Novel dimeric β-helical model of an ice nucleation protein with bridged active sites

<p>Abstract</p> <p>Background</p> <p>Ice nucleation proteins (INPs) allow water to freeze at high subzero temperatures. Due to their large size (>120 kDa), membrane association, and tendency to aggregate, an experimentally-determined tertiary structure of an INP has yet to be reported. How they function at the molecular level therefore remains unknown.</p> <p>Results</p> <p>Here we have predicted a novel β-helical fold for the INP produced by the bacterium <it>Pseudomonas borealis</it>. The protein uses internal serine and glutamine ladders for stabilization and is predicted to dimerize via the burying of a solvent-exposed tyrosine ladder to make an intimate hydrophobic contact along the dimerization interface. The manner in which <it>Pb</it>INP dimerizes also allows for its multimerization, which could explain the aggregation-dependence of INP activity. Both sides of the <it>Pb</it>INP structure have tandem arrays of amino acids that can organize waters into the ice-like clathrate structures seen on antifreeze proteins.</p> <p>Conclusions</p> <p>Dimerization dramatically increases the 'ice-active' surface area of the protein by doubling its width, increasing its length, and presenting identical ice-forming surfaces on both sides of the protein. We suggest that this allows sufficient anchored clathrate waters to align on the INP surface to nucleate freezing. As <it>Pb</it>INP is highly similar to all known bacterial INPs, we predict its fold and mechanism of action will apply to these other INPs.</p

Spatiotemporal Analysis of Flow-Induced Intermediate Filament Displacement in Living Endothelial Cells

The distribution of hemodynamic shear stress throughout the arterial tree is transduced by the endothelium into local cellular responses that regulate vasoactivity, vessel wall remodeling, and atherogenesis. Although the exact mechanisms of mechanotransduction remain unknown, the endothelial cytoskeleton has been implicated in transmitting extracellular force to cytoplasmic sites of signal generation via connections to the lumenal, intercellular, and basal surfaces. Direct observation of intermediate filament (IF) displacement in cells expressing green fluorescent protein-vimentin has suggested that cytoskeletal mechanics are rapidly altered by the onset of fluid shear stress. Here, restored images from time-lapse optical sectioning fluorescence microscopy were analyzed as a four-dimensional intensity distribution function that represented IF positions. A displacement index, related to the product moment correlation coefficient as a function of time and subcellular spatial location, demonstrated patterns of IF displacement within endothelial cells in a confluent monolayer. Flow onset induced a significant increase in IF displacement above the nucleus compared with that measured near the coverslip surface, and displacement downstream from the nucleus was larger than in upstream areas. Furthermore, coordinated displacement of IF near the edges of adjacent cells suggested the existence of mechanical continuity between cells. Thus, quantitative analysis of the spatiotemporal patterns of flow-induced IF displacement suggests redistribution of intracellular force in response to alterations in hemodynamic shear stress acting at the lumenal surface

Towards reducing the capital cost of manufacturing Laminated Veneer Lumbers: Investigating finger jointing solutions

The capital cost of setting up a Laminated Veneer Lumber (LVL) plant which produces continuous LVL billet products, through a continuous veneer assembly and hot-pressing processes, is significant. However, the utilisation of batch-type presses, similar to those employed in the plywood industry, could significantly reduce this initial cost and may provide new opportunities for small to medium scale operations. This process would produce shorter billet lengths which would need to be joined together to produce lengths viable for structural products. Scarf joints have been used commercially to join some veneer-based engineered wood products but have limitations, while finger joints are a common method for jointing sawn timber products and offer some key advantages but is not a common method to join veneer-based products. Consequently, this paper focusses on investigating the influence of key manufacturing parameters on the performance of finger jointed LVL. The effect of the joint orientation (horizontal or vertical), the finger length, the gluing pressure and the adhesive type on the joint strength and stiffness were investigated. The finger jointed LVL were tested in edge bending, flat bending and tension, and the results were compared to reference unjointed LVL. The bending performance of the finger jointed LVL was also compared to scarfed jointed LVL. In total 304 tests were performed. The results indicated that the average strength values of finger jointed LVL can reach up to 99% of the average strength of unjointed LVL and compares to scarf jointed LVL on flat bending. Horizontal joints, being more practical to produce for deep beams, performed similarly to vertical joints. The 25 mm joints were found to have no mechanical advantages over the 20 mm investigated finger joints. A gluing pressure lower than the Eurocode's recommended level for solid timber achieved sufficient bonding for the products to be utilised. The gluing pressure was also found not to influence the performance of the joint, for the range of pressures investigated. Both polyurethane and resorcinol-formaldehyde adhesives produced high performing products, with the latter displaying superior adhesive bond durability. The paper concludes that finger jointing LVL represents a viable solution to manufacture usable LVL lengths from short LVL billets, but have lower edge bending efficiency than scarf jointed LVL

Probing Spectral Line Gradients Beyond One Effective Radius in NGC 3610

The outer region (0.75--1.25 r_e in the B-band) of the merger-remnant elliptical NGC 3610 is studied using extremely high signal to noise Keck spectra, with a supplementary spectrum of the galaxy center. Stellar population parameters -- age, [Z/H], [$\alpha$/Fe] -- are measured in several apertures along the slit. Using the multi-index simultaneous fitting method of Proctor et al. (2004), no significant stellar population gradients are detected in the outer parts of the galaxy. The overall gradients relative to the galaxy center are consistent with those found in many other early-type galaxies, though the metallicity gradient is much steeper than would be expected if NGC 3610 formed in a major merger event. Standard analysis methods using the H$\beta$ index are found to produce spurious radially variable gradients.Comment: 15 pages, 9 figures, accepted by A

A metal-poor damped Ly-alpha system at redshift 6.4

We identify a strong Ly-alpha damping wing profile in the spectrum of the quasar P183+05 at z=6.4386. Given the detection of several narrow metal absorption lines at z=6.40392, the most likely explanation for the absorption profile is that it is due to a damped Ly-alpha system. However, in order to match the data a contribution of an intergalactic medium 5-38% neutral or additional weaker absorbers near the quasar is also required. The absorption system presented here is the most distant damped Ly-alpha system currently known. We estimate an HI column density ($10^{20.68\pm0.25}\,$cm$^{-2}$), metallicity ([O/H]$=-2.92\pm 0.32$), and relative chemical abundances of a system consistent with a low-mass galaxy during the first Gyr of the universe. This object is among the most metal-poor damped Ly-alpha systems known and, even though it is observed only ~850 Myr after the big bang, its relative abundances do not show signatures of chemical enrichment by Population III stars.Comment: Updated to match published versio

The JSpecView Project: an Open Source Java viewer and converter for JCAMP-DX, and XML spectral data files

The JSpecView Open Source project began with the intention of providing both a teaching and research tool for the display of JCAMP-DX spectra. The development of the Java source code commenced under license in 2001 and was released as Open Source in March 2006. The scope was then broadened to take advantage of the XML initiative in Chemistry and routines to read and write AnIML and CMLspect documents were added

Dynamical description of quantum computing: generic nonlocality of quantum noise

We develop dynamical non-Markovian description of quantum computing in weak coupling limit, in lowest order approximation. We show that long range memory of quantum reservoir produces strong interrelation between structure of noise and quantum algorithm, implying nonlocal attacks of noise. We then argue that the quantum error correction method fails to protect quantum computation against electromagnetic or phonon vacuum which exhibit $1/t^4$ memory. This shows that the implicit assumption of quantum error correction theory -- independence of noise and self-dynamics -- fails in long time regimes. We also use our approach to present {\it pure} decoherence and decoherence accompanied by dissipation in terms of spectral density of reservoir. The so-called {\it dynamical decoupling} method is discussed in this context. Finally, we propose {\it minimal decoherence model}, in which the only source of decoherence is vacuum. We optimize fidelity of quantum information processing under the trade-off between speed of gate and strength of decoherence.Comment: 12 pages, minor corrections, softened interpretation of the result

The peculiar motions of early-type galaxies in two distant regions - II. The spectroscopic data

We present the spectroscopic data for the galaxies studied in the EFAR project, which is designed to measure the properties and peculiar motions of early-type galaxies in two distant regions. We have obtained 1319 spectra of 714 early-type galaxies over 33 observing runs on 10 different telescopes. We describe the observations and data reductions used to measure redshifts, velocity dispersions and the Mgb and Mg2 Lick linestrength indices. Detailed simulations and intercomparison of the large number of repeat observations lead to reliable error estimates for all quantities. The measurements from different observing runs are calibrated to a common zeropoint or scale before being combined, yielding a total of 706 redshifts, 676 velocity dispersions, 676 Mgb linestrengths and 582 Mg2 linestrengths. The median estimated errors in the combined measurements are dcz=20 km/s, dsigma/sigma=9.1%, dMgb/Mgb=7.2% and dMg2=0.015 mag. Comparison of our measurements with published datasets shows no systematic errors in the redshifts or velocity dispersions and only small zeropoint corrections to bring our linestrengths onto the standard Lick system. We have assigned galaxies to physical clusters by examining the line-of-sight velocity distributions based on EFAR and ZCAT redshifts, together with the projected distributions on the sky. We derive mean redshifts and velocity dispersions for these clusters, which will be used in estimating distances and peculiar velocities and to test for trends in the galaxy population with cluster mass. The spectroscopic parameters presented here for 706 galaxies combine high quality data, uniform reduction and measurement procedures, and detailed error analysis. They form the largest single set of velocity dispersions and linestrengths for early-type galaxies published to date.Comment: 27 pages, 18 figures, accepted by MNRA