Large-scale genomic 2D visualization reveals extensive CG-AT skew correlation in bird genomes

<p>Abstract</p> <p>Background</p> <p>Bird genomes have very different compositional structure compared with other warm-blooded animals. The variation in the base skew rules in the vertebrate genomes remains puzzling, but it must relate somehow to large-scale genome evolution. Current research is inclined to relate base skew with mutations and their fixation. Here we wish to explore base skew correlations in bird genomes, to develop methods for displaying and quantifying such correlations at different scales, and to discuss possible explanations for the peculiarities of the bird genomes in skew correlation.</p> <p>Results</p> <p>We have developed a method called Base Skew Double Triangle (BSDT) for exhibiting the genome-scale change of AT/CG skew as a two-dimensional square picture, showing base skews at many scales simultaneously in a single image. By this method we found that most chicken chromosomes have high AT/CG skew correlation (symmetry in 2D picture), except for some microchromosomes. No other organisms studied (18 species) show such high skew correlations. This visualized high correlation was validated by three kinds of quantitative calculations with overlapping and non-overlapping windows, all indicating that chicken and birds in general have a special genome structure. Similar features were also found in some of the mammal genomes, but clearly much weaker than in chickens. We presume that the skew correlation feature evolved near the time that birds separated from other vertebrate lineages. When we eliminated the repeat sequences from the genomes, the AT and CG skews correlation increased for some mammal genomes, but were still clearly lower than in chickens.</p> <p>Conclusion</p> <p>Our results suggest that BSDT is an expressive visualization method for AT and CG skew and enabled the discovery of the very high skew correlation in bird genomes; this peculiarity is worth further study. Computational analysis indicated that this correlation might be a compositional characteristic, present not only in chickens, but also remained or developed in some mammals during evolution. Special aspects of bird metabolism related to e.g. flight may be the reason why birds evolved or retained the skew correlation. Our analysis also indicated that repetitive DNA sequence elements need to be taken into account in studying the evolution of the correlation between AT and CG skews.</p

Method and system for providing beam polarization

A radiation polarizer, controller, and a method of radiation polarization and beam control, are disclosed. The radiation polarizer includes a substrate, at least one anti-reflection coating layer communicatively coupled to the substrate, at least two nanostructures communicatively coupled to the at least one anti-reflection coating layer, and at least two groove layers, wherein each one of the at least two groove layers is interstitial to a respective one of the at least two nanostructures. The method may include the steps of communicatively coupling at least one anti-reflection coating layer to a substrate, communicatively coupling at least two nanostructures to at least one of the at least one anti-reflection coating layer, providing interstitially to a respective one of the at least two nanostructures at least two groove layers, coupling the at least two groove layers and the at least two nanostructures to provide a pass wavelength in the range of about 250 nm to less than about a microwave wavelength, and allowing for examining of radiation having a wavelength in a range of about 250 nm to less than about a microwave wavelength, and having an electric field orthogonal to the at least two groove layers, by allowing for a passing of the radiation through said coupling of the at least two groove layers and the at least two nanostructures.Published versio

Precision phase retardation devices and method of making same

A birefringent device of substantially uniform thickness less than about 10 microns, and being suitable for operating in a wavelength range about a central wavelength is disclosed. The device includes a base substrate, a layer of periodic index regions of alternating refractive indices applied to a first surface of the base substrate, and a cap substrate located substantially adjacent to the layer distal to the base substrate. The layer of periodic index regions has a periodicity of less than the central wavelength. The device being suitable to produce an arbitrary phase retardation between 0 and 2Published versio

Films for optical use and methods of making such films

Films for optical use, articles containing such films, methods for making such films, and systems that utilize such films, are disclosedPublished versio

Comparison of metagenomic samples using sequence signatures

BACKGROUND: Sequence signatures, as defined by the frequencies of k-tuples (or k-mers, k-grams), have been used extensively to compare genomic sequences of individual organisms, to identify cis-regulatory modules, and to study the evolution of regulatory sequences. Recently many next-generation sequencing (NGS) read data sets of metagenomic samples from a variety of different environments have been generated. The assembly of these reads can be difficult and analysis methods based on mapping reads to genes or pathways are also restricted by the availability and completeness of existing databases. Sequence-signature-based methods, however, do not need the complete genomes or existing databases and thus, can potentially be very useful for the comparison of metagenomic samples using NGS read data. Still, the applications of sequence signature methods for the comparison of metagenomic samples have not been well studied. RESULTS: We studied several dissimilarity measures, including d(2), d(2)(*) and d(2)(S) recently developed from our group, a measure (hereinafter noted as Hao) used in CVTree developed from Hao’s group (Qi et al., 2004), measures based on relative di-, tri-, and tetra-nucleotide frequencies as in Willner et al. (2009), as well as standard l(p) measures between the frequency vectors, for the comparison of metagenomic samples using sequence signatures. We compared their performance using a series of extensive simulations and three real next-generation sequencing (NGS) metagenomic datasets: 39 fecal samples from 33 mammalian host species, 56 marine samples across the world, and 13 fecal samples from human individuals. Results showed that the dissimilarity measure d(2)(S) can achieve superior performance when comparing metagenomic samples by clustering them into different groups as well as recovering environmental gradients affecting microbial samples. New insights into the environmental factors affecting microbial compositions in metagenomic samples are obtained through the analyses. Our results show that sequence signatures of the mammalian gut are closely associated with diet and gut physiology of the mammals, and that sequence signatures of marine communities are closely related to location and temperature. CONCLUSIONS: Sequence signatures can successfully reveal major group and gradient relationships among metagenomic samples from NGS reads without alignment to reference databases. The d(2)(S) dissimilarity measure is a good choice in all application scenarios. The optimal choice of tuple size depends on sequencing depth, but it is quite robust within a range of choices for moderate sequencing depths

High performance wavelength-division multiplexing schemes for optical networks

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Sketch map of the 12 paired diagonals for calculating total skew correlation

<p><b>Copyright information:</b></p><p>Taken from "Large-scale genomic 2D visualization reveals extensive CG-AT skew correlation in bird genomes"</p><p>http://www.biomedcentral.com/1471-2148/7/234</p><p>BMC Evolutionary Biology 2007;7():234-234.</p><p>Published online 23 Nov 2007</p><p>PMCID:PMC2212660.</p><p></p> See text for explanation. The arrows show the fourth line pair as an example

The chromatogram (color scale) drawn using the color function of Table 4

<p><b>Copyright information:</b></p><p>Taken from "Large-scale genomic 2D visualization reveals extensive CG-AT skew correlation in bird genomes"</p><p>http://www.biomedcentral.com/1471-2148/7/234</p><p>BMC Evolutionary Biology 2007;7():234-234.</p><p>Published online 23 Nov 2007</p><p>PMCID:PMC2212660.</p><p></p> The numbers at the bottom correspond to the skew value, for example 26.0 means when base skew is 26.0, the color in BSDT is deep green