Evidence for an ancient whole genome duplication in the cycad lineage

Contrary to the many whole genome duplication events recorded for angiosperms (flowering plants), whole genome duplications in gymnosperms (non-flowering seed plants) seem to be much rarer. Although ancient whole genome duplications have been reported for most gymnosperm lineages as well, some are still contested and need to be confirmed. For instance, data for ginkgo, but particularly cycads have remained inconclusive so far, likely due to the quality of the data available and flaws in the analysis. We extracted and sequenced RNA from both the cycad Encephalartos natalensis and Ginkgo biloba. This was followed by transcriptome assembly, after which these data were used to build paralog age distributions. Based on these distributions, we identified remnants of an ancient whole genome duplication in both cycads and ginkgo. The most parsimonious explanation would be that this whole genome duplication event was shared between both species and had occurred prior to their divergence, about 300 million years ago

Non-ideal artificial phase discontinuity in long Josephson 0-kappa-junctions

We investigate the creation of an arbitrary $\kappa$-discontinuity of the Josephson phase in a long Nb-AlO_x-Nb Josephson junction (LJJ) using a pair of tiny current injectors, and study the formation of fractional vortices formed at this discontinuity. The current I_inj, flowing from one injector to the other, creates a phase discontinuity kappa ~ I_inj. The calibration of injectors is discussed in detail. The small but finite size of injectors leads to some deviations of the properties of such a 0-kappa-LJJ from the properties of a LJJ with an ideal kappa-discontinuity. These experimentally observed deviations in the dependence of the critical current on I_inj$ and magnetic field can be well reproduced by numerical simulation assuming a finite injector size. The physical origin of these deviations is discussed.Comment: Submitted to Phys. Rev. B (12 figures). v 2: refs updated, long eqs fixed v 3: major changes, fractional vortex dynamics exclude

Dynamics of semifluxons in Nb long Josephson 0-pi junctions

We propose, implement and test experimentally long Josephson 0-pi junctions fabricated using conventional Nb-AlOx-Nb technology. We show that using a pair of current injectors, one can create an arbitrary discontinuity of the Josephson phase and in particular a pi-discontinuity, just like in d-wave/s-wave or in d-wave/d-wave junctions, and study fractional Josephson vortices which spontaneously appear. Moreover, using such junctions, we can investigate the \emph{dynamics} of the fractional vortices -- a domain which is not yet available for natural 0-pi-junctions due to their inherently high damping. We observe half-integer zero-field steps which appear on the current-voltage characteristics due to hopping of semifluxons.Comment: Fractional vortices in conventional superconductors ;-

A molecular insight into algal-oomycete warfare: cDNA analysis of <i>Ectocarpus siliculosus</i> infected with the basal oomycete <i>Eurychasma dicksonii</i>

Brown algae are the predominant primary producers in coastal habitats, and like land plants are subject to disease and parasitism. Eurychasma dicksonii is an abundant, and probably cosmopolitan, obligate biotrophic oomycete pathogen of marine brown algae. Oomycetes (or water moulds) are pathogenic or saprophytic non-photosynthetic Stramenopiles, mostly known for causing devastating agricultural and aquacultural diseases. Whilst molecular knowledge is restricted to crop pathogens, pathogenic oomycetes actually infect hosts from most eukaryotic lineages. Molecular evidence indicates that Eu. dicksonii belongs to the most early-branching oomycete clade known so far. Therefore Eu. dicksonii is of considerable interest due to its presumed environmental impact and phylogenetic position. Here we report the first large scale functional molecular data acquired on the most basal oomycete to date. 9873 unigenes, totalling over 3.5Mb of sequence data, were produced from Sanger-sequenced and pyrosequenced EST libraries of infected Ectocarpus siliculosus. 6787 unigenes (70%) were of algal origin, and 3086 (30%) oomycete origin. 57% of Eu. dicksonii sequences had no similarity to published sequence data, indicating that this dataset is largely unique. We were unable to positively identify sequences belonging to the RXLR and CRN groups of oomycete effectors identified in higher oomycetes, however we uncovered other unique pathogenicity factors. These included putative algal cell wall degrading enzymes, cell surface proteins, and cyclophilin-like proteins. A first look at the host response to infection has also revealed movement of the host nucleus to the site of infection as well as expression of genes responsible for strengthening the cell wall, and secretion of proteins such as protease inhibitors. We also found evidence of transcriptional reprogramming of E. siliculosus transposable elements and of a viral gene inserted in the host genome

The Older the Better: Infanticide Is Age-Related for Both Victims and Perpetrators in Captive Long-Tailed Macaques

In wild primates, infanticide is a risk that is especially prevalent when a new male takes over the alpha position. Insight into risk factors related to infanticide may decrease the incidence of infanticide in captivity during male introductions. We investigated several risk factors of infanticide derived from hypotheses explaining infanticide in the wild and tested this in captive long-tailed macaques (Macaca fascicularis) using demographic data spanning a 25.5-year period. Factors that are related to infanticide in the wild explained a large proportion, but not all incidences, of infanticide in captivity. Consistent with the wild data, infants young enough to decrease the interbirth interval (<215 days) were at risk of being killed. In contrast to studies from the wild, infanticidal males were more than 2.5 years younger than non-infanticidal males. This indicates that captive settings can lead to new risks since relatively young males may gain the alpha position, promoting infanticide. Therefore, we propose the adolescent male risk hypothesis as a captive risk factor in which subadult males pose a risk of infanticide. In conclusion, the ages of both males and infants are related to infanticide in captivity and have to be taken into account during male introductions

First-Order System Least Squares and the Energetic Variational Approach for Two-Phase Flow

This paper develops a first-order system least-squares (FOSLS) formulation for equations of two-phase flow. The main goal is to show that this discretization, along with numerical techniques such as nested iteration, algebraic multigrid, and adaptive local refinement, can be used to solve these types of complex fluid flow problems. In addition, from an energetic variational approach, it can be shown that an important quantity to preserve in a given simulation is the energy law. We discuss the energy law and inherent structure for two-phase flow using the Allen-Cahn interface model and indicate how it is related to other complex fluid models, such as magnetohydrodynamics. Finally, we show that, using the FOSLS framework, one can still satisfy the appropriate energy law globally while using well-known numerical techniques.Comment: 22 pages, 8 figures submitted to Journal of Computational Physic

On the Divergence-Free Condition in Godunov-Type Schemes for Ideal Magnetohydrodynamics: the Upwind Constrained Transport Method

We present a general framework to design Godunov-type schemes for multidimensional ideal magnetohydrodynamic (MHD) systems, having the divergence-free relation and the related properties of the magnetic field B as built-in conditions. Our approach mostly relies on the 'Constrained Transport' (CT) discretization technique for the magnetic field components, originally developed for the linear induction equation, which assures div(B)=0 and its preservation in time to within machine accuracy in a finite-volume setting. We show that the CT formalism, when fully exploited, can be used as a general guideline to design the reconstruction procedures of the B vector field, to adapt standard upwind procedures for the momentum and energy equations, avoiding the onset of numerical monopoles of O(1) size, and to formulate approximate Riemann solvers for the induction equation. This general framework will be named here 'Upwind Constrained Transport' (UCT). To demonstrate the versatility of our method, we apply it to a variety of schemes, which are finally validated numerically and compared: a novel implementation for the MHD case of the second order Roe-type positive scheme by Liu and Lax (J. Comp. Fluid Dynam. 5, 133, 1996), and both the second and third order versions of a central-type MHD scheme presented by Londrillo and Del Zanna (Astrophys. J. 530, 508, 2000), where the basic UCT strategies have been first outlined

Reducing quantum control for spin-spin entanglement distribution

We present a protocol that sets maximum stationary entanglement between remote spins through scattering of mobile mediators without initialization, post-selection or feedback of the mediators' state. No time-resolved tuning is needed and, counterintuitively, the protocol generates two-qubit singlet states even when classical mediators are used. The mechanism responsible for such effect is resilient against non-optimal coupling strengths and dephasing affecting the spins. The scheme uses itinerant particles and scattering centres and can be implemented in various settings. When quantum dots and photons are used a striking result is found: injection of classical mediators, rather than quantum ones, improves the scheme efficiency.Comment: 7 pages, 5 figures, replaced with published versio

Boomwortels: de verschillende ondergrondse strategieën van bomen

Planten kunnen zich aanpassen aan veranderende omstandigheden. Zo kunnen bomen grotere bladeren maken in de schaduw, of dikkere bij droogte. Hoe en of een boom ook de wortels kan aanpassen, is veel min- der duidelijk. Wij keken daarom in een onderzoek of je bij verschillende boomsoorten en onder verschillende omstandigheden andere wortels aan- treft in de bodem

Phase synchronization in tilted deterministic ratchets

We study phase synchronization for a ratchet system. We consider the deterministic dynamics of a particle in a tilted ratchet potential with an external periodic forcing, in the overdamped case. The ratchet potential has to be tilted in order to obtain a rotator or self-sustained nonlinear oscillator in the absence of external periodic forcing. This oscillator has an intrinsic frequency that can be entrained with the frequency of the external driving. We introduced a linear phase through a set of discrete time events and the associated average frequency, and show that this frequency can be synchronized with the frequency of the external driving. In this way, we can properly characterize the phenomenon of synchronization through Arnold tongues, which represent regions of synchronization in parameter space, and discuss their implications for transport in ratchets.Comment: 14 pages, 6 figures, Physica A, in pres