Identification of six new photoactive yellow proteins--diversity and structure-function relationships in a bacterial blue light photoreceptor

Photoactive yellow proteins (PYP) are bacterial photoreceptors with a Per-Arnt-Sim (PAS) domain fold. We report the identification of six new PYPs, thus nearly doubling the size of this protein family. This extends the taxonomic diversity of PYP-containing bacteria from photosynthetic to nonphotosynthetic bacteria, from aquatic to soil-dwelling organisms, and from Proteobacteria to Salinibacter ruber from the phylum Bacteriodetes. The new PYPs greatly increase the sequence diversity of the PYP family, reducing the most prevalent pair-wise identity from 45% to 25%. Sequence alignments and analysis indicate that all 14 PYPs share a common structure with 13 highly conserved residues that form the chromophore binding pocket. Nevertheless, the functional properties of the PYPs vary greatly--the absorbance maximum extends from 432 to 465 nm, the pK(a) of the chromophore varies from pH 2.8 to 10.2, and the lifetime of the presumed PYP signaling state ranges from 1 ms to 1 h. Thus, the PYP family offers an excellent opportunity to investigate how functional properties are tuned over a wide range, while maintaining the same overall protein structural fold. We discuss the implications of these results for structure-function relationships in the PYP family.     

Thrombin allostery

Thrombin is a Na(+)-activated, allosteric serine protease that plays multiple functional roles in blood pathophysiology. Binding of Na(+) is the major driving force behind the procoagulant, prothrombotic and signaling functions of the enzyme. This review summarizes our current understanding of the molecular basis of thrombin allostery with special emphasis on the kinetic aspects of Na(+) activation. The molecular mechanism of thrombin allostery is a remarkable example of long-range communication that offers a paradigm for many other biological systems.     

Analytical discrimination between sources of ginseng using Raman spectroscopy

Ginseng is a widely used medicinal product that grows mainly in Korea, China and America. American ginseng is classified as an endangered species, and so the import and export of this type of ginseng is illegal in certain countries. Due to this restriction it is becoming increasingly important to be able to distinguish between different types of ginseng. FT-Raman spectroscopy has the ability to discriminate between ginseng specimens according to the country of origin and the effects of processing on the ginseng material. The ginsenoside content of ginseng differs in both conformation and concentration depending on the source of the ginseng, which means that ginseng grown in different countries should express unique spectral features. The presence or absence of these features, therefore, could indicate the geographical origin of the sample. Several spectral features were identified for a range of ginsengs, such as a peak at 980 cm(-1) that was only found in Chinese ginseng, and the different wavenumber positions of characteristic ginseng bands near 1600 cm(-1). This indicates that Raman spectroscopy can be used to pinpoint the origin of an unknown ginseng sample and that it would provide a rapid nondestructive analytical technique for formally discriminating between restricted and permitted imports.     

Analysis of testosterone and dihydrotestosterone from biological fluids as the oxime derivatives using high-performance liquid chromatography/tandem mass spectrometry

A sensitive liquid chromatography/electrospray ionization tandem mass spectrometry (LC/ESI-MS/MS) method for the simultaneous quantitative analysis of dihydrotestosterone (DHT) and testosterone (T) from biological fluids has been developed. Commercially available deuterated analogues were used as internal standards. Steroids were extracted from serum or testicular fluid with hexane/ethyl acetate, evaporated to dryness, and treated with hydroxylamine to form their oxime derivatives. Upon chromatographic separation, the compounds were quantified using selected reaction monitoring (SRM). For T, the [M+H](+) ion at m/z 304 and the fragment ion at m/z 124 were used as the precursor and product ions. For DHT the ion cluster [M+H+ACN](+) at m/z 347 and the dissociated ion [M+H](+) at m/z 306 were used as the precursor and product ions, respectively. The limits of detectability on-column were in the sub-femtomole range for both compounds and the intra-day coefficient of variation (CV) for analysis from serum was less than 7% for both compounds. Given its high reproducibility, sensitivity, and relative simplicity, this assay should be of use in determining androgen levels in biospecimens, particularly in settings where sample quantity or steroid concentration are low.     

Copper and iron interactions with angiotensin-converting enzyme inhibitors. A study by fast-atom bombardment tandem mass spectrometry

Fast atom bombardment, combined with high-energy collision-induced tandem mass spectrometry, has been used to investigate gas-phase metal-ion interactions with captopril, enalaprilat and lisinopril, all angiotensin-converting enzyme inhibitors.Suggestions for the location of metal-binding sites are presented. For captopril, metal binding occurs most likely at both the sulphur and the nitrogen atom. For enalaprilat and lisinopril, binding preferably occurs at the amine nitrogen. Copyright 1999 John Wiley & Sons, Ltd.     

Transmission of ultrasound through a single layer of bubbles

We investigate, both experimentally and theoretically, the effect of coupling between resonant scatterers on the transmission coefficient of a model system of isotropic scatterers. The model system consists of a monodisperse layer of bubbles, which exhibit a strong monopole scattering resonance at low ultrasonic frequencies. The layer was a true 2D structure obtained by injecting very monodisperse bubbles (with radius a ∼ 100 μm) into a yield-stress polymer gel. Even for a layer with a low concentration of bubbles (areal fraction, n a ² , of 10-20%, where n is the number of bubbles per unit area), the ultrasonic transmission was found to be significantly reduced by the presence of bubbles (-20 to -50 dB) and showed a sharp minimum at a particular frequency. Interestingly, this frequency did not correspond to the resonance frequency of the individual, isolated bubbles, but depended markedly on the concentration. This frequency shift is an indication of strong coupling between the bubbles. We propose a simple model, based on a self-consistent relation, which takes into account the coupling between the bubbles and gives good agreement with the measured transmission coefficient.     

Voltammetric Antioxidant Analysis in Mineral Oil Samples Immobilized into Boron‐Doped Diamond Micropore Array Electrodes

Mineral oil microdroplets containing the model antioxidant N,N‐didodecyl‐N′,N′‐diethyl‐phenylene‐diamine (DDPD) are immobilized into a 100×100 pore‐array (ca. 10 μm individual pore diameter, 100 μm pitch) in a boron‐doped diamond electrode surface. The robust diamond surface allows pore filling, cleaning, and reuse without damage to the electrode surface. The electrode is immersed into aqueous electrolyte media, and voltammetric responses for the oxidation of DDPD are obtained. In order to further improve the current responses, 20 wt% of carbon nanofibers are co‐deposited with the oil into the pore array. Voltammetric signals are consistent with the oxidation of DDPD and the associated transfer of perchlorate anions (in aqueous 0.1 M NaClO₄) or the transfer of protons (in aqueous 0.1 M HClO₄). From the magnitude of the current response, the DDPD content in the mineral oil can be determined down to less than 1 wt% levels. Perhaps surprisingly, the reversible (or midpoint) potential for the DDPD oxidation in mineral oil (when immersed in 0.1 NaClO₄) is shown to be concentration‐dependent and to shift to more positive potential values for more dilute DDPD in mineral oil solutions. An extraction mechanism and the formation of a separate organic product phase are proposed to explain this behavior.     

Convergence of adaptive FEM for elliptic obstacle problems

We treat the convergence of adaptive lowest-order FEM for some elliptic obstacle problem with affine obstacle. For error estimation, we use a residual error estimator which is an extended version of the estimator from [2] and additionally controls the data oscillations. The main result states that an appropriately weighted sum of energy error, edge residuals, and data oscillations satisfies a contraction property that leads to convergence. In addition, we discuss the generalization to the case of inhomogeneous Dirichlet data and non-affine obstacles χ ∈ H²(Ω) for which similar results are obtained. (© 2011 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim)     

Proton Emission——-Recent Results and Future Prospects

Considerable progress has been made in the study of proton-emitting nuclei since the first observation of direct proton emission nearly half a century ago. This has led to improvements in our understanding of this rare decay process and provided invaluable nuclear structure data far from the valley of beta stability. This paper reviews the implications of some recent results for exotic iridium, rhenium and tantalum isotopes and considers prospects for future experimental studies of proton-emitting nuclei located at and above the N =82 neutron shell closure.     

Biologically driven neural platform invoking parallel electrophoretic separation and urinary metabolite screening

This work reveals a computational framework for parallel electrophoretic separation of complex biological macromolecules and model urinary metabolites. More specifically, the implementation of a particle swarm optimization (PSO) algorithm on a neural network platform for multiparameter optimization of multiplexed 24-capillary electrophoresis technology with UV detection is highlighted. Two experimental systems were examined: (1) separation of purified rabbit metallothioneins and (2) separation of model toluene urinary metabolites and selected organic acids. Results proved superior to the use of neural networks employing standard back propagation when examining training error, fitting response, and predictive abilities. Simulation runs were obtained as a result of metaheuristic examination of the global search space with experimental responses in good agreement with predicted values. Full separation of selected analytes was realized after employing optimal model conditions. This framework provides guidance for the application of metaheuristic computational tools to aid in future studies involving parallel chemical separation and screening. Adaptable pseudo-code is provided to enable users of varied software packages and modeling framework to implement the PSO algorithm for their desired use.