An insight into iTRAQ: where do we stand now?

The iTRAQ (isobaric tags for relative and absolute quantification) technique is widely employed in proteomic workflows requiring relative quantification. Here, we review the iTRAQ literature; in particular, we focus on iTRAQ usage in relation to other commonly used quantitative techniques e.g. stable isotope labelling in culture (SILAC), label-free methods and selected reaction monitoring (SRM). As a result, we identify several issues arising with respect to iTRAQ. Perhaps frustratingly, iTRAQ's attractiveness has been undermined by a number of technical and analytical limitations: it may not be truly quantitative, as the changes in abundance reported will generally be underestimated. We discuss weaknesses and strengths of iTRAQ as a methodology for relative quantification in the light of this and other technical issues. We focus on technical developments targeted at iTRAQ accuracy and precision, use of 4-plex over 8-plex reagents and application of iTRAQ to post-translational modification (PTM) workflows. We also discuss iTRAQ in relation to label-free approaches, to which iTRAQ is losing ground.     

A solvation-based screening approach for metabolite arrays

This paper explores a new method for screening metabolites in an array format based on relative polarity using selective solvent dissolution. A synthetic cocktail of metabolites was spotted onto a hydrophobic silicon surface, and solubilised with solvents of varying polarity. The metabolites retained on the silicon surface after the solvent treatments were detected using time-of-flight static secondary ion mass spectrometry (ToF-sSIMS). Solvent-specific metabolite retention was clearly evident on multivariate analysis of the dataset, using principal component analysis. Selective removal of metabolites was observed when solvents with different polarity were used, with the metabolite retention or removal in most cases correlating to the polarity of the solvent used, although consideration of other forces in operation may be needed to arrive at fully predictable behaviours. This approach provides the basis for development of a technique to separate complex metabolites into simpler constituents in a metabolite array prior to identification and quantification using mass spectrometry. It is an analytical approach that is intermediate between the more rapid but less informative direct analysis methods (such as DIMS) that do not involve any analyte separations and the more comprehensive but time consuming methods (such as GC- and LC-MS) that involve chromatographic or electrophoretic separations. The approach has the potential to be successfully developed for rapid, yet informative screening of metabolomes.     

Diruthenium(III,III) ethynyl-phenyleneimine molecular wires: preparation via on-complex Schiff base condensation

The diruthenium compound trans-Ru(2)(DMBA)(4)(C≡C-C(6)H(4)-4-CHO)(2) (1; DMBA is N,N'-dimethylbenzamidinate) was prepared from the reaction between Ru(2)(DMBA)(4)(NO(3))(2) and HC≡C-C(6)H(4)-4-CHO under the weak base conditions. The aldehyde groups of 1 undergo a condensation reaction with NH(2)C(6)H(4)-4-Y (Y = H and NH(2)) to afford new compounds trans-Ru(2)(DMBA)(4)(C≡C-C(6)H(4)-4-CH═N-C(6)H(4)-4'-Y)(2) (Y = H (2) and NH(2) (3)). A related compound, Ru(2)(DMBA)(4)(C≡C-C(6)H(4)-4-N═C(Me)Fc)(2) (4), was also prepared from the reaction between Ru(2)(DMBA)(4)(NO(3))(2) and HC≡C-C(6)H(4)-N═C(Me)Fc. X-ray structural studies of compounds 1 and 2 revealed significant deviation from an idealized D(4h) geometry in the coordination sphere of the Ru(2) core. Voltammetric measurements revealed four one electron redox processes for compounds 1-3: the Ru(2) centered oxidation and reduction, and a pair of reductions of the imine or aldehyde groups. Compound 4 displays an additional oxidation attributed to the Fc groups. DFT calculations were performed on model compounds to gain a more thorough understanding of the interaction of the organic functional groups across the diruthenium bridge.     

Diruthenium(III,III) bis(alkynyl) compounds with donor/acceptor-substituted geminal-diethynylethene ligands

Reported in this contribution are the preparation and characterization of a series of Ru(2)(DMBA)(4) (DMBA = N,N'-dimethylbenzamidinate) bis(alkynyl) compounds, trans-Ru(2)(DMBA)(4)(X-gem-DEE)(2) [gem-DEE = σ-geminal-diethynylethene; X = H (1), Si(i)Pr(3) (2), Fc (3); 4-C(6)H(4)NO(2) (4), and 4-C(6)H(4)NMe(2) (5)]. Compounds 1-5 were characterized by spectroscopic and voltammetric techniques as well as the single-crystal X-ray diffraction studies of 2 and 3. Both the single-crystal structural data of compounds 2 and 3 and the spectroscopic/voltammetric data indicate that the gem-DEE ligands are similar to simple acetylides in their impact on the molecular and electronic structures of the Ru(2)(DMBA)(4) core. Furthermore, density functional theory calculations revealed more extensive π delocalization in aryl-donor-substituted gem-DEEs and that the hole-transfer mechanism will likely dominate the charge delocalization in Ru(2)-gem-DEE-based wires.     

Transferable pair potentials for CdS and ZnS crystals

A set of interatomic pair potentials is developed for CdS and ZnS crystals. We show that a simple energy function, which has been used to describe the properties of CdSe [E. Rabani, J. Chem. Phys. 116, 258 (2002)], can be parametrized to accurately describe the lattice and elastic constants, and phonon dispersion relations of bulk CdS and ZnS in the wurtzite and rocksalt crystal structures. The predicted coexistence pressure of the wurtzite and rocksalt structures as well as the equation of state are in good agreement with experimental observations. These new pair potentials enable the study of a wide range of processes in bulk and nanocrystalline II-VI semiconductor materials.     

Threshold reduction in a cyclic photonic molecule laser composed of identical microdisks with whispering-gallery modes

Lasing modes in cyclic photonic molecules (CPMs) composed of several identical thin semiconductor microdisks in free space are studied in a linear approximation. Maxwell's equations with exact boundary conditions and the radiation condition at infinity are considered as a specific eigenvalue problem that enables one to find natural frequencies and threshold gains. It is demonstrated that careful tuning of the distance between the disks in CPMs is able to drastically reduce the lasing thresholds of the whispering-gallery modes having small azimuth indices.     

Effect of water density on methanol oxidation kinetics in supercritical water

We oxidized methanol in supercritical water at 500 degrees C to explore the influence of the water concentration (or density) on the kinetics. The rate increased as the water concentration increased from 1.8 to 5.7 mol/L. This effect of water density on the kinetics observed experimentally was quantitatively reproduced by a previously validated mechanism-based, detailed chemical kinetics model. In this model, reactions of OH radicals with methanol were the fastest methanol removal steps. The rates of these removal steps increased with water density at 500 degrees C because the OH radical concentration increased. The OH radical concentration increased with density because the rates of the steps H + H2O = OH + H2 and CH3 + H2O = OH + CH4, which produce OH radicals, increased. Thus, the main role of water in accelerating methanol oxidation kinetics at 500 degrees C is as a hydrogen donor to a radical (R) in steps such as R + H2O = OH + RH. This system provides a striking example of SCW being involved on the molecular level in the free-radical oxidation as a reactant in elementary steps.     

Combustion chemistry of enols: possible ethenol precursors in flames

Before the recent discovery that enols are intermediates in many flames, they appeared in no combustion models. Furthermore, little is known about enols' flame chemistry. Enol formation in low-pressure flames takes place in the preheat zone, and its precursors are most likely fuel species or the early products of fuel decomposition. The OH + ethene reaction has been shown to dominate ethenol production in ethene flames although this reaction has appeared insufficient to describe ethenol formation in all hydrocarbon oxidation systems. In this work, the mole fraction profiles of ethenol in several representative low-pressure flames are correlated with those of possible precursor species as a means for judging likely formation pathways in flames. These correlations and modeling suggest that the reaction of OH with ethene is in fact the dominant source of ethenol in many hydrocarbon flames, and that addition-elimination reactions of OH with other alkenes are also likely to be responsible for enol formation in flames. On this basis, enols are predicted to be minor intermediates in most flames and should be most prevalent in olefinic flames where reactions of the fuel with OH can produce enols directly.     

Development and characterization of Au-YSZ surface plasmon resonance based sensing materials: high temperature detection of CO

Au-YSZ nanocomposite films exhibited a surface plasmon resonance absorption band around 600 nm that underwent a reversible blue shift and narrowed upon exposure to CO in air at 500 degrees C. A linear dependence of the sensing signal was observed for CO concentrations ranging between 0.1 and 1 vol % in an air carrier gas. This behavior of the SPR band, upon exposure to CO, was not observed when using nitrogen as the carrier gas, indicating an oxygen-dependent reaction mechanism. Additionally, the SPR band showed no measurable signal change upon exposure to CO at temperatures below approximately 400 degrees C. The oxygen and temperature-dependent characteristics, coupled with the oxygen ion formation and conduction properties of the YSZ matrix, are indicative of charge-transfer reactions occurring at the three-phase boundary region between oxygen, Au, and YSZ, which result in charge transfer into the Au nanoparticles. These reactions are associated with the oxidation of CO and a corresponding reduction of the YSZ matrix. The chemical-reaction-induced charge injection into the Au nanoparticles results in the observed blue shift and narrowing of the SPR band.     

Alkylation of inorganic oxo compounds and insights on preventing DNA damage

Metabolism of food- and tobacco-borne procarcinogens results in the exposure of DNA to toxic alkylating agents. These assaults can bring about DNA alkylation damage, mutations, and cancer. Dietary inorganic compounds such as selenium and vanadium are known to prevent cancer, possibly by reacting directly with alkylating agents, thereby preventing DNA damage. To understand potential interactions between oxo species and alkylating toxins, we reacted a series of alkylating agents with varied classes of oxo compounds (i.e., vanadates, selenate, phosphate, sulfate, acetate, nitrate, and nitrite). A new organic-soluble selenate, [(C6H5)4P]3(O3SeOCH2OSeO3)(HSeO4), was synthesized and characterized for these studies. Vanadates were found to convert ethylating agents into ethanol, whereas other anions formed esters upon alkylation. General trends show that oxo anions of the greatest charge density were the most reactive. These studies suggest that the design of new compounds for cancer prevention should incorporate reactive oxo groups with high anionic charge density.