Catalytic strategies of self-cleaving ribozymes

[Structure: see text]. Five naturally occurring nucleolytic ribozymes have been identified: the hammerhead, hairpin, glmS, hepatitis delta virus (HDV), and Varkud satellite (VS) ribozymes. All of these RNA enzymes catalyze self-scission of the RNA backbone using a chemical mechanism equivalent to that of RNase A. RNase A uses four basic strategies to promote this reaction: geometric constraints, activation of the nucleophile, transition-state stabilization, and leaving group protonation. In this Account, we discuss the current thinking on how nucleolytic ribozymes harness RNase A's four sources of catalytic power. The geometry of the phosphodiester cleavage reaction constrains the nucleotides flanking the scissile phosphate so that they are unstacked from a canonical A-form helix and thus require alternative stabilization. Crystal structures and mutational analysis reveal that cross-strand base pairing, along with unconventional stacking and tertiary hydrogen-bonding interactions, work to stabilize the splayed conformation in nucleolytic ribozymes. Deprotonation of the 2'-OH nucleophile greatly increases its nucleophilicity in the strand scission reaction. Crystal structures of the hammerhead, hairpin, and glmS ribozymes reveal the N1 of a G residue within hydrogen-bonding distance of the 2'-OH. In each case, this residue has also been shown to be important for catalysis. In the HDV ribozyme, a hydrated magnesium has been implicated as the general base. Catalysis by the VS ribozyme requires both an A and a G, but the precise role of either has not been elucidated. Enzymes can lower the energy of a chemical reaction by binding more tightly to the transition state than to the ground states. Comparison of the hairpin ground- and transition-state mimic structures reveal greater hydrogen bonding to the transition-state mimic structure, suggesting transition-state stabilization as a possible catalytic strategy. However, the hydrogen-bonding pattern in the glmS ribozyme transition-state mimic structure and the ground-state structures are equivalent. Protonation of the 5'-O leaving group by a variety of functional groups can promote the cleavage reaction. In the HDV ribozyme, the general acid is a conserved C residue. In the hairpin ribozyme, a G residue has been implicated in protonation of the leaving group. An A in the hammerhead ribozyme probably plays a similar role. In the glmS ribozyme, an exogenous cofactor may provide the general acid. This diversity is in contrast to the relatively small number of functional groups that serve as a general base, where at least three of the nucleolytic ribozymes may use the N1 of a G.     

Productivity potential of an inline deposition system for amorphous and microcrystalline silicon solar cells

Amorphous and microcrystalline silicon single layers and p-i-n solar cells were produced dynamically using an inline deposition system called “line source”. A highly uniform deposition of thin-film silicon layers with layer-thickness variations of less than ±5% was achieved. Amorphous and microcrystalline silicon single junction solar cells were dynamically fabricated with initial efficiencies of 8.3% and 6.3%, respectively. The dynamic deposition rate of these solar cells is 6.75 nm m/min in case of a-Si:H and 3.3 nm m/min for μc-Si:H. In this work it will be shown that an enhancement of the deposition rate up to 15.6 nm m/min during the i-layer deposition of a-Si:H solar cells has only a weak negative influence on the initial efficiencies of the cells. Further on, the effect of substrate velocity on solar cell characteristics of a-Si:H solar cells is investigated. Finally, a productivity estimation of the line source concept is presented.     

Modification of the sterol profile in milk through feeding

The fortification of milk with phytosterols is an increasingly common practice to enhance the sterol profile and offer consumers potential health benefits. This study investigated whether cattle feed can influence the profile of phytosterols and cholesterol in the milk produced as an alternative to direct fortification of milk. Five experiments were performed using feeds commonly used by Australian dairy farmers and selected formulated rumen-protected feeds. Statistical significances were observed for some individual plant sterols and cholesterol in milk under these differing feeding regimens compared with the respective controls. In the case of the phytosterols, where the daily recommended consumption is typically 2 g per day, the total phytosterols were <0.12 mg/100 mL of milk. An experiment using a rumen-protected feed with high phytosterol levels suggested a decreased transfer of cholesterol to the milk by as much as 20%, although further work is required to confirm these preliminary results. Overall, the study suggests that different feeding practices have minimal effect on the resulting sterol profile of the milk.     

Quantitative image analysis of acoustic tomography in woods

The development of acoustic techniques for wood analysis through tomography has enabled the generation of images by means of nondestructive techniques. These images allow for the evaluation of the internal condition of wood trunks. This type of evaluation provides valuable information since the internal defects (e.g. holes) in the wood are difficult to identify—especially in its early stages of development. Whereas there is a substantial body of work that aims to improve these images by applying new interpolation and inspection techniques, the assessment of these techniques has traditionally been carried out via a bare visual analysis or inspection of the real wood trunk. In this work, an approach is proposed to quantitatively assess interpolation methods regarding their ability to correctly detect faults in the wood. This approach is based on a confusion matrix that allows for the computation of accuracy, reliability and recall. An experiment is presented using images from the cross-section of wood trunks generated by two interpolation methods applied for internal-hole detection: (1) an interpolation method using surrounding points and (2) the Ellipse Based Spatial Interpolation. The results demonstrated the effectiveness of the approach in quantitatively assessing and comparing these methods.     

Magnesium-Containing Bioactive Glasses for Biomedical Applications

The importance of Mg in the human body, its key role in bone tissue development, in addition to its application to improve and modify physical, thermal, and mechanical properties of bioactive silicate glasses, make Mg a very interesting element as a component of bioactive glasses for medical applications. Although Mg is a typical element in the composition of numerous developed bioactive glasses, the analysis of the literature reveals that further research is required to gain comprehensive understanding about the effects of MgO on bioactive glass structure and properties. This article presents a comprehensive overview of the field of Mg-containing bioactive glasses discussing available compositions and summarizing existing knowledge on effects of MgO on glass properties. The biomedical applications of several developed glasses are discussed highlighting the distinct effects of Mg in relevant areas, such as bioactivity and cell response, and focusing on the most common applications for these glasses, such as bone cements, bioactive coatings, and scaffolds for bone tissue engineering. The effect of Mg on bone development is discussed and avenues for future research in the field are proposed, emphasizing the need to investigate unstudied properties of (already developed) Mg-containing glass compositions, such as angiogenesis-stimulating action and the effect on osteoclast functions, to develop new Mg-containing bioactive glasses as well as to make products of different shape designs such as nanoparticles, fibers, and complex porous structures.     

Biological variation of prostate specific antigen levels in serum: an evaluation of day-to-day physiological fluctuations in a well-defined cohort of 24 patients

PURPOSE: We evaluated the daily biological variation of serum prostate specific antigen (PSA) concentrations to determine the critical difference required between 2 consecutive PSA measurements that would indicate a significant elevation. MATERIALS AND METHODS: A total of 24 men, grouped according to clinical diagnosis and PSA, underwent phlebotomy for 10 consecutive weekdays. Duplicate serum samples were measured using 3 separate lots of Tandem-E and IMx PSA assays. The biological variation was calculated and the 2 PSA assay systems were compared. The critical difference was examined to determine the percent elevation necessary to indicate (with 95% confidence) that PSA had increased beyond what would be expected from biological and analytical variation. RESULTS: The biological variation, defined in terms of percent coefficient of variation, had a log-normal distribution with a geometric mean of 7.3% coefficient of variation and a 95th percentile value of 19.2% coefficient of variation using the Tandem-E PSA assay. Assuming an analytical variation of 5% coefficient of variation, the median critical difference was 20.5% and the 95th percentile critical difference was 45.8%. There was no significant difference between the 2 PSA assay systems in biological variation. However, PSA concentrations measured by the IMx assay were consistently lower compared to values measured by the Tandem-E assay. CONCLUSIONS: Characterizing the biological variation of serum PSA assists in evaluating the significance of changes in serial PSA measurements. The degree of biological variation differs among patients, such that an increase between 2 consecutive PSA levels that is less than 20 to 46% may be due to biological and analytical variation. These data influence interpretation of repeated measurements of serum PSA with time.     

Evolution of nanocluster ensembles: Computer simulation of diffusion and reaction controlled Ostwald ripening

The Ion Beam Synthesis (IBS) of nanoclusters can be controlled by the flux and the fluence of ions as well as by the implantation and/or annealing temperature. The evolution of the precipitates, mainly described by their particle radius distribution (PRD), the number of remaining particles and the critical radius, depends on these parameters. However, the evolution is expected to behave different for systems like SiO₂ and CoSi₂ clusters in Si, because they are characterized by quite different ratios of diffusion to reaction constants. Here we present a unified model of Ostwald ripening of nanoclusters, which describes the pure diffusion and reaction controlled limits as well as all intermediate, mixed processes. Expressing the exact solution of the adiabatic diffusion equation by multipole moments we derive the governing equation for the evolution of an ensemble of nanoclusters in the leading monopole approximation. Whereas in the diffusion controlled regime we have the well known infinite range 1/r interaction among the nanoclusters, 1/r² interactions come into play in the reaction limited regime. Computer simulations for ensembles of several thousands of nanoclusters demonstrate the evolution for typical cases.     

Electrochemical and surface properties of nanocrystalline β-MnO2 in aqueous electrolyte

Surface and electrochemical properties of micrometric and nanometric tetragonal β-MnO₂ of, respectively, 4 and 61 m² g⁻¹ surface area were studied. The monodispersed nanocrystalline phase prepared by spray pyrolysis and characterized by transmission electron microscopy (TEM), is made of facetted crystals with 70 nm × 40 nm edges. Three types of energy domains were identified by surface acid-base titration. Slow step linear voltammetry reduction (10 mV/2 h scan rate) showed one current peak at −0.6 V (versus Hg-HgO 1 M KOH) for the micrometric phase, but three current peaks at −0.18, −0.36 and −0.55 V for the nanometric phase. They were assigned to the reduction of: (1) surface Mn atoms related to 〈1 1 1〉 and 〈3 1 1〉 faces; (2) more stable surface Mn atoms related to 〈1 0 0〉 and 〈1 1 0〉 faces; (3) bulk Mn atoms, respectively. The presence of new reduction peaks at higher potential is ascribed to the increase in Gibbs free energy caused by the surface energy of the nanometric particle.