Two-stage Off-Gel isoelectric focusing: protein followed by peptide fractionation and application to proteome analysis of human plasma

This paper presents the recently introduced Off-Gel electrophoresis (OGE) technology as a versatile tool to reproducibly fractionate intact proteins and peptides into discrete liquid fractions. The coupling of two stages of OGE, i.e., the separation of intact proteins in a first-stage followed by fractionation of peptides derived from each protein fraction after proteolysis in a second stage, results in an array of 15 x 15 fractions that are directly amenable to additional peptide fractionation like reverse-phase liquid chromatography (RPC). The analysis of all second-stage peptide fractions from only the first-stage protein fraction representing pH 5.0 -5.15 by on-line reverse-phase LC-tandem mass spectrometry resulted in the identification of 53 proteins (337 peptides), of which 10 were on different immunoglobulin (Ig) chains, with an input of only 1.5 mg human blood plasma proteins. Increasing the protein load to approximately 12 mg increased the number of identified proteins in the same protein fraction to 73 proteins (449 peptides), of which 15 were Ig-related. Immunodepletion of six of the most abundant proteins (albumin, transferrin, haptoglobin, IgG, IgA, and alpha-1-antitrypsin) prior to first-stage OGE with an input of 1.5 mg of protein (equivalent to approximately 10 mg nondepleted plasma) resulted in the identification of 81 proteins (660 peptides), of which three were still Ig fragments. The pI-based separation of peptides appears to be nonuniform based on the theoretically determined pI values of identified peptides. This observation specifically accounts for the neutral zone (pI 5-8) and can be accounted for by the physicochemical properties of the peptides given by their amino acid composition. The power of OGE separation of proteins and peptides is discussed with a focus on the use of the knowledge about the pI of proteins and peptides that assist the validation of correct identifications together with the retention time of peptides on RPC.     

用于真实蛋白质结构预测的一种新的优化方法

用“相对熵”作为优化函数 ,提出了一个有效快速的折叠预测优化算法 .使用了非格点模型 ,预测只关心蛋白质主链的走向 .其中只用到了蛋白质主链上的两两连续的Cα 原子间的距离信息以及 2 0种氨基酸的接触势的一个扩展形式 .对几个真实蛋白质做了算法测试 ,预测的初始结构都为比较大的去折叠态 ,预测构象相对于它们天然结构的均方根偏差 (RMSD)为 5～ 7 .从原理上讲 ,该方法是对能量优化的改进 .     

ORSIS – News and further developments

The paper deals with the simulation program Off Road Systems Interactive Simulation (ORSIS) which is the w,orldwide leading simulation tool for off road driving of wheeled vehicles. Even though the present state of development allows a very realistic simulation of the man–vehicle–terrain system, there is continuous further improvement in the computer program’s detail. Some of the recent innovations integrated into the program are presented in this paper. These examples were chosen in a way that the scope of the further developments can be demonstrated. They represent three main directions of the work carried out: the refining of the tire–soil-model, the integration of new technologies and subsystems into the vehicle model and the improvement of the man–machine–interface especially in driving simulators.The first part of the paper describes a further development of the tire–soil-model. A significant improvement has been achieved to include the influence of slippery surfaces on traction in combination with the tire tread pattern. Results from finite element method (FEM) as well as real measurements were used to build up an approach, which qualitatively allows the influence of the positive–negative portion of the tire tread and the lug height of the tire tread on traction to be considered. The basic idea is very simple and straightforward. Moreover the calculation costs are very low, so the enhancement does not affect real time operation.In the second part a physical model for the central tire inflation system (CTIS) is presented. With this model it is possible to simulate the complete pneumatic system of a CTIS, including the air compressor with an accumulator, the pressure line and the wheel valves. The components are modelled by their physical parameters, so an adaptation to different existing tire-pressure-control-systems (TPC) can be made. The paper presents a short review of the modelling and a first validation using real measurements. Furthermore the influence of each parameter, e.g. the discharge flow of the compressor on the inflation time, is presented.The third part of the paper describes a further development of the visualization system. The ORSIS OpenGL graphic engine was separated from the main ORSIS simulation and can be run on different PCs controlled via a network. It is therefore possible to build up very cheap multi-channel visualization systems using consumer PCs running under LinuX. The fact that ORSIS itself is running on a normal PC allows the assembly of comparatively cheap driving simulators of a high end simulation quality.     

The effect of velocity on rigid wheel performance

A simulation model to predict the effect of velocity on rigid-wheel performance for off-road terrain was examined. The soil–wheel simulation model is based on determining the forces acting on a wheel in steady state conditions. The stress distribution at the interface was analyzed from the instantaneous equilibrium between wheel and soil elements. The soil was presented by its reaction to penetration and shear. The simulation model describes the effect of wheel velocity on the soil–wheel interaction performances such as: wheel sinkage, wheel slip, net tractive ratio, gross traction ratio, tractive efficiency and motion resistance ratio. Simulation results from several soil-wheel configurations corroborate that the effect of velocity should be considered. It was found that wheel performance such as net tractive ratio and tractive efficiency, increases with increasing velocity. Both, relative wheel sinkage and relative free rolling wheel force ratio, decrease as velocity increases. The suggested model improves the performance prediction of off-road operating vehicles and can be used for applications such as controlling and improving off-road vehicle performance.     

Nanocomposites based on cationic polyelectrolytes and silver nanoparticles: Synthesis,characterization, molybdate retention and antimicrobial activity

The objective of this work was to synthesize nanocomposites based on cationic polyelectrolytes and silver nanoparticles using poly(N-vinylbenzyl-N-triethylammonium chloride) as polymer phase. For that, a nanostructured crosslinker was synthesized from silver nanoparticles (AgNPs) and acrylic acid. Molybdate retention properties of nanocomposites were studied in function of pH and ionic strength. In addition, their antimicrobial properties were evaluated against E. coli and S. aureus. It was evidenced that AgNPs can be stabilized using acrylic acid and that this material can be incorporated to the polymer phase during polymerization by free radical of cationic monomers. The effect of pH on retention of molybdate, by the nanostructured polymer, was significant only to low ionic strength (the order seen was pH 5.0 > pH 7.0 > pH 9.0 for 0.0% NaCl). Results suggest that the main interaction influencing the molybdate retention is electrostatic in nature. Finally, antimicrobial activity was enhanced by incorporation of polymerizable nanostructured crosslinker based on AgNPs.     

Homonuclear correlation experiments for quadrupolar nuclei, spinning away from the magic angle

We present a set of homonuclear correlation experiments for half-integer quadrupolar spins in solids. In all these exchange-type experiments, the dipolar interaction is retained during the mixing time by spinning the sample at angles other than the “regular magic angle” (54.7°). The second-order quadrupolar interaction is averaged by different strategies for the different experiments. The multiple-quantum off magic angle spinning (MQOMAS) exchange experiment is essentially a regular MQMAS experiment where the quadrupolar interaction is averaged by combining magic angle spinning with a multiple- to single-quantum correlation scheme. The sample is spun at the magic angle at all times except during the mixing time which is added to establish homonuclear correlation. In the multiple-quantum P₄ magic angle spinning (MQP₄MAS) exchange experiment, the sample is spun at one of the angles at which the fourth-order Legendre polynomial vanishes (P₄ magic angle), the remaining second-order quadrupolar interaction now governed by a second-rank tensor is refocussed by the multiple to single-quantum correlation scheme. In the dynamic angle spinning (DAS) exchange experiment, the second-order quadrupolar interaction is averaged by correlating the evolution from two complementary angles. These experiments are demonstrated and compared, in view of their specific advantages and disadvantages, for ²³Na in the model compound Na₂SO₃.     

Heavy traffic analysis of a storage model with long range dependent On/Off sources

We consider a fluid queueing system with infinite storage capacity and constant output rate offered a superposition ofN identical On/Off sources, where the ratio of input to output rate is small. The On and/or Off periods have heavy tailed distributions with infinite variance, giving rise to Long Range Dependence in the arrival process. In the limit of a large number of sources and high load, it is shown that the tail of the stationary queue content distribution is Weibullian, implying much larger queue contents than in the classical case of exponential tails. Noting that similar results were recently found by I. Norros for a storage system input by a Fractional Brownian Motion, we then show how the two models are related, thus providing a further physical motivation for the Fractional Brownian Motion model.     

An extension of the edge covering problem

In this paper we define a weightedr-covering problem, and show that there exists an optimum solution of ther-covering problem which can be decomposed into the sum of a rounded down solution of its linear relaxation and an optimal solution of a weighted edge covering problem on a reduced graph. Vertexr-packing problem can also be reduced to ther-covering problem.     

Stimuli-Responsive Catenane-Based Catalysts

Rotaxanes and molecular knots exhibit particular properties resulting from the presence of a mechanical bond within their structure that maintains the molecular components interlocked in a permanent manner. On the other hand, the disassembly of the interlocked architecture through the breakdown of the mechanical bond can activate properties which are masked in the parent compound. Herein, we present the development of stimuli-responsive Cu^I-complexed [2]catenanes as OFF/ON catalysts for the copper-catalyzed alkyne-azide cycloaddition (CuAAC) reaction. The encapsulation of the Cu^I ion inside the [2]catenanes inhibits its ability to catalyze the formation of triazoles. In contrast, the controlled opening of the two macrocycles induces the breaking of the mechanical bond, thereby restoring the catalytic activity of the Cu^I ion for the CuAAC reaction. Such OFF/ON catalysts can be involved in signal amplification processes with various potential applications.     

三能级系统电子分布转移的数值模拟

原子能级中的分布可以人为的加以控制,受激拉曼迁移过程为我们提供了一种有效转移电子分布的方法,特别是可以有选择地实现分子高振动能级的分布转移.要对该过程有一个全面的了解,就必须对偏离共振和激光强度对电子分布转移所产生的影响有深刻的认识.使用数值模拟的方法系统地分析了三能级系统在受激拉曼迁移过程中电子分布的转移情况,计算了系统处于双光子共振时和偏离共振时的转移率,分析了偏离双光子共振、偏离单光子共振以及两束激光相对强度对转移率的影响.计算结果表明在双光子共振时可以完全转移;当偏离双光子共振很小的时候,基本可以达到完全转移;转移率对两束激光的相对强度不是很敏感.