High-throughput SNP genotyping in the highly heterozygous genome of Eucalyptus: assay success, polymorphism and transferability across species

Background: High-throughput SNP genotyping has become an essential requirement for molecular breeding and population genomics studies in plant species. Large scale SNP developments have been reported for several mainstream crops. A growing interest now exists to expand the speed and resolution of genetic analysis to outbred species with highly heterozygous genomes. When nucleotide diversity is high, a refined diagnosis of the target SNP sequence context is needed to convert queried SNPs into high-quality genotypes using the Golden Gate Genotyping Technology (GGGT). This issue becomes exacerbated when attempting to transfer SNPs across species, a scarcely explored topic in plants, and likely to become significant for population genomics and inter specific breeding applications in less domesticated and less funded plant genera. Results: We have successfully developed the first set of 768 SNPs assayed by the GGGT for the highly heterozygous genome of Eucalyptus from a mixed Sanger/454 database with 1,164,695 ESTs and the preliminary 4.5X draft genome sequence for E. grandis. A systematic assessment of in silico SNP filtering requirements showed that stringent constraints on the SNP surrounding sequences have a significant impact on SNP genotyping performance and polymorphism. SNP assay success was high for the 288 SNPs selected with more rigorous in silico constraints; 93% of them provided high quality genotype calls and 71% of them were polymorphic in a diverse panel of 96 individuals of five different species. SNP reliability was high across nine Eucalyptus species belonging to three sections within subgenus Symphomyrtus and still satisfactory across species of two additional subgenera, although polymorphism declined as phylogenetic distance increased. Conclusions: This study indicates that the GGGT performs well both within and across species of Eucalyptus notwithstanding its nucleotide diversity >= 2%. The development of a much larger array of informative SNPs across multiple Eucalyptus species is feasible, although strongly dependent on having a representative and sufficiently deep collection of sequences from many individuals of each target species. A higher density SNP platform will be instrumental to undertake genome-wide phylogenetic and population genomics studies and to implement molecular breeding by Genomic Selection in Eucalyptus.

Variations on a theme: diversification of cuticular hydrocarbons in a clade of cactophilic Drosophila

Background: We characterized variation and chemical composition of epicuticular hydrocarbons (CHCs) in the seven species of the Drosophila buzzatii cluster with gas chromatography/mass spectrometry. Despite the critical role of CHCs in providing resistance to desiccation and involvement in communication, such as courtship behavior, mating, and aggregation, few studies have investigated how CHC profiles evolve within and between species in a phylogenetic context. We analyzed quantitative differences in CHC profiles in populations of the D. buzzatii species cluster in order to assess the concordance of CHC differentiation with species divergence. Results: Thirty-six CHC components were scored in single fly extracts with carbon chain lengths ranging from C(29) to C(39), including methyl-branched alkanes, n alkenes, and alkadienes. Multivariate analysis of variance revealed that CHC amounts were significantly different among all species and canonical discriminant function (CDF) analysis resolved all species into distinct, non-overlapping groups. Significant intraspecific variation was found in different populations of D. serido suggesting that this taxon is comprised of at least two species. We summarized CHC variation using CDF analysis and mapped the first five CHC canonical variates (CVs) onto an independently derived period (per) gene + chromosome inversion + mtDNA COI gene for each sex. We found that the COI sequences were not phylogenetically informative due to introgression between some species, so only per + inversion data were used. Positive phylogenetic signal was observed mainly for CV1 when parsimony methods and the test for serial independence (TFSI) were used. These results changed when no outgroup species were included in the analysis and phylogenetic signal was then observed for female CV3 and/or CV4 and male CV4 and CV5. Finally, removal of divergent populations of D. serido significantly increased the amount of phylogenetic signal as up to four out of five CVs then displayed positive phylogenetic signal. Conclusions: CHCs were conserved among species while quantitative differences in CHC profiles between populations and species were statistically significant. Most CHCs were species-, population-, and sex-specific. Mapping CHCs onto an independently derived phylogeny revealed that a significant portion of CHC variation was explained by species' systematic affinities indicating phylogenetic conservatism in the evolution of these hydrocarbon arrays, presumptive waterproofing compounds and courtship signals as in many other drosophilid species.

Integration and visualization of systems biology data in context of the genome

Background: High-density tiling arrays and new sequencing technologies are generating rapidly increasing volumes of transcriptome and protein-DNA interaction data. Visualization and exploration of this data is critical to understanding the regulatory logic encoded in the genome by which the cell dynamically affects its physiology and interacts with its environment. Results: The Gaggle Genome Browser is a cross-platform desktop program for interactively visualizing high-throughput data in the context of the genome. Important features include dynamic panning and zooming, keyword search and open interoperability through the Gaggle framework. Users may bookmark locations on the genome with descriptive annotations and share these bookmarks with other users. The program handles large sets of user-generated data using an in-process database and leverages the facilities of SQL and the R environment for importing and manipulating data. A key aspect of the Gaggle Genome Browser is interoperability. By connecting to the Gaggle framework, the genome browser joins a suite of interconnected bioinformatics tools for analysis and visualization with connectivity to major public repositories of sequences, interactions and pathways. To this flexible environment for exploring and combining data, the Gaggle Genome Browser adds the ability to visualize diverse types of data in relation to its coordinates on the genome. Conclusions: Genomic coordinates function as a common key by which disparate biological data types can be related to one another. In the Gaggle Genome Browser, heterogeneous data are joined by their location on the genome to create information-rich visualizations yielding insight into genome organization, transcription and its regulation and, ultimately, a better understanding of the mechanisms that enable the cell to dynamically respond to its environment.

Localized modes of binary mixtures of Bose-Einstein condensates in nonlinear optical lattices

The properties of the localized states of a two-component Bose-Einstein condensate confined in a nonlinear periodic potential (nonlinear optical lattice) are investigated. We discuss the existence of different types of solitons and study their stability by means of analytical and numerical approaches. The symmetry properties of the localized states with respect to nonlinear optical lattices are also investigated. We show that nonlinear optical lattices allow the existence of bright soliton modes with equal symmetry in both components and bright localized modes of mixed symmetry type, as well as dark-bright bound states and bright modes on periodic backgrounds. In spite of the quasi-one-dimensional nature of the problem, the fundamental symmetric localized modes undergo a delocalizing transition when the strength of the nonlinear optical lattice is varied. This transition is associated with the existence of an unstable solution, which exhibits a shrinking (decaying) behavior for slightly overcritical (undercritical) variations in the number of atoms.

The electromagnetics of light transmission through subwavelength slits in metallic films

By numerically calculating the relevant electromagnetic fields and charge current densities, we show how local charges and currents near subwavelength structures govern light transmission through subwavelength apertures in a real metal film. The illumination of a single aperture generates surface waves; and in the case of slits, generates them with high efficiency and with a phase close to - pi with respect to a reference standing wave established at the metal film front facet. This phase shift is due to the direction of induced charge currents running within the slit walls. The surface waves on the entrance facet interfere with the standing wave. This interference controls the profile of the transmission through slit pairs as a function of their separation. We compare the calculated transmission profile for a two-slit array to simple interference models and measurements [Phys. Rev. B 77(11), 115411 (2008)]. (C) 2011 Optical Society of America

LATENT RANK CHANGE DETECTION FOR ANALYSIS OF SPLICE-JUNCTION MICROARRAYS WITH NONLINEAR EFFECTS

Alternative splicing of gene transcripts greatly expands the functional capacity of the genome, and certain splice isoforms may indicate specific disease states such as cancer. Splice junction microarrays interrogate thousands of splice junctions, but data analysis is difficult and error prone because of the increased complexity compared to differential gene expression analysis. We present Rank Change Detection (RCD) as a method to identify differential splicing events based upon a straightforward probabilistic model comparing the over-or underrepresentation of two or more competing isoforms. RCD has advantages over commonly used methods because it is robust to false positive errors due to nonlinear trends in microarray measurements. Further, RCD does not depend on prior knowledge of splice isoforms, yet it takes advantage of the inherent structure of mutually exclusive junctions, and it is conceptually generalizable to other types of splicing arrays or RNA-Seq. RCD specifically identifies the biologically important cases when a splice junction becomes more or less prevalent compared to other mutually exclusive junctions. The example data is from different cell lines of glioblastoma tumors assayed with Agilent microarrays.

Analytical calculation of the transition to complete phase synchronization in coupled oscillators

Here we present a system of coupled phase oscillators with nearest neighbors coupling, which we study for different boundary conditions. We concentrate at the transition to the total synchronization. We are able to develop exact solutions for the value of the coupling parameter when the system becomes completely synchronized, for the case of periodic boundary conditions as well as for a chain with fixed ends. We compare the results with those calculated numerically.

STATISTICAL EVALUATION OF MATURE LANDFILL LEACHATE TREATMENT BY HOMOGENEOUS CATALYTIC OZONATION

This study presents the results of a mature landfill leachate treated by a homogeneous catalytic ozonation process with ions Fe(2+) and Fe(3+) at acidic pH. Quality assessments were performed using Taguchi`s method (L(8) design). Strong synergism was observed statistically between molecular ozone and ferric ions, pointing to their catalytic effect on (center dot)OH generation. The achievement of better organic matter depollution rates requires an ozone flow of 5 L h(-1) (590 mg h(-1) O(3)) and a ferric ion concentration of 5 mg L(-1).

Sensor arrays to detect humic substances and Cu(II) in waters

The interaction between poly(o-ethoxyaniline) (POEA) adsorbed onto solid substrates and humic substances (HS) and Cu(2+) ions has been investigated using UV-vis spectroscopy and atomic force microscopy (AFM). Both HS and Cu(2+) are able to dope POEA and change film morphology. This interaction was exploited in a sensor array made with nanostructured films of POEA, sulfonated lignin and HS, which could detect small concentrations of HS and Cu(2+) in water. (C) 2009 Elsevier B.V. All rights reserved.

A BEM model applied to failure analysis of multi-fractured structures

Due to manufacturing or damage process, brittle materials present a large number of micro-cracks which are randomly distributed. The lifetime of these materials is governed by crack propagation under the applied mechanical and thermal loadings. In order to deal with these kinds of materials, the present work develops a boundary element method (BEM) model allowing for the analysis of multiple random crack propagation in plane structures. The adopted formulation is based on the dual BEM, for which singular and hyper-singular integral equations are used. An iterative scheme to predict the crack growth path and crack length increment is proposed. This scheme enables us to simulate the localization and coalescence phenomena, which are the main contribution of this paper. Considering the fracture mechanics approach, the displacement correlation technique is applied to evaluate the stress intensity factors. The propagation angle and the equivalent stress intensity factor are calculated using the theory of maximum circumferential stress. Examples of multi-fractured domains, loaded up to rupture, are considered to illustrate the applicability of the proposed method. (C) 2011 Elsevier Ltd. All rights reserved.

Structural behaviour of three-pile caps subjected to axial compressive loading

This work presents a comparative analysis about the behaviour of pile caps supported by 3 piles subjected to axial loading. Piles with 20 cm and 30 cm diameters were analysed. The main reinforcement was maintained in all the specimens, however, the arrangement of the secondary reinforcement varied. The main reinforcement consisted of steel bars connecting the piles. The secondary reinforcement was made up of: (a) bars going through the piles and through the projection of the column, (b) bars forming a network, and (c) vertical and horizontal stirrups. The main objective was the observation of the pile cap behaviour regarding the cracks and the modes of rupture. The real scale specimens were subjected to experimental tests until failure by rupture. Instruments were placed with the aim to obtain the displacement of the bases, the strains in the main and secondary reinforcement bars, in the compression struts, in the lower and upper nodal zones and in the sides of the caps. None of the caps reached failure by rupture with a load less than 1.12 times the theoretical load. The specimens ruptured due to the cracking of the compression strut and/or the yielding of the reinforcement bars in one direction.

Evaluation of rock mechanical behaviors under uniaxial compression with reference to assessed weathering grades

A weathering classification for granitic rock materials from southeastern Brazil was framed based on core characteristics. The classification was substantiated by a detailed petrographic study. Indirect assessment of weathering grades by density, ultrasonic and Schmidt hammer index tests was performed. Rebound values due to Schmidt hammer multiple impacts at one representative point were more efficient in predicting weathering grades than averaged single impact rebound values, P-wave velocities and densities. Uniaxial compression tests revealed that a large range of uniaxial compressive strength (214-153 MPa) exists in Grade I category where weathering does not seem to have played any role. It was concluded that variability in occurrences of quartz intragranular cracks and in biotite percentage, distribution and orientation might have played a key role in accelerating or decelerating the failure processes of the Grade I specimens. Deterioration of uniaxial compressive strength and elastic modulus and increase in Poisson`s ratio with increasing weathering intensity could be attributed to alteration of minerals, disruption of rock skeleton and microcrack augmentation. A crude relation between failure modes and weathering grades also emerged.

Fatigue behaviour of friction stir welded AA2024-T3 alloy: longitudinal and transverse crack growth

The fatigue crack growth properties of friction stir welded joints of 2024-T3 aluminium alloy have been studied under constant load amplitude (increasing-Delta K), with special emphasis on the residual stress (inverse weight function) effects on longitudinal and transverse crack growth rate predictions (Glinka`s method). In general, welded joints were more resistant to longitudinally growing fatigue cracks than the parent material at threshold Delta K values, when beneficial thermal residual stresses decelerated crack growth rate, while the opposite behaviour was observed next to K-C instability, basically due to monotonic fracture modes intercepting fatigue crack growth in weld microstructures. As a result, fatigue crack growth rate (FCGR) predictions were conservative at lower propagation rates and non-conservative for faster cracks. Regarding transverse cracks, intense compressive residual stresses rendered welded plates more fatigue resistant than neat parent plate. However, once the crack tip entered the more brittle weld region substantial acceleration of FCGR occurred due to operative monotonic tensile modes of fracture, leading to non-conservative crack growth rate predictions next to K-C instability. At threshold Delta K values non-conservative predictions values resulted from residual stress relaxation. Improvements on predicted FCGR values were strongly dependent on how the progressive plastic relaxation of the residual stress field was considered.

Finite element analysis of concrete cracking at early age

The study of the early age concrete properties is becoming more important, as the thermal effects and the shrinkage, even in the first hours, could generate cracks, increasing the permeability of the structure and being able to induce problems of durability and functionality in the same ones. The detailed study of the stresses development during the construction process can be decisive to keep low the cracking levels. In this work a computational model, based on the finite element method, was implemented to simulate the early age concrete behavior and, specially, the evaluation of the cracking risk. The finite element analysis encloses the computational modeling of the following phenomena: chemical, thermal, moisture diffusion and mechanical which occur at the first days after the concrete cast. The developed software results were compared with experimental values found in the literature, demonstrating an excellent approach for all the implemented analysis.

2D evaluation of crack openings using smeared and embedded crack models

This work deals with the determination of crack openings in 2D reinforced concrete structures using the Finite Element Method with a smeared rotating crack model or an embedded crack model In the smeared crack model, the strong discontinuity associated with the crack is spread throughout the finite element As is well known, the continuity of the displacement field assumed for these models is incompatible with the actual discontinuity However, this type of model has been used extensively due to the relative computational simplicity it provides by treating cracks in a continuum framework, as well as the reportedly good predictions of reinforced concrete members` structural behavior On the other hand, by enriching the displacement field within each finite element crossed by the crack path, the embedded crack model is able to describe the effects of actual discontinuities (cracks) This paper presents a comparative study of the abilities of these 2D models in predicting the mechanical behavior of reinforced concrete structures Structural responses are compared with experimental results from the literature, including crack patterns, crack openings and rebar stresses predicted by both models