. They end up in the LHC tunnel at CERN, Geneva, Switzerland in 2012. Two experimentalists tell them about colliders and our heroes watch live as the Higgs boson is produced and decays. The show was presented in English at Oxford University and University College London, as well as Padua University and ICTP Trieste. It was 1st performed in German at the Deutsche Museum, Bonn (5/'14). The show has eleven speaking parts and involves in total 20 people.Comment: 113 pages, 88 figures. An up to date version of the paper with high resolution pictures can be found at http://www.th.physik.uni-bonn.de/People/dreiner/Downloads/. In v2 the acknowledgements and a citation are correcte