10,838 research outputs found
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 AĂ 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
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