蛋白质组学技术前沿进展

蛋白质组学是以生物体系整体蛋白质为研究对象的新的研究领域,已经成为后基因时代中生命科学最重要研究方向之一。 近年来,蛋白质组学研究取得了令人鼓舞的进展,一系列新技术与新方法得到了快速的发展。 本文总结了2013年以来蛋白质组学研究的有关新技术,并对其发展进行了展望。     

Application of Anodic Stripping Differential Alternative Pulses Voltammetry for Simultaneous Species Quantification

The second order voltammetric technique Differential Alternative Pulses Voltammetry (DAPV) was applied in anodic stripping mode for simultaneous quantification of traces of species having close E_1/2. The potential‐time waveform and the signal processing allowing the DAPV application in stripping mode are presented. The pulses widths and amplitudes were optimized to obtain maximal sensitivity and resolution at traces of In³⁺ and Cd²⁺ (having E_1/2 difference of 45 mV) simultaneous quantification in presence of excess of Pb²⁺. Precise results for both species concentrations were obtained up to In³⁺ to Cd²⁺ concentration ratio as high as 1 to 10 without any sample pre‐treatment in purified industrial waste waters using 0.1 mol L⁻¹ HCl as supporting electrolyte.     

Global quantification of phosphoproteins combining metabolic labeling and gel‐based proteomics in B. pumilus

Differential proteomics targeting the protein abundance is commonly used to follow changes in biological systems. Differences in localization and degree of post‐translational modifications of proteins including phosphorylations are of tremendous interest due to the anticipated role in molecular regulatory processes. Because of their particular low abundance in prokaryotes, identification and quantification of protein phosphorylation is traditionally performed by either comparison of spot intensities on two‐dimensional gels after differential phosphoprotein staining or gel‐free by stable isotope labeling, sequential phosphopeptide enrichment and following LC‐MS analysis. In the current work, we combined in a proof‐of‐principle experiment these techniques using ¹⁴N/¹⁵N metabolic labeling with succeeding protein separation on 2D gels. The visualization of phosphorylations on protein level by differential staining was followed by protein identification and determination of phosphorylation sites and quantification by LC‐MS/MS. This approach should avoid disadvantages of traditional workflows, in particular the limited capability of peptide‐based gel‐free methods to quantify isoforms of proteins. Comparing control and stress conditions allowed for relative quantification in protein phosphorylation in Bacillus pumilus exposed to hydrogen peroxide. Altogether, we quantified with this method 19 putatively phosphorylated proteins.     

Isolation,characterization, and quantification of curcuminoids and their comparative effects in cerebral ischemia

The study reports a rapid and short analytical technique for separation, characterization, and quantitation along with comparative pharmacological effect of curcuminoids in cerebral ischemia. Flash chromatography, using silica and diol columns along with gradient mobile phase, was utilized to separate three curcuminoids, i.e., curcumin (Cur), demethoxycurcumin (DMC), and bisdemethoxycurcumin (BDMC) for the first time. The separated peaks were monitored at 200–360?nm, whereas the purity of compounds (96.2–97.6%) was determined through qualitative analysis such as infrared and ¹H and ¹³C-nuclear magnetic resonance spectroscopy, mass spectrometry (MS), and differential scanning calorimetry. Furthermore, chitosan nanoparticles (CS-NPs) for curcuminoids were prepared and characterized through zeta sizer, zeta potential, scanning electron microscopy, and transmission electron microscopy. The developed ultra performance of liquid chromatography-electrospray ionization-quadrupole-time of flight-mass spectrometry/mass spectrometry (UPLC-ESI-Q-TOF-MS/MS) method showed simplified automation and shorter run time for Combi flash over conventional separation techniques. The CS-NPs for all the three curcuminoids and combined-curcuminoids (CCr) (combined and administered together for a synergistic effect), following intranasal administration in middle cerebral artery–occluded rats were evaluated for grip strength, locomotor activity, and histopathological examination where the anti-ischemic activity was observed, in terms of potency, for all three CS-NPs and CCr as CCr>Cur>DMC>>BDMC. Cur-CS-NPs exhibited more potency among Cur, DMC, and BDMC, whereas CCr was the more potent anti-ischemic drug compared to Cur, DMC, and BDMC. For Cur the characteristic activity is proposed because of the presence of methoxy group on the phenyl ring whereas for CCr it is synergistic effect of curcuminoids.     

Simultaneous quantification of curcuminoids and xanthorrhizol in Curcuma xanthorrhiza by high-performance liquid chromatography

A new method for simultaneous quantification of curcuminoids and xanthorrhizol (XNT) in Curcuma xanthorrhiza was developed and validated using high-performance liquid chromatography with diode-array UV–Vis detector. The chromatographic separation was achieved on a Phenomenex C18 at room temperature with the mobile-phase acetonitrile ?0.001% formic acid in gradient elution system and delivered at a flow rate of 1?mL/min. Detection wavelength 425?nm was used for curcuminoids and 224?nm for XNT. System suitability, linearity, precision, accuracy, limit of detection, limit of quantitation, and stability were evaluated and were found in good agreement with Association of Official Analytical Chemists guidelines for single-laboratory validation. The proposed method was found to be precise, accurate, and reliable and also could be applied for the simultaneous quantitative analysis of curcuminoids and XNT in C. xanthorriza raw material and its herbal medicinal product.     

A Study of Hyperbolicity of Kinetic Stochastic Galerkin System for the Isentropic Euler Equations with Uncertainty

The authors study the fluid dynamic behavior of the stochastic Galerkin (SG for short) approximation to the kinetic Fokker-Planck equation with random uncertainty. While the SG system at the kinetic level is hyperbolic, its fluid dynamic limit, as the Knudsen number goes to zero and the underlying kinetic equation approaches to the uncertain isentropic Euler equations, is not necessarily hyperbolic, as will be shown in the case study fashion for various orders of the SG approximations.     

Is mortality or interest rate the most important risk in annuity models? A comparison of sensitivity analysis methods

Demographic and financial factors are key risk-drivers for insurance companies and pension funds. This paper proposes a systematic investigation for deepening our understanding how these risk drivers affect the annuity cost. We employ local and global sensitivity methods. For local sensitivity, we derive closed form expressions for the differential importance measures of perturbed annuities and connect them to the entropy of the annuity cost. For global sensitivity, we compare variance-based, moment-independent sensitivity measures and Shapley effects. In particular, moment-independent sensitivity measures and Shapley effects are compared for the first time in the case of dependent risk factors. Our framework encompasses and extends several previous results on the sensitivity analysis of annuity models. From a methodological viewpoint, the techniques compared in this paper can support analysts in building annuity models and in verifying the impact of risk drivers in their models. Numerical results using the U.S. 1990 and the U.K. 1990–1994 mortality tables show that the demographic factor is the most important risk source in low-interest rate contexts. However, when uncertainty on the two risk sources is taken into account, the financial factor becomes the global key-driver of risk. Also, interactions among the two factors appear quantitatively significant.     

Large deviation theory for a homogenized and “corrected” elliptic ODE

We study a one-dimensional elliptic problem with highly oscillatory random diffusion coefficient. We derive a homogenized solution and a so-called Gaussian corrector. We also prove a “pointwise” large deviation principle (LDP) for the full solution and approximate this LDP with a more tractable form. Applications to uncertainty quantification are considered.