Nitrilases catalyze key step to conformationally constrained GABA analogous gamma-amino acids in high optical purity

Five- and six-membered carbocyclic gamma-amino acids were prepared in high enantiomeric purity by nitrilase-mediated transformation of hitherto unreported gamma-amino nitriles. The nitrilases investigated reveal a strong enantiopreference for cis-isomers (up to 99% ee), whereas trans-isomers were available in up to 86% ee. The biocatalytic enantioselective syntheses of cis-3-aminocyclohexanecarboxylic acid (3b), trans-3-aminocyclohexanecarboxylic acids (4b, 6b, 8b) as well as trans-3-aminocylopentanecarboxylic acid (2b) are hereby reported for the first time.     

Design of new plasmepsin inhibitors: a virtual high throughput screening approach on the EGEE grid

Though different species of the genus Plasmodium may be responsible for malaria, the variant caused by P. falciparum is often very dangerous and even fatal if untreated. Hemoglobin degradation is one of the key metabolic processes for the survival of the Plasmodium parasite in its host. Plasmepsins, a family of aspartic proteases encoded by the Plasmodium genome, play a prominent role in host hemoglobin cleavage. In this paper we demonstrate the use of virtual screening, in particular molecular docking, employed at a very large scale to identify novel inhibitors for plasmepsins II and IV. A large grid infrastructure, the EGEE grid, was used to address the problem of large computation resources required for docking hundreds of thousands of chemical compounds on different plasmepsin targets of P. falciparum. A large compound library of about 1 million chemical compounds was docked on 5 different targets of plasmepsins using two different docking software, namely FlexX and AutoDock. Several strategies were employed to analyze the results of this virtual screening approach including docking scores, ideal binding modes, and interactions to key residues of the protein. Three different classes of structures with thiourea, diphenylurea, and guanidino scaffolds were identified to be promising hits. While the identification of diphenylurea compounds is in accordance with the literature and thus provides a sort of "positive control", the identification of novel compounds with a guanidino scaffold proves that high throughput docking can be effectively used to identify novel potential inhibitors of P. falciparum plasmepsins. Thus, with the work presented here, we do not only demonstrate the relevance of computational grids in drug discovery but also identify several promising small molecules which have the potential to serve as candidate inhibitors for P. falciparum plasmepsins. With the use of the EGEE grid infrastructure for the virtual screening campaign against the malaria causing parasite P. falciparum we have demonstrated that resource sharing on an eScience infrastructure such as EGEE provides a new model for doing collaborative research to fight diseases of the poor.     

Influence of roughness and capillary size on the zeta potential values obtained by streaming potential measurements

Streaming potential measurements are performed to determine the zeta potential of flat surfaces, particles, or fibers. Although the zeta potential is a well-defined property of solid surfaces in a liquid, there are indications that the absolute values of the zeta potential calculated using the Helmholtz-Smoluchowski equation are affected by surface roughness and—in case of particle or fiber assemblies—their packing density. The study at hand investigates these influences using flat polymer surfaces with different roughness and topography and assemblies of basalt spheres. It was found that increasing roughness of the flat surface and larger size or smaller number of particles in particle assemblies result in flatter slopes of the streaming potential versus pressure and thus lower apparent absolute values of the zeta potential. The interpretation of streaming potential measurements should therefore not focus on absolute zeta potential values but on trends in pH- and concentration-dependent measurements.     

Assessing the effect of oxygen and microbial inhibitors to optimize ferricyanide-mediated BOD assay

Methods for short-term BOD analysis (BOD_st) based on ferricyanide mediator reduction have succeeded in overcoming some problems associated with the standard BOD test analysis (BOD₅) such as long-term incubations (5 days), the need to dilute samples and low reproducibility. Here we present a bioassay where a Klebsiella pneumoniae environmental strain successfully reduces ferricyanide without de-aeration of the samples with linear BOD₅ ranges between 30 and 500 mg L⁻¹ or 30 and 200 mg L⁻¹, using glucose-glutamic acid solution (GGA) or OECD standards respectively. We further propose a new assay termination solution that allows higher reproducibility and standardization of the cell-based assay, employing formaldehyde (22.7 g L⁻¹) or other compounds in order to stop ferricyanide reduction without affecting the amperometric detection and therefore replace the centrifugation step normally used to stop microbial-driven reactions in ferricyanide-mediated bioassays. These improvements led to an accurate determination of real municipal wastewater samples.     

Separation of Sr in combination of ion exchange and Sr resin with alcohol-nitric acid solution and rapid determination of <Superscript>90</Superscript>Sr in wine and soil samples

This paper describes the procedures of isolating strontium from wine and soil samples which enable creating of procedure for rapid determination of ⁹⁰Sr. The method of determination of ⁹⁰Sr includes binding of Sr on the cationic exchanger IR-120 from the sample and simultaneous elution from the cation column and binding on the Sr column, separation of Sr on Sr resin with HNO₃ even in presence of alcohols and subsequent Cherenkov counting. Sr can be efficiently bind on Sr resin and separated from the other elements with lower acid concentrations in the presence of a low portion of alcohol, or even from a wine sample without the loss of Sr resin capacity. The binding strength of Sr on Sr resin decreases with the rising of HNO₃ concentration (1–5 M) in the presence of 13% of ethanol or methanol, and with the rising of the alcohol portion in constant concentration of HNO₃. Application of cation exchanger for Sr binding in phase of sample preparation decreases Sr column loading and improve Sr recovery. The method allows the determination of ⁹⁰Sr activities in wine and soil sample lower than 10 mBq in reasonable time.     

Isolation and Structural Elucidation of Armeniaspirols A–C: Potent Antibiotics against Gram‐Positive Pathogens

In an antibiotic lead discovery program, the known strain Streptomyces armeniacus DSM19369 has been found to produce three new natural products when cultivated on a malt‐containing medium. The challenging structural elucidation of the isolated compounds was achieved by using three independent methods, that is, chemical degradation followed by NMR spectroscopy, a computer‐assisted structure prediction algorithm, and X‐ray crystallography. The compounds, named armeniaspirol A–C ( 2 – 4 ), exhibit a compact, hitherto unprecedented chlorinated spiro[4.4]non‐8‐ene scaffold. Labeling experiments with [1‐¹³C] acetate, [1,2‐¹³C2] acetate, and [U‐¹³C] proline suggest a biosynthesis through a rare two‐chain mechanism. Armeniaspirols displayed moderate to high in vitro activities against Gram‐positive pathogens such as methicillin‐resistant S. aureus (MRSA) or vancomycin resistant E. faecium (VRE). As analogue 2 was active in vivo in an MRSA sepsis model, and showed no development of resistance in a serial passaging experiment, it represents a new antibiotic lead structure.     

Modelling methyl tertiary butyl ether and tertiary butyl alcohol biodegradation by a bacterial consortium

The widespread use of methyl tertiary butyl ether (MTBE) as an additive in gasoline has resulted in serious soil and groundwater pollution. To tackle MTBE contamination in groundwater, bioremediation is considered a cost-effective and energy-efficient option. The design of an efficient, reliable and reproducible bioremediation strategy requires a thorough understanding of the (microbial) degradation kinetics of both MTBE and tertiary butyl alcohol (TBA), that is, the main intermediate during bioremediation of MTBE. To assist the design procedure, this research focuses on building a mathematical model to describe MTBE/TBA degradation kinetics by a bacterial consortium, that is, the VITO M-consortium.

For the presented case study, the information obtained from experimental data is combined with knowledge regarding the biodegradation reactions in order to obtain a low-complexity, accurate mathematical model. The resulting model accurately describes MTBE/TBA degradation and has successfully been validated on independent experimental data. Since the model is of the mass balance type, it can easily be extended to other types of operation by defining the transport terms of the new system. This makes the model a very useful tool in the design procedure for large-scale bioremediation strategies. Furthermore, the model provides insight into the MTBE/TBA degradation kinetics and biodegradation mechanisms by hypothesis testing.     

Normal-state hourglass dispersion of the spin excitations in FeSexTe(1-x)

We use cold neutron spectroscopy to study the low-energy spin excitations of superconducting (SC) FeSe0.4Te0.6 and essentially nonsuperconducting (NSC) FeSe0.45Te0.55. In contrast with BaFe2-x(Co,Ni)xAs2, where the low-energy spin excitations are commensurate both in the SC and normal state, the normal-state spin excitations in SC FeSe0.4Te0.6 are incommensurate and show an hourglass dispersion near the resonance energy. Since similar hourglass dispersion is also found in the NSC FeSe0.45Te0.55, we argue that the observed incommensurate spin excitations in FeSe(1-x)Tex are not directly associated with superconductivity. Instead, the results can be understood within a picture of Fermi surface nesting assuming extremely low Fermi velocities and spin-orbital coupling.