Screening,Molecular Cloning,and Biochemical Characterization of an Alcohol Dehydrogenase from Pichia pastoris Useful for the Kinetic Resolution of a Racemic β‐Hydroxy‐β‐trifluoromethyl Ketone

The stereoselective synthesis of chiral 1,3‐diols with the aid of biocatalysts is an attractive tool in organic chemistry. Besides the reduction of diketones, an alternative approach consists of the stereoselective reduction of β‐hydroxy ketones (aldols). Thus, we screened for an alcohol dehydrogenase (ADH) that would selectively reduce a β‐hydroxy‐β‐trifluoromethyl ketone. One potential starting material for this process is readily available by aldol addition of acetone to 2,2,2‐trifluoroacetophenone. Over 200 strains were screened, and only a few yeast strains showed stereoselective reduction activities. The enzyme responsible for the reduction of the β‐hydroxy‐β‐trifluoromethyl ketone was identified after purification and subsequent MALDI‐TOF mass spectrometric analysis. As a result, a new NADP⁺‐dependent ADH from Pichia pastoris (PPADH) was identified and confirmed to be capable of stereospecific and diastereoselective reduction of the β‐hydroxy‐β‐trifluoromethyl ketone to its corresponding 1,3‐diol. The gene encoding PPADH was cloned and heterologously expressed in Escherichia coli BL21(DE3). To determine the influence of an N‐ or C‐terminal His‐tag fusion, three different recombinant plasmids were constructed. Interestingly, the variant with the N‐terminal His‐tag showed the highest activity; consequently, this variant was purified and characterized. Kinetic parameters and the dependency of activity on pH and temperature were determined. PPADH shows a substrate preference for the reduction of linear and branched aliphatic aldehydes. Surprisingly, the enzyme shows no comparable activity towards ketones other than the β‐hydroxy‐β‐trifluoromethyl ketone.     

Higher Hydrocarbon Production through Oxidative Coupling of Methane Combined with Hydrogenation of Carbon Oxides

In the production of higher hydrocarbons, combining oxidative coupling of methane (OCM) with hydrogenation of the formed carbon oxides in a separate reactor provides an alternative to the currently applied methane conversion to syngas followed by Fischer‐Tropsch synthesis. The effects of CH₄:O₂ feed ratio in the OCM reactor and partial pressures of H₂ or/and H₂O in the hydrogenation reactor were analyzed to maximize production of C₂₊ hydrocarbons and reduce CO_x formation. The highest C₂₊ yield was achieved with low CH₄:O₂ feed ratio for OCM and removal of the formed water before entering the hydrogenation reactor.     

Binding Mode and Structure–Activity Relationships around Direct Inhibitors of the Nrf2–Keap1 Complex

An X‐ray crystal structure of Kelch‐like ECH‐associated protein (Keap1) co‐crystallised with (1S,2R)‐2‐[(1S)‐1‐[(1,3‐dioxo‐2,3‐dihydro‐1H‐isoindol‐2‐yl)methyl]‐1,2,3,4‐tetrahydroisoquinolin‐2‐carbonyl]cyclohexane‐1‐carboxylic acid (compound (S,R,S)‐ 1 a ) was obtained. This X‐ray crystal structure provides breakthrough experimental evidence for the true binding mode of the hit compound (S,R,S)‐ 1 a , as the ligand orientation was found to differ from that of the initial docking model, which was available at the start of the project. Crystallographic elucidation of this binding mode helped to focus and drive the drug design process more effectively and efficiently.     

Cluster-grouping: from subgroup discovery to clustering

We introduce the problem of cluster-grouping and show that it can be considered a subtask in several important data mining tasks, such as subgroup discovery, mining correlated patterns, clustering and classification. The algorithm CG for solving cluster-grouping problems is then introduced, and it is incorporated as a component in several existing and novel algorithms for tackling subgroup discovery, clustering and classification. The resulting systems are empirically compared to state-of-the-art systems such as CN2, CBA, Ripper, Autoclass and CobWeb. The results indicate that the CG algorithm can be useful as a generic local pattern mining component in a wide variety of data mining and machine learning algorithms.     

Mathematical programs with complementarity constraints in the context of inverse optimal control for locomotion

In this paper an inverse optimal control problem in the form of a mathematical program with complementarity constraints (MPCC) is considered and numerical experiences are discussed. The inverse optimal control problem arises in the context of human navigation where the body is modelled as a dynamical system and it is assumed that the motions are optimally controlled with respect to an unknown cost function. The goal of the inversion is now to find a cost function within a given parametrized family of candidate cost functions such that the corresponding optimal motion minimizes the deviation from given data. MPCCs are known to be a challenging class of optimization problems typically violating all standard constraint qualifications (CQs). We show that under certain assumptions the resulting MPCC fulfills CQs for MPCCs being the basis for theory on MPCC optimality conditions and consequently for numerical solution techniques. Finally, numerical results are presented for the discretized inverse optimal control problem of locomotion using different solution techniques based on relaxation and lifting.     

Design and characterization of a current sensing platform for silicon-based nanopores with integrated tunneling nanoelectrodes

Solid-state nanopores have been gaining popularity in nano-biotechnology for single molecule detection, in particular for label-free high-throughput DNA sequencing. In order to address the improvement of the resolution/speed trade-off critical in this application, here we present a new two-channel current amplifier tailored for solid-state nanopore devices with integrated tunneling electrodes. The simultaneous detection of ion and tunneling currents provides enhanced molecule tracking capability. We describe the system design starting from a detailed noise analysis and device modeling, highlighting the detrimental role of the conductive silicon substrate and of all the stray capacitive couplings between the electrodes. Given the high input capacitance (0.1–1 nF), the input voltage noise has been carefully minimized choosing a discrete couple of matched low-noise JFETs as input stage, thus achieving an equivalent input noise of 1.5 nV/√Hz (corresponding to a current noise floor of 15 fA/√Hz at 10 kHz). Low-noise performance (11 pA rms noise integrated over a 75 kHz bandwidth) is preserved at a wide bandwidth (300 kHz) and high gain (100 MΩ) thanks to the adoption of an improved integrator/differentiator cascade topology. Furthermore, along with biasing networks and selectable low-pass filters, an AC-coupled channel providing additional gain has been introduced in order to “zoom” in the current signature during pore blockade events. Together with an experimental characterization of the system (and comparison with the noise performance of other instruments), the platform is validated by demonstrating the detection of λ-DNA with 20 nm pores.     

In vitro biotransformation of (R)- and (S)-thalidomide: application of circular dichroism spectroscopy to the stereochemical characterization of the hydroxylated metabolites

Circular dichroism (CD) spectroscopy was successfully used for the stereochemical characterization of the hydroxylated metabolites formed during the in vitro biotransformation of (R)- and (S)-thalidomide. Incubation extracts of the individual enantiomers were analyzed by HPLC on an achiral stationary phase combined with CD detection. The CD data of the almost enantiopure eluates of the metabolites were compared with the CD spectra quantum chemically calculated for the respective structures. The results allowed us a reliable determination of the absolute stereostructure for all of the metabolites. The chiral center of thalidomide is unaffected by the stereoselective biotransformation process. (3'R,5'R)-trans-5'-hydroxythalidomide is the main metabolite of (R)-thalidomide, which epimerizes spontaneously to give the more stable (3'S,5'R)-cis isomer. On the contrary, (S)-thalidomide is preferentially metabolized by hydroxylation in the phthalimide moiety, resulting in the formation of (S)-5-hydroxythalidomide.     

Two-color photorefractive effect in Mg-doped lithium niobate

The two-color photorefractive response of near stoichiometric lithium niobate (SLN) doped with Mg above a critical threshold has been investigated. Striking differences as compared with non Mg-doped material were observed: The intermediate level in the two-color writing process has approximately a two orders of magnitude longer lifetime in SLN:Mg than in nominally undoped SLN, the grating is written in a shallower level but can be fixed via a simple thermal process and complementary electron-hole gratings are formed. It is proposed that the Fe impurity level moves from below the small-polaron level in nonMgO-doped material to above it, resulting in the increased lifetime of the small polaron. These changes are associated with a shift of the Fe from a Li site to a Nb site. The two-color sensitivity is higher than in the absence of MgO but the dynamic range is much lower.     

Cartilage degeneration in relation to repetitive pressure: case study of a unilateral hip hemiarthroplasty patient

The mitochondrial, inner-membrane-associated, reversible NADPH-->NAD transhydrogenase of adult Hymenolepis diminuta physiologically couples matrix-localized, NADP-specific "malic" enzyme with NADH-dependent anaerobic electron transport. Employing submitochondrial particles (SMP) as the source of enzyme activity and both spectrophotometric and fluorometric assessments, the present study made evident that in its catalysis of transhydrogenation between NADPH and NAD, the cestode enzyme engages in the concomitant transmembrane translocation of protons. As assessed spectrophotometrically, the catalysis of NADPH-dependent NAD reduction by H. diminuta SMP was stimulated significantly by carbonyl cyanide 3-chlorophenylhydrazone (CCCP), carbonyl cyanide 4-(trifluoromethoxy) phenylhydrazone (FCCP), as well as by the protonophoric anthelmintic, niclosamide. In addition, N,N'-dicyclohexylcarbodiimide (DCCD) markedly diminished SMP-catalyzed hydride ion transfer between NADPH and NAD. The catalysis by SMP of concomitant, transhydrogenase-mediated proton translocation was evaluated more directly via fluorometric assays using 8-anilino-1-napthalenesulfonic acid (ANS) as the probe. These latter evaluations revealed a transhydrogenase-dependent enhancement of ANS fluorescence in accord with an intravesicular accumulation of protons. ANS fluorescence was quenched rapidly when the assay system was supplemented with CCCP, FCCP, or niclosamide. Consistent with the helminth transhydrogenase acting as a proton pump, transhydrogenase-mediated enhanced fluorescence also was inhibited by DCCD. Considered collectively, these data indicated, apparently for the first time for any invertebrate system, that the transhydrogenase, in catalyzing the NADPH-->NAD reaction, acts in the translocation of protons from the matrix to the intermembrane space mitochondrial compartment.