Evaluation of the gaussian beam model for prediction of LDV fringe fields

A simple model is developed to estimate the fringe field geometry at the intersection of two Gaussian laser beams. Comparison of the model results to experimentally measured fringe spacing demonstrates that while the model predicts the fringe geometry well when the beam waists are far from the intersection volume, it performs poorly under nominally ideal conditions- when the beam waists are located at the intersection. Data obtained with two different laser sources indicate that the discrepancies between the theory and experiment are likely due to deviations of the laser beam from an ideal Gaussian beam. With a high quality laser, the details of the fringe field geometry are still not well duplicated by the Gaussian beam model, although the magnitude of the variation in fringe spacing and the effect of the controlling system parameters are correctly predicted

Determination of pyridoxal-5′-phosphate (PLP)-bonding sites in proteins: a peptide mass fingerprinting approach based on diagnostic tandem mass spectral features of PLP-modified peptides

Peptides modified by pyridoxal-5′-phosphate (PLP), linked to a lysine residue via reductive amination, exhibit distinct spectral characteristics in the collision-induced dissociation (CID) tandem mass (MS/MS) spectra that are described here. The MS/MS spectra typically display two dominant peaks whose m/z values correspond to neutral losses of [H 3 PO 4 ] (−98 Da) and the PLP moiety as [C 8 H 10 NO 5 P] (−231 Da) from the precursor peptide ion, respectively. Few other peaks are observed. Recognition of this distinct fragmentation behavior is imperative since determining sequences and sites of modifications relies on the formation of amide backbone cleavage products for subsequent interpretation via proteome database searching. Additionally, PLP-modified peptides exhibit suppressed precursor ionization efficiency which diminishes their detection in complex mixtures. Presented here is a protocol which describes an enrichment strategy for PLP-modified peptides combined with neutral loss screening and peptide mass fingerprinting to map the PLP-bonding site in a known PLP-dependent protein. This approach represents an efficient alternative to site-directed mutagenesis which has been the traditional method used for PLP-bonding site localization in proteins. Copyright © 2009 John Wiley & Sons, Ltd.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/64342/1/4270_ftp.pd

Wnt5a induces ROR1 to complex with HS1 to enhance migration of chronic lymphocytic leukemia cells.

ROR1 (receptor tyrosine kinase-like orphan receptor 1) is a conserved, oncoembryonic surface antigen expressed in chronic lymphocytic leukemia (CLL). We found that ROR1 associates with hematopoietic-lineage-cell-specific protein 1 (HS1) in freshly isolated CLL cells or in CLL cells cultured with exogenous Wnt5a. Wnt5a also induced HS1 tyrosine phosphorylation, recruitment of ARHGEF1, activation of RhoA and enhanced chemokine-directed migration; such effects could be inhibited by cirmtuzumab, a humanized anti-ROR1 mAb. We generated truncated forms of ROR1 and found its extracellular cysteine-rich domain or kringle domain was necessary for Wnt5a-induced HS1 phosphorylation. Moreover, the cytoplamic, and more specifically the proline-rich domain (PRD), of ROR1 was required for it to associate with HS1 and allow for F-actin polymerization in response to Wnt5a. Accordingly, we introduced single amino acid substitutions of proline (P) to alanine (A) in the ROR1 PRD at positions 784, 808, 826, 841 or 850 in potential SH3-binding motifs. In contrast to wild-type ROR1, or other ROR1P→︀A mutants, ROR1P(841)A had impaired capacity to recruit HS1 and ARHGEF1 to ROR1 in response to Wnt5a. Moreover, Wnt5a could not induce cells expressing ROR1P(841)A to phosphorylate HS1 or activate ARHGEF1, and was unable to enhance CLL-cell motility. Collectively, these studies indicate HS1 plays an important role in ROR1-dependent Wnt5a-enhanced chemokine-directed leukemia-cell migration

Revolutionary systems for catalytic combustion and diesel catalytic particulate traps.

This report is a summary of an LDRD project completed for the development of materials and structures conducive to advancing the state of the art for catalyst supports and diesel particulate traps. An ancillary development for bio-medical bone scaffolding was also realized. Traditionally, a low-pressure drop catalyst support, such as a ceramic honeycomb monolith, is used for catalytic reactions that require high flow rates of gases at high-temperatures. A drawback to the traditional honeycomb monoliths under these operating conditions is poor mass transfer to the catalyst surface in the straight-through channels. ''Robocasting'' is a unique process developed at Sandia National Laboratories that can be used to manufacture ceramic monoliths with alternative 3-dimensional geometries, providing tortuous pathways to increase mass transfer while maintaining low-pressure drops. These alternative 3-dimensional geometries may also provide a foundation for the development of self-regenerating supports capable of trapping and combusting soot particles from a diesel engine exhaust stream. This report describes the structures developed and characterizes the improved catalytic performance that can result. The results show that, relative to honeycomb monolith supports, considerable improvement in mass transfer efficiency is observed for robocast samples synthesized using an FCC-like geometry of alternating rods. Also, there is clearly a trade-off between enhanced mass transfer and increased pressure drop, which can be optimized depending on the particular demands of a given application. Practical applications include the combustion of natural gas for power generation, production of syngas, and hydrogen reforming reactions. The robocast lattice structures also show practicality for diesel particulate trapping. Preliminary results for trapping efficiency are reported as well as the development of electrically resistive lattices that can regenerate the structure by combusting the trapped soot. During this project an ancillary bio-medical application was discovered for lattices of hydroxyapatite. These structures show promise as bone scaffolds for the reparation of damaged bone. A case study depicting the manufacture of a customized device that fits into a damaged mandible is described

Barrel swirl breakdown in spark-ignition engines: Insights from particle image velocimetry measurements

This is an article from the journal, Proceedings of the Institution of Mechanical Engineers, Part D: Journal of Automobile Engineering [© IMechE ]. It is also available at: http://dx.doi.org/10.1243/0954407991527134Particle image velocimetry (PIV) has been used here to study the formation and breakdown of barrel swirl ('tumble') in a production geometry, four-stroke, four-valve, motored, spark-ignition, optically accessed internal combustion (IC) engine. The barrel swirl ratio (BSR) of the cylinder head could be enhanced by means of a port face inducer gasket so that the flow processes taking place at low and high swirl ratios could be investigated conveniently. Double-exposed images from planes both parallel and perpendicular to the cylinder axis were recorded at selected crank angles through the induction and compression strokes at a motored engine speed of 1000 r/min, with a wide open throttle, for both high and low BSR cases. The recorded images were interrogated by digital autocorrelation to give two-dimensional maps of instantaneous velocity. In both high and low BSR cases, a barrel or tumbling vortex motion is generated during induction, which is shown to persist throughout the majority of the compression stroke. The details of barrel swirl formation during induction and its subsequent modification during compression, however, differ strongly between the two cases. These differences can be explained qualitatively in terms of two main events; the first being competition during induction between vortices of unequal strength and the second being competition between the large-scale swirl motion and the local flow field generated by piston motion during compression. In the low barrel swirl case, significant dissipation occurs owing to these interactions and consequently the large-scale motion exhibits lower mean velocities and undergoes significant distortion. In the case of high BSR, the competition effects are minimized and a single ordered vertical vortex exhibiting high velocity magnitudes is observed to avoid piston induced distortion. It then moves into the apex of the pent roof combustion chamber where it survives as a single ordered vortex until at least 40° crank angle (CA) before top dead centre (TDC). Limitations and developments of the PIV technique are discussed

Hydrazines as versatile chemical biology probes and drug-discovery tools for cofactor-dependent enzymes [preprint]

Known chemoproteomic probes generally use warheads that tag a single type of amino acid or modified form thereof to identify cases in which its hyper-reactivity underpins function. Much important biochemistry derives from electron-poor enzyme cofactors, transient intermediates and chemically-labile regulatory modifications, but probes for such species are underdeveloped. Here, we have innovated a versatile class of chemoproteomic probes for this less charted hemisphere of the proteome by using hydrazine as the common chemical warhead. Its electron-rich nature allows it to react by both polar and radicaloid mechanisms and to target multiple, pharmacologically important functional classes of enzymes bearing diverse organic and inorganic cofactors. Probe attachment can be blocked by active-site-directed inhibitors, and elaboration of the warhead supports connection of a target to a lead compound. The capacity of substituted hydrazines to profile, discover and inhibit diverse cofactor-dependent enzymes enables cell and tissue imaging and makes this platform useful for enzyme and drug discovery

Computational refinement of post-translational modifications predicted from tandem mass spectrometry

Motivation: A post-translational modification (PTM) is a chemical modification of a protein that occurs naturally. Many of these modifications, such as phosphorylation, are known to play pivotal roles in the regulation of protein function. Henceforth, PTM perturbations have been linked to diverse diseases like Parkinson's, Alzheimer's, diabetes and cancer. To discover PTMs on a genome-wide scale, there is a recent surge of interest in analyzing tandem mass spectrometry data, and several unrestrictive (so-called ‘blind’) PTM search methods have been reported. However, these approaches are subject to noise in mass measurements and in the predicted modification site (amino acid position) within peptides, which can result in false PTM assignments

On-board, time-resolved diesel particulate measurements by laser-induced incandescence

NRC publication: Ye

Power and limitations of electrophoretic separations in proteomics strategies

Proteomics can be defined as the large-scale analysis of proteins. Due to the complexity of biological systems, it is required to concatenate various separation techniques prior to mass spectrometry. These techniques, dealing with proteins or peptides, can rely on chromatography or electrophoresis. In this review, the electrophoretic techniques are under scrutiny. Their principles are recalled, and their applications for peptide and protein separations are presented and critically discussed. In addition, the features that are specific to gel electrophoresis and that interplay with mass spectrometry (i.e., protein detection after electrophoresis, and the process leading from a gel piece to a solution of peptides) are also discussed