The aspartic proteinase family of three Phytophthora species

Background - Phytophthora species are oomycete plant pathogens with such major social and economic impact that genome sequences have been determined for Phytophthora infestans, P. sojae and P. ramorum. Pepsin-like aspartic proteinases (APs) are produced in a wide variety of species (from bacteria to humans) and contain conserved motifs and landmark residues. APs fulfil critical roles in infectious organisms and their host cells. Annotation of Phytophthora APs would provide invaluable information for studies into their roles in the physiology of Phytophthora species and interactions with their hosts. Results - Genomes of Phytophthora infestans, P. sojae and P. ramorum contain 11-12 genes encoding APs. Nine of the original gene models in the P. infestans database and several in P. sojae and P. ramorum (three and four, respectively) were erroneous. Gene models were corrected on the basis of EST data, consistent positioning of introns between orthologues and conservation of hallmark motifs. Phylogenetic analysis resolved the Phytophthora APs into 5 clades. Of the 12 sub-families, several contained an unconventional architecture, as they either lacked a signal peptide or a propart region. Remarkably, almost all APs are predicted to be membrane-bound. Conclusions - One of the twelve Phytophthora APs is an unprecedented fusion protein with a putative G-protein coupled receptor as the C-terminal partner. The others appear to be related to well-documented enzymes from other species, including a vacuolar enzyme that is encoded in every fungal genome sequenced to date. Unexpectedly, however, the oomycetes were found to have both active and probably-inactive forms of an AP similar to vertebrate BACE, the enzyme responsible for initiating the processing cascade that generates the Aß peptide central to Alzheimer's Disease. The oomycetes also encode enzymes similar to plasmepsin V, a membrane-bound AP that cleaves effector proteins of the malaria parasite Plasmodium falciparum during their translocation into the host red blood cell. Since the translocation of Phytophthora effector proteins is currently a topic of intense research activity, the identification in Phytophthora of potential functional homologues of plasmepsin V would appear worthy of investigation. Indeed, elucidation of the physiological roles of the APs identified here offers areas for future study. The significant revision of gene models and detailed annotation presented here should significantly facilitate experimental design

Coarse-graining polymers as soft colloids

We show how to coarse grain polymers in a good solvent as single particles, interacting with density-independent or density-dependent interactions. These interactions can be between the centres of mass, the mid-points or end-points of the polymers. We also show how to extend these methods to polymers in poor solvents and mixtures of polymers. Treating polymers as soft colloids can greatly speed up the simulation of complex many-polymer systems, including polymer-colloid mixtures.Comment: to appear in Physica A, special STATPHYS 2001 edition. Content of invited talk by AA

Density profiles and surface tensions of polymers near colloidal surfaces

The surface tension of interacting polymers in a good solvent is calculated theoretically and by computer simulations for a planar wall geometry and for the insertion of a single colloidal hard-sphere. This is achieved for the planar wall and for the larger spheres by an adsorption method, and for smaller spheres by a direct insertion technique. Results for the dilute and semi-dilute regimes are compared to results for ideal polymers, the Asakura-Oosawa penetrable-sphere model, and to integral equations, scaling and renormalization group theories. The largest relative changes with density are found in the dilute regime, so that theories based on non-interacting polymers rapidly break down. A recently developed ``soft colloid'' approach to polymer-colloid mixtures is shown to correctly describe the one-body insertion free-energy and the related surface tension

Accurate effective pair potentials for polymer solutions

Dilute or semi-dilute solutions of non-intersecting self-avoiding walk (SAW) polymer chains are mapped onto a fluid of ``soft'' particles interacting via an effective pair potential between their centers of mass. This mapping is achieved by inverting the pair distribution function of the centers of mass of the original polymer chains, using integral equation techniques from the theory of simple fluids. The resulting effective pair potential is finite at all distances, has a range of the order of the radius of gyration, and turns out to be only moderately concentration-dependent. The dependence of the effective potential on polymer length is analyzed in an effort to extract the scaling limit. The effective potential is used to derive the osmotic equation of state, which is compared to simulation data for the full SAW segment model, and to the predictions of renormalization group calculations. A similar inversion procedure is used to derive an effective wall-polymer potential from the center of mass density profiles near the wall, obtained from simulations of the full polymer segment model. The resulting wall-polymer potential turns out to depend strongly on bulk polymer concentration when polymer-polymer correlations are taken into account, leading to a considerable enhancement of the effective repulsion with increasing concentration. The effective polymer-polymer and wall-polymer potentials are combined to calculate the depletion interaction induced by SAW polymers between two walls. The calculated depletion interaction agrees well with the ``exact'' results from much more computer-intensive direct simulation of the full polymer-segment model, and clearly illustrates the inadequacy -- in the semi-dilute regime -- of the standard Asakura-Oosawa approximation based on the assumption of non-interacting polymer coils.Comment: 18 pages, 24 figures, ReVTeX, submitted to J. Chem. Phy

Stable isotope quality assurance using the 'Calibrated IRMS' strategy

Procedures in our laboratory have always been directed towards complete understanding of all processes involved and corrections needed etc., instead of relying fully on laboratory reference materials. This rather principal strategy (or attitude) is probably not optimal in the economic sense, and is not necessarily more accurate either. Still, it has proven to be very rewarding in its capability to detect caveats that go undiscovered in the standard way of measurement, but that do influence the accuracy or reliability of the measurement procedure. An additional benefit of our laboratory procedures is that it makes us capable of assisting the International Atomic Energy Agency (IAEA) with primary questions like mutual scale assignments and comparison of isotope ratios of the same isotope in different matrices (like delta(18)O in water, carbonates and atmospheric CO(2)), establishment of the (17)O-(18)O relation, and the replenishment of the calibration standards. Finally, for manual preparation systems with a low sample throughput ( and thus only few reference materials analysed) it may well be the only way to produce reliable results

Probing molecular dynamics at the nanoscale via an individual paramagnetic center

Understanding the dynamics of molecules adsorbed to surfaces or confined to small volumes is a matter of increasing scientific and technological importance. Here, we demonstrate a pulse protocol using individual paramagnetic nitrogen vacancy (NV) centers in diamond to observe the time evolution of 1H spins from organic molecules located a few nanometers from the diamond surface. The protocol records temporal correlations among the interacting 1H spins, and thus is sensitive to the local system dynamics via its impact on the nuclear spin relaxation and interaction with the NV. We are able to gather information on the nanoscale rotational and translational diffusion dynamics by carefully analyzing the time dependence of the NMR signal. Applying this technique to various liquid and solid samples, we find evidence that liquid samples form a semi-solid layer of 1.5 nm thickness on the surface of diamond, where translational diffusion is suppressed while rotational diffusion remains present. Extensions of the present technique could be adapted to highlight the chemical composition of molecules tethered to the diamond surface or to investigate thermally or chemically activated dynamical processes such as molecular folding

Magnetic imaging with an ensemble of Nitrogen Vacancy centers in diamond

The nitrogen-vacancy (NV) color center in diamond is an atom-like system in the solid-state which specific spin properties can be efficiently used as a sensitive magnetic sensor. An external magnetic field induces Zeeman shifts of the NV center levels which can be measured using Optically Detected Magnetic Resonance (ODMR). In this work, we exploit the ODMR signal of an ensemble of NV centers in order to quantitatively map the vectorial structure of a magnetic field produced by a sample close to the surface of a CVD diamond hosting a thin layer of NV centers. The reconstruction of the magnetic field is based on a maximum-likelihood technique which exploits the response of the four intrinsic orientations of the NV center inside the diamond lattice. The sensitivity associated to a 1 {\mu}m^2 area of the doped layer, equivalent to a sensor consisting of approximately 10^4 NV centers, is of the order of 2 {\mu}T/sqrt{Hz}. The spatial resolution of the imaging device is 400 nm, limited by the numerical aperture of the optical microscope which is used to collect the photoluminescence of the NV layer. The versatility of the sensor is illustrated by the accurate reconstruction of the magnetic field created by a DC current inside a copper wire deposited on the diamond sample.Comment: 11 pages, 5 figures, figure 4 added, results unchange

Competition between Spin-Orbit Interaction and Zeeman Coupling in Rashba 2DEGs

We investigate systematically how the interplay between Rashba spin-orbit interaction and Zeeman coupling affects the electron transport and the spin dynamics in InGaAs-based 2D electron gases. From the quantitative analysis of the magnetoconductance, measured in the presence of an in-plane magnetic field, we conclude that this interplay results in a spin-induced breaking of time reversal symmetry and in an enhancement of the spin relaxation time. Both effects, due to a partial alignment of the electron spin along the applied magnetic field, are found to be in excellent agreement with recent theoretical predictions.Comment: 4 figures and 4 page