Analysis of the genetic diversity and structure across a wide range of germplasm reveals prominent gene flow in apple at the European level

Abstract Background: The amount and structure of genetic diversity in dessert apple germplasm conserved at a European level is mostly unknown, since all diversity studies conducted in Europe until now have been performed on regional or national collections. Here, we applied a common set of 16 SSR markers to genotype more than 2,400 accessions across 14 collections representing three broad European geographic regions (North+East, West and South) with the aim to analyze the extent, distribution and structure of variation in the apple genetic resources in Europe. Results: A Bayesian model-based clustering approach showed that diversity was organized in three groups, although these were only moderately differentiated (FST=0.031). A nested Bayesian clustering approach allowed identification of subgroups which revealed internal patterns of substructure within the groups, allowing a finer delineation of the variation into eight subgroups (FST=0.044). The first level of stratification revealed an asymmetric division of the germplasm among the three groups, and a clear association was found with the geographical regions of origin of the cultivars. The substructure revealed clear partitioning of genetic groups among countries, but also interesting associations between subgroups and breeding purposes of recent cultivars or particular usage such as cider production. Additional parentage analyses allowed us to identify both putative parents of more than 40 old and/or local cultivars giving interesting insights in the pedigree of some emblematic cultivars. Conclusions: The variation found at group and sub-group levels may reflect a combination of historical processes of migration/selection and adaptive factors to diverse agricultural environments that, together with genetic drift, have resulted in extensive genetic variation but limited population structure. The European dessert apple germplasm represents an important source of genetic diversity with a strong historical and patrimonial value. The present work thus constitutes a decisive step in the field of conservation genetics. Moreover, the obtained data can be used for defining a European apple core collection useful for further identification of genomic regions associated with commercially important horticultural traits in apple through genome-wide association studies.

VISTA Variables in the Via Lactea (VVV): The public ESO near-IR variability survey of the Milky Way

We describe the public ESO near-IR variability survey (VVV) scanning the Milky Way bulge and an adjacent section of the mid-plane where star formation activity is high. The survey will take 1929 h of observations with the 4-m VISTA telescope during 5 years (2010-2014), covering similar to 10(9) point sources across an area of 520 deg(2), including 33 known globular clusters and similar to 350 open clusters. The final product will be a deep near-IR atlas in five passbands (0.9-2.5 mu m) and a catalogue of more than 106 variable point sources. Unlike single-epoch surveys that, in most cases, only produce 2-D maps, the VVV variable star survey will enable the construction of a 3-D map of the surveyed region using well-understood distance indicators such as RR Lyrae stars, and Cepheids. It will yield important information on the ages of the populations. The observations will be combined with data from MACHO, OGLE, EROS, VST, Spitzer, HST, Chandra, INTEGRAL, WISE, Fermi LAT, XMM-Newton, GAIA and ALMA for a complete understanding of the variable sources in the inner Milky Way. This public survey will provide data available to the whole community and therefore will enable further studies of the history of the Milky Way, its globular cluster evolution, and the population census of the Galactic Bulge and center, as well as the investigations of the star forming regions in the disk. The combined variable star catalogues will have important implications for theoretical investigations of pulsation properties of stars. (C) 2009 Elsevier B.V. All rights reserved.

The role of carbohydrates in seed germination and seedling establishment of Himatanthus sucuuba, an Amazonian tree with populations adapted to flooded and non-flooded conditions

Background and Aims In the Amazonian floodplains plants withstand annual periods of flooding which can last 7 months. Under these conditions seedlings remain submerged in the dark for long periods since light penetration in the water is limited. Himatanthus sucuuba is a tree species found in the `varzea` (VZ) floodplains and adjacent non-flooded `terra-firme` (TF) forests. Biochemical traits which enhance flood tolerance and colonization success of H. sucuuba in periodically flooded environments were investigated. Methods Storage carbohydrates of seeds of VZ and TF populations were extracted and analysed by HPAEC/PAD. Starch was analysed by enzyme (glucoamylase) degradation followed by quantification of glucose oxidase. Carbohydrate composition of roots of VZ and TF seedlings was studied after experimental exposure to a 15-d period of submersion in light versus darkness. Key Results The endosperm contains a large proportion of the seed reserves, raffinose being the main nonstructural carbohydrate. Around 93% of the cell wall storage polysaccharides (percentage dry weight basis) in the endosperm of VZ seeds was composed of mannose, while soluble sugars accounted for 2.5%. In contrast, 74% of the endosperm in TF seeds was composed of galactomannans, while 22% of the endosperm was soluble sugars. This suggested a larger carbohydrate allocation to germination in TF populations whereas VZ populations allocate comparatively more to carbohydrates mobilized during seedling development. The concentration of root non-structural carbohydrates in non-flooded seedlings strongly decreased after a 15-d period of darkness, whereas flooded seedlings were less affected. These effects were more pronounced in TF seedlings, which showed significantly lower root non-structural carbohydrate concentrations. Conclusions There seem to be metabolic adjustments in VZ but not TF seedlings that lead to adaptation to the combined stresses of darkness and flooding. This seems to be important for the survival of the species in these contrasting environments, leading these populations to different directions during evolution.

A DNA Vaccine Encoding the Enterohemorragic Escherichia coli Shiga-Like Toxin 2 A(2) and B Subunits Confers Protective Immunity to Shiga Toxin Challenge in the Murine Model

Production of verocytotoxin or Shiga-like toxin (Stx), particularly Stx2, is the basis of hemolytic uremic syndrome, a frequently lethal outcome for subjects infected with Stx2-producing enterohemorrhagic Escherichia coli (EHEC) strains. The toxin is formed by a single A subunit, which promotes protein synthesis inhibition in eukaryotic cells, and five B subunits, which bind to globotriaosylceramide at the surface of host cells. Host enzymes cleave the A subunit into the A(1) peptide, endowed with N-glycosidase activity to the 28S rRNA, and the A(2) peptide, which confers stability to the B pentamer. We report the construction of a DNA vaccine (pStx2 Delta AB) that expresses a nontoxic Stx2 mutated form consisting of the last 32 amino acids of the A(2) sequence and the complete B subunit as two nonfused polypeptides. Immunization trials carried out with the DNA vaccine in BALB/c mice, alone or in combination with another DNA vaccine encoding granulocyte-macrophage colony-stimulating factor, resulted in systemic Stx-specific antibody responses targeting both A and B subunits of the native Stx2. Moreover, anti-Stx2 antibodies raised in mice immunized with pStx2 Delta AB showed toxin neutralization activity in vitro and, more importantly, conferred partial protection to Stx2 challenge in vivo. The present vector represents the second DNA vaccine so far reported to induce protective immunity to Stx2 and may contribute, either alone or in combination with other procedures, to the development of prophylactic or therapeutic interventions aiming to ameliorate EHEC infection-associated sequelae.

Comparative genomics of the neglected human malaria parasite Plasmodium vivax

The human malaria parasite Plasmodium vivax is responsible for 25 - 40% of the similar to 515 million annual cases of malaria worldwide. Although seldom fatal, the parasite elicits severe and incapacitating clinical symptoms and often causes relapses months after a primary infection has cleared. Despite its importance as a major human pathogen, P. vivax is little studied because it cannot be propagated continuously in the laboratory except in non- human primates. We sequenced the genome of P. vivax to shed light on its distinctive biological features, and as a means to drive development of new drugs and vaccines. Here we describe the synteny and isochore structure of P. vivax chromosomes, and show that the parasite resembles other malaria parasites in gene content and metabolic potential, but possesses novel gene families and potential alternative invasion pathways not recognized previously. Completion of the P. vivax genome provides the scientific community with a valuable resource that can be used to advance investigation into this neglected species.

Estimating the number of ozone peaks in Mexico City using a non-homogeneous Poisson model

In this paper, we consider the problem of estimating the number of times an air quality standard is exceeded in a given period of time. A non-homogeneous Poisson model is proposed to analyse this issue. The rate at which the Poisson events occur is given by a rate function lambda(t), t >= 0. This rate function also depends on some parameters that need to be estimated. Two forms of lambda(t), t >= 0 are considered. One of them is of the Weibull form and the other is of the exponentiated-Weibull form. The parameters estimation is made using a Bayesian formulation based on the Gibbs sampling algorithm. The assignation of the prior distributions for the parameters is made in two stages. In the first stage, non-informative prior distributions are considered. Using the information provided by the first stage, more informative prior distributions are used in the second one. The theoretical development is applied to data provided by the monitoring network of Mexico City. The rate function that best fit the data varies according to the region of the city and/or threshold that is considered. In some cases the best fit is the Weibull form and in other cases the best option is the exponentiated-Weibull. Copyright (C) 2007 John Wiley & Sons, Ltd.

Laurdan Spectrum Decomposition as a Tool for the Analysis of Surface Bilayer Structure and Polarity: a Study with DMPG, Peptides and Cholesterol

The highly hydrophobic fluorophore Laurdan (6-dodecanoyl-2-(dimethylaminonaphthalene)) has been widely used as a fluorescent probe to monitor lipid membranes. Actually, it monitors the structure and polarity of the bilayer surface, where its fluorescent moiety is supposed to reside. The present paper discusses the high sensitivity of Laurdan fluorescence through the decomposition of its emission spectrum into two Gaussian bands, which correspond to emissions from two different excited states, one more solvent relaxed than the other. It will be shown that the analysis of the area fraction of each band is more sensitive to bilayer structural changes than the largely used parameter called Generalized Polarization, possibly because the latter does not completely separate the fluorescence emission from the two different excited states of Laurdan. Moreover, it will be shown that this decomposition should be done with the spectrum as a function of energy, and not wavelength. Due to the presence of the two emission bands in Laurdan spectrum, fluorescence anisotropy should be measured around 480 nm, to be able to monitor the fluorescence emission from one excited state only, the solvent relaxed state. Laurdan will be used to monitor the complex structure of the anionic phospholipid DMPG (dimyristoyl phosphatidylglycerol) at different ionic strengths, and the alterations caused on gel and fluid membranes due to the interaction of cationic peptides and cholesterol. Analyzing both the emission spectrum decomposition and anisotropy it was possible to distinguish between effects on the packing and on the hydration of the lipid membrane surface. It could be clearly detected that a more potent analog of the melanotropic hormone alpha-MSH (Ac-Ser(1)-Tyr(2)-Ser(3)-Met(4)-Glu(5)-His(6)-Phe(7)-Arg(8)-Trp(9)-Gly(10)-Lys(11)-Pro(12)-Val(13)-NH(2)) was more effective in rigidifying the bilayer surface of fluid membranes than the hormone, though the hormone significantly decreases the bilayer surface hydration.

X-ray spectrometry: a powerful tool for the measurement of complete fusion of weakly bound nuclei

We describe how the method of detection of delayed K x-rays produced by the electron capture decay of the residual nuclei can be a powerful tool in the investigation of the effect of the breakup process on the complete fusion (CF) cross-section of weakly bound nuclei at energies close to the Coulomb barrier. This is presently one of the most interesting subjects under investigation in the field of low-energy nuclear reactions, and the difficult experimental task of separating CF from the incomplete fusion (ICF) of one of the breakup fragments can be achieved by the x-ray spectrometry method. We present results for the fusion of the (9)Be + (144)Sm system. Copyright (c) 2008 John Wiley & Sons, Ltd.

Fermion perturbations in string theory black holes

In this paper we study fermion perturbations in four-dimensional black holes of string theory, obtained either from a non-extreme configuration of three intersecting five-branes with a boost along the common string or from a non-extreme intersecting system of two two-branes and two five-branes. The Dirac equation for the massless neutrino field, after conformal re-scaling of the metric, is written as a wave equation suitable to study the time evolution of the perturbation. We perform a numerical integration of the evolution equation, and with the aid of Prony fitting of the time-domain profile, we calculate the complex frequencies that dominate the quasinormal ringing stage, and also determine these quantities by the semi-analytical sixth-order WKB method. We also find numerically the decay factor of fermion fields at very late times, and show that the falloff is identical to those showing for massless fields in other four-dimensional black hole spacetimes.

Quasinormal modes of semiclassical electrically charged black holes

We report the results concerning the influence of vacuum polarization due to quantum massive vector, scalar and spinor fields on the scalar sector of quasinormal modes in spherically symmetric charged black holes. The vacuum polarization from quantized fields produces a shift in the values of the quasinormal frequencies, and correspondingly the semiclassical system becomes a better oscillator with respect to the classical Reissner-Nordstrom black hole.

VACUUM POLARIZATION EFFECTS ON QUASINORMAL MODES IN ELECTRICALLY CHARGED BLACK HOLE SPACE-TIMES

We investigate the influence of vacuum polarization of quantum massive fields on the scalar sector of quasinormal modes in spherically symmetric black holes. We consider the evolution of a massless scalar field on the space-time corresponding to a charged semiclassical black hole, consisting of the quantum-corrected geometry of a Reissner-Nordstrom black hole dressed by a quantum massive scalar field in the large mass limit. Using a sixth order WKB approach we find a shift in the quasinormal mode frequencies due to vacuum polarization.

Goethite (alpha-FeOOH) Nanorods as Suitable Antiferromagnetic Substrates

We propose goethite nanorods as suitable anti-ferromagnetic substrates. The great advantage of using these inorganic nanostructures as building blocks comes from the fact that it permits the design and fabrication of colloidal and supracolloidal assemblies knowing first their magnetic characteristics. As a proof of concept, we have developed mix multifunctional systems, driving on the surface of these AFM substrates, cobalt ferrite nanoparticles (the study of bimagnetic systems opens new degrees of freedom to tailor the overall properties and offers the Meiklejohn-Bean paradigm, but inverted), a silica shell (protection purposes, but also as a tailored spacer that permits controlling magnetic interactions), and metallic gold clusters (seeds that can favor the acquisition of optical or catalytic properties).

Columnar joints in the Patino Formation sandstones, Eastern Paraguay: a dynamic interaction between dyke intrusion, quartz dissolution and cooling-induced fractures

The Patino Formation sandstones, which crop out in Aregua neighborhood in Eastern Paraguay and show columnar joints near the contact zone with a nephelinite dyke, have as their main characteristics the high proportion of syntaxial quartz overgrowth and a porosity originated from different processes, initially by dissolution and later by partial filling and fracturing. Features like the presence of floating grains in the syntaxial cement, the transitional interpenetrative contact between the silica-rich cement and grains as well as the intense fracture porosity are strong indications that the cement has been formed by dissolution and reprecipitation of quartz from the framework under the effect of thermal expansion followed by rapid contraction. The increase of the silica-rich cement towards the dyke in association with the orthogonal disposition of the columns relative to dyke walls are indicative that the igneous body may represent the main heat source for the interstitial aqueous solutions previously existing in the sediments. At macroscopic scale, the increasing of internal tensions in the sandstones is responsible for the nucleation of polygons, leading to the individualization of prisms, which are interconnected by a system of joints, formed firstly on isotherm surfaces of low temperature and later on successive adjacent planes towards the dyke heat source.

Density-Profile Processes Describing Biological Signaling Networks: Almost Sure Convergence to Deterministic Trajectories

We introduce jump processes in R(k), called density-profile processes, to model biological signaling networks. Our modeling setup describes the macroscopic evolution of a finite-size spin-flip model with k types of spins with arbitrary number of internal states interacting through a non-reversible stochastic dynamics. We are mostly interested on the multi-dimensional empirical-magnetization vector in the thermodynamic limit, and prove that, within arbitrary finite time-intervals, its path converges almost surely to a deterministic trajectory determined by a first-order (non-linear) differential equation with explicit bounds on the distance between the stochastic and deterministic trajectories. As parameters of the spin-flip dynamics change, the associated dynamical system may go through bifurcations, associated to phase transitions in the statistical mechanical setting. We present a simple example of spin-flip stochastic model, associated to a synthetic biology model known as repressilator, which leads to a dynamical system with Hopf and pitchfork bifurcations. Depending on the parameter values, the magnetization random path can either converge to a unique stable fixed point, converge to one of a pair of stable fixed points, or asymptotically evolve close to a deterministic orbit in Rk. We also discuss a simple signaling pathway related to cancer research, called p53 module.

On the Hamilton-Jacobi equation in the framework of generalized functions

In this work we study, in the framework of Colombeau`s generalized functions, the Hamilton-Jacobi equation with a given initial condition. We have obtained theorems on existence of solutions and in some cases uniqueness. Our technique is adapted from the classical method of characteristics with a wide use of generalized functions. We were led also to obtain some general results on invertibility and also on ordinary differential equations of such generalized functions. (C) 2011 Elsevier Inc. All rights reserved.