Increasing the thermostability of sucrose phosphorylase by a combination of sequence- and structure-based mutagenesis

Sucrose phosphorylase is a promising biocatalyst for the glycosylation of a wide variety of acceptor molecules, but its low thermostability is a serious drawback for industrial applications. In this work, the stability of the enzyme from Bifidobacterium adolescentis has been significantly improved by a combination of smart and rational mutagenesis. The former consists of substituting the most flexible residues with amino acids that occur more frequently at the corresponding positions in related sequences, while the latter is based on a careful inspection of the enzyme's crystal structure to promote electrostatic interactions. In this way, a variant enzyme could be created that contains six mutations and whose half-life at the industrially relevant temperature of 60 °C has more than doubled compared with the wild-type enzyme. An increased stability in the presence of organic co-solvents could also be observed, although these effects were most noticeable at low temperatures.     

Variation in Herbivory-induced Volatiles Among Cucumber (<Emphasis Type="Italic">Cucumis sativus</Emphasis> L.) Varieties has Consequences for the Attraction of Carnivorous Natural Enemies

In response to herbivory by arthropods, plants emit herbivory-induced volatiles that attract carnivorous enemies of the inducing herbivores. Here, we compared the attractiveness of eight cucumber varieties (Cucumis sativus L.) to Phytoseiulus persimilis predatory mites after infestation of the plants with herbivorous spider mites (Tetranychus urticae) under greenhouse conditions. Attractiveness differed considerably, with the most attractive variety attracting twice as many predators as the least attractive variety. Chemical analysis of the volatiles released by the infested plants revealed significant differences among varieties, both in quantity and quality of the emitted blends. Comparison of the attractiveness of the varieties with the amounts of volatiles emitted indicated that the quality (composition) of the blend is more important for attraction than the amount of volatiles emitted. The amount of (E)-β-ocimene, (E,E)-TMTT, and two other, yet unidentified compounds correlated positively with the attraction of predatory mites. Quantities of four compounds negatively correlated with carnivore attraction, among them methyl salicylate, which is known to attract the predatory mite P. persimilis. The emission of methyl salicylate correlated with an unknown compound that had a negative correlation with carnivore attraction and hence could be masking the attractiveness of methyl salicylate. The results imply that the foraging success of natural enemies of pests can be enhanced by breeding for crop varieties that release specific volatiles.     

Solution-processed germanium nanowire-positioned Schottky solar cells

Germanium nanowire (GeNW)-positioned Schottky solar cell was fabricated by a solution process. A GeNW-containing solution was spread out onto asymmetric metal electrodes to produce a rectifying current flow. Under one-sun illumination, the GeNW-positioned Schottky solar cell yields an open-circuit voltage of 177 mV and a short-circuit current of 19.2 nA. Schottky and ohmic contacts between a single GeNW and different metal electrodes were systematically investigated. This solution process may provide a route to the cost-effective nanostructure solar architecture.     

Behavioral and Chemical Investigations of Contact Kairomones Released by the Mud Dauber Wasp <Emphasis Type="Italic">Trypoxylon politum</Emphasis>, a Host of the Parasitoid <Emphasis Type="Italic">Melittobia digitata</Emphasis>

Contact kairomones from the host mud dauber wasp Trypoxylon politum Say (Hymenoptera: Crabronidae) that mediate behavioral responses of its ectoparasitoid Melittobia digitata Dahms (Hymenoptera: Eulophidae) were investigated. Chemical residues from host by-products, the cocoon, and the meconium, induced arrestment behavior of macropterous female parasitoids, while those from the host stage attacked, i.e., the prepupa, did not. Melittobia digitata response to polar and apolar extracts of host by-products indicated kairomone(s) solubility mainly in hexane. GC and GC/MS analysis of cocoon and meconium apolar extracts revealed a mixture of linear carboxylic acids from C₆ to C₁₈, and both extracts contained almost identical compounds. When a reconstructed blend of host by-product carboxylic acids was tested, M. digitata females showed only a weak response, thus suggesting that other unidentified compounds present in small quantities also may be involved. Melittobia digitata’s response to contact kairomones was innate and not affected by previous host exposure experience. Our results provide evidence of contact kairomone exploitation in the genus Melittobia. The ecological significance of these findings in the host selection process of M. digitata is discussed.     

Experimental Validation of a Fundamental Model for PCR Efficiency

Recently a theoretical analysis of PCR efficiency has been published by Booth et al. (2010). The PCR yield is the product of three efficiencies: (i) the annealing efficiency is the fraction of templates that form binary complexes with primers during annealing, (ii) the polymerase binding efficiency is the fraction of binary complexes that bind to polymerase to form ternary complexes and (iii) the elongation efficiency is the fraction of ternary complexes that extend fully. Yield is controlled by the smallest of the three efficiencies and control could shift from one type of efficiency to another over the course of a PCR experiment. Experiments have been designed that are specifically controlled by each one of the efficiencies and the results are consistent with the mathematical model. The experimental data has also been used to quantify six key parameters of the theoretical model. An important application of the fully characterized model is to calculate initial template concentration from real-time PCR data. Given the PCR protocol, the midpoint cycle number (where the template concentration is half that of the final concentration) can be theoretically determined and graphed for a variety of initial DNA concentrations. Real-time results can be used to calculate the midpoint cycle number and consequently the initial DNA concentration, using this graph. The application becomes particularly simple if a conservative PCR protocol is followed where only the annealing efficiency is controlling.     

The analysis of repeated multivariate binary quality of life data: a hierarchical model approach

Many quality of life measuring instruments consist of a number of questions that are answered on ordinal scales. Often these responses are then totalled to give a summary score for each quality of life domain within the instrument. This, however, may lose valuable information about individual aspects of patient quality of life and also can have little intuitive meaning. Here we present an alternative analysis, in which dichotomized individual items of the questionnaire are analyzed. We first show how a hierarchical logistic regression model for repeated binary data can be extended to the multivariate case. We then use such a model for analyzing the prevalence of six symptoms in a palliative treatment trial in non-small-cell lung cancer. The analysis provides information about the correlations between symptoms, both between and within person. If appropriate, it also permits the estimation of a treatment effect common to all symptoms. Methods for model checking are discussed. We conclude that this methodology can provide a more intuitive and informative analysis of quality of life data than that obtained by considering summary scores.     

Structural and kinetic studies on ligand binding in wild-type and active-site mutants of penicillin acylase

Penicillin acylase catalyses the condensation of Calpha-substituted phenylacetic acids with beta-lactam nucleophiles, producing semi-synthetic beta-lactam antibiotics. For efficient synthesis a low affinity for phenylacetic acid and a high affinity for Calpha-substituted phenylacetic acid derivatives is desirable. We made three active site mutants, alphaF146Y, betaF24A and alphaF146Y/betaF24A, which all had a 2- to 10-fold higher affinity for Calpha-substituted compounds than wild-type enzyme. In addition, betaF24A had a 20-fold reduced affinity for phenylacetic acid. The molecular basis of the improved properties was investigated by X-ray crystallography. These studies showed that the higher affinity of alphaF146Y for (R)-alpha-methylphenylacetic acid can be explained by van der Waals interactions between alphaY146:OH and the Calpha-substituent. The betaF24A mutation causes an opening of the phenylacetic acid binding site. Only (R)-alpha-methylphenylacetic acid, but not phenylacetic acid, induces a conformation with the ligand tightly bound, explaining the weak binding of phenylacetic acid. A comparison of the betaF24A structure with other open conformations of penicillin acylase showed that betaF24 has a fixed position, whereas alphaF146 acts as a flexible lid on the binding site and reorients its position to achieve optimal substrate binding.