iMolTalk: an interactive, internet-based protein structure analysis server

iMolTalk (http://i.moltalk.org) is a new and interactive web server for protein structure analysis. It addresses the need to identify and highlight biochemically important regions in protein structures. As input, the server requires only the four-digit Protein Data Bank (PDB) identifier, of an experimentally determined structure or a structure file in PDB format stemming e.g. from comparative modelling. iMolTalk offers a wide range of implemented tools (i) to extract general information from PDB files, such as generic header information or the sequence derived from three-dimensional co-ordinates; (ii) to map corresponding residues from sequence to structure; (iii) to search for contacts of residues (amino or nucleic acids) or heterogeneous groups to the protein, present cofactors and substrates; and (iv) to identify protein-protein interfaces between chains in a structure. The server provides results as user-friendly two-dimensional graphical representations and in textual format, ideal for further processing. At any time during the analysis, the user can choose, for the following step, from the set of implemented tools or submit his/her own script to the server to extend the functionality of iMolTalk

Using public participation to sample trace metals in lake surface sediments: the OPAL Metals Survey

Members of the public in England were invited in 2010 to take part in a national metals survey, by collecting samples of littoral sediment from a standing water body for geochemical analysis. To our knowledge, this is the first national sediment metals survey using public participation and reveals a snapshot of the extent of metals contamination in ponds and lakes across England. Hg, Ni, Cu, Zn and Pb concentrations exceeding sediment quality guidelines for the health of aquatic biota are ubiquitous in ponds and lakes, not just in areas with a legacy of industrial activity. To validate the public sampling approach, a calibration exercise was conducted at ten water bodies selected to represent a range of lakes found across England. Sediment concentrations of Hg, Ni, Cu, Zn and Pb were measured in samples of soil, stream and littoral and deep water sediment to assess inputs. Significant differences between littoral sediment metal concentrations occur due to local variability, but also organic content, especially in upland, peat soil catchments. Variability of metal concentrations between littoral samples is shown to be low in small (<20 ha) lowland lakes. Larger and upland lakes with more complex inputs and variation in organic content of littoral samples have a greater variability. Collection of littoral sediments in small lakes and ponds, with or without voluntary participation, can provide a reliable sampling technique for the preliminary assessment of metal contamination in standing waters. However, the heterogeneity of geology, soils and history/extent of metal contamination in the English landscape, combined with the random nature of sample collection, shows that systematic sampling for evaluating the full extent of metal contamination in lakes is still required

Comment on "Raman spectroscopy study of NaxCoO2 and superconducting NaxCoO2 yH2O"

The effect of surface degradation of the thermolectric cobaltite on Raman spectra is discussed and compared to experimental results from Co3O4 single crystals. We conclude that on NaCl flux grown NaxCoO2 crystals a surface layer of Co3O4 easily forms that leads to the observation of an intense phonon around 700 cm-1 [Phys. Rev. B 70, 052502 (2004)]. Raman spectra on freshly cleaved crystals from optical floating zone ovens do not show such effects and have a high frequency phonon cut-off at approximately 600 cm -1 [Phys. Rev. Lett 96, 167204 (2006)]. We discuss the relation of structural dimensionality, electronic correlations and the high frequency phonon cut-off of the thermolectric cobaltite.Comment: 2 pages, 1 figure, to be published in Phys. Rev. B (2007

Quality assurance in stereotactic radiosurgery/radiotherapy according to DIN 6875-1

The new DIN (' Deutsche Industrie- Norm') 6875- 1, which is currently being finalised, deals with quality assurance ( QA) criteria and tests methods for linear accelerator and Gamma Knife stereotactic radiosurgery/ radiotherapy including treatment planning, stereotactic frame and stereotactic imaging and a system test to check the whole chain of uncertainties. Our existing QA program, based on dedicated phantoms and test procedures, has been refined to fulfill the demands of this new DIN. The radiological and mechanical isocentre corresponded within 0.2 mm and the measured 50% isodose lines were in agreement with the calculated ones within less than 0.5 mm. The measured absorbed dose was within 3%. The resultant output factors measured for the 14-, 8- and 4- mm collimator helmet were 0.9870 +/- 0.0086, 0.9578 +/- 0.0057 and 0.8741 +/- 0.0202, respectively. For 170 consecutive tests, the mean geometrical accuracy was 0.48 +/- 0.23 mm. Besides QA phantoms and analysis software developed in- house, the use of commercially available tools facilitated the QA according to the DIN 6875- 1 with which our results complied. Copyright (C) 2004 S. Karger AG, Basel

Structural Insight into How Bacteria Prevent Interference between Multiple Divergent Type IV Secretion Systems

Prokaryotes use type IV secretion systems (T4SSs) to translocate substrates (e.g., nucleoprotein, DNA, and protein) and/or elaborate surface structures (i.e., pili or adhesins). Bacterial genomes may encode multiple T4SSs, e.g., there are three functionally divergent T4SSs in some Bartonella species (vir, vbh, and trw). In a unique case, most rickettsial species encode a T4SS (rvh) enriched with gene duplication. Within single genomes, the evolutionary and functional implications of cross-system interchangeability of analogous T4SS protein components remains poorly understood. To lend insight into cross-system interchangeability, we analyzed the VirB8 family of T4SS channel proteins. Crystal structures of three VirB8 and two TrwG Bartonella proteins revealed highly conserved C-terminal periplasmic domain folds and dimerization interfaces, despite tremendous sequence divergence. This implies remarkable structural constraints for VirB8 components in the assembly of a functional T4SS. VirB8/TrwG heterodimers, determined via bacterial two-hybrid assays and molecular modeling, indicate that differential expression of trw and vir systems is the likely barrier to VirB8-TrwG interchangeability. We also determined the crystal structure of Rickettsia typhi RvhB8-II and modeled its coexpressed divergent paralog RvhB8-I. Remarkably, while RvhB8-I dimerizes and is structurally similar to other VirB8 proteins, the RvhB8-II dimer interface deviates substantially from other VirB8 structures, potentially preventing RvhB8-I/RvhB8-II heterodimerization. For the rvh T4SS, the evolution of divergent VirB8 paralogs implies a functional diversification that is unknown in other T4SSs. Collectively, our data identify two different constraints (spatiotemporal for Bartonella trw and vir T4SSs and structural for rvh T4SSs) that mediate the functionality of multiple divergent T4SSs within a single bacterium. IMPORTANCE:&nbsp; Assembly of multiprotein complexes at the right time and at the right cellular location is a fundamentally important task for any organism. In this respect, bacteria that express multiple analogous type IV secretion systems (T4SSs), each composed of around 12 different components, face an overwhelming complexity. Our work here presents the first structural investigation on factors regulating the maintenance of multiple T4SSs within a single bacterium. The structural data imply that the T4SS-expressing bacteria rely on two strategies to prevent cross-system interchangeability: (i) tight temporal regulation of expression or (ii) rapid diversification of the T4SS components. T4SSs are ideal drug targets provided that no analogous counterparts are known from eukaryotes. Drugs targeting the barriers to cross-system interchangeability (i.e., regulators) could dysregulate the structural and functional independence of discrete systems, potentially creating interference that prevents their efficient coordination throughout bacterial infection.</p

"I am your mother and your father!": In vitro derived gametes and the ethics of solo reproduction

In this paper, we will discuss the prospect of human reproduction achieved with gametes originating from only one person. According to statements by a minority of scientists working on the generation of gametes in vitro, it may become possible to create eggs from men’s non-reproductive cells and sperm from women’s. This would enable, at least in principle, the creation of an embryo from cells obtained from only one individual: ‘solo reproduction’. We will consider what might motivate people to reproduce in this way, and the implications that solo reproduction might have for ethics and policy. We suggest that such an innovation is unlikely to revolutionise reproduction and parenting. Indeed, in some respects it is less revolutionary than in vitro fertilisation as a whole. Furthermore, we show that solo reproduction with in vitro created gametes is not necessarily any more ethically problematic than gamete donation—and probably less so. Where appropriate, we draw parallels with the debate surrounding reproductive cloning. We note that solo reproduction may serve to perpetuate reductive geneticised accounts of reproduction, and that this may indeed be ethically questionable. However, in this it is not unique among other technologies of assisted reproduction, many of which focus on genetic transmission. It is for this reason that a ban on solo reproduction might be inconsistent with continuing to permit other kinds of reproduction that also bear the potential to strengthen attachment to a geneticised account of reproduction. Our claim is that there are at least as good reasons to pursue research towards enabling solo reproduction, and eventually to introduce solo reproduction as an option for fertility treatment, as there are to do so for other infertility related purposes

Searching a Dark Photon with HADES

We present a search for the e+e- decay of a hypothetical dark photon, also names U vector boson, in inclusive dielectron spectra measured by HADES in the p (3.5 GeV) + p, Nb reactions, as well as the Ar (1.756 GeV/u) + KCl reaction. An upper limit on the kinetic mixing parameter squared epsilon^{2} at 90% CL has been obtained for the mass range M(U) = 0.02 - 0.55 GeV/c2 and is compared with the present world data set. For masses 0.03 - 0.1 GeV/c^2, the limit has been lowered with respect to previous results, allowing now to exclude a large part of the parameter region favoured by the muon g-2 anomaly. Furthermore, an improved upper limit on the branching ratio of 2.3 * 10^{-6} has been set on the helicity-suppressed direct decay of the eta meson, eta-> e+e-, at 90% CL

An upper limit on hypertriton production in collisions of Ar(1.76 AGeV)+KCl

A high-statistic data sample of Ar(1.76 AGeV)+KCl events recorded with HADES is used to search for a hypertriton signal. An upper production limit per centrality-triggered event of $1.04$ x $10^{-3}$ on the $3\sigma$ level is derived. Comparing this value with the number of successfully reconstructed $\Lambda$ hyperons allows to determine an upper limit on the ratio $N_{_{\Lambda}^3H}/N_{\Lambda}$, which is confronted with statistical and coalescence-type model calculations