Alteration of product specificity of Aeropyrum pernix farnesylgeranyl diphosphate synthase (Fgs) by directed evolution

Directed evolution of the C25 farnesylgeranyl diphosphate synthase of Aeropyrum pernix (Fgs) was carried out by error-prone PCR with an in vivo color complementation screen utilizing carotenoid biosynthetic pathway enzymes. Screening yielded 12 evolved clones with C20 geranylgeranyl diphosphate synthase activity which were isolated and characterized in order to understand better the chain elongation mechanism of this enzyme. Analysis of these mutants revealed three different mechanisms of product chain length specificity. Two mutants (A64T and A64V) have a single mutation at the 8th amino acid upstream of a conserved first aspartate-rich motif (FARM), which is involved in the mechanism for chain elongation reaction of all prenyl diphosphate synthases. One mutant (A135T) carries a single mutation at the 7th amino acid upstream of another conserved region (141GQ142), which was recently found to be another important region controlling chain elongation of a type III C20 geranylgeranyl diphosphate synthase and Escherichia coli C15 farnesyl diphosphate synthase. Finally, one mutant carrying four mutations (V84I, H88R, I177 M and M191V) is of interest. Molecular modeling, site-directed mutagenesis and in vitro assays of this mutant suggest that product chain-length distribution can be also controlled by a structural change provoked by a cooperative interaction of amino acids.     

Determination of the threshold of gravity for inducing kinetosis in fish: A drop-tower experiment

It has been repeatedly shown earlier that some fish of a given batch reveal motion sickness (a kinetosis) at the transition from 1 g to microgravity. In the course of parabolic aircraft flight experiments, it has been demonstrated that kinetosis susceptibility is correlated with asymmetric inner ear otoliths (i.e., differently weighed statoliths on the right and the left side of the head) or with genetically predispositioned malformed cells within the sensory epithelia of the inner ear. Hitherto, the threshold of gravity perception for inducing kinetotic behaviour as well as the relative importance of asymmetric otoliths versus malformed epithelia for kinetosis susceptibility has yet not been determined. The following experiment using the ZARM drop-tower facility in Bremen, Germany, is proposed to be carried out in order to answer the aforementioned questions. Larval cichlid fish (Oreochromis mossambicus) will be kept in a camcorder-equipped centrifuge during the microgravity phases of the drops and thus receive various gravity environments ranging from 0.1 to 0.9 g. Videographed controls will be housed outside of the centrifuge receiving 0 g. Based on the videorecordings, animals will be grouped into kinetotically and normally swimming samples. Subsequently, otoliths will be dissected and their size and asymmetry will be measured. Further investigations will focus on the numerical quantification of inner ear supporting and sensory cells as well as on the quantification of inner ear carbonic anhydrase reactivity. A correlation between (1) the results to be obtained concerning the g-loads inducing kinetosis and (2) the corresponding otolith asymmetry/morphology of sensory epithelia/carbonic anhydrase reactivity will further contribute to the understanding of the origin of kinetosis susceptibility. Besides an outline of the proposed principal experiments, the present study reports on a first series of drop-tower tests which were undertaken to elucidate the feasibility of the proposal (especially concerning the question, if some 4.7 s of microgravity are sufficient to induce kinetotic behaviour in larval fish).     

Subroutines for some plasma surface interaction processes: physical sputtering, chemical erosion, radiation enhanced sublimation, backscattering and thermal evaporation

A suite of FORTRAN subroutines/functions to generate data using empirical formulas for physical sputtering of mono-atomic targets for any elemental incident ion (atom), chemical erosion of graphite, Radiation Enhanced Sublimation (RES) of graphite, the number and energy backscattering coefficients for any elemental incident ion (atom) on a compound target and thermal evaporation of graphite is presented. Since chemical erosion, RES and thermal evaporation depend on the surface temperature of graphite, a subroutine implementing the 1-D heat diffusion equation to determine the temperature of any plasma-facing graphite surface is implemented. As an example to illustrate the use of these subroutines/functions, a simple model for the erosion of a plasma-facing surface, consisting of a simple collisionless sheath model, a 1-dimensional steady state heat diffusion model and 0-dimensional steady state particle balance at the target is developed and a sample listing of the program is presented.

Program summary

Title of program: Plasma Surface Interaction Codes (PSIC)Catalog identifier: ADTRProgram summary URL:http://cpc.cs.qub.ac.uk/summaries/ADTRProgram obtainable from: CPC Program Library, Queen's University of Belfast, N. IrelandComputers for which the program has been designed for and others on which it has been tested: Program is designed for any computer with a FORTRAN-77 compiler. It has been tested on a Linux PC with g77, Absoft f77, f90, f95, Fujitsu f95, Lahey f95Operating systems under which the program has been tested: Linux, UNIXProgramming language used: FORTRAN-77Memory required to execute with typical data: Negligible (executable is 178 861 bytes; add to it the memory used by the Fortran library linked to)No. of bits in a word: 16No. of processors used: 1Has the code been vectorized or parallelized?: NoNo. of bytes in distributed program, including test data, etc.: 11 619No. of lines in distributed program, including test data, etc.: 1015Distribution format: tar gzip fileNature of physical problems: 0-D plasma surface interaction model used to demonstrate calls to subroutines for physical sputtering yield, chemical erosion yield of graphite, RES of graphite, backscattering coefficients, thermal evaporation of graphite and 1-D heat diffusion in graphite.Method of solution: Semi-empirical formulas are used for the PSIs and analytical formulas are used for thermal evaporation and 1-D heat diffusion in graphite.Restrictions on the complexity of the problem: All the PSIs (except for the backscattering coefficients) are valid only for a monoatomic target. The heat diffusion solution is not valid for non-uniform plasmas and for targets for which the heat diffusion is not isotropic.Typical running time: Example program takes much less than 0.01 secondUniversal features of the program: None     

Model Checking

Die Gewährleistung der korrekten Funktionsweise von Hard- und Software ist ein entscheidender Faktor bei der heutigen Systementwicklung. Dies trifft ganz besonders auf das Gebiet der sog. sicherheitskritischen Systeme zu, bei dem ein Systemversagen Menschenleben gefährden kann.     

Reinforcement learning on explicitly specified time scales

In recent years hierarchical concepts of temporal abstraction have been integrated in the reinforcement learning framework to improve scalability. However, existing approaches are limited to domains where a decomposition into subtasks is known a priori. In this article we propose the concept of explicitly selecting time scale related abstract actions if no subgoal related abstract actions are available. This concept is realised with multi-step actions on different time scales that are combined in one single action set. We exploit the special structure of the action set in the MSA-Q-learning algorithm. This approach is suited for learning optimal policies in unstructured domains where a decomposition into subtasks is not known in advance or does not exist at all. By learning different explicitly specified time scales simultaneously, we achieve a considerable improvement of learning speed, which we demonstrate on several benchmark problems.     

DDT-related compounds bound to the nonextractable particulate matter in sediments of the Teltow Canal,Germany

Sediment samples of the Teltow Canal (Berlin, Germany) were analyzed with respect to extractable and nonextractable organic compounds. The study focused on the identification and quantitation of bound 2,2-bis(chlorophenyl)-1,1,1-trichlorethane (DDT) residues in order to obtain further information about the fate of DDT-derived compounds within the particulate matter of the aquatic environment. Various chemical degradation techniques and a complementary online pyrolysis-GC/MS method were applied to the pre-extracted sediment residues. Generally, the distribution of the bound DDT-related compounds was found to differ distinctly from the substances distribution within the extractable fraction. The main metabolite of the anaerobic degradation pathway (2,2-bis(chlorophenyl)-1,1-dichlorethane, DDD) is most abundant in the sediment extracts but occurred only in insignificant concentrations in the degradation products of all procedures applied. The most abundant DDT-metabolites released after the degradation procedures were 4,4'-DBP, 4,4'-DDA, and 4,4'-DDM. In addition, 4,4'-DDM was detected at rather high concentrations by pyrolytic analysis. The results imply a weak association to the nonextractable particulate matter based on noncovalent interactions for the observed DDT-related contaminants. The release of these compounds was initiated by the modification and degradation of the organic macromolecular matrix as well as of the inorganic material. Furthermore, numerous methoxychlor-related compounds were detected not only in the extracts but also in parts of the hydrolysis products.     

Interferometry at the physical limit: how to measure sub-parts-per-million optical homogeneity in fused silica

Inspection of the refractive-index distribution in fused silica is very sensitive to thermally induced measurement errors. A model is derived for the estimation and interpretation of thermal errors applicable to interferometric homogeneity investigations. The outlines of the model are supported by experimental investigations and numerical calculations. The results state a mandatory temperature stability of deltaT = 0.02 K for a required reproducibility of sigma(delta(n)) < or = 1 x 10(-7) and a lower sensitivity of higher-order Zernike terms. Requirements of the interferometer environment include spatial and temporal stability. Only a small part of the frequency spectrum of temporal instabilities contributes significantly to the measurement error and is therefore critical for the system. Experimental values are given for different environmental conditions.     

Ultrasensitive detection of unstained proteins in acrylamide gels by native UV fluorescence

Visualization of proteins inside acrylamide and other gels usually relies on different staining methods. To omit the protein-staining procedure, we visualized unstained proteins inside acrylamide gels by laser excitation with ultraviolet (UV) light (280 nm, 35 mJ/cm2) and directly detected native UV fluorescence. In one-dimensional gels, a detection limit as low as 1 ng for bovine serum albumin and 5 ng for other proteins with a linear dynamic range (2.7 orders of magnitude) comparable to state of the art fluorescent dyes could be achieved. In addition, the application of this method to 20 microg of a whole cell lysate separated in a two-dimensional gel showed more than 600 spots. Since protein labeling always represents a serious obstacle in protein identification technologies, the working efficiency with our procedure can be considered as a significant improvement for protein visualization and reproducibility in proteomics.     

Synthesis of cubic zirconium and hafnium nitride having Th3P4 structure

High-pressure synthesis is a powerful method for the preparation of novel materials with high elastic moduli and hardness. Additionally, such materials may exhibit interesting thermal, optoelectronic, semiconductuing, magnetic or superconducting properties. Here, we report on the high-pressure synthesis of zirconium and hafnium nitrides with the stoichiometry M3N4, where M = Zr, Hf. Synthesis experiments were performed in a laser-heated diamond anvil cell at pressures up to 18 GPa and temperatures up to 3,000 K. We observed formation of cubic Zr3N4 and Hf3N4 (c-M3N4) with a Th3P4-structure, where M-cations are eightfold coordinated by N anions. The c-M3N4 phases are the first binary nitrides with such a high coordination number. Both compounds exhibit high bulk moduli around 250 GPa, which indicates high hardness. Moreover, the new nitrides, c-Zr3N4 and c-Hf3N4, may be the first members of a larger group of transition metal and/or lanthanide nitrides with interesting ferromagnetic or superconducting behaviour.     

Robustness of radial basis functions

Neural networks are intended to be used in future nanoelectronic technology since these architectures seem to be robust to malfunctioning elements and noise in its inputs and parameters. In this work, the robustness of radial basis function networks is analyzed in order to operate in noisy and unreliable environment. Furthermore, upper bounds on the mean square error under noise contaminated parameters and inputs are determined if the network parameters are constrained. To achieve robuster neural network architectures fundamental methods are introduced to identify sensitive parameters and neurons.