Quantitative Proteomic Approach Reveals Altered Metabolic Pathways in Response to the Inhibition of Lysine Deacetylases in A549 Cells under Normoxia and Hypoxia

Growing evidence is showing that acetylation plays an essential role in cancer, but studies on the impact of KDAC inhibition (KDACi) on the metabolic profile are still in their infancy. Here, we analyzed, by using an iTRAQ-based quantitative proteomics approach, the changes in the proteome of KRAS-mutated non-small cell lung cancer (NSCLC) A549 cells in response to trichostatin-A (TSA) and nicotinamide (NAM) under normoxia and hypoxia. Part of this response was further validated by molecular and biochemical analyses and correlated with the proliferation rates, apoptotic cell death, and activation of ROS scavenging mechanisms in opposition to the ROS production. Despite the differences among the KDAC inhibitors, up-regulation of glycolysis, TCA cycle, oxidative phosphorylation and fatty acid synthesis emerged as a common metabolic response underlying KDACi. We also observed that some of the KDACi effects at metabolic levels are enhanced under hypoxia. Furthermore, we used a drug repositioning machine learning approach to list candidate metabolic therapeutic agents for KRAS mutated NSCLC. Together, these results allow us to better understand the metabolic regulations underlying KDACi in NSCLC, taking into account the microenvironment of tumors related to hypoxia, and bring new insights for the future rational design of new therapies.     

Positional distribution of fatty acids in cardiolipin of mitochondria from 21-day-old rats

Pure cardiolipins (1,3-diphosphatidylglycerol) were prepared from mitochondria of heart, liver and kidney from 21-day-old male Wistar rats and submitted toNaja naja venom phospholipase A₂ (EC 3.1.1.4) action. Incubation conditions were controlled carefully, and a complete hydrolysis of cardiolipin to lysocardiolipin {di [1 (1″) acylsn-glycero-3-phosphoryl] 1′, 3′-sn-glycerol} and fatty acids from positions 2 (2″) was obtained in less than two hr practically without side reactions. Cardiolipins from the three organs contained low levels of saturated fatty acids; stearic acid accounted for 0.4–0.7% and palmitic acid for 1.4–3.5% of total fatty acids. These percentages apparently depended on the organ. In all three cases, linoleic acid was the major component, but its percentage varied from 62–78% of total fatty acids. Acyl chains linked to positions 1 (1″) of all three cardiolipin preparations exhibited a similar pattern; they were composed of linoleic acid for 85–89%. This fatty acid also was the main component esterified at position 2 (2″), but its percentage was much more variable: from 39.8% in heart to 51.2% in kidney and 67.8% in liver mitochondria. The remaining acids comprised octadecenoic and polyunsaturated fatty acids with more than 18 carbon atoms in different proportions. As opposed to other phospholipids,cis-vaccenic acid, and not oleic acid, was the main octadecenoic acid present in cardiolipins. Octadecenoic acids were nine- to 10-fold more concentrated at positions 2 (2″) than at positions 1 (1″). The percentage ofcis-vaccenic acid was four- to five-fold higher than that of oleic acid at positions 2 (2″), whereas oleic acid dominated at positions 1 (1″). From results presented in this study and selected literature data, it may be concluded that fatty acids are asymmetrically distributed in cardiolipins of different origins, with linoleic acid showing a definite preference for position 1 (1″).     

Local residence time,residence revolution,and residence volume distributions in twin‐screw extruders

This work was aimed at studying the overall, partial, and local residence time distributions (RTD); overall, partial and local residence revolution distributions (RRD) and overall, partial and local residence volume distributions (RVD) in a co‐rotating twin screw extruder, on the one hand; and establishing the relationships among them, on the other hand. Emphasis was placed on the effects of the type and geometry of mixing elements (a gear block and various types of kneading elements differing in staggering angle) and process parameters on the RTD, RRD and RVD. The overall and partial RTD were directly measured in‐line during the extrusion process and the local ones were calculated by deconvolution based on a statistical theory. The local RTD allowed comparing the mixing performance of mixing elements. Also it was confirmed both experimentally and theoretically that specific throughput, defined as a ratio of throughput (Q) over screw speed (N), controlled all the above three types of residence distributions, be they local, partial or overall. The RRD and RVD do not provide more information on an extrusion process than the corresponding RTD. Rather they are different ways of representing the same phenomena. POLYM. ENG. SCI., 48:19–28, 2008. © 2007 Society of Plastics Engineers     

JaTS: a fully portable seismic tomography software based on Fresnel wavepaths and a probabilistic reconstruction approach

JaTS, a Java 2D seismic tomography software, is presented. It implements original algorithms achieving optimal accuracy with reasonable computing costs. A second-order Fast Marching Method (FMM) is used for solving the eikonal equation, therefore enabling a fast and robust computation of seismic traveltimes between sources and receivers. The wavepaths are materialized by Fresnel volumes rather than by conventional rays. This approach accounts for complex velocity models and has the advantage of considering the effects of the wave frequency in the velocity model resolution. The model is computed by a Simultaneous Iterative Reconstruction Technique (SIRT) which has been reformulated to integrate Fresnel wavepaths by using a probabilistic approach. In addition, various utilities are implemented, such as a tapering filter, used to decrease artifact effects occurring in the vicinity of the sources and receivers. The software also offers the possibility of reconstructing the velocity field on a grid larger than the one used for the wave propagation computation. This contributes to stabilize the estimated values. All of the seismic processing tools have been integrated with a user-friendly graphical interface. JaTS represents a tightly integrated tool suite that supports the entire process of importing the SG2 field records, first-break picking, forward modeling and velocity-field computing across multiple platforms.     

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Reliable Computing -     

A time-domain test for some types of nonlinearity

The bispectrum and third-order moment can be viewed as equivalent tools for testing for the presence of nonlinearity in stationary time series. This is because the bispectrum is the Fourier transform of the third-order moment. An advantage of the bispectrum is that its estimator comprises terms that are asymptotically independent at distinct bifrequencies under the hypothesis of linearity. An advantage of the third-order moment is that its values in any subset of joint lags can be used in the test, whereas when using the bispectrum the entire (or truncated) third-order moment is required to construct the Fourier transform. We propose a test for nonlinearity based upon the estimated third-order moment. We use the phase scrambling bootstrap method to give a nonparametric estimate of the variance of our test statistic under the hypothesis. Using a simulation study, we demonstrate that the test obtains its target significance level, with large power, when compared to an existing standard parametric test that uses the bispectrum. Further we show how the proposed test can be used to identify the source of nonlinearity due to interactions at specific frequencies. We also investigate implications for heuristic diagnosis of nonstationarity.     

Polymerase chain reaction versus culture for detection of Ureaplasma urealyticum and Mycoplasma hominis in the urogenital tract of adults and the respiratory tract of newborns

The efficiency of the polymerase chain reaction (PCR) was compared with that of culture for detection of Ureaplasma urealyticum and Mycoplasma hominis in 726 clinical specimens comprising 189 gynecological samples, 362 urological samples, and 175 samples from newborn infants. The sensitivity of PCR versus culture was 95% for both organisms, while the sensitivity of culture versus PCR was 91% for Ureaplasma urealyticum and 84% for Mycoplasma hominis. Furthermore, PCR tests were faster than culture tests, allowing the time to diagnosis to be reduced from two to five days to 24 h.     

Modification of alkenyl chain profile in plasmalogens of rat heart mitochondria by dietary trielaidin

Effects of dietary trielaidin upon the alkenyl chain profile of plasmalogens were studied using heart mitochondria of rats fed a semi-purified diet containing 10% of fat supplement in which elaidic acid accounted for 69% of total fatty acids. Alkyl substituted dioxane (ASD) derivatives of the alkenyl groups of plasmalogens were prepared and analyzed by silver nitrate TLC and by GLC on different phases (BDS and OV-275). After two months of feeding the experimental diet, 40% of the ASD contained atrans-octadecenyl chain, suggesting that dietary elaidic acid was reduced in vivo to the corresponding alcohol and incorporated into plasmalogens. There was a simultaneous decrease in the percentage of ASD containing saturated chains, but the percentage of ASD substituted withcis-octadecenyl chains was not significantly affected. These observations suggested that elaidic acid may compete with saturated fatty acids, but not withcis-octadecenoic acids during the plasmalogen biosynthesis. Feeding trielaidin did not seem to have any significant influence on the relative proportions of plasmalogens, which accounted for 11–12%, on a phosphorus basis, of total heart mitochondria phospholipids.     

Scalarization of dyadic spectral Green's functions and networkformalism for three-dimensional full-wave analysis of planar lines andantennas

A novel and systematic method is presented for the complete determination of dyadic spectral Green's functions directly from Maxwell's equations. With the use of generalized scalarizations developed in this paper, four general and concise expressions for the spectral Green's functions for one-dimensionally inhomogeneous multilayer structures, excited by three-dimensional electric and magnetic current sources, are given in terms of modal amplitudes together with appropriate explicit singular terms at the source region. It is shown that Maxwell's equations in spectral-domain can be reduced, by using dyadic spectral eigenfunctions, to two sets of z-dependent inhomogeneous transmission-line equations for the modal amplitudes. One set of the transmission-line equations are due to the transverse current sources and the other set due to the vertical current sources. Utilizing these equations, network schematizations of the excitation, transmission and reflection processes of three-dimensional electromagnetic waves in one-dimensionally inhomogeneous multilayer structures are achieved in a full-wave manner. The determination of the spectral Green's functions becomes so simple that it is accomplished by the investigation of voltages and currents on the derived equivalent circuits. Examples of singleand multilayer structures are used to validate the general expressions and the equivalent circuits     

Contribution oftrans-18∶1 acids from dairy fat to european diets

Twelve commercial samples of French butter, purchased in October–November, and 12 other samples, purchased in May–June, were analyzed with particular attention to theirtrans-octadecenoic acid contents. The isomeric fatty acids were quantitated by a combination of gas-liquid chromatography (GLC) of total fatty acids as isopropyl esters on a polar capillary column (CPSil 88) and of silver nitrate-impregnated thin-layer chromatography followed by GLC of the pooled saturated (used as internal standards) andtrans-octadecenoic acid fractions. Autumn butters contained 3.22±0.44%trans-octadecenoic acids (relative to total fatty acids), whereas those collected during the spring contained 4.28±0.47% (P<0.01). Minimum and maximum values for the two sets of butters were 2.46 (autumn) and 5.10% (spring), respectively. The annual mean value for thetrans-octadecenoic acid content in all butter samples was 3.8% of total fatty acids (ca. 2% for thetrans-11 18∶1 acid). This value allows calculation of the daily individual intake oftrans-octadecenoic acids from dairy products by populations of member states of the European Economic Community (EEC). It varies from 0.57 g (Portugal) to 1.66 g (Denmark). The mean value for the twelve countries of the EEC is 1.16 g/person/d, which is close to data published for the United States. In France, the consumption oftrans octadecenoic acids from dairy fat is higher than that from margarines (ca. 1.5 vs. 1.1 g/person/d).