Detection of phosphorylated peptides in proteomic analyses using microfluidic compact disk technology

A compact disk (CD)-based microfluidic method for selective detection of phosphopeptides by mass spectrometry is described. It combines immobilized metal affinity chromatography (IMAC) and enzymatic dephosphorylation. Phosphoproteins are digested with trypsin and processed on the CD using nanoliter scale IMAC with and without subsequent in situ alkaline phosphatase treatment. This is followed by on-CD matrix-assisted laser desorption/ionization (MALDI) mass spectrometry. Dephosphorylation of the IMAC-enriched peptides allows selective phosphopeptide detection based on the differential mass maps generated (mass shifts of 80 Da or multiples of 80 Da). The CD contains 96 microstructures, each with a 16 nL IMAC microfluidic column. Movement of liquid is controlled by differential spinning of the disk. Up to 48 samples are distributed onto the CD in two equal sets. One set is for phosphopeptide enrichment only, the other for identical phosphopeptide enrichment but combined with in situ dephosphorylation. Peptides are eluted from the columns directly into MALDI target areas, still on the CD, using a solvent containing the MALDI matrix. After crystallization, the CD is inserted into a MALDI mass spectrometer for analysis down to the femtomole level. The average success rate in phosphopeptide detection is over 90%. Applied to noncharacterized samples, the method identified two novel phosphorylation sites, Thr 735 and Ser 737, in the ligand-binding domain of the human mineralocorticoid receptor.     

Water and Solute Movement in Air Pollution Control Residues Measured by Time-Domain Reflectometry

The mobility of pollutants from air pollution control (APC) residues is strongly influenced by its contact with water. This study aims to verify the applicability of time-domain reflectometry (TDR) to infer water and solute movement in situ in an APC residue–compost mixture in a laboratory column. The calibrated dielectric permittivity–volumetric water content relationship (K?θv) for the material shows a distinct plateau at midrange volumetric water contents, which are underestimated by Topp’s K?θv model throughout the studied range. The coating of probes enables a clear TDR signal collection and analysis up to electrical conductivity values of 280?mS?cm?1. Heterogeneities in packing and channel flow in the column are revealed by TDR measurements. Water contents inferred by TDR signal analysis require careful interpretation when used in materials such as APC residues, due to the high amount of water bound in the hydration shells of ions released into the pore water.     

Simple and accurate four-node axisymmetric element

Based on the assumed strain method, a simple four-node axisymmetric solid element is introduced. The assumed strain field is carefully selected to preserve the correct rank of the element stiffness matrix and to achieve high accuracy. The strain field is developed in conjunction with orthogonal projections and no matrix inversions are needed. The coarse mesh accuracy in bending and in typical axisymmetric load cases is excellent even for nearly incompressible materials. The strain-driven format obtained is well suited for materials with non-linear stress–strain relations. Several numerical examples are presented where the excellent performance of the proposed simple element is verified. Copyright © 2006 John Wiley & Sons, Ltd.     

Strategies to obtain pattern fidelity in nanowire growth from large-area surfaces patterned using nanoimprint lithography

Position controlled nanowire growth is important for nanowire-based optoelectronic components which rely on light emission or light absorption. For solar energy harvesting applications, dense arrays of nanowires are needed; however, a major obstacle to obtaining dense nanowire arrays is seed particle displacement and coalescing during the annealing stage prior to nanowire growth. Here, we explore three different strategies to improve pattern preservation of large-area catalyst particle arrays defined by nanoimprint lithography for nanowire growth. First, we see that heat treating the growth substrate prior to nanoimprint lithography improves pattern preservation. Second, we explore the possibility of improving pattern preservation by fixing the seed particles in place prior to annealing by modifying the growth procedure. And third, we show that a SiN _x growth mask can fully prevent seed particle displacement. We show how these strategies allow us to greatly improve the pattern fidelity of grown InP nanowire arrays with dimensions suitable for solar cell applications, ultimately achieving 100% pattern preservation over the sampled area. The generic nature of these strategies is supported through the synthesis of GaAs and GaP nanowires.

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The robust vehicle routing problem with time windows

This paper addresses the robust vehicle routing problem with time windows. We are motivated by a problem that arises in maritime transportation where delays are frequent and should be taken into account. Our model only allows routes that are feasible for all values of the travel times in a predetermined uncertainty polytope, which yields a robust optimization problem. We propose two new formulations for the robust problem, each based on a different robust approach. The first formulation extends the well-known resource inequalities formulation by employing adjustable robust optimization. We propose two techniques, which, using the structure of the problem, allow to reduce significantly the number of extreme points of the uncertainty polytope. The second formulation generalizes a path inequalities formulation to the uncertain context. The uncertainty appears implicitly in this formulation, so that we develop a new cutting plane technique for robust combinatorial optimization problems with complicated constraints. In particular, efficient separation procedures are discussed. We compare the two formulations on a test bed composed of maritime transportation instances. These results show that the solution times are similar for both formulations while being significantly faster than the solutions times of a layered formulation recently proposed for the problem.     

Trajectory planning in the infinity norm for linear control systems

When planning trajectories, a reasonable demand on the generated curves is that they interpolate through given points, or given intervals, at given specified times, or that they go through these points or intervals at times lying in specified time windows. This problem is addressed here as an optimal control problem, minimizing the infinity norm of the inputs of a discretized linear control system since the infinity norm minimization problem arises naturally when doing trajectory planning for both controlled switching systems and non-holonomic robotic systems.     

A GC–MS-based metabonomic investigation of blood serum from irritable bowel syndrome patients undergoing intervention with acidified milk products

In the present study, the use of gas chromatography mass spectrometry (GC–MS)-based metabonomics to characterize blood serum in an intervention study of patients suffering from the common gastrointestinal disorder irritable bowel syndrome (IBS) was investigated. The patients included in the study consumed an acidified milk product with (n = 30) or without probiotics (n = 31) (Lactobacillus paracasei F19, Lactobacillus acidophilus LA-5 and Bifidobacterium lactis BB-12) for an 8-week period, and blood serum samples were collected before and after the intervention. Acidified milk is commonly used as a delivering vector for probiotics in commercial consumer settings. The serum samples were extracted and derivatized using N-Methyl-N-(trimethylsilyl) trifluoroacetamide (MSTFA), and GC–MS analysis was carried out. Multivariate data analysis including principal component analysis (PCA), orthogonal partial least squares-discriminant analysis (OPLS-DA), and S-plot was applied on the obtained GC–MS data, which revealed higher serum lactate, glutamine, proline creatinine/creatine, and aspartic acid levels and lower serum glucose levels after the intervention period for both treatment groups. Consequently, the present study indicated an effect of acidified milk consumption on the plasma metabolite profile, which was independent of a concomitant intake of probiotics. In addition, the present study demonstrates that GC–MS is a useful analytical technique for metabonomics studies of blood serum.     

Essential functional role of the polysaccharide intercellular adhesin of Staphylococcus epidermidis in hemagglutination

Hemagglutination of erythrocytes is a common property of Staphylococcus epidermidis strains, which is related to adherence and biofilm formation and may be essential for the pathogenesis of biomaterial-associated infections caused by S. epidermidis. In three independent biofilm-producing, hemagglutination-positive S. epidermidis isolates, interruption of the icaADBC operon essential for polysaccharide intercellular adhesin (PIA) synthesis by Tn917 insertions led to a hemagglutination-negative phenotype. An immunoglobulin G fraction of antiserum to PIA greatly reduced hemagglutination. Purified PIA led to a 64-fold decrease of hemagglutination titers of these strains; however, it did not mediate hemagglutination by itself. These observations define PIA as the hemagglutinin of S. epidermidis or at least as its major functional component.