Computing the nonabelian tensor squares of polycyclic groups

In this paper we develop a theory for computing the nonabelian tensor square and related computations for finitely presented groups and specialize it to polycyclic groups. This theory provides a framework for making nonabelian tensor square computations for polycyclic groups and is the basis of an algorithm for computing the nonabelian tensor square for any polycyclic group.     

Accuracy of SUPREX (stability of unpurified proteins from rates of H/D exchange) and MALDI mass spectrometry-derived protein unfolding free energies determined under non-EX2 exchange conditions

Described here is the impact of so-called non-EX2 exchange behavior on the accuracy of protein unfolding free energies (i.e., DeltaG u values) and m values (i.e.,-deltaDeltaG u/delta[denaturant] values) determined by an H/D exchange and mass spectrometry-based technique termed stability of unpurified proteins from rates of H/D exchange (SUPREX). Both experimental and theoretical results on a model protein, ubiquitin, reveal that reasonably accurate thermodynamic parameters for its folding reaction can be determined by SUPREX even when H/D exchange data is collected in a non-EX2 regime. Not surprisingly, the theoretical results reported here on a series of hypothetical protein systems with a wide range of biophysical properties show that the accuracy of SUPREX-derived DeltaG u and m values is compromised for many proteins when analyses are performed at high pH (e.g., pH 9) and for selected proteins with specific biophysical parameters (e.g., slow folding rates) when analyses are performed at lower pH. Of more significance is that the experimental and theoretical results reveal a means by which problems with non-EX2 exchange behavior can be detected in the SUPREX experiment without prior knowledge of the protein's biophysical properties. The results of this work also reveal that such problems with non-EX2 exchange behavior can generally be minimized if appropriate H/D exchange times are employed in the SUPREX experiment to yield SUPREX curve transition midpoints at chemical denaturant concentrations less than 2 M.     

An efficient synthesis of a potent PPARpan agonist

An efficient synthesis of 2-{4-[({4-{[4-(4-methoxyphenyl)piperazin-1-yl]methyl}-2-[4-(trifluoromethyl)phenyl]-1,3-thiazol-5-yl}methyl)thio]phenoxy}-2-methylpropanoic acid (1), a potent PPARpan agonist, is described. The seven-step synthesis, which afforded 1 in 30% overall yield, includes a highly regioselective carbon-sulfur bond formation via coupling of a bishydroxymethylthiazole (3) with 4-hydroxythiophenol, displacement of the remaining alcohol through a three-step telescoped sequence involving an efficient cleavage of an aryl mesylate, and an efficient and practical method of introducing an isobutyric acid fragment.     

Myosin-cross-reactive antigen (MCRA) protein from <Emphasis Type="Italic">Bifidobacterium breve</Emphasis> is a FAD-dependent fatty acid hydratase which has a function in stress protection

Background  

The aim of this study was to determine the catalytic activity and physiological role of myosin-cross-reactive antigen (MCRA) from Bifidobacterium breve NCIMB 702258. MCRA from B. breve NCIMB 702258 was cloned, sequenced and expressed in heterologous hosts (Lactococcus and Corynebacterium) and the recombinant proteins assessed for enzymatic activity against fatty acid substrates.     

The morphology and structure of PS‐b‐P4VP block copolymer films by solvent annealing: effect of the solvent parameter

Lamellae (symmetric) forming polystyrene‐b‐poly(4‐vinylpyridine) (PS‐b‐P4VP) block copolymers (BCPs) were used to produce nanostructured thin films by solvent (toluene) casting (spin‐coating) onto silicon substrates. As expected, strong micellization of PS‐P4VP in toluene results in poorly ordered hexagonally structures films. Following deposition the films were solvent annealed in various solvents and mixtures thereof. A range of both morphologies including micelle and microphase separated structures were observed. It was found that nanostructures typical of films of regular thickness (across the substrate) and demonstrating microphase separation occurred only for relatively few solvents and mixtures. The data demonstrate that simple models of solvent annealing based on swelling of the polymer promoting higher polymer chain mobility are not appropriate and more careful rationalization is required to understand these data. Analysis suggests that regular phase separated films can only be achieved when the copolymer Hildebrand solubility parameter is very similar to the value of the solvent. It is suggested that the solvent anneal method used is best considered as a liquid phase technique rather than a vapor phase method. The results show that solvent annealing methods can be a very powerful means to control structure and in some circumstances dominate other factors such as surface chemistry and surface energies. Copyright © 2009 John Wiley & Sons, Ltd.     

Thermodynamic Analysis of the Geldanamycin–Hsp90 Interaction in a Whole Cell Lysate Using a Mass Spectrometry-Based Proteomics Approach

Geldanamycin is a natural product with well-established and potent anti-cancer activities. Heat shock protein 90 (Hsp90) is the known target of geldanamycin, which directly binds to Hsp90’s N-terminal ATP binding domain and inhibits Hsp90’s ATPase activity. The affinity of geldanamycin for Hsp90 has been measured in multiple studies. However, there have been large discrepancies between the reported dissociation constants (i.e., K_d values), which have ranged from low nanomolar to micromolar. Here the stability of proteins from rates of oxidation (SPROX) technique was used in combination with an isobaric mass tagging strategy to measure the binding affinity of geldanamycin to unpurified Hsp90 in an MCF-7 cell lysate. The K_d values determined here were dependent on how long geldanamycin was equilibrated with the lysate prior to SPROX analysis. The K_d values determined using equilibration times of 0.5 and 24 h were 1 and 0.03 μM, respectively. These K_d values, which are similar to those previously reported in a geldanamycin–Hsp90 binding study that involved the use of a fluorescently labeled geldanamycin analogue, establish that the slow-tight binding behavior previously observed for the fluorescently labeled geldanamycin analogue is not an artifact of the fluorescent label, but rather an inherent property of the geldanamycin–Hsp90 binding interaction. The slow-tight binding property of this complex may be related to time-dependent conformational changes in Hsp90 and/or to time-dependent chemical changes in geldanamycin, both of which have been previously proposed to explain the slow-tight binding behavior of the geldanamycin–Hsp90 complex.

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SEM and ECIS Investigation of Cells Cultured on Nanopillar Modified Interdigitated Impedance Electrodes for Analysis of Cell Growth and Cytotoxicity of Potential Anticancer Drugs

Cell‐based biosensors treat living cells as sensing elements and are able to detect the functional information of biologically active analytes. Monitoring cytotoxicity with high sensitivity, rapidity and at low cost is of great interest in the fields of clinical diagnostics, environmental monitoring, food safety and security. This research investigates the behaviour of different cell types on nanostructured architectures. The development of cell‐based assays using bioimpedance devices has the potential of screening anti‐cancer drugs; these have a potential impact for developing new techniques and tools for the analysis of cells in the bio‐pharma industry. Gold impedance electrodes have been successfully fabricated for impedance measurement on cells cultured on the electrode surface which was modified with gold nanopillars with a height of 60 nm and 150 nm diameter in a highly ordered layout thanks to the e‐beam lithography technique. This article investigates the effects on the sensitivity achieved with the ECIS (Electric Cell‐substrate Impedance Spectroscopy) measurements while monitoring the cytotoxicity of two different drugs (Antrodia Camphorata extract and Nicotine) on different cell lines (HeLa, A549 and BALBc 3T3) cultured on the nanostructured devices. The change of morphology of cells growing on the nanostructured electrodes was also investigated through SEM imaging.     

Isotope ratio monitoring gas chromatography/Mass spectrometry of D/H by high temperature conversion isotope ratio mass spectrometry

Of all the elements, hydrogen has the largest naturally occurring variations in the ratio of its stable isotopes (D/H). It is for this reason that there has been a strong desire to add hydrogen to the list of elements amenable to isotope ratio monitoring gas chromatography/mass spectrometry (irm-GC/MS). In irm-GC/MS the sample is entrained in helium as the carrier gas, which is also ionized and separated in the isotope ratio mass spectrometer (IRMS). Because of the low abundance of deuterium in nature, precise and accurate on-line monitoring of D/H ratios with an IRMS requires that low energy helium ions be kept out of the m/z 3 collector, which requires the use of an energy filter. A clean mass 3 (HD(+.)) signal which is independent of a large helium load in the electron impact ion source is essential in order to reach the sensitivity required for D/H analysis of capillary GC peaks. A new IRMS system, the DELTA(plus)XL(trade mark), has been designed for high precision, high accuracy measurements of transient signals of hydrogen gas. It incorporates a retardation lens integrated into the m/z 3 Faraday cup collector. Following GC separation, the hydrogen bound in organic compounds must be quantitatively converted into H(2) gas prior to analysis in the IRMS. Quantitative conversion is achieved by high temperature conversion (TC) at temperatures >1400 degrees C. Measurements of D/H ratios of individual organic compounds in complicated natural mixtures can now be made to a precision of 2 per thousand (delta notation) or, better, with typical sample amounts of approximately 200 ng per compound. Initial applications have focused on compounds of interest to petroleum research (biomarkers and natural gas components), food and flavor control (vanillin and ethanol), and metabolic studies (fatty acids and steroids). Copyright 1999 John Wiley & Sons, Ltd.