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

Effects of electrostatic screening on the conformation of single DNA molecules confined in a nanochannel

Single T4-DNA molecules were confined in rectangular-shaped channels with a depth of 300 nm and a width in the range 150-300 nm casted in a poly(dimethylsiloxane) nanofluidic chip. The extensions of the DNA molecules were measured with fluorescence microscopy as a function of the ionic strength and composition of the buffer as well as the DNA intercalation level by the YOYO-1 dye. The data were interpreted with scaling theory for a wormlike polymer in good solvent, including the effects of confinement, charge, and self-avoidance. It was found that the elongation of the DNA molecules with decreasing ionic strength can be interpreted in terms of an increase of the persistence length. Self-avoidance effects on the extension are moderate, due to the small correlation length imposed by the channel cross-sectional diameter. Intercalation of the dye results in an increase of the DNA contour length and a partial neutralization of the DNA charge, but besides effects of electrostatic origin it has no significant effect on the bare bending rigidity. In the presence of divalent cations, the DNA molecules were observed to contract, but they do not collapse into a condensed structure. It is proposed that this contraction results from a divalent counterion mediated attractive force between the segments of the DNA molecule.Comment: 38 pages, 10 figures, accepted for publication in The Journal of Chemical Physic

From a vortex gas to a vortex crystal in instability-driven two-dimensional turbulence

We study structure formation in two-dimensional turbulence driven by an external force, interpolating between linear instability forcing and random stirring, subject to nonlinear damping. Using extensive direct numerical simulations, we uncover a rich parameter space featuring four distinct branches of stationary solutions: large-scale vortices, hybrid states with embedded shielded vortices (SVs) of either sign, and two states composed of many similar SVs. Of the latter, the first is a dense vortex gas where all SVs have the same sign and diffuse across the domain. The second is a hexagonal vortex crystal forming from this gas when the instability is sufficiently weak. These solutions coexist stably over a wide parameter range. The late-time evolution of the system from small-amplitude initial conditions is nearly self-similar, involving three phases: initial inverse cascade, random nucleation of SVs from turbulence and, once a critical number of vortices is reached, a phase of explosive nucleation of SVs, leading to a statistically stationary state. The vortex gas is continued in the forcing parameter, revealing a sharp transition towards the crystal state as the forcing strength decreases. This transition is analysed in terms of the diffusion of individual vortices and tools from statistical physics. The crystal can also decay via an inverse cascade resulting from the breakdown of shielding or insufficient nonlinear damping acting on SVs. Our study highlights the importance of the forcing details in two-dimensional turbulence and reveals the presence of nontrivial SV states in this system, specifically the emergence and melting of a vortex crystal

The thermal equation of state of FeTiO_3 ilmenite based on in situ X-ray diffraction at high pressures and temperatures

We present in situ measurements of the unit-cell volume of a natural terrestrial ilmenite (Jagersfontein mine, South Africa) and a synthetic reduced ilmenite (FeTiO_3) at simultaneous high pressure and high temperature up to 16 GPa and 1273 K. Unit-cell volumes were determined using energy-dispersive synchrotron X-ray diffraction in a multi-anvil press. Mössbauer analyses show that the synthetic sample contained insignificant amounts of Fe^(3+) both before and after the experiment. Results were fit to Birch-Murnaghan thermal equations of state, which reproduce the experimental data to within 0.5 and 0.7 GPa for the synthetic and natural samples, respectively. At ambient conditions, the unit-cell volume of the natural sample [V_0 = 314.75 ± 0.23 (1 ) Å^3] is significantly smaller than that of the synthetic sample [V_0 = 319.12 ± 0.26 Å^3]. The difference can be attributed to the presence of impurities and Fe^(3+) in the natural sample. The 1 bar isothermal bulk moduli K_(T0) for the reduced ilmenite is slightly larger than for the natural ilmenite (181 ± 7 and 165 ± 6 GPa, respectively), with pressure derivatives K_0' = 3 ± 1. Our results, combined with literature data, suggest that the unit-cell volume of reduced ilmenite is significantly larger than that of oxidized ilmenite, whereas their thermoelastic parameters are similar. Our data provide more appropriate input parameters for thermo-chemical models of lunar interior evolution, in which reduced ilmenite plays a critical role

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 Aβ 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.Fil: Kay, John. Cardiff University; Reino UnidoFil: Meijer, Harold J. G.. Wageningen University; Reino UnidoFil: Ten Have, Arjen. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Mar del Plata. Instituto de Investigaciones Biológicas; Argentina. Universidad Nacional de Mar del Plata. Facultad de Ciencias Exactas y Naturales; ArgentinaFil: van Kan, Jan A. L.. Wageningen University; Reino Unid

Effect of H-NS on the elongation and compaction of single DNA molecules in a nanospace

10.1039/c3sm51214bSoft Matter9409593-960

Sensitivity Analysis of List Scheduling Heuristics

When jobs have to be processed on a set of identical parallel machines so as to minimize the makespan of the schedule, list scheduling rules form a popular class of heuristics. The order in which jobs appear on the list is assumed here to be determined by the relative size of their processing times; well known special cases are the LPT rule and the SPT rule, in which the jobs are ordered according to non-increasing and non-decreasing processing time respectively. When one of the job processing times is gradually increased, the schedule produced by a list scheduling rule will be affected in a manner reflecting its sensitivity to data perturbations. We analyze this phenomenon and obtain analytical support for the intuitively plausible notion that the sensitivity of a list scheduling rule increases with the quality of the schedule produced

The Radial Orbit Instability in Collisionless N-Body Simulations

Using a suite of self-gravitating, collisionless N-body models, we systematically explore a parameter space relevant to the onset and behavior of the radial orbit instability (ROI), whose strength is measured by the systemic axis ratios of the models. We show that a combination of two initial conditions, namely the velocity anisotropy and the virial ratio, determines whether a system will undergo ROI and exactly how triaxial the system will become. A third initial condition, the radial shape of the density profile, plays a smaller, but noticeable role. Regarding the dynamical development of the ROI, the instability a) begins after systems collapse to their most compact configuration and b) evolves fastest when a majority of the particles have radially anisotropic orbits while there is a lack of centrally-concentrated isotropic orbits. We argue that this is further evidence that self-reinforcing torques are the key to the onset of the ROI. Our findings support the idea that a separate orbit instability plays a role in halting the ROI.Comment: accepted for publication in ApJ. 9 figures in emulateapj styl

Optics-less smart sensors and a possible mechanism of cutaneous vision in nature

Optics-less cutaneous (skin) vision is not rare among living organisms, though its mechanisms and capabilities have not been thoroughly investigated. This paper demonstrates, using methods from statistical parameter estimation theory and numerical simulations, that an array of bare sensors with a natural cosine-law angular sensitivity arranged on a flat or curved surface has the ability to perform imaging tasks without any optics at all. The working principle of this type of optics-less sensor and the model developed here for determining sensor performance may be used to shed light upon possible mechanisms and capabilities of cutaneous vision in nature