Rapid detection of antigen binding by antibody fragments expressed in the periplasm of Escherichia coli

Bacterial expression systems can greatly facilitate proteinengineering of antibodies. We have developed a system for high-levelexpression of antibodies, antibody fragments, or hybrid antibodieswith novel effector functions in the periplasm of Escherichiacoli. From 5 ml of cells, a simple extraction yields sufficientmaterial for SDS-gel electro-phoresis, detection and characterizationof hapten binding. To demonstrate our system, heavy-chain variableregions and 1 light chains of a mouse anti-NP antibody weresynthesized as hybrid proteins with a bacterial signal peptide(Omp F). Each chain is secreted into the periplasm where processing(cleavage of the signal peptide), folding and heterodimer associationtake place. Periplasmic proteins are released by cold osmoticshock, and hapten-binding activity is easily detected withoutfurther manipulation. The ease of genetic engineering in thissystem will facilitate the production of immunoglobulin derivativesdesigned for specific applications, and expression of thesemolecules in a native state will allow the rapid screening ofcombinatorial libraries and the results of mutagenesis.     

The mechanism of CO oxidation over Cu(110): Effect of CO gas energy

The effect of the temperature of gas phase CO upon the kinetics of the oxygen titration reaction: CO_g +O_a CO_2,g, has been studied. It is found that the reaction's rate is independant of CO gas temperature between 300 and 623 K. The activation energy (6.5 kcal/mole), dependence upon CO pressure (first-order), and independence upon oxygen coverage for 0.1 _o 0.4 are all independant of the CO gas phase temperature. This result rules out any Eley-Rideal type mechanism whereby CO reacts directly from the gas phase with an oxygen adatom without first being accommodated to the surface temperature in an absorbed state. The result is instead interpretable in terms of a Langmuir-Hinshelwood mechanism.Camille and Henry Dreyfus Foundation Teacher-Scholar Fellowship.     

基于图嵌入与拓扑结构信息的蛋白质复合物识别算法

蛋白质复合物是细胞结构和生化机制的研究基础,如何准确识别蛋白质复合物成为近年来的研究热点。针对传统算法根据结构信息对蛋白质复合物进行搜索存在敏感度和F-measure低的问题,以及现有监督学习算法根据人为构造特征进行蛋白质复合物识别存在特征构造不能较好地反映图的真实信息等不足,提出了graph2vec-SVM识别算法。将蛋白质复合物看作稠密子图并考虑子图模块度大小,利用graph2vec将图信息转换为向量,并进一步采用SVM分类器对蛋白质复合物进行识别,提高了蛋白质复合物识别的敏感度和F-measure。该算法分别与目前流行的4种非监督学习算法(ClusterOne、CMC、HC-PIN和COACH)和3种监督学习算法(SCI-BN、SCI-SVM和RM)进行比较,在精准度、敏感度和F-measure 3项指标上都显示出了良好的性能。     

Protein interaction networks: centrality,modularity, dynamics,and applications

In the post-genomic era, proteomics has achieved significant theoretical and practical advances with the development of high-throughput technologies. Especially the rapid accumulation of protein-protein interactions (PPIs) provides a foundation for constructing protein interaction networks (PINs), which can furnish a new perspective for understanding cellular organizations, processes, and functions at network level. In this paper, we present a comprehensive survey on three main characteristics of PINs: centrality, modularity, and dynamics. 1) Different centrality measures, which are used to calculate the importance of proteins, are summarized based on the structural characteristics of PINs or on the basis of its integrated biological information; 2) Different modularity definitions and various clustering algorithms for predicting protein complexes or identifying functional modules are introduced; 3) The dynamics of proteins, PPIs and sub-networks are discussed, respectively. Finally, the main applications of PINs in the complex diseases are reviewed, and the challenges and future research directions are also discussed.     

基于加权网络和局部适应度的蛋白质复合物识别算法

蛋白质复合物识别对分析蛋白质网络的结构特征和模块功能具有重要意义。通常在蛋白质网络中挖掘稠密子图或模块来识别其中的蛋白质复合物,限制了其应用范围和识别的准确性。针对该问题,提出了一种基于加权网络和局部适应度的蛋白质复合物识别算法,该算法综合稠密子图的密度指标和模块性定义了新的局部适应度函数,并基于边聚集系数构建加权的蛋白质网络,根据权值选择边,在加权蛋白质网络中将种子边不断聚类扩展,从而获取具有最大综合适应度的子图作为蛋白质复合物。在酵母蛋白质等多个实际网络中试验表明,该算法能够有效提升蛋白质复合物识别的准确性。     

Intergranular oxidation of silicon in 20Cr-25Ni niobium-stabilized stainless steel at 1140–1230 K

The kinetics of intergranular oxidation of silicon in a 20Cr-25Ni Nb-stabilized stainless steel are reported, at temperatures in the range 1140–1230 K, in CO₂ at 40 bar pressure. The depth of attack increased parabolically with respect to time, with an activation energy of 335±30 kJ/mol. The mechanism of growth is discussed in terms of classical internal-oxidation theories, and an alternative explanation based on an available-space theory is developed. The internal oxidation rates in a number of different alloys are compared with diffusivities of metals in the base alloy. It is proposed that intergranular oxidation in the 20–25 Nb steel is controlled by the rate of outward diffusion of iron or chromium in the alloy.     

Evolution of insoluble eutectic Si particles in anodic oxidation films during adipic-sulfuric acid anodizing processes of ZL114A aluminum alloys

The effects of insoluble eutectic Si particles on the growth of anodic oxide films on ZL114A aluminum alloy substrates were in-vestigated by optical microscopy (OM) and scanning electron microscopy (SE...     

Oxidation behavior and mechanism of aluminum oxynitride (AlON) at elevated temperatures

The oxidation behavior and mechanism of aluminum oxynitride (AlON) powder exposed to air at elevated temperatures between 800°C and 1300°C was investigated by X-ray diffractometry (XRD), scanning electron microscope (SEM), electron spin resonance (ESR), nuclear magnetic resonance (NMR), and simultaneous thermogravimetry, differential thermal analysis, and mass spectrometry techniques (TG-DTA-MS). The weight of AlON gradually increases to a maximum value at 1150°C and then decreases with further heating. Meanwhile, AlON powder undergoes chemical changes, as evidenced by lattice expansion, and turns eventually into alumina. ESR spectra reveal the occurrence of lone pair electrons in the oxidized products and the intensity of corresponding resonance signal increases before disappearing with the increase in temperature. Combined with the results of NMR and TG-DTA-MS, the measured data suggest that Al-N in [AlO₃N] tetrahedron and [AlO₅N] octahedron are gradually oxidized into Al-O-N group with lone pair electrons, which causes continuous weight gain and lattice expansion. Further oxidation at higher temperatures results in alumina and N₂.     

Localized swelling of Fe-Cr-Ni alloy rollers in high-temperature applications

Localized swelling has been observed in 24Cr-24Ni-Nb steel transportation rollers used in the normalizing furnace of a plate mill after prolonged service at high temperature. Due to high localized thermal and mechanical stresses, the chromia layer formed on the roller surface ruptures, exposing the roller substrate to furnace oxygen. Oxidation of second-phase carbides results in the formation of carbon monoxide at very high partial pressure. This leads to formation of voids, leading in turn to localized swelling of the roller material.     

Numerical Simulation of Internal Oxidation of Steels during Annealing Treatments

This paper presents a new model for simultaneous diffusion and precipitation of chemical elements in metallic matrices, a scheme for its numerical solution, and several applications to problems of internal oxidation. The model basically stands as an extension of the classical Wagner model for internal oxidation of steels, but is more much general in that it allows for an arbitrary number of diffusing chemical elements, an arbitrary number of precipitate phases with arbitrary compositions, dependence of diffusion coefficients and solubility products upon (time-dependent) temperature, etc., thus allowing for a much broader range of applications. As a counterpart, it is generally impossible to solve the complex, non-linear equations of the model analytically, but this can be done numerically. The simple but efficient numerical scheme proposed is based on explicit 1D finite differences. Experience has shown that this scheme, in spite of its rusticity and the restrictions it imposes on the time-step, is more efficient than more elaborate strategies based on the finite-element method. The applications presented are concerned with internal oxidation of steels during annealing processes. The model and associated numerical scheme allow for evaluation of the amounts of the various oxide precipitates in the external layer of the sheet. This opens the way, through numerical parametric studies of the influence of the process parameters and the chemical composition, to the improvement of existing treatments and the development of new steel grades.