Different cleavage sites are aligned differently in the active site of M1 RNA, the catalytic subunit of Escherichia coli RNase P.

We have studied RNase P RNA (M1 RNA) cleavage of model tRNA precursors that are cleaved at two independent positions. Here we present data demonstrating that cleavage at both sites depends on the 2'-OH immediately 5' of the respective cleavage site. However, we show that the 2-amino group of a guanosine at the cleavage site plays a significant role in cleavage at one of these sites but not at the other. These data suggest that these two cleavage sites are handled differently by the ribozyme. This theory is supported by our finding that the cross-linking pattern between Ml RNA and tRNA precursors carrying 4-thioU showed distinct differences, depending on the location of the 4-thioU relative to the respective cleavage site. These findings lead us to suggest that different cleavage sites are aligned differently in the active site, possibly as a result of different binding modes of a substrate to M1 RNA. We discuss a model in which the interaction between the 3'-terminal "RCCA" motif (first three residues interact) of a tRNA precursor and M1 RNA plays a significant role in this process.

Electrochemical Behaviour of PSS-Functionalized Silica Films Prepared by Electroassisted Deposition of Sol–Gel Precursors

Porous, electrically insulating SiO2 layers containing polystyrene sulfonate (PSS) were deposited on glassy carbon electrodes by an electrochemically assisted deposition method. The obtained material was characterized by microscopic, spectroscopic and thermal techniques. Silica-PSS films modify the electrochemical response of the glassy carbon electrodes against selected redox probes. Positively charged species show reduced diffusivities across the SiO2-PSS pores, which resulted in a concentration ratio higher than 1 for these species. The opposite behaviour was found for negatively charged redox probes. These observations can be interpreted in terms of the different affinity of the GC/SiO2-PSS-modified electrode for the electroactive species, as a consequence of the negatively charged porous silica.

Rheological Properties of Organoclay Suspensions in Epoxy Network Precursors

This paper deals with the evolution of the state of dispersion of organically modified montmorillonites in epoxy or amine precursors. The epoxy prepolymer is a diglycidyl ether of bisphenol A (DGEBA) and the curing agent is an aliphatic diamine with a polyoxypropylene backbone (Jeffamine D2000). The clay dispersion is evaluated at the platelet scale (nanoscopic scale) from X-ray spectrometry [wide-angle X-ray diffraction (WAXD) and small-angle X-ray scattering (SAXS)] and at the aggregates scale (microscopic scale) from rheological analysis. The organoclays used form gels in the monomers above the percolation threshold if no shear is applied and present a mechanical gel/sol transition when shear stress increases. Gel strength and viscosity at high shear rates are linked to the nanometric state of dispersion and reveal the existence of two different organizations depending on organoclay/monomer interactions: (i) When the clay shows good interactions with the monomer, a significant swelling of the clay galleries by the monomer is obtained. These swollen particles lead to formation of weak gels which after shearing give high relative viscosity fluids. (ii) When the clay develops poor interactions with the monomer, the clay tends to reduce its exchange surface with the monomer and leads to a strongly connected gel. Shear breaks down this physical network leading to a very low relative viscosity fluid composed of nonswollen particles keeping a high aspect ratio. (C) 2003 Elsevier B.V All rights reserved.

Optical precursors and Beer's law violations; non-exponential propagation losses in water

We develop a model for exponential decay of broadband pulses, and examine its implications for experiments on optical precursors. One of the signature features of Brillouin precursors is attenuation with a less rapid decay than that predicted by Beer's Law. Depending on the pulse parameters and the model that is adopted for the dielectric properties of the medium, the limiting z-dependence of the loss has been described as z(-1/2), z(-1/3), exponential, or, in more detailed descriptions, some combination of the above. Experimental results in the search for precursors are examined in light of the different models, and a stringent test for sub-exponential decay is applied to data on propagation of 500 femtosecond pulses through 1-5 meters of water. (C) 2005 Optical Society of America.

Effect of different preparation routes on the structure and properties of rigid polyurethane-layered silicate nanocomposites

To identify the effect of reactive preparation on the structure and properties of rigid polyurethane (PU)layered silicate nanocomposite, a range of nanocomposites were prepared by combining the various precursors in different sequences. The morphology of the samples was characterized by XRD and TEM. Tensile properties and dynamic mechanical thermal properties were measured. The reactions between the layered silicates and PU precursors were monitored via FTIR to gain an understanding of the participation of nanofiller in the polymerization reaction, and the impact of this on system stoichiometry. The XRD and TEM results provided evidence that morphology can differ significantly if different synthesis methods are used. However, the mechanical properties are dominated by the stoichiometry imbalance induced by the addition of the layered silicates. (c) 2006 Wiley Periodicals, Inc.

The precursors and impacts of BSR on AMT acquisition and implementation

This paper reports on the results of research into the connections between transaction attributes and buyer-supplier relationships (BSRs) in advanced manufacturing technology (AMT) acquisition and implementation. The investigation began by examining the impact of the different patterns of BSR on the performance of the AMT acquisition. In understanding the phenomena, the study drew upon and integrated the literature of transaction cost economics theory, BSRs, and AMT, and used this as the basis for a theoretical framework and hypotheses development. This framework was then empirically tested using data that were gathered through a questionnaire survey with 147 companies and analyzed using a structural equation modeling technique. The results of the analysis indicated that the higher the level of technological specificity and uncertainty, the more firms are likely to engage in a stronger relationship with technology suppliers. However, the complexity of the technology being implemented was associated with BSR only indirectly through its association with the level of uncertainty (which has a direct impact upon BSR). The analysis also provided strong support for the premise that developing strong BSR could lead to an improved performance in acquiring and implementing AMT. The implications of the study are offered for both the academic and practitioner audience.

Impurity profiling and synthesis of precursors to the hallucinogenic amphetamine DOB

DOB (4‐bromo‐2,5‐dimethoxyamphetamine) is a newly emerging hallucinogenic amphetamine that sparked serious health warnings in Ireland, following its first seizure back in 2003. Known more commonly as “snowball”, this drug is highly potent and may be used as a substitute to ecstasy (MDMA) and lysergic acid diethylamide (LSD). To date, the work carried out on the impurity profiling of DOB is limited in comparison to amphetamine, methamphetamine and MDMA. In this work, the impurity profile of 4‐bromo‐2,5‐dimethoxyphenyl‐2‐propanone (4‐Br‐2,5‐P2P) is explored. This ketone is a direct precursor to DOB. Its more versatile non‐bromo analogue, 2,5‐ dimethoxyphenyl‐2‐propanone (2,5‐P2P) is also examined, as in addition to DOB, it may be used in the synthesis of a range of several other hallucinogenic amphetamines. A number of different routes to both 2,5‐P2P and 4‐Br‐2,5‐P2P were investigated. For each of these routes, the impurities produced were carefully isolated. Following isolation, the impurities were fully characterised (by 1H‐NMR/13C‐NMR spectroscopy, IR, MS), in order to aid structure elucidation. Compounds not easily resolved by flash column chromatography were analysed by LC‐MS and/or independently synthesised for the purpose of attaining reference standards. Adaptation of the well‐known ‘phenylacetic acid route’ to synthesis of both 2,5‐P2P and 4‐Br‐2,5‐P2P, was found to provide low yields of the expected ketone products. Four impurities were isolated during the preparation of both ketones. The yield of one of these impurities (possessing a dibenzylketone core), was greatly influenced by the amount of acetic anhydride reagent used during the reaction. Having carried out the reaction with several different equivalents of acetic anhydride, it was found that formation of the ‘dibenzylketone’ could not be eliminated. This may increase its likelihood of being detected in the final drug product. The ‘Darzens route’, having very recently emerged as a synthetic route to amphetamine and MDMA precursors, was discovered to be a viable route for manufacture of 2,5‐P2P and 4‐Br‐2,5‐P2P. Despite execution of the reaction being more tedious, the route provides superior yields (≈50–60%) to those achieved using the ‘phenylacetic acid route’ (≈35–38%). Incorporation of a bromine atom (at the aromatic 4‐position) is required at some stage during synthesis of DOB. The bromination of many intermediates/starting materials was therefore also examined in detail. Bromination of the acid starting material 2,5‐dimethoxyphenylacetic acid (2,5‐PAA) was found to be clean and high yielding. This was in stark contrast to the bromination of the benzaldehyde starting material, the ketone precursor 2,5‐P2P and the dibenzylketone‐based impurity. Numerous brominated products were isolated from each of these reactions, many of which were novel compounds, and previously unreported as impurities in the literature. The unpredictable/nondescript nature of these brominations is likely to have a significant impact on the impurity profile of illicitly produced DOB.

Investigating routes toward atomic layer deposition of silicon carbide: Ab initio screening of potential silicon and carbon precursors

Silicon carbide (SiC) is a promising material for electronics due to its hardness, and ability to carry high currents and high operating temperature. SiC films are currently deposited using chemical vapor deposition (CVD) at high temperatures 1500–1600 °C. However, there is a need to deposit SiC-based films on the surface of high aspect ratio features at low temperatures. One of the most precise thin film deposition techniques on high-aspect-ratio surfaces that operates at low temperatures is atomic layer deposition (ALD). However, there are currently no known methods for ALD of SiC. Herein, the authors present a first-principles thermodynamic analysis so as to screen different precursor combinations for SiC thin films. The authors do this by calculating the Gibbs energy ΔGΔG of the reaction using density functional theory and including the effects of pressure and temperature. This theoretical model was validated for existing chemical reactions in CVD of SiC at 1000 °C. The precursors disilane (Si2H6), silane (SiH4), or monochlorosilane (SiH3Cl) with ethyne (C2H2), carbontetrachloride (CCl4), or trichloromethane (CHCl3) were predicted to be the most promising for ALD of SiC at 400 °C.

Automatic learning of pre-miRNAs from different species.

Discovery of microRNAs (miRNAs) relies on predictive models for characteristic features from miRNA precursors (pre-miRNAs). The short length of miRNA genes and the lack of pronounced sequence features complicate this task. To accommodate the peculiarities of plant and animal miRNAs systems, tools for both systems have evolved differently. However, these tools are biased towards the species for which they were primarily developed and, consequently, their predictive performance on data sets from other species of the same kingdom might be lower. While these biases are intrinsic to the species, their characterization can lead to computational approaches capable of diminishing their negative effect on the accuracy of pre-miRNAs predictive models. We investigate in this study how 45 predictive models induced for data sets from 45 species, distributed in eight subphyla/classes, perform when applied to a species different from the species used in its induction. Results: Our computational experiments show that the separability of pre-miRNAs and pseudo pre-miRNAs instances is species-dependent and no feature set performs well for all species, even within the same subphylum/class. Mitigating this species dependency, we show that an ensemble of classifiers reduced the classification errors for all 45 species. As the ensemble members were obtained using meaningful, and yet computationally viable feature sets, the ensembles also have a lower computational cost than individual classifiers that rely on energy stability parameters, which are of prohibitive computational cost in large scale applications. Conclusion: In this study, the combination of multiple pre-miRNAs feature sets and multiple learning biases enhanced the predictive accuracy of pre-miRNAs classifiers of 45 species. This is certainly a promising approach to be incorporated in miRNA discovery tools towards more accurate and less species-dependent tools.

Using Different Co-Adjuvant Activating Agents to Improve Activated Carbon Adsorption Capacities

Activated carbon (AC) has proved to be an effective adsorbent for the removal of an assortment of organic and inorganic pollutants from aqueous or gaseous media. However, the pursuit for more effective and cheaper AC is still very active and a diversity of textural and chemical treatments are described as a way to expand their applications. It is well known that the surface area and surface chemistry of AC strongly affect their adsorption capacity [1-3]. In particular, an increase in the nitrogen content has been related to an increase of the basic character and also to the development of the porous structure. In most published work this was achieved through an AC post treatment, including either a reaction with nitrogen containing reagents, such as ammonia, nitric acid, or a diversity of amines. However, the AC prepared directly from a nitrogen rich precursor through a physical or chemical activation is referred to as presenting the best characteristics, namely high nitrogen content, high basic character, low nitrogen leaching and also a good thermal stability [4]. To improve the AC adsorption capacities for acidic pesticide removal from the aqueous phase, we intend to improve the porous structure and introduce nitrogenated groups directly into the AC matrix, using different co-adjuvant activating agents as a nitrogen source, by chemical activation, with potassium hydroxide, of cork or poly(ethyleneterephthalate) (PET) precursors.