5,568 research outputs found
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
Circulating non-coding RNAs in renal cell carcinoma—pathogenesis and potential implications as clinical biomarkers
ALMA Multi-line Imaging of the Nearby Starburst Galaxy NGC 253
We present spatially resolved (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/CO isotopic line ratio (350), we
show that CO(1-0) has moderate optical depths. A comparison of the HCN
and HCO with their C-substituted isotopologues shows that the
HCN(1-0) and HCO(1-0) lines have optical depths at least comparable to
CO(1-0). HCN/HCO (and HCN/HNC) 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
CH 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 recombination lines that, like their counterparts,
show compact, centrally peaked morphologies, distinct from the molecular gas
tracers. A number of sulfur based species are mapped (CS, SO, NS, CS,
HCS and CHSH) 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 of a Werner state, on
the one hand, and (ii) the temperature of the one-dimensional Heisenberg
two-spin chain with a magnetic field along the axis, on the other one.
This is true for each value of below a certain critical value . The
pertinent mapping depends on the particular 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
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