A Model-Based Analysis of GC-Biased Gene Conversion in the Human and Chimpanzee Genomes

GC-biased gene conversion (gBGC) is a recombination-associated process that favors the fixation of G/C alleles over A/T alleles. In mammals, gBGC is hypothesized to contribute to variation in GC content, rapidly evolving sequences, and the fixation of deleterious mutations, but its prevalence and general functional consequences remain poorly understood. gBGC is difficult to incorporate into models of molecular evolution and so far has primarily been studied using summary statistics from genomic comparisons. Here, we introduce a new probabilistic model that captures the joint effects of natural selection and gBGC on nucleotide substitution patterns, while allowing for correlations along the genome in these effects. We implemented our model in a computer program, called phastBias, that can accurately detect gBGC tracts about 1 kilobase or longer in simulated sequence alignments. When applied to real primate genome sequences, phastBias predicts gBGC tracts that cover roughly 0.3% of the human and chimpanzee genomes and account for 1.2% of human-chimpanzee nucleotide differences. These tracts fall in clusters, particularly in subtelomeric regions; they are enriched for recombination hotspots and fast-evolving sequences; and they display an ongoing fixation preference for G and C alleles. They are also significantly enriched for disease-associated polymorphisms, suggesting that they contribute to the fixation of deleterious alleles. The gBGC tracts provide a unique window into historical recombination processes along the human and chimpanzee lineages. They supply additional evidence of long-term conservation of megabase-scale recombination rates accompanied by rapid turnover of hotspots. Together, these findings shed new light on the evolutionary, functional, and disease implications of gBGC. The phastBias program and our predicted tracts are freely available. © 2013 Capra et al

Reconnection Outflows and Current Sheet Observed with Hinode/XRT in the 2008 April 9 "Cartwheel CME" Flare

Supra-arcade downflows (SADs) have been observed with Yohkoh/SXT (soft X-rays (SXR)), TRACE (extreme ultra-violet (EUV)), SoHO/LASCO (white light), SoHO/SUMER (EUV spectra), and Hinode/XRT (SXR). Characteristics such as low emissivity and trajectories which slow as they reach the top of the arcade are consistent with post-reconnection magnetic flux tubes retracting from a reconnection site high in the corona until they reach a lower-energy magnetic configuration. Viewed from a perpendicular angle, SADs should appear as shrinking loops rather than downflowing voids. We present XRT observations of supra-arcade downflowing loops (SADLs) following a coronal mass ejection (CME) on 2008 April 9 and show that their speeds and decelerations are consistent with those determined for SADs. We also present evidence for a possible current sheet observed during this flare that extends between the flare arcade and the CME. Additionally, we show a correlation between reconnection outflows observed with XRT and outgoing flows observed with LASCO.Comment: 32 pages, 23 figures, Accepted for publication by the Astrophysical Journal (Oct. 2010

Islands of linkage in an ocean of pervasive recombination reveals two-speed evolution of human cytomegalovirus genomes

Human cytomegalovirus (HCMV) infects most of the population worldwide, persisting throughout the host's life in a latent state with periodic episodes of reactivation. While typically asymptomatic, HCMV can cause fatal disease among congenitally infected infants and immunocompromised patients. These clinical issues are compounded by the emergence of antiviral resistance and the absence of an effective vaccine, the development of which is likely complicated by the numerous immune evasins encoded by HCMV to counter the host's adaptive immune responses, a feature that facilitates frequent super-infections. Understanding the evolutionary dynamics of HCMV is essential for the development of effective new drugs and vaccines. By comparing viral genomes from uncultivated or low-passaged clinical samples of diverse origins, we observe evidence of frequent homologous recombination events, both recent and ancient, and no structure of HCMV genetic diversity at the whole-genome scale. Analysis of individual gene-scale loci reveals a striking dichotomy: while most of the genome is highly conserved, recombines essentially freely and has evolved under purifying selection, 21 genes display extreme diversity, structured into distinct genotypes that do not recombine with each other. Most of these hyper-variable genes encode glycoproteins involved in cell entry or escape of host immunity. Evidence that half of them have diverged through episodes of intense positive selection suggests that rapid evolution of hyper-variable loci is likely driven by interactions with host immunity. It appears that this process is enabled by recombination unlinking hyper-variable loci from strongly constrained neighboring sites. It is conceivable that viral mechanisms facilitating super-infection have evolved to promote recombination between diverged genotypes, allowing the virus to continuously diversify at key loci to escape immune detection, while maintaining a genome optimally adapted to its asymptomatic infectious lifecycle

VLC system for the determination of a vehicle’s position and speed

In recent years, lighting solutions have gradually been replaced by more efficient features, taking advantage of Light Emitting Diodes (LEDs) that have progressively conquered the market with increasingly high optical powers, low energy consumption and variable color temperatures. Along with this evolution, Visible Light Communication (VLC) technology has also been developed to use this existing lighting infrastructure and the inherent characteristic of LEDs being easily switched to high frequency to build data transmission systems. The applications of this communication technology using electromagnetic signals in the visible range are currently in a development stage with promising applications in several domains.This paper intends to study an optical communication system based on VLC to establish communication between road infrastructures and. vehicles. For this purpose, four communication channels established through the modulation of white trichromatic LED emitters are used. Detection of the optical signals is performed with a photodiode based on two stacked pin structures made of a-Si:H and a-SiC:H. This device works as an optical filter in the visible spectrum and its spectral sensitivity can be adjusted through stationary optical bias. On-Off-Keying (OOK) modulation is used. The structure of the data blocks to be transmitted was designed to avoid undesirable effects related to ambient light (flickering and/or perceptible variations in color temperature of the white light). The experimental tests of the proposed model were performed using a small-scale prototype. The results show that with the proposed system it is possible to transmit information between road infrastructure and vehicles. 

Evaluation of phylogenetic reconstruction methods using bacterial whole genomes: a simulation based study

Background: Phylogenetic reconstruction is a necessary first step in many analyses which use whole genome sequence data from bacterial populations. There are many available methods to infer phylogenies, and these have various advantages and disadvantages, but few unbiased comparisons of the range of approaches have been made. Methods: We simulated data from a defined "true tree" using a realistic evolutionary model. We built phylogenies from this data using a range of methods, and compared reconstructed trees to the true tree using two measures, noting the computational time needed for different phylogenetic reconstructions. We also used real data from Streptococcus pneumoniae alignments to compare individual core gene trees to a core genome tree. Results: We found that, as expected, maximum likelihood trees from good quality alignments were the most accurate, but also the most computationally intensive. Using less accurate phylogenetic reconstruction methods, we were able to obtain results of comparable accuracy; we found that approximate results can rapidly be obtained using genetic distance based methods. In real data we found that highly conserved core genes, such as those involved in translation, gave an inaccurate tree topology, whereas genes involved in recombination events gave inaccurate branch lengths. We also show a tree-of-trees, relating the results of different phylogenetic reconstructions to each other. Conclusions: We recommend three approaches, depending on requirements for accuracy and computational time. Quicker approaches that do not perform full maximum likelihood optimisation may be useful for many analyses requiring a phylogeny, as generating a high quality input alignment is likely to be the major limiting factor of accurate tree topology. We have publicly released our simulated data and code to enable further comparisons

Shape Animation with Combined Captured and Simulated Dynamics

We present a novel volumetric animation generation framework to create new types of animations from raw 3D surface or point cloud sequence of captured real performances. The framework considers as input time incoherent 3D observations of a moving shape, and is thus particularly suitable for the output of performance capture platforms. In our system, a suitable virtual representation of the actor is built from real captures that allows seamless combination and simulation with virtual external forces and objects, in which the original captured actor can be reshaped, disassembled or reassembled from user-specified virtual physics. Instead of using the dominant surface-based geometric representation of the capture, which is less suitable for volumetric effects, our pipeline exploits Centroidal Voronoi tessellation decompositions as unified volumetric representation of the real captured actor, which we show can be used seamlessly as a building block for all processing stages, from capture and tracking to virtual physic simulation. The representation makes no human specific assumption and can be used to capture and re-simulate the actor with props or other moving scenery elements. We demonstrate the potential of this pipeline for virtual reanimation of a real captured event with various unprecedented volumetric visual effects, such as volumetric distortion, erosion, morphing, gravity pull, or collisions

Precision measurements of the top quark mass from the Tevatron in the pre-LHC era

The top quark is the heaviest of the six quarks of the Standard Model. Precise knowledge of its mass is important for imposing constraints on a number of physics processes, including interactions of the as yet unobserved Higgs boson. The Higgs boson is the only missing particle of the Standard Model, central to the electroweak symmetry breaking mechanism and generation of particle masses. In this Review, experimental measurements of the top quark mass accomplished at the Tevatron, a proton-antiproton collider located at the Fermi National Accelerator Laboratory, are described. Topologies of top quark events and methods used to separate signal events from background sources are discussed. Data analysis techniques used to extract information about the top mass value are reviewed. The combination of several most precise measurements performed with the two Tevatron particle detectors, CDF and \D0, yields a value of \Mt = 173.2 \pm 0.9 GeV/$c^2$.Comment: This version contains the most up-to-date top quark mass averag