Integrating gene and protein expression data with genome-scale metabolic networks to infer functional pathways

This article has been made available through the Brunel Open Access Publishing Fund. Copyright @ 2013 Pey et al.; licensee BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.Background: The study of cellular metabolism in the context of high-throughput -omics data has allowed us to decipher novel mechanisms of importance in biotechnology and health. To continue with this progress, it is essential to efficiently integrate experimental data into metabolic modeling. Results: We present here an in-silico framework to infer relevant metabolic pathways for a particular phenotype under study based on its gene/protein expression data. This framework is based on the Carbon Flux Path (CFP) approach, a mixed-integer linear program that expands classical path finding techniques by considering additional biophysical constraints. In particular, the objective function of the CFP approach is amended to account for gene/protein expression data and influence obtained paths. This approach is termed integrative Carbon Flux Path (iCFP). We show that gene/protein expression data also influences the stoichiometric balancing of CFPs, which provides a more accurate picture of active metabolic pathways. This is illustrated in both a theoretical and real scenario. Finally, we apply this approach to find novel pathways relevant in the regulation of acetate overflow metabolism in Escherichia coli. As a result, several targets which could be relevant for better understanding of the phenomenon leading to impaired acetate overflow are proposed. Conclusions: A novel mathematical framework that determines functional pathways based on gene/protein expression data is presented and validated. We show that our approach is able to provide new insights into complex biological scenarios such as acetate overflow in Escherichia coli.Basque Governmen

Structural Characterization of Rapid Thermal Oxidized Si\u3csub\u3e1−x−y\u3c/sub\u3eGe\u3csub\u3ex\u3c/sub\u3eC\u3csub\u3ey\u3c/sub\u3e Alloy Films Grown by Rapid Thermal Chemical Vapor Deposition

The structural properties of as-grown and rapid thermal oxidized Si1−x−yGexCy epitaxial layers have been examined using a combination of infrared, x-ray photoelectron, x-ray diffraction, secondary ion mass spectroscopy, and Raman spectroscopy techniques. Carbon incorporation into the Si1−x−yGexCy system can lead to compressive or tensile strain in the film. The structural properties of the oxidized Si1−x−yGexCy film depend on the type of strain (i.e., carbon concentration) of the as-prepared film. For compressive or fully compensated films, the oxidation process drastically reduces the carbon content so that the oxidized films closely resemble to Si1−xGex films. For tensile films, two broad regions, one with carbon content higher and the other lower than that required for full strain compensation, coexist in the oxidized films

NAD(P)H quinone oxidoreductase (NQO1): an enzyme which needs just enough mobility, in just the right places

NAD(P)H quinone oxidoreductase 1 (NQO1) catalyses the two electron reduction of quinones and a wide range of other organic compounds. Its physiological role is believed to be partly the reduction of free radical load in cells and the detoxification of xenobiotics. It also has non-enzymatic functions stabilising a number of cellular regulators including p53. Functionally, NQO1 is a homodimer with two active sites formed from residues from both polypeptide chains. Catalysis proceeds via a substituted enzyme mechanism involving a tightly bound FAD cofactor. Dicoumarol and some structurally related compounds act as competitive inhibitors of NQO1. There is some evidence for negative cooperativity in quinine oxidoreductases which is most likely to be mediated at least in part by alterations to the mobility of the protein. Human NQO1 is implicated in cancer. It is often over-expressed in cancer cells and as such is considered as a possible drug target. Interestingly, a common polymorphic form of human NQO1, p.P187S, is associated with an increased risk of several forms of cancer. This variant has much lower activity than the wild-type, primarily due to its substantially reduced affinity for FAD which results from lower stability. This lower stability results from inappropriate mobility of key parts of the protein. Thus, NQO1 relies on correct mobility for normal function, but inappropriate mobility results in dysfunction and may cause disease.This work was supported by the Junta de Andalucía [grant number P11-CTS-07187 (to A.L.P.)]

Path finding methods accounting for stoichiometry in metabolic networks

Graph-based methods have been widely used for the analysis of biological networks. Their application to metabolic networks has been much discussed, in particular noting that an important weakness in such methods is that reaction stoichiometry is neglected. In this study, we show that reaction stoichiometry can be incorporated into path-finding approaches via mixed-integer linear programming. This major advance at the modeling level results in improved prediction of topological and functional properties in metabolic networks

Cathodoluminescence Contrast of Localized Defects Part I. Numerical Model for Simulation

A three-dimensional model has been developed for cathodoluminescence contrast of localized defects in semiconductors. The numerical model incorporates electron-solid interaction effects, charge transport phenomena and optical losses. Electron-solid interaction is modelled by a Monte Carlo method. Three-dimensional continuity equation and derivative boundary conditions are discretized by a central-difference quotients scheme. Localized defects are represented by regions of enhanced non-radiative recombination. The discretized linear difference equations of the boundary value problem are solved by the successive-over-relaxation method. A method for avoiding the divergence problem during the successive-over-relaxation calculation is illustrated. The solutions of the model are compared with the analytical results of several established models

Investigation of Dislocations in GaAs Using Cathodoluminescence in the Scanning Electron Microscope

Electrically active dislocations in Si-doped {100} GaAs substrates were observed using the cathodoluminescence (CL) technique in the scanning electron microscope (SEM). CL contrast profiles were experimentally obtained from the dislocations at different beam energies. Based on the CL model for localized defects in semiconductors developed earlier by Pey, the depths of the dislocations were found by locating the beam energy at which maximum CL contrast occurred. A preferential etching technique for {100} GaAs was employed to reveal the dislocations and to measure their depths. The etched depths obtained were compared to the predicted results from the theoretical model developed. The discrepancies in the results were attributed to a Cottrell atmosphere of point defects around the dislocation core

Cathodoluminescence Contrast of Localized Defects Part II. Defect Investigation

Cathodoluminescence contrast from defects with different geometrical and electronic properties have been studied using the numerical model developed in Part I. The contrast of a localized subsurface defect exhibits a maxima at a specific beam energy Emax which corresponds to the depth of the defect. The contrast of a dis-location which intersects the top surface perpendicularly is a decreasing function of beam energy. The differences in the image profiles of the two different kinds of defects allow the two types of imperfections to be distinguished. In addition, the resolution of a subsurface defect at beam energies lower than Emax is only a function of defect size and is insensitive to the defect strength. The defect depth, size and strength can therefore be extracted sequentially. The extension of the model to the investigation of complex or multiple defects such as dot and halo contrast is also illustrated

Trends of particulate matter (PM₂.₅) and chemical composition at a regional background site in the Western Mediterranean over the last nine years (2002-2010)

The time variability and long term trends of PM₂.₅ (particulate matter of diameter <2.5 μm) at various regional background (RB) sites across Europe are studied and interpreted in this work. Data on mean annual levels of PM₂.₅ measured at Montseny (MSY, North East Spain) and various RB sites in Spain and Europe are evaluated and compared, and subsequently analysed for statistically significant trends. The MSY site registered higher average PM₂.₅ levels than those measured at a selection of other RB sites across Spain, Portugal, Germany and Scandinavia by percentage compared to the mean of all the stations in these countries, but lower than those measured in Switzerland, Italy and Austria. Reductions in PM₂.₅ were observed across all stations in Spain and Europe to varying degrees (7-49%). MSY underwent a statistically significant reduction since measurements began, indicating a year-on-year gradual decrease (−3.7 μgm¯³, calculated from the final year of data compared to the mean). Similar trends were observed in other RB sites across Spain (−1.9 μgm¯³). Reductions recorded in PM₂.₅ across Europe were varied, with many experiencing gradual, year-on-year decreases (−1.8 μgm¯³). These reductions have been attributed to various causes: the introduction and implementation of pollution abatement strategies in EU member states, the effect of the current economic crisis on emissions of PM₂.₅ and the influence of meteorology observed during the winters of 2009 and 2010. In addition, the North Atlantic Oscillation (NAO), a large scale meteorological phenomenon most prevalent during winter, was observed to influence the frequency of Saharan dust intrusions across the Iberian Peninsula. Chemical composition of PM₂.₅ at MSY is characterised by high levels of organic matter (OM) and sulphate, followed by crustal material, nitrate and ammonia. Sea Spray and elemental carbon (EC) comprised a minor part of the total PM₂.₅ mass. Statistical trend analysis was performed on the various chemical components of PM₂.₅ recorded at MSY to determine which components were accountable for the decrease in PM₂.₅ concentration. It is shown that OM underwent the largest decrease over the time period with a statistically significant trend (−1.3 μgm¯³ compared to the mean), followed by sulphate (−0.8 μgm¯³), ammonium (−0.5 μgm¯³) and nitrate (−0.4 μgm¯³). Conversely, sea spray, EC and crustal a material reductions were found to be negligible

Source apportionment of fine PM and sub-micron particle number concentrations at a regional background site in the western Mediterranean: a 2.5 year study

The chemical composition and sources of ambient fine particulate matter (PM₁) over a period of 2.5 years for a regional background site in the western Mediterranean are presented in this work. Furthermore, sub-micron particle number concentrations and the sources of these particles are also presented. The mean PM₁ concentration for the measurement period was 8.9 μgm¯³, with organic matter (OM) and sulphate comprising most of the mass (3.2 and 1.5 μgm¯³ respectively). Six sources were identified in PM₁ by Positive Matrix Factorisation (PMF): secondary organic aerosol, secondary nitrate, industrial, traffic + biomass burning, fuel oil combustion and secondary sulphate. Typically anthropogenic sources displayed elevated concentrations during the week with reductions at weekends. Nitrate levels were elevated in winter and negligible in summer, whereas secondary sulphate levels underwent a contrasting seasonal evolution with highest concentrations in summer, similar to the fuel oil combustion source. The SOA source was influenced by episodes of sustained pollution as a result of anticyclonic conditions occurring during winter, giving rise to thermal inversions and the accumulation of pollutants in the mixing layer. Increased levels in summer were owing to higher biogenic emissions and regional recirculation of air masses. The industrial source decreased in August due to decreased emissions during the vacation period. Increases in the traffic + biomass burning source were recorded in January, April and October, which were attributed to the occurrence of the aforementioned pollution episodes and local biomass burning emission sources, which include agriculture and domestic heating systems. Average particle number concentrations (N₉_₈₂₅ nm) from 5/11/2010 to 01/06/2011 and from 15/10/2011 to 18/12/2011 reached 3097 cm¯³. Five emission sources of particle of sub-micron particles were determined by Principal Component Analysis (PCA); industrial + traffic + biomass burning, new particle formation + growth, secondary sulphate + fuel oil combustion, crustal material and secondary nitrate. The new particle formation + growth source dominated the particle number concentration (56% of total particle number concentration), especially for particles 100 nm) and thus did not influence the particle number concentration significantly