Evaluation of structural similarity based on reduced dimensionality representations of protein structure

Protein similarity estimations can be achieved using reduced dimensional representations and we describe a new application for the generation of two-dimensional maps from the three-dimensional structure. The code for the dimensionality reduction is based on the concept of pseudo-random generation of two-dimensional coordinates and Monte Carlo-like acceptance criteria for the generated coordinates. A new method for calculating protein similarity is developed by introducing a distance-dependent similarity field. Similarity of two proteins is derived from similarity field indices between amino acids based on various criteria such as hydrophobicity, residue replacement factors and conformational similarity, each showing a one factor Gaussian dependence. Results on comparisons of misfolded protein models with data sets of correctly folded structures show that discrimination between correctly folded and misfolded structures is possible. Tests were carried out on five different proteins, comparing a misfolded protein structure with members of the same topology, architecture, family and domain according to the CATH classification.     

On the efficient implementation of conditional critical regions and the construction of monitors

Summary A method is presented that allows the efficient implementation of conditional critical regions combined with scheduling of the waiting processes. It is based on the knowledge of static and invariant relations that exist among the conditional critical regions of a process system. Mathematical methods are applied in order to show the nature of these relations, and to determine them for practical applications.By collecting the conditional critical regions in a program module, a monitor is obtained. Its rather abstract user level allows clear and well structured programming style. It also shows some advantages in comparison to other monitor proposals on the implementation level.Work done mainly at the Fakultät für Informatik, Universität Karlsruhe, Karlsruhe, and also at the Department of Computer Science, University of Toronto, Toronto.     

Molecular structure and evolution of the conjugative multiresistance plasmid pRE25 of Enterococcus faecalis isolated from a raw-fermented sausage

Plasmid pRE25 from Enterococcus faecalis transfers resistances against kanamycin, neomycin, streptomycin, clindamycin, lincomycin, azithromycin, clarithromycin, erythromycin, roxithromycin, tylosin, chloramphenicol, and nourseothricin sulfate by conjugation in vitro to E. faecalis JH2-2, Lactococcus lactis Bu2, and Listeria innocua L19. Its nucleotide sequence of 50237 base pairs represents the largest, fully sequenced conjugative multiresistance plasmid of enterococci (Plasmid 46 (2001) 170). The gene for chloramphenicol resistance (cat) was identified as an acetyltransferase identical to the one of plasmid pIP501 of Streptococcus agalactiae. Erythromycin resistance is due to a 23S ribosomal RNA methyl transferase, again as found in pIP501 (ermB). The aminoglycoside resistance genes are packed in tandem as in transposon Tn5405 of Staphylococcus aureus: an aminoglycoside 6-adenyltransferase, a streptothricin acetyl transferase, and an aminoglycoside phosphotransferase.). Identical resistance genes are known from pathogens like Streptococcus pyogenes, S. agalactiae, S. aureus, Campylobacter coli, Clostridium perfringens, and Clostridium difficile. pRE25 is composed of a 30.5-kbp segment almost identical to pIP501. Of the 15 genes involved in conjugative transfer, 10 codes for putative transmembrane proteins (e.g. trsB, traC, trsF, trsJ, and trsL). The enterococcal part is joined into the pIP501 part by insertion elements IS1216V of E. faecium Tn1545 (three copies), and homologs of IS1062 (E. faecalis) and IS1485 (E. faecium). pRE25 demonstrates that enterococci from fermented food do participate in the molecular communication between Gram-positive and Gram-negative bacteria of the human and animal microflora.     

Flip the tip: an automated,high quality,cost-effective patch clamp screen

The race for creating an automated patch clamp has begun. Here, we present a novel technology to produce true gigaseals and whole cell preparations at a high rate. Suspended cells are flushed toward the tip of glass micropipettes. Seal, whole-cell break-in, and pipette/liquid handling are fully automated. Extremely stable seals and access resistance guarantee high recording quality. Data obtained from different cell types sealed inside pipettes show long-term stability, voltage clamp and seal quality, as well as block by compounds in the pM range. A flexible array of independent electrode positions minimizes consumables consumption at maximal throughput. Pulled micropipettes guarantee a proven gigaseal substrate with ultra clean and smooth surface at low cost.     

Electrical, optical and morphological properties of nanoparticle indium-tin-oxide layers

Porous layers were prepared from DEGUSSA's ITO (In₂O₃:Sn) nanoparticle dispersion by doctor blading followed by annealing in air. We investigated the influence of various annealing parameters on electrical, optical and morphological thin film properties.Conductance rises with increasing annealing temperature and time by more than three orders of magnitude up to 44 Ω^− 1cm^− 1. Besides this we found an abrupt decrease in free charge carrier concentration above a critical annealing temperature of 250 °C, which leads to a step in conductance curve. In spite of particle growing during annealing no decrease in porosity was observed and in opposite to compact material, nanoparticle layers do not exhibit an appreciable shrinkage below recrystallisation temperature. These both indicate a densification hindering particle pinning effect, which is believed to be currently the main obstruction to achieve higher electrical conductivities.     

Bindemittelfreie zeolithische Molekularsiebe der Typen LTA und FAU

Zeolite molecular sieves belong to the most important adsorbents. For dynamic, technical adsorption processes the use of shaped bodies is required. In conventional molecular sieves usually clay type minerals are used as binder. In this paper novel binderless zeolite molecular sieves and their advantages in comparison to binder containing molecular sieves are shown.