A Multiplex Assay to Assess the Transaminase Activity toward Chemically Diverse Amine Donors

The development of methods to engineer and immobilize amine transaminases (ATAs) to improve their functionality and operational stability is gaining momentum. The quest for robust, fast, and easy-to-use methods to screen the activity of large collections of transaminases, is essential. This work presents a novel and multiplex fluorescence-based kinetic assay to assess ATA activity using 4-dimethylamino-1-naphthaldehyde as an amine acceptor. The developed assay allowed us to screen a battery of amine donors using free and immobilized ATAs from different microbial sources as biocatalysts. As a result, using chromatographic methods, 4-hydroxybenzylamine was identified as the best amine donor for the amination of 5-(hydroxymethyl)furfural. Finally, we adapted this method to determine the apparent Michaelis-Menten parameters of a model immobilized ATA at the microscopic (single-particle) level. Our studies promote the use of this multiplex, multidimensional assay to screen ATAs for further improvement.     

A new generation of fibers from alginic acid for dressing materials

We developed and elaborated manufacturing conditions for the production of alginic acid fibers with high sorption properties. The fibers' tenacity obtained at a level of 16 cN/tex is suitable for textile processing these fibers, and will make it possible to produce a new generation of highly absorptive dressing materials. The presence of acid groups in the fiber‐forming material allows us to use them for the addition of new generation antibiotics, which makes it possible to extend the antibacterial effects of these fibers. © 2007 Wiley Periodicals, Inc. J Appl Polym Sci, 2008     

Label-Free Quantitative Proteomics Reveals Differences in Molecular Mechanism of Atherosclerosis Related and Non-Related to Chronic Kidney Disease

The major cause of mortality in patients with chronic kidney disease (CKD) is atherosclerosis related to traditional and non-traditional risk factors. However, the understanding of the molecular specificity that distinguishes the risk factors for classical cardiovascular disease (CVD) and CKD-related atherosclerosis (CKD-A) is far from complete. In this study we investigated the disease-related differences in the proteomes of patients with atherosclerosis related and non-related to CKD. Plasma collected from patients in various stages of CKD, CVD patients without symptoms of kidney dysfunction, and healthy volunteers (HVs), were analyzed by a coupled label-free and mass spectrometry approach. Dysregulated proteins were confirmed by an enzyme-linked immunosorbent assay (ELISA). All proteomic data were correlated with kidney disease development and were subjected to bioinformatics analysis. One hundred sixty-two differentially expressed proteins were identified. By directly comparing the plasma proteomes from HVs, CKD, and CVD patients in one study, we demonstrated that proteins involved in inflammation, blood coagulation, oxidative stress, vascular damage, and calcification process exhibited greater alterations in patients with atherosclerosis related with CKD. These data indicate that the above nontraditional risk factors are strongly specific for CKD-A and appear to be less essential for the development of “classical” CVD.     

Electrochemical and density functional theory study of bis(cyclopentadienyl) mono(β-diketonato) titanium(IV) cationic complexes

The electrochemical behaviour of fluorinated bis(cyclopentadienyl) mono(β-diketonato) titanium(IV) complexes, of general formula [Cp₂Ti(R′COCHCOR)]⁺ClO₄⁻ with Cp = cyclopentadienyl and R′, R = CF₃, C₄H₃S; CF₃, C₄H₃O; CF₃, Ph (C₆H₅); CF₃, CH₃; CH₃, CH₃; Ph, Ph and Ph, CH₃ is described. Both metal and ligand based redox processes are observed. The chemically and electrochemically reversible Ti^IV/Ti^III couple is followed by an irreversible ligand reduction at a considerably more negative (cathodic) potential. A comparison of the ligand reduction in its free and chelated state indicates that the β-diketonato ligand (R′COCHCOR)⁻ in [Cp₂Ti(R′COCHCOR)]⁺ClO₄⁻ is electroactive at more negative potentials. A theoretical density functional theory (DFT) study shows that a highly localized metal centred frontier orbital dominates the Ti^IV/Ti^III redox chemistry resulting in a non-linear relationship between the formal redox potential (E°′) and the sum of the group electronegativities of the R and R′ groups, χ_R + χ_R′, of the ligand. Linear relationships, however, are obtained between the DFT calculated electron affinity (EA) of the complexes and χ_R + χ_R′, the pK_a of the free β-diketones R′COCH₂COR and the carbonyl stretching frequency, v_CO, of the complexes. The DFT calculated electronic structure of the second reduced species [Cp₂Ti(β-diketonato)]⁻ shows that it is best described as Ti(III) coupled to a β-diketonato radical.     

The Semantic Web: Collective Intelligence on the Web

The World Wide Web has turned hypertext into a success story by enabling world-wide sharing of unstructured information and informal knowledge. The Semantic Web targets the sharing of structured information and formal knowledge pursuing objectives of achieving collective intelligence on the Web. Germane to the structure of the Semantic Web is a layering and standardization of concerns. These concerns are reflected by an architecture of the Semantic Web that we present through a common use case. Semantic Web data for the use case is now found on the Web and is part of a quickly growing set of Semantic Web resources available for formal processing.     

Production of Polyunsaturated Fatty Acids by Mortierella alpina Using Submerse and Solid State Fermentation

A new isolate of Mortierella alpina, > 98 % identical with M. alpina ATCC 16266, was cultivated in a defined glucose‐based medium with three organic nitrogen sources (glycine, urea and Na‐L‐glutamate) at three different concentrations in shaking flasks at 20 °C. The results were compared to the cultivation in complex medium with yeast extract as nitrogen source. In the defined media, high yields of polyunsaturated fatty acids (PUFAs) and arachidonic acid (ARA), respectively, were obtained with Na‐L‐glutamate. However, the absolute highest yields of PUFA and ARA were measured with the yeast extract medium. An optimized yeast extract complex medium was used for a submerse bioreactor cultivation in a 45‐L scale. Furthermore, M. alpina was cultivated in a solid state fermenter, using an oat bran water mixture as substrate.     

Multipose Binding in Molecular Docking

Molecular docking has been extensively applied in virtual screening of small molecule libraries for lead identification and optimization. A necessary prerequisite for successful differentiation between active and non-active ligands is the accurate prediction of their binding affinities in the complex by use of docking scoring functions. However, many studies have shown rather poor correlations between docking scores and experimental binding affinities. Our work aimed to improve this correlation by implementing a multipose binding concept in the docking scoring scheme. Multipose binding, i.e., the property of certain protein-ligand complexes to exhibit different ligand binding modes, has been shown to occur in nature for a variety of molecules. We conducted a high-throughput docking study and implemented multipose binding in the scoring procedure by considering multiple docking solutions in binding affinity prediction. In general, improvement of the agreement between docking scores and experimental data was observed, and this was most pronounced in complexes with large and flexible ligands and high binding affinities. Further developments of the selection criteria for docking solutions for each individual complex are still necessary for a general utilization of the multipose binding concept for accurate binding affinity prediction by molecular docking.     

A decomposition method for multi-product kanban systems with setup times and lost sales

We consider kanban controlled production systems with three or more different products processed on a single manufacturing facility. Customers for a product arrive according to a Poisson process. If a customer's demand cannot be met from stock, the customer leaves and satisfies his demand elsewhere (lost sales). Between the production of different products setup changes must be performed that take a significant time. Setup times and processing times are product-specific and follow exponential distributions. A production run continues until the target inventory level given by the number of kanbans for the product has been reached (exhaustive processing). Then the manufacturing facility is set up for the next product according to a fixed setup cycle. The exact model is mathematically intractable even for smaller systems. Therefore, we propose a decomposition-based approximation method for estimating steady-state performance measures     

Real-Time Noncoherent UWB Positioning Radar With Millimeter Range Accuracy: Theory and Experiment

In this paper, we propose a novel architecture for ultra-wideband (UWB) positioning systems, which combines the architectures of carrier-based UWB systems and traditional energy detection-based UWB systems. By implementing the novel architecture, we have successfully developed a standalone noncoherent system for positioning both static and dynamic targets in an indoor environment with approximately 2 and 5 mm of 3-D accuracy, respectively. The results are considered a great milestone in developing such technology. 1-D and 3-D experiments have been carried out and validated using an optical reference system, which provides better than 0.3-mm 3-D accuracy. This type of indoor high-accuracy wireless localization system has many unique applications including robot control, surgical navigation, sensitive material monitoring, and asset tracking.