A two-phase approach for detecting recombination in nucleotide sequences

Genetic recombination can produce heterogeneous phylogenetic histories within a set of homologous genes. Delineating recombination events is important in the study of molecular evolution, as inference of such events provides a clearer picture of the phylogenetic relationships among different gene sequences or genomes. Nevertheless, detecting recombination events can be a daunting task, as the performance of different recombinationdetecting approaches can vary, depending on evolutionary events that take place after recombination. We recently evaluated the effects of postrecombination events on the prediction accuracy of recombination-detecting approaches using simulated nucleotide sequence data. The main conclusion, supported by other studies, is that one should not depend on a single method when searching for recombination events. In this paper, we introduce a two-phase strategy, applying three statistical measures to detect the occurrence of recombination events, and a Bayesian phylogenetic approach in delineating breakpoints of such events in nucleotide sequences. We evaluate the performance of these approaches using simulated data, and demonstrate the applicability of this strategy to empirical data. The two-phase strategy proves to be time-efficient when applied to large datasets, and yields high-confidence results.Comment: 5 pages, 3 figures. Chan CX, Beiko RG and Ragan MA (2007). A two-phase approach for detecting recombination in nucleotide sequences. In Hazelhurst S and Ramsay M (Eds) Proceedings of the First Southern African Bioinformatics Workshop, 28-30 January, Johannesburg, 9-1

Parton recombination and fluctuations of conserved charges

We study various fluctuation and correlation signals of the deconfined state using a dynamical recombination approach (quark Molecular Dynamics, qMD). We analyse charge ratio fluctuations, charge transfer fluctuations and baryon-strangeness correlations as a function of the center of mass energy with a set of central Pb+Pb/Au+Au events from AGS energies on (Elab = 4 AGeV) up to the highest RHIC energy available (V sNN = 200 GeV) and as a function of time with a set of central Au+Au qMD events at V sNN = 200 GeV with and without applying our hadronization procedure. For all studied quantities, the results start from values compatible with a weakly coupled QGP in the early stage and end with values compatible with the hadronic result in the final state. We show that the loss of the signal occurs at the same time as hadronization and trace it back to the dynamical recombination process implemented in our model

Study of the transition from conduction to injection in an electrohydrodynamic flow in blade-plane geometry

A dielectric fluid can be set into motion with the help of electric forces, mainly Coulomb force. This phenomenon, called electroconvection, can be induced by electrohydrodynamic conduction, injection, and induction. Conduction is based on the dissociation/recombination phenomenon, generates heterocharge layers, and occurs for low electric field values. Injection produces homocharge layers in the electrode vicinity and requires stronger electric fields to be initiated. This study is an experimental observation of the transition from conduction to injection of a dielectric liquid in blade-plane geometry using Particle Image Velocimetry. In addition, the electric current is measured to completely understand the flow behavior

First Time-dependent Study of H2 and H3+ Ortho-Para Chemistry in the Diffuse Interstellar Medium: Observations Meet Theoretical Predictions

The chemistry in the diffuse interstellar medium initiates the gradual increase of molecular complexity during the life cycle of matter. A key molecule that enables build-up of new molecular bonds and new molecules via proton-donation is H3+. Its evolution is tightly related to molecular hydrogen and thought to be well understood. However, recent observations of ortho and para lines of H2 and H3+ in the diffuse ISM showed a puzzling discrepancy in nuclear spin excitation temperatures and populations between these two key species. H3+, unlike H2, seems to be out of thermal equilibrium, contrary to the predictions of modern astrochemical models. We conduct the first time-dependent modeling of the para-fractions of H2 and H3+ in the diffuse ISM and compare our results to a set of line-of-sight observations, including new measurements presented in this study. We isolate a set of key reactions for H3+ and find that the destruction of the lowest rotational states of H3+ by dissociative recombination largely control its ortho/para ratio. A plausible agreement with observations cannot be achieved unless a ratio larger than 1:5 for the destruction of (1,1)- and (1,0)-states of H3+ is assumed. Additionally, an increased CR ionization rate to 10(-15) 1/s further improves the fit whereas variations of other individual physical parameters, such as density and chemical age, have only a minor effect on the predicted ortho/para ratios. Thus our study calls for new laboratory measurements of the dissociative recombination rate and branching ratio of the key ion H3+ under interstellar conditions.Comment: 27 pages, 6 figures, 3 table

HI Absorption Toward HII Regions at Small Galactic Longitudes

We make a comprehensive study of HI absorption toward HII regions located within Galactic longitudes less than 10 degrees. Structures in the extreme inner Galaxy are traced using the longitude-velocity space distribution of this absorption. We find significant HI absorption associated with the Near and Far 3kpc Arms, the Connecting Arm, Banias Clump 1 and the H I Tilted Disk. We also constrain the line of sight distances to HII regions, by using HI absorption spectra together with the HII region velocities measured by radio recombination lines.Comment: Complete figure set available in online version of journal. Accepted by ApJ August 8, 201

The formation of voids in a universe with cold dark matter and a cosmological constant

A spherical Lagrangian hydrodynamical code has been written to study the formation of cosmological structures in the early Universe. In this code we take into account the presence of collisionless non-baryonic cold dark matter (CDM), the cosmological constant and a series of physical processes present during and after the recombination era, such as photon drag resulting from the cosmic background radiation and hydrogen molecular production. We follow the evolution of the structure since the recombination era until the present epoch. As an application of this code we study the formation of voids starting from negative density perturbations which evolved during and after the recombination era. We analyse a set of COBE-normalized models, using different spectra to see their influence on the formation of voids. Our results show that large voids with diameters ranging from 10h^{-1} Mpc up to 50h^{-1} Mpc can be formed in a universe model dominated by the cosmological constant (\Omega_\Lambda ~ 0.8). This particular scenario is capable of forming large and deep empty regions (with density contrasts \delta < -0.6). Our results also show that the physical processes acting on the baryonic matter produce a transition region where the radius of the dark matter component is greater than the baryonic void radius. The thickness of this transition region ranges from about tens of kiloparsecs up to a few megaparsecs, depending on the spectrum considered. Putative objects formed near voids and within the transition region would have a different amount of baryonic/dark matter when compared with \Omega_b/\Omega_d. If one were to use these galaxies to determine, by dynamical effects or other techniques, the quantity of dark matter present in the Universe, the result obtained would be only local and not representative of the Universe as a whole.Comment: MNRAS (in press); 9 pages, no figure