Correcting ligands, metabolites, and pathways

BACKGROUND: A wide range of research areas in bioinformatics, molecular biology and medicinal chemistry require precise chemical structure information about molecules and reactions, e.g. drug design, ligand docking, metabolic network reconstruction, and systems biology. Most available databases, however, treat chemical structures more as illustrations than as a datafield in its own right. Lack of chemical accuracy impedes progress in the areas mentioned above. We present a database of metabolites called BioMeta that augments the existing pathway databases by explicitly assessing the validity, correctness, and completeness of chemical structure and reaction information. DESCRIPTION: The main bulk of the data in BioMeta were obtained from the KEGG Ligand database. We developed a tool for chemical structure validation which assesses the chemical validity and stereochemical completeness of a molecule description. The validation tool was used to examine the compounds in BioMeta, showing that a relatively small number of compounds had an incorrect constitution (connectivity only, not considering stereochemistry) and that a considerable number (about one third) had incomplete or even incorrect stereochemistry. We made a large effort to correct the errors and to complete the structural descriptions. A total of 1468 structures were corrected and/or completed. We also established the reaction balance of the reactions in BioMeta and corrected 55% of the unbalanced (stoichiometrically incorrect) reactions in an automatic procedure. The BioMeta database was implemented in PostgreSQL and provided with a web-based interface. CONCLUSION: We demonstrate that the validation of metabolite structures and reactions is a feasible and worthwhile undertaking, and that the validation results can be used to trigger corrections and improvements to BioMeta, our metabolite database. BioMeta provides some tools for rational drug design, reaction searches, and visualization. It is freely available at provided that the copyright notice of all original data is cited. The database will be useful for querying and browsing biochemical pathways, and to obtain reference information for identifying compounds. However, these applications require that the underlying data be correct, and that is the focus of BioMeta

Extended Star Formation and Molecular Gas in the Tidal Arms near NGC3077

We report the detection of ongoing star formation in the prominent tidal arms near NGC 3077 (member of the M 81 triplet). In total, 36 faint compact HII regions were identified, covering an area of ~4x6 kpc^2. Most of the HII regions are found at HI column densities above 1x10^21 cm^-2 (on scales of 200 pc), well within the range of threshold columns measured in normal galaxies. The HII luminosity function resembles the ones derived for other low-mass dwarf galaxies in the same group; we derive a total star formation rate of 2.6x10^-3 M_sun/yr in the tidal feature. We also present new high-resolution imaging of the molecular gas distribution in the tidal arm using CO observations obtained with the OVRO interferometer. We recover about one sixth of the CO flux (or M_H2~2x10^6 M_sun, assuming a Galactic conversion factor) originally detected in the IRAM 30m single dish observations, indicating the presence of a diffuse molecular gas component in the tidal arm. The brightest CO peak in the interferometer map (comprising half of the detected CO flux) is coincident with one of the brightest HII regions in the feature. Assuming a constant star formation rate since the creation of the tidal feature (presumably ~3x10^8 years ago), a total mass of ~7x10^5 M_sun has been transformed from gas into stars. Over this period, the star formation in the tidal arm has resulted in an additional enrichment of Delta(Z)>0.002. The reservoir of atomic and molecular gas in the tidal arm is ~3x10^8 M_sun, allowing star formation to continue at its present rate for a Hubble time. Such wide-spread, low-level star formation would be difficult to image around more distant galaxies but may be detectable through intervening absorption in quasar spectra.Comment: Accepted for publication in the Astronomical Journa

The Nature of Nearby Counterparts to Intermediate Redshift Luminous Compact Blue Galaxies I. Optical/H I Properties and Dynamical Masses

We present single-dish H I spectra obtained with the Green Bank Telescope, along with optical photometric properties from the Sloan Digital Sky Survey, of 20 nearby (D < 70 Mpc) Luminous Compact Blue Galaxies (LCBGs). These ~L*, blue, high surface brightness, starbursting galaxies were selected with the same criteria used to define LCBGs at higher redshifts. We find these galaxies are gas-rich, with M(HI) ranging from 5*10^8 to 8*10^9 M_sun, and M(HI)/L_B ranging from 0.2 to 2 M_sun/L_sun, consistent with a variety of morphological types of galaxies. We find the dynamical masses (measured within R_25) span a wide range, from 3*10^9 to 1*10^11 M_sun. However, at least half have dynamical mass-to-light ratios smaller than nearby galaxies of all Hubble types, as found for LCBGs at intermediate redshifts. By comparing line widths and effective radii with local galaxy populations, we find that LCBGs are consistent with the dynamical mass properties of Magellanic (low luminosity) spirals, and the more massive irregulars and dwarf ellipticals, such as NGC 205.Comment: 33 pages, 8 figures, accepted by Ap

Ammonia (J,K) = (1,1) to (4,4) and (6,6) inversion lines detected in the Seyfert 2 galaxy NGC 1068

We present the detection of the ammonia (NH3) (J,K) = (1,1) to (4,4) and (6,6) inversion lines toward the prototypical Seyfert 2 galaxy NGC 1068, made with the Green Bank Telescope (GBT). This is the first detection of ammonia in a Seyfert galaxy. The ortho-to-para-NH3 abundance ratio suggests that the molecule was formed in a warm medium of at least 20 K. For the NH3 column density and fractional abundance, we find (1.09\pm0.23)\times10^14 cm^-2 and (2.9\pm0.6)\times10^-8, respectively, from the inner 1.2 kpc of NGC 1068. The kinetic temperature can be constrained to 80\pm20 K for the bulk of the molecular gas, while some fraction has an even higher temperature of 140\pm30 K.Comment: 5 pages, 3 figures, accepted by A&

Disentangling the Circumnuclear Environs of Centaurus A: III. An Inner Molecular Ring, Nuclear Shocks and the CO to warm H2 interface

We present the distribution and kinematics of the molecular gas in the circumnuclear disk (CND, 400 pc x 200 pc) of Centaurus A with resolutions of ~5 pc (0.3 arcsec) and shed light onto the mechanism feeding the Active Galactic Nucleus (AGN) using CO(3-2), HCO+(4-3), HCN(4-3), and CO(6-5) observations obtained with ALMA. Multiple filaments or streamers of tens to a hundred parsec scale exist within the CND, which form a ring-like structure with an unprojected diameter of 9 x 6 arcsec (162pc x 108pc) and a position angle PA = 155deg. Inside the nuclear ring, there are two leading and straight filamentary structures with lengths of about 30-60pc at PA = 120deg on opposite sides of the AGN, with a rotational symmetry of 180deg and steeper position-velocity diagrams, which are interpreted as nuclear shocks due to non-circular motions. Along the filaments, and unlike other nearby AGNs, several dense molecular clumps present low HCN/HCO+(4-3) ratios (~0.5). The filaments abruptly end in the probed transitions at r = 20pc from the AGN, but previous near-IR H2 (J=1-0) S(1) maps show that they continue in an even ~1000 K), winding up in the form of nuclear spirals, and forming an inner ring structure with another set of symmetric filaments along the N-S direction and within r = 10pc. The molecular gas is governed primarily by non-circular motions, being the successive shock fronts at different scales where loss of angular momentum occurs, a mechanism which may feed efficiently powerful radio galaxies down to parsec scales.Comment: 46 pages. Accepted for publication in Ap

ALMA Multi-line Imaging of the Nearby Starburst Galaxy NGC 253

We present spatially resolved ($\sim$50 pc) imaging of molecular gas species in the central kiloparsec of the nearby starburst galaxy NGC 253, based on observations taken with the Atacama Large Millimeter/submillimeter Array (ALMA). A total of 50 molecular lines are detected over a 13 GHz bandwidth imaged in the 3 mm band. Unambiguous identifications are assigned for 27 lines. Based on the measured high CO/C$^{17}$O isotopic line ratio ($\gtrsim$350), we show that $^{12}$CO(1-0) has moderate optical depths. A comparison of the HCN and HCO$^{+}$ with their $^{13}$C-substituted isotopologues shows that the HCN(1-0) and HCO$^{+}$(1-0) lines have optical depths at least comparable to CO(1-0). H$^{13}$CN/H$^{13}$CO$^{+}$ (and H$^{13}$CN/HN$^{13}$C) line ratios provide tighter constraints on dense gas properties in this starburst. SiO has elevated abundances across the nucleus. HNCO has the most distinctive morphology of all the bright lines, with its global luminosity dominated by the outer parts of the central region. The dramatic variation seen in the HNCO/SiO line ratio suggests that some of the chemical signatures of shocked gas are being erased in the presence of dominating central radiation fields (traced by C$_{2}$H and CN). High density molecular gas tracers (including HCN, HCO$^+$, and CN) are detected at the base of the molecular outflow. We also detect hydrogen $\beta$ recombination lines that, like their $\alpha$ counterparts, show compact, centrally peaked morphologies, distinct from the molecular gas tracers. A number of sulfur based species are mapped (CS, SO, NS, C$_{2}$S, H$_{2}$CS and CH$_{3}$SH) and have morphologies similar to SiO.Comment: 20 pages, 10 figures, accepted to the Astrophysical Journa

Werner states and the two-spinors Heisenberg anti-ferromagnet

We ascertain, following ideas of Arnesen, Bose, and Vedral concerning thermal entanglement [Phys. Rev. Lett. {\bf 87} (2001) 017901] and using the statistical tool called {\it entropic non-triviality} [Lamberti, Martin, Plastino, and Rosso, Physica A {\bf 334} (2004) 119], that there is a one to one correspondence between (i) the mixing coefficient $x$ of a Werner state, on the one hand, and (ii) the temperature $T$ of the one-dimensional Heisenberg two-spin chain with a magnetic field $B$ along the $z-$axis, on the other one. This is true for each value of $B$ below a certain critical value $B_c$. The pertinent mapping depends on the particular $B-$value one selects within such a range

Science-Policy Briefing Paper and Event 1

The first briefing paper summarizing work being carried-out in AtlantOS. The outcome will be presented to the stakeholders in a briefing even

Three-dimensional simulations of the interstellar medium in dwarf galaxies - II. Galactic wind

We study the hydrodynamical evolution of galactic winds in disky dwarf galaxies moving through an intergalactic medium. In agreement with previous investigations,we find that when the ram pressure stripping does not disrupt the ISM, it usually has a negligible effect on the galactic wind dynamics. Only when the IGM ram pressure is comparable to the central ISM thermal pressure the stripping and the superwind influence each other increasing the gas removal rate. In this case several parameters regulate the ISM ejection process, as the original distribution of the ISM and the geometry of the IGM-galaxy interaction. When the ISM is not removed by the ram pressure or the wind, it loses memory of the starburst episode and recovers almost its pre-burst distribution in a timescale of 50-200 Myr. After this time another star formation episode becomes, in principle, possible. Evidently, galactic winds are consistent with a recurrent bursts star formation history. Contrary to the ISM content, the amount of the metal-rich ejecta retained by the galaxy is more sensitive to the ram pressure action. Part of the ejecta is first trapped in a low density, extraplanar gas produced by the IGM-ISM interaction, and then pushed back onto the galactic disc. The amount of trapped metals in a moving galaxy may be up to three times larger than in a galaxy at rest. This prediction may be tested comparing metallicity of dwarf galaxies in nearby poor clusters or groups, such as Virgo or Fornax, with the field counterpart. The sensitivity of the metal entrapment efficiency on the geometry of the interaction may explain part of the observed scatter in the metallicity-luminosity relation for dwarf galaxies.Comment: Accepted MNRAS, 9 color figure