Platelet PECAM-1 inhibits thrombus formation in vivo

Platelet endothelial cell adhesion molecule-1 (PECAM-1) is a cell surface glycoprotein receptor expressed on a range of blood cells, including platelets, and on vascular endothelial cells. PECAM-1 possesses adhesive and signaling properties, the latter being mediated by immunoreceptor tyrosine-based inhibitory motifs present on the cytoplasmic tail of the protein. Recent studies in vitro have demonstrated that PECAM-1 signaling inhibits the aggregation of platelets. In the present study we have used PECAM-1-deficient mice and radiation chimeras to investigate the function of this receptor in the regulation of thrombus formation. Using intravital microscopy and laser-induced injury to cremaster muscle arterioles, we show that thrombi formed in PECAM-1-deficient mice were larger, formed more rapidly than in control mice, and were more stable. Larger thrombi were also formed in control mice that received transplants of PECAM-1-deficient bone marrow, in comparison to mice that received control transplants. A ferric chloride model of thrombosis was used to investigate thrombus formation in carotid arteries. In PECAM-1-deficient mice the time to 75% vessel occlusion was significantly shorter than in control mice. These data provide evidence for the involvement of platelet PECAM-1 in the negative regulation of thrombus formation.

Factors required for the uridylylation of the foot-and-mouth disease virus 3B1, 3B2, and 3B3 peptides by the RNA-dependent RNA polymerase (3D(pol)) in vitro

The 5' terminus of picornavirus genomic RNA is covalently linked to the virus-encoded peptide 313 (VTg). Foot-and-mouth disease virus (FMDV) is unique in encoding and using 3 distinct forms of this peptide. These peptides each act as primers for RNA synthesis by the virus-encoded RNA polymerase 3D(pol). To act as the primer for positive-strand RNA synthesis, the 3B peptides have to be uridylylated to form VPgpU(pU). For certain picornaviruses, it has been shown that this reaction is achieved by the 3D(pol) in the presence of the 3CD precursor plus an internal RNA sequence termed a cis-acting replication element (cre). The FMDV ere has been identified previously to be within the 5' untranslated region, whereas all other picornavirus cre structures are within the viral coding region. The requirements for the in vitro uridylylation of each of the FMDV 313 peptides has now been determined, and the role of the FMDV ere (also known as the 3B-uridylylation site, or bus) in this reaction has been analyzed. The poly(A) tail does not act as a significant template for FMDV 3B uridylylation.

The poliovirus 2C cis-acting replication element-mediated uridylylation of VPg is not required for synthesis of negative-sense genomes

Nucleotides in the terminal loop of the poliovirus 2C cis-acting replication element (2C(CRE)), a 61 nt structured RNA, function as the template for the addition of two uridylate (U) residues to the viral protein VPg. This uridylylation reaction leads to the formation of VPgpUpU, which is used by the viral RNA polymerase as a nucleotide-peptide primer for genome replication. Although VPg primes both positive- and negative-strand replication, the specific requirement for 2C(CRE)-mediated uridylylation for one or both events has not been demonstrated. We have used a cell-free in vitro translation and replication reaction to demonstrate that 2C(CRE) is not required for the initiation of the negative-sense strand, which is synthesized in the absence of 2C(CRE)-mediated VPgpUpU formation. We propose that the 3' poly(A) tail could serve as the template for the formation of a VPg-poly(U) primer that functions in the initiation of negative-sense strands.

Synthesis and structure-activity relationship studies of CD4 down-modulating cyclotriazadisulfonamide (CADA) analogues

HIV attachment via the CD4 receptor is an important target for developing novel approaches to HIV chemotherapy. Cyclotriazadisulfonamide (CADA) inhibits HIV at submicromolar levels by specifically down-modulating cell-surface and intracellular CD4. An effective five-step synthesis of CADA in 30% overall yield is reported. This synthesis has also been modified to produce more than 50 analogues. Many tail-group analogues have been made by removing the benzyl tail of CADA and replacing it with various alkyl, acyl, alkoxycarbonyl and aminocarbonyl substituents. A series of sidearm analogues, including two unsymmetrical compounds, have also been prepared by modifying the CADA synthesis, replacing the toluenesulfonyl sidearms with other sulfonyl groups. Testing 30 of these compounds in MT-4 cells shows a wide range of CD4 down-modulation potency, which correlates with ability to inhibit HIV-1. Three-dimensional quantitative structure-activity relationship (3D-QSAR) models were constructed using comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) approaches. The X-ray crystal structures of four compounds, including CADA, show the same major conformation of the central 12-membered ring. The solid-state structure of CADA was energy minimized and used to generate the remaining 29 structures, which were similarly minimized and aligned to produce the 3D-QSAR models. Both models indicate that steric bulk of the tail group, and, to a lesser extent, the sidearms mainly determine CD4 down-modulation potency in this series of compounds.

Dicaesium pentacyanotricuprate(I), Cs2Cu3(CN)(5)

Cs2Cu3(CN)(5) has a layered structure consisting of [Cu-3(CN)(5)](2-) sheets stacked in an ABAB fashion along the c axis, with Cs+ cations lying between the sheets. The sheets are generated by linking -(CuCN) - chains, in which the C N groups are ordered, via [Cu(CN)(3)](2-) units. The two bridging cyanide groups of each [Cu(CN)(3)](2-) unit show partial 'head-to-tail' disorder of C and N, whilst the third C N group is terminal and ordered with C bonded to Cu.

Conformational and self-assembly studies of helix forming hexapeptides containing two alpha-amino isobutyric acids

Single crystal X-ray diffraction studies reveal that three hexapeptides with general formula Boc-Ile-Aib-Xx-Ile-Aib-Yy-OMe, where Xx and Yy are Leu in peptide I, Len and Phe in peptide II, and Phe and Leu in peptide III, respectively, adopt equivalent conformations that can be described as mixed 3(10)/alpha-helice with two 4 -> 1 and two 5 -> 1 intramolecular N-H center dot center dot center dot O=C H-bonds. The peptides do not generate any helixterminating Schellman motif despite having Aib at the penultimate position from C-terminus. In the crystalline state, the helices are packed in head-to-tail fashion through intermolecular hydrogen bonds to create supramolecular helical structures. The CD Studies of the three hexapeptides in acetonitrile indicate that they are folded in well-developed 3(10)-helical structures. NMR studies of peptide I in CDCl3 also suggest the formation of a homogeneous 3 m-helical structure. The field emission scanning electron microscopic (FE-SEM) images of peptide 11 in the solid state reveal a non-twisted ribbon-like morphology, which is formed through lateral association of non-twisted filaments. (c) 2007 Elsevier Ltd. All rights reserved.

Overlapping double turn conformations adopted by tetrapeptides containing non-coded alpha-Amino Isobutyric Acid (AIB) and formation of tape-like structures through supramolecular helix mediated self-assembly

Single crystal X-ray diffraction studies and solvent dependent H-1 NMR titrations reveal that a set of four tetrapeptides with general formula Boc-Xx(1)-Aib(2)-Yy(3)-Zz(4)-OMe, where Xx, Yy and Zz are coded L- amino acids, adopt equivalent conformations that can be described as overlapping double turn conformations stabilized by two 4 -> 1 intramolecular hydrogen bonds between Yy(3)-NH and Boc C=O and Zz(4)-NH and Xx(1)C=O. In the crystalline state, the double turn structures are packed in head-to-tail fashion through intermolecular hydrogen bonds to create supramolecular helical structures. Field emission scanning electron microscopic (FE-SEM) images of the tetrapeptides in the solid state reveal that they can form flat tape-like structures. The results establish that synthetic Aib containing supramolecular helices can form highly ordered self-aggregated amyloid plaque like human amylin.

Interactions of an anionic surfactant with poly(oxyalkylene) copolymers in aqueous solution

The interactions of sodium dodecyl sulfate (SDS) with poly(ethylene oxide)/poly(alkylene oxide) (E/A) block copolymers are explored in this study: With respect to the specific compositional characteristics of the copolymer, introduction of SDS can induce fundamentally different effects to the self-assembly behavior of E/A copolymer solutions. In the case of the E18B10-SDS system (E = poly(ethylene oxide) and B = poly(butylene oxide)) development of large surfactant-polymer aggregates was observed. In the case of B20E610-SDS, B12E227B12-SDS, E40B10E40-SDS, E19P43E19-SDS (P = poly(propylene oxide)), the formation of smaller particles compared to pure polymeric micelles points to micellar suppression induced by the ionic surfactant. This effect can be ascribed to a physical binding between the hydrophobic block of unassociated macromolecules and the non-polar tail of the surfactant. Analysis of critical micelle concentrations (cmc*) of polymer-surfactant aqueous solutions within the framework of regular solution theory for binary surfactants revealed negative deviations from ideal behavior for E40B10E40-SDS and E19P43E19-SDS, but positive deviations for E18B10-SDS. Ultrasonic studies performed for the E19P43E19-SDS system enabled the identification of three distinct regions, corresponding to three main steps of the complexation; SDS absorption to the hydrophobic backbone of polymer, development of polymer-surfactant complexes and gradual breakdown of the mixed aggregates. (C) 2008 Elsevier Inc. All rights reserved.

Influence of environmental stress on distributions of times to first division in Escherichia coli populations, as determined by digital-image analysis of individual cells

The distributions of times to first cell division were determined for populations of Escherichia coli stationary-phase cells inoculated onto agar media. This was accomplished by using automated analysis of digital images of individual cells growing on agar and calculation of the "box area ratio." Using approximately 300 cells per experiment, the mean time to first division and standard deviation for cells grown in liquid medium at 37 degrees C and inoculated on agar and incubated at 20 degrees C were determined as 3.0 h and 0.7 h, respectively. Distributions were observed to tail toward the higher values, but no definitive model distribution was identified. Both preinoculation stress by heating cultures at 50 degrees C and postinoculation stress by growth in the presence of higher concentrations of NaCl increased mean times to first division. Both stresses also resulted in an increase in the spread of the distributions that was proportional to the mean division time, the coefficient of variation being constant at approximately 0.2 in all cases. The "relative division time," which is the time to first division for individual cells expressed in terms of the cell size doubling time, was used as measure of the "work to be done" to prepare for cell division. Relative division times were greater for heat-stressed cells than for those growing under osmotic stress.

New mathematical modeling approach for predicting microbial inactivation by high hydrostatic pressure

A new primary model based on a thermodynamically consistent first-order kinetic approach was constructed to describe non-log-linear inactivation kinetics of pressure-treated bacteria. The model assumes a first-order process in which the specific inactivation rate changes inversely with the square root of time. The model gave reasonable fits to experimental data over six to seven orders of magnitude. It was also tested on 138 published data sets and provided good fits in about 70% of cases in which the shape of the curve followed the typical convex upward form. In the remainder of published examples, curves contained additional shoulder regions or extended tail regions. Curves with shoulders could be accommodated by including an additional time delay parameter and curves with tails shoulders could be accommodated by omitting points in the tail beyond the point at which survival levels remained more or less constant. The model parameters varied regularly with pressure, which may reflect a genuine mechanistic basis for the model. This property also allowed the calculation of (a) parameters analogous to the decimal reduction time D and z, the temperature increase needed to change the D value by a factor of 10, in thermal processing, and hence the processing conditions needed to attain a desired level of inactivation; and (b) the apparent thermodynamic volumes of activation associated with the lethal events. The hypothesis that inactivation rates changed as a function of the square root of time would be consistent with a diffusion-limited process.

Perceptual compensation for effects of echo and of reverberation on speech identification

In an ideal "reverberant" room, the energy of the impulse responses decays smoothly, at a constant rate of dB/s, so that gradually-decaying tails are added at the ends of sounds. Conversely, a single echo gives a flat energy-decay up to the echo's arrival time, which then drops abruptly, so that sounds with only echoes lack the decaying-tail feature of reverberation. The perceptual effects of these types of reflection pattern were measured with test-words from a continuum of steps between "sir" and "stir", which were each embedded in a carrier phrase. When the proportion of reflected sound in test-words is increased, to a level above the amount in the carrier, the test words sound more like "sir". However, when the proportion of reflected sound in the carrier is also increased, to match the amount in the test word, there can be a perceptual compensation where test words sound more like "stir" again. A reference condition used real-room reverberation from recordings at different source to receiver distances. In a synthetic-reverberation condition, the reflection pattern was from a "colorless" impulse response, comprising exponentially-decaying reflections that were spaced at intervals. In a synthetic-echo condition, the reflection pattern was obtained from the synthetic reverberation by removing the intervals between reflections before delaying the resulting cluster relative to the direct sound. Compensation occurred in the reference condition and in different types of synthetic reverberation, but not in synthetic-echo conditions. This result indicates that the presence of tails from reverberation informs the compensation mechanism.

Liquid flow over a substrate structured by seeded nanoparticles

Recent experiments have demonstrated that nanoparticles which sparsely distributed over a solid substrate can substantially change the flow conditions at the solid surface in the presence of slip. Inspired by these observations, the flow past tiny particles seeded on a solid substrate is investigated theoretically in the framework of an interface formation model. It has been shown, that even a single seeded nanoparticle can reduce significantly the measurable tangential component of hydrodynamic velocity at the substrate and affect the amount of the observed apparent slippage of the liquid. The effect from the particle manifests in a form of a long relaxation tail defined by the characteristic time of the interface formation process. A comparison with experiments has demonstrated a good agreement between theoretically predicted and experimentally observed values of the relaxation tail length scale.

Differential recognition of Staphylococcus aureus quorum-sensing signals depends on both extracellular loops 1 and 2 of the transmembrane sensor AgrC.

Virulence in Staphylococcus aureus is regulated via agr-dependent quorum sensing in which an autoinducing peptide (AIP) activates AgrC, a histidine protein kinase. AIPs are usually thiolactones containing seven to nine amino acid residues in which the thiol of the central cysteine is linked to the alpha-carboxyl of the C-terminal amino acid residue. The staphylococcal agr locus has diverged such that the AIPs of the four different S. aureus agr groups self-activate but cross-inhibit. Consequently, although the agr system is conserved among the staphylococci, it has undergone significant evolutionary divergence whereby to retain functionality, any changes in the AIP-encoding gene (agrD) that modifies AIP structure must be accompanied by corresponding changes in the AgrC receptor. Since AIP-1 and AIP-4 only differ by a single amino acid, we compared the transmembrane topology of AgrC1 and AgrC4 to identify amino acid residues involved in AIP recognition. As only two of the three predicted extracellular loops exhibited amino acid differences, site-specific mutagenesis was used to exchange the key AgrC1 and AgrC4 amino acid residues in each loop either singly or in combination. A novel lux-based agrP3 reporter gene fusion was constructed to evaluate the response of the mutated AgrC receptors. The data obtained revealed that while differential recognition of AIP-1 and AIP-4 depends primarily on three amino acid residues in loop 2, loop 1 is essential for receptor activation by the cognate AIP. Furthermore, a single mutation in the AgrC1 loop 2 resulted in conversion of (Ala5)AIP-1 from a potent antagonist to an activator, essentially resulting in the forced evolution of a new AIP group. Taken together, our data indicate that loop 2 constitutes the predicted hydrophobic pocket that binds the AIP thiolactone ring while the exocyclic amino acid tail interacts with loop 1 to facilitate receptor activation.

A comparison of extreme European daily precipitation simulated by a global and a regional climate model for present and future climates

The intensity and distribution of daily precipitation is predicted to change under scenarios of increased greenhouse gases (GHGs). In this paper, we analyse the ability of HadCM2, a general circulation model (GCM), and a high-resolution regional climate model (RCM), both developed at the Met Office's Hadley Centre, to simulate extreme daily precipitation by reference to observations. A detailed analysis of daily precipitation is made at two UK grid boxes, where probabilities of reaching daily thresholds in the GCM and RCM are compared with observations. We find that the RCM generally overpredicts probabilities of extreme daily precipitation but that, when the GCM and RCM simulated values are scaled to have the same mean as the observations, the RCM captures the upper-tail distribution more realistically. To compare regional changes in daily precipitation in the GHG-forced period 2080-2100 in the GCM and the RCM, we develop two methods. The first considers the fractional changes in probability of local daily precipitation reaching or exceeding a fixed 15 mm threshold in the anomaly climate compared with the control. The second method uses the upper one-percentile of the control at each point as the threshold. Agreement between the models is better in both seasons with the latter method, which we suggest may be more useful when considering larger scale spatial changes. On average, the probability of precipitation exceeding the 1% threshold increases by a factor of 2.5 (GCM and RCM) in winter and by I .7 (GCM) or 1.3 (RCM) in summer.

A comparison of extreme value theory approaches for determining value at risk

This paper compares a number of different extreme value models for determining the value at risk (VaR) of three LIFFE futures contracts. A semi-nonparametric approach is also proposed, where the tail events are modeled using the generalised Pareto distribution, and normal market conditions are captured by the empirical distribution function. The value at risk estimates from this approach are compared with those of standard nonparametric extreme value tail estimation approaches, with a small sample bias-corrected extreme value approach, and with those calculated from bootstrapping the unconditional density and bootstrapping from a GARCH(1,1) model. The results indicate that, for a holdout sample, the proposed semi-nonparametric extreme value approach yields superior results to other methods, but the small sample tail index technique is also accurate.