Compound prioritization methods increase rates of chemical probe discovery in model organisms

Preselection of compounds that are more likely to induce a phenotype can increase the efficiency and reduce the costs for model organism screening. To identify such molecules, we screened ~81,000 compounds in Saccharomyces cerevisiae and identified ~7500 that inhibit cell growth. Screening these growth-inhibitory molecules across a diverse panel of model organisms resulted in an increased phenotypic hit-rate. These data were used to build a model to predict compounds that inhibit yeast growth. Empirical and in silico application of the model enriched the discovery of bioactive compounds in diverse model organisms. To demonstrate the potential of these molecules as lead chemical probes, we used chemogenomic profiling in yeast and identified specific inhibitors of lanosterol synthase and of stearoyl-CoA 9-desaturase. As community resources, the ~7500 growth-inhibitory molecules have been made commercially available and the computational model and filter used are provided.     

Direct quantitative analysis of peptides using matrix assisted laser desorption ionization

The protocol and various matrices were examined for quantification of biomolecules in both the low ca. 1200 amu and mid mass 6000–12000 amu ranges using an internal standard. Comparative studies of different matrices of MALDI quantitative analysis showed that the best accuracy and standard curve linearity were obtained for two matrices: (a) 2,5-dihydroxybenzoic acid (DHB) combined with a comatrix of fucose and 5-methoxysalicylic acid (MSA) and (b) ferulic acid/fucose. In the low mass range, the quantitative limit was in the 30 fmol range and in the mid mass range the quantitative limit was in the 250 fmol range. Linear response was observed over 2–3 decades of analyte concentration. The relative error of the standard curve slope was 1.3–1.8% with correlation coefficients of 0.996–0.998.The main problem for quantitative measurement was suppression of the signal of the less concentrated component (analyte or internal standard) by the more concentrated component. The effect was identified with saturation of the matrix by the analyte. The threshold of matrix saturation was found to be in the range of 1/(3000–5000) analyte/matrix molar ratio. To avoid matrix saturation the (analyte+internal standard) to matrix molar ratio should be below this threshold. Thus the internal standard concentration should be as low as possible.DHB/MSA/fucose and ferulic acid/fucose matrices demonstrated good accuracy and linearity for standard curves even when the internal standard had chemical properties different from the analyte. However, use of an internal standard with different chemical properties requires highly stable instrumental parameters as well as constant (analyte+internal standard)/matrix molar ratio for all samples.     

Laser-interrogated dichroic spectroscopy: A sensitive probe of molecular anisotropies

A technique for measuring the parameters which characterise the anisotropic spatial distributions of angular momentum vectors of molecules in dilute ga     

Reactive properties of trans-dichlorooxirane in relation to the contrasting carcinogenicities of vinyl chloride and trans-dichloroethylen

Our objective in this work is to gain insight into the contrasting carcinogenic activities of vinyl chloride (definitely carcinogenic) and trans-dichloroethylene (apparently inactive). The initial metabolic step for each molecule is believed to be epoxidation of the double bond, and there is evidence indicating that for vinyl chloride, this epoxide (chlorooxirane) is its ultimate (direct-acting) carcinogenic form. This article presents the findings of a computational study of the reactive properties of trans-dichlorooxirane (the epoxide of trans-dichloroethylene). An ab initio SCF -MO procedure was used to determine the energy requirements for stretching the C? O and C? Cl bonds (S_N1 reactivity) and to study the epoxide's S_N2 interactions with ammonia, taken as a model nucleophile. The starting points were the oxygen- and chlorine-protonated forms of the epoxide. The structure of the system was reoptimized at each step along the various reaction pathways. The results of this work are compared to an analogous earlier study of the reactive properties of chlorooxirane. The chlorineprotonated C? Cl bonds are found to have much lower energy barriers to stretching than do the oxygen-protonated C? O bonds. In the S_N2 processes, intermediate complexes are formed with ammonia by both the oxygen- and the chlorine-protonated epoxides; the latter complexes are the more stable. Based on our results, we propose two mechanisms (one S_N1 and the other S_N2) whereby trans-dichlorooxirane can interact with N₇ of guanine to produce an adduct analogous to one formed by chlorooxirane, which has been found to be the primary in vivo DNA alkylation product of vinyl chloride and to which has been attributed the carcinogenicity of the latter. Overall, trans-dichlorooxirane is found to be chemically more reactive than chlorooxirane; this may help to account for the much lesser carcinogenic and mutagenic activities of trans-dichloroethylene, since the epoxide may be reacting with other cellular nucleophiles before it reaches the key site(s) at which the carcinogenic or mutagenic interaction would occur. We also offer some speculations concerning other possible factors related to the differing carcinogenicities of vinyl chloride and trans-dichloroethylene, such as ease of epoxide formation and the likelihood of oxygen protonation.     

Ultrasonic-shear-wave measurement of known residual stress in aluminum

Ultrasonic-shear-wave time-of-flight measurements were made at a nominal frequency of 4 MHz on both stressed and nonstressed sample disks of 2024 aluminum alloy. The stressed state of the first sample was produced by shrink-fitting a plug and ring to produce a calculated 130-MPa region of uniform compression in the plug, and a concomitant nonuniform tension and compression in the ring. Time-of-flight measurement scans across sample diameters were made using a piezoelectric-shear transducer with a viscous couplant, and repeated using a contactless electromagnetic-acoustic transducer. The ultrasonic results were then compared with elasticity theory, assuming the acoustoelastic relationship between sound velocity and material strain.     

X-ray photoelectron spectroscopic studies of carbon fibre surfaces. I. carbon fibre spectra and the effects of heat treatment

The use of X-ray photoelectron spectroscopy for the study of carbon fibre surfaces is first discussed in general terms, and then with emphasis on untreated fibre samples heated to 1400°C in vacuo. Preliminary theoretical calculations show that a graphitic environment does have some modifying effect upon expected C 1s binding energy shifts for surface groups when compared with those obtained from other systems. Differences in surface chemistry cause only very small changes in the C 1s region, but these changes are shown to be detectable when appropriate data and data analysis techniques are used. Heat treatment causes loss of some oxide groups from the surface of the fibres and some nitrogen from the bulk of the fibres, although the resulting fibres do contain some CO groupings absent in the original fibres.     

Correlation and prediction of partition coefficient between the gas phase and water, and the solvents dry methyl acetate, dry and wet ethyl acetate, and dry and wet butyl acetate

Experimental partition coefficient data have been compiled from the published literature for the water/methyl acetate, water/ethyl acetate and water/butyl acetate partition systems, log P data, and for the gas/methyl acetate, gas/ethyl acetate and gas/butyl acetate partition systems, log K data. Application of the Abraham solvation parameter model to the sets of partition coefficients leads to equations that correlate the log P data and log K data to 0.18 log units for the three dry alkyl acetate solvents. Slightly larger deviations were noted for solute partition into both wet ethyl acetate and wet butyl acetate. The derived correlations were validated using training set and test set analyses.