ConSole: using modularity of contact maps to locate solenoid domains in protein structures.

BackgroundPeriodic proteins, characterized by the presence of multiple repeats of short motifs, form an interesting and seldom-studied group. Due to often extreme divergence in sequence, detection and analysis of such motifs is performed more reliably on the structural level. Yet, few algorithms have been developed for the detection and analysis of structures of periodic proteins.ResultsConSole recognizes modularity in protein contact maps, allowing for precise identification of repeats in solenoid protein structures, an important subgroup of periodic proteins. Tests on benchmarks show that ConSole has higher recognition accuracy as compared to Raphael, the only other publicly available solenoid structure detection tool. As a next step of ConSole analysis, we show how detection of solenoid repeats in structures can be used to improve sequence recognition of these motifs and to detect subtle irregularities of repeat lengths in three solenoid protein families.ConclusionsThe ConSole algorithm provides a fast and accurate tool to recognize solenoid protein structures as a whole and to identify individual solenoid repeat units from a structure. ConSole is available as a web-based, interactive server and is available for download at http://console.sanfordburnham.org

Cancer3D: understanding cancer mutations through protein structures.

The new era of cancer genomics is providing us with extensive knowledge of mutations and other alterations in cancer. The Cancer3D database at http://www.cancer3d.org gives an open and user-friendly way to analyze cancer missense mutations in the context of structures of proteins in which they are found. The database also helps users analyze the distribution patterns of the mutations as well as their relationship to changes in drug activity through two algorithms: e-Driver and e-Drug. These algorithms use knowledge of modular structure of genes and proteins to separately study each region. This approach allows users to find novel candidate driver regions or drug biomarkers that cannot be found when similar analyses are done on the whole-gene level. The Cancer3D database provides access to the results of such analyses based on data from The Cancer Genome Atlas (TCGA) and the Cancer Cell Line Encyclopedia (CCLE). In addition, it displays mutations from over 14,700 proteins mapped to more than 24,300 structures from PDB. This helps users visualize the distribution of mutations and identify novel three-dimensional patterns in their distribution

PDBFlex: exploring flexibility in protein structures.

The PDBFlex database, available freely and with no login requirements at http://pdbflex.org, provides information on flexibility of protein structures as revealed by the analysis of variations between depositions of different structural models of the same protein in the Protein Data Bank (PDB). PDBFlex collects information on all instances of such depositions, identifying them by a 95% sequence identity threshold, performs analysis of their structural differences and clusters them according to their structural similarities for easy analysis. The PDBFlex contains tools and viewers enabling in-depth examination of structural variability including: 2D-scaling visualization of RMSD distances between structures of the same protein, graphs of average local RMSD in the aligned structures of protein chains, graphical presentation of differences in secondary structure and observed structural disorder (unresolved residues), difference distance maps between all sets of coordinates and 3D views of individual structures and simulated transitions between different conformations, the latter displayed using JSMol visualization software

MTO1 mediates tissue specificity of OXPHOS defects via tRNA modification and translation optimization, which can be bypassed by dietary intervention

Mitochondrial diseases often exhibit tissue-specific pathologies, but this phenomenon is poorly understood. Here we present regulation of mitochondrial translation by the Mitochondrial Translation Optimization Factor 1, MTO1, as a novel player in this scenario. We demonstrate that MTO1 mediates tRNA modification and controls mitochondrial translation rate in a highly tissue-specific manner associated with tissue-specific OXPHOS defects. Activation of mitochondrial proteases, aberrant translation products, as well as defects in OXPHOS complex assembly observed in MTO1 deficient mice further imply that MTO1 impacts translation fidelity. In our mouse model, MTO1-related OXPHOS deficiency can be bypassed by feeding a ketogenic diet. This therapeutic intervention is independent of the MTO1-mediated tRNA modification and involves balancing of mitochondrial and cellular secondary stress responses. Our results thereby establish mammalian MTO1 as a novel factor in the tissue-specific regulation of OXPHOS and fine tuning of mitochondrial translation accurac

Seizures, ataxia and parvalbumin-expressing interneurons respond to selenium supply in Selenop-deficient mice

Mice with constitutive disruption of the Selenop gene have been key to delineate the importance of selenoproteins in neurobiology. However, the phenotype of this mouse model is exquisitely dependent on selenium supply and timing of selenium supplementation. Combining biochemical, histological, and behavioral methods, we tested the hypothesis that parvalbumin-expressing interneurons in the primary somatosensory cortex and hippocampus depend on dietary selenium availability in Selenop−/− mice. Selenop-deficient mice kept on adequate selenium diet (0.15 mg/kg, i.e. the recommended dietary allowance, RDA) developed ataxia, tremor, and hyperexcitability between the age of 4–5 weeks. Video-electroencephalography demonstrated epileptic seizures in Selenop−/− mice fed the RDA diet, while Selenop ± heterozygous mice behaved normally. Both neurological phenotypes, hyperexcitability/seizures and ataxia/dystonia were successfully prevented by selenium supplementation from birth or transgenic expression of human SELENOP under a hepatocyte-specific promoter. Selenium supplementation with 10 μM selenite in the drinking water on top of the RDA diet increased the activity of glutathione peroxidase in the brains of Selenop−/− mice to control levels. The effects of selenium supplementation on the neurological phenotypes were dose- and time-dependent. Selenium supplementation after weaning was apparently too late to prevent ataxia/dystonia, while selenium withdrawal from rescued Selenop−/− mice eventually resulted in ataxia. We conclude that SELENOP expression is essential for preserving interneuron survival under limiting Se supply, while SELENOP appears dispensable under sufficiently high Se status

Damage tolerant design of additively manufactured metallic components subjected to cyclic loading:State of the art and challenges

none21siUndoubtedly, a better understanding and the further development of approaches for damage tolerant component design of AM parts are among the most significant challenges currently facing the use of these new technologies. This article presents a thorough overview of the workshop discussions. It aims to provide a review of the parameters affecting the damage tolerance of parts produced by additive manufacturing (shortly, AM parts) with special emphasis on the process parameters intrinsic to the AM technologies, the resulting defects and the residual stresses. Based on these aspects, basic concepts are reviewed and critically discussed specifically for AM materials: - Criteria for damage tolerant component design; - Criteria for the determination of fatigue and fracture properties; - Strategies for the determination of the fatigue life in dependence of different manufacturing conditions; - Methods for the quantitative characterization of microstructure and defects; - Methods for the determination of residual stresses; - Effect of the defects and the residual stresses on the fatigue life and behaviour. We see that many of the classic concepts need to be expanded in order to fit with the particular microstructure (grain size and shape, crystal texture) and defect distribution (spatial arrangement, size, shape, amount) present in AM (in particular laser powder bed fusion). For instance, 3D characterization of defects becomes essential, since the defect shapes in AM are diverse and impact the fatigue life in a different way than in the case of conventionally produced components. Such new concepts have immediate consequence on the way one should tackle the determination of the fatigue life of AM parts; for instance, since a classification of defects and a quantification of the tolerable shapes and sizes is still missing, a new strategy must be defined, whereby theoretical calculations (e.g. FEM) allow determining the maximum tolerable defect size, and non-destructive testing (NDT) techniques are required to detect whether such defects are indeed present in the component. Such examples show how component design, damage and failure criteria, and characterization (and/or NDT) become for AM parts fully interlinked. We conclude that the homogenization of these fields represents the current challenge for the engineer and the materials scientist.noneZerbst, Uwe; Bruno, Giovanni; Buffiere, Jean-Yves; Wegener, Thomas; Niendorf, Thomas; Wu, Tao; Zhang, Xiang; Kashaev, Nikolai; Meneghetti, Giovanni; Hrabe, Nik; Madia, Mauro; Werner, Tiago; Hilgenberg, Kai; Koukolíková, Martina; Procházka, Radek; Džugan, Jan; Möller, Benjamin; Beretta, Stefano; Evans, Alexander; Wagener, Rainer; Schnabel, KaiZerbst, Uwe; Bruno, Giovanni; Buffiere, Jean-Yves; Wegener, Thomas; Niendorf, Thomas; Wu, Tao; Zhang, Xiang; Kashaev, Nikolai; Meneghetti, Giovanni; Hrabe, Nik; Madia, Mauro; Werner, Tiago; Hilgenberg, Kai; Koukolíková, Martina; Procházka, Radek; Džugan, Jan; Möller, Benjamin; Beretta, Stefano; Evans, Alexander; Wagener, Rainer; Schnabel, Ka

Normalised model-based processing diagrams for additive layer manufacture of engineering alloys

Additive Layer Manufacturing (ALM) is becoming a more widely accepted method for the production of near net-shape products across a range of industries and alloys. Depending on the end application, a level of process substantiation is required for new parts or alloys. Prior knowledge of the likely process parameter ranges that will provide a target region for the process integrity can save valuable time and resource during initial ALM trials. In this paper, the parameters used during the powder bed ALM process have been taken from the literature and the present study to construct normalised process maps for the ALM process by building on an approach taken by Ion et al. in the early 1990's (J.C. Ion, H.R. Shercliff, M.F. Ashby, Acta Metallurgica et Materialia 40 (1992) 1539e1551). These process maps present isopleths of normalised equivalent energy density (E0*) and are designed to provide a practical framework for comparing a range of ALM platforms, alloys and process parameters and provide a priori information on microstructure. The diagrams provide a useful reference and methodology to aid in the selection of appropriate processing parameters during the early development stages. This paper also applies the methodology to worked examples of Tie6Ale4V depositions processed using different Electron Beam Melting parameters

Bioaerosols in the Amazon rain forest: temporal variations and vertical profiles of Eukarya, Bacteria, and Archaea

The Amazon rain forest plays a major role in global hydrological cycling, and biogenic aerosols are likely to influence the formation of clouds and precipitation. Information about the sources and altitude profiles of primary biological aerosol particles, however, is sparse. We used fluorescence in situ hybridization (FISH), a molecular biological staining technique largely unexplored in aerosol research, to investigate the sources and spatiotemporal distribution of Amazonian bioaerosols on the domain level. We found wet season bioaerosol number concentrations in the range of 1–5 × 105 m−3 accounting for &gt; 70 % of the coarse mode aerosol. Eukaryotic and bacterial particles predominated, with fractions of ∼ 56 % and ∼ 26 % of the intact airborne cells. Archaea occurred at very low concentrations. Vertical profiles exhibit a steep decrease in bioaerosol numbers from the understory to 325 m height on the Amazon Tall Tower Observatory (ATTO), with a stronger decrease in Eukarya compared to Bacteria. Considering earlier investigations, our results can be regarded as representative for near-pristine Amazonian wet season conditions. The observed concentrations and profiles provide new insights into the sources and dispersion of different types of Amazonian bioaerosols as a solid basis for model studies on biosphere–atmosphere interactions such as bioprecipitation cycling.</p

Broad AOX expression in a genetically tractable mouse model does not disturb normal physiology

Plants and many lower organisms, but not mammals, express alternative oxidases (AOXs) that branch the mitochondrial respiratory chain, transferring electrons directly from ubiquinol to oxygen without proton pumping. Thus, they maintain electron flow under conditions when the classical respiratory chain is impaired, limiting excess production of oxygen radicals and supporting redox and metabolic homeostasis. AOX from Ciona intestinalis has been used to study and mitigate mitochondrial impairments in mammalian cell lines, Drosophila disease models and, most recently, in the mouse, where multiple lentivector-AOX transgenes conferred substantial expression in specific tissues. Here, we describe a genetically tractable mouse model in which Ciona AOX has been targeted to the Rosa26 locus for ubiquitous expression. The AOX(Rosa26) mouse exhibited only subtle phenotypic effects on respiratory complex formation, oxygen consumption or the global metabolome, and showed an essentially normal physiology. AOX conferred robust resistance to inhibitors of the respiratory chain in organello; moreover, animals exposed to a systemically applied LD50 dose of cyanide did not succumb. The AOX(Rosa26) mouse is a useful tool to investigate respiratory control mechanisms and to decipher mitochondrial disease aetiology in vivo.Peer reviewe