Protein domains as units of genetic transfer

Genomes evolve as modules. In prokaryotes (and some eukaryotes), genetic material can be transferred between species and integrated into the genome via homologous or illegitimate recombination. There is little reason to imagine that the units of transfer correspond to entire genes; however, such units have not been rigorously characterized. We examined fragmentary genetic transfers in single-copy gene families from 144 prokaryotic genomes and found that breakpoints are located significantly closer to the boundaries of genomic regions that encode annotated structural domains of proteins than expected by chance, particularly when recombining sequences are more divergent. This correlation results from recombination events themselves and not from differential nucleotide substitution. We report the first systematic study relating genetic recombination to structural features at the protein level

A Library for Declarative Resolution-Independent 2D Graphics

The design of most 2D graphics frameworks has been guided by what the computer can draw efficiently, instead of by how graphics can best be expressed and composed. As a result, such frameworks restrict expressivity by providing a limited set of shape primitives, a limited set of textures and only affine transformations. For example, non-affine transformations can only be added by invasive modification or complex tricks rather than by simple composition. More general frameworks exist, but they make it harder to describe and analyze shapes. We present a new declarative approach to resolution-independent 2D graphics that generalizes and simplifies the functionality of traditional frameworks, while preserving their efficiency. As a real-world example, we show the implementation of a form of focus+context lenses that gives better image quality and better performance than the state-of-the-art solution at a fraction of the code. Our approach can serve as a versatile foundation for the creation of advanced graphics and higher level frameworks

Magnetic stimulation for non-homogeneous biological structures

BACKGROUND: Magnetic stimulation has gained relatively wide application in studying nervous system structures. This technology has the advantage of reduced excitation of sensory nerve endings, and hence results in quasi-painless action. It has become clinically accepted modality for brain stimulation. However, theoretical and practical solutions for assessment of induced current distribution need more detailed and accurate consideration. Some possible analyses are proposed for distribution of the current induced from excitation current contours of different shape and disposition. Relatively non-difficult solutions are shown, applicable for two- and three-dimensional analysis. METHODS: The boundary conditions for field analysis by the internal Dirichlet problem are introduced, based on the vector potential field excited by external current coils. The feedback from the induced eddy currents is neglected. Finite element modeling is applied for obtaining the electromagnetic fields distribution in a non-homogeneous domain. RESULTS: The distributions were obtained in a non-homogeneous structure comprised of homogeneous layers. A tendency was found of the induced currents to follow paths in lower resistivity layers, deviating from the expected theoretical course for a homogeneous domain. Current density concentrations occur at the boundary between layers, suggesting the possibility for focusing on, or predicting of, a zone of stimulation. CONCLUSION: The theoretical basis and simplified approach for generation of 3D FEM networks for magnetic stimulation analysis are presented, applicable in non-homogeneous and non-linear media. The inconveniences of introducing external excitation currents are avoided. Thus, the possibilities are improved for analysis of distributions induced by time-varying currents from contours of various geometry and position with respect to the medium

ATLASGAL - star forming efficiencies and the Galactic star formation rate

The ATLASGAL survey has characterized the properties of approximately 1000 embedded H ii regions and found an empirical relationship between the clump mass and bolometric luminosity that covers 3-4 orders of magnitude. Comparing this relation with simulated clusters drawn from an initial mass function and using different star formation efficiencies we find that a single value is unable to fit the observed luminosity to mass (L/M) relation. We have used a Monte Carlo simulation to generate 200 000 clusters using the L/M-ratio as a constraint to investigate how the star formation efficiency changes as a function of clump mass. This has revealed that the star formation efficiency decreases with increasing clump mass with a value of 0.2 for clumps with masses of a few hundred solar masses and dropping to 0.08 for clumps with masses of a few thousand solar masses. We find good agreement between our results and star formation efficiencies determined from counts of embedded objects in nearby molecular clouds. Using the star formation efficiency relationship and the infrared excess time for embedded star formation of 2 ± 1 Myr we estimate the Galactic star formation rate to be approximately 0.9 ± 0.45 M· yr-1, which is in good agreement with previously reported values. This model has the advantage of providing a direct means of determining the star formation rate and avoids the difficulties encountered in converting infrared luminosities to stellar mass that affect previous galactic and extragalactic studies

Phylogeny of Prokaryotes and Chloroplasts Revealed by a Simple Composition Approach on All Protein Sequences from Complete Genomes Without Sequence Alignment

The complete genomes of living organisms have provided much information on their phylogenetic relationships. Similarly, the complete genomes of chloroplasts have helped to resolve the evolution of this organelle in photosynthetic eukaryotes. In this paper we propose an alternative method of phylogenetic analysis using compositional statistics for all protein sequences from complete genomes. This new method is conceptually simpler than and computationally as fast as the one proposed by Qi et al. (2004b) and Chu et al. (2004). The same data sets used in Qi et al. (2004b) and Chu et al. (2004) are analyzed using the new method. Our distance-based phylogenic tree of the 109 prokaryotes and eukaryotes agrees with the biologists tree of life based on 16S rRNA comparison in a predominant majority of basic branching and most lower taxa. Our phylogenetic analysis also shows that the chloroplast genomes are separated to two major clades corresponding to chlorophytes s.l. and rhodophytes s.l. The interrelationships among the chloroplasts are largely in agreement with the current understanding on chloroplast evolution

A Benchmark of Parametric Methods for Horizontal Transfers Detection

Horizontal gene transfer (HGT) has appeared to be of importance for prokaryotic species evolution. As a consequence numerous parametric methods, using only the information embedded in the genomes, have been designed to detect HGTs. Numerous reports of incongruencies in results of the different methods applied to the same genomes were published. The use of artificial genomes in which all HGT parameters are controlled allows testing different methods in the same conditions. The results of this benchmark concerning 16 representative parametric methods showed a great variety of efficiencies. Some methods work very poorly whatever the type of HGTs and some depend on the conditions or on the metrics used. The best methods in terms of total errors were those using tetranucleotides as criterion for the window methods or those using codon usage for gene based methods and the Kullback-Leibler divergence metric. Window methods are very sensitive but less specific and detect badly lone isolated gene. On the other hand gene based methods are often very specific but lack of sensitivity. We propose using two methods in combination to get the best of each category, a gene based one for specificity and a window based one for sensitivity

CHIMPS: Physical properties of molecular clumps across the inner Galaxy

The latest generation of high-angular-resolution unbiased Galactic plane surveys in molecular-gas tracers are enabling the interiors of molecular clouds to be studied across a range of environments. The CO Heterodyne Inner MilkyWay Plane Survey (CHIMPS) simultaneously mapped a sector of the inner Galactic plane, within 27:8 . 46:2 and jbj 0: 5, in 13CO (3-2) and C18O (3-2) at an angular resolution of 15 arcsec. The combination of the CHIMPS data with 12CO (3-2) data from the CO High Resolution Survey (COHRS) has enabled us to perform a voxel-by-voxel local-thermodynamic-equilibrium (LTE) analysis, determining the excitation temperature, optical depth, and column density of 13CO at each; b; v position. Distances to discrete sources identified by FELLWALKER in the 13CO (3-2) emission maps were determined, allowing the calculation of numerous physical properties of the sources, and we present the first source catalogues in this paper.We find that, in terms of size and density, the CHIMPS sources represent an intermediate population between large-scale molecular clouds identified by CO and dense clumps seen in thermal dust continuum emission, and therefore represent the bulk transition from the diffuse to the dense phase of molecular gas.We do not find any significant systematic variations in the masses, column densities, virial parameters, mean excitation temperature, or the turbulent pressure over the range of Galactocentric distance probed, but we do find a shallow increase in the mean volume density with increasing Galactocentric distance. We find that inter-arm clumps have significantly narrower linewidths, and lower virial parameters and excitation temperatures than clumps located in spiral arms. When considering the most reliable distance-limited subsamples, the largest variations occur on the clump-to-clump scale, echoing similar recent studies that suggest that the star-forming process is largely insensitive to the Galactic-scale environment, at least within the inner disc

A Genome-Wide Analysis of Promoter-Mediated Phenotypic Noise in Escherichia coli

Gene expression is subject to random perturbations that lead to fluctuations in the rate of protein production. As a consequence, for any given protein, genetically identical organisms living in a constant environment will contain different amounts of that particular protein, resulting in different phenotypes. This phenomenon is known as “phenotypic noise.” In bacterial systems, previous studies have shown that, for specific genes, both transcriptional and translational processes affect phenotypic noise. Here, we focus on how the promoter regions of genes affect noise and ask whether levels of promoter-mediated noise are correlated with genes' functional attributes, using data for over 60% of all promoters in Escherichia coli. We find that essential genes and genes with a high degree of evolutionary conservation have promoters that confer low levels of noise. We also find that the level of noise cannot be attributed to the evolutionary time that different genes have spent in the genome of E. coli. In contrast to previous results in eukaryotes, we find no association between promoter-mediated noise and gene expression plasticity. These results are consistent with the hypothesis that, in bacteria, natural selection can act to reduce gene expression noise and that some of this noise is controlled through the sequence of the promoter region alon

A Library for Declarative Resolution-Independent 2D Graphics

htmlabstractThe design of most 2D graphics frameworks has been guided by what the computer can draw efficiently, instead of by how graphics can best be expressed and composed. As a result, such frameworks restrict expressivity by providing a limited set of shape primitives, a limited set of textures and only affine transformations. For example, non-affine transformations can only be added by invasive modification or complex tricks rather than by simple composition. More general frameworks exist, but they make it harder to describe and analyze shapes. We present a new declarative approach to resolution-independent 2D graphics that generalizes and simplifies the functionality of traditional frameworks, while preserving their efficiency. As a real-world example, we show the implementation of a form of focus+context lenses that gives better image quality and better performance than the state-of-the-art solution at a fraction of the code. Our approach can serve as a versatile foundation for the creation of advanced graphics and higher level frameworks