www.rnaworkbench.com: A new program for analyzing RNA interference

RNA interference (RNAi) has become an important tool to study and utilize gene silencing by introducing short interfering RNA (siRNA). In order to predict the most efficient siRNAs, a new software tool, RNA Workbench (RNAWB), has been designed and is freely available (after registration) on http://www.rnaworkbench.com. In addition to the standard selection rules, RNAWB includes the possibility of statistical analyses of the applied selection rules (criteria). The role of RNA secondary structures in the RNA interference process as well as the application of sequence rules are discussed to show the applicability of the software.     

The Role of Filippi’s Glands in the Silk Moths Cocoon Construction

Filippi’s glands (FGs), formerly also called Lyonet’s glands, are accessory secretory structures of the labial (silk) glands of lepidopteran caterpillars, which were implicated to play an important role in the maturation of the silk material and the construction of the cocoon. In our previous study, we have identified several species of giant silk moths that completely lack the FGs. Interestingly, the absence of FGs in these species correlates with the construction of a loose cocoon architecture. We investigated the functions of FGs by their surgical extirpation in the last instar larvae of the silkworm, Bombyx mori. We found that the absence of FGs altered the structure of the resulting cocoon, in which the different layers of silk were separated. In further experiments, we found no effects of the absence of FGs on larval cocoon formation behavior or on changes in cocoon mass or lipid content. Differential proteomic analysis revealed no significant contribution of structural proteins from FGs to silk cocoon material, but we identified several low abundance proteins that may play a role in posttranslational modifications of some silk proteins. Proteomic analysis also revealed a difference in phosphorylation of the N-terminal sequence of fibroin-heavy chain molecule. Thus, FGs appear to affect silk stickiness during spinning by regulating posttranslational modifications. This could also explain the link that exists between the absence of these glands and the formation of loose cocoons in some giant silk moth species.     

Surface morphology of contact lenses probed with microscopy techniques.

The present study is bringing a comparison of surface morphology for various types of contact lenses. A novel method--scanning electron microscopy under aqueous conditions (cryo-SEM)--was tested for visualization of lenses at magnifications up to 2000x. For imaging lens surface on nanometre scale, we employed atomic force microscopy (AFM) in aqueous media. Various materials of lenses, based on silicone hydrogels or conventional hydrogels, were investigated. Total, 10 types of contact lenses from five manufacturers were selected and probed. We found that different methods of lens manufacture (lathe-cutting, cast-moulding, and spin casting) led to different values of surface roughness. In the swollen state, roughness values of lens surfaces lie between 4 and 140 nm. Lenses manufactured by lathe-cutting exhibit notable higher values, so that they could be easily distinguished from others. In cast-moulded lenses, the surface roughness decreased with increasing water content. Moreover, additional treatments of lenses introduced unique structural motifs onto surface. For instance, porous structure was found on lens surface finalized with plasma oxidation.     

The influence of temperature and cyclic loading on adhesion in polycarbonate-polyurethane-glass adhesive joint

The paper deals with the influence of temperature and cyclic loading on adhesion and transparency of the adhesive joint consisting of soda-lime-silica glass and polycarbonate (PC) bonded with polyurethane (PU) adhesive film. The tested joint represents critical part of transparent armored glass used in vehicles. Dynamic tension creep tests were performed at temperatures to which armored glass is commonly exposed (25, 50, 60, 70, and 80?°C). Sawtooth loading mode was performed to 650?N and the sine loading in the force range 0–1550?N. The aim of the paper was to discover conditions causing delamination of the adhesive joint and glass milky appearance during the use. Delamination of soda-lime-silica glass/PU adhesive interface occurred at 25?°C after load to 1550?N without the change of transparency. Both dynamic and static tension creep tests performed to 400?N led to plastic deformation of PU adhesive at and above 70?°C, in preference at both ends and circumference edges of adhesive joint, and thus, to loss of transparency, but extent of deformation differed. Milky maps observed after sawtooth load to 650?N at 80?°C reflected delaminated areas of highly deformed PU adhesive. Temperature of 70?°C was found out to be the critical parameter being in synergy effect with different thermal expansion of PC and PU adhesive.     

Quantitative analysis of pores of two types in a plasma-sprayed coating

Quantitative microstructural analyses of thermally sprayed coatings are reviewed. Then a ceramic plasma-sprayed coating is analysed using light microscopy and image analysis. Globular pores and interlamellar flat pores are reconstructed from serial sections of a specimen and their volume and surface area histograms are estimated. The spatial distribution of pores is described using a method based on 3D distances and testing of complete spatial randomness is performed. Interpretations of results in terms of the physical background of the material are discussed.     

Numerical modelling of incompressible flows for Newtonian and non-Newtonian fluids

This paper deals with numerical solution of two-dimensional and three-dimensional steady and unsteady laminar incompressible flows for Newtonian and non-Newtonian shear thickening fluids flow through a branching channel. The mathematical model used in this work is the generalized system of Navier–Stokes equations. The right hand side of this system is defined by the power-law model. The finite volume method combined with artificial compressibility method is used for numerical simulations of generalized Newtonian fluids flow. Numerical solution is divided into two parts, steady state and unsteady. Steady state solution is achieved for t→∞$t\to \infty$ using steady boundary conditions and followed by steady residual behaviour. For unsteady solution high artificial compressibility coefficient β²${\beta }^2$ is considered. An artificial compressibility method with a pulsation of the pressure in the outlet boundary is used.     

A Tandem Enzymatic sp2‐C‐Methylation Process: Coupling in Situ S‐Adenosyl‐l‐Methionine Formation with Methyl Transfer

A one‐pot, two‐step biocatalytic platform for the regiospecfic C‐methylation and C‐ethylation of aromatic substrates is described. The tandem process utilises SalL (Salinospora tropica) for in situ synthesis of S‐adenosyl‐l ‐methionine (SAM), followed by alkylation of aromatic substrates by the C‐methyltransferase NovO (Streptomyces spheroides). The application of this methodology is demonstrated for the regiospecific labelling of aromatic substrates by the transfer of methyl, ethyl and isotopically labelled ¹³CH_3, ¹³CD₃ and CD₃ groups from their corresponding SAM analogues formed in situ.