Line Defects in Molybdenum Disulfide Layers

Layered molecular materials and especially MoS2 are already accepted as promising candidates for nanoelectronics. In contrast to the bulk material, the observed electron mobility in single-layer MoS2 is unexpectedly low. Here we reveal the occurrence of intrinsic defects in MoS2 layers, known as inversion domains, where the layer changes its direction through a line defect. The line defects are observed experimentally by atomic resolution TEM. The structures were modeled and the stability and electronic properties of the defects were calculated using quantum-mechanical calculations based on the Density-Functional Tight-Binding method. The results of these calculations indicate the occurrence of new states within the band gap of the semiconducting MoS2. The most stable non-stoichiometric defect structures are observed experimentally, one of which contains metallic Mo-Mo bonds and another one bridging S atoms

Aberration-corrected electron microscopy of nanoparticles

The early history of scanning transmission electron microscopy (STEM) is reviewed as a way to frame the technical issues that make aberration correction an essential upgrade for the study of nanoparticles using STEM. The principles of aberration correction are explained, and the use of aberration-corrected microscopy in the study of nanostructures is exemplified in order to remark the features and challenges in the use of this measuring techniqu

Tensor Decomposition Reveals Concurrent Evolutionary Convergences and Divergences and Correlations with Structural Motifs in Ribosomal RNA

Evolutionary relationships among organisms are commonly described by using a hierarchy derived from comparisons of ribosomal RNA (rRNA) sequences. We propose that even on the level of a single rRNA molecule, an organism's evolution is composed of multiple pathways due to concurrent forces that act independently upon different rRNA degrees of freedom. Relationships among organisms are then compositions of coexisting pathway-dependent similarities and dissimilarities, which cannot be described by a single hierarchy. We computationally test this hypothesis in comparative analyses of 16S and 23S rRNA sequence alignments by using a tensor decomposition, i.e., a framework for modeling composite data. Each alignment is encoded in a cuboid, i.e., a third-order tensor, where nucleotides, positions and organisms, each represent a degree of freedom. A tensor mode-1 higher-order singular value decomposition (HOSVD) is formulated such that it separates each cuboid into combinations of patterns of nucleotide frequency variation across organisms and positions, i.e., “eigenpositions” and corresponding nucleotide-specific segments of “eigenorganisms,” respectively, independent of a-priori knowledge of the taxonomic groups or rRNA structures. We find, in support of our hypothesis that, first, the significant eigenpositions reveal multiple similarities and dissimilarities among the taxonomic groups. Second, the corresponding eigenorganisms identify insertions or deletions of nucleotides exclusively conserved within the corresponding groups, that map out entire substructures and are enriched in adenosines, unpaired in the rRNA secondary structure, that participate in tertiary structure interactions. This demonstrates that structural motifs involved in rRNA folding and function are evolutionary degrees of freedom. Third, two previously unknown coexisting subgenic relationships between Microsporidia and Archaea are revealed in both the 16S and 23S rRNA alignments, a convergence and a divergence, conferred by insertions and deletions of these motifs, which cannot be described by a single hierarchy. This shows that mode-1 HOSVD modeling of rRNA alignments might be used to computationally predict evolutionary mechanisms

L11 domain rearrangement upon binding to RNA and thiostrepton studied by NMR spectroscopy

Ribosomal proteins are assumed to stabilize specific RNA structures and promote compact folding of the large rRNA. The conformational dynamics of the protein between the bound and unbound state play an important role in the binding process. We have studied those dynamical changes in detail for the highly conserved complex between the ribosomal protein L11 and the GTPase region of 23S rRNA. The RNA domain is compactly folded into a well defined tertiary structure, which is further stabilized by the association with the C-terminal domain of the L11 protein (L11(ctd)). In addition, the N-terminal domain of L11 (L11(ntd)) is implicated in the binding of the natural thiazole antibiotic thiostrepton, which disrupts the elongation factor function. We have studied the conformation of the ribosomal protein and its dynamics by NMR in the unbound state, the RNA bound state and in the ternary complex with the RNA and thiostrepton. Our data reveal a rearrangement of the L11(ntd), placing it closer to the RNA after binding of thiostrepton, which may prevent binding of elongation factors. We propose a model for the ternary L11–RNA–thiostrepton complex that is additionally based on interaction data and conformational information of the L11 protein. The model is consistent with earlier findings and provides an explanation for the role of L11(ntd) in elongation factor binding

Synthesis of 5-Hydroxyectoine from Ectoine: Crystal Structure of the Non-Heme Iron(II) and 2-Oxoglutarate-Dependent Dioxygenase EctD

As a response to high osmolality, many microorganisms synthesize various types of compatible solutes. These organic osmolytes aid in offsetting the detrimental effects of low water activity on cell physiology. One of these compatible solutes is ectoine. A sub-group of the ectoine producer's enzymatically convert this tetrahydropyrimidine into a hydroxylated derivative, 5-hydroxyectoine. This compound also functions as an effective osmostress protectant and compatible solute but it possesses properties that differ in several aspects from those of ectoine. The enzyme responsible for ectoine hydroxylation (EctD) is a member of the non-heme iron(II)-containing and 2-oxoglutarate-dependent dioxygenases (EC 1.14.11). These enzymes couple the decarboxylation of 2-oxoglutarate with the formation of a high-energy ferryl-oxo intermediate to catalyze the oxidation of the bound organic substrate. We report here the crystal structure of the ectoine hydroxylase EctD from the moderate halophile Virgibacillus salexigens in complex with Fe3+ at a resolution of 1.85 Å. Like other non-heme iron(II) and 2-oxoglutarate dependent dioxygenases, the core of the EctD structure consists of a double-stranded β-helix forming the main portion of the active-site of the enzyme. The positioning of the iron ligand in the active-site of EctD is mediated by an evolutionarily conserved 2-His-1-carboxylate iron-binding motif. The side chains of the three residues forming this iron-binding site protrude into a deep cavity in the EctD structure that also harbours the 2-oxoglutarate co-substrate-binding site. Database searches revealed a widespread occurrence of EctD-type proteins in members of the Bacteria but only in a single representative of the Archaea, the marine crenarchaeon Nitrosopumilus maritimus. The EctD crystal structure reported here can serve as a template to guide further biochemical and structural studies of this biotechnologically interesting enzyme family

A thermopiezomechanical finite rotation shell element

A finite rotation shell element is presented which can be used to analyse thermopiezomechanical phenomena when dealing with thin-walled smart structures. Initially, the underlying theory is explained in order to illustrate the simplifying assumptions that are eventually made. Several locking phenomena are avoided by deploying ANS and EAS techniques. The rotations are described by the Rodriguez parametrisation. The transverse distribution of the electric potential is assumed to be quadratic, and the temperature field to be cubic. The Reissner-Mindlin hypothesis is used for the displacement field in the transverse direction. Finally, a numerical example is discussed to demonstrate the field of application. ɠ2010 Taylor & Francis Group, London

DEVELOPMENT OF A HABITAT SUITABILITY INDEX FOR THE NOBLE CRAYFISH ASTACUS ASTACUS USING FUZZY MODELLING

A Geographic Information System (GIS) and fuzzy modelling were used to develop a habitat suitability index for the noble crayfish, Astacus astacus. The model is based on crayfish distribution data for the federal state Hesse, Germany, which had been recorded between 1988 and 1996. It includes 185 sites with noble crayfish in 126 watercourses. Official data on the morphological quality of surface waters recorded between 1996 and 1998 by order of the Ministry of Hesse for Environment, Rural Areas and Consumers Protection was used to describe the habitat features. One third of the crayfish sites was selected by chance to determine habitat properties significantly associated with crayfish occurrence by means of the Kolmogorov-Smirnoff test and frequency analysis. Meaningless associations were excluded based on expert knowledge. Five parameters related to the structure of the riverbed and the bankside were incorporated in the fuzzy model. The model was complemented by a number of parameters known to exclude the occurrence of the noble crayfish (e.g. pipes, concrete embankments). Finally, a habitat suitability index for every stretch of water in Hesse was calculated. The predictive power of the fuzzy model was tested on the remaining distribution data set for Astacus astacus. The habitat suitability index differed slightly but significantly (p < 0.001) between sites with and sites without crayfish occurrence. Fuzzy modelling proved to be useful for assessing habitat suitability with respect to crayfish, though further improvements of the model appeared to be necessary for a more reliable prediction of noble crayfish sites

DEVELOPMENT OF A HABITAT SUITABILITY INDEX FOR THE NOBLE CRAYFISH ASTACUS ASTACUS USING FUZZY MODELLING

A Geographic Information System (GIS) and fuzzy modelling were used to develop a habitat suitability index for the noble crayfish, Astacus astacus. The model is based on crayfish distribution data for the federal state Hesse, Germany, which had been recorded between 1988 and 1996. It includes 185 sites with noble crayfish in 126 watercourses. Official data on the morphological quality of surface waters recorded between 1996 and 1998 by order of the Ministry of Hesse for Environment, Rural Areas and Consumers Protection was used to describe the habitat features. One third of the crayfish sites was selected by chance to determine habitat properties significantly associated with crayfish occurrence by means of the Kolmogorov-Smirnoff test and frequency analysis. Meaningless associations were excluded based on expert knowledge. Five parameters related to the structure of the riverbed and the bankside were incorporated in the fuzzy model. The model was complemented by a number of parameters known to exclude the occurrence of the noble crayfish (e.g. pipes, concrete embankments). Finally, a habitat suitability index for every stretch of water in Hesse was calculated. The predictive power of the fuzzy model was tested on the remaining distribution data set for Astacus astacus. The habitat suitability index differed slightly but significantly (p < 0.001) between sites with and sites without crayfish occurrence. Fuzzy modelling proved to be useful for assessing habitat suitability with respect to crayfish, though further improvements of the model appeared to be necessary for a more reliable prediction of noble crayfish sites