Sequential interval motif search: unrestricted database surveys of global MS/MS data sets for detection of putative post-translational modifications

Tandem mass spectrometry is the prevailing approach for large-scale peptide sequencing in high-throughput proteomic profiling studies. Effective database search engines have been developed to identify peptide sequences from MS/MS fragmentation spectra. Since proteins are polymorphic and subject to post-translational modifications (PTM), however, computational methods for detecting unanticipated variants are also needed to achieve true proteome-wide coverage. Different from existing "unrestrictive" search tools, we present a novel algorithm, termed SIMS (for Sequential Motif Interval Search), that interprets pairs of product ion peaks, representing potential amino acid residues or "intervals", as a means of mapping PTMs or substitutions in a blind database search mode. An effective heuristic software program was likewise developed to evaluate, rank, and filter optimal combinations of relevant intervals to identify candidate sequences, and any associated PTM or polymorphism, from large collections of MS/MS spectra. The prediction performance of SIMS was benchmarked extensively against annotated reference spectral data sets and compared favorably with, and was complementary to, current state-of-the-art methods. An exhaustive discovery screen using SIMS also revealed thousands of previously overlooked putative PTMs in a compendium of yeast protein complexes and in a proteome-wide map of adult mouse cardiomyocytes. We demonstrate that SIMS, freely accessible for academic research use, addresses gaps in current proteomic data interpretation pipelines, improving overall detection coverage, and facilitating comprehensive investigations of the fundamental multiplicity of the expressed proteome.     

Analysis of major protein-protein and protein-metal complexes of erythrocytes directly from cell lysate utilizing capillary electrophoresis mass spectrometry

The separation and detection of the major protein-protein and protein-metal complexes of erythrocytes directly from cell lysate under native conditions has been accomplished for the first time using capillary electrophoresis electrospray ionization-mass spectrometry (CE/ESI-MS). All three major protein-protein and protein-metal complexes in human red blood cells (RBCs) with a concentration dynamic range of approximately 3 orders of magnitude were successfully detected. Intact complexes detected in lysed RBCs included carbonic anhydrase II (CAII-Zn at approximately 0.8 amol/cell) complexed with its zinc cofactor, carbonic anhydrase I (CAI-Zn at approximately 7 amol/cell) complexed with its zinc cofactor, and hemoglobin A (Hb-tetramer at approximately 450 amol/cell)a tetramer formed by two alpha-beta-subunits and four heme groups. The average molecular weights measured for these complexes were consistent with their theoretical values within 0.01% mass accuracy. The use of Polybrene as a self-coating reagent in conjunction with ammonium acetate at pH approximately 7.4, narrow capillary for high separation efficiency, and forward polarity CE to avoid acid production at the tip of the capillary were overriding experimental factors for successful analysis of protein complexes. Diluting the lysed blood sample in ammonium acetate for a minimum of 6 h before injecting the sample into the CE was essential for obtaining the mass accuracy consistent with their theoretical average molecular weights. At physiological pH, the mass spectrum of the electrophoretic peak of Hb-tetramer included a small amount of the monomers and Hb-dimer. The migration time and peak profile of these species were almost identical to that of the tetramer, indicating that they are formed from decomposition of the Hb-tetramer during the ESI process. A separate electrophoretic peak for the Hb-dimer was only detected when the pH of the BGE was lowered from 7.4 to approximately 6.6. Running CE in forward polarity mode was essential for detection of the intact Hb-tetramer as well as CAI-Zn and CAII-Zn complexes. Under forward polarity mode, CE outlet/ESI shared electrode acts as the cathode of the CE circuit and the anode (positive voltage for positive ions) of the ESI circuit, thereby maintaining approximately neutral pH at the CE outlet/ESI electrode. In addition, under forward polarity mode, CAII-Zn and CAI-Zn migrated ahead of Hb-tetramer, avoiding being masked by 562x and 64x, respectively, molar excess of Hb-tetramer.     

New Raman spectrometer using a digital micromirror device and a photomultiplier tube detector for rapid on-line industrial analysis. Part I: description of the prototype and preliminary results

In this paper, a prototype of a new generation of Raman spectrometers, based on the use of a monochromator, a digital micromirror device as light modulator, and a photomultiplier tube as detector of the Raman light, is described. This spectrometer, containing no moving parts, is inexpensive, robust, and very precise. New in concept, this spectrometer makes it possible to record, in addition to classical Raman spectra, the intensity at several selected points of the spectrum and/or the total intensity in several selected intervals at the same time with great accuracy, thus giving new possibilities for analytical applications. Also, the work presented demonstrates the possibilities of this very simple prototype for rapid on-line industrial analysis, with an example of quantitative analysis of binary and ternary mixtures of xylene isomers. The precision obtained is satisfactory (errors of prediction approximately 3% in 5-6 seconds per sample).     

Adsorption of polyanions on nanostructured polypyrrole submonolayer grafted on semiconducting transparent support

Polypyrrole submonolayers are formed on three different supports: indium oxide (In₂O₃), indium tin oxide (ITO) and tin oxide (SnO₂). It is seen that this formation is a function of the nature of the substrates. Nanometric film scale has been checked by AFM measurements. These polypyrrole submonolayers allowed self-assembling with polyoxometalate and played a determining role in the adsorption characteristics.     

Smooth finite element methods: Convergence,accuracy and properties

A stabilized conforming nodal integration finite element method based on strain smoothing stabilization is presented. The integration of the stiffness matrix is performed on the boundaries of the finite elements. A rigorous variational framework based on the Hu–Washizu assumed strain variational form is developed. We prove that solutions yielded by the proposed method are in a space bounded by the standard, finite element solution (infinite number of subcells) and a quasi‐equilibrium finite element solution (a single subcell). We show elsewhere the equivalence of the one‐subcell element with a quasi‐equilibrium finite element, leading to a global a posteriori error estimate. We apply the method to compressible and incompressible linear elasticity problems. The method can always achieve higher accuracy and convergence rates than the standard finite element method, especially in the presence of incompressibility, singularities or distorted meshes, for a slightly smaller computational cost. It is shown numerically that the one‐cell smoothed four‐noded quadrilateral finite element has a convergence rate of 2.0 in the energy norm for problems with smooth solutions, which is remarkable. For problems with rough solutions, this element always converges faster than the standard finite element and is free of volumetric locking without any modification of integration scheme. Copyright © 2007 John Wiley & Sons, Ltd.     

基于管内填充方法的客车侧翻安全性改进研究

按照欧洲ECE R66法规,建立了客车整车有限元模型,利用LS_DYNA软件模拟了客车侧翻时车身的动态响应。针对原车身结构侧翻存在的问题,提出了基于管内填充方法的结构改进方案,并进行了仿真分析和试验验证。仿真及试验结果表明,在适当位置的矩形钢管内填充石蜡、松香或环氧树脂与木屑及固化剂的混合物,都可使车身上部结构刚度提高。考虑到高温时的稳定性,环氧树脂与木屑及固化剂的混合物效果更佳。改进后的客车车身骨架在侧翻时没有与乘员生存空间发生相互穿透,满足法规要求。     

An experimental study on micro-EDM in low-resistivity deionized water using short voltage pulses

Deionized water has been used as dielectric fluid for micro-electrical discharge machining (micro-EDM) because it gives higher material removal rate and lower tool wear than hydrocarbon oil. Moreover, it is a relatively low-cost and eco-friendly substance. Therefore, deionized water tends to be more favorable for micro-EDM. However, it causes weak electrochemical reaction during micro-EDM due to its slight conductivity. This leads to the unanticipated additional material removal from the workpiece which affects the machining shape and quality. The study in this paper aims to suppress the electrochemical reaction in die-sinking micro-EDM using deionized water by employing short voltage pulse. Experiments were carried out to fabricate micro-holes using the developed nanosecond pulse circuit. Different pulse parameters were applied to identify the main factor affecting the electrochemical reaction rate. Machining gap was found to be thinner and workpiece surface adjacent to the rim of micro-holes were found to be free of defects caused by material dissolution when pulse duration reached a critical value. Moreover, the influence of pulse parameters on material removal rate and machined shape was also investigated. Besides, energy-dispersive X-ray spectroscopy analysis showed that the machined surface using deionized water was less affected from material migration during micro-EDM process in comparison to hydrocarbon oil.     

Effect of biogas technology on nutrient flows for small- and medium-scale pig farms in Vietnam

Increased demand for meat products has led to increased livestock production in Vietnam, which now risks environmental pollution from inappropriate animal manure management on livestock farms. Biogas technology is generally considered an efficient solution for such farms to produce renewable biofuel for use in the household and to reduce the pollution impact from animal waste. However, with biogas technology, farmers may reduce their use of manure for fertilising crops. This field survey investigated nutrient flows on small- and medium-scale livestock farms with and without biogas in Northern Vietnam, in order to identify existing problems and possibilities for sustainable livestock production. A field survey was conducted on 12 pig farms with biogas and 12 pig farms without biogas in Quoc Oai district, Hanoi city. In general, the non-biogas pig farms used on average 3.8 ton compost and 3.1 ton fresh solid manure ha^?1?crop^?1 for each of three crops typically grown per year on their arable land. They discharged on average 16?% of the total manure produced into the environment in liquid form through the public sewage system. On biogas pig farms, the use of fresh solid manure for crops and discharge of liquid manure was lower, as manure was used to produce biogas. However, excessive use of washing water on several of these farms resulted in very dilute slurry (solid manure:water ratio 1:11) entering the biogas digester. This lowered the retention time in the digester (below the optimum range of 35?C55?days), leading to low biogas production rates and possible accumulation of sediment. The digestate was also highly diluted and hence difficult and costly to transport and apply to crops, so it was largely (60?%) discharged to the environment. The input volume of washing water should therefore be reduced to a ratio of 1:5. For better sustainability, appropriate technologies are needed to absorb nutrients from the digestate before discharge and to recycle these nutrients to crops.     

Musk fragrances, DEHP and heavy metals in a 20 years old sludge treatment reed bed system

The Sludge Treatment Reed Bed (STRB) technology is a cost-efficient and environmentally friendly technology to dewater and mineralize surplus sludge from conventional wastewater treatment systems. Primary and secondary liquid sludge is loaded onto the surface of the bed over several years, where it is dewatered, mineralized and turned into a biosolid with a high dry matter content for use as an organic fertilizer on agricultural land. We analysed the concentrations of five organic micropollutants (galaxolide, tonalide, cashmeran, celestolide and DEHP) and six heavy metals (Pb, Ni, Cu, Cd, Zn and Cr) in the accumulated sludge in a 20-year old STRB in Denmark in order to assess the degradation and fate of these contaminants in a STRB and the relation to sludge composition. The results showed that the deposited sludge was dewatered to reach a dry matter content of 29%, and that up to a third of the organic content of the sludge was mineralized. The concentrations of heavy metals generally increased with depth in the vertical sludge profile due to the dewatering and mineralization of organic matter, but in all cases the concentrations were below the European Union legal limits for agricultural land disposal. The concentrations of fragrances and DEHP ranged from 10 to 9000 ng g⁻¹ dry mass. The attenuation of hydrophobic micropollutants from the top to the bottom layer of the reed bed ranged from 40 to 98%, except for tonalide which increased significantly with sludge depth, and consequently showed an unusual depth distribution of the galaxolide/tonalide ratio. This unexpected pattern may reflect changes imposed by a long storage time and/or different composition of the fresh sludge in the past. The lack of a significant decreasing DEHP concentration with sludge age might indicate that this compound is very persistent in STRBs. In conclusion the STRB was a feasible technology for sludge treatment before its land disposal.