Analysis of the reaction mechanism and substrate specificity of haloalkane dehalogenases by sequential and structural comparisons

Haloalkane dehalogenases catalyse environmentally importantdehalogenation reactions. These microbial enzymes representobjects of interest for protein engineering studies, attemptingto improve their catalytic efficiency or broaden their substratespecificity towards environmental pollutants. This paper presentsthe results of a comparative study of haloalkane dehalogenasesoriginating from different organisms. Protein sequences andthe models of tertiary structures of haloalkane dehalogenaseswere compared to investigate the protein fold, reaction mechanismand substrate specificity of these enzymes. Haloalkane dehalogenasescontain the structural motifs of /ß-hydrolases and epoxidaseswithin their sequences. They contain a catalytic triad withtwo different topological arrangements. The presence of a structurallyconserved oxyanion hole suggests the two-step reaction mechanismpreviously described for haloalkane dehalogenase from Xanthobacterautotrophicus GJ10. The differences in substrate specificityof haloalkane dehalogenases originating from different speciesmight be related to the size and geometry of an active siteand its entrance and the efficiency of the transition stateand halide ion stabilization by active site residues. Structurallyconserved motifs identified within the sequences can be usedfor the design of specific primers for the experimental screeningof haloalkane dehalogenases. Those amino acids which were predictedto be functionally important represent possible targets forfuture site-directed mutagenesis experiments.     

On the existence of chaos in the electronically adjustable structures of the state variable filters

As demonstrated in the paper, chaotic motion can appear in state variable filters, that is, common network structures dedicated for analog signal processing. In particular, two Kerwin–Huelsman–Newcomb biquadratic filtering sections are considered for theoretical, numerical and experimental analysis. Mathematical models are designed, and conditions for evolution of typical strange attractors are provided. The corresponding largest Lyapunov exponent is calculated and visualized as a function of internal system parameters and the shape of input harmonic waveform. Mutual connection between the mathematical model and the real lumped electronic circuit is discussed in detail. Copyright © 2016 John Wiley & Sons, Ltd.     

CFD Process Modeling of the Industrial Calcination of Diatomite

Calcination of diatomite is an expensive process frequently resulting in products with unpredictable structure. Alternatively, calcination in swirling flow is an energy‐saving option. Computational fluid dynamics modeling of an experimental calcination process unit is presented. Experimental results and systematic collection of process data were used to define boundary condition for steady‐state and transient simulation runs. The comparison of experimental and simulation results shows the complexity of the calcination process. The results can be used for further process optimization.     

A Novel Nanoprobe for Multimodal Imaging Is Effectively Incorporated into Human Melanoma Metastatic Cell Lines

To facilitate efficient drug delivery to tumor tissue, several nanomaterials have been designed, with combined diagnostic and therapeutic properties. In this work, we carried out fundamental in vitro and in vivo experiments to assess the labeling efficacy of our novel theranostic nanoprobe, consisting of glycogen conjugated with a red fluorescent probe and gadolinium. Microscopy and resazurin viability assays were used to study cell labeling and cell viability in human metastatic melanoma cell lines. Fluorescence lifetime correlation spectroscopy (FLCS) was done to investigate nanoprobe stability. Magnetic resonance imaging (MRI) was performed to study T₁ relaxivity in vitro, and contrast enhancement in a subcutaneous in vivo tumor model. Efficient cell labeling was demonstrated, while cell viability, cell migration, and cell growth was not affected. FLCS showed that the nanoprobe did not degrade in blood plasma. MRI demonstrated that down to 750 cells/μL of labeled cells in agar phantoms could be detected. In vivo MRI showed that contrast enhancement in tumors was comparable between Omniscan contrast agent and the nanoprobe. In conclusion, we demonstrate for the first time that a non-toxic glycogen-based nanoprobe may effectively visualize tumor cells and tissue, and, in future experiments, we will investigate its therapeutic potential by conjugating therapeutic compounds to the nanoprobe.     

Stepwise dissection and visualization of the catalytic mechanism of haloalkane dehalogenase LinB using molecular dynamics simulations and computer graphics

The different steps of the dehalogenation reaction carried out by LinB on three different substrates have been characterized using a combination of quantum mechanical calculations and molecular dynamics simulations. This has allowed us to obtain information in atomic detail about each step of the reaction mechanism, that is, substrate entrance and achievement of the near-attack conformation, transition state stabilization within the active site, halide stabilization, water molecule activation and subsequent hydrolytic attack on the ester intermediate with formation of alcohol, and finally product release. Importantly, no bias or external forces were applied during the whole procedure so that both intermediates and products were completely free to sample configuration space in order to adapt to the plasticity of the active site and/or search for an exit. Differences in substrate reactivity were found to be correlated with the ease of adopting the near-attack conformation and two different exit pathways were found for product release that do not interfere with substrate entrance. Additional support for the different entry and exit pathways was independently obtained from an examination of the enzyme's normal modes.     

Detection of bubbles as concentric circular arrangements

The paper proposes a method for the detection of bubble-like transparent objects in a liquid. The detection problem is non-trivial since bubble appearance varies considerably due to different lighting conditions causing contrast reversal and multiple interreflections. We formulate the problem as the detection of concentric circular arrangements (CCA). The CCAs are recovered in a hypothesize-optimize-verify framework. The hypothesis generation is based on sampling from the partially linked components of the non-maximum suppressed responses of oriented ridge filters, and is followed by the CCA parameter estimation. Parameter optimization is carried out by minimizing a novel cost-function. The performance was tested on gas dispersion images of pulp suspension and oil dispersion images. The mean error of gas/oil volume estimation was used as a performance criterion due to the fact that the main goal of the applications driving the research was the bubble volume estimation. The method achieved 28 and 13 % of gas and oil volume estimation errors correspondingly outperforming the OpenCV Circular Hough Transform in both cases and the WaldBoost detector in gas volume estimation.