Dimethyl isotope-coded affinity selection for the analysis of free and blocked N-termini of proteins using LC-MS/MS

Because of enhanced a(1) ion signals, dimethyl labeling is useful for identifying the N-termini of proteins or peptides. Herein, we describe a novel strategy that uses dimethyl isotope-coded affinity selection (DICAS) to isolate peptides that contain either the dimethylated or in vivo blocked N-termini of proteins for comprehensive sequence analyses by LC-MS/MS. In this method, dimethyl labeling at the protein level was first performed using formaldehyde-d(2) to label all unblocked protein N-termini and lysine residues, followed by trypsin digestion. The free N-terminal amines of internal peptides generated by digestion were captured by solid supports with aldehyde functionalities through reductive amination. The flow-through fractions, which contained either in vivo or in vitro blocked N-terminal peptides, were subjected to sequence analyses by LC-MS/MS. Owing to the unique feature of a1 signal enhancement associated with dimethylated peptides and the use of the deuterium reagent, the in vitro blocked (or in vivo free) N-termini of proteins could be easily differentiated from the in vivo blocked N-termini. Thus, their sequences and N-terminal modifications could be assigned unambiguously from MS/MS spectra. In this study, the completeness of the labeling and the efficiency of the isolation method were first confirmed by the use of a mixture of model proteins composed of hemoglobin, myoglobin, and alpha-lactalbumin. The N-termini of all three proteins, including both alpha and beta chains of hemoglobin as well as a signal sequence located in the N-termini of alpha-lactalbumin, were successfully identified. The protocol was then applied to the analysis of an unfractionated lysate of MCF-7 cells. Results indicate that more than 80% of the isolated peptides contained the N-termini of unique proteins, and many of them were consistent with known or inferred N-terminal processing such as methionine removal and acetylation. In addition, using the DICAS approach, we identified a novel N-terminal formylation for the Ig kappa chain V-III region SIE protein and a novel N-terminal signal sequence (1th-32th amino acid) for profilin.     

Optimum power-saving method for power MOSFET width of DC/DC converters

An optimum power metal-oxide-semiconductor field effect transistor (MOSFET) width technique is proposed for enhancing the efficiency characteristics of switching DC-DC converters. By implementing a one-cycle buck DC-DC converter, it is demonstrated that the dynamic power MOSFET width controlling technique has a much improved power reduction whether the load current is light or heavy. The maximum efficiency of the buck converter is ~92% with a 3% efficiency improvement for the heavy load condition. The efficiency is further improved by ~16% for the light load condition as a result of the power reduction from the large power MOSFET transistors. Also proposed is a new error-correction loop circuit to enable a better load regulation than that of previous designs. Compared with the adaptive gate driver voltage technique, the optimum power MOSFET width can achieve a significant improvement in power saving. It is also superior to the low-voltage-swing MOSFET gate drive technique for switching DC-DC converters     

Stabilized space–time computation of wind-turbine rotor aerodynamics

We show how we use the Deforming-Spatial-Domain/Stabilized Space–Time (DSD/SST) formulation for accurate 3D computation of the aerodynamics of a wind-turbine rotor. As the test case, we use the NREL 5MW offshore baseline wind-turbine rotor. This class of computational problems are rather challenging, because they involve large Reynolds numbers and rotating turbulent flows, and computing the correct torque requires an accurate and meticulous numerical approach. We compute the problem with both the original version of the DSD/SST formulation and a recently introduced version with an advanced turbulence model. The DSD/SST formulation with the advanced turbulence model is a space–time version of the residual-based variational multiscale method. We compare our results to those reported recently, which were obtained with the residual-based variational multiscale Arbitrary Lagrangian–Eulerian method using NURBS for spatial discretization and which we take as the reference solution. While the original DSD/SST formulation yields torque values not far from the reference solution, the DSD/SST formulation with the variational multiscale turbulence model yields torque values very close to the reference solution.     

Particle-reinforced aluminum matrix composites produced from powder mixtures via friction stir processing

Particle-reinforced aluminum matrix composites were produced from powder mixtures of aluminum and silicon by using multiple passages of friction stir processing (FSP). In the composites, the Si particles with an average size of ∼1.5 μm are uniformly dispersed in the aluminum matrix which has a fine-grained structure (∼2 μm). The strengthening mechanism of the composites is discussed. It indicates that the fine grain size of aluminum, the Orowan strengthening due to intragranular particles and the dislocations generated by thermal mismatch all contribute significantly to the composite yield strength.     

Phononic plate waves

In the past two decades, phononic crystals (PCs) which consist of periodically arranged media have attracted considerable interest because of the existence of complete frequency band gaps and maneuverable band structures. Recently, Lamb waves in thin plates with PC structures have started to receive increasing attention for their potential applications in filters, resonators, and waveguides. This paper presents a review of recent works related to phononic plate waves which have recently been published by the authors and coworkers. Theoretical and experimental studies of Lamb waves in 2-D PC plate structures are covered. On the theoretical side, analyses of Lamb waves in 2-D PC plates using the plane wave expansion (PWE) method, finite-difference time-domain (FDTD) method, and finite-element (FE) method are addressed. These methods were applied to study the complete band gaps of Lamb waves, characteristics of the propagating and localized wave modes, and behavior of anomalous refraction, called negative refraction, in the PC plates. The theoretical analyses demonstrated the effects of PC-based negative refraction, lens, waveguides, and resonant cavities. We also discuss the influences of geometrical parameters on the guiding and resonance efficiency and on the frequencies of waveguide and cavity modes. On the experimental side, the design and fabrication of a silicon-based Lamb wave resonator which utilizes PC plates as reflective gratings to form the resonant cavity are discussed. The measured results showed significant improvement of the insertion losses and quality factors of the resonators when the PCs were applied.     

Gas-bubbled nano zero-valent iron process for high concentration arsenate removal

In this study, batch experiments were performed to investigate a novel process for high concentration arsenate removal in the presence of air and/or CO(2) bubbling. The pretreatment step, CO(2) bubbling at 300 mL/min for 5 min, was taken to adjust the solution pH to an acidic environment, followed by air bubbling at 300 mL/min for 10 min to increase dissolved oxygen in the solution. In the treatment period, the nano-scale zero-valent iron was applied to remove aqueous arsenate of 3000 μg/L, while the treatment system was continuously bubbled by 300 mL/min of air. Such a process resulted in outstanding performance in arsenate removal. Furthermore, in the field groundwater application, the arsenate removal rate for the proposed process was 5 times faster than the rate measured when the system was pretreated by acidic chemical species only.     

Development of a multi-pathway probabilistic health risk assessment model for swimmers exposed to chloroform in indoor swimming pools

For swimmers, exposure to chloroform, a probable carcinogen, in indoor swimming pools can be through different pathways such as ingestion, dermal absorption, inhalation during swimming, and inhalation during resting. In order to evaluate health risk results from excessive exposure to chloroform, concentrations of chloroform in pool water were first collected and analyzed. Then, a two-layer model is used, which is capable of estimating the concentrations of chloroform in the boundary layer adjacent to the water surface and the concentrations of chloroform in indoor swimming pool air. The use of stratification model is important for estimating the risks for swimmers since they are exposed to these kinds of situations while performing swimming and resting in indoor swimming pools environment. The incremental lifetime cancer risk (ILCR) was then estimated using the multi-pathway exposure model. The results showed that the 95th percentile of ILCRs calculated for male and female swimmers were 2.80 × 10(-4) and 2.47 × 10(-4), respectively. The major exposure routes were found to be inhalation during swimming which contributes to more than 99% of the total health risk. Our study suggested that to protect swimmers from excessive exposure to chloroform, alternative methods or processes of disinfection should be considered for swimming pool managers.     

Study and fabrication of ZnNb2O6 thin films by sol-gel method

Zinc niobium oxide (ZnNb₂O₆) thin films were grown on ITO/glass substrate by sol-gel process. Microstructure and surface morphology of the ZnNb₂O₆ thin films have been studied by X-ray diffraction and scanning electron microscopy. Optical properties of the ZnNb₂O₆ thin films were obtained by UV-visible recording spectrophotometer. The dependence of the microstructure, optical transmittance spectra, optical band gap on annealing temperature was also investigated.     

Identification of di-isononyl phthalate metabolites for exposure marker discovery using in vitro/in vivo metabolism and signal mining strategy with LC-MS data

Di-isononyl phthalate esters (DINPs) are endocrine-disrupting chemicals and have replaced di(2-ethylhexyl) phthalate (DEHP) as the major plasticizer for poly(vinyl chloride) (PVC) products in recent years. Exposure marker discovery of DINPs is crucial, because of their high potential for human exposure and toxicity. Here, we propose an alternative approach for tracing signals derived from stable isotope-labeled precursors with varied labeling ratios to efficiently filter probable metabolite signals. The statistical process, which involves a signal mining algorithm with isotope tracing (SMAIT), has effectively filtered 13 probable DINP metabolite signals out of the 8867 peaks in the LC-MS data obtained from incubated stable isotope-labeled precursors with liver enzymes. Seven of the 13 probable metabolite signals were confirmed as DINP structure-related metabolites by preliminary MS/MS analyses. These 7 structure-related metabolite signals were validated as effective DINP exposure markers, using urine samples collected from DINP-administered rats without time-consuming comprehensive structure identification. We propose that the 7 identified possible DINP metabolite signals of m/z 279.1, 293.1, 305.1, 307.1, 321.1, 365.1, and 375.1 are potential markers for DINP exposure and should be investigated further. The integrated approach described here can efficiently, and systematically, filter probable metabolite signals from a complex LC-MS dataset for toxic exposure marker discovery. It is a relatively low-cost/rapid workflow for exposure marker discovery.     

High-affinity capture of proteins by diamond nanoparticles for mass spectrometric analysis

Carboxylated/oxidized diamond nanoparticles (nominal size 100 nm) exhibit exceptionally high affinity for proteins through both hydrophilic and hydrophobic forces. The affinity is so high that proteins in dilute solution can be easily captured by diamonds, simply separated by centrifugation, and directly analyzed by matrix-assisted laser desorption/ionization (MALDI) time-of-flight (TOF) mass spectrometry (MS). No preseparation of the adsorbed molecules from diamonds is required for the mass spectrometric analysis. Compared to conventional MALDI-TOF-MS, an enhancement in detection sensitivity by more than 2 orders of magnitude is achieved for dilute solution containing cytochrome c, myoglobin, and albumin because of preconcentration of the probed molecules. The lowest concentration detectable is 100 pM for a 1-mL solution. Aside from the enhanced sensitivity, the overall performance of this technique does not show any sign of deterioration for highly contaminated protein solutions, and furthermore, no significant peak broadening and band shift were observed in the mass spectra. The promise of this new method for clinical proteomics research is demonstrated with an application to human blood serum.