Lithium abundances among solar-type pre-main-sequence stars

NASA Technical Reports Server (NTRS)

Strom, Karen M.; Wilkin, Francis P.; Strom, Stephen E.; Seaman, Robert L.

1989-01-01

Measurements of Li I 6707 A line strengths were carried out for two samples of pre-main-sequence (PMS) stars (L 1641 and Taurus-Auriga), and the Li abundances estimated for PMS stars are compared with those deduced from observations of Li line strengths for main-sequence stars in the Alpha Persei cluster. It was found that the maximum Li abundances among the PMS stars with solar mass values greater than 1.0 exceed the maximum abundances for Alpha Per stars by at least 0.3 dex. Some PMS stars, including few apparently young stars, showed large (greater than 1.0 dex) Li depletion, and some apparently old PMS stars showed little or no depletion.

ORBITAL SOLUTIONS FOR TWO YOUNG, LOW-MASS SPECTROSCOPIC BINARIES IN OPHIUCHUS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rosero, V.; Prato, L.; Wasserman, L. H.

2011-01-15

We report the orbital parameters for ROXR1 14 and RX J1622.7-2325Nw, two young, low-mass, and double-lined spectroscopic binaries recently discovered in the Ophiuchus star-forming region. Accurate orbital solutions were determined from over a dozen high-resolution spectra taken with the Keck II and Gemini South telescopes. These objects are T Tauri stars with mass ratios close to unity and periods of {approx}5 and {approx}3 days, respectively. In particular, RX J1622.7-2325Nw shows a non-circularized orbit with an eccentricity of 0.30, higher than any other short-period pre-main-sequence (PMS) spectroscopic binary known to date. We speculate that the orbit of RX J1622.7-2325Nw has notmore » yet circularized because of the perturbing action of a {approx}1'' companion, itself a close visual pair. A comparison of known young spectroscopic binaries (SBs) and main-sequence (MS) SBs in the eccentricity-period plane shows an indistinguishable distribution of the two populations, implying that orbital circularization occurs in the first 1 Myr of a star's lifetime. With the results presented in this paper we increase by {approx}4% the small sample of PMS spectroscopic binary stars with known orbital elements.« less

Photometric search for variable stars in the young open cluster Berkeley 59

NASA Astrophysics Data System (ADS)

Lata, Sneh; Pandey, A. K.; Maheswar, G.; Mondal, Soumen; Kumar, Brijesh

2011-12-01

We present the time series photometry of stars located in the extremely young open cluster Berkeley 59. Using the 1.04-m telescope at Aryabhatta Research Institute of Observational Sciences (ARIES), Nainital, we have identified 42 variables in a field of ˜13 × 13 arcmin2 around the cluster. The probable members of the cluster have been identified using a (V, V-I) colour-magnitude diagram and a (J-H, H-K) colour-colour diagram. 31 variables have been found to be pre-main-sequence stars associated with the cluster. The ages and masses of the pre-main-sequence stars have been derived from the colour-magnitude diagram by fitting theoretical models to the observed data points. The ages of the majority of the probable pre-main-sequence variable candidates range from 1 to 5 Myr. The masses of these pre-main-sequence variable stars have been found to be in the range of ˜0.3 to ˜3.5 M⊙, and these could be T Tauri stars. The present statistics reveal that about 90 per cent T Tauri stars have period <15 d. The classical T Tauri stars are found to have a larger amplitude than the weak-line T Tauri stars. There is an indication that the amplitude decreases with an increase in mass, which could be due to the dispersal of the discs of relatively massive stars.

YSOVAR: Six Pre-main-sequence Eclipsing Binaries in the Orion Nebula Cluster

DTIC Science & Technology

2012-06-25

reserved. Printed in the U.S.A. YSOVAR: SIX PRE-MAIN-SEQUENCE ECLIPSING BINARIES IN THE ORION NEBULA CLUSTER M. Morales-Calderón1,2, J. R. Stauffer1, K. G...multi-color light curves for∼2400 candidate Orion Nebula Cluster (ONC) members from our Warm Spitzer Exploration Science Program YSOVAR, we have...readable tables 1. INTRODUCTION The Orion Nebula Cluster (ONC) contains several thousand members, and since it is nearby, it provides an excellent em

Pre-main-sequence isochrones - II. Revising star and planet formation time-scales

NASA Astrophysics Data System (ADS)

Bell, Cameron P. M.; Naylor, Tim; Mayne, N. J.; Jeffries, R. D.; Littlefair, S. P.

2013-09-01

We have derived ages for 13 young (<30 Myr) star-forming regions and find that they are up to a factor of 2 older than the ages typically adopted in the literature. This result has wide-ranging implications, including that circumstellar discs survive longer (≃ 10-12 Myr) and that the average Class I lifetime is greater (≃1 Myr) than currently believed. For each star-forming region, we derived two ages from colour-magnitude diagrams. First, we fitted models of the evolution between the zero-age main sequence and terminal-age main sequence to derive a homogeneous set of main-sequence ages, distances and reddenings with statistically meaningful uncertainties. Our second age for each star-forming region was derived by fitting pre-main-sequence stars to new semi-empirical model isochrones. For the first time (for a set of clusters younger than 50 Myr), we find broad agreement between these two ages, and since these are derived from two distinct mass regimes that rely on different aspects of stellar physics, it gives us confidence in the new age scale. This agreement is largely due to our adoption of empirical colour-Teff relations and bolometric corrections for pre-main-sequence stars cooler than 4000 K. The revised ages for the star-forming regions in our sample are: ˜2 Myr for NGC 6611 (Eagle Nebula; M 16), IC 5146 (Cocoon Nebula), NGC 6530 (Lagoon Nebula; M 8) and NGC 2244 (Rosette Nebula); ˜6 Myr for σ Ori, Cep OB3b and IC 348; ≃10 Myr for λ Ori (Collinder 69); ≃11 Myr for NGC 2169; ≃12 Myr for NGC 2362; ≃13 Myr for NGC 7160; ≃14 Myr for χ Per (NGC 884); and ≃20 Myr for NGC 1960 (M 36).

Mid-IR Spectra Herbig Ae/Be Stars

NASA Technical Reports Server (NTRS)

Wooden, Diane; Witteborn, Fred C. (Technical Monitor)

1997-01-01

Herbig Ae/Be stars are intermediate mass pre-main sequence stars, the higher mass analogues to the T Tauri stars. Because of their higher mass, they are expected form more rapidly than the T Tauri stars. Whether the Herbig Ae/Be stars accrete only from collapsing infalling envelopes or whether accrete through geometrically flattened viscous accretion disks is of current debate. When the Herbig Ae/Be stars reach the main sequence they form a class called Vega-like stars which are known from their IR excesses to have debris disks, such as the famous beta Pictoris. The evolutionary scenario between the pre-main sequence Herbig Ae/Be stars and the main sequence Vega-like stars is not yet revealed and it bears on the possibility of the presence of Habitable Zone planets around the A stars. Photometric studies of Herbig Ae/Be stars have revealed that most are variable in the optical, and a subset of stars show non-periodic drops of about 2 magnitudes. These drops in visible light are accompanied by changes in their colors: at first the starlight becomes reddened, and then it becomes bluer, the polarization goes from less than 0.1 % to roughly 1% during these minima. The theory postulated by V. Grinnin is that large cometary bodies on highly eccentric orbits occult the star on their way to being sublimed, for systems that are viewed edge-on. This theory is one of several controversial theories about the nature of Herbig Ae/Be stars. A 5 year mid-IR spectrophotometric monitoring campaign was begun by Wooden and Butner in 1992 to look for correlations between the variations in visible photometry and mid-IR dust emission features. Generally the approximately 20 stars that have been observed by the NASA Ames HIFOGS spectrometer have been steady at 10 microns. There are a handful, however, that have shown variable mid-IR spectra, with 2 showing variations in both the continuum and features anti-correlated with visual photometry, and 3 showing variations in the emission features only while the continuum level remained unchanged. The first 2 stars mentioned probably have reprocessing envelopes. The other 3 stars gives important clues to the controversy over the geometry of the gas and dust around these pre-main sequence stars: the steady underlying 10 microns continuum and variable features indicates that an optically thick continuum probably arising from an accretion disk is decoupled from the optically thin emission features which may arise in a disk atmosphere. Bernadette Rodgers has joined this monitoring campaign in the near-IR using GRIMII with the goal of detecting variations in the hot dust continuum and the gas density in the dense accretion region close to these stars.

Pre-main sequence sun: a dynamic approach

DOE Office of Scientific and Technical Information (OSTI.GOV)

Newman, M.J.; Winkler, K.H.A.

1979-01-01

The classical pre-main sequence evolutionary behavior found by Hayashi and his coworkers for the Sun depends crucially on the choice of initial conditions. The Hayashi picture results from beginning the calculation with an already centrally condensed, highly Jeans unstable object not terribly far removed from the stellar state initially. The present calculation follows the work of Larson in investigating the hydrodynamic collapse and self-gravitational accretion of an initially uniform, just Jeans unstable interstellar gas-dust cloud. The resulting picture for the early history of the Sun is quite different from that found by Hayashi. A rather small (R approx. = 2more » R/sub sun/), low-luminosity (L greater than or equal to L/sub sun/) protostellar core develops. A fully convective stellar core, characteristic of Hayashi's work, is not found during the accretion process, and can only develop, if at all, in the subsequent pre-main sequence Kelvin-Helmholtz contraction of the core. 3 figures, 1 table.« less

The dot{M}-M_* relation of pre-main-sequence stars: a consequence of X-ray driven disc evolution

NASA Astrophysics Data System (ADS)

Ercolano, B.; Mayr, D.; Owen, J. E.; Rosotti, G.; Manara, C. F.

2014-03-01

We analyse current measurements of accretion rates on to pre-main-sequence stars as a function of stellar mass, and conclude that the steep dependence of accretion rates on stellar mass is real and not driven by selection/detection threshold, as has been previously feared. These conclusions are reached by means of statistical tests including a survival analysis which can account for upper limits. The power-law slope of the dot{M}-M_* relation is found to be in the range of 1.6-1.9 for young stars with masses lower than 1 M⊙. The measured slopes and distributions can be easily reproduced by means of a simple disc model which includes viscous accretion and X-ray photoevaporation. We conclude that the dot{M}-M_* relation in pre-main-sequence stars bears the signature of disc dispersal by X-ray photoevaporation, suggesting that the relation is a straightforward consequence of disc physics rather than an imprint of initial conditions.

Evolution of Pre-Main Sequence Accretion Disks

NASA Technical Reports Server (NTRS)

Hartmann, Lee W.

2004-01-01

The aim of this project is to develop a comprehensive global picture of the physical conditions in, and evolutionary timescales of, pre-main sequence accretion disks. The results of this work will help constrain the initial conditions for planet formation. To this end we are developing much larger samples of 3-10 Myr-old stars to provide better empirical constraints on protoplanetary disk evolution; measuring disk accretion rates in these systems; and constructing detailed model disk structures consistent with observations to infer physical conditions such as grain growth in protoplanetary disks.

Evolution of Pre-Main Sequence Accretion Disks

NASA Technical Reports Server (NTRS)

Hartmann, Lee W.

2003-01-01

The aim of this project is to develop a comprehensive global picture of the physical conditions in, and evolutionary timescales of, pre-main sequence accretion disks. The results of this work will help constrain the initial conditions for planet formation. To this end we are developing much larger samples of 3-10 Myr-old stars to provide better empirical constraints on protoplanetary disk evolution; measuring disk accretion rates in these systems; and constructing detailed model disk structures consistent with observations to infer physical conditions such as grain growth in protoplanetary disks.

Evolution Models of Helium White Dwarf–Main-sequence Star Merger Remnants

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Xianfei; Bi, Shaolan; Hall, Philip D.

It is predicted that orbital decay by gravitational-wave radiation and tidal interaction will cause some close binary stars to merge within a Hubble time. The merger of a helium-core white dwarf with a main-sequence (MS) star can produce a red giant branch star that has a low-mass hydrogen envelope when helium is ignited and thus become a hot subdwarf. Because detailed calculations have not been made, we compute post-merger models with a stellar evolution code. We find the evolutionary paths available to merger remnants and find the pre-merger conditions that lead to the formation of hot subdwarfs. We find thatmore » some such mergers result in the formation of stars with intermediate helium-rich surfaces. These stars later develop helium-poor surfaces owing to diffusion. Combining our results with a model population and comparing to observed stars, we find that some observed intermediate helium-rich hot subdwarfs can be explained as the remnants of the mergers of helium-core white dwarfs with low-mass MS stars.« less

A search for pre-main-sequence stars in high-latitude molecular clouds. 3: A survey of the Einstein database

NASA Technical Reports Server (NTRS)

Caillault, Jean-Pierre; Magnani, Loris; Fryer, Chris

1995-01-01

In order to discern whether the high-latitude molecular clouds are regions of ongoing star formation, we have used X-ray emission as a tracer of youthful stars. The entire Einstein database yields 18 images which overlap 10 of the clouds mapped partially or completely in the CO (1-0) transition, providing a total of approximately 6 deg squared of overlap. Five previously unidentified X-ray sources were detected: one has an optical counterpart which is a pre-main-sequence (PMS) star, and two have normal main-sequence stellar counterparts, while the other two are probably extragalactic sources. The PMS star is located in a high Galactic latitude Lynds dark cloud, so this result is not too suprising. The translucent clouds, though, have yet to reveal any evidence of star formation.

Pre-main sequence variables in young cluster Stock 18

NASA Astrophysics Data System (ADS)

Sinha, Tirthendu; Sharma, Saurabh; Pandey, Rakesh; Pandey, Anil Kumar

2018-04-01

We have carried out multi-epoch deep I band photometry of the open cluster Stock 18 to search for variable stars in star forming regions. In the present study, we identified 65 periodic and 217 non-periodic variable stars. The periods of most of the periodic variables are between 2 hours to 15 days and their magnitude varies between 0.05 to 0.6 mag. We have derived spectral energy distributions for 48 probable pre-main sequence variables. Their average age and mass are 2.7 ± 0.3 Myrs and 2.7 ± 0.2 Mo, respectively.

VizieR Online Data Catalog: NGC 7129 pre-main sequence stars (Stelzer+, 2009)

NASA Astrophysics Data System (ADS)

Stelzer, B.; Scholz, A.

2010-09-01

We make use of X-ray and IR imaging observations to identify the pre-main sequence stars in NGC 7129. We define a sample of young stellar objects based on color-color diagrams composed from IR photometry between 1.6 and 8um, from 2MASS and Spitzer, and based on X-ray detected sources from a Chandra observation. A 22ks long Chandra observation targeting the Herbig star SVS 12 was carried out on Mar 11, 2006 (start of observation UT 14h29m18s). (5 data files).

Pre-processing SAR image stream to facilitate compression for transport on bandwidth-limited-link

DOEpatents

Rush, Bobby G.; Riley, Robert

2015-09-29

Pre-processing is applied to a raw VideoSAR (or similar near-video rate) product to transform the image frame sequence into a product that resembles more closely the type of product for which conventional video codecs are designed, while sufficiently maintaining utility and visual quality of the product delivered by the codec.

The intermediate-age pre-cataclysmic variables SDSS J172406+562003 and RE J2013+4002

NASA Astrophysics Data System (ADS)

Shimansky, V. V.; Borisov, N. V.; Nurtdinova, D. N.; Mitrofanova, A. A.; Vlasyuk, V. V.; Spiridonova, O. I.

2012-06-01

We have analyzed the physical status of the pre-cataclysmic variables SDSSJ172406+562003 and RE J2013+4002, which have evolved after their common-envelope stage a time t = 106-107 years. Spectroscopy and photometry of these systems were performed with the 6-m and 1-m telescopes of the Special Astrophysical Observatory. We demonstrate that emission lines in the spectra were formed solely by the reflection of radiation emitted by the white dwarfs on the surfaces of their cool companions, under conditions close to local thermodynamic equilibrium. These effects are also responsible for most of the objects' photometric variability amplitude. However, comparing the light curves of SDSS 172406 from different epochs, we find aperiodic brightness variations, probably due to spottedness of the surface of the secondary. Jointly analyzing the spectra, radial-velocity curves, and light curves of the pre-cataclysmic variables and modeling the reflection effects, we have derived their fundamental parameters. We demonstrate that the secondaries in these systems are consistent with evolutionary models for main-sequence stars and do not have the luminosity excesses characteristic of cool stars in young pre-cataclysmic variables.

Detectable close-in planets around white dwarfs through late unpacking

NASA Astrophysics Data System (ADS)

Veras, Dimitri; Gänsicke, Boris T.

2015-02-01

Although 25-50 per cent of white dwarfs (WDs) display evidence for remnant planetary systems, their orbital architectures and overall sizes remain unknown. Vibrant close-in (≃1 R⊙) circumstellar activity is detected at WDs spanning many Gyr in age, suggestive of planets further away. Here we demonstrate how systems with 4 and 10 closely packed planets that remain stable and ordered on the main sequence can become unpacked when the star evolves into a WD and experience pervasive inward planetary incursions throughout WD cooling. Our full-lifetime simulations run for the age of the Universe and adopt main-sequence stellar masses of 1.5, 2.0 and 2.5 M⊙, which correspond to the mass range occupied by the progenitors of typical present-day WDs. These results provide (i) a natural way to generate an ever-changing dynamical architecture in post-main-sequence planetary systems, (ii) an avenue for planets to achieve temporary close-in orbits that are potentially detectable by transit photometry and (iii) a dynamical explanation for how residual asteroids might pollute particularly old WDs.

Discovery and Characterization of Eclipsing Binary Stars and Transiting Planets in Young Benchmark Clusters: The Pleiades and Hyades

NASA Astrophysics Data System (ADS)

Stassun, Keivan; David, Trevor J.; Conroy, Kyle E.; Hillenbrand, Lynne; Stauffer, John R.; Pepper, Joshua; Rebull, Luisa M.; Cody, Ann Marie

2016-06-01

Prior to K2, only one eclipsing binary in the Pleiades was known (HD 23642). We present the discovery and characterization of three additional eclipsing binaries (EBs) in this ~120 Myr old benchmark open cluster. Unlike HD 23642, all three of the new EBs are low mass (Mtot < 1 M⊙) and thus their components are still undergoing pre-main-sequence contraction at the Pleiades age. Low mass EBs are rare, especially in the pre-main-sequence phase, and thus these systems are valuable for constraining theoretical stellar evolution models. One of the three new EBs is single-lined with a K-type primary (HII 2407). The second (HCG 76) comprises two nearly equal-mass 0.3 M⊙ stars, with masses and radii measured with precisions of better than 3% and 5%, respectively. The third (MHO 9) has an M-type primary with a secondary that is possibly quite close to the hydrogen-burning limit, but needs additional follow-up observations to better constrain its parameters. We use the precise parameters of HCG 76 to test the predictions of stellar evolution models, and to derive an independent distance to the Pleiades of 132±5 pc. Finally, we present tentative evidence for differential rotation in the primary component of the newly discovered Pleiades EB HII 2407, and we also characterize a newly discovered transiting Neptune-sized planet orbiting an M-dwarf in the Hyades.

Stellar and Circumstellar Properties of the Pre-Main-Sequence Binary GV Tau from Infrared Spectroscopy

NASA Astrophysics Data System (ADS)

Doppmann, Greg W.; Najita, Joan R.; Carr, John S.

2008-09-01

We report spatially resolved spectroscopy of both components of the low-mass pre-main-sequence binary GV Tau. High-resolution spectroscopy in the K and L bands is used to characterize the stellar properties of the binary and to explore the nature of the circumstellar environment. We find that the southern component, GV Tau S, is a radial velocity variable, possibly as a result of an unseen low-mass companion. The strong warm gaseous HCN absorption reported previously by Gibb and coworkers toward GV Tau S was not present during the epoch of our observations. Instead, we detect warm (~500 K) molecular absorption with similar properties toward the northern infrared companion, GV Tau N. At the epoch of our observations, the absorbing gas toward GV Tau N was approximately at the radial velocity of the GV Tau molecular envelope, but it was redshifted with respect to the star by ~13 km s-1. One interpretation of our results is that GV Tau N is also a binary and that most of the warm molecular absorption arises in a circumbinary disk viewed close to edge-on. Data presented herein were obtained at the W. M. Keck Observatory from telescope time allocated to the National Aeronautics and Space Administration through the agency's scientific partnership with the California Institute of Technology and the University of California. The Observatory was made possible by the generous financial support of the W. M. Keck Foundation.

Measuring the Mass of a Pre-Main Sequence Binary Star Through the Orbit of TWA 5A

NASA Astrophysics Data System (ADS)

Konopacky, Q. M.; Ghez, A. M.; McCabe, C.; Duchene, G.; Macintosh, B. A.

2005-12-01

We present the results of a five year monitoring campaign of the close binary TWA 5Aab in the TW Hydrae association, using speckle and adaptive optics on the W.M. Keck 10 m telescopes. These measurements were taken as part of our ongoing monitoring of pre-main sequence (PMS) binaries in an effort to increase the number of dynamically determined PMS masses and thereby calibrate the theoretical PMS evolutionary tracks. Our observations have allowed us to obtain the first determination of this system's astrometric orbit. We find an orbital period of 5.55 ± 0.07 years and a semi-major axis of 0.063 arcsec ± 0.004 arcsec. Combining these results with a kinematic distance, we calculate a total mass of 0.70 ± 0.24 M⊙ for this system. This mass measurement, as well as the estimated age of this system, are in best agreement with the model predictions of Baraffe et al. (1998), but are also consistent to within 1.6σ of all other models considered. Our formal significance is low due to our proper accounting of correlated uncertainties; these correlations are important and generally not accounted for in comparisons of this kind. Nonetheless, with only a few more years of observation, these models will be easily distinguished. Support for this work was provided by the NASA Astrobiology Institute, the NSF Science & Technology Center for AO, managed by UCSC (AST-9876783), and the Packard Foundation.

Photometry and spectroscopy in the open cluster Alpha Persei, 2

NASA Technical Reports Server (NTRS)

Prosser, Charles F.

1993-01-01

Results from a combination of new spectroscopic and photometric observations in the lower main-sequence and pre-main sequence of the open cluster alpha Persei are presented. New echelle spectroscopy has provided radial and rotational velocity information for thirteen candidate members, three of which are nonmembers based on radial velocity, absence of a Li 6707A feature, and absence of H-alpha emission. A set of revised rotational velocity estimates for several slowly rotating candidates identified earlier is given, yielding rotational velocities as low as 7 km/s for two apparent cluster members. VRI photometry for several pre-main sequence members is given; the new (V,V-I(sub K)) photometry yields a more clearly defined pre-main sequence. A list of approximately 43 new faint candidate members based on the (V,V-I(sub K)) CCD photometry is presented in an effort to identify additional cluster members at very low masses. Low-dispersion spectra obtained for several of these candidates provide in some cases supporting evidence for cluster membership. The single brown dwarf candidate in this cluster is for the first time placed in a color-magnitude diagram with other cluster members, providing a better means for establishing its true status. Stars from among the list of new photometric candidates may provide the means for establishing a sequence of cluster members down to very faint magnitudes (V approximately 21) and consequently very low masses. New coordinate determinations for previous candidate members and finding charts for the new photometric candidates are provided in appendices.

Zodiacal Exoplanets in Time (ZEIT). III. A Short-period Planet Orbiting a Pre-main-sequence Star in the Upper Scorpius OB Association

NASA Astrophysics Data System (ADS)

Mann, Andrew W.; Newton, Elisabeth R.; Rizzuto, Aaron C.; Irwin, Jonathan; Feiden, Gregory A.; Gaidos, Eric; Mace, Gregory N.; Kraus, Adam L.; James, David J.; Ansdell, Megan; Charbonneau, David; Covey, Kevin R.; Ireland, Michael J.; Jaffe, Daniel T.; Johnson, Marshall C.; Kidder, Benjamin; Vanderburg, Andrew

2016-09-01

We confirm and characterize a close-in ({P}{{orb}} = 5.425 days), super-Neptune sized ({5.04}-0.37+0.34 {R}\\oplus ) planet transiting K2-33 (2MASS J16101473-1919095), a late-type (M3) pre-main-sequence (11 Myr old) star in the Upper Scorpius subgroup of the Scorpius-Centaurus OB association. The host star has the kinematics of a member of the Upper Scorpius OB association, and its spectrum contains lithium absorption, an unambiguous sign of youth (\\lt 20 Myr) in late-type dwarfs. We combine photometry from K2 and the ground-based MEarth project to refine the planet’s properties and constrain the host star’s density. We determine K2-33’s bolometric flux and effective temperature from moderate-resolution spectra. By utilizing isochrones that include the effects of magnetic fields, we derive a precise radius (6%-7%) and mass (16%) for the host star, and a stellar age consistent with the established value for Upper Scorpius. Follow-up high-resolution imaging and Doppler spectroscopy confirm that the transiting object is not a stellar companion or a background eclipsing binary blended with the target. The shape of the transit, the constancy of the transit depth and periodicity over 1.5 yr, and the independence with wavelength rule out stellar variability or a dust cloud or debris disk partially occulting the star as the source of the signal; we conclude that it must instead be planetary in origin. The existence of K2-33b suggests that close-in planets can form in situ or migrate within ˜10 Myr, e.g., via interactions with a disk, and that long-timescale dynamical migration such as by Lidov-Kozai or planet-planet scattering is not responsible for all short-period planets.

The evolution of the lithium abundances of solar-type stars. II - The Ursa Major Group

NASA Technical Reports Server (NTRS)

Soderblom, David R.; Pilachowski, Catherine A.; Fedele, Stephen B.; Jones, Burton F.

1993-01-01

We draw upon a recent study of the membership of the Ursa Major Group (UMaG) to examine lithium among 0.3 Gyr old solar-type stars. For most G and K dwarfs, Li confirms the conclusions about membership in UMaG reached on the basis of kinematics and chromospheric activity. G and K dwarfs in UMaG have less Li than comparable stars in the Pleiades. This indicates that G and K dwarfs undergo Li depletion while they are on the main sequence, in addition to any pre-main-sequence depletion they may have experienced. Moreover, the Li abundances of the Pleiades K dwarfs cannot be attributed to main-sequence depletion alone, demonstrating that pre-main-sequence depletion of Li also takes place. The sun's Li abundance implies that the main-sequence mechanism becomes less effective with age. The hottest stars in UMaG have Li abundances like those of hot stars in the Pleiades and Hyades and in T Tauris, and the two genuine UMaG members with temperatures near Boesgaard's Li chasm have Li abundances consistent with that chasm developing fully by 0.3 Gyr for stars with UMaG's metallicity. We see differences in the abundance of Li between UMaG members of the same spectral types, indicating that a real spread in the lithium abundance exists within this group.

Tidal Dissipation In Rotating Low Mass Stars: Implications For The Orbital Evolution Of Close In Planets

NASA Astrophysics Data System (ADS)

Gallet, Florian; Bolmont, Emeline; Mathis, Stéphane; Charbonnel, Corinne; Amard, Louis; Alibert, Yann

2017-10-01

Close-in planets represent a large fraction of the population of confirmed exoplanets. To understand the dynamical evolution of these planets, star-planet interactions must be taken into account. In particular, the dependence of the tidal interactions on the structural parameters of the star, its rotation, and its metallicity should be treated in the models. We quantify how the tidal dissipation in the convective envelope of rotating low-mass stars evolves in time. We also investigate the possible consequences of this evolution on planetary orbital evolution. In Gallet et al. (2017) and Bolmont et al. (2017) we generalized the work of Bolmont & Mathis (2016) by following the orbital evolution of close-in planets using the new tidal dissipation predictions for advanced phases of stellar evolution and non-solar metallicity. We find that during the pre-main sequence the evolution of tidal dissipation is controlled by the evolution of the internal structure of the star through the stellar contraction. On the main-sequence tidal dissipation is strongly driven by the evolution of the surface rotation that is impacted by magnetized stellar winds braking. Finally, during the more evolved phases, the tidal dissipation sharply decreases as radiative core retreats in mass and radius towards the red-giant branch. Using an orbital evolution model, we also show that changing the metallicity leads to diUerent orbital evolutions (e.g., planets migrate farther out from an initially fast rotating metal rich star). By using this model, we qualitatively reproduced the observational trends of the population of hot Jupiters with the metallicity of their host stars. However, more work still remain to be do so as to be able to quantitatively fit our results to the observations.

The incidence of stellar mergers and mass gainers among massive stars

DOE Office of Scientific and Technical Information (OSTI.GOV)

De Mink, S. E.; Sana, H.; Langer, N.

2014-02-10

Because the majority of massive stars are born as members of close binary systems, populations of massive main-sequence stars contain stellar mergers and products of binary mass transfer. We simulate populations of massive stars accounting for all major binary evolution effects based on the most recent binary parameter statistics and extensively evaluate the effect of model uncertainties. Assuming constant star formation, we find that 8{sub −4}{sup +9}% of a sample of early-type stars are the products of a merger resulting from a close binary system. In total we find that 30{sub −15}{sup +10}% of massive main-sequence stars are the productsmore » of binary interaction. We show that the commonly adopted approach to minimize the effects of binaries on an observed sample by excluding systems detected as binaries through radial velocity campaigns can be counterproductive. Systems with significant radial velocity variations are mostly pre-interaction systems. Excluding them substantially enhances the relative incidence of mergers and binary products in the non-radial velocity variable sample. This poses a challenge for testing single stellar evolutionary models. It also raises the question of whether certain peculiar classes of stars, such as magnetic O stars, are the result of binary interaction and it emphasizes the need to further study the effect of binarity on the diagnostics that are used to derive the fundamental properties (star-formation history, initial mass function, mass-to-light ratio) of stellar populations nearby and at high redshift.« less

From protostellar to pre-main-sequence evolution

NASA Astrophysics Data System (ADS)

D'Antona, F.

I summarize the status of pre-main-sequence evolutionary tracks starting from the first steps dating back to the concept of Hayashi track. Understanding of the dynamical protostellar phase in the vision of Palla & Stahler, who introduced the concept of the deuterium burning thermostat and of stellar birthline, provided for a long time a link between the dynamical and hydrostatic evolution. Disk accretion however changed considerably the view, but re-introducing some ambiguities which must still be solved. The limitations and uncertainties in the mass and age determination from models for young stellar objects are summarized, but the burning of light elements is still a powerful observational signature.

The sdA problem - I. Physical properties

NASA Astrophysics Data System (ADS)

Pelisoli, Ingrid; Kepler, S. O.; Koester, D.

2018-04-01

The so-called sdA stars are defined by having H-rich spectra and surface gravities similar to hot subdwarf stars, but effective temperature below the zero-age horizontal branch. Their evolutionary history is an enigma: their surface gravity is too high for main-sequence stars, but too low for single evolution white dwarfs. They are most likely byproducts of binary evolution, including blue-stragglers, extremely-low mass white dwarf stars (ELMs) and their precursors (pre-ELMs). A small number of ELMs with similar properties to sdAs is known. Other possibilities include metal-poor A/F dwarfs, second generation stars, or even stars accreted from dwarf galaxies. In this work, we analyse colours, proper motions, and spacial velocities of a sample of sdAs from the Sloan Digital Sky Survey to assess their nature and evolutionary origin. We define a probability of belonging to the main sequence and a probability of being a (pre-)ELM based on these properties. We find that 7 per cent of the sdAs are more likely to be (pre-)ELMs than main-sequence stars. However, the spacial velocity distribution suggests that over 35 per cent of them cannot be explained as single metal-poor A/F stars.

MicroRNA categorization using sequence motifs and k-mers.

PubMed

Yousef, Malik; Khalifa, Waleed; Acar, İlhan Erkin; Allmer, Jens

2017-03-14

Post-transcriptional gene dysregulation can be a hallmark of diseases like cancer and microRNAs (miRNAs) play a key role in the modulation of translation efficiency. Known pre-miRNAs are listed in miRBase, and they have been discovered in a variety of organisms ranging from viruses and microbes to eukaryotic organisms. The computational detection of pre-miRNAs is of great interest, and such approaches usually employ machine learning to discriminate between miRNAs and other sequences. Many features have been proposed describing pre-miRNAs, and we have previously introduced the use of sequence motifs and k-mers as useful ones. There have been reports of xeno-miRNAs detected via next generation sequencing. However, they may be contaminations and to aid that important decision-making process, we aimed to establish a means to differentiate pre-miRNAs from different species. To achieve distinction into species, we used one species' pre-miRNAs as the positive and another species' pre-miRNAs as the negative training and test data for the establishment of machine learned models based on sequence motifs and k-mers as features. This approach resulted in higher accuracy values between distantly related species while species with closer relation produced lower accuracy values. We were able to differentiate among species with increasing success when the evolutionary distance increases. This conclusion is supported by previous reports of fast evolutionary changes in miRNAs since even in relatively closely related species a fairly good discrimination was possible.

INTRINSIC COLORS, TEMPERATURES, AND BOLOMETRIC CORRECTIONS OF PRE-MAIN-SEQUENCE STARS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pecaut, Mark J.; Mamajek, Eric E.

2013-09-01

We present an analysis of the intrinsic colors and temperatures of 5-30 Myr old pre-main-sequence (pre-MS) stars using the F0- through M9-type members of nearby, negligibly reddened groups: the η Cha cluster, the TW Hydra Association, the β Pic Moving Group, and the Tucana-Horologium Association. To check the consistency of spectral types from the literature, we estimate new spectral types for 52 nearby pre-MS stars with spectral types F3 through M4 using optical spectra taken with the SMARTS 1.5 m telescope. Combining these new types with published spectral types and photometry from the literature (Johnson-Cousins BVI{sub C} , 2MASS JHK{submore » S} and WISE W1, W2, W3, and W4), we derive a new empirical spectral type-color sequence for 5-30 Myr old pre-MS stars. Colors for pre-MS stars match dwarf colors for some spectral types and colors, but for other spectral types and colors, deviations can exceed 0.3 mag. We estimate effective temperatures (T {sub eff}) and bolometric corrections (BCs) for our pre-MS star sample through comparing their photometry to synthetic photometry generated using the BT-Settl grid of model atmosphere spectra. We derive a new T {sub eff} and BC scale for pre-MS stars, which should be a more appropriate match for T Tauri stars than often-adopted dwarf star scales. While our new T {sub eff} scale for pre-MS stars is within ≅100 K of dwarfs at a given spectral type for stars« less

The Gaia-ESO Survey: the present-day radial metallicity distribution of the Galactic disc probed by pre-main-sequence clusters

NASA Astrophysics Data System (ADS)

Spina, L.; Randich, S.; Magrini, L.; Jeffries, R. D.; Friel, E. D.; Sacco, G. G.; Pancino, E.; Bonito, R.; Bravi, L.; Franciosini, E.; Klutsch, A.; Montes, D.; Gilmore, G.; Vallenari, A.; Bensby, T.; Bragaglia, A.; Flaccomio, E.; Koposov, S. E.; Korn, A. J.; Lanzafame, A. C.; Smiljanic, R.; Bayo, A.; Carraro, G.; Casey, A. R.; Costado, M. T.; Damiani, F.; Donati, P.; Frasca, A.; Hourihane, A.; Jofré, P.; Lewis, J.; Lind, K.; Monaco, L.; Morbidelli, L.; Prisinzano, L.; Sousa, S. G.; Worley, C. C.; Zaggia, S.

2017-05-01

Context. The radial metallicity distribution in the Galactic thin disc represents a crucial constraint for modelling disc formation and evolution. Open star clusters allow us to derive both the radial metallicity distribution and its evolution over time. Aims: In this paper we perform the first investigation of the present-day radial metallicity distribution based on [Fe/H] determinations in late type members of pre-main-sequence clusters. Because of their youth, these clusters are therefore essential for tracing the current interstellar medium metallicity. Methods: We used the products of the Gaia-ESO Survey analysis of 12 young regions (age < 100 Myr), covering Galactocentric distances from 6.67 to 8.70 kpc. For the first time, we derived the metal content of star forming regions farther than 500 pc from the Sun. Median metallicities were determined through samples of reliable cluster members. For ten clusters the membership analysis is discussed in the present paper, while for other two clusters (I.e. Chamaeleon I and Gamma Velorum) we adopted the members identified in our previous works. Results: All the pre-main-sequence clusters considered in this paper have close-to-solar or slightly sub-solar metallicities. The radial metallicity distribution traced by these clusters is almost flat, with the innermost star forming regions having [Fe/H] values that are 0.10-0.15 dex lower than the majority of the older clusters located at similar Galactocentric radii. Conclusions: This homogeneous study of the present-day radial metallicity distribution in the Galactic thin disc favours models that predict a flattening of the radial gradient over time. On the other hand, the decrease of the average [Fe/H] at young ages is not easily explained by the models. Our results reveal a complex interplay of several processes (e.g. star formation activity, initial mass function, supernova yields, gas flows) that controlled the recent evolution of the Milky Way. Based on observations made with the ESO/VLT, at Paranal Observatory, under program 188.B-3002 (The Gaia-ESO Public Spectroscopic Survey).Full Table 1 is only available at the CDS via anonymous ftp to http://cdsarc.u-strasbg.fr (http://130.79.128.5) or via http://cdsarc.u-strasbg.fr/viz-bin/qcat?J/A+A/601/A70

Paleomagnetic and AMS study of Permian and Triassic rocks from the Hronic Nappe and Paleogene rocks from the Central Carpathian Paleogene Basin, Western Carpathians

NASA Astrophysics Data System (ADS)

Márton, Emö; Madzin, Jozef; Bučová, Jana; Grabowski, Jacek; Plašienka, Dušan; Aubrecht, Roman

2017-04-01

The Hronic (Choč) units form the highest cover nappe system of the Central Western Carpathians which was emplaced over the Fatric (Krížna) nappe system during the Late Cretaceous. The Permian (red beds and lava flows) and Triassic (sediments) rocks, the main targets of our study, were affected only by diagenetic or very low-grade, burial-related recrystallization and were tilted and transported together. The pre-late Cretaceous sequence is overlapped by Paleogene mainly flysch sequences. Three laboratories (Bratislava, Budapest and Warsaw) were involved in standard paleomagnetic processing and AMS measurements of the samples, while Curie-points were determined in Budapest. The site/locality mean paleomagnetic directions obtained were significantly different from the local direction of the present Earth magnetic field, indicating the long term stability of the paleomagnetic signal. The magnetic fabrics varied from un-oriented to dominantly schistose with well-defined lineations. The latter were normally subhorizontal, although subvertical maxima also occurred among the Triassic sediments. Shallow inclinations, after tilt corrections, suggest near-equatorial position for most of the Permian and Lower Triassic, while around 20°N for the Middle-Upper Triassic localities. The paleomagnetic declinations are interpreted in terms of CW tectonic rotations, which are normally larger for the Permian than for the Triassic samples, although there are some differences within the same age groups. This may be attributed to differential movements during nappe emplacement or subsequent tectonic disturbances. For two localities from the Paleogene cover sequence of the Hronic units, close to the main sampling area (Low Tatra Mts) of the present study documented fairly large CCW rotations, thus obtained additional evidence for the general CCW rotation of the Central Western Carpathians during the Cenozoic. Thus, we conclude that the Cenozoic CCW rotation was pre-dated by large CW rotations, probably connected to the nappe emplacement. In addition, a pre-Jurassic moderate CW rotation is inferred from the difference in declinations between Triassic and Permian palaeomagnetic declinations. Acknowledgement: This work was financially supported by the Slovak Research and Development Agency under the contract No. APVV-0212-12 and by the Hungarian Scientific Research Fund OTKA K105245.

The complete Einstein Observatory X-ray survey of the Orion Nebula region.

NASA Technical Reports Server (NTRS)

Gagne, Marc; Caillault, Jean-Pierre

1994-01-01

We have analyzed archival Einstein Observatory images of a roughly 4.5 square degree region centered on the Orion Nebula. In all, 245 distinct X-ray sources have been detected in six High Resolution Imager (HRI) and 17 Imaging Proportional Counter (IPC) observations. An optical database of over 2700 stars has been assembled to search for candidate counterparts to the X-ray sources. Roughly half the X-ray sources are identified with a single Orion Nebula cluster member. The 10 main-sequence O6-B5 cluster stars detected in Orion have X-ray activity levels comparable to field O and B stars. X-ray emission has also been detected in the direction of four main-sequence late-B and early-A type stars. Since the mechanisms producing X-rays in late-type coronae and early-type winds cannot operate in the late-B and early-A type atmospheres, we argue that the observed X-rays, with L(sub X) approximately = 3 x 10(exp 30) ergs/s, are probably produced in the coronae of unseen late-type binary companions. Over 100 X-ray sources have been associated with late-type pre-main sequence stars. The upper envelope of X-ray activity rises sharply from mid-F to late-G, with L(sub x)/L(sub bol) in the range 10(exp -4) to 2 x 10(exp -3) for stars later than approximately G7. We have looked for variability of the late-type cluster members on timescales of a day to a year and find that 1/4 of the stars show significantly variable X-ray emission. A handful of the late-type stars have published rotational periods and spectroscopic rotational velocities; however, we see no correlation between X-ray activity and rotation. Thus, for this sample of pre-main-sequence stars, the large dispersion in X-ray activity does not appear to be caused by the dispersion in rotation, in contrast with results obtained for low-mass main-sequence stars in the Pleiades and pre-main-sequence stars in Taurus-Auriga.

Theory of winds in late-type evolved and pre-main-sequence stars

NASA Technical Reports Server (NTRS)

Macgregor, K. B.

1983-01-01

Recent observational results confirm that many of the physical processes which are known to occur in the Sun also occur among late-type stars in general. One such process is the continuous loss of mass from a star in the form of a wind. There now exists an abundance of either direct or circumstantial evidence which suggests that most (if not all) stars in the cool portion of the HR diagram possess winds. An attempt is made to assess the current state of theoretical understanding of mass loss from two distinctly different classes of late-type stars: the post-main-sequence giant/supergiant stars and the pre-main-sequence T Tauri stars. Toward this end, the observationally inferred properties of the wind associated with each of the two stellar classes under consideration are summarized and compared against the predictions of existing theoretical models. Although considerable progress has been made in attempting to identify the mechanisms responsible for mass loss from cool stars, many fundamental problems remain to be solved.

THE YOUNG OPEN CLUSTERS KING 12, NGC 7788, AND NGC 7790: PRE-MAIN-SEQUENCE STARS AND EXTENDED STELLAR HALOS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Davidge, T. J.

2012-12-20

The stellar contents of the open clusters King 12, NGC 7788, and NGC 7790 are investigated using MegaCam images. Comparisons with isochrones yield an age <20 Myr for King 12, 20-40 Myr for NGC 7788, and 60-80 Myr for NGC 7790 based on the properties of stars near the main-sequence turnoff (MSTO) in each cluster. The reddening of NGC 7788 is much larger than previously estimated. The luminosity functions (LFs) of King 12 and NGC 7788 show breaks that are attributed to the onset of pre-main-sequence (PMS) objects, and comparisons with models of PMS evolution yield ages that are consistentmore » with those measured from stars near the MSTO. In contrast, the r' LF of main-sequence stars in NGC 7790 is matched to r' = 20 by a model that is based on the solar neighborhood mass function. The structural properties of all three clusters are investigated by examining the two-point angular correlation function of blue main-sequence stars. King 12 and NGC 7788 are each surrounded by a stellar halo that extends out to a radius of 5 arcmin ({approx}3.4 pc). It is suggested that these halos form in response to large-scale mass ejection early in the evolution of the clusters, as predicted by models. In contrast, blue main-sequence stars in NGC 7790 are traced out to a radius of {approx}7.5 arcmin ({approx}5.5 pc), with no evidence of a halo. It is suggested that all three clusters may have originated in the same star-forming complex, but not in the same giant molecular cloud.« less

The discovery of low-mass pre-main-sequence stars in Cepheus OB3b

NASA Astrophysics Data System (ADS)

Pozzo, M.; Naylor, T.; Jeffries, R. D.; Drew, J. E.

2003-05-01

We report the discovery of a low-mass pre-main-sequence (PMS) stellar population in the younger subgroup of the Cepheus OB3 association, Cep OB3b, using UBVI CCD photometry and follow-up spectroscopy. The optical survey covers approximately 1300 arcmin2 on the sky and gives a global photometric and astrometric catalogue for more than 7000 objects. The location of a PMS population is well defined in a V versus (V-I) colour-magnitude diagram. Multifibre spectroscopic results for optically selected PMS candidates confirm the T Tauri nature for 10 objects, with equal numbers of classical TTS (CTTS) and weak-line TTS (WTTS). There are six other objects that we classify as possible PMS stars. The newly discovered TTS stars have masses in the range ~0.9-3.0 Msolar and ages from <1 to nearly 10 Myr, based on the Siess, Dufour & Forestini isochrones. Their location close to the O and B stars of the association (especially the O7n star) demonstrates that low-mass star formation is indeed possible in such an apparently hostile environment dominated by early-type stars and that the latter must have been less effective in eroding the circumstellar discs of their lower-mass siblings compared with other OB associations (e.g. λ-Ori). We attribute this to the nature of the local environment, speculating that the bulk of molecular material, which shielded low-mass stars from the ionizing radiation of their early-type siblings, has only recently been removed.

On the Lack of Circumbinary Planets Orbiting Isolated Binary Stars

NASA Astrophysics Data System (ADS)

Fleming, David P.; Barnes, Rory; Graham, David E.; Luger, Rodrigo; Quinn, Thomas R.

2018-05-01

We outline a mechanism that explains the observed lack of circumbinary planets (CBPs) via coupled stellar–tidal evolution of isolated binary stars. Tidal forces between low-mass, short-period binary stars on the pre-main sequence slow the stellar rotations transferring rotational angular momentum to the orbit as the stars approach the tidally locked state. This transfer increases the binary orbital period, expanding the region of dynamical instability around the binary, and destabilizing CBPs that tend to preferentially orbit just beyond the initial dynamical stability limit. After the stars tidally lock, we find that angular momentum loss due to magnetic braking can significantly shrink the binary orbit, and hence the region of dynamical stability, over time, impacting where surviving CBPs are observed relative to the boundary. We perform simulations over a wide range of parameter space and find that the expansion of the instability region occurs for most plausible initial conditions and that, in some cases, the stability semimajor axis doubles from its initial value. We examine the dynamical and observable consequences of a CBP falling within the dynamical instability limit by running N-body simulations of circumbinary planetary systems and find that, typically, at least one planet is ejected from the system. We apply our theory to the shortest-period Kepler binary that possesses a CBP, Kepler-47, and find that its existence is consistent with our model. Under conservative assumptions, we find that coupled stellar–tidal evolution of pre-main sequence binary stars removes at least one close-in CBP in 87% of multi-planet circumbinary systems.

SEARCHING FOR YOUNG JUPITER ANALOGS AROUND AP COL: L-BAND HIGH-CONTRAST IMAGING OF THE CLOSEST PRE-MAIN-SEQUENCE STAR

DOE Office of Scientific and Technical Information (OSTI.GOV)

Quanz, Sascha P.; Avenhaus, Henning; Meyer, Michael R.

2012-08-01

The nearby M-dwarf AP Col was recently identified by Riedel et al. as a pre-main-sequence star (age 12-50 Myr) situated only 8.4 pc from the Sun. The combination of its youth, distance, and intrinsically low luminosity make it an ideal target to search for extrasolar planets using direct imaging. We report deep adaptive optics observations of AP Col taken with VLT/NACO and Keck/NIRC2 in the L band. Using aggressive speckle suppression and background subtraction techniques, we are able to rule out companions with mass m {>=} 0.5-1 M{sub Jup} for projected separations a > 4.5 AU, and m {>=} 2more » M{sub Jup} for projected separations as small as 3 AU, assuming an age of 40 Myr using the COND theoretical evolutionary models. Using a different set of models, the mass limits increase by a factor of {approx}>2. The observations presented here are the deepest mass-sensitivity limits yet achieved within 20 AU on a star with direct imaging. While Doppler radial velocity surveys have shown that Jovian bodies with close-in orbits are rare around M-dwarfs, gravitational microlensing studies predict that 17{sup +6}{sub -9}% of these stars host massive planets with orbital separations of 1-10 AU. Sensitive high-contrast imaging observations, like those presented here, will help to validate results from complementary detection techniques by determining the frequency of gas giant planets on wide orbits around M-dwarfs.« less

Evolution of Pre-Main Sequence Accretion Disks

NASA Technical Reports Server (NTRS)

Hartmann, Lee W.

2000-01-01

The aim of this project was to develop a comprehensive global picture of the physical conditions in, and evolutionary timescales of, pre-main sequence accretion disks. The results of this work will help constrain the initial conditions for planet formation. To this end we: (1) Developed detailed calculations of disk structure to study physical conditions and investigate the observational effects of grain growth in T Tauri disks; (2) Studied the dusty emission and accretion rates in older disk systems, with ages closer to the expected epoch of (giant) planet formation at 3-10 Myr, and (3) Began a project to develop much larger samples of 3-10 Myr-old stars to provide better empirical constraints on protoplanetary disk evolution.

ASCA X-ray observations of pre-main-sequence stars

NASA Technical Reports Server (NTRS)

Skinner, S. L.; Walter, F. M.; Yamauchi, S.

1996-01-01

The results of recent Advanced Satellite for Cosmology and Astrophysics (ASCA) X-ray observations of two pre-main sequence stars are presented: the weak emission line T Tauri star HD 142361, and the Herbig Ae star HD 104237. The solid state imaging spectrometer spectra for HD 142361 shows a clear emission line from H-like Mg 7, and spectral fits reveal a multiple temperature plasma with a hot component of at least 16 MK. The spectra of HD 104237 show a complex temperature structure with the hottest plasma at temperatures of greater than 30 MK. It is concluded that mechanisms that predict only soft X-ray emission can be dismissed for Herbig Ae stars.

High Resolution X-ray Spectroscopy and Star Formation: HETG Observations of the Pre-Main Sequence Stellar Cluster IC 348

NASA Astrophysics Data System (ADS)

Principe, David; Huenemoerder, David P.; Schulz, Norbert; Kastner, Joel H.; Weintraub, David; Preibisch, Thomas

2018-01-01

We present Chandra High Energy Transmission Grating (HETG) observations of the ∼3 Myr old pre-main sequence (pre-MS) stellar cluster IC 348. With 400-500 cluster members at a distance of ∼300 pc, IC 348 is an ideal target to observe a large number of X-ray sources in a single pointing and is thus an extremely efficient use of Chandra-HETG. High resolution X-ray spectroscopy offers a means to investigate detailed spectral characteristic of X-ray emitting plasmas and their surrounding environments. We present preliminary results where we compare X-ray spectral signatures (e.g., luminosity, temperature, column density, abundance) of the X-ray brightest pre-MS stars in IC 348 with spectral type, multiwavelength signatures of accretion, and the presence of circumstellar disks at multiple stages of pre-MS stellar evolution. Assuming all IC 348 members formed from the same primordial molecular cloud, any disparity between coronal abundances of individual members, as constrained by the identification and strength of emission lines, will constrain the source(s) of coronal chemical evolution at a stage of pre-MS evolution vital to the formation of planets.

Evolution of multi-drug resistant HCV clones from pre-existing resistant-associated variants during direct-acting antiviral therapy determined by third-generation sequencing

NASA Astrophysics Data System (ADS)

Takeda, Haruhiko; Ueda, Yoshihide; Inuzuka, Tadashi; Yamashita, Yukitaka; Osaki, Yukio; Nasu, Akihiro; Umeda, Makoto; Takemura, Ryo; Seno, Hiroshi; Sekine, Akihiro; Marusawa, Hiroyuki

2017-03-01

Resistance-associated variant (RAV) is one of the most significant clinical challenges in treating HCV-infected patients with direct-acting antivirals (DAAs). We investigated the viral dynamics in patients receiving DAAs using third-generation sequencing technology. Among 283 patients with genotype-1b HCV receiving daclatasvir + asunaprevir (DCV/ASV), 32 (11.3%) failed to achieve sustained virological response (SVR). Conventional ultra-deep sequencing of HCV genome was performed in 104 patients (32 non-SVR, 72 SVR), and detected representative RAVs in all non-SVR patients at baseline, including Y93H in 28 (87.5%). Long contiguous sequences spanning NS3 to NS5A regions of each viral clone in 12 sera from 6 representative non-SVR patients were determined by third-generation sequencing, and showed the concurrent presence of several synonymous mutations linked to resistance-associated substitutions in a subpopulation of pre-existing RAVs and dominant isolates at treatment failure. Phylogenetic analyses revealed close genetic distances between pre-existing RAVs and dominant RAVs at treatment failure. In addition, multiple drug-resistant mutations developed on pre-existing RAVs after DCV/ASV in all non-SVR cases. In conclusion, multi-drug resistant viral clones at treatment failure certainly originated from a subpopulation of pre-existing RAVs in HCV-infected patients. Those RAVs were selected for and became dominant with the acquisition of multiple resistance-associated substitutions under DAA treatment pressure.

X-Raying the Coronae of HD 155555

NASA Technical Reports Server (NTRS)

Lalitha, S.; Singh, K.P.; Drake, S. A.; Kashyap, V.

2015-01-01

We present an analysis of the high-resolution Chandra observation of the multiple system, HD 155555 (an RS CVn type binary system, HD 155555 AB, and its spatially resolved low-mass companion HD 155555 C). This is an intriguing system which shows properties of both an active pre-main sequence star and a synchronised (main sequence) binary. We obtain the emission measure distribution, temperature structures, plasma densities, and abundances of this system and compare them with the coronal properties of other young/active stars. HD 155555 AB and HD 155555 C produce copious X-ray emission with log L(sub x) of 30.54 and 29.30, respectively, in the 0.3-6.0 kiloelectronvolt energy band. The light curves of individual stars show variability on timescales of few minutes to hours. We analyse the dispersed spectra and reconstruct the emission measure distribution using spectral line analysis. The resulting elemental abundances exhibit inverse first ionisation potential effect in both cases. An analysis of He-like triplets yields a range of coronal electron densities 1010 - 1013 per cubic centimeter. Since HD 155555 AB is classified both as an RS CVn and a PMS star, we compare our results with those of other slightly older active main-sequence stars and T Tauri stars, which indicates that the coronal properties of HD 155555 AB closely resemble that of an older RS CVn binary rather than a younger PMS star. Our results also suggests that the properties of HD 155555 C is very similar to those of other active M dwarfs.

No Evidence for Protoplanetary Disk Destruction By OB Stars in the MYStIX Sample

NASA Astrophysics Data System (ADS)

Richert, Alexander J. W.; Feigelson, Eric D.; Getman, Konstantin V.; Kuhn, Michael A.

2015-09-01

Hubble Space Telescope images of proplyds in the Orion Nebula, as well as submillimeter/radio measurements, show that the dominant O7 star {θ }1Ori C photoevaporates nearby disks around pre-main-sequence stars. Theory predicts that massive stars photoevaporate disks within distances of the order of 0.1 pc. These findings suggest that young, OB-dominated massive H ii regions are inhospitable to the survival of protoplanetary disks and, subsequently, to the formation and evolution of planets. In the current work, we test this hypothesis using large samples of pre-main-sequence stars in 20 massive star-forming regions selected with X-ray and infrared photometry in the MYStIX survey. Complete disk destruction would lead to a deficit of cluster members with an excess in JHKS and Spitzer/IRAC bands in the vicinity of O stars. In four MYStIX regions containing O stars and a sufficient surface density of disk-bearing sources to reliably test for spatial avoidance, we find no evidence for the depletion of inner disks around pre-main-sequence stars in the vicinity of O-type stars, even very luminous O2-O5 stars. These results suggest that massive star-forming regions are not very hostile to the survival of protoplanetary disks and, presumably, to the formation of planets.

On the apparent positions of T Tauri stars in the H-R diagram

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kenyon, S.J.; Hartmann, L.W.

1990-01-01

The spread in apparent luminosities of T Tauri stars caused by occultation and emission from protostellar disks is investigated. A random distribution of disk inclination angles, coupled with a plausible range of accretion rates, introduces a significant scatter in apparent luminosities for intrinsically identical stars. The observed dispersion of luminosities for K7-M1 Hayashi track stars thought to have disks in Taurus-Auriga is similar to predictions of the simple accretion disk model, which suggets that age determinations form many pre-main-sequence stars are uncertain. The results also suggest that Stahler's birthline for convective track pre-main-sequence stars may be located at slightly lowermore » luminosities than previously thought. 38 refs.« less

Evolution of Pre-Main Sequence Accretion Disks

NASA Technical Reports Server (NTRS)

Hartmann, Lee W.

2002-01-01

The aim of this project is to develop a comprehensive global picture of the physical conditions in, and evolutionary timescales of, pre-main sequence accretion disks. The results of this work will help constrain the initial conditions for planet formation. To this end we plan to: (1) Develop much larger samples of 3-10 Myr-old stars to provide better empirical constraints on protoplanetary disk evolution; (2) Study the dusty emission and accretion rates in these systems, with ages closer to the expected epoch of (giant) planet formation at 3-10 Myr; and (3) Develop detailed model disk structures consistent with observations to infer physical conditions in protoplanetary disks and to constrain possible grain growth as the first stage of planetesimal formation.

A Rapidly Moving Shell in the Orion Nebula

NASA Technical Reports Server (NTRS)

Walter, Donald K.; O'Dell, C. R.; Hu, Xihai; Dufour, Reginald J.

1995-01-01

A well-resolved elliptical shell in the inner Orion Nebula has been investigated by monochromatic imaging plus high- and low-resolution spectroscopy. We find that it is of low ionization and the two bright ends are moving at -39 and -49 km/s with respect to OMC-1. There is no central object, even in the infrared J bandpass although H2 emission indicates a possible association with the nearby very young pre-main-sequence star J&W 352, which is one of the youngest pre-main-sequence stars in the inner Orion Nebula. Many of the characteristics of this object (low ionization, blue shift) are like those of the Herbig-Haro objects, although the symmetric form would make it an unusual member of that class.

Supernova SN 2011fe from an exploding carbon-oxygen white dwarf star.

PubMed

Nugent, Peter E; Sullivan, Mark; Cenko, S Bradley; Thomas, Rollin C; Kasen, Daniel; Howell, D Andrew; Bersier, David; Bloom, Joshua S; Kulkarni, S R; Kandrashoff, Michael T; Filippenko, Alexei V; Silverman, Jeffrey M; Marcy, Geoffrey W; Howard, Andrew W; Isaacson, Howard T; Maguire, Kate; Suzuki, Nao; Tarlton, James E; Pan, Yen-Chen; Bildsten, Lars; Fulton, Benjamin J; Parrent, Jerod T; Sand, David; Podsiadlowski, Philipp; Bianco, Federica B; Dilday, Benjamin; Graham, Melissa L; Lyman, Joe; James, Phil; Kasliwal, Mansi M; Law, Nicholas M; Quimby, Robert M; Hook, Isobel M; Walker, Emma S; Mazzali, Paolo; Pian, Elena; Ofek, Eran O; Gal-Yam, Avishay; Poznanski, Dovi

2011-12-14

Type Ia supernovae have been used empirically as 'standard candles' to demonstrate the acceleration of the expansion of the Universe even though fundamental details, such as the nature of their progenitor systems and how the stars explode, remain a mystery. There is consensus that a white dwarf star explodes after accreting matter in a binary system, but the secondary body could be anything from a main-sequence star to a red giant, or even another white dwarf. This uncertainty stems from the fact that no recent type Ia supernova has been discovered close enough to Earth to detect the stars before explosion. Here we report early observations of supernova SN 2011fe in the galaxy M101 at a distance from Earth of 6.4 megaparsecs. We find that the exploding star was probably a carbon-oxygen white dwarf, and from the lack of an early shock we conclude that the companion was probably a main-sequence star. Early spectroscopy shows high-velocity oxygen that slows rapidly, on a timescale of hours, and extensive mixing of newly synthesized intermediate-mass elements in the outermost layers of the supernova. A companion paper uses pre-explosion images to rule out luminous red giants and most helium stars as companions to the progenitor.

The preS deletion of hepatitis B virus (HBV) is associated with liver fibrosis progression in patients with chronic HBV infection.

PubMed

Li, Fan; Li, Xiaodong; Yan, Tao; Liu, Yan; Cheng, Yongqian; Xu, Zhihui; Shao, Qing; Liao, Hao; Huang, Pengyu; Li, Jin; Chen, Guo-Feng; Xu, Dongping

2018-03-01

Limited data are available regarding the association of hepatitis B virus (HBV) mutations with liver fibrosis in HBV infection. The study aimed to clarify whether HBV preS deletion mutation is associated with liver fibrosis progression. A total of 469 patients were enrolled, including 324 with chronic hepatitis B (CHB), 28 with HBV-related compensated liver cirrhosis (LC), and 117 with HBV-related decompensated LC. All CHB and compensated LC patients received liver biopsy. Fibrosis grade was assessed using METAVIR score. HBV preS deletion was determined by direct sequencing and verified by clonal sequencing. Overall preS deletion was detected in 12.6% (59/469) patients, specifically, in 7.51% (13/173), 10.60% (16/151), and 20.69% (30/145) of patients with no-to-mild liver fibrosis (F0-1), moderate-to-severe liver fibrosis (F2-3), and cirrhosis (F4), respectively (p < 0.01). Patients with preS-deleted HBV had lower serum HBV DNA and albumin levels compared to patients with wild-type HBV. The median length of preS deletion was 39-base pairs (bp) (3-204 bp) and the deletion most frequently emerged in preS2 initial region. Multivariate analysis identified the preS2 deletion rather than preS1 deletion to be an independent risk factor of significant fibrosis, i.e., METAVIR F ≥ 2 (p = 0.007). In addition, preS-deleted viral sequences were detected in the pool of intrahepatic HBV covalently closed circular DNA. HBV preS deletion is positively associated with liver fibrosis progression in chronic HBV-infected patients. HBV preS2 deletion may serve as a warning indicator for liver fibrosis progression.

CBrowse: a SAM/BAM-based contig browser for transcriptome assembly visualization and analysis.

PubMed

Li, Pei; Ji, Guoli; Dong, Min; Schmidt, Emily; Lenox, Douglas; Chen, Liangliang; Liu, Qi; Liu, Lin; Zhang, Jie; Liang, Chun

2012-09-15

To address the impending need for exploring rapidly increased transcriptomics data generated for non-model organisms, we developed CBrowse, an AJAX-based web browser for visualizing and analyzing transcriptome assemblies and contigs. Designed in a standard three-tier architecture with a data pre-processing pipeline, CBrowse is essentially a Rich Internet Application that offers many seamlessly integrated web interfaces and allows users to navigate, sort, filter, search and visualize data smoothly. The pre-processing pipeline takes the contig sequence file in FASTA format and its relevant SAM/BAM file as the input; detects putative polymorphisms, simple sequence repeats and sequencing errors in contigs and generates image, JSON and database-compatible CSV text files that are directly utilized by different web interfaces. CBowse is a generic visualization and analysis tool that facilitates close examination of assembly quality, genetic polymorphisms, sequence repeats and/or sequencing errors in transcriptome sequencing projects. CBrowse is distributed under the GNU General Public License, available at http://bioinfolab.muohio.edu/CBrowse/ liangc@muohio.edu or liangc.mu@gmail.com; glji@xmu.edu.cn Supplementary data are available at Bioinformatics online.

XMM-NEWTON MONITORING OF THE CLOSE PRE-MAIN-SEQUENCE BINARY AK SCO. EVIDENCE OF TIDE-DRIVEN FILLING OF THE INNER GAP IN THE CIRCUMBINARY DISK

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gomez de Castro, Ana Ines; Lopez-Santiago, Javier; Talavera, Antonio

2013-03-20

AK Sco stands out among pre-main-sequence binaries because of its prominent ultraviolet excess, the high eccentricity of its orbit, and the strong tides driven by it. AK Sco consists of two F5-type stars that get as close as 11 R{sub *} at periastron passage. The presence of a dense (n{sub e} {approx} 10{sup 11} cm{sup -3}) extended envelope has been unveiled recently. In this article, we report the results from an XMM-Newton-based monitoring of the system. We show that at periastron, X-ray and UV fluxes are enhanced by a factor of {approx}3 with respect to the apastron values. The X-raymore » radiation is produced in an optically thin plasma with T {approx} 6.4 Multiplication-Sign 10{sup 6} K and it is found that the N{sub H} column density rises from 0.35 Multiplication-Sign 10{sup 21} cm{sup -2} at periastron to 1.11 Multiplication-Sign 10{sup 21} cm{sup -2} at apastron, in good agreement with previous polarimetric observations. The UV emission detected in the Optical Monitor band seems to be caused by the reprocessing of the high-energy magnetospheric radiation on the circumstellar material. Further evidence of the strong magnetospheric disturbances is provided by the detection of line broadening of 278.7 km s{sup -1} in the N V line with Hubble Space Telescope/Space Telescope Imaging Spectrograph. Numerical simulations of the mass flow from the circumbinary disk to the components have been carried out. They provide a consistent scenario with which to interpret AK Sco observations. We show that the eccentric orbit acts like a gravitational piston. At apastron, matter is dragged efficiently from the inner disk border, filling the inner gap and producing accretion streams that end as ring-like structures around each component of the system. At periastron, the ring-like structures come into contact, leading to angular momentum loss, and thus producing an accretion outburst.« less

Structure and immune recognition of trimeric pre-fusion HIV-1 Env

DOE PAGES

Pancera, Marie; Zhou, Tongqing; Druz, Aliaksandr; ...

2014-10-08

The human immunodeficiency virus type 1 (HIV-1) envelope (Env) spike, comprising three gp120 and three gp41 subunits, is a conformational machine that facilitates HIV-1 entry by rearranging from a mature unliganded state, through receptor-bound intermediates, to a post-fusion state. As the sole viral antigen on the HIV-1 virion surface, Env is both the target of neutralizing antibodies and a focus of vaccine efforts. Here we report the structure at 3.5 Å resolution for an HIV-1 Env trimer captured in a mature closed state by antibodies PGT122 and 35O22. This structure reveals the pre-fusion conformation of gp41, indicates rearrangements needed formore » fusion activation, and defines parameters of immune evasion and immune recognition. Pre-fusion gp41 encircles amino- and carboxy-terminal strands of gp120 with four helices that form a membrane-proximal collar, fastened by insertion of a fusion peptide-proximal methionine into a gp41-tryptophan clasp. Spike rearrangements required for entry involve opening the clasp and expelling the termini. In conclusion, N-linked glycosylation and sequence-variable regions cover the pre-fusion closed spike; we used chronic cohorts to map the prevalence and location of effective HIV-1-neutralizing responses, which were distinguished by their recognition of N-linked glycan and tolerance for epitope-sequence variation.« less

Structure and immune recognition of trimeric pre-fusion HIV-1 Env

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pancera, Marie; Zhou, Tongqing; Druz, Aliaksandr

The human immunodeficiency virus type 1 (HIV-1) envelope (Env) spike, comprising three gp120 and three gp41 subunits, is a conformational machine that facilitates HIV-1 entry by rearranging from a mature unliganded state, through receptor-bound intermediates, to a post-fusion state. As the sole viral antigen on the HIV-1 virion surface, Env is both the target of neutralizing antibodies and a focus of vaccine efforts. Here we report the structure at 3.5 Å resolution for an HIV-1 Env trimer captured in a mature closed state by antibodies PGT122 and 35O22. This structure reveals the pre-fusion conformation of gp41, indicates rearrangements needed formore » fusion activation, and defines parameters of immune evasion and immune recognition. Pre-fusion gp41 encircles amino- and carboxy-terminal strands of gp120 with four helices that form a membrane-proximal collar, fastened by insertion of a fusion peptide-proximal methionine into a gp41-tryptophan clasp. Spike rearrangements required for entry involve opening the clasp and expelling the termini. In conclusion, N-linked glycosylation and sequence-variable regions cover the pre-fusion closed spike; we used chronic cohorts to map the prevalence and location of effective HIV-1-neutralizing responses, which were distinguished by their recognition of N-linked glycan and tolerance for epitope-sequence variation.« less

Revising Star and Planet Formation Timescales

NASA Astrophysics Data System (ADS)

Bell, Cameron P. M.; Naylor, Tim; Mayne, N. J.; Jeffries, R. D.; Littlefair, S. P.

2013-07-01

We have derived ages for 13 young (<30 Myr) star-forming regions and find that they are up to a factor of 2 older than the ages typically adopted in the literature. This result has wide-ranging implications, including that circumstellar discs survive longer (≃ 10-12 Myr) and that the average Class I lifetime is greater (≃1 Myr) than currently believed. For each star-forming region, we derived two ages from colour-magnitude diagrams. First, we fitted models of the evolution between the zero-age main sequence and terminal-age main sequence to derive a homogeneous set of main-sequence ages, distances and reddenings with statistically meaningful uncertainties. Our second age for each star-forming region was derived by fitting pre-main-sequence stars to new semi-empirical model isochrones. For the first time (for a set of clusters younger than 50 Myr), we find broad agreement between these two ages, and since these are derived from two distinct mass regimes that rely on different aspects of stellar physics, it gives us confidence in the new age scale. This agreement is largely due to our adoption of empirical colour-Teff relations and bolometric corrections for pre-main-sequence stars cooler than 4000 K. The revised ages for the star-forming regions in our sample are: 2 Myr for NGC 6611 (Eagle Nebula; M 16), IC 5146 (Cocoon Nebula), NGC 6530 (Lagoon Nebula; M 8) and NGC 2244 (Rosette Nebula); 6 Myr for σ Ori, Cep OB3b and IC 348; ≃10 Myr for λ Ori (Collinder 69); ≃11 Myr for NGC 2169; ≃12 Myr for NGC 2362; ≃13 Myr for NGC 7160; ≃14 Myr for χ Per (NGC 884); and ≃20 Myr for NGC 1960 (M 36).

Three years of ULTRASPEC at the Thai 2.4-m telescope: Capabilities and scientific highlights

NASA Astrophysics Data System (ADS)

Yadav, Ram Kesh; Richichi, Andrea; Irawati, Puji; Dhillon, Vikram Singh; Marsh, Thomas R.; Soonthornthum, Boonrucksar

2018-04-01

High temporal resolution observations enable the study of rapid phenomena such as the flux variations in binary system objects, e.g. cataclysmic variables, compact binary systems, the flux variations in young star clusters, stellar occultations and more. The 2.4-m Thai National Telescope (TNT) is ideally suited for this niche research, being the largest facility in Southeast Asia and being equipped with ULTRASPEC, a high-speed imager based on a low-noise frame transfer electron-multiplying CCD. In the sub-window mode, ULTRASPEC can record uninterrupted sequences with frame rates as fast as few milliseconds. We present some of the key results obtained in the area of high time resolution with ULTRASPEC. We also present the results of a recent worldwide campaign to observe the current series of lunar occultations of Aldebaran (α Tauri) carried out in close collaboration with the Devasthal facilities, the out-of-eclipse variations on the post common-envelope system J1021+1744, and pre-main-sequence variables in young open cluster Stock 8.

Setting up a probe based, closed tube real-time PCR assay for focused detection of variable sequence alterations.

PubMed

Becságh, Péter; Szakács, Orsolya

2014-10-01

During diagnostic workflow when detecting sequence alterations, sometimes it is important to design an algorithm that includes screening and direct tests in combination. Normally the use of direct test, which is mainly sequencing, is limited. There is an increased need for effective screening tests, with "closed tube" during the whole process and therefore decreasing the risk of PCR product contamination. The aim of this study was to design such a closed tube, detection probe based screening assay to detect different kind of sequence alterations in the exon 11 of the human c-kit gene region. Inside this region there are variable possible deletions and single nucleotide changes. During assay setup, more probe chemistry formats were screened and tested. After some optimization steps the taqman probe format was selected.

A near infrared classification of pre-main sequence stars

NASA Astrophysics Data System (ADS)

Alonso-Martínez, M.; Meeus, G.; Eiroa, C.

2017-03-01

T Tauri stars are young solar analogues (M ≤ 1.5M_{⊙}), harbouring a disc and with ongoing accretion. The T Tauri phase has been estimated to last around 10 Myr. We have obtained J and K band spectra with WHT/LIRIS and NOT/NOTCam of 112 T Tauri stars in the Taurus star forming region. By measuring the equivalent widths of common and strong spectral features, known to follow a tight relation with temperature, we aim at providing a direct and fast method to derive stellar effective temperatures. Line ratios of strong absorption features relatively close in wavelength are used to overcome the effects of veiling. Besides, the Al I (1.313μm) line is strongly gravity-dependent and used to discern between surface gravities. Finally, we estimate accretion rates using the H-lines Pa-β and Br-γ.

Complete Genome Sequences of Isolates of Enterococcus faecium Sequence Type 117, a Globally Disseminated Multidrug-Resistant Clone

PubMed Central

Tedim, Ana P.; Lanza, Val F.; Manrique, Marina; Pareja, Eduardo; Ruiz-Garbajosa, Patricia; Cantón, Rafael; Baquero, Fernando; Tobes, Raquel

2017-01-01

ABSTRACT The emergence of nosocomial infections by multidrug-resistant sequence type 117 (ST117) Enterococcus faecium has been reported in several European countries. ST117 has been detected in Spanish hospitals as one of the main causes of bloodstream infections. We analyzed genome variations of ST117 strains isolated in Madrid and describe the first ST117 closed genome sequences. PMID:28360174

Probabilistic Reasoning Over Seismic Time Series: Volcano Monitoring by Hidden Markov Models at Mt. Etna

NASA Astrophysics Data System (ADS)

Cassisi, Carmelo; Prestifilippo, Michele; Cannata, Andrea; Montalto, Placido; Patanè, Domenico; Privitera, Eugenio

2016-07-01

From January 2011 to December 2015, Mt. Etna was mainly characterized by a cyclic eruptive behavior with more than 40 lava fountains from New South-East Crater. Using the RMS (Root Mean Square) of the seismic signal recorded by stations close to the summit area, an automatic recognition of the different states of volcanic activity (QUIET, PRE-FOUNTAIN, FOUNTAIN, POST-FOUNTAIN) has been applied for monitoring purposes. Since values of the RMS time series calculated on the seismic signal are generated from a stochastic process, we can try to model the system generating its sampled values, assumed to be a Markov process, using Hidden Markov Models (HMMs). HMMs analysis seeks to recover the sequence of hidden states from the observations. In our framework, observations are characters generated by the Symbolic Aggregate approXimation (SAX) technique, which maps RMS time series values with symbols of a pre-defined alphabet. The main advantages of the proposed framework, based on HMMs and SAX, with respect to other automatic systems applied on seismic signals at Mt. Etna, are the use of multiple stations and static thresholds to well characterize the volcano states. Its application on a wide seismic dataset of Etna volcano shows the possibility to guess the volcano states. The experimental results show that, in most of the cases, we detected lava fountains in advance.

New radio detections of early-type pre-main-sequence stars

NASA Technical Reports Server (NTRS)

Skinner, Stephen L.; Brown, Alexander; Linsky, Jeffrey L.

1990-01-01

Results of VLA radio continuum observations of 13 early-type pre-main-sequence stars selected from the 1984 catalog of Finkenzeller and Mundt are presented. The stars HD 259431 and MWC 1080 were detected at 3.6 cm, while HD 200775 and TY CrA were detected at both 3.6 and 6 cm. The flux density of HD 200775 has a frequency dependence consistent with the behavior expected for free-free emission originating in a fully ionized wind. However, an observation in A configuration suggests that the source geometry may not be spherically symmetric. In contrast, the spectral index of TY CrA is negative with a flux behavior implying nonthermal emission. The physical mechanism responsible for the nonthermal emission has not yet been identified, although gyrosynchrotron and synchrotron processes cannot be ruled out.

Forming spectroscopic massive protobinaries by disc fragmentation

NASA Astrophysics Data System (ADS)

Meyer, D. M.-A.; Kuiper, R.; Kley, W.; Johnston, K. G.; Vorobyov, E.

2018-01-01

The surroundings of massive protostars constitute an accretion disc which has numerically been shown to be subject to fragmentation and responsible for luminous accretion-driven outbursts. Moreover, it is suspected to produce close binary companions which will later strongly influence the star's future evolution in the Hertzsprung-Russel diagram. We present three-dimensional gravitation-radiation-hydrodynamic numerical simulations of 100 M⊙ pre-stellar cores. We find that accretion discs of young massive stars violently fragment without preventing the (highly variable) accretion of gaseous clumps on to the protostars. While acquiring the characteristics of a nascent low-mass companion, some disc fragments migrate on to the central massive protostar with dynamical properties showing that its final Keplerian orbit is close enough to constitute a close massive protobinary system, having a young high- and a low-mass components. We conclude on the viability of the disc fragmentation channel for the formation of such short-period binaries, and that both processes - close massive binary formation and accretion bursts - may happen at the same time. FU-Orionis-type bursts, such as observed in the young high-mass star S255IR-NIRS3, may not only indicate ongoing disc fragmentation, but also be considered as a tracer for the formation of close massive binaries - progenitors of the subsequent massive spectroscopic binaries - once the high-mass component of the system will enter the main-sequence phase of its evolution. Finally, we investigate the Atacama Large (sub-)Millimeter Array observability of the disc fragments.

YOUNG STELLAR CLUSTERS CONTAINING MASSIVE YOUNG STELLAR OBJECTS IN THE VVV SURVEY

DOE Office of Scientific and Technical Information (OSTI.GOV)

Borissova, J.; Alegría, S. Ramírez; Kurtev, R.

The purpose of this research is to study the connections of the global properties of eight young stellar clusters projected in the Vista Variables in the Via Lactea (VVV) ESO Large Public Survey disk area and their young stellar object (YSO) populations. The analysis is based on the combination of spectroscopic parallax-based reddening and distance determinations with main-sequence and pre-main-sequence ishochrone fitting to determine the basic parameters (reddening, age, distance) of the sample clusters. The lower mass limit estimations show that all clusters are low or intermediate mass (between 110 and 1800  M {sub ⊙}), the slope Γ of themore » obtained present-day mass functions of the clusters is close to the Kroupa initial mass function. The YSOs in the cluster’s surrounding fields are classified using low resolution spectra, spectral energy distribution fits with theoretical predictions, and variability, taking advantage of multi-epoch VVV observations. All spectroscopically confirmed YSOs (except one) are found to be massive (more than 8 M {sub ⊙}). Using VVV and GLIMPSE color–color cuts we have selected a large number of new YSO candidates, which are checked for variability and 57% are found to show at least low-amplitude variations. In few cases it was possible to distinguish between YSO and AGB classifications on the basis of light curves.« less

Definition and empirical structure of the range of stellar chromospheres-coronae across the H-R diagram: Cool stars

NASA Technical Reports Server (NTRS)

Linsky, J. L.

1986-01-01

Major advances in our understanding of non-radiative heating and other activity in stars cooler than T sub eff = 10,000K has occured in the last few years. This observational evidence is reviewed and the trends that are now becoming apparent are discussed. The evidence for non-radiatively heated outer atmospheric layers (chromospheres, transition regions, and coronae) in dwarf stars cooler than spectral type A7, in F and G giants, pre-main sequence stars, and close bindary systems is unambiguous, as is the evidence for chromospheres in the K and M giants and supergiants. The existence of non-radiative heating in the outer layers of the A stars remains undetermined despite repeated searches at all wavelengths. Two important trends in the data are the decrease in plasma emission measure with age on the main sequence and decreasing rotational velocity. Variability and atmospheric inhomogeneity are commonly seen, and there is considerable evidence that magnetic fields define the geometry and control the energy balance in the outer atmospheric layers. In addition, the microwave observations imply that non-thermal electrons are confined in coronal magnetic flux tubes in at least the cool dwarfs and RS CVn systems. The chromospheres in the K and M giants and supergiants are geometrically extended, as are the coronae in the RS CVn systems and probably also in other stars.

A VLT/NACO survey for triple and quadruple systems among visual pre-main sequence binaries

NASA Astrophysics Data System (ADS)

Correia, S.; Zinnecker, H.; Ratzka, Th.; Sterzik, M. F.

2006-12-01

Aims.This paper describes a systematic search for high-order multiplicity among wide visual Pre-Main Sequence (PMS) binaries. Methods: .We conducted an Adaptive Optics survey of a sample of 58 PMS wide binaries from various star-forming regions, which include 52 T Tauri systems with mostly K- and M-type primaries, with the NIR instrument NACO at the VLT. Results: .Of these 52 systems, 7 are found to be triple (2 new) and 7 quadruple (1 new). The new close companions are most likely physically bound based on their probability of chance projection and, for some of them, on their position on a color-color diagram. The corresponding degree of multiplicity among wide binaries (number of triples and quadruples divided by the number of systems) is 26.9 ± 7.2% in the projected separation range ~0.07 arcsec -12'', with the largest contribution from the Taurus-Auriga cloud. We also found that this degree of multiplicity is twice in Taurus compared to Ophiuchus and Chamaeleon for which the same number of sources are present in our sample. Considering a restricted sample composed of systems at distance 140-190 pc, the degree of multiplicity is 26.8 ± 8.1%, in the separation range 10/14 AU-1700/2300 AU (30 binaries, 5 triples, 6 quadruples). The observed frequency agrees with results from previous multiplicity surveys within the uncertainties, although a significant overabundance of quadruple systems compared to triple systems is apparent. Tentatively including the spectroscopic pairs in our restricted sample and comparing the multiplicity fractions to those measured for solar-type main-sequence stars in the solar neighborhood leads to the conclusion that both the ratio of triples to binaries and the ratio of quadruples to triples seems to be in excess among young stars. Most of the current numerical simulations of multiple star formation, and especially smoothed particles hydrodynamics simulations, over-predict the fraction of high-order multiplicity when compared to our results. The circumstellar properties around the individual components of our high-order multiple systems tend to favor mixed systems (i.e. systems including components of wTTS and cTTS type), which is in general agreement with previous studies of disks in binaries, with the exception of Taurus, where we find a preponderance of similar type of components among the multiples studied.

The Relationship Between X-Ray Radiance and Magnetic Flux

NASA Astrophysics Data System (ADS)

Pevtsov, Alexei A.; Fisher, George H.; Acton, Loren W.; Longcope, Dana W.; Johns-Krull, Christopher M.; Kankelborg, Charles C.; Metcalf, Thomas R.

2003-12-01

We use soft X-ray and magnetic field observations of the Sun (quiet Sun, X-ray bright points, active regions, and integrated solar disk) and active stars (dwarf and pre-main-sequence) to study the relationship between total unsigned magnetic flux, Φ, and X-ray spectral radiance, LX. We find that Φ and LX exhibit a very nearly linear relationship over 12 orders of magnitude, albeit with significant levels of scatter. This suggests a universal relationship between magnetic flux and the power dissipated through coronal heating. If the relationship can be assumed linear, it is consistent with an average volumetric heating rate Q~B/L, where B is the average field strength along a closed field line and L is its length between footpoints. The Φ-LX relationship also indicates that X-rays provide a useful proxy for the magnetic flux on stars when magnetic measurements are unavailable.

Orbital motion in pre-main sequence binaries

DOE Office of Scientific and Technical Information (OSTI.GOV)

Schaefer, G. H.; Prato, L.; Simon, M.

2014-06-01

We present results from our ongoing program to map the visual orbits of pre-main sequence (PMS) binaries in the Taurus star forming region using adaptive optics imaging at the Keck Observatory. We combine our results with measurements reported in the literature to analyze the orbital motion for each binary. We present preliminary orbits for DF Tau, T Tau S, ZZ Tau, and the Pleiades binary HBC 351. Seven additional binaries show curvature in their relative motion. Currently, we can place lower limits on the orbital periods for these systems; full solutions will be possible with more orbital coverage. Five othermore » binaries show motion that is indistinguishable from linear motion. We suspect that these systems are bound and might show curvature with additional measurements in the future. The observations reported herein lay critical groundwork toward the goal of measuring precise masses for low-mass PMS stars.« less

The Search for Pre-Main Sequence Eclipsing Binary Stars in the Lagoon Nebula

NASA Astrophysics Data System (ADS)

Henderson, Calen B.; Stassun, K. G.

2009-01-01

We report time-series CCD I-band photometry for the pre-main-sequence cluster NGC 6530, located within the Lagoon Nebula. The data were obtained with the 4Kx4K imager on the SMARTS 1.0m telescope at CTIO on 36 nights over the summers of 2005 and 2006. In total we have light curves for 50,000 stars in an area 1 deg2, with a sampling cadence of 1 hour. The stars in our sample have masses in the range 0.25-4.0 Msun, assuming a distance of 1.25 kpc to the cluster. Our goals are to look for stars with rotation periods and to identify eclipsing binary candidates. Here we present light curves of photometrically variable stars and potential eclipsing binary star systems. This work has been supported by the National Science Foundation under Career grant AST-0349075.

Searching for δ Scuti-type pulsation and characterising northern pre-main-sequence field stars

NASA Astrophysics Data System (ADS)

Díaz-Fraile, D.; Rodríguez, E.; Amado, P. J.

2014-08-01

Context. Pre-main-sequence (PMS) stars are objects evolving from the birthline to the zero-age main sequence (ZAMS). Given a mass range near the ZAMS, the temperatures and luminosities of PMS and main-sequence stars are very similar. Moreover, their evolutionary tracks intersect one another causing some ambiguity in the determination of their evolutionary status. In this context, the detection and study of pulsations in PMS stars is crucial for differentiating between both types of stars by obtaining information of their interiors via asteroseismic techniques. Aims: A photometric variability study of a sample of northern field stars, which previously classified as either PMS or Herbig Ae/Be objects, has been undertaken with the purpose of detecting δ Scuti-type pulsations. Determination of physical parameters for these stars has also been carried out to locate them on the Hertzsprung-Russell diagram and check the instability strip for this type of pulsators. Methods: Multichannel photomultiplier and CCD time series photometry in the uvby Strömgren and BVI Johnson bands were obtained during four consecutive years from 2007 to 2010. The light curves have been analysed, and a variability criterion has been established. Among the objects classified as variable stars, we have selected those which present periodicities above 4 d-1, which was established as the lowest limit for δ Scuti-type pulsations in this investigation. Finally, these variable stars have been placed in a colour-magnitude diagram using the physical parameters derived with the collected uvbyβ Strömgren-Crawford photometry. Results: Five PMS δ Scuti- and three probable β Cephei-type stars have been detected. Two additional PMS δ Scuti stars are also confirmed in this work. Moreover, three new δ Scuti- and two γ Doradus-type stars have been detected among the main-sequence objects used as comparison or check stars.

Prophylaxis against the systemic hypotension induced by propofol during rapid-sequence intubation.

PubMed

el-Beheiry, H; Kim, J; Milne, B; Seegobin, R

1995-10-01

The objective of this study was to determine the effectiveness of two prophylactic approaches against the anticipated hypotension induced by propofol during rapid-sequence intubation. Thirty-six male or female nonpremedicated ASA class I-II patients aged 21-60 yr undergoing elective outpatient surgery were included in the study. Patients were randomly allocated to receive pre-induction ephedrine sulphate (70 micrograms x kg(-1)iv), pre-induction volume loading (12 ml x kg(-1) Ringer's lactate) or no treatment. Rapid-sequence intubation with cricoid pressure was then performed with propofol (2.5 mg. x kg(-1)) and succinylcholine (1.5 mg x kg(-1). The lungs were subsequently ventilated with 0.25-0.5% isoflurane in a 2:1 N2O/O2 mixture. Vecuronium was given once neuromuscular function had recovered from the succinylcholine. Heart rate and systemic arterial blood pressure were measured non-invasively before induction, after propofol administration and every minute for ten minutes after intubation. Pre-induction volume loading prevented the hypotension observed before surgical stimulation in control and ephedrine groups. Moreover, pre-induction volume loading was not associated with increases in heart rate after intubation as was ephedrine administration. The intubating conditions were excellent to satisfactory in most patients and the overall incidence of adverse events during intubation was mainly due to pain during injection of propofol. The present study showed that preoperative volume loading is more efficacious than pre-induction administration of ephedrine sulphate in maintaining haemodynamic stability during rapid-sequence induction with propofol and succinylcholine. In addition, propofol in combination with succinylcholine provides excellent conditions for rapid-sequence intubation.

Age Spreads and the Temperature Dependence of Age Estimates in Upper Sco

NASA Astrophysics Data System (ADS)

Fang, Qiliang; Herczeg, Gregory J.; Rizzuto, Aaron

2017-06-01

Past estimates for the age of the Upper Sco Association are typically 11–13 Myr for intermediate-mass stars and 4–5 Myr for low-mass stars. In this study, we simulate populations of young stars to investigate whether this apparent dependence of estimated age on spectral type may be explained by the star formation history of the association. Solar and intermediate mass stars begin their pre-main sequence evolution on the Hayashi track, with fully convective interiors and cool photospheres. Intermediate-mass stars quickly heat up and transition onto the radiative Henyey track. As a consequence, for clusters in which star formation occurs on a timescale similar to that of the transition from a convective to a radiative interior, discrepancies in ages will arise when ages are calculated as a function of temperature instead of mass. Simple simulations of a cluster with constant star formation over several Myr may explain about half of the difference in inferred ages versus photospheric temperature; speculative constructions that consist of a constant star formation followed by a large supernova-driven burst could fully explain the differences, including those between F and G stars where evolutionary tracks may be more accurate. The age spreads of low-mass stars predicted from these prescriptions for star formation are consistent with the observed luminosity spread of Upper Sco. The conclusion that a lengthy star formation history will yield a temperature dependence in ages is expected from the basic physics of pre-main sequence evolution, and is qualitatively robust to the large uncertainties in pre-main sequence evolutionary models.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fang Qiliang; Herczeg, Gregory J.; Rizzuto, Aaron

Past estimates for the age of the Upper Sco Association are typically 11–13 Myr for intermediate-mass stars and 4–5 Myr for low-mass stars. In this study, we simulate populations of young stars to investigate whether this apparent dependence of estimated age on spectral type may be explained by the star formation history of the association. Solar and intermediate mass stars begin their pre-main sequence evolution on the Hayashi track, with fully convective interiors and cool photospheres. Intermediate-mass stars quickly heat up and transition onto the radiative Henyey track. As a consequence, for clusters in which star formation occurs on amore » timescale similar to that of the transition from a convective to a radiative interior, discrepancies in ages will arise when ages are calculated as a function of temperature instead of mass. Simple simulations of a cluster with constant star formation over several Myr may explain about half of the difference in inferred ages versus photospheric temperature; speculative constructions that consist of a constant star formation followed by a large supernova-driven burst could fully explain the differences, including those between F and G stars where evolutionary tracks may be more accurate. The age spreads of low-mass stars predicted from these prescriptions for star formation are consistent with the observed luminosity spread of Upper Sco. The conclusion that a lengthy star formation history will yield a temperature dependence in ages is expected from the basic physics of pre-main sequence evolution, and is qualitatively robust to the large uncertainties in pre-main sequence evolutionary models.« less

Evolutionary status of isolated B[e] stars

NASA Astrophysics Data System (ADS)

Lee, Chien-De; Chen, Wen-Ping; Liu, Sheng-Yuan

2016-08-01

Aims: We study a sample of eight B[e] stars with uncertain evolutionary status to shed light on the origin of their circumstellar dust. Methods: We performed a diagnostic analysis on the spectral energy distribution beyond infrared wavelengths, and conducted a census of neighboring region of each target to ascertain its evolutionary status. Results: In comparison to pre-main sequence Herbig stars, these B[e] stars show equally substantial excess emission in the near-infrared, indicative of existence of warm dust, but much reduced excess at longer wavelengths, so the dusty envelopes should be compact in size. Isolation from star-forming regions excludes the possibility of their pre-main sequence status. Six of our targets, including HD 50138, HD 45677, CD-24 5721, CD-49 3441, MWC 623, and HD 85567, have been previously considered as FS CMa stars, whereas HD 181615/6 and HD 98922 are added to the sample by this work. We argue that the circumstellar grains of these isolated B[e] stars, already evolved beyond the pre-main sequence phase, should be formed in situ. This is in contrast to Herbig stars, which inherit large grains from parental molecular clouds. It has been thought that HD 98922, in particular, is a Herbig star because of its large infrared excess, but we propose it being in a more evolved stage. Because dust condenses out of stellar mass loss in an inside-out manner, the dusty envelope is spatially confined, and anisotropic mass flows, or anomalous optical properties of tiny grains, lead to the generally low line-of-sight extinction toward these stars.

A NEAR-INFRARED STUDY OF THE STAR-FORMING REGION RCW 34

DOE Office of Scientific and Technical Information (OSTI.GOV)

Van der Walt, D. J.; De Villiers, H. M.; Czanik, R. J.

2012-07-15

We report the results of a near-infrared imaging study of a 7.8 Multiplication-Sign 7.8 arcmin{sup 2} region centered on the 6.7 GHz methanol maser associated with the RCW 34 star-forming region using the 1.4 m IRSF telescope at Sutherland. A total of 1283 objects were detected simultaneously in J, H, and K for an exposure time of 10,800 s. The J - H, H - K two-color diagram revealed a strong concentration of more than 700 objects with colors similar to what is expected of reddened classical T Tauri stars. The distribution of the objects on the K versus Jmore » - K color-magnitude diagram is also suggestive that a significant fraction of the 1283 objects is made up of lower mass pre-main-sequence stars. We also present the luminosity function for the subset of about 700 pre-main-sequence stars and show that it suggests ongoing star formation activity for about 10{sup 7} years. An examination of the spatial distribution of the pre-main-sequence stars shows that the fainter (older) part of the population is more dispersed over the observed region and the brighter (younger) subset is more concentrated around the position of the O8.5V star. This suggests that the physical effects of the O8.5V star and the two early B-type stars on the remainder of the cloud out of which they formed could have played a role in the onset of the more recent episode of star formation in RCW 34.« less

Primate-specific evolution of an LDLR enhancer

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Qian-Fei; Prabhakar, Shyam; Wang, Qianben

2005-12-01

Sequence changes in regulatory regions have often been invoked to explain phenotypic divergence among species, but molecular examples of this have been difficult to obtain. In this study we identified an anthropoid primate-specific sequence element that contributed to the regulatory evolution of the low-density lipoprotein receptor. Using a combination of close and distant species genomic sequence comparisons coupled with in vivo and in vitro studies, we found that a functional cholesterol-sensing sequence motif arose and was fixed within a pre-existing enhancer in the common ancestor of anthropoid primates. Our study demonstrates one molecular mechanism by which ancestral mammalian regulatory elementsmore » can evolve to perform new functions in the primate lineage leading to human.« less

Previously unclassified bacteria dominate during thermophilic and mesophilic anaerobic pre-treatment of primary sludge.

PubMed

Pervin, Hasina M; Batstone, Damien J; Bond, Philip L

2013-06-01

Thermophilic biological pre-treatment enables enhanced anaerobic digestion for treatment of wastewater sludges but, at present, there is limited understanding of the hydrolytic-acidogenic microbial composition and its contribution to this process. In this study, the process was assessed by comparing the microbiology of thermophilic (50-65 °C) and mesophilic (35 °C) pre-treatment reactors treating primary sludge. A full-cycle approach for the 16S rRNA genes was applied in order to monitor the diversity of bacteria and their abundance in a thermophilic pre-treatment reactor treating primary sludge. For the thermophilic pre-treatment (TP), over 90% of the sequences were previously undetected and these had less than 97% sequence similarity to cultured organisms. During the first 83 days, members of the Betaproteobacteria dominated the community sequences and a newly designed probe was used to monitor a previously unknown bacterium affiliated with the genus Brachymonas. Between days 85 and 183, three phylotypes that affiliated with the genera Comamonas, Clostridium and Lysobacter were persistently dominant in the TP community, as revealed by terminal-restriction fragment length polymorphism (T-RFLP). Hydrolytic and fermentative functions have been speculated for these bacteria. Mesophilic pre-treatment (MP) and TP communities were different but they were both relatively dynamic. Statistical correlation analysis and the function of closely allied reference organisms indicated that previously unclassified bacteria dominated the TP community and may have been functionally involved in the enhanced hydrolytic performance of thermophilic anaerobic pre-treatment. This study is the first to reveal the diversity and dynamics of bacteria during anaerobic digestion of primary sludge. Copyright © 2013 Elsevier GmbH. All rights reserved.

Mass loss from solar-type stars

NASA Technical Reports Server (NTRS)

Hartmann, L.

1985-01-01

The present picture of mass loss from solar-type (low-mass) stars is described, with special emphasis on winds from pre-main-sequence stars. Attention is given to winds from T Tauri stars and to angular momentum loss. Prospects are good for further advances in our understanding of the powerful mass loss observed from young stars; ultraviolet spectra obtainable with the Space Telescope should provide better estimates of mass loss rates and a clearer picture of physical conditions in the envelopes of these stars. To understand the mass ejection from old, slowly rotating main-sequence stars, we will have to study the sun.

Lithium in lower-main-sequence stars of the Alpha Persei cluster

NASA Technical Reports Server (NTRS)

Balachandran, Suchitra; Lambert, David L.; Stauffer, John R.

1988-01-01

Lithium abundances are presented for main-sequence stars of spectral types F, G, and K in the young open cluster Alpha Per. For 46 cluster members, a correlation between Li abundance and projected rotational velocity v sin i is found: all of the Li-poor stars are slow rotators. Two explanations are proposed to account for the correlation: (1) that the Li depletion is introduced following a rapid spin-down phase experienced by young low-mass stars, and that this episode of Li depletion may be the dominant one determining the spread of Li abundances among young low-mass main-sequence stars, and (2) that star formation has occurred over a finite period such that the older stars have undergone a spin-down and depletion of Li by a means that may or may not depend on rotation. The Li abundance in the warm and rapidly rotating stars appears to be undepleted, as is predicted by recent models of pre-main-sequence stars. The depletion observed in the cool stars exceeds the level predicted by these models.

High levels of variation in Salix lignocellulose genes revealed using poplar genomic resources

PubMed Central

2013-01-01

Background Little is known about the levels of variation in lignin or other wood related genes in Salix, a genus that is being increasingly used for biomass and biofuel production. The lignin biosynthesis pathway is well characterized in a number of species, including the model tree Populus. We aimed to transfer the genomic resources already available in Populus to its sister genus Salix to assess levels of variation within genes involved in wood formation. Results Amplification trials for 27 gene regions were undertaken in 40 Salix taxa. Twelve of these regions were sequenced. Alignment searches of the resulting sequences against reference databases, combined with phylogenetic analyses, showed the close similarity of these Salix sequences to Populus, confirming homology of the primer regions and indicating a high level of conservation within the wood formation genes. However, all sequences were found to vary considerably among Salix species, mainly as SNPs with a smaller number of insertions-deletions. Between 25 and 176 SNPs per kbp per gene region (in predicted exons) were discovered within Salix. Conclusions The variation found is sizeable but not unexpected as it is based on interspecific and not intraspecific comparison; it is comparable to interspecific variation in Populus. The characterisation of genetic variation is a key process in pre-breeding and for the conservation and exploitation of genetic resources in Salix. This study characterises the variation in several lignocellulose gene markers for such purposes. PMID:23924375

The Low-Mass Stellar Content of the Scorpius-Centaurus OB Association

NASA Technical Reports Server (NTRS)

Yorke, H.; Kunkel, M.; Brander, W.; Zinnecker, H.; Neuhauser, R.; Schmitt, J.; Mayor, M.; Udry, S.

2000-01-01

Based on ROSAT observations and data obtained with ground-based telescopes, we have carried out an extensive study of the low-mass pre-main-sequence population in Upper Scorpius, the youngest subgroup of the Scorpius-Centaurus OB association.

Orbital Decay in Binaries with Evolved Stars

NASA Astrophysics Data System (ADS)

Sun, Meng; Arras, Phil; Weinberg, Nevin N.; Troup, Nicholas; Majewski, Steven R.

2018-01-01

Two mechanisms are often invoked to explain tidal friction in binary systems. The ``dynamical tide” is the resonant excitation of internal gravity waves by the tide, and their subsequent damping by nonlinear fluid processes or thermal diffusion. The ``equilibrium tide” refers to non-resonant excitation of fluid motion in the star’s convection zone, with damping by interaction with the turbulent eddies. There have been numerous studies of these processes in main sequence stars, but less so on the subgiant and red giant branches. Motivated by the newly discovered close binary systems in the Apache Point Observatory Galactic Evolution Experiment (APOGEE-1), we have performed calculations of both the dynamical and equilibrium tide processes for stars over a range of mass as the star’s cease core hydrogen burning and evolve to shell burning. Even for stars which had a radiative core on the main sequence, the dynamical tide may have very large amplitude in the newly radiative core in post-main sequence, giving rise to wave breaking. The resulting large dynamical tide dissipation rate is compared to the equilibrium tide, and the range of secondary masses and orbital periods over which rapid orbital decay may occur will be discussed, as well as applications to close APOGEE binaries.

On the Lack of Circumbinary Planets Orbiting Isolated Binary Stars

NASA Astrophysics Data System (ADS)

Fleming, David; Barnes, Rory; Graham, David E.; Luger, Rodrigo; Quinn, Thomas R.

2018-04-01

To date, no binary star system with an orbital period less than 7.5 days has been observed to host a circumbinary planet (CBP), a puzzling observation given the thousands of binary stars with orbital periods < 10 days discovered by the Kepler mission (Kirk et al., 2016) and the observational biases that favor their detection (Munoz & Lai, 2015). We outline a mechanism that explains the observed lack of CBPs via coupled stellar-tidal evolution of isolated binary stars. Tidal forces between low-mass, short-period binary stars on the pre-main sequence slow the stellar rotations, transferring rotational angular momentum to the orbit as the stars approach the tidally locked state. This transfer increases the binary orbital period, expanding the region of dynamical instability around the binary, and destabilizing CBPs that tend to preferentially orbit just beyond the initial dynamical stability limit. After the stars tidally lock, we find that angular momentum loss due to magnetic braking can significantly shrink the binary orbit, and hence the region of dynamical stability, over time impacting where surviving CBPs are observed relative to the boundary. We perform simulations over a wide range of parameter space and find that the expansion of the instability region occurs for most plausible initial conditions and that in some cases, the stability semi-major axis doubles from its initial value. We examine the dynamical and observable consequences of a CBP falling within the dynamical instability limit by running N-body simulations of circumbinary planetary systems and find that typically, at least one planet is ejected from the system. We apply our theory to the shortest period Kepler binary that possesses a CBP, Kepler-47, and find that its existence is consistent with our model. Under conservative assumptions, we find that coupled stellar-tidal evolution of pre-main sequence binary stars removes at least one close-in CBP in 87% of multi-planet circumbinary systems.

Spectroscopic Characterization of a Newborn Neptune-Sized Planet

NASA Astrophysics Data System (ADS)

Benneke, Bjoern

2016-10-01

The study of planet formation as it occurs has remained an elusive frontier, until now. Our team recently identified a newly-born planet orbiting a young, 5-10 Myr old, pre-main-sequence M star in the Upper Scorpius star-forming region. In its early stage, the close-in planet is about 50% larger than Neptune. Models predict that it will contract over the coming 100-1000 Myr to become a member of the intriguingly abundant class of close-in sub-Neptunes. Spectroscopic observations of this newborn planet will give us the unprecedented opportunity to probe the formation and evolution of low-mass, close-in planets at this early stage. Here, we propose to a reconnaissance study to probe the adolescent state of the gravitationally-bound atmosphere using near-infrared transit spectroscopy and the planet's hydrogen loss rate using far-UV transit spectroscopy. Together, our observations will give us unparalleled insights into the initial state of a young close-in planet as well as into the competing timescales of Kelvin-Helmholtz contraction and envelope mass-loss involved in the early evolution of close-in sub-Neptunes and Neptunes. If the proposed reconnaissance observations detect that molecular absorption in the atmosphere of USco 1610-1919b, then USco 1610-1919b will be one of the prime targets for the 200-hour JWST/NIRISS GTO program to probe the formation and evolution of exoplanets. Mid-cycle observations are required because the final target list for JWST/GTO programs must be locked in by June 2017 before the beginning of HST Cycle 25.

Magma degassing and eruption dynamics of the Avellino pumice Plinian eruption of Somma-Vesuvius (Italy). Comparison with the Pompeii eruption

NASA Astrophysics Data System (ADS)

Balcone-Boissard, H.; Boudon, G.; Ucciani, G.; Villemant, B.; Cioni, R.; Civetta, L.; Orsi, G.

2012-05-01

The eruptive history of Mt. Somma-Vesuvius is characterised by large explosive events: Pomici di Base eruption (22,030 ± 175 yr cal BP), Mercato (8890 ± 90 yr cal BP), Avellino (3945 ± 10 yr cal BP) and Pompeii (79 AD). Pre-eruptive conditions and sin-eruptive degassing processes of the Avellino eruption, the highest-magnitude Plinian event, have been investigated, using volatile contents (F, Cl, H2O) in melt inclusions and residual glass, and textural characteristics of pumice clasts of the 9 fallout layers sampled in detail in a representative sequence. The sequence displays an up-section sharp colour change from white to grey, corresponding to variations in both magma composition and textural characteristics. The pre-eruptive conditions have been constrained by systematic measurements of Cl content in both melt inclusions and matrix glass of pumice clasts. The pumice glass composition varies from Na-rich phonolite (white pumice) to K-rich phonolite (grey pumice). The measured Cl values constantly cluster at 5200 ± 400 ppm (buffer value), whatever the composition of the melt, suggesting that the entire magma body was saturated with sub-critical fluids. This Cl saturation constrains the pre-eruptive pressures and maximum H2O contents at 200 ± 10 MPa and 6.3 ± 0.2 wt.% H2O for the white pumice melt and 195 ± 15 MPa and 5.2 ± 0.2 wt.% H2O for the grey pumice melt. The fluid phase, mainly composed of a H2O-rich vapour phase and brine, probably accumulated at the top of the reservoir and generated an overpressure able to trigger the onset of the eruption. Magma degassing was rather homogeneous for the white and grey eruptive units, mostly occurring through closed-system processes, leading to a typical Plinian eruptive style. A steady-state withdrawal of an H2O-saturated magma may explain the establishment of a sustained Plinian column. Variation from white to grey pumice is accompanied by decrease of mean vesicularity and increase of mean microcrystallinity and permeability related to significant vesicle coalescence. Despite this, the ascending magma column still evolves under closed-system degassing, without significant gas loss through conduit walls. The Avellino eruption shows numerous similarities with the 79 AD Pompeii eruption in pre-eruptive conditions, degassing processes and eruptive style which are discussed here.

The effect of starspots on the radii of low-mass pre-main-sequence stars

NASA Astrophysics Data System (ADS)

Jackson, R. J.; Jeffries, R. D.

2014-07-01

A polytropic model is used to investigate the effects of dark photospheric spots on the evolution and radii of magnetically active, low-mass (M < 0.5 M⊙), pre-main-sequence (PMS) stars. Spots slow the contraction along Hayashi tracks and inflate the radii of PMS stars by a factor of (1 - β)-N compared to unspotted stars of the same luminosity, where β is the equivalent covering fraction of dark starspots and N ≃ 0.45 ± 0.05. This is a much stronger inflation than predicted by Spruit & Weiss for main-sequence stars with the same β, where N ˜ 0.2-0.3. These models have been compared to radii determined for very magnetically active K- and M-dwarfs in the young Pleiades and NGC 2516 clusters, and the radii of tidally locked, low-mass eclipsing binary components. The binary components and zero-age main-sequence K-dwarfs have radii inflated by ˜10 per cent compared to an empirical radius-luminosity relation that is defined by magnetically inactive field dwarfs with interferometrically measured radii; low-mass M-type PMS stars, that are still on their Hayashi tracks, are inflated by up to ˜40 per cent. If this were attributable to starspots alone, we estimate that an effective spot coverage of 0.35 < β < 0.51 is required. Alternatively, global inhibition of convective flux transport by dynamo-generated fields may play a role. However, we find greater consistency with the starspot models when comparing the loci of active young stars and inactive field stars in colour-magnitude diagrams, particularly for the highly inflated PMS stars, where the large, uniform temperature reduction required in globally inhibited convection models would cause the stars to be much redder than observed.

76 FR 6575 - Airworthiness Directives; BAE Systems (Operations) Limited Model BAe 146 and Avro 146-RJ Airplanes

Federal Register 2010, 2011, 2012, 2013, 2014

2011-02-07

.... One operator reported a crack in a pre-modification main fitting. Shot peening was not present, as... received additional reports of cracked NLG main fittings. One operator reported a crack in a... optional closing action of EASA AD 2010-0001-E is embodiment of M-D B 146-32-150 (polishing and shot...

Early-type objects in NGC 6611 and the Eagle Nebula

NASA Astrophysics Data System (ADS)

Martayan, C.; Floquet, M.; Hubert, A. M.; Neiner, C.; Frémat, Y.; Baade, D.; Fabregat, J.

2008-10-01

Aims: An important question about Be stars is whether they are born as such or whether they have become Be stars during their evolution. It is necessary to observe young clusters to answer this question. Methods: To this end, observations of stars in NGC 6611 and the star-formation region of Eagle Nebula were carried out with the ESO-WFI in slitless spectroscopic mode and at the VLT-GIRAFFE (R ≃ 6400-17 000). The targets for the GIRAFFE observations were pre-selected from the literature and our catalogue of emission-line stars based on the WFI study. GIRAFFE observations allowed us to study the population of the early-type stars accurately both with and without emission lines. For this study, we determined the fundamental parameters of OBA stars thanks to the GIRFIT code. We also studied the status of the objects (main sequence or pre-main sequence stars) by using IR data, membership probabilities, and location in HR diagrams. Results: The nature of the early-type stars with emission-line stars in NGC 6611 and its surrounding environment is derived. The slitless observations with the WFI clearly indicate a small number of emission-line stars in M16. We observed with GIRAFFE 101 OBA stars, among them 9 are emission-line stars with circumstellar emission in Hα. We found that W080 could be a new He-strong star, like W601. W301 is a possible classical Be star, W503 is a mass-transfer eclipsing binary with an accretion disk, and the other ones are possible Herbig Ae/Be stars. We also found that the rotational velocities of main sequence B stars are 18% lower than those of pre-main sequence B stars, in good agreement with theory about the evolution of rotational velocities. Combining adaptive optics, IR data, spectroscopy, and radial velocity indications, we found that 27% of the B-type stars are binaries. We also redetermined the age of NGC 6611 found equal to 1.2-1.8 Myears, in good agreement with the most recent determinations.

Speciation and Neutral Molecular Evolution in One-Dimensional Closed Population

NASA Astrophysics Data System (ADS)

Semovski, Sergei V.; Bukin, Yuri S.; Sherbakov, Dmitry Yu.

Models are presented suitable for a description of speciation processes arising due to reproductive isolation depending on genetic distance. The main attention is paid to the model of a one-dimensional closed population, which describes the evolution of littoral benthic organisms. In order to correspond the modeling results to the results obtained in the course of experimental phylogenetic studies, all individual-based models described here involve neutrally evolving and maternally inherited DNA sequence. Sub-samples of the resulting sequences were used for a posteriori phylogenetic inferences which then were compared to the "true" evolutionary histories.

A NEW CLASS OF NASCENT ECLIPSING BINARIES WITH EXTREME MASS RATIOS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Moe, Maxwell; Stefano, Rosanne Di, E-mail: mmoe@cfa.harvard.edu

2015-03-10

Early B-type main-sequence (MS) stars (M {sub 1} ≈ 5-16 M {sub ☉}) with closely orbiting low-mass stellar companions (q = M {sub 2}/M {sub 1} < 0.25) can evolve to produce Type Ia supernovae, low-mass X-ray binaries, and millisecond pulsars. However, the formation mechanism and intrinsic frequency of such close extreme mass-ratio binaries have been debated, especially considering none have hitherto been detected. Utilizing observations of the Large Magellanic Cloud galaxy conducted by the Optical Gravitational Lensing Experiment, we have discovered a new class of eclipsing binaries in which a luminous B-type MS star irradiates a closely orbiting low-massmore » pre-MS companion that has not yet fully formed. The primordial pre-MS companions have large radii and discernibly reflect much of the light they intercept from the B-type MS primaries (ΔI {sub refl} ≈ 0.02-0.14 mag). For the 18 definitive MS + pre-MS eclipsing binaries in our sample with good model fits to the observed light-curves, we measure short orbital periods P = 3.0-8.5 days, young ages τ ≈ 0.6-8 Myr, and small secondary masses M {sub 2} ≈ 0.8-2.4 M {sub ☉} (q ≈ 0.07-0.36). The majority of these nascent eclipsing binaries are still associated with stellar nurseries, e.g., the system with the deepest eclipse ΔI {sub 1} = 2.8 mag and youngest age τ = 0.6 ± 0.4 Myr is embedded in the bright H II region 30 Doradus. After correcting for selection effects, we find that (2.0 ± 0.6)% of B-type MS stars have companions with short orbital periods P = 3.0-8.5 days and extreme mass ratios q ≈ 0.06-0.25. This is ≈10 times greater than that observed for solar-type MS primaries. We discuss how these new eclipsing binaries provide invaluable insights, diagnostics, and challenges for the formation and evolution of stars, binaries, and H II regions.« less

A tale of two anomalies: Depletion, dispersion, and the connection between the stellar lithium spread and inflated radii on the pre-main sequence

DOE Office of Scientific and Technical Information (OSTI.GOV)

Somers, Garrett; Pinsonneault, Marc H., E-mail: somers@astronomy.ohio-state.edu, E-mail: pinsono@astronomy.ohio-state.edu

2014-07-20

We investigate lithium depletion in standard stellar models (SSMs) and main sequence (MS) open clusters, and explore the origin of the Li dispersion in young, cool stars of equal mass, age, and composition. We first demonstrate that SSMs accurately predict the Li abundances of solar analogs at the zero-age main sequence (ZAMS) within theoretical uncertainties. We then measure the rate of MS Li depletion by removing the [Fe/H]-dependent ZAMS Li pattern from three well-studied clusters, and comparing the detrended data. MS depletion is found to be mass-dependent, in the sense of more depletion at low mass. A dispersion in Limore » abundance at fixed T{sub eff} is nearly universal, and sets in by ∼200 Myr. We discuss mass and age dispersion trends, and the pattern is mixed. We argue that metallicity impacts the ZAMS Li pattern, in agreement with theoretical expectations but contrary to the findings of some previous studies, and suggest Li as a test of cluster metallicity. Finally, we argue that a radius dispersion in stars of fixed mass and age, during the epoch of pre-MS Li destruction, is responsible for the spread in Li abundances and the correlation between rotation and Li in young cool stars, most well known in the Pleiades. We calculate stellar models, inflated to match observed radius anomalies in magnetically active systems, and the resulting range of Li abundances reproduces the observed patterns of young clusters. We discuss ramifications for pre-MS evolutionary tracks and age measurements of young clusters, and suggest an observational test.« less

The Structure of the Young Star Cluster NGC 6231. I. Stellar Population

NASA Astrophysics Data System (ADS)

Kuhn, Michael A.; Medina, Nicolás; Getman, Konstantin V.; Feigelson, Eric D.; Gromadzki, Mariusz; Borissova, Jordanka; Kurtev, Radostin

2017-09-01

NGC 6231 is a young cluster (age ˜2-7 Myr) dominating the Sco OB1 association (distance ˜1.59 kpc) with ˜100 O and B stars and a large pre-main-sequence stellar population. We combine a reanalysis of archival Chandra X-ray data with multiepoch near-infrared (NIR) photometry from the VISTA Variables in the Vía Lactéa (VVV) survey and published optical catalogs to obtain a catalog of 2148 probable cluster members. This catalog is 70% larger than previous censuses of probable cluster members in NGC 6231. It includes many low-mass stars detected in the NIR but not in the optical and some B stars without previously noted X-ray counterparts. In addition, we identify 295 NIR variables, about half of which are expected to be pre-main-sequence stars. With the more complete sample, we estimate a total population in the Chandra field of 5700-7500 cluster members down to 0.08 {M}⊙ (assuming a universal initial mass function) with a completeness limit at 0.5 {M}⊙ . A decrease in stellar X-ray luminosities is noted relative to other younger clusters. However, within the cluster, there is little variation in the distribution of X-ray luminosities for ages less than 5 Myr. The X-ray spectral hardness for B stars may be useful for distinguishing between early-B stars with X-rays generated in stellar winds and B-star systems with X-rays from a pre-main-sequence companion (>35% of B stars). A small fraction of catalog members have unusually high X-ray median energies or reddened NIR colors, which might be explained by absorption from thick or edge-on disks or being background field stars.

Are Avellino (4365 cal BP) and Pompeii twin plinian eruptions? Pre-eruptive constraints and degassing history

NASA Astrophysics Data System (ADS)

Boudon, Georges; Balcone-Boissard, Hélène; Villemant, Benoît.; Ucciani, Guillaume; Cioni, Raffaello

2010-05-01

Somma-Vesuvius activity started 35 ky ago and is characterized by numerous eruptions of variable composition and eruptive style, sometimes interrupted by long periods of unrest. The main explosive eruptions are represented by four plinian eruptions: Pomici di Base eruption (22 cal ky), Mercato (~8900 cal BP), Avellino (4365 cal BP) and Pompeii (79 AD). The 79 AD eruption embodies the most famous eruption since it's responsible of the destruction of Pompeii and Herculanum and it's the first described eruption. The Avellino eruption represents the last plinian event that preceded the Pompeii eruption. The eruptive sequence is similar to the 79 AD plinian eruption, with an opening phase preceding a main plinian fallout activity which ended by a phreatomagmatic phase. The fallout deposit displays a sharp colour contrast from white to grey pumice, corresponding to a magma composition evolution. We focus our study on the main fallout deposit that we sampled in detail in the Traianello quarry, 9 km North-North East of the crater, to investigate the degassing processes during the eruption, using volatile content and textural observations. Density and vesicularity measurements were obtained on a minimum of 100 pumice clasts sampled in 10 stratigraphic levels in the fallout deposit. On the basis of the density distribution, bulk geochemical data, point analytical measurements on glasses (melt inclusions and residual glass) and textural observations were obtained simultaneously on a minimum of 5 pumice clasts per eruptive unit. The glass composition, in particular the Na/K ratio, evolves from Na-rich phonolite for white pumices to a more K-rich phonolite for grey pumices. The pre-eruptive conditions are constrained by systematic Cl measurements in melt inclusions and matrix glass of pumice clasts. The entire magma was saturated relative to sub-critical fluids (a Cl-rich H2O vapour phase and a brine), with a Cl melt content buffered at ~6000 ppm, and a mean pre-eruptive H2O content depending of the magma composition. Most of the pumices of the different eruptive units show that H2O degassing during the eruption followed a typical closed-system evolution as expected for plinian eruption. Contrary to H2O, Cl was not efficiently degassed during the plinian phase of the eruption: the matrix glass composition remains close to the pre-eruptive content. Compared to the 79AD eruption the degassing processes showed by the whole Avellino plinian phase is more homogeneous and similar to the white pumice phase of the Pompeii eruption whereas the open-system degassing mode identified from the grey pumices of the 79AD eruption is not represented during the Avellino eruption.

ABSOLUTE PROPERTIES OF THE PRE-MAIN-SEQUENCE ECLIPSING BINARY STAR NP PERSEI

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lacy, Claud H. Sandberg; Fekel, Francis C.; Muterspaugh, Matthew W.

2016-07-01

NP Per is a well-detached, 2.2 day eclipsing binary whose components are both pre-main-sequence stars that are still contracting toward the main-sequence phase of evolution. We report extensive photometric and spectroscopic observations with which we have determined their properties accurately. Their surface temperatures are quite different: 6420 ± 90 K for the larger F5 primary star and 4540 ± 160 K for the smaller K5e star. Their masses and radii are 1.3207 ± 0.0087 solar masses and 1.372 ± 0.013 solar radii for the primary, and 1.0456 ± 0.0046 solar masses and 1.229 ± 0.013 solar radii for the secondary. The orbital period is variable over long periods of time. A comparisonmore » of the observations with current stellar evolution models from MESA indicates that the stars cannot be fit at a single age: the secondary appears significantly younger than the primary. If the stars are assumed to be coeval and to have the age of the primary (17 Myr), then the secondary is larger and cooler than predicted by current models. The H α spectral line of the secondary component is completely filled by, presumably, chromospheric emission due to a magnetic activity cycle.« less

Let-7 miRNA Precursors Co-express with LIN28B in Cervical Cells.

PubMed

Zamora-Contreras, Aida Margarita; Alvarez-Salas, Luis Marat

2018-01-01

The let-7 microRNAs (miRNAs) are frequently dysregulated in carcinogenic processes, including cervical cancer. LIN28 proteins regulate let-7 biogenesis by binding to conserved sequences within the pre-miRNA structure. Nevertheless, recent research has shown that some let-7 miRNAs may escape LIN28 regulation. Correlate pre-let-7 miRNAs and LIN28B levels in cervical cell lines with different malignancy and HPV content. Pre-let-7 levels were determined by RTqPCR. LIN28B and other let-7 targets were analyzed by immunoblot. In silico tools were used to correlate let-7 and LIN28B expression and to analyze prelet- 7 sequences and structures. Lin28B protein was detected in all tested cell lines although it was more expressed in tumor cell lines. High levels of pre-let-7c/f-1 and pre-miR-98 were present in almost all cell lines regardless malignancy and LIN28B expression. Pre-let-7g/i were mainly expressed in tumor cell lines, pre-let-7e and pre-let-7-a3 were absent in all cell lines and pre-let-7a-2 showed indistinct expression. LIN28B showed positive correlation with pre-let-7i/g/f-1 and pre-miR-98 in tumor cell lines, suggesting escape from regulation. Sequence alignment and analysis of pre-let-7 miRNAs showed distinctive structural features within the preE region that may influence the ideal pre-let-7 structuring for LIN28B interaction. Short preE-stems were present in pre-let-7 that may escape LIN28B regulation, but long preEstems were mostly associated with high-level pre-let-7 miRNAs. The observed differences of pre-let-7 levels in cervical cell lines may be the result of alternative preE structuring affecting interaction with LIN28B thus resulting in differential let-7 regulation. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Substantial reservoirs of molecular hydrogen in the debris disks around young stars.

PubMed

Thi, W F; Blake, G A; van Dishoeck, E F; van Zadelhoff, G J; Horn, J M; Becklin, E E; Mannings, V; Sargent, A I; van Den Ancker, M E; Natta, A

2001-01-04

Circumstellar accretion disks transfer matter from molecular clouds to young stars and to the sites of planet formation. The disks observed around pre-main-sequence stars have properties consistent with those expected for the pre-solar nebula from which our own Solar System formed 4.5 Gyr ago. But the 'debris' disks that encircle more than 15% of nearby main-sequence stars appear to have very small amounts of gas, based on observations of the tracer molecule carbon monoxide: these observations have yielded gas/dust ratios much less than 0.1, whereas the interstellar value is about 100 (ref. 9). Here we report observations of the lowest rotational transitions of molecular hydrogen (H2) that reveal large quantities of gas in the debris disks around the stars beta Pictoris, 49 Ceti and HD135344. The gas masses calculated from the data are several hundreds to a thousand times greater than those estimated from the CO observations, and yield gas/dust ratios of the same order as the interstellar value.

IUE observations of pre-main-sequence stars. I - Mg II and Ca II resonance line fluxes for T Tauri stars

NASA Technical Reports Server (NTRS)

Giampapa n, M. S.

1981-01-01

IUE satellite and Lick 3 m reflector image tube scanner measurements of the Mg II and Ca II resonance lines in a sample of T Tauri stars are the basis of a discussion of the Mg II h and k line emission and the Ca II H and K line emission, within the context of stellar chromospheres. Corroborative evidence is presented for the chromospheric origin of these resonance lines, and chromospheric radiative loss rates in the Mg II and Ca II resonance lines are derived. It is found that the degree of nonradiative heating present in the outer atmospheres of T Tauri stars generally exceeds that of the RS CVn systems, as well as the dMe stars and other active chromospheric dwarfs, and it is inferred that the surfaces of such pre-main sequence stars are covered by regions similar to solar plages. The mean chromospheric electron density of T Tauri stars is determined as 10 to the 11th/cu cm.

Rates and delay times of Type Ia supernovae in the helium-enriched main-sequence donor scenario

NASA Astrophysics Data System (ADS)

Liu, Zheng-Wei; Stancliffe, Richard J.

2018-04-01

The nature of the progenitors of Type Ia supernovae (SNe Ia) remains a mystery. Comparing theoretical rates and delay-time distributions of SNe Ia with those inferred observationally can constrain their progenitor models. In this work, taking thermohaline mixing into account in the helium-enriched main-sequence (HEMS) donor scenario, we address rates and delay times of SNe Ia in this channel by combining the results of self-consistent binary evolution calculations with population synthesis models. We find that the Galactic SN Ia rate from the HEMS donor scenario is around 0.6-1.2 × 10-3 yr-1, which is about 30 per cent of the observed rate. Delay times of SNe Ia in this scenario cover a wide range of 0.1-1.0 Gyr. We also present the pre-explosion properties of companion stars in the HEMS donor scenario, which will be helpful for placing constraints on SN Ia progenitors through analysing their pre-explosion images.

A Critical Assessment of Ages Derived Using Pre-Main-Sequence Isochrones in Colour-Magnitude Diagrams

NASA Astrophysics Data System (ADS)

Bell, Cameron P. M.

2012-11-01

In this thesis a critical assessment of the ages derived using theoretical pre-main-sequence (pre-MS) stellar evolutionary models is presented by comparing the predictions to the low-mass pre-MS population of 14 young star-forming regions (SFRs) in colour-magnitude diagrams (CMDs). Deriving pre-MS ages requires precise distances and estimates of the reddening. Therefore, the main-sequence (MS) members of the SFRs have been used to derive a self-consistent set of statistically robust ages, distances and reddenings with associated uncertainties using a maximum-likelihood fitting statistic and MS evolutionary models. A photometric method for de-reddening individual stars - known as the Q-method - in regions where the extinction is spatially variable has been updated and is presented. The effects of both the model dependency and the SFR composition on these derived parameters are also discussed. The problem of calibrating photometric observations of red pre-MS stars is examined and it is shown that using observations of MS stars to transform the data into a standard photometric system can introduce significant errors in the position of the pre-MS locus in CMD space. Hence, it is crucial that precise photometric studies - especially of pre-MS objects - be carried out in the natural photometric system of the observations. This therefore requires a robust model of the system responses for the instrument used, and thus the calculated responses for the Wide-Field Camera on the Isaac Newton Telescope are presented. These system responses have been tested using standard star observations and have been shown to be a good representation of the photometric system. A benchmark test for the pre-MS evolutionary models is performed by comparing them to a set of well-calibrated CMDs of the Pleiades in the wavelength regime 0.4-2.5 μm. The masses predicted by these models are also tested against dynamical masses using a sample of MS binaries by calculating the system magnitude in a given photometric bandpass. This analysis shows that for Teff ≤ 4000 K the models systematically overestimate the flux by a factor of 2 at 0.5 μm, though this decreases with wavelength, becoming negligible at 2.2 μm. Thus before the pre-MS models are used to derive ages, a recalibration of the models is performed by incorporating an empirical colour-Teff relation and bolometric corrections based on the Ks-band luminosity of Pleiades members, with theoretical corrections for the dependence on the surface gravity (log g). The recalibrated pre-MS model isochrones are used to derive ages from the pre-MS populations of the SFRs. These ages are then compared with the MS derivations, thus providing a powerful diagnostic tool with which to discriminate between the different pre-MS age scales that arise from a much stronger model dependency in the pre-MS regime. The revised ages assigned to each of the 14 SFRs are up to a factor two older than previous derivations, a result with wide-ranging implications, including that circumstellar discs survive longer and that the average Class II lifetime is greater than currently believed.

Massive pre-main-sequence stars in M17

NASA Astrophysics Data System (ADS)

Ramírez-Tannus, M. C.; Kaper, L.; de Koter, A.; Tramper, F.; Bik, A.; Ellerbroek, L. E.; Ochsendorf, B. B.; Ramírez-Agudelo, O. H.; Sana, H.

2017-08-01

The formation process of massive stars is still poorly understood. Massive young stellar objects (mYSOs) are deeply embedded in their parental clouds; these objects are rare, and thus typically distant, and their reddened spectra usually preclude the determination of their photospheric parameters. M17 is one of the best-studied H II regions in the sky, is relatively nearby, and hosts a young stellar population. We have obtained optical to near-infrared spectra of previously identified candidate mYSOs and a few OB stars in this region with X-shooter on the ESO Very Large Telescope. The large wavelength coverage enables a detailed spectroscopic analysis of the photospheres and circumstellar disks of these candidate mYSOs. We confirm the pre-main-sequence (PMS) nature of six of the stars and characterise the O stars. The PMS stars have radii that are consistent with being contracting towards the main sequence and are surrounded by a remnant accretion disk. The observed infrared excess and the double-peaked emission lines provide an opportunity to measure structured velocity profiles in the disks. We compare the observed properties of this unique sample of young massive stars with evolutionary tracks of massive protostars and propose that these mYSOs near the western edge of the H II region are on their way to become main-sequence stars ( 6-20 M⊙) after having undergone high mass accretion rates (Ṁacc 10-4-10-3M⊙yr-1). Their spin distribution upon arrival at the zero age main-sequence is consistent with that observed for young B stars, assuming conservation of angular momentum and homologous contraction. Based on observations collected at the European Southern Observatory at Paranal, Chile (ESO programmes 60.A-9404(A), 085.D-0741, 089.C-0874(A), and 091.C-0934(B)).The full normalised X-shooter spectra are available at the CDS via anonymous ftp to http://cdsarc.u-strasbg.fr (http://130.79.128.5) or via http://cdsarc.u-strasbg.fr/viz-bin/qcat?J/A+A/604/A78

Overview of Petroleum Settings in Deep Waters of the Brazilian South Atlantic Margin

NASA Astrophysics Data System (ADS)

Anjos, Sylvia; Penteado, Henrique; Oliveira, Carlos M. M.

2015-04-01

The objective of this work is to present an overall view of the tectonic and stratigraphic evolution of the western South Atlantic with focus on the Brazilian marginal basins. It includes the structural evolution, stratigraphic sequences, depositional environments and petroleum systems model along the Brazilian marginal basins. In addition, a description of the main petroleum provinces and selected plays including the pre-salt carbonates and post-salt turbidite reservoirs is presented. Source-rock ages and types, trap styles, main reservoir characteristics, petroleum compositions, and recent exploration results are discussed. Finally, an outlook and general assessment of the impact of the large pre-salt discoveries on the present-day and future production curves are given.

Monitoring volcano activity through Hidden Markov Model

NASA Astrophysics Data System (ADS)

Cassisi, C.; Montalto, P.; Prestifilippo, M.; Aliotta, M.; Cannata, A.; Patanè, D.

2013-12-01

During 2011-2013, Mt. Etna was mainly characterized by cyclic occurrences of lava fountains, totaling to 38 episodes. During this time interval Etna volcano's states (QUIET, PRE-FOUNTAIN, FOUNTAIN, POST-FOUNTAIN), whose automatic recognition is very useful for monitoring purposes, turned out to be strongly related to the trend of RMS (Root Mean Square) of the seismic signal recorded by stations close to the summit area. Since RMS time series behavior is considered to be stochastic, we can try to model the system generating its values, assuming to be a Markov process, by using Hidden Markov models (HMMs). HMMs are a powerful tool in modeling any time-varying series. HMMs analysis seeks to recover the sequence of hidden states from the observed emissions. In our framework, observed emissions are characters generated by the SAX (Symbolic Aggregate approXimation) technique, which maps RMS time series values with discrete literal emissions. The experiments show how it is possible to guess volcano states by means of HMMs and SAX.

X-Ray Flare Oscillations Track Plasma Sloshing along Star-disk Magnetic Tubes in the Orion Star-forming Region

NASA Astrophysics Data System (ADS)

Reale, Fabio; Lopez-Santiago, Javier; Flaccomio, Ettore; Petralia, Antonino; Sciortino, Salvatore

2018-03-01

Pulsing X-ray emission tracks the plasma “echo” traveling in an extremely long magnetic tube that flares in an Orion pre-main sequence (PMS) star. On the Sun, flares last from minutes to a few hours and the longest-lasting ones typically involve arcades of closed magnetic tubes. Long-lasting X-ray flares are observed in PMS stars. Large-amplitude (∼20%), long-period (∼3 hr) pulsations are detected in the light curve of day-long flares observed by the Advanced CCD Imaging Spectrometer on-board Chandra from PMS stars in the Orion cluster. Detailed hydrodynamic modeling of two flares observed on V772 Ori and OW Ori shows that these pulsations may track the sloshing of plasma along a single long magnetic tube, triggered by a sufficiently short (∼1 hr) heat pulse. These magnetic tubes are ≥20 solar radii long, enough to connect the star with the surrounding disk.

Phylogenetic relationships among the major lineages of the birds-of-paradise (Paradisaeidae) using mitochondrial DNA gene sequences.

PubMed

Nunn, G B; Cracraft, J

1996-06-01

Complete mitochondrial cytochrome b gene sequences were determined from 12 species of the Australo-Papuan birds-of-paradise (Paradisaeidae) representing 9 genera. Phylogenetic analysis of these and 5 previously published sequences reveals a radiation of the main paradisaeinine lineages that took place over a relatively short evolutionary time scale. The core paradisaeinines are resolved as the monophyletic sister-group to the crow-like manucodines. The genus Parotia is basal to other paradisaeinines and is not closely related to the morphologically similar genera Ptiloris and Lophorina. Three major clades within the paradisaeinine ingroup include: (1) Cicinnurus and Diphyllodes, (2) Ptiloris and Lophorina, and (3) the genus Paradisaea. The monotypic genus Seleucidis is apparently closely related to clades (1) and (2). Cytochrome b sequences did not provide evidence for the monophyly of the sicklebill genera Epimachus and Drepanornis. The paradisaeid tree is characterized by short internodal distances. Thus, some clades cannot be strongly resolved by cytochrome b sequences alone.

The Complete Mitochondrial Genome of Gossypium hirsutum and Evolutionary Analysis of Higher Plant Mitochondrial Genomes

PubMed Central

Su, Aiguo; Geng, Jianing; Grover, Corrinne E.; Hu, Songnian; Hua, Jinping

2013-01-01

Background Mitochondria are the main manufacturers of cellular ATP in eukaryotes. The plant mitochondrial genome contains large number of foreign DNA and repeated sequences undergone frequently intramolecular recombination. Upland Cotton (Gossypium hirsutum L.) is one of the main natural fiber crops and also an important oil-producing plant in the world. Sequencing of the cotton mitochondrial (mt) genome could be helpful for the evolution research of plant mt genomes. Methodology/Principal Findings We utilized 454 technology for sequencing and combined with Fosmid library of the Gossypium hirsutum mt genome screening and positive clones sequencing and conducted a series of evolutionary analysis on Cycas taitungensis and 24 angiosperms mt genomes. After data assembling and contigs joining, the complete mitochondrial genome sequence of G. hirsutum was obtained. The completed G.hirsutum mt genome is 621,884 bp in length, and contained 68 genes, including 35 protein genes, four rRNA genes and 29 tRNA genes. Five gene clusters are found conserved in all plant mt genomes; one and four clusters are specifically conserved in monocots and dicots, respectively. Homologous sequences are distributed along the plant mt genomes and species closely related share the most homologous sequences. For species that have both mt and chloroplast genome sequences available, we checked the location of cp-like migration and found several fragments closely linked with mitochondrial genes. Conclusion The G. hirsutum mt genome possesses most of the common characters of higher plant mt genomes. The existence of syntenic gene clusters, as well as the conservation of some intergenic sequences and genic content among the plant mt genomes suggest that evolution of mt genomes is consistent with plant taxonomy but independent among different species. PMID:23940520

The complete mitochondrial genome of Gossypium hirsutum and evolutionary analysis of higher plant mitochondrial genomes.

PubMed

Liu, Guozheng; Cao, Dandan; Li, Shuangshuang; Su, Aiguo; Geng, Jianing; Grover, Corrinne E; Hu, Songnian; Hua, Jinping

2013-01-01

Mitochondria are the main manufacturers of cellular ATP in eukaryotes. The plant mitochondrial genome contains large number of foreign DNA and repeated sequences undergone frequently intramolecular recombination. Upland Cotton (Gossypium hirsutum L.) is one of the main natural fiber crops and also an important oil-producing plant in the world. Sequencing of the cotton mitochondrial (mt) genome could be helpful for the evolution research of plant mt genomes. We utilized 454 technology for sequencing and combined with Fosmid library of the Gossypium hirsutum mt genome screening and positive clones sequencing and conducted a series of evolutionary analysis on Cycas taitungensis and 24 angiosperms mt genomes. After data assembling and contigs joining, the complete mitochondrial genome sequence of G. hirsutum was obtained. The completed G.hirsutum mt genome is 621,884 bp in length, and contained 68 genes, including 35 protein genes, four rRNA genes and 29 tRNA genes. Five gene clusters are found conserved in all plant mt genomes; one and four clusters are specifically conserved in monocots and dicots, respectively. Homologous sequences are distributed along the plant mt genomes and species closely related share the most homologous sequences. For species that have both mt and chloroplast genome sequences available, we checked the location of cp-like migration and found several fragments closely linked with mitochondrial genes. The G. hirsutum mt genome possesses most of the common characters of higher plant mt genomes. The existence of syntenic gene clusters, as well as the conservation of some intergenic sequences and genic content among the plant mt genomes suggest that evolution of mt genomes is consistent with plant taxonomy but independent among different species.

An Anatomy of a Seismic Sequence in a Deep Gold Mine

NASA Astrophysics Data System (ADS)

Gibowicz, S. J.

1997-12-01

An unusual swarm-like seismic sequence occurred in April 1993 at the Western Deep Levels gold mine, South Africa. Altogether 199 events with moment magnitude from -0.5 to 3.1 were recorded and located by the mine seismic network. The sequence lasted 12 days and was composed in fact of four main shock-aftershocks sequences, closely following each other in space and time. The events were confined to a volume of rock extending to 670 m in the N-S, 630 m in the E-W, and 390 m in the vertical directions. The first sequence lasted 179 hours and the second only 13 hours, being interrupted by the third sequence which lasted 31 hours, being in turn interrupted by the fourth sequence. The parameter p, describing the rate of occurrence of aftershocks, ranged from 0.7 to 1. The first sequence is characterized by the lowest value of the fractal correlation dimension D = 1.75 and the second by the highest value of D = 2.4, whereas the third and fourth sequences are characterized by the middle value of D = 1.9.¶The corner frequencies of P and S waves are in close proximity and range from 14 to 220 Hz. A display of source parameters as a function of time shows that the four main shocks are most distinctly marked by their source radius. For 46 events a moment tensor inversion was performed. In most cases the double-couple component is dominant, ranging from 60 to 90 percent of the solution. The double-couple solutions correspond to the same number of normal and reverse faults and oblique-slip focal mechanisms. An analysis of space distribution of P, T and B axes reveals that the distribution of B axes is the most regular.

MESA models of the evolutionary state of the interacting binary epsilon Aurigae

NASA Astrophysics Data System (ADS)

Gibson, Justus L.; Stencel, Robert E.

2018-06-01

Using MESA code (Modules for Experiments in Stellar Astrophysics, version 9575), an evaluation was made of the evolutionary state of the epsilon Aurigae binary system (HD 31964, F0Iap + disc). We sought to satisfy several observational constraints: (1) requiring evolutionary tracks to pass close to the current temperature and luminosity of the primary star; (2) obtaining a period near the observed value of 27.1 years; (3) matching a mass function of 3.0; (4) concurrent Roche lobe overflow and mass transfer; (5) an isotopic ratio 12C/13C = 5 and, (6) matching the interferometrically determined angular diameter. A MESA model starting with binary masses of 9.85 + 4.5 M⊙, with a 100 d initial period, produces a 1.2 + 10.6 M⊙ result having a 547 d period, and a single digit 12C/13C ratio. These values were reached near an age of 20 Myr, when the donor star comes close to the observed luminosity and temperature for epsilon Aurigae A, as a post-RGB/pre-AGB star. Contemporaneously, the accretor then appears as an upper main-sequence, early B-type star. This benchmark model can provide a basis for further exploration of this interacting binary, and other long-period binary stars.

Characterizing Intermediate-Mass, Pre-Main-Sequence Stars via X-Ray Emision

NASA Astrophysics Data System (ADS)

Haze Nunez, Evan; Povich, Matthew Samuel; Binder, Breanna Arlene; Broos, Patrick; Townsley, Leisa K.

2018-01-01

The X-ray emission from intermediate-mass, pre-main-sequence stars (IMPS) can provide useful constraints on the ages of very young (${<}5$~Myr) massive star forming regions. IMPS have masses between 2 and 8 $M_{\\odot}$ and are getting power from the gravitational contraction of the star. Main-sequence late-B and A-type stars are not expected to be strong X-ray emitters, because they lack the both strong winds of more massive stars and the magneto-coronal activity of lower-mass stars. There is, however, mounting evidence that IMPS are powerful intrinsic x-ray emitters during their convection-dominated early evolution, before the development and rapid growth of a radiation zone. We present our prime candidates for intrinsic, coronal X-ray emission from IMPS identified in the Chandra Carina Complex Project. The Carina massive star-forming complex is of special interest due to the wide variation of star formation stages within the region. Candidate IMPS were identified using infrared spectral energy distribution (SED) models. X-ray properties, including thermal plasma temperatures and absorption-corrected fluxes, were derived from XSPEC fits performed using absorption ($N_{H}$) constrained by the extinction values returned by the infrared SED fits. We find that IMPS have systematically higher X-ray luminosities compared to their lower-mass cousins, the TTauri stars.This work is supported by the National Science Foundation under grant CAREER-1454334 and by NASA through Chandra Award 18200040.

The detectability of radio emission from exoplanets

NASA Astrophysics Data System (ADS)

Lynch, C. R.; Murphy, Tara; Lenc, E.; Kaplan, D. L.

2018-05-01

Like the magnetised planets in our Solar System, magnetised exoplanets should emit strongly at radio wavelengths. Radio emission directly traces the planetary magnetic fields and radio detections can place constraints on the physical parameters of these features. Large comparative studies of predicted radio emission characteristics for the known population of exoplanets help to identify what physical parameters could be key for producing bright, observable radio emission. Since the last comparative study, many thousands of exoplanets have been discovered. We report new estimates for the radio flux densities and maximum emission frequencies for the current population of known exoplanets orbiting pre-main sequence and main-sequence stars with spectral types F-M. The set of exoplanets predicted to produce observable radio emission are Hot Jupiters orbiting young stars. The youth of these system predicts strong stellar magnetic fields and/or dense winds, which are key for producing bright, observable radio emission. We use a new all-sky circular polarisation Murchison Widefield Array survey to place sensitive limits on 200 MHz emission from exoplanets, with 3σ values ranging from 4.0 - 45.0 mJy. Using a targeted Giant Metre Wave Radio Telescope observing campaign, we also report a 3σ upper limit of 4.5 mJy on the radio emission from V830 Tau b, the first Hot Jupiter to be discovered orbiting a pre-main sequence star. Our limit is the first to be reported for the low-frequency radio emission from this source.

Optical spectroscopy of X-ray sources in the Taurus molecular cloud: discovery of ten new pre-main sequence stars

NASA Astrophysics Data System (ADS)

Scelsi, L.; Sacco, G.; Affer, L.; Argiroffi, C.; Pillitteri, I.; Maggio, A.; Micela, G.

2008-11-01

Aims: We have analyzed optical spectra of 25 X-ray sources identified as potential new members of the Taurus molecular cloud (TMC), in order to confirm their membership in this star-forming region. Methods: Fifty-seven candidate members were previously selected among the X-ray sources in the XEST survey, having a 2MASS counterpart compatible with a pre-main sequence star based on color-magnitude and color-color diagrams. We obtained high-resolution optical spectra for 7 of these candidates with the SARG spectrograph at the TNG telescope, which were used to search for lithium absorption and to measure the Hα line and the radial and rotational velocities. Then, 18 low-resolution optical spectra obtained with the instrument DOLORES for other candidate members were used for spectral classification, for Hα measurements, and to assess membership together with IR color-color and color-magnitude diagrams and additional information from the X-ray data. Results: We found that 3 sources show lithium absorption, with equivalent widths (EWs) of 500 mÅ, broad spectral line profiles, indicating rotational velocities of 20{-}40 km s-1, radial velocities consistent with those for known members, and Hα emission. Two of them are classified as new weak-lined T Tauri stars, while the EW ( -9 Å) of the Hα line and its broad asymmetric profile clearly indicate that the third star (XEST-26-062) is a classical T Tauri star. Fourteen sources observed with DOLORES are M-type stars. Fifteen sources show Hα emission. Six of them have spectra that indicate surface gravity lower than in main sequence stars, and their de-reddened positions in IR color-magnitude diagrams are consistent with their derived spectral type and with pre-main sequence models at the distance of the TMC. The K-type star XEST-11-078 is confirmed as a new member on the basis of the strength of the Hα emission line. Overall, we confirm membership to the TMC for 10 out of 25 X-ray sources observed in the optical. Three sources remain uncertain. Based on data collected with the Italian Telescopio Nazionale Galileo (TNG) operated on the island of La Palma by the Centro Galileo Galilei of INAF (Istituto Nazionale di Astrofisica) at the Spanish Observatorio del Roque del los Muchachos of the Instituto de Astrofìsica de Canarias.

HUBBLE TARANTULA TREASURY PROJECT. V. THE STAR CLUSTER HODGE 301: THE OLD FACE OF 30 DORADUS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cignoni, M.; Sabbi, E.; Marel, R. P. van der

Based on color–magnitude diagrams (CMDs) from the Hubble Space Telescope  Hubble Tarantula Treasury Project (HTTP) survey, we present the star formation history of Hodge 301, the oldest star cluster in the Tarantula Nebula. The HTTP photometry extends faint enough to reach, for the first time, the cluster pre-main sequence (PMS) turn-on, where the PMS joins the main sequence. Using the location of this feature, along with synthetic CMDs generated with the latest PARSEC models, we find that Hodge 301 is older than previously thought, with an age between 26.5 and 31.5 Myr. From this age, we also estimate that between 38 andmore » 61 Type II supernovae exploded in the region. The same age is derived from the main sequence turn-off, whereas the age derived from the post-main sequence stars is younger and between 20 and 25 Myr. Other relevant parameters are a total stellar mass of ≈8800 ± 800  M {sub ⊙} and average reddening E ( B − V ) ≈ 0.22–0.24 mag, with a differential reddening δE ( B − V ) ≈ 0.04 mag.« less

Hubble Tarantula Treasury Project V. The Star Cluster Hodge 301: The Old Face of 30 Doradus

NASA Astrophysics Data System (ADS)

Cignoni, M.; Sabbi, E.; van der Marel, R. P.; Lennon, D. J.; Tosi, M.; Grebel, E. K.; Gallagher, J. S., III; Aloisi, A.; de Marchi, G.; Gouliermis, D. A.; Larsen, S.; Panagia, N.; Smith, L. J.

2016-12-01

Based on color-magnitude diagrams (CMDs) from the Hubble Space Telescope Hubble Tarantula Treasury Project (HTTP) survey, we present the star formation history of Hodge 301, the oldest star cluster in the Tarantula Nebula. The HTTP photometry extends faint enough to reach, for the first time, the cluster pre-main sequence (PMS) turn-on, where the PMS joins the main sequence. Using the location of this feature, along with synthetic CMDs generated with the latest PARSEC models, we find that Hodge 301 is older than previously thought, with an age between 26.5 and 31.5 Myr. From this age, we also estimate that between 38 and 61 Type II supernovae exploded in the region. The same age is derived from the main sequence turn-off, whereas the age derived from the post-main sequence stars is younger and between 20 and 25 Myr. Other relevant parameters are a total stellar mass of ≈8800 ± 800 M ⊙ and average reddening E(B - V) ≈ 0.22-0.24 mag, with a differential reddening δE(B - V) ≈ 0.04 mag. Based on observations with the NASA/ESA Hubble Space Telescope, obtained at the Space Telescope Science Institute, which is operated by AURA Inc., under NASA contract NAS 5-26555.

First results of the SONS survey: submillimetre detections of debris discs

NASA Astrophysics Data System (ADS)

Panić, O.; Holland, W. S.; Wyatt, M. C.; Kennedy, G. M.; Matthews, B. C.; Lestrade, J. F.; Sibthorpe, B.; Greaves, J. S.; Marshall, J. P.; Phillips, N. M.; Tottle, J.

2013-10-01

New detections of debris discs at submillimetre wavelengths present highly valuable complementary information to prior observations of these sources at shorter wavelengths. Characterization of discs through spectral energy distribution modelling including the submillimetre fluxes is essential for our basic understanding of disc mass and temperature, and presents a starting point for further studies using millimetre interferometric observations. In the framework of the ongoing SCUBA-2 Observations of Nearby Stars, the instrument SCUBA-2 on the James Clerk Maxwell Telescope was used to provide measurements of 450 and 850 μm fluxes towards a large sample of nearby main-sequence stars with debris discs detected previously at shorter wavelengths. We present the first results from the ongoing survey, concerning 850 μm detections and 450 μm upper limits towards 10 stars, the majority of which are detected at submillimetre wavelengths for the first time. One, or possibly two, of these new detections is likely a background source. We fit the spectral energy distributions of the star+disc systems with a blackbody emission approach and derive characteristic disc temperatures. We use these temperatures to convert the observed fluxes to disc masses. We obtain a range of disc masses from 0.001 to 0.1 M⊕, values similar to the prior dust mass measurements towards debris discs. There is no evidence for evolution in dust mass with age on the main sequence, and indeed the upper envelope remains relatively flat at ≈0.5 M⊕ at all ages. The inferred disc masses are lower than those from disc detections around pre-main-sequence stars, which may indicate a depletion of solid mass. This may also be due to a change in disc opacity, though limited sensitivity means that it is not yet known what fraction of pre-main-sequence stars have discs with dust masses similar to debris disc levels. New, high-sensitivity detections are a path towards investigating the trends in dust mass evolution.

Discovery of Par 1802 as a Low-Mass, Pre-Main-Sequence Eclipsing Binary in the Orion Star-Forming Region

NASA Astrophysics Data System (ADS)

Cargile, P. A.; Stassun, K. G.; Mathieu, R. D.

2008-02-01

We report the discovery of a pre-main-sequence (PMS), low-mass, double-lined, spectroscopic, eclipsing binary in the Orion star-forming region. We present our observations, including radial velocities derived from optical high-resolution spectroscopy, and present an orbit solution that permits the determination of precise empirical masses for both components of the system. We find that Par 1802 is composed of two equal-mass (0.39 +/- 0.03, 0.40 +/- 0.03 M⊙) stars in a circular, 4.7 day orbit. There is strong evidence, such as the system exhibiting strong Li lines and a center-of-mass velocity consistent with cluster membership, that this system is a member of the Orion star-forming region and quite possibly the Orion Nebula Cluster, and therefore has an age of only a few million years. As there are currently only a few empirical mass and radius measurements for low-mass, PMS stars, this system presents an interesting test for the predictions of current theoretical models of PMS stellar evolution.

Lactobacillus delbrueckii subsp. bulgaricus CRL 454 cleaves allergenic peptides of β-lactoglobulin.

PubMed

Pescuma, Micaela; Hébert, Elvira M; Haertlé, Thomas; Chobert, Jean-Marc; Mozzi, Fernanda; Font de Valdez, Graciela

2015-03-01

Whey, a cheese by-product used as a food additive, is produced worldwide at 40.7 million tons per year. β-Lactoglobulin (BLG), the main whey protein, is poorly digested and is highly allergenic. We aimed to study the contribution of Lactobacillus delbrueckii subsp. bulgaricus CRL 454 to BLG digestion and to analyse its ability to degrade the main allergenic sequences of this protein. Pre-hydrolysis of BLG by L. delbrueckii subsp. bulgaricus CRL 454 increases digestion of BLG assayed by an in vitro simulated gastrointestinal system. Moreover, peptides from hydrolysis of the allergenic sequences V41-K60, Y102-R124, C121-L140 and L149-I162 were found when BLG was hydrolysed by this strain. Interestingly, peptides possessing antioxidant, ACE inhibitory, antimicrobial and immuno-modulating properties were found in BLG degraded by both the Lactobacillus strain and digestive enzymes. To conclude, pre-hydrolysis of BLG by L. delbrueckii subsp. bulgaricus CRL 454 has a positive effect on BLG digestion and could diminish allergenic reactions. Copyright © 2014 Elsevier Ltd. All rights reserved.

preAssemble: a tool for automatic sequencer trace data processing.

PubMed

Adzhubei, Alexei A; Laerdahl, Jon K; Vlasova, Anna V

2006-01-17

Trace or chromatogram files (raw data) are produced by automatic nucleic acid sequencing equipment or sequencers. Each file contains information which can be interpreted by specialised software to reveal the sequence (base calling). This is done by the sequencer proprietary software or publicly available programs. Depending on the size of a sequencing project the number of trace files can vary from just a few to thousands of files. Sequencing quality assessment on various criteria is important at the stage preceding clustering and contig assembly. Two major publicly available packages--Phred and Staden are used by preAssemble to perform sequence quality processing. The preAssemble pre-assembly sequence processing pipeline has been developed for small to large scale automatic processing of DNA sequencer chromatogram (trace) data. The Staden Package Pregap4 module and base-calling program Phred are utilized in the pipeline, which produces detailed and self-explanatory output that can be displayed with a web browser. preAssemble can be used successfully with very little previous experience, however options for parameter tuning are provided for advanced users. preAssemble runs under UNIX and LINUX operating systems. It is available for downloading and will run as stand-alone software. It can also be accessed on the Norwegian Salmon Genome Project web site where preAssemble jobs can be run on the project server. preAssemble is a tool allowing to perform quality assessment of sequences generated by automatic sequencing equipment. preAssemble is flexible since both interactive jobs on the preAssemble server and the stand alone downloadable version are available. Virtually no previous experience is necessary to run a default preAssemble job, on the other hand options for parameter tuning are provided. Consequently preAssemble can be used as efficiently for just several trace files as for large scale sequence processing.

Brockia lithotrophica gen. nov., sp. nov., an anaerobic thermophilic bacterium from a terrestrial hot spring.

PubMed

Perevalova, Anna A; Kublanov, Ilya V; Baslerov, R V; Zhang, Gengxin; Bonch-Osmolovskaya, Elizaveta A

2013-02-01

A novel thermophilic bacterium, strain Kam1851(T), was isolated from a terrestrial hot spring of the Uzon Caldera, Kamchatka Peninsula, Russia. Cells of strain Kam1851(T) were spore-forming rods with a gram-positive type of cell wall. Growth was observed between 46 and 78 °C, and pH 5.5-8.5. The optimal growth (doubling time, 6.0 h) was at 60-65 °C and pH 6.5. The isolate was an obligate anaerobe growing in pre-reduced medium only. It grew on mineral medium with molecular hydrogen or formate as electron donors, and elemental sulfur, thiosulfate or polysulfide as electron acceptors. The main cellular fatty acids were C(16 : 0) (34.2 %), iso-C(16 : 0) (18 %), C(18 : 0) (12.8 %) and iso-C(17 : 0) (11.1 %). The G+C content of the genomic DNA of strain Kam1851(T) was 63 mol%. 16S rRNA gene sequence analysis showed that strain Kam1851(T) belonged to the order Thermoanaerobacterales, but it was not closely related to representatives of any genera with validly published names. The most closely related strains, which had no more than 89.2 % sequence similarity, were members of the genera Ammonifex and Caldanaerobacter. On the basis of its phylogenetic position and novel phenotypic features, isolate Kam1851(T) is proposed to represent a novel species in a new genus, Brockia lithotrophica gen. nov., sp. nov.; the type strain of Brockia lithotrophica is Kam1851(T) ( = DSM 22653(T) = VKM B-2685(T)).

SeqTrim: a high-throughput pipeline for pre-processing any type of sequence read

PubMed Central

2010-01-01

Background High-throughput automated sequencing has enabled an exponential growth rate of sequencing data. This requires increasing sequence quality and reliability in order to avoid database contamination with artefactual sequences. The arrival of pyrosequencing enhances this problem and necessitates customisable pre-processing algorithms. Results SeqTrim has been implemented both as a Web and as a standalone command line application. Already-published and newly-designed algorithms have been included to identify sequence inserts, to remove low quality, vector, adaptor, low complexity and contaminant sequences, and to detect chimeric reads. The availability of several input and output formats allows its inclusion in sequence processing workflows. Due to its specific algorithms, SeqTrim outperforms other pre-processors implemented as Web services or standalone applications. It performs equally well with sequences from EST libraries, SSH libraries, genomic DNA libraries and pyrosequencing reads and does not lead to over-trimming. Conclusions SeqTrim is an efficient pipeline designed for pre-processing of any type of sequence read, including next-generation sequencing. It is easily configurable and provides a friendly interface that allows users to know what happened with sequences at every pre-processing stage, and to verify pre-processing of an individual sequence if desired. The recommended pipeline reveals more information about each sequence than previously described pre-processors and can discard more sequencing or experimental artefacts. PMID:20089148

Molecular characterisation of an avihepadnavirus isolated from Psittacula krameri (ring-necked parrot).

PubMed

Piasecki, Tomasz; Kurenbach, Brigitta; Chrząstek, Klaudia; Bednarek, Karolina; Kraberger, Simona; Martin, Darren P; Varsani, Arvind

2012-03-01

Avihepadnaviruses have been documented previously in ducks, herons, geese, storks and cranes. Here, we describe the full genome of a new avihepadnavirus isolated from Psittacula krameri (ring-necked parrot) in Poland. The parrot hepatitis B virus (PHBV) genome (3042 bp) shares <76% sequence identity with other avihepadnavirus isolates and is phylogenetically most closely related to heron and stork hepatitis B viruses isolates. PHBV has a genome organization similar to that of other hepadnaviruses and contains ORFs for a preC/C, preS/S and polyprotein. Additionally, we identified an X-like ORF in the genome of PHBV. The full-genome data will be useful in developing screening tools for avihepadnaviruses in parrots.

High Contrast X-ray Flares In The Anchors Database

NASA Astrophysics Data System (ADS)

McCleary, Jacqueline; Wolk, S.

2010-01-01

The X-ray light curves of pre-main sequence stars can show variability in the form of flares altering a baseline characteristic activity level; the largest X-ray flares are characterized by a rapid rise to 10 or more times the characteristic count rate, followed by a slower quasi-exponential decay. Analysis of these high-contrast X-ray flares enables the study of the innermost magnetic fields of pre-main sequence stars. We have scanned the ANCHORS database of Chandra observations of star-forming regions to extend the study of flare events on pre-main sequence stars both in sky coverage and in volume. We developed a sample of 30 high-contrast flares out of the 14,000 stars available in ANCHORS at the time of our study. By not biasing our sample by cluster, age, or spectral type, we increased the number of X-ray flare events studied and subsequently the strength of any statements about their properties. Applying the generally accepted methods of time-resolved spectral analysis developed by Reale et al. (1997), we measured the temperatures, confining magnetic field strengths, and loop lengths of these large flares. The results of the flare analysis were compared to the 2MASS and Spitzer data available for the stars in our sample. We found that the longest flare loop lengths (of order several stellar radii) are only seen on stars whose IR data indicates the presence of disks, which suggests that the longest flares may stretch all the way to the disk. Such long flares tend to be more tenuous (rarified) than the other large flares studied. A wide range of loop lengths were observed, indicating that two types of flares may occur on disked young stellar objects: either compact and analogous to flares on evolved stars, or long and the result of star-disk magnetic connections.

Accreting Planets in the Habitable Zones of M-Stars Are Too Hot to Retain Liquid Water

NASA Astrophysics Data System (ADS)

Ramirez, R. M.; Kopparapu, R. K.; Kasting, J. F.

2014-12-01

Previous studies1,2 have shown that young accreting planets in the habitable zones (HZ) of pre-main sequence M-stars face major dynamical hurdles in both the retention and acquisition of volatiles. High collision rates with other bodies, short planetary formation timescales, and inefficient radial mixing are among the major problems encountered. However, another equally-important concern is the high temperatures predicted within the circumstellar disk, greatly hindering volatile delivery. We use a 1-D radiative-convective climate model to demonstrate that the fluxes received by accreting planets orbiting late K-M stars exceed the runaway greenhouse threshold. Given that M-stars are disproportionately brighter in their pre main-sequence lifetimes as compared to Sun-like stars (i.e. G-class insolation), planets orbiting M-stars are especially susceptible to the runaway, with intensity and duration increasing for cooler M-stars. Thus, accreting planetesimals in the HZs of M-stars could be too hot to maintain liquid water on their surfaces. In contrast, accreting planets located at Earth's distance (or farther) from a pre-main sequence solar analogue (i.e. G2 spectral class) receive stellar fluxes well below that of the runaway point. Our results suggest that future missions and surveys can improve their prospects of finding alien life by targeting HZ planets orbiting Sun-like stars. Moreover, our findings support recent claims that Venus may have lost its water during accretion3. REFERENCES1. Lissauer, Jack J. "Planets formed in habitable zones of M dwarf stars probably are deficient in volatiles." The Astrophysical Journal Letters 660.2 (2007): L149. 2. Raymond, Sean N., John Scalo, and Victoria S. Meadows. "A decreased probability of habitable planet formation around low-mass stars." The Astrophysical Journal 669.1 (2007): 606. 3. Hamano, Keiko, Yutaka Abe, and Hidenori Genda. "Emergence of two types of terrestrial planet on solidification of magma ocean." Nature 497.7451 (2013): 607-610.

Observations of suspected low-mass post-T Tauri stars and their evolutionary status

NASA Technical Reports Server (NTRS)

Mundt, R.; Walter, F. M.; Feigelson, E. D.; Finkenzeller, U.; Herbig, G. H.; Odell, A. P.

1983-01-01

The results of a study of five X-ray discovered weak emission pre-main-sequence stars in the Taurus-Auriga star formation complex are presented. All are of spectral type K7-M0, and about 1-2 mag above the main sequence. One is a double-lined spectroscopic binary, the first spectroscopic binary PMS star to be confirmed. The ages, masses, and radii of these stars as determined by photometry and spectroscopy are discussed. The difference in emission strength between these and the T Tauri stars is investigated, and it is concluded that these 'post-T Tauri' stars do indeed appear more evolved than the T Tauri stars, although there is no evidence of any significant difference in ages.

Paired moraine-dammed lakes: a key landform for glaciated high mountain areas in the tropical Andes of Peru

NASA Astrophysics Data System (ADS)

Iturrizaga, Lasafam

2016-04-01

The tropical mountain range of the Cordillera Blanca hosts one of the main concentrations of proglacial lakes in high-mountain settings worldwide, which have formed as a result of the dominant trend of modern glacier retreat. Based on empirical data from field research in over 20 valleys and the analysis of air and satellite images, a genetic classification of major lake types with their barriers and a generalized model for the distribution of the present lakes and paleolakes was set up. The origin of the lakes and their recurrent distribution pattern are associated with the individual stages of the Pleistocene to modern glaciation and their corresponding geomorphological landforms. Characteristic repetitive moraine sequences are found in the upper parts of numerous valleys of the Cordillera Blanca. In terms of the spatial arrangement of the lake types, combined lakes are classified as a distinct composite lake type. These lakes occur at nearly the same elevation or at successively lower elevations, and form characteristic lake sequences of two or more lakes. They may occur as multi-moraine-dammed lakes or mixed combined lakes such as moraine-rock-dammed lakes or multi-debris-dammed lakes. From special interest are in this study the paired moraine-dammed lakes (e.g. Lagunas Qoyllurcochas, Lagunas Safuna Alta and Baja). They are composed of the Great Endmoraine (GEM), primarily formed during the Little Ice Age and earlier, and the pre-GEM, formed during the Holocene. Both moraines are located in rather close vicinity to each other at a distance of 1-3 km. In contrast to the prominent sharp-crested GEM, the pre-GEM is a low-amplitude end-moraine complex, which usually does not exceed a few meters to tens of meters in height. The latter is often composed of several inserted moraine ridges or an irregular hummocky moraine landscape. It is argued here that the process of formation of these combined lakes is mainly controlled by a combination of distinct topographical and climatic factors.

Evolution of Pre-Main Sequence Accretion Disks

NASA Technical Reports Server (NTRS)

Hartmann, Lee W.

2005-01-01

The aim of this project was to develop a comprehensive global picture of the physical conditions in, and evolutionary timescales of, premain sequence accretion disks. The results of this work will help constrain the initial conditions for planet formation. To this end we developed much larger samples of 3-10 Myr-old stars to provide better empirical constraints on protoplanetary disk evolution; measured disk accretion rates in these systems; and constructed detailed model disk structures consistent with observations to infer physical conditions such as grain growth in protoplanetary disks.

Hubble Tarantula Treasury Project - VI. Identification of Pre-Main-Sequence Stars using Machine Learning techniques

NASA Astrophysics Data System (ADS)

Ksoll, Victor F.; Gouliermis, Dimitrios A.; Klessen, Ralf S.; Grebel, Eva K.; Sabbi, Elena; Anderson, Jay; Lennon, Daniel J.; Cignoni, Michele; de Marchi, Guido; Smith, Linda J.; Tosi, Monica; van der Marel, Roeland P.

2018-05-01

The Hubble Tarantula Treasury Project (HTTP) has provided an unprecedented photometric coverage of the entire star-burst region of 30 Doradus down to the half Solar mass limit. We use the deep stellar catalogue of HTTP to identify all the pre-main-sequence (PMS) stars of the region, i.e., stars that have not started their lives on the main-sequence yet. The photometric distinction of these stars from the more evolved populations is not a trivial task due to several factors that alter their colour-magnitude diagram positions. The identification of PMS stars requires, thus, sophisticated statistical methods. We employ Machine Learning Classification techniques on the HTTP survey of more than 800,000 sources to identify the PMS stellar content of the observed field. Our methodology consists of 1) carefully selecting the most probable low-mass PMS stellar population of the star-forming cluster NGC2070, 2) using this sample to train classification algorithms to build a predictive model for PMS stars, and 3) applying this model in order to identify the most probable PMS content across the entire Tarantula Nebula. We employ Decision Tree, Random Forest and Support Vector Machine classifiers to categorise the stars as PMS and Non-PMS. The Random Forest and Support Vector Machine provided the most accurate models, predicting about 20,000 sources with a candidateship probability higher than 50 percent, and almost 10,000 PMS candidates with a probability higher than 95 percent. This is the richest and most accurate photometric catalogue of extragalactic PMS candidates across the extent of a whole star-forming complex.

Keck Adaptive Optics Imaging of Nearby Young Stars: Detection of Close Multiple Systems

NASA Astrophysics Data System (ADS)

Brandeker, Alexis; Jayawardhana, Ray; Najita, Joan

2003-10-01

Using adaptive optics on the Keck II 10 m telescope on Mauna Kea, we have surveyed 24 of the nearest young stars known in search of close companions. Our sample includes members of the MBM 12 and TW Hydrae young associations and the classical T Tauri binary UY Aurigae in the Taurus star-forming region. We present relative photometry and accurate astrometry for 10 close multiple systems. The multiplicity frequency in the TW Hydrae and MBM 12 groups are high in comparison to other young regions, although the significance of this result is low because of the small number statistics. We resolve S18 into a triple system, including a tight 63 mas (projected separation of 17 AU at a distance of 275 pc) binary, for the first time, with a hierarchical configuration reminiscent of VW Chamaeleontis and T Tauri. Another tight binary in our sample-TWA 5Aab (54 mas or 3 AU at 55 pc)-offers the prospect of dynamical mass measurement using astrometric observations within a few years and thus could be important for testing pre-main-sequence evolutionary models. Our observations confirm with 9 σ confidence that the brown dwarf TWA 5B is bound to TWA 5A. We find that the flux ratio of UY Aur has changed dramatically, by more than a magnitude in the H band, possibly as a result of variable extinction. With the smaller flux difference, the system may once again become detectable as an optical binary, as it was at the time of its discovery in 1944. Taken together, our results demonstrate that adaptive optics on large telescopes is a powerful tool for detecting tight companions and thus exploring the frequency and configurations of close multiple systems.

Pre-frontal control of closed-loop limbic neurostimulation by rodents using a brain-computer interface

NASA Astrophysics Data System (ADS)

Widge, Alik S.; Moritz, Chet T.

2014-04-01

Objective. There is great interest in closed-loop neurostimulators that sense and respond to a patient's brain state. Such systems may have value for neurological and psychiatric illnesses where symptoms have high intraday variability. Animal models of closed-loop stimulators would aid preclinical testing. We therefore sought to demonstrate that rodents can directly control a closed-loop limbic neurostimulator via a brain-computer interface (BCI). Approach. We trained rats to use an auditory BCI controlled by single units in prefrontal cortex (PFC). The BCI controlled electrical stimulation in the medial forebrain bundle, a limbic structure involved in reward-seeking. Rigorous offline analyses were performed to confirm volitional control of the neurostimulator. Main results. All animals successfully learned to use the BCI and neurostimulator, with closed-loop control of this challenging task demonstrated at 80% of PFC recording locations. Analysis across sessions and animals confirmed statistically robust BCI control and specific, rapid modulation of PFC activity. Significance. Our results provide a preliminary demonstration of a method for emotion-regulating closed-loop neurostimulation. They further suggest that activity in PFC can be used to control a BCI without pre-training on a predicate task. This offers the potential for BCI-based treatments in refractory neurological and mental illness.

Accretion-induced luminosity spreads in young clusters: evidence from stellar rotation

NASA Astrophysics Data System (ADS)

Littlefair, S. P.; Naylor, Tim; Mayne, N. J.; Saunders, Eric; Jeffries, R. D.

2011-05-01

We present an analysis of the rotation of young stars in the associations Cepheus OB3b, NGC 2264, 2362 and the Orion Nebula Cluster (ONC). We discover a correlation between rotation rate and position in a colour-magnitude diagram (CMD) such that stars which lie above an empirically determined median pre-main sequence rotate more rapidly than stars which lie below this sequence. The same correlation is seen, with a high degree of statistical significance, in each association studied here. If position within the CMD is interpreted as being due to genuine age spreads within a cluster, then the stars above the median pre-main sequence would be the youngest stars. This would in turn imply that the most rapidly rotating stars in an association are the youngest, and hence those with the largest moments of inertia and highest likelihood of ongoing accretion. Such a result does not fit naturally into the existing picture of angular momentum evolution in young stars, where the stars are braked effectively by their accretion discs until the disc disperses. Instead, we argue that, for a given association of young stars, position within the CMD is not primarily a function of age, but of accretion history. We show that this hypothesis could explain the correlation we observe between rotation rate and position within the CMD.

Evolution models of helium white dwarf-main-sequence star merger remnants: the mass distribution of single low-mass white dwarfs

NASA Astrophysics Data System (ADS)

Zhang, Xianfei; Hall, Philip D.; Jeffery, C. Simon; Bi, Shaolan

2018-02-01

It is not known how single white dwarfs with masses less than 0.5Msolar -- low-mass white dwarfs -- are formed. One way in which such a white dwarf might be formed is after the merger of a helium-core white dwarf with a main-sequence star that produces a red giant branch star and fails to ignite helium. We use a stellar-evolution code to compute models of the remnants of these mergers and find a relation between the pre-merger masses and the final white dwarf mass. Combining our results with a model population, we predict that the mass distribution of single low-mass white dwarfs formed through this channel spans the range 0.37 to 0.5Msolar and peaks between 0.45 and 0.46Msolar. Helium white dwarf--main-sequence star mergers can also lead to the formation of single helium white dwarfs with masses up to 0.51Msolar. In our model the Galactic formation rate of single low-mass white dwarfs through this channel is about 8.7X10^-3yr^-1. Comparing our models with observations, we find that the majority of single low-mass white dwarfs (<0.5Msolar) are formed from helium white dwarf--main-sequence star mergers, at a rate which is about $2$ per cent of the total white dwarf formation rate.

Planets around pulsars - Implications for planetary formation

NASA Technical Reports Server (NTRS)

Bodenheimer, Peter

1993-01-01

Data on planets around pulsars are summarized, and different models intended to explain the formation mechanism are described. Both theoretical and observational evidence suggest that very special circumstances are required for the formation of planetary systems around pulsars, namely, the prior presence of a millisecond pulsar with a close binary companion, probably a low mass main-sequence star. It is concluded that the discovery of two planets around PSR 1257+12 is important for better understanding the problems of dynamics and stellar evolution. The process of planetary formation should be learned through intensive studies of the properties of disks near young objects and application of techniques for detection of planets around main-sequence solar-type stars.

Characterisation of monotreme caseins reveals lineage-specific expansion of an ancestral casein locus in mammals.

PubMed

Lefèvre, Christophe M; Sharp, Julie A; Nicholas, Kevin R

2009-01-01

Using a milk-cell cDNA sequencing approach we characterised milk-protein sequences from two monotreme species, platypus (Ornithorhynchus anatinus) and echidna (Tachyglossus aculeatus) and found a full set of caseins and casein variants. The genomic organisation of the platypus casein locus is compared with other mammalian genomes, including the marsupial opossum and several eutherians. Physical linkage of casein genes has been seen in the casein loci of all mammalian genomes examined and we confirm that this is also observed in platypus. However, we show that a recent duplication of beta-casein occurred in the monotreme lineage, as opposed to more ancient duplications of alpha-casein in the eutherian lineage, while marsupials possess only single copies of alpha- and beta-caseins. Despite this variability, the close proximity of the main alpha- and beta-casein genes in an inverted tail-tail orientation and the relative orientation of the more distant kappa-casein genes are similar in all mammalian genome sequences so far available. Overall, the conservation of the genomic organisation of the caseins indicates the early, pre-monotreme development of the fundamental role of caseins during lactation. In contrast, the lineage-specific gene duplications that have occurred within the casein locus of monotremes and eutherians but not marsupials, which may have lost part of the ancestral casein locus, emphasises the independent selection on milk provision strategies to the young, most likely linked to different developmental strategies. The monotremes therefore provide insight into the ancestral drivers for lactation and how these have adapted in different lineages.

HAT-P-65b and HAT-P-66b: Two Transiting Inflated Hot Jupiters and Observational Evidence for the Reinflation of Close-in Giant Planets

NASA Astrophysics Data System (ADS)

Hartman, J. D.; Bakos, G. Á.; Bhatti, W.; Penev, K.; Bieryla, A.; Latham, D. W.; Kovács, G.; Torres, G.; Csubry, Z.; de Val-Borro, M.; Buchhave, L.; Kovács, T.; Quinn, S.; Howard, A. W.; Isaacson, H.; Fulton, B. J.; Everett, M. E.; Esquerdo, G.; Béky, B.; Szklenar, T.; Falco, E.; Santerne, A.; Boisse, I.; Hébrard, G.; Burrows, A.; Lázár, J.; Papp, I.; Sári, P.

2016-12-01

We present the discovery of the transiting exoplanets HAT-P-65b and HAT-P-66b, with orbital periods of 2.6055 and 2.9721 days, masses of 0.527+/- 0.083 {M}{{J}} and 0.783+/- 0.057 {M}{{J}}, and inflated radii of 1.89+/- 0.13 {R}{{J}} and {1.59}-0.10+0.16 {R}{{J}}, respectively. They orbit moderately bright (V=13.145+/- 0.029 and V=12.993+/- 0.052) stars of mass 1.212+/- 0.050 {M}⊙ and {1.255}-0.054+0.107 {M}⊙ . The stars are at the main-sequence turnoff. While it is well known that the radii of close-in giant planets are correlated with their equilibrium temperatures, whether or not the radii of planets increase in time as their hosts evolve and become more luminous is an open question. Looking at the broader sample of well-characterized close-in transiting giant planets, we find that there is a statistically significant correlation between planetary radii and the fractional ages of their host stars, with a false-alarm probability of only 0.0041%. We find that the correlation between the radii of planets and the fractional ages of their hosts is fully explained by the known correlation between planetary radii and their present-day equilibrium temperatures; however, if the zero-age main-sequence equilibrium temperature is used in place of the present-day equilibrium temperature, then a correlation with age must also be included to explain the planetary radii. This suggests that, after contracting during the pre-main-sequence, close-in giant planets are reinflated over time due to the increasing level of irradiation received from their host stars. Prior theoretical work indicates that such a dynamic response to irradiation requires a significant fraction of the incident energy to be deposited deep within the planetary interiors. Based on observations obtained with the Hungarian-made Automated Telescope Network. Based on observations obtained at the W. M. Keck Observatory, which is operated by the University of California and the California Institute of Technology. Keck time has been granted by NOAO (A289Hr, A245Hr) and NASA (N029Hr, N154Hr, N130Hr, N133Hr, N169Hr, N186Hr). Based on observations obtained with the Tillinghast Reflector 1.5 m telescope and the 1.2 m telescope, both operated by the Smithsonian Astrophysical Observatory at the Fred Lawrence Whipple Observatory in Arizona. Based on observations made with the Nordic Optical Telescope, operated by the Nordic Optical Telescope Scientific Association at the Observatorio del Roque de los Muchachos, La Palma, Spain, of the Intituto de Astrofísica de Canarias. Based on observations made with the SOPHIE spectrograph on the 1.93 m telescope at Observatoire de Haute-Provence (OHP, CNRS/AMU), France (programs 15A.PNP.HEBR and 15B.PNP.HEBR). Data presented herein were obtained at the WIYN Observatory from telescope time allocated to NN-EXPLORE through the scientific partnership of the National Aeronautics and Space Administration, the National Science Foundation, and the National Optical Astronomy Observatory. This work was supported by a NASA WIYN PI Data Award, administered by the NASA Exoplanet Science Institute.

Virtual plate pre-bending for the long bone fracture based on axis pre-alignment.

PubMed

Liu, Bin; Luo, Xinjian; Huang, Rui; Wan, Chao; Zhang, Bingbing; Hu, Weihua; Yue, Zongge

2014-06-01

In this paper, a modeling and visualizing system for assisting surgeons in correctly registering for the closed fracture reduction surgery is presented. By using this system, the geometric parameters of the target fixation plate before the long bone fracture operation can be obtained. The main processing scheme consists of following steps: firstly (image data process), utilize the Curvelet transform to denoise the CT images of fracture part and then reconstruct the 3D models of the broken bones. Secondly (pre-alignment), extract the axial lines of the broken bones and spatially align them. Then drive the broken bone models to be pre-aligned. Thirdly (mesh segmentation), a method based on vertex normal feature is utilized to obtain the broken bone cross-sections mesh models. Fourthly (fine registration), the ICP (Iterative Closest Point) algorithm is used to register the cross-sections and the broken bone models are driven to achieve the fine registration posture. Lastly (plate fitting), an accurate NURBS surface fitting method is used to construct the virtual plate. The experiment proved that the obtained models of the pre-bended plates were closely bonded to the surface of the registered long bone models. Finally, the lengths, angles and other interested geometric parameters can be measured on the plate models. Copyright © 2014 Elsevier Ltd. All rights reserved.

Taxonomic and predicted metabolic profiles of the human gut microbiome in pre-Columbian mummies.

PubMed

Santiago-Rodriguez, Tasha M; Fornaciari, Gino; Luciani, Stefania; Dowd, Scot E; Toranzos, Gary A; Marota, Isolina; Cano, Raul J

2016-11-01

Characterization of naturally mummified human gut remains could potentially provide insights into the preservation and evolution of commensal and pathogenic microorganisms, and metabolic profiles. We characterized the gut microbiome of two pre-Columbian Andean mummies dating to the 10-15th centuries using 16S rRNA gene high-throughput sequencing and metagenomics, and compared them to a previously characterized gut microbiome of an 11th century AD pre-Columbian Andean mummy. Our previous study showed that the Clostridiales represented the majority of the bacterial communities in the mummified gut remains, but that other microbial communities were also preserved during the process of natural mummification, as shown with the metagenomics analyses. The gut microbiome of the other two mummies were mainly comprised by Clostridiales or Bacillales, as demonstrated with 16S rRNA gene amplicon sequencing, many of which are facultative anaerobes, possibly consistent with the process of natural mummification requiring low oxygen levels. Metagenome analyses showed the presence of other microbial groups that were positively or negatively correlated with specific metabolic profiles. The presence of sequences similar to both Trypanosoma cruzi and Leishmania donovani could suggest that these pathogens were prevalent in pre-Columbian individuals. Taxonomic and functional profiling of mummified human gut remains will aid in the understanding of the microbial ecology of the process of natural mummification. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

The Exoplant Migration Timescale from K2 Young Clusters

NASA Astrophysics Data System (ADS)

Rizzuto, Aaron C.; Mann, Andrew; Kraus, Adam L.; Ireland, Michael

2017-01-01

Planetary Migration models for close-in exoplanets(a < 0.1 AU, P < 20 days) can be loosely divided into three categories: Disk-driven migration, binary-star planet interaction, and planet-planet interaction. Disk migration, occurs over the lifetime of the protoplanetary disk (<5 Myr), while migration involving dynamical multi-body interactions operate on timescales of ~100’s of Myr to ~1Gyr, a lengthier process than disk migration. It is unclear which of these is the dominating mechanism.The K2 mission has measured planet formation timescales and migration pathways by sampling groups of stars at key pre-main-sequence ages: Over the past 10 campaigns, multiple groups of young stars have been observed by K2, ranging from the 10 Myr Upper Scorpius OB association, through the ˜120 Myr Pleiades, the ˜600-800 Myr Hyades and Praesepe moving groups, to the original Kepler Field. The frequency, orbital and compositional properties of the exoplanet population in these samples of different age, with careful treatment of detection completeness, will be sufficient to address the question of exoplanet migration as their host stars are settling onto the main sequence.We will present the initial results of a program to directly address the question of planet migration with a uniform injection-recovery tests on a new K2 detrending pipeline that is optimized for the particular case of young, rotationally variable stars in K2 to robustly measure the detectability of planets of differing size and orbit. Initial results point towards a migration timescale of 200-700 Myr, which is consistent with the slower planet-planet scattering or Kozai migration models.

Molecular characterization of two genotypes of a new polerovirus infecting brassicas in China.

PubMed

Xiang, Hai-Ying; Dong, Shu-Wei; Shang, Qiao-Xia; Zhou, Cui-Ji; Li, Da-Wei; Yu, Jia-Lin; Han, Cheng-Gui

2011-12-01

The genomic RNA sequences of two genotypes of a brassica-infecting polerovirus from China were determined. Sequence analysis revealed that the virus was closely related to but significantly different from turnip yellows virus (TuYV). This virus and other poleroviruses, including TuYV, had less than 90% amino acid sequence identity in all gene products except the coat protein. Based on the molecular criterion (>10% amino acid sequence difference) for species demarcation in the genus Polerovirus, the virus represents a distinct species for which the name Brassica yellows virus (BrYV) is proposed. Interestingly, there were two genotypes of BrYV, which mainly differed in the 5'-terminal half of the genome.

Simulating Electron Cyclotron Maser Emission for Low Mass Stars

NASA Astrophysics Data System (ADS)

Llama, Joe; Jardine, Moira

2018-01-01

Zeeman-Doppler Imaging (ZDI) is a powerful technique that enables us to map the large-scale magnetic fields of stars spanning the pre- and main-sequence. Coupling these magnetic maps with field extrapolation methods allow us to investigate the topology of the closed, X-ray bright corona, and the cooler, open stellar wind.Using ZDI maps of young M dwarfs with simultaneous radio light curves obtained from the VLA, we present the results of modeling the Electron-Cyclotron Maser (ECM) emission from these systems. We determine the X-ray luminosity and ECM emission that is produced using the ZDI maps and our field extrapolation model. We compare these findings with the observed radio light curves of these stars. This allows us to predict the relative phasing and amplitude of the stellar X-ray and radio light curves.This benchmarking of our model using these systems allows us to predict the ECM emission for all stars that have a ZDI map and an observed X-ray luminosity. Our model allows us to understand the origin of transient radio emission observations and is crucial for disentangling stellar and exoplanetary radio signals.

Analysis of potential risks from the bacterial communities associated with air-contact surfaces from tilapia (Oreochromis niloticus) fish farming.

PubMed

Grande Burgos, Maria Jose; Romero, Jose Luis; Pérez Pulido, Rubén; Cobo Molinos, Antonio; Gálvez, Antonio; Lucas, Rosario

2018-01-01

Tilapia farming is a promising growing sector in aquaculture. Yet, there are limited studies on microbiological risks associated to tilapia farms. The aim of the present study was to analyse the bacterial communities from solid surfaces in contact with air in a tilapia farm in order to evaluate the presence of bacteria potentially toxinogenic or pathogenic to humans or animals. Samples from a local tilapia farm (tank wall, aerator, water outlets, sink and floor) were analyzed by high throughput sequencing technology. Sequences were assigned to operational taxonomic units (OTUs). Proteobacteria was the main phylum represented in most samples (except for one). Cyanobacteria were a relevant phylum in the inner wall from the fattening tank and the wet floor by the pre-fattening tank. Bacteroidetes were the second phylum in relative abundance for samples from the larval rearing tank and the pre-fattening tank and one sample from the fattening tank. Fusobacteria showed highest relative abundances in samples from the larval rearing tank and pre-fattening tank. Other phyla (Verrucomicrobia, Actinobacteria, Firmicutes, Planktomycetes, Acidobacteria, Chloroflexi, Chlorobi, Gemmatiomonadetes or Fibrobacters) had lower relative abundances. A large fraction of the reads (ranging from 43.67% to 72.25%) were assigned to uncultured bacteria. Genus Acinetobacter (mainly A. calcoaceticus/baumanni) was the predominant OTU in the aerator of the fattening tank and also in the nearby sink on the floor. The genera Cetobacterium and Bacteroides showed highest relative abundances in the samples from the larval rearing tank and the pre-fattening tank. Genera including fish pathogens (Fusobacterium, Aeromonas) were only detected at low relative abundances. Potential human pathogens other than Acinetobacter were either not detected or had very low relative abundances (< 0.01%). The results of the study suggest that the main risk factors to be monitored in tilapia farm are putative human pathogenic Acinetobacter and potential cyanotoxin-producing cyanobacteria. Copyright © 2017 Elsevier Inc. All rights reserved.

Fine-Scale Movements of the Broadnose Sevengill Shark and Its Main Prey, the Gummy Shark

PubMed Central

Barnett, Adam; Abrantes, Kátya G.; Stevens, John D.; Bruce, Barry D.; Semmens, Jayson M.

2010-01-01

Information on the fine-scale movement of predators and their prey is important to interpret foraging behaviours and activity patterns. An understanding of these behaviours will help determine predator-prey relationships and their effects on community dynamics. For instance understanding a predator's movement behaviour may alter pre determined expectations of prey behaviour, as almost any aspect of the prey's decisions from foraging to mating can be influenced by the risk of predation. Acoustic telemetry was used to study the fine-scale movement patterns of the Broadnose Sevengill shark Notorynchus cepedianus and its main prey, the Gummy shark Mustelus antarcticus, in a coastal bay of southeast Tasmania. Notorynchus cepedianus displayed distinct diel differences in activity patterns. During the day they stayed close to the substrate (sea floor) and were frequently inactive. At night, however, their swimming behaviour continually oscillated through the water column from the substrate to near surface. In contrast, M. antarcticus remained close to the substrate for the entire diel cycle, and showed similar movement patterns for day and night. For both species, the possibility that movement is related to foraging behaviour is discussed. For M. antarcticus, movement may possibly be linked to a diet of predominantly slow benthic prey. On several occasions, N. cepedianus carried out a sequence of burst speed events (increased rates of movement) that could be related to chasing prey. All burst speed events during the day were across the substrate, while at night these occurred in the water column. Overall, diel differences in water column use, along with the presence of oscillatory behaviour and burst speed events suggest that N. cepedianus are nocturnal foragers, but may opportunistically attack prey they happen to encounter during the day. PMID:21151925

New Hepatitis B Virus of Cranes That Has an Unexpected Broad Host Range

PubMed Central

Prassolov, Alexej; Hohenberg, Heinz; Kalinina, Tatyana; Schneider, Carola; Cova, Lucyna; Krone, Oliver; Frölich, Kai; Will, Hans; Sirma, Hüseyin

2003-01-01

All hepadnaviruses known so far have a very limited host range, restricted to their natural hosts and a few closely related species. This is thought to be due mainly to sequence divergence in the large envelope protein and species-specific differences in host components essential for virus propagation. Here we report an infection of cranes with a novel hepadnavirus, designated CHBV, that has an unexpectedly broad host range and is only distantly evolutionarily related to avihepadnaviruses of related hosts. Direct DNA sequencing of amplified CHBV DNA as well a sequencing of cloned viral genomes revealed that CHBV is most closely related to, although distinct from, Ross' goose hepatitis B virus (RGHBV) and slightly less closely related to duck hepatitis B virus (DHBV). Phylogenetically, cranes are very distant from geese and ducks and are most closely related to herons and storks. Naturally occurring hepadnaviruses in the last two species are highly divergent in sequence from RGHBV and DHBV and do not infect ducks or do so only marginally. In contrast, CHBV from crane sera and recombinant CHBV produced from LMH cells infected primary duck hepatocytes almost as efficiently as DHBV did. This is the first report of a rather broad host range of an avihepadnavirus. Our data imply either usage of similar or identical entry pathways and receptors by DHBV and CHBV, unusual host and virus adaptation mechanisms, or divergent evolution of the host genomes and cellular components required for virus propagation. PMID:12525630

New hepatitis B virus of cranes that has an unexpected broad host range.

PubMed

Prassolov, Alexej; Hohenberg, Heinz; Kalinina, Tatyana; Schneider, Carola; Cova, Lucyna; Krone, Oliver; Frölich, Kai; Will, Hans; Sirma, Hüseyin

2003-02-01

All hepadnaviruses known so far have a very limited host range, restricted to their natural hosts and a few closely related species. This is thought to be due mainly to sequence divergence in the large envelope protein and species-specific differences in host components essential for virus propagation. Here we report an infection of cranes with a novel hepadnavirus, designated CHBV, that has an unexpectedly broad host range and is only distantly evolutionarily related to avihepadnaviruses of related hosts. Direct DNA sequencing of amplified CHBV DNA as well a sequencing of cloned viral genomes revealed that CHBV is most closely related to, although distinct from, Ross' goose hepatitis B virus (RGHBV) and slightly less closely related to duck hepatitis B virus (DHBV). Phylogenetically, cranes are very distant from geese and ducks and are most closely related to herons and storks. Naturally occurring hepadnaviruses in the last two species are highly divergent in sequence from RGHBV and DHBV and do not infect ducks or do so only marginally. In contrast, CHBV from crane sera and recombinant CHBV produced from LMH cells infected primary duck hepatocytes almost as efficiently as DHBV did. This is the first report of a rather broad host range of an avihepadnavirus. Our data imply either usage of similar or identical entry pathways and receptors by DHBV and CHBV, unusual host and virus adaptation mechanisms, or divergent evolution of the host genomes and cellular components required for virus propagation.

On the phylogenetic placement of human T cell leukemia virus type 1 sequences associated with an Andean mummy.

PubMed

Coulthart, Michael B; Posada, David; Crandall, Keith A; Dekaban, Gregory A

2006-03-01

Recently, the putative finding of ancient human T cell leukemia virus type 1 (HTLV-1) long terminal repeat (LTR) DNA sequences in association with a 1500-year-old Chilean mummy has stirred vigorous debate. The debate is based partly on the inherent uncertainties associated with phylogenetic reconstruction when only short sequences of closely related genotypes are available. However, a full analysis of what phylogenetic information is present in the mummy data has not previously been published, leaving open the question of what precisely is the range of admissible interpretation. To fulfill this need, we re-analyzed the mummy data in a new way. We first performed phylogenetic analysis of 188 published LTR DNA sequences from extant strains belonging to the HTLV-1 Cosmopolitan clade, using the method of statistical parsimony which is designed both to optimize phylogenetic resolution among sequences with little evolutionary divergence, and to permit precise mapping of individual sequence mutations onto branches of a divergence network. We then deduced possible phylogenetic positions for the two main categories of published Chilean mummy sequences, based on their published 157-nucleotide LTR sequences. The possible phylogenetic placements for one of the mummy sequence categories are consistent with a modern origin. However, one of these placements for the other mummy sequence category falls very close to the root of the Cosmopolitan clade, consistent with an ancient origin for both this mummy sequence and the Cosmopolitan clade.

Stellar Clusters in the NGC 6334 Star-Forming Complex

NASA Astrophysics Data System (ADS)

Feigelson, Eric D.; Martin, Amanda L.; McNeill, Collin J.; Broos, Patrick S.; Garmire, Gordon P.

2009-07-01

The full stellar population of NGC 6334, one of the most spectacular regions of massive star formation in the nearby Galaxy, has not been well sampled in past studies. We analyze here a mosaic of two Chandra X-ray Observatory images of the region using sensitive data analysis methods, giving a list of 1607 faint X-ray sources with arcsecond positions and approximate line-of-sight absorption. About 95% of these are expected to be cluster members, most lower mass pre-main-sequence stars. Extrapolating to low X-ray levels, the total stellar population is estimated to be 20,000-30,000 pre-main-sequence stars. The X-ray sources show a complicated spatial pattern with ~10 distinct star clusters. The heavily obscured clusters are mostly associated with previously known far-infrared sources and radio H II regions. The lightly obscured clusters are mostly newly identified in the X-ray images. Dozens of likely OB stars are found, both in clusters and dispersed throughout the region, suggesting that star formation in the complex has proceeded over millions of years. A number of extraordinarily heavily absorbed X-ray sources are associated with the active regions of star formation.

Soft X-ray observations of pre-main sequence stars in the chamaeleon dark cloud

NASA Technical Reports Server (NTRS)

Feigelson, Eric D.; Kriss, Gerard A.

1987-01-01

Einstein IPC observations of the nearby Chamaeleon I star forming cloud show 22 well-resolved soft X-ray sources in a 1x2 deg region. Twelve are associated with H-alpha emission line pre-main sequence (PMS) stars, and four with optically selected PMS stars. Several X-ray sources have two or more PMS stars in their error circles. Optical spectra were obtained at CTIO of possible stellar counterparts of the remaining X-ray sources. They reveal 5 probable new cloud members, K7-MO stars with weak or absent emission lines. These naked X-ray selected PMS stars are similar to those found in the Taurus-Auriga cloud. The spatial distributions and H-R diagrams of the X-ray and optically selected PMS stars in the cloud are very similar. Luminosity functions indicate the Chamaeleon stars are on average approximately 5 times more X-ray luminous than Pleiad dwarfs. A significant correlation between L sub x and optical magnitude suggests this trend may continue within the PMS phase of stellar evolution. The relation of increasing X-ray luminosity with decreasing stellar ages is thus extended to stellar ages as young as 1 million years.

Nuclear Mitochondrial DNA Activates Replication in Saccharomyces cerevisiae

PubMed Central

Chatre, Laurent; Ricchetti, Miria

2011-01-01

The nuclear genome of eukaryotes is colonized by DNA fragments of mitochondrial origin, called NUMTs. These insertions have been associated with a variety of germ-line diseases in humans. The significance of this uptake of potentially dangerous sequences into the nuclear genome is unclear. Here we provide functional evidence that sequences of mitochondrial origin promote nuclear DNA replication in Saccharomyces cerevisiae. We show that NUMTs are rich in key autonomously replicating sequence (ARS) consensus motifs, whose mutation results in the reduction or loss of DNA replication activity. Furthermore, 2D-gel analysis of the mrc1 mutant exposed to hydroxyurea shows that several NUMTs function as late chromosomal origins. We also show that NUMTs located close to or within ARS provide key sequence elements for replication. Thus NUMTs can act as independent origins, when inserted in an appropriate genomic context or affect the efficiency of pre-existing origins. These findings show that migratory mitochondrial DNAs can impact on the replication of the nuclear region they are inserted in. PMID:21408151

Nuclear mitochondrial DNA activates replication in Saccharomyces cerevisiae.

PubMed

Chatre, Laurent; Ricchetti, Miria

2011-03-08

The nuclear genome of eukaryotes is colonized by DNA fragments of mitochondrial origin, called NUMTs. These insertions have been associated with a variety of germ-line diseases in humans. The significance of this uptake of potentially dangerous sequences into the nuclear genome is unclear. Here we provide functional evidence that sequences of mitochondrial origin promote nuclear DNA replication in Saccharomyces cerevisiae. We show that NUMTs are rich in key autonomously replicating sequence (ARS) consensus motifs, whose mutation results in the reduction or loss of DNA replication activity. Furthermore, 2D-gel analysis of the mrc1 mutant exposed to hydroxyurea shows that several NUMTs function as late chromosomal origins. We also show that NUMTs located close to or within ARS provide key sequence elements for replication. Thus NUMTs can act as independent origins, when inserted in an appropriate genomic context or affect the efficiency of pre-existing origins. These findings show that migratory mitochondrial DNAs can impact on the replication of the nuclear region they are inserted in.

Microprocessor activity controls differential miRNA biogenesis In Vivo.

PubMed

Conrad, Thomas; Marsico, Annalisa; Gehre, Maja; Orom, Ulf Andersson

2014-10-23

In miRNA biogenesis, pri-miRNA transcripts are converted into pre-miRNA hairpins. The in vivo properties of this process remain enigmatic. Here, we determine in vivo transcriptome-wide pri-miRNA processing using next-generation sequencing of chromatin-associated pri-miRNAs. We identify a distinctive Microprocessor signature in the transcriptome profile from which efficiency of the endogenous processing event can be accurately quantified. This analysis reveals differential susceptibility to Microprocessor cleavage as a key regulatory step in miRNA biogenesis. Processing is highly variable among pri-miRNAs and a better predictor of miRNA abundance than primary transcription itself. Processing is also largely stable across three cell lines, suggesting a major contribution of sequence determinants. On the basis of differential processing efficiencies, we define functionality for short sequence features adjacent to the pre-miRNA hairpin. In conclusion, we identify Microprocessor as the main hub for diversified miRNA output and suggest a role for uncoupling miRNA biogenesis from host gene expression. Copyright © 2014 The Authors. Published by Elsevier Inc. All rights reserved.

Substrate recognition by ribonucleoprotein ribonuclease MRP

PubMed Central

Esakova, Olga; Perederina, Anna; Quan, Chao; Berezin, Igor; Krasilnikov, Andrey S.

2011-01-01

The ribonucleoprotein complex ribonuclease (RNase) MRP is a site-specific endoribonuclease essential for the survival of the eukaryotic cell. RNase MRP closely resembles RNase P (a universal endoribonuclease responsible for the maturation of the 5′ ends of tRNA) but recognizes distinct substrates including pre-rRNA and mRNA. Here we report the results of an in vitro selection of Saccharomyces cerevisiae RNase MRP substrates starting from a pool of random sequences. The results indicate that RNase MRP cleaves single-stranded RNA and is sensitive to sequences in the immediate vicinity of the cleavage site requiring a cytosine at the position +4 relative to the cleavage site. Structural implications of the differences in substrate recognition by RNases P and MRP are discussed. PMID:21173200

Substrate recognition by ribonucleoprotein ribonuclease MRP.

PubMed

Esakova, Olga; Perederina, Anna; Quan, Chao; Berezin, Igor; Krasilnikov, Andrey S

2011-02-01

The ribonucleoprotein complex ribonuclease (RNase) MRP is a site-specific endoribonuclease essential for the survival of the eukaryotic cell. RNase MRP closely resembles RNase P (a universal endoribonuclease responsible for the maturation of the 5' ends of tRNA) but recognizes distinct substrates including pre-rRNA and mRNA. Here we report the results of an in vitro selection of Saccharomyces cerevisiae RNase MRP substrates starting from a pool of random sequences. The results indicate that RNase MRP cleaves single-stranded RNA and is sensitive to sequences in the immediate vicinity of the cleavage site requiring a cytosine at the position +4 relative to the cleavage site. Structural implications of the differences in substrate recognition by RNases P and MRP are discussed.

Intermediate to low-mass stellar content of Westerlund 1

NASA Astrophysics Data System (ADS)

Brandner, W.; Clark, J. S.; Stolte, A.; Waters, R.; Negueruela, I.; Goodwin, S. P.

2008-01-01

We have analysed near-infrared NTT/SofI observations of the starburst cluster Westerlund 1, which is among the most massive young clusters in the Milky Way. A comparison of colour-magnitude diagrams with theoretical main-sequence and pre-main sequence evolutionary tracks yields improved extinction and distance estimates of AKs = 1.13 ± 0.03 mag and d = 3.55 ± 0.17 kpc (DM = 12.75 ± 0.10 mag). The pre-main sequence population is best fit by a Palla & Stahler isochrone for an age of 3.2 Myr, while the main sequence population is in agreement with a cluster age of 3 to 5 Myr. An analysis of the structural parameters of the cluster yields that the half-mass radius of the cluster population increases towards lower mass, indicative of the presence of mass segregation. The cluster is clearly elongated with an eccentricity of 0.20 for stars with masses between 10 and 32 M_⊙, and 0.15 for stars with masses in the range 3 to 10 M_⊙. We derive the slope of the stellar mass function for stars with masses between 3.4 and 27 M_⊙. In an annulus with radii between 0.75 and 1.5 pc from the cluster centre, we obtain a slope of Γ = -1.3. Closer in, the mass function of Westerlund 1 is shallower with Γ = -0.6. The extrapolation of the mass function for stars with masses from 0.08 to 120 M_⊙ yields an initial total stellar mass of ≈52 000 M_⊙, and a present-day mass of 20 000 to 45 000 M_⊙ (about 10 times the stellar mass of the Orion nebula cluster, and 2 to 4 times the mass of the NGC 3603 young cluster), indicating that Westerlund 1 is the most massive starburst cluster identified to date in the Milky Way. Based on observations collected at the European Southern Observatory, La Silla, Chile, and retrieved from the ESO archive (Prog ID 67.C-0514).

Estudio de la población estelar de varios cúmulos en Carina

NASA Astrophysics Data System (ADS)

Molina-Lera, J. A.; Baume, G. L.; Carraro, G.; Costa, E.

2015-08-01

Based on deep photometric data in the bands, complemented with infrared 2MASS data, we conducted an analysis of the fundamental parameters of six open clusters located in the Carina region. To perform a systematic study we developed a specialized code. In particular, we investigated the behavior of the respective lower main sequences. Our analysis indicated the presence of a significant population of pre-sequence stars in several of the clusters. We therefore obtained estimated values of contraction ages. Furthermore, we have determined the slopes of the initial mass functions of the studied clusters.

The influence of radiative core growth on coronal X-ray emission from pre-main-sequence stars

NASA Astrophysics Data System (ADS)

Gregory, Scott G.; Adams, Fred C.; Davies, Claire L.

2016-04-01

Pre-main-sequence (PMS) stars of mass ≳0.35 M⊙ transition from hosting fully convective interiors to configurations with a radiative core and outer convective envelope during their gravitational contraction. This stellar structure change influences the external magnetic field topology and, as we demonstrate herein, affects the coronal X-ray emission as a stellar analogue of the solar tachocline develops. We have combined archival X-ray, spectroscopic, and photometric data for ˜1000 PMS stars from five of the best studied star-forming regions: the Orion Nebula Cluster, NGC 2264, IC 348, NGC 2362, and NGC 6530. Using a modern, PMS calibrated, spectral type-to-effective temperature and intrinsic colour scale, we de-redden the photometry using colours appropriate for each spectral type, and determine the stellar mass, age, and internal structure consistently for the entire sample. We find that PMS stars on Henyey tracks have, on average, lower fractional X-ray luminosities (LX/L*) than those on Hayashi tracks, where this effect is driven by changes in LX. X-ray emission decays faster with age for higher mass PMS stars. There is a strong correlation between L* and LX for Hayashi track stars but no correlation for Henyey track stars. There is no correlation between LX and radiative core mass or radius. However, the longer stars have spent with radiative cores, the less X-ray luminous they become. The decay of coronal X-ray emission from young early K to late G-type PMS stars, the progenitors of main-sequence A-type stars, is consistent with the dearth of X-ray detections of the latter.

Rescaled Range analysis of Induced Seismicity: rapid classification of clusters in seismic crisis

NASA Astrophysics Data System (ADS)

Bejar-Pizarro, M.; Perez Lopez, R.; Benito-Parejo, M.; Guardiola-Albert, C.; Herraiz, M.

2017-12-01

Different underground fluid operations, mainly gas storing, fracking and water pumping, can trigger Induced Seismicity (IS). This seismicity is normally featured by small-sized earthquakes (M<2.5), although particular cases reach magnitude as great as 5. It has been up for debate whether earthquakes greater than 5 can be triggered by IS or this level of magnitude only corresponds to tectonic earthquakes caused by stress change. Whatever the case, the characterization of IS for seismic clusters and seismic series recorded close but not into the gas storage, is still under discussion. Time-series of earthquakes obey non-linear patterns where the Hurst exponent describes the persistency or anti-persistency of the sequence. Natural seismic sequences have an H-exponent close to 0.7, which combined with the b-value time evolution during the time clusters, give us valuable information about the stationarity of the phenomena. Tectonic earthquakes consist in a main shock with a decay of time-occurrence of seismic shocks obeying the Omori's empirical law. On the contrary, IS does not exhibit a main shock and the time occurrence depends on the injection operations instead of on the tectonic energy released. In this context, the H-exponent can give information about the origin of the sequence. In 2013, a seismic crisis was declared from the Castor underground gas storing located off-shore in the Mediterranean Sea, close to the Northeastern Spanish cost. The greatest induced earthquake was 3.7. However, a 4.2 earthquake, probably of tectonic origin, occurred few days after the operations stopped. In this work, we have compared the H-exponent and the b-value time evolution according to the timeline of gas injection. Moreover, we have divided the seismic sequence into two groups: (1) Induced Seismicity and (2) Triggered Seismicity. The rescaled range analysis allows the differentiation between natural and induced seismicity and gives information about the persistency and long-term memory of the seismic crisis. These results are a part of the Spanish project SISMOSIMA (CGL2013-47412-C2-2P).

A Synthetic Self-Oscillating Vocal Fold Model Platform for Studying Augmentation Injection

PubMed Central

Murray, Preston R.; Thomson, Scott L.; Smith, Marshall E.

2013-01-01

Objective Design and evaluate a platform for studying the mechanical effects of augmentation injections using synthetic self-oscillating vocal fold models. Study Design Basic science. Methods Life-sized, synthetic, multi-layer, self-oscillating vocal fold models were created that simulated bowing via volumetric reduction of the body layer relative to that of a normal, unbowed model. Material properties of the layers were unchanged. Models with varying degrees of bowing were created and paired with normal models. Following initial acquisition of data (onset pressure, vibration frequency, flow rate, and high-speed image sequences), bowed models were injected with silicone that had material properties similar to those used in augmentation procedures. Three different silicone injection quantities were tested: sufficient to close the glottal gap, insufficient to close the glottal gap, and excess silicone to create convex bowing of the bowed model. The above-mentioned metrics were again taken and compared. Pre- and post-injection high-speed image sequences were acquired using a hemilarynx setup, from which medial surface dynamics were quantified. Results The models vibrated with mucosal wave-like motion and at onset pressures and frequencies typical of human phonation. The models successfully exhibited various degrees of bowing which were then mitigated by injecting filler material. The models showed general pre- to post-injection decreases in onset pressure, flow rate, and open quotient, and a corresponding increase in vibration frequency. Conclusion The model may be useful in further explorations of the mechanical consequences of augmentation injections. PMID:24476985

The energy balance in coronal holes and average quiet-sun regions

NASA Technical Reports Server (NTRS)

Raymond, J. C.; Doyle, J. G.

1981-01-01

Emission measure curves are presented for average coronal hole and quiet-sun spectra taken during the Skylab mission by Vernazza and Reeves (1978), and the curves are used to discuss the energy balance in each region. Close-coupling calculations are used for the Be sequence, assuming a 10 level ion; for B sequence ions mainly distorted wave calculations in an 11 level ion are used, but close-coupling cross sections are used for some ions; for C and Mg sequence ions, distorted wave calculations are used with 15 and 10 level ions, respectively, and close-coupling results are used for Li-like ions with two levels. Results are presented and include the following: the coronal hole spectrum shows a smaller slope in the emission measure distribution, consistent with the expected outflow effects. It is concluded that the simple constant pressure models of static coronal loops of constant cross section are basically able to match the observed emission measure distribution of the average quiet sun between 1,000,000 and 10,000,000 K. However, the cell center and network distributions are respectively steeper and shallower than predicted by the detailed cooling curve.

Absolute Transition Probabilities of Lines in the Spectra of Astrophysical Atoms, Molecules, and Ions

NASA Technical Reports Server (NTRS)

Parkinson, W. H.; Smith, P. L.; Yoshino, K.

1984-01-01

Progress in the investigation of absolute transition probabilities (A-values or F values) for ultraviolet lines is reported. A radio frequency ion trap was used for measurement of transition probabilities for intersystem lines seen in astronomical spectra. The intersystem line at 2670 A in Al II, which is seen in pre-main sequence stars and symbiotic stars, was studied.

Hiding in plain sight

NASA Astrophysics Data System (ADS)

Riedel, Adric Richard

2012-05-01

Since the first successful measurements of stellar trigonometric parallax in the 1830s, the study of nearby stars has focused on the highest proper motion stars (micro > 0.18″ yr-1). Those high proper motion stars have formed the backbone of the last 150 years of study of the Solar Neighborhood and the composition of the Galaxy. Statistically speaking, though, there is a population of stars that will have low proper motions when their space motions have been projected onto the sky. At the same time, over the last twenty years, populations of relatively young stars (less than ˜ 100 Myr), most of them with low proper motions, have been revealed near (< 100 pc) the Sun. This dissertation is the result of two related projects: A photometric search for nearby (< 25pc) southern-hemisphere M dwarf stars with low proper motions (micro < 0.18″ yr-1), and a search for nearby (< 100 pc) pre-main-sequence (< 125 Myr old) M dwarf systems. The projects rely on a variety of photometric, spectroscopic, and astrometric analyses (including parallaxes from our program) using data from telescopes at CTIO via the SMARTS Consortium and at Lowell Observatory. Within this dissertation, I describe the identification and confirmation of 23 new nearby low proper motion M dwarf systems within 25 pc, 8 of which are within 15 pc (50% of the anticipated low-proper-motion 15 pc sample). I also report photometric, spectroscopic, and astrometric parameters and identifications for a selection of 25 known and new candidate nearby young M dwarfs, including new low-mass members of the TW Hydra, beta Pictoris, Tucana-Horologium, Argus, and AB Doradus associations, following the methods of my Riedel et al. (2011) paper and its discovery of AP Col, the closest pre-main-sequence star to the Solar System. These low proper motion and nearby star discoveries are put into the context of the Solar Neighborhood as a whole by means of the new RECONS 25 pc Database, to which I have now added (including my Riedel et al. (2010) paper) 81 star systems (4% of the total). INDEX WORDS: Astronomy, Astrometry, Photometry, Spectroscopy, Kinematics, Proper motion, Parallax, Nearby stars, Low-mass stars, Young stars, Pre-main-sequence stars.

New direct measurement of the 10B(p,α)7Be reaction with the activation technique

NASA Astrophysics Data System (ADS)

Depalo, Rosanna; Caciolli, Antonio; Broggini, Carlo; La Cognata, Marco; Lamia, Livio; Menegazzo, Roberto; Mou, Liliana; Puglia, Sebastiana Maria Regina; Rigato, Valentino; Romano, Stefano; Alvarez, Carlos Rossi; Sergi, Maria Letizia; Spitaleri, Claudio; Tumino, Aurora

2018-01-01

Boron plays an important role in astrophysics and, together with lithium and beryllium, is a probe of stellar structure during the pre-main sequence and main-sequence phases. In this context, the 10B(p,α)7 Be reaction is of particular interest. The literature data show discrepancies in the energy range between 100 keV and 2 MeV. This also poses a normalization problem for indirect data obtained with the Trojan Horse Method. A new measurement of the 10B(p,α)7 Be reaction cross section was performed at Legnaro National Laboratories (LNL). At LNL, the cross section was determined with the activation technique by measuring the activated samples at a low-background counting facility. The analysis of that experiment is now complete and the results are here presented.

Ancient Recombination Events between Human Herpes Simplex Viruses

PubMed Central

Burrel, Sonia; Boutolleau, David; Ryu, Diane; Agut, Henri; Merkel, Kevin; Leendertz, Fabian H.

2017-01-01

Abstract Herpes simplex viruses 1 and 2 (HSV-1 and HSV-2) are seen as close relatives but also unambiguously considered as evolutionary independent units. Here, we sequenced the genomes of 18 HSV-2 isolates characterized by divergent UL30 gene sequences to further elucidate the evolutionary history of this virus. Surprisingly, genome-wide recombination analyses showed that all HSV-2 genomes sequenced to date contain HSV-1 fragments. Using phylogenomic analyses, we could also show that two main HSV-2 lineages exist. One lineage is mostly restricted to subSaharan Africa whereas the other has reached a global distribution. Interestingly, only the worldwide lineage is characterized by ancient recombination events with HSV-1. Our findings highlight the complexity of HSV-2 evolution, a virus of putative zoonotic origin which later recombined with its human-adapted relative. They also suggest that coinfections with HSV-1 and 2 may have genomic and potentially functional consequences and should therefore be monitored more closely. PMID:28369565

Microbial communities of biomethanization digesters fed with raw and heat pre-treated microalgae biomasses.

PubMed

Sanz, Jose Luis; Rojas, Patricia; Morato, Ana; Mendez, Lara; Ballesteros, Mercedes; González-Fernández, Cristina

2017-02-01

Microalgae biomasses are considered promising feedstocks for biofuel and methane productions. Two Continuously Stirred Tank Reactors (CSTR), fed with fresh (CSTR-C) and heat pre-treated (CSTR-T) Chlorella biomass were run in parallel in order to determine methane productions. The methane yield was 1.5 times higher in CSTR-T with regard to CSTR-C. Aiming to understand the microorganism roles within of the reactors, the sludge used as an inoculum (I), plus raw (CSTR-C) and heat pre-treated (CSTR-T) samples were analyzed by high-throughput pyrosequencing. The bacterial communities were dominated by Proteobacteria, Bacteroidetes, Chloroflexi and Firmicutes. Spirochaetae and Actinobacteria were only detected in sample I. Proteobacteria, mainly Alfaproteobacteria, were by far the dominant phylum within of the CSTR-C bioreactor. Many of the sequences retrieved were related to bacteria present in activated sludge treatment plants and they were absent after thermal pre-treatment. Most of the sequences affiliated to the Bacteroidetes were related to uncultured groups. Anaerolineaceae was the sole family found of the Chloroflexi phylum. All of the genera identified of the Firmicutes phylum carried out macromolecule hydrolysis and by-product fermentation. The proteolytic bacteria were prevalent over the saccharolytic microbes. The percentage of the proteolytic genera increased from the inoculum to the CSTR-T sample in a parallel fashion with an available protein increase owing to the high protein content of Chlorella. To relate the taxa identified by high-throughput sequencing to their functional roles remains a future challenge. Copyright © 2016 Elsevier Ltd. All rights reserved.

Clinical, Morphological, and Molecular Characterization of Penicillium canis sp. nov., Isolated from a Dog with Osteomyelitis

PubMed Central

Sutton, Deanna A.; Swenson, Cheryl L.; Bailey, Chris J.; Wiederhold, Nathan P.; Nelson, Nathan C.; Thompson, Elizabeth H.; Wickes, Brian L.; French, Stephanie; Fu, Jianmin; Vilar-Saavedra, Paulo

2014-01-01

Infections caused by Penicillium species are rare in dogs, and the prognosis in these cases is poor. An unknown species of Penicillium was isolated from a bone lesion in a young dog with osteomyelitis of the right ilium. Extensive diagnostic evaluation did not reveal evidence of dissemination. Resolution of lameness and clinical stability of disease were achieved with intravenous phospholipid-complexed amphotericin B initially, followed by long-term combination therapy with terbinafine and ketoconazole. A detailed morphological and molecular characterization of the mold was undertaken. Sequence analysis of the internal transcribed spacer revealed the isolate to be closely related to Penicillium menonorum and Penicillium pimiteouiense. Additional sequence analysis of β-tubulin, calmodulin, minichromosome maintenance factor, DNA-dependent RNA polymerase, and pre-rRNA processing protein revealed the isolate to be a novel species; the name Penicillium canis sp. nov. is proposed. Morphologically, smooth, ovoid conidia, a greenish gray colony color, slow growth on all media, and a failure to form ascomata distinguish this species from closely related Penicillium species. PMID:24789186

Clinical, morphological, and molecular characterization of Penicillium canis sp. nov., isolated from a dog with osteomyelitis.

PubMed

Langlois, Daniel K; Sutton, Deanna A; Swenson, Cheryl L; Bailey, Chris J; Wiederhold, Nathan P; Nelson, Nathan C; Thompson, Elizabeth H; Wickes, Brian L; French, Stephanie; Fu, Jianmin; Vilar-Saavedra, Paulo; Peterson, Stephen W

2014-07-01

Infections caused by Penicillium species are rare in dogs, and the prognosis in these cases is poor. An unknown species of Penicillium was isolated from a bone lesion in a young dog with osteomyelitis of the right ilium. Extensive diagnostic evaluation did not reveal evidence of dissemination. Resolution of lameness and clinical stability of disease were achieved with intravenous phospholipid-complexed amphotericin B initially, followed by long-term combination therapy with terbinafine and ketoconazole. A detailed morphological and molecular characterization of the mold was undertaken. Sequence analysis of the internal transcribed spacer revealed the isolate to be closely related to Penicillium menonorum and Penicillium pimiteouiense. Additional sequence analysis of β-tubulin, calmodulin, minichromosome maintenance factor, DNA-dependent RNA polymerase, and pre-rRNA processing protein revealed the isolate to be a novel species; the name Penicillium canis sp. nov. is proposed. Morphologically, smooth, ovoid conidia, a greenish gray colony color, slow growth on all media, and a failure to form ascomata distinguish this species from closely related Penicillium species. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

Revolution evolution: tracing angular momentum during star and planetary system formation

NASA Astrophysics Data System (ADS)

Davies, Claire Louise

2015-04-01

Stars form via the gravitational collapse of molecular clouds during which time the protostellar object contracts by over seven orders of magnitude. If all the angular momentum present in the natal cloud was conserved during collapse, stars would approach rotational velocities rapid enough to tear themselves apart within just a few Myr. In contrast to this, observations of pre-main sequence rotation rates are relatively slow (∼ 1 - 15 days) indicating that significant quantities of angular momentum must be removed from the star. I use observations of fully convective pre-main sequence stars in two well-studied, nearby regions of star formation (namely the Orion Nebula Cluster and Taurus-Auriga) to determine the removal rate of stellar angular momentum. I find the accretion disc-hosting stars to be rotating at a slower rate and contain less specific angular momentum than the disc-less stars. I interpret this as indicating a period of accretion disc-regulated angular momentum evolution followed by near-constant rotational evolution following disc dispersal. Furthermore, assuming that the age spread inferred from the Hertzsprung-Russell diagram constructed for the star forming region is real, I find that the removal rate of angular momentum during the accretion-disc hosting phase to be more rapid than that expected from simple disc-locking theory whereby contraction occurs at a fixed rotation period. This indicates a more efficient process of angular momentum removal must operate, most likely in the form of an accretion-driven stellar wind or outflow emanating from the star-disc interaction. The initial circumstellar envelope that surrounds a protostellar object during the earliest stages of star formation is rotationally flattened into a disc as the star contracts. An effective viscosity, present within the disc, enables the disc to evolve: mass accretes inwards through the disc and onto the star while momentum migrates outwards, forcing the outer regions of the disc to expand. I used spatially resolved submillimetre detections of the dust and gas components of protoplanetary discs, gathered from the literature, to measure the radial extent of discs around low-mass pre-main sequence stars of ∼ 1-10 Myr and probe their viscous evolution. I find no clear observational evidence for the radial expansion of the dust component. However, I find tentative evidence for the expansion ofthe gas component. This suggests that the evolution of the gas and dust components of protoplanetary discs are likely governed by different astrophysical processes. Observations of jets and outflows emanating from protostars and pre-main sequence stars highlight that it may also be possible to remove angular momentum from the circumstellar material. Using the sample of spatially resolved protoplanetary discs, I find no evidence for angular momentum removal during disc evolution. I also use the spatially resolved debris discs from the Submillimetre Common-User Bolometer Array-2 Observations of Nearby Stars survey to constrain the amount of angular momentum retained within planetary systems. This sample is compared to the protoplanetary disc angular momenta and to the angular momentum contained within pre-stellar cores. I find that significant quantities of angular momentum must be removed during disc formation and disc dispersal. This likely occurs via magnetic braking during the formation of the disc, via the launching of a disc or photo-evaporative wind, and/or via ejection of planetary material following dynamical interactions.

[Genetic diversity and phylogeny of rhizobia isolated from peanut (Arachis hypogaea)].

PubMed

Yang, Jiang-Ke; Xie, Fu-Li; Zhou, Jun-Chu

2002-12-01

Forty three rhizobium strains isolated from peanut (Arachis hypogaea) and 15 reference strains from other genus and species were analyzed by the method of 16S rRNA RFLP, 16S rRNA sequencing and 16S-23S IGS PCR RFLP. The results of the 16S rRNA RFLP shown that 43 strains tested were all ascribed to the genus of Bradyrhizobium phylogenetically. Strains tested were adjacent to the B. japonicum and far from B. elkanii 16S rRNA genotype. The genotypes generated by the 4 restriction endonucleases, Mbo I, Dde I, Hae III and Msp I, were same as the representatives of B. japonicum. The dendrogram generated by 16S rRNA sequence and Neighbor-joining method shown that peanut rhizobia clustered into the subcluster represented by B. japonicum and B. liaoningense, were more close to B. liaoningense genetically, and the sequence difference between them was less than 1%. High sequence similarity was also determined between B. liaoningense and B. japonicum. JZ1, representative strain of peanut rhizobia were systematically far from the B. elkanii, and the sequence divergence about 2%. The results from IGS RFLP analysis indicated that although they were phylogenetically close to B. japonicum and B. elkanii, peanut rhizobia forming an independent group at the similarity of 71% could be further divided into four subgroups, A, B, C and D. Subgroup A consisted of strains from different region, subgroup B was composed of strains from Wuchang, Qianjiang and Jingzhou, subgroup C was mainly composed of strains from Jingzhou and starins of subgroup D mainly from Neijiang. Reference strains from B. japonicum and B. elkanii were independently clustered into the subgroup E at the similarity of 71%. The geographical factor effect on genetic diversity of rhizobia was found.

Effect of pre-strain on precipitation and exfoliation corrosion resistance in an Al-Zn-Mg alloy

NASA Astrophysics Data System (ADS)

Lu, Xianghan; Du, Zhiwei; Han, Xiaolei; Li, Ting; Wang, Guojun; Lu, Liying; Bai, Xiaoxia; Zhou, Tietao

2017-12-01

To investigate the effect of pre-strain on behaviors in a specially developed Al-4.5Zn-1.2Mg alloy, transmission electron microscopy (TEM) bright field (BF) imaging combined with select area electron diffraction (SAED), Vickers-hardness tests and electrical conductivity tests was conducted for insight into precipitation in aluminum (Al) matrix during two step ageing, and standard exfoliation corrosion (EXCO) test combined with high-angle angular dark field scanning transmission electron microscopy (HAADF-STEM) and scanning electron microscopy (SEM) was carried out for corrosion behavior. Results showed that pre-strain accelerated precipitation during two step ageing as the sequence of: (i) supersaturated solid solution (SSS), GPI zones precipitations, GPI dissolution; (ii) SSS, fcc precipitates, η’ phases or η phases. And the precipitation hardening of the fcc precipitates was not effective as GPI zones. Pre-strain also accelerated EXCO developing, which was mainly attributed to the coverage ratio of η phases on high-angle grain boundaries (HAGBs) increasing as pre-strain increase.

40 CFR 98.433 - Calculating GHG contained in pre-charged equipment or closed-cell foams.

Code of Federal Regulations, 2014 CFR

2014-07-01

...-charged equipment or closed-cell foams. 98.433 Section 98.433 Protection of Environment ENVIRONMENTAL... Exporters of Fluorinated Greenhouse Gases Contained in Pre-Charged Equipment or Closed-Cell Foams § 98.433 Calculating GHG contained in pre-charged equipment or closed-cell foams. (a) The total mass of each...

40 CFR 98.433 - Calculating GHG contained in pre-charged equipment or closed-cell foams.

Code of Federal Regulations, 2013 CFR

2013-07-01

...-charged equipment or closed-cell foams. 98.433 Section 98.433 Protection of Environment ENVIRONMENTAL... Exporters of Fluorinated Greenhouse Gases Contained in Pre-Charged Equipment or Closed-Cell Foams § 98.433 Calculating GHG contained in pre-charged equipment or closed-cell foams. (a) The total mass of each...

40 CFR 98.433 - Calculating GHG contained in pre-charged equipment or closed-cell foams.

Code of Federal Regulations, 2011 CFR

2011-07-01

...-charged equipment or closed-cell foams. 98.433 Section 98.433 Protection of Environment ENVIRONMENTAL... Exporters of Fluorinated Greenhouse Gases Contained in Pre-Charged Equipment or Closed-Cell Foams § 98.433 Calculating GHG contained in pre-charged equipment or closed-cell foams. (a) The total mass of each...

40 CFR 98.433 - Calculating GHG contained in pre-charged equipment or closed-cell foams.

Code of Federal Regulations, 2012 CFR

2012-07-01

...-charged equipment or closed-cell foams. 98.433 Section 98.433 Protection of Environment ENVIRONMENTAL... Exporters of Fluorinated Greenhouse Gases Contained in Pre-Charged Equipment or Closed-Cell Foams § 98.433 Calculating GHG contained in pre-charged equipment or closed-cell foams. (a) The total mass of each...

Genomes of diverse isolates of the marine cyanobacterium Prochlorococcus

PubMed Central

Biller, Steven J.; Berube, Paul M.; Berta-Thompson, Jessie W.; Kelly, Libusha; Roggensack, Sara E.; Awad, Lana; Roache-Johnson, Kathryn H.; Ding, Huiming; Giovannoni, Stephen J.; Rocap, Gabrielle; Moore, Lisa R.; Chisholm, Sallie W.

2014-01-01

The marine cyanobacterium Prochlorococcus is the numerically dominant photosynthetic organism in the oligotrophic oceans, and a model system in marine microbial ecology. Here we report 27 new whole genome sequences (2 complete and closed; 25 of draft quality) of cultured isolates, representing five major phylogenetic clades of Prochlorococcus. The sequenced strains were isolated from diverse regions of the oceans, facilitating studies of the drivers of microbial diversity—both in the lab and in the field. To improve the utility of these genomes for comparative genomics, we also define pre-computed clusters of orthologous groups of proteins (COGs), indicating how genes are distributed among these and other publicly available Prochlorococcus genomes. These data represent a significant expansion of Prochlorococcus reference genomes that are useful for numerous applications in microbial ecology, evolution and oceanography. PMID:25977791

Solar and stellar coronal plasmas

NASA Technical Reports Server (NTRS)

Golub, L.

1985-01-01

Progress made in describing and interpreting coronal plasma processes and the relationship between the solar corona and its stellar counterparts is reported. Topics covered include: stellar X-ray emission, HEAO 2 X-ray survey of the Pleiades, closed coronal structures, X-ray survey of main-sequence stars with shallow convection zones, implications of the 1400 MHz flare emission, and magnetic field stochasticity.

Comparative modeling without implicit sequence alignments.

PubMed

Kolinski, Andrzej; Gront, Dominik

2007-10-01

The number of known protein sequences is about thousand times larger than the number of experimentally solved 3D structures. For more than half of the protein sequences a close or distant structural analog could be identified. The key starting point in a classical comparative modeling is to generate the best possible sequence alignment with a template or templates. With decreasing sequence similarity, the number of errors in the alignments increases and these errors are the main causes of the decreasing accuracy of the molecular models generated. Here we propose a new approach to comparative modeling, which does not require the implicit alignment - the model building phase explores geometric, evolutionary and physical properties of a template (or templates). The proposed method requires prior identification of a template, although the initial sequence alignment is ignored. The model is built using a very efficient reduced representation search engine CABS to find the best possible superposition of the query protein onto the template represented as a 3D multi-featured scaffold. The criteria used include: sequence similarity, predicted secondary structure consistency, local geometric features and hydrophobicity profile. For more difficult cases, the new method qualitatively outperforms existing schemes of comparative modeling. The algorithm unifies de novo modeling, 3D threading and sequence-based methods. The main idea is general and could be easily combined with other efficient modeling tools as Rosetta, UNRES and others.

A spectroscopic and photometric study of the unique pre- main sequence system KH 15D

NASA Astrophysics Data System (ADS)

Hamilton, Catrina Marie

2004-09-01

As a class, T Tauri stars are YSOs, some which are surrounded by circumstellar disks, and are recognized as the final stage of low-mass star formation. They also represent the earliest stage of stellar evolution that is optically visible, and, therefore, can be easily studied in detail. Understanding the processes through which these young stars interact with and eventually disperse their circumstellar disks is critical for understanding how they evolve from the T Tauri phase to the zero age main sequence (ZAMS), and how this affects the formation of planets, as well as their rotational evolution. KH 15D is a unique eclipsing system that could provide invaluable insight into the evolution of circumstellar disk material, as well as clues to the close stellar environment. Discovered in 1997, this star system has been observed to undergo an eclipse every 48 days in which the star's light is diminished by 3.5 magnitudes. What is so unusual about the eclipse is that the length of the eclipse has evolved over time, growing in length from 16 days initially, to ˜25 days in 2002/2003. Evolution of disk material on these timescales has never been observed before, and therefore provides us with a unique opportunity to refine our theories about remnant disks around young stars, how they transition, possibly into planets, and what role they play as the star matures and arrives on the zero age main sequence. Additionally, high resolution spectra obtained at specific phases during the December 2001 eclipse showed that as the obscuring matter cut across the star, dramatic spectral changes in the Hα and Hβ lines were seen. Its unique eclipse produces a “natural coronographic” effect in which the stellar photosphere is occulted, revealing details of its magnetosphere and surroundings during eclipse. There is evidence that the weak-lined T Tauri star (WTTS) central to the system is actively accreting gas, although probably not at the rate of a typical classical T Tauri star, calling into question the common practice of associating WTTS characteristics with the absence of an accretion disk. Here I present an investigation of the photometric and spectroscopic properties of the KH 15D eclipsing system, and discuss the implications that this system holds for the future research of T Tauri stars.

Effects of pre- and pro-sequence of thaumatin on the secretion by Pichia pastoris.

PubMed

Ide, Nobuyuki; Masuda, Tetsuya; Kitabatake, Naofumi

2007-11-23

Thaumatin is a 22-kDa sweet-tasting protein containing eight disulfide bonds. When thaumatin is expressed in Pichia pastoris using the thaumatin cDNA fused with both the alpha-factor signal sequence and the Kex2 protease cleavage site from Saccharomyces cerevisiae, the N-terminal sequence of the secreted thaumatin molecule is not processed correctly. To examine the role of the thaumatin cDNA-encoded N-terminal pre-sequence and C-terminal pro-sequence on the processing of thaumatin and efficiency of thaumatin production in P. pastoris, four expression plasmids with different pre-sequence and pro-sequence were constructed and transformed into P. pastoris. The transformants containing pre-thaumatin gene that has the native plant signal, secreted thaumatin molecules in the medium. The N-terminal amino acid sequence of the secreted thaumatin molecule was processed correctly. The production yield of thaumatin was not affected by the C-terminal pro-sequence, and the pro-sequence was not processed in P. pastoris, indicating that pro-sequence is not necessary for thaumatin synthesis.

Chromobacterium sphagni sp. nov., an insecticidal bacterium isolated from Sphagnum bogs.

PubMed

Blackburn, Michael B; Farrar, Robert R; Sparks, Michael E; Kuhar, Daniel; Mitchell, Ashaki; Gundersen-Rindal, Dawn E

2017-09-01

Sixteen isolates of Gram-reaction-negative, motile, violet-pigmented bacteria were isolated from Sphagnum bogs in West Virginia and Maine, USA. 16S rRNA gene sequences and fatty acid analysis revealed a high degree of relatedness among the isolates, and genome sequencing of two isolates, IIBBL 14B-1T and IIBBL 37-2 (from West Virginia and Maine, respectively), revealed highly similar genomic sequences. The average nucleotide identity (gANI) calculated for these two isolates was found to be in excess of 99 %, but did not exceed 88 % when comparing either isolate with genomic sequences of Chromobacterium violaceum ATCC 12472T, C. haemolyticum DSM 19808T, C. piscinae ND17, C. subtsugae PRAA4-1T, C. vaccinii MWU205T or C. amazonense CBMAI 310T. Collectively, gANI and 16S rRNA gene sequence comparisons suggested that isolates IIBBL 14B-1T and IIBBL 37-2 were most closely related to C. subtsugae, but represented a distinct species. We propose the name Chromobacterium sphagni sp. nov. for this taxon; the type strain is IIBBL 14B-1T (=NRRL B-67130T=JCM 31882T).

Constraints on pre-main-sequence evolution from stellar pulsations

NASA Astrophysics Data System (ADS)

Casey, M. P.; Zwintz, K.; Guenther, D. B.

2014-02-01

Pulsating pre-main-sequence (PMS) stars afford the earliest opportunity in the lifetime of a star to which the concepts of asteroseismology can be applied. PMS stars should be structurally simpler than their evolved counterparts, thus (hopefully!) making any asteroseismic analysis relatively easier. Unfortunately, this isn't necessarily the case. The majority of these stars (around 80) are δ Scuti pulsators, with a couple of γ Doradus, γ Doradus - δ Scuti hybrids, and slowly pulsating B stars thrown into the mix. The majority of these stars have only been discovered within the last ten years, with the community still uncovering the richness of phenomena associated with these stars, many of which defy traditional asteroseismic analysis. A systematic asteroseismic analysis of all of the δ Scuti PMS stars was performed in order to get a better handle on the properties of these stars as a group. Some strange results have been found, including one star pulsating up to the theoretical acoustic cut-off frequency of the star, and a number of stars in which the most basic asteroseismic analysis suggests problems with the stars' positions in the Hertzsprung-Russell diagram. From this we get an idea of the\\break constraints - or lack thereof - that these results can put on PMS stellar evolution.

Course 6: Star Formation

NASA Astrophysics Data System (ADS)

Natta, A.

Contents 1 Introduction 2 Collapse of molecular cores 2.1 Giant molecular clouds and cores 2.2 Conditions for collapse 2.3 Free-fall collapse 2.4 Collapse of an isothermal sphere of gas 2.5 Collapse of a slowly rotating core 3 Observable properties of protostars 3.1 Evidence of infall from molecular line profiles 3.2 SEDs of protostars 3.3 The line spectrumof a protostar 4 Protostellar and pre-main-sequence evolution 4.1 The protostellar phase 4.2 Pre-main-sequence evolution 4.3 The birthline 5 Circumstellar disks 5.1 Accretion disks 5.2 Properties of steady accretion disks 5.3 Reprocessing disks 5.4 Disk-star interaction 6 SEDs of disks 6.1 Power-law disks 6.2 Long-wavelength flux and disk mass 6.3 Comparison with TTS observations: Heating mechanism 7 Disk properties from observations 7.1 Mass accretion rate 7.2 Inner radius 7.3 Masses 7.4 Sizes 8 Disk lifetimes 8.1 Ground-based near and mid-infrared surveys 8.2 Mid-infrared ISOCAMsurveys 8.3 ISOPHOT 60 microm survey 8.4 Surveys at millimeter wavelengths 9 Disk evolution 9.1 Can we observe the early planet formation phase? 9.2 Evidence for grain growth 9.3 Evidence of planetesimals 9.4 Where is the diskmass? 10 Secondary or debris disks 11 Summary

V474 Car: A RARE HALO RS CVn BINARY IN RETROGRADE GALACTIC ORBIT

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bubar, Eric J.; Mamajek, Eric E.; Jensen, Eric L. N.

We report the discovery that the star V474 Car is an extremely active, high velocity halo RS CVn system. The star was originally identified as a possible pre-main-sequence star in Carina, given its enhanced stellar activity, rapid rotation (10.3 days), enhanced Li, and absolute magnitude which places it above the main sequence (MS). However, its extreme radial velocity (264 km s{sup -1}) suggested that this system was unlike any previously known pre-MS system. Our detailed spectroscopic analysis of echelle spectra taken with the CTIO 4 m finds that V474 Car is both a spectroscopic binary with an orbital period similarmore » to the photometric rotation period and metal-poor ([Fe/H] {approx_equal}-0.99). The star's Galactic orbit is extremely eccentric (e {approx_equal} 0.93) with a perigalacticon of only {approx}0.3 kpc of the Galactic center-and the eccentricity and smallness of its perigalacticon are surpassed by only {approx}0.05% of local F/G-type field stars. The observed characteristics are consistent with V474 Car being a high-velocity, metal-poor, tidally locked, chromospherically active binary, i.e., a halo RS CVn binary, and one of only a few such specimens known.« less

PEERING INTO THE GIANT-PLANET-FORMING REGION OF THE TW HYDRAE DISK WITH THE GEMINI PLANET IMAGER

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rapson, Valerie A.; Kastner, Joel H.; Millar-Blanchaer, Maxwell A.

2015-12-20

We present Gemini Planet Imager (GPI) adaptive optics near-infrared images of the giant-planet-forming regions of the protoplanetary disk orbiting the nearby (D = 54 pc), pre-main-sequence (classical T Tauri) star TW Hydrae. The GPI images, which were obtained in coronagraphic/polarimetric mode, exploit starlight scattered off small dust grains to elucidate the surface density structure of the TW Hya disk from ∼80 AU to within ∼10 AU of the star at ∼1.5 AU resolution. The GPI polarized intensity images unambiguously confirm the presence of a gap in the radial surface brightness distribution of the inner disk. The gap is centered near ∼23 AU,more » with a width of ∼5 AU and a depth of ∼50%. In the context of recent simulations of giant-planet formation in gaseous, dusty disks orbiting pre-main-sequence stars, these results indicate that at least one young planet with a mass ∼0.2 M{sub J} could be present in the TW Hya disk at an orbital semimajor axis similar to that of Uranus. If this (proto)planet is actively accreting gas from the disk, it may be readily detectable by GPI or a similarly sensitive, high-resolution infrared imaging system.« less

THE SOLAR NEIGHBORHOOD. XXVI. AP Col: THE CLOSEST (8.4 pc) PRE-MAIN-SEQUENCE STAR

DOE Office of Scientific and Technical Information (OSTI.GOV)

Riedel, Adric R.; Henry, Todd J.; Jao, Wei-Chun

2011-10-15

We present the results of a multi-technique investigation of the M4.5Ve flare star AP Col, which we discover to be the nearest pre-main-sequence star. These include astrometric data from the CTIO 0.9 m, from which we derive a proper motion of 342.0 {+-} 0.5 mas yr{sup -1}, a trigonometric parallax of 119.21 {+-} 0.98 mas (8.39 {+-} 0.07 pc), and photometry and photometric variability at optical wavelengths. We also provide spectroscopic data, including radial velocity (22.4 {+-} 0.3 km s{sup -1}), lithium equivalent width (EW) (0.28 {+-} 0.02 A), H{alpha} EW (-6.0 to -35 A), vsin i (11 {+-} 1more » km s{sup -1}), and gravity indicators from the Siding Spring 2.3 m WiFeS, Lick 3 m Hamilton echelle, and Keck-I HIRES echelle spectrographs. The combined observations demonstrate that AP Col is the closer of only two known systems within 10 pc of the Sun younger than 100 Myr. Given its space motion and apparent age of 12-50 Myr, AP Col is likely a member of the recently proposed {approx}40 Myr old Argus/IC 2391 Association.« less

Experimental Investigations on Subsequent Yield Surface of Pure Copper by Single-Sample and Multi-Sample Methods under Various Pre-Deformation.

PubMed

Liu, Gui-Long; Huang, Shi-Hong; Shi, Che-Si; Zeng, Bin; Zhang, Ke-Shi; Zhong, Xian-Ci

2018-02-10

Using copper thin-walled tubular specimens, the subsequent yield surfaces under pre-tension, pre-torsion and pre-combined tension-torsion are measured, where the single-sample and multi-sample methods are applied respectively to determine the yield stresses at specified offset strain. The rule and characteristics of the evolution of the subsequent yield surface are investigated. Under the conditions of different pre-strains, the influence of test point number, test sequence and specified offset strain on the measurement of subsequent yield surface and the concave phenomenon for measured yield surface are studied. Moreover, the feasibility and validity of the two methods are compared. The main conclusions are drawn as follows: (1) For the single or multi-sample method, the measured subsequent yield surfaces are remarkably different from cylindrical yield surfaces proposed by the classical plasticity theory; (2) there are apparent differences between the test results from the two kinds of methods: the multi-sample method is not influenced by the number of test points, test order and the cumulative effect of residual plastic strain resulting from the other test point, while those are very influential in the single-sample method; and (3) the measured subsequent yield surface may appear concave, which can be transformed to convex for single-sample method by changing the test sequence. However, for the multiple-sample method, the concave phenomenon will disappear when a larger offset strain is specified.

Facies and log signatures of sequence boundaries in Sembakung area, Tarakan Basin, East Kalimantan, Indonesia

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bambang, P.; Hardjono, M.; Silalahi, L.

1996-08-01

Tarakan basin is one of the basins in East Kalimantan having a complicated geological condition. Tectonic repetition developed in this area constructed various stratigraphic traps. Sedimentary development in log data shows continuous regression in Meliat and Tabul Formations (Middle Meocene), Santul Formation (Late Miocene), Tarakan Formation (Pliocene) and Bunyu Formation (Pleistocene), Supported by seismic data, stratigraphic sequence in the basin is obvious, especially in Sembakung-Bangkudulis area. The sequence boundaries, mainly {open_quotes}lowstand{close_quotes} distribution as good prospective trap, can be mapped by applying tract systems and studying wavelet extract as seismic expression character of a reservoir. Subtle changes in pattern of stratigraphicmore » sequences can become a hint of sedimentary environment and its lithology content, supporting both exploration and exploitation planning.« less

Predicting earthquakes by analyzing accelerating precursory seismic activity

USGS Publications Warehouse

Varnes, D.J.

1989-01-01

During 11 sequences of earthquakes that in retrospect can be classed as foreshocks, the accelerating rate at which seismic moment is released follows, at least in part, a simple equation. This equation (1) is {Mathematical expression},where {Mathematical expression} is the cumulative sum until time, t, of the square roots of seismic moments of individual foreshocks computed from reported magnitudes;C and n are constants; and tfis a limiting time at which the rate of seismic moment accumulation becomes infinite. The possible time of a major foreshock or main shock, tf,is found by the best fit of equation (1), or its integral, to step-like plots of {Mathematical expression} versus time using successive estimates of tfin linearized regressions until the maximum coefficient of determination, r2,is obtained. Analyzed examples include sequences preceding earthquakes at Cremasta, Greece, 2/5/66; Haicheng, China 2/4/75; Oaxaca, Mexico, 11/29/78; Petatlan, Mexico, 3/14/79; and Central Chile, 3/3/85. In 29 estimates of main-shock time, made as the sequences developed, the errors in 20 were less than one-half and in 9 less than one tenth the time remaining between the time of the last data used and the main shock. Some precursory sequences, or parts of them, yield no solution. Two sequences appear to include in their first parts the aftershocks of a previous event; plots using the integral of equation (1) show that the sequences are easily separable into aftershock and foreshock segments. Synthetic seismic sequences of shocks at equal time intervals were constructed to follow equation (1), using four values of n. In each series the resulting distributions of magnitudes closely follow the linear Gutenberg-Richter relation log N=a-bM, and the product n times b for each series is the same constant. In various forms and for decades, equation (1) has been used successfully to predict failure times of stressed metals and ceramics, landslides in soil and rock slopes, and volcanic eruptions. Results of more recent experiments and theoretical studies on crack propagation, fault mechanics, and acoustic emission can be closely reproduced by equation (1). Rate-process theory and continuum damage mechanics offer leads toward understanding the physical processes. ?? 1989 Birkha??user Verlag.

Mass spectrometry-based protein identification by integrating de novo sequencing with database searching.

PubMed

Wang, Penghao; Wilson, Susan R

2013-01-01

Mass spectrometry-based protein identification is a very challenging task. The main identification approaches include de novo sequencing and database searching. Both approaches have shortcomings, so an integrative approach has been developed. The integrative approach firstly infers partial peptide sequences, known as tags, directly from tandem spectra through de novo sequencing, and then puts these sequences into a database search to see if a close peptide match can be found. However the current implementation of this integrative approach has several limitations. Firstly, simplistic de novo sequencing is applied and only very short sequence tags are used. Secondly, most integrative methods apply an algorithm similar to BLAST to search for exact sequence matches and do not accommodate sequence errors well. Thirdly, by applying these methods the integrated de novo sequencing makes a limited contribution to the scoring model which is still largely based on database searching. We have developed a new integrative protein identification method which can integrate de novo sequencing more efficiently into database searching. Evaluated on large real datasets, our method outperforms popular identification methods.

HII 2407: AN ECLIPSING BINARY REVEALED BY K2 OBSERVATIONS OF THE PLEIADES

DOE Office of Scientific and Technical Information (OSTI.GOV)

David, Trevor J.; Hillenbrand, Lynne A.; Zhang, Celia

2015-11-20

The star HII 2407 is a member of the relatively young Pleiades star cluster and was previously discovered to be a single-lined spectroscopic binary. It is newly identified here within Kepler/K2 photometric time series data as an eclipsing binary system. Mutual fitting of the radial velocity and photometric data leads to an orbital solution and constraints on fundamental stellar parameters. While the primary has arrived on the main sequence, the secondary is still pre-main sequence and we compare our results for the M/M{sub ⊙} and R/R{sub ⊙} values with stellar evolutionary models. We also demonstrate that the system is likelymore » to be tidally synchronized. Follow-up infrared spectroscopy is likely to reveal the lines of the secondary, allowing for dynamically measured masses and elevating the system to benchmark eclipsing binary status.« less

The Age Related Properties of Solar Type Stars

NASA Technical Reports Server (NTRS)

Soderblom, David

1999-01-01

The studies of lithium in solar-type stars in clusters of a wide range of ages has provided critical information on a tracer of convective processes, especially among very young stars. Our most recent work has been on a pre-main sequence cluster (NGC 2264) that took place after this grant expired, but was founded on it. The spread seen in Li in Zero-Age Main Sequence clusters like the Pleiades is huge and possibly related to rotation. No clear spread in seen in NGC 2264, so it does not have its origins in the conditions of formation but is instead a result of processes occurring during PMS evolution. Our observations of M67 were particularly interesting because this cluster is the same age as the Sun, i.e.,very old. Clear evidence was seen for a spread in Li there too, indicating that the spread seen in very young stars perpetuates itself into old age.

Pre-main-sequence stars in the young cluster IC 2391

NASA Technical Reports Server (NTRS)

Stauffer, John; Hartmann, Lee W.; Jones, Burton F.; Mcnamara, Brian R.

1989-01-01

Seven or eight new, late-type members of the poor open cluster IC 2391 are identified, and membership is confirmed for two other stars. The new members fall approximately along a 3 x 10 to the 7th yr isochrone, which is the age estimated for the cluster on the basis of it super main-seqence turnoff. Echelle spectra were obtained for the most probable cluster members. Most show H-alpha in emission and a strong Li 6707 A absorption line, and a few are rapid rotators. The Li abundances for cluster stars cooler than the sun are considerably less than the primordial Li abundance, providing the first direct evidence for substantial premain-sequence Li burning. The rotational velocities show a range from about 15 to 150 km/s, with a distribution of rotational velocities not significantly different from that observed for low-mass stars in the Pleiades.

10 micron Spectroscopy with OSCIR: Silicate Minerology and The Origins of Disks & Protoplanetesimals

NASA Astrophysics Data System (ADS)

Woodward, Chick; Wooden, Diane; Harker, David; Rodgers, Bernadette; Butner, Harold

1999-02-01

The analysis of the silicate mineralogy of pre-main sequence Herbig Ae/Be (HeAeBe) stars to main sequence (beta)-Pic systems, probes the chemical and physical conditions in these potentially planet-forming environments, the condensation of dust from the gas-disk, and the aggregation and accretion of these solids into planetesimals and comets. We propose to obtain 10 micron OSCIR spectra of a selected list of HeAeBe and (beta)-Pic like systems. Use of our ground-based data, combined with the ISO SWS database, and our extensive analytical modeling efforts will permit us to develop a fundamental understanding of connections between silicate mineralogy and the origins and evolution of disks and protoplanetesimals. This program will provide a framework to extend our understanding of planetary formation processes and the mineralogy of dust in differing circumstellar environs and comets to be studied with the NASA STARDUST and SIRTF missions.

40 CFR 98.436 - Data reporting requirements.

Code of Federal Regulations, 2014 CFR

2014-07-01

... Contained in Pre-Charged Equipment or Closed-Cell Foams § 98.436 Data reporting requirements. (a) Each importer of fluorinated GHGs contained in pre-charged equipment or closed-cell foams must submit an annual...) Total mass in metric tons of each fluorinated GHG imported in pre-charged equipment or closed-cell foams...

40 CFR 98.436 - Data reporting requirements.

Code of Federal Regulations, 2013 CFR

2013-07-01

... Contained in Pre-Charged Equipment or Closed-Cell Foams § 98.436 Data reporting requirements. (a) Each importer of fluorinated GHGs contained in pre-charged equipment or closed-cell foams must submit an annual...) Total mass in metric tons of each fluorinated GHG imported in pre-charged equipment or closed-cell foams...

40 CFR 98.436 - Data reporting requirements.

Code of Federal Regulations, 2011 CFR

2011-07-01

... Contained in Pre-Charged Equipment or Closed-Cell Foams § 98.436 Data reporting requirements. (a) Each importer of fluorinated GHGs contained in pre-charged equipment or closed-cell foams must submit an annual...) Total mass in metric tons of each fluorinated GHG imported in pre-charged equipment or closed-cell foams...

A white dwarf cooling age of 8 Gyr for NGC 6791 from physical separation processes.

PubMed

García-Berro, Enrique; Torres, Santiago; Althaus, Leandro G; Renedo, Isabel; Lorén-Aguilar, Pablo; Córsico, Alejandro H; Rohrmann, René D; Salaris, Maurizio; Isern, Jordi

2010-05-13

NGC 6791 is a well studied open cluster that it is so close to us that can be imaged down to very faint luminosities. The main-sequence turn-off age ( approximately 8 Gyr) and the age derived from the termination of the white dwarf cooling sequence ( approximately 6 Gyr) are very different. One possible explanation is that as white dwarfs cool, one of the ashes of helium burning, (22)Ne, sinks in the deep interior of these stars. At lower temperatures, white dwarfs are expected to crystallize and phase separation of the main constituents of the core of a typical white dwarf ((12)C and (16)O) is expected to occur. This sequence of events is expected to introduce long delays in the cooling times, but has not hitherto been proven. Here we report that, as theoretically anticipated, physical separation processes occur in the cores of white dwarfs, resolving the age discrepancy for NGC 6791.

Emission performance of ceramic preconverters evaluated by FTP and Euro Stage III emission test cycle

DOE Office of Scientific and Technical Information (OSTI.GOV)

Locker, R.J.; Then, P.M.; Zink, U.

1996-09-01

Preconverters and close-coupled main converters are viewed as key components in advanced emission systems to help the auto industry comply with tightened emission regulations in North America and Europe. Due to their close position to the exhaust manifold when compared to current main catalysts, the mechanical and thermal durability requirements on such close-coupled converters are significantly increased. A set of representative preconverter systems, with respect to back pressure and surface area, ceramic and metal substrate material was exposed to a 100 hour engine aging cycle, which is equivalent to approximately 80,000 kilometers under European driving conditions. This aging cycle ismore » used by the German Autoconsortium (ZDAKW). In order to address the high thermal load in a close-coupled position, the preconverter inlet gas temperature has been elevated to a maximum of 950 C at stoichiometry. Maximum preconverter midbed temperature has been found close to 1,000 C. State-of-the-art catalytic coatings were used on the preconverters (Pd-only) and main converters (Trimetal). Emission tests using the new European test cycle (EDC 99), as well as the FTP 75 test cycle have been used to evaluate the catalytic performance. These tests were done during the aging at 20, 60 and 100 hours on the preconverters alone and on the combination of pre- and main converters. The impact of air injection has been studied on the complete preconverter/mainconverter system. The Celcor XT{trademark} ceramic preconverter proved mechanically and catalytically intact during the severe 100 hour aging cycle. The metallic and ceramic preconverter systems demonstrated equivalent catalytic performance.« less

Hot subdwarfs in (eclipsing) binaries with brown dwarf or low-mass main-sequence companions

NASA Astrophysics Data System (ADS)

Schaffenroth, Veronika; Geier, Stephan; Heber, Uli

2014-09-01

The formation of hot subdwarf stars (sdBs), which are core helium-burning stars located on the extended horizontal branch, is not yet understood. Many of the known hot subdwarf stars reside in close binary systems with short orbital periods of between a few hours and a few days, with either M-star or white-dwarf companions. Common-envelope ejection is the most probable formation channel. Among these, eclipsing systems are of special importance because it is possible to constrain the parameters of both components tightly by combining spectroscopic and light-curve analyses. They are called HW Virginis systems. Soker (1998) proposed that planetary or brown-dwarf companions could cause the mass loss necessary to form an sdB. Substellar objects with masses greater than >10 M_J were predicted to survive the common-envelope phase and end up in a close orbit around the stellar remnant, while planets with lower masses would entirely evaporate. This raises the question if planets can affect stellar evolution. Here we report on newly discovered eclipsing or not eclipsing hot subdwarf binaries with brown-dwarf or low-mass main-sequence companions and their spectral and photometric analysis to determine the fundamental parameters of both components.

Investigating ChaMPlane X-Ray Sources in the Galactic Bulge with Magellan LDSS2 Spectra

NASA Astrophysics Data System (ADS)

Koenig, Xavier; Grindlay, Jonathan E.; van den Berg, Maureen; Laycock, Silas; Zhao, Ping; Hong, JaeSub; Schlegel, Eric M.

2008-09-01

We have carried out optical and X-ray spectral analyses on a sample of 136 candidate optical counterparts of X-ray sources found in five Galactic bulge fields included in our Chandra Multiwavelength Plane Survey. We use a combination of optical spectral fitting and quantile X-ray analysis to obtain the hydrogen column density toward each object, and a three-dimensional dust model of the Galaxy to estimate the most probable distance in each case. We present the discovery of a population of stellar coronal emission sources, likely consisting of pre-main-sequence, young main-sequence, and main-sequence stars, as well as a component of active binaries of RS CVn or BY Dra type. We identify one candidate quiescent low-mass X-ray binary with a subgiant companion; we note that this object may also be an RS CVn system. We report the discovery of three new X-ray-detected cataclysmic variables (CVs) in the direction of the Galactic center (at distances lesssim2 kpc). This number is in excess of predictions made with a simple CV model based on a local CV space density of lesssim10-5 pc-3, and a scale height ~200 pc. We discuss several possible reasons for this observed excess.

Anodal transcranial direct current stimulation enhances the effects of motor imagery training in a finger tapping task.

PubMed

Saimpont, Arnaud; Mercier, Catherine; Malouin, Francine; Guillot, Aymeric; Collet, Christian; Doyon, Julien; Jackson, Philip L

2016-01-01

Motor imagery (MI) training and anodal transcranial direct current stimulation (tDCS) applied over the primary motor cortex can independently improve hand motor function. The main objective of this double-blind, sham-controlled study was to examine whether anodal tDCS over the primary motor cortex could enhance the effects of MI training on the learning of a finger tapping sequence. Thirty-six right-handed young human adults were assigned to one of three groups: (i) who performed MI training combined with anodal tDCS applied over the primary motor cortex; (ii) who performed MI training combined with sham tDCS; and (iii) who received tDCS while reading a book. The MI training consisted of mentally rehearsing an eight-item complex finger sequence for 13 min. Before (Pre-test), immediately after (Post-test 1), and at 90 min after (Post-test 2) MI training, the participants physically repeated the sequence as fast and as accurately as possible. An anova showed that the number of sequences correctly performed significantly increased between Pre-test and Post-test 1 and remained stable at Post-test 2 in the three groups (P < 0.001). Furthermore, the percentage increase in performance between Pre-test and Post-test 1 and Post-test 2 was significantly greater in the group that performed MI training combined with anodal tDCS compared with the other two groups (P < 0.05). As a potential physiological explanation, the synaptic strength within the primary motor cortex could have been reinforced by the association of MI training and tDCS compared with MI training alone and tDCS alone. © 2015 Federation of European Neuroscience Societies and John Wiley & Sons Ltd.

Deformation-based augmented reality for hepatic surgery.

PubMed

Haouchine, Nazim; Dequidt, Jérémie; Berger, Marie-Odile; Cotin, Stéphane

2013-01-01

In this paper we introduce a method for augmenting the laparoscopic view during hepatic tumor resection. Using augmented reality techniques, vessels, tumors and cutting planes computed from pre-operative data can be overlaid onto the laparoscopic video. Compared to current techniques, which are limited to a rigid registration of the pre-operative liver anatomy with the intra-operative image, we propose a real-time, physics-based, non-rigid registration. The main strength of our approach is that the deformable model can also be used to regularize the data extracted from the computer vision algorithms. We show preliminary results on a video sequence which clearly highlights the interest of using physics-based model for elastic registration.

Additives influence on spinning solution and nano web properties

NASA Astrophysics Data System (ADS)

Kukle, S.; Jegina, S.; Sutka, A.; Makovska, R.

2017-10-01

Needleless electrospinning operated as a one-stage process producing nanofibres webs from spinning solutions with the corresponding to the final use properties seems has a good future prospects. Complicated spinning solution designing started with the selection of composition and components proportion, pre-processing sequence and parameters establishing for every component and for their mixing. Spinning solution viscosity and electro conductivity together with the spinning distance and intensity of electromagnetic field are main parameters determined spin ability and properties of obtained nanofibers. Influence of some pre-processing parameters of components, combinations of organic and non-organic components and their concentration influence on spinning solution viscosity and conductivity, as well on fibres diameters are under discussion.

1961-2011: Fifty years of Hayashi tracks

NASA Astrophysics Data System (ADS)

Palla, Francesco

2012-09-01

Fifty years after the seminal paper by Prof. C. Hayashi, the field of pre-main sequence (PMS) evolution still plays a fundamental role in observational and theoretical astrophysics. In this contribution, I highlight the contribution made by Hayashi in establishing the theoretical foundation of early stellar evolution. Then, I discuss the changes of the classical theory introduced by the inclusion of protostellar evolution in PMS models and present selected results on young stars.

Coseismic Surface Cracks Produced By the Mw8.1 Pisagua Earthquake Sequence

NASA Astrophysics Data System (ADS)

Allmendinger, R. W.; Scott, C. P.; Gonzalez, G.; Loveless, J. P.

2014-12-01

The April 1, 2014 Mw8.1 Pisagua earthquake filled a relatively small part of the Iquique Gap, a segment of the the Nazca-South America plate boundary that had not experienced a great earthquake since 1877. The slip maximum for the event occurred south of the hypocenter offshore of the village of Pisagua. To document the permanent surface deformation, we measured more than 3,700 co- or post seismic cracks, spanning 220 km of coast length, during three field excursions 2 weeks, 6 weeks, and 3 months after the main shock. Thanks to the hyperarid climate of the region, many fresh cracks are still visible 3.5 months after the main event but eolian processes and sloughing of the side-walls are rapidly obscuring these fragile features. The distribution of crack strikes is noisy for several reasons: (1) the vast majority of new cracks reactivated pre-existing cracks in many cases with less than ideal orientations; (2) both the April 1 main shock and the April 2 Mw7.7 aftershock 70 km to the south probably produced cracks; (3) several smaller crustal aftershocks occurred on EW reverse faults and may have enhanced cracking on EW scarps; and (4) cracking is locally enhanced along sharp topographic features. Nonetheless, there is a tendency for NNE striking cracks S of the slip maximum and NNW cracks to the north. We measured crack aperture and calculate strain in transects of 500-1000 m length at 3 localities along the earthquake rupture length. Those close to the slip maximum have permanent coseismic extensional strains on the order of 1e-4 and even a site 60 km S of the Mw7.7 event has crack strain of 5e-5. These strains are not homogenous, but diminish eastward. These data indicate that surface cracking caused by any one event utilizes the most suitably pre-existing weaknesses, Presumably, over time earthquakes with similar slip characteristics will add constructively in the geological record to produce a crack population characteristic of the long term average earthquake in the region.

Study pre-earthquake features in the Earth atmosphere-ionosphere environment associated with 2016 Amatrice-Norcia (Central Italy) seismic sequence

NASA Astrophysics Data System (ADS)

Ouzounov, Dimitar; Pulinets, Sergey; Giuliani, Gioacchino; Hernández-Pajares, Manuel; García-Rigo, Alberto

2017-04-01

The 2016 Amatrice-Norcia (Central Italy) seismic sequence (M6.3, M6.1 and M6.5), became one of the unusual and important modern earthquake events. Recent studies indicate (including April 6th 2009 Abruzzo earthquake) an enhanced coupling between the atmospheric boundary layer and the ionosphere, which have been proposed to be related with large (>M6) earthquakes. This relationship has been studied for the 2016 Central Italy sequence using an integrated set of observations of five physical and environmental parameters. We present observational data from January to November 2016 of five physical parameters- radon, seismicity, temperature of the atmosphere boundary layer, outgoing earth infrared radiation and GPS/TEC and their temporal and spatial variations several days before the onset of the Amatrice-Norcia earthquake sequence. The Aug 24 M6.2 foreshock was situated about 70 kilometers from the 2 stations of radon near L'Aquila. These data show an increase prior to the main earthquake beginning in July-August this enhancement of radon coincides (with some delay) with an increase in the atmospheric chemical potential (Aug 11) measured near the epicentral area from satellite. And subsequently from Aug12 there was an association with the acceleration of outgoing infrared radiation observed on the top of the atmosphere from EOS satellite (Aug 16). The GPS/Total Electron Content data indicate an increase of electron concentration in ionosphere on August 22 and October 26, 1-2 days before the M6.2 foreshock and the M6.5 main shock on Oct 30, 2016. Both ground and satellite data have in common that they were evident in about the last ten days before the M6.2 foreshock of Aug 24 and continuously up to the main shock of Oct 30, although the radon variations started 2 months earlier. We examined the possible correlation between different pre-earthquake signals in the frame of a multidisciplinary investigation of Lithosphere -Atmosphere -Ionosphere coupling concept.

Effects of Main-Sequence Mass Loss on Stellar and Galactic Chemical Evolution.

NASA Astrophysics Data System (ADS)

Guzik, Joyce Ann

1988-06-01

L. A. Willson, G. H. Bowen and C. Struck -Marcell have proposed that 1 to 3 solar mass stars may experience evolutionarily significant mass loss during the early part of their main-sequence phase. The suggested mass-loss mechanism is pulsation, facilitated by rapid rotation. Initial mass-loss rates may be as large as several times 10^{-9}M o/yr, diminishing over several times 10^8 years. We attempted to test this hypothesis by comparing some theoretical implications with observations. Three areas are addressed: Solar models, cluster HR diagrams, and galactic chemical evolution. Mass-losing solar models were evolved that match the Sun's luminosity and radius at its present age. The most extreme viable models have initial mass 2.0 M o, and mass-loss rates decreasing exponentially over 2-3 times 10^8 years. Compared to a constant -mass model, these models require a reduced initial ^4He abundance, have deeper envelope convection zones and higher ^8B neutrino fluxes. Early processing of present surface layers at higher interior temperatures increases the surface ^3He abundance, destroys Li, Be and B, and decreases the surface C/N ratio following first dredge-up. Evolution calculations incorporating main-sequence mass loss were completed for a grid of models with initial masses 1.25 to 2.0 Mo and mass loss timescales 0.2 to 2.0 Gyr. Cluster HR diagrams synthesized with these models confirm the potential for the hypothesis to explain observed spreads or bifurcations in the upper main sequence, blue stragglers, anomalous giants, and poor fits of main-sequence turnoffs by standard isochrones. Simple closed galactic chemical evolution models were used to test the effects of main-sequence mass loss on the F and G dwarf distribution. Stars between 3.0 M o and a metallicity -dependent lower mass are assumed to lose mass. The models produce a 30 to 60% increase in the stars to stars-plus -remnants ratio, with fewer early-F dwarfs and many more late-F dwarfs remaining on the main sequence to the present. The ratio of stars to stellar remnants and the white dwarf age distribution may prove valuable in distinguishing between explanations for the observed bimodal present-day stellar mass function.

Ancient Recombination Events between Human Herpes Simplex Viruses.

PubMed

Burrel, Sonia; Boutolleau, David; Ryu, Diane; Agut, Henri; Merkel, Kevin; Leendertz, Fabian H; Calvignac-Spencer, Sébastien

2017-07-01

Herpes simplex viruses 1 and 2 (HSV-1 and HSV-2) are seen as close relatives but also unambiguously considered as evolutionary independent units. Here, we sequenced the genomes of 18 HSV-2 isolates characterized by divergent UL30 gene sequences to further elucidate the evolutionary history of this virus. Surprisingly, genome-wide recombination analyses showed that all HSV-2 genomes sequenced to date contain HSV-1 fragments. Using phylogenomic analyses, we could also show that two main HSV-2 lineages exist. One lineage is mostly restricted to subSaharan Africa whereas the other has reached a global distribution. Interestingly, only the worldwide lineage is characterized by ancient recombination events with HSV-1. Our findings highlight the complexity of HSV-2 evolution, a virus of putative zoonotic origin which later recombined with its human-adapted relative. They also suggest that coinfections with HSV-1 and 2 may have genomic and potentially functional consequences and should therefore be monitored more closely. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Extensional vs. compressional deformation in the Central High Atlas salt province: A paleomagnetic approach

NASA Astrophysics Data System (ADS)

Calvín, P.; Casas-Sainz, A. M.; Villalaín, J. J.; Moussaid, B.

2018-06-01

In this paper we address the problem of the distinction between diapiric, salt-driven and compressional structures, using the outstanding example of the Central High Atlas (Morocco). A remagnetized component carried by magnetite has been isolated in 32 new paleomagnetic sites. It is characterized by: maximum unblocking temperatures around 450 °C, syn-folding behavior and normal polarity. These 33 mean paleomagnetic directions were analyzed together with other 68 from published works around the study area to construct a robust paleomagnetic dataset along a cross-section perpendicular to the main structures. The remagnetization direction (n: 100, Dec: 332.2°, Inc: 34.5°, η: 6.2°, ξ: 2.0°, A/n: 6.427°) and the paleo-dip of beds (the attitude of the beds at the remagnetization occurrence) were calculated through small circle methods. The remagnetization can be dated as ca. 100 Ma. Because of its occurrence between the extensional and compressional periods, this remagnetization offers the possibility of restore the basin to its pre-inversion geometry. Comparison between present-day and pre-inversion structure allows discriminating three different evolutionary patterns: (i) thrusted and welded salt-walls mainly structured during the extensional stage (Ikkou ridge) with steep limbs close to the salt-wall core. (ii) Jurassic salt-walls with weaker deformation, restricted to the areas adjacent to the structure (Tadaghmamt and Timedouine); in this case, Cenozoic compression is limited to welding of the salt-walls and buttressing of the sedimentary sequences against faults. (iii) salt-rollers gently initiated during the Jurassic (Toumliline diapir), thrusted during the Cenozoic compression. Results show the importance of salt tectonics both during extension and compression, as well as the control of the compressional features by the inherited extensional structures. The performed restorations prove that paleomagnetism is a useful, independent tool to obtain palinspastic restorations and to separate, and quantify, the imprint generated during the basinal stage from the inversional features.

Centromere and telomere sequence alterations reflect the rapid genome evolution within the carnivorous plant genus Genlisea.

PubMed

Tran, Trung D; Cao, Hieu X; Jovtchev, Gabriele; Neumann, Pavel; Novák, Petr; Fojtová, Miloslava; Vu, Giang T H; Macas, Jiří; Fajkus, Jiří; Schubert, Ingo; Fuchs, Joerg

2015-12-01

Linear chromosomes of eukaryotic organisms invariably possess centromeres and telomeres to ensure proper chromosome segregation during nuclear divisions and to protect the chromosome ends from deterioration and fusion, respectively. While centromeric sequences may differ between species, with arrays of tandemly repeated sequences and retrotransposons being the most abundant sequence types in plant centromeres, telomeric sequences are usually highly conserved among plants and other organisms. The genome size of the carnivorous genus Genlisea (Lentibulariaceae) is highly variable. Here we study evolutionary sequence plasticity of these chromosomal domains at an intrageneric level. We show that Genlisea nigrocaulis (1C = 86 Mbp; 2n = 40) and G. hispidula (1C = 1550 Mbp; 2n = 40) differ as to their DNA composition at centromeres and telomeres. G. nigrocaulis and its close relative G. pygmaea revealed mainly 161 bp tandem repeats, while G. hispidula and its close relative G. subglabra displayed a combination of four retroelements at centromeric positions. G. nigrocaulis and G. pygmaea chromosome ends are characterized by the Arabidopsis-type telomeric repeats (TTTAGGG); G. hispidula and G. subglabra instead revealed two intermingled sequence variants (TTCAGG and TTTCAGG). These differences in centromeric and, surprisingly, also in telomeric DNA sequences, uncovered between groups with on average a > 9-fold genome size difference, emphasize the fast genome evolution within this genus. Such intrageneric evolutionary alteration of telomeric repeats with cytosine in the guanine-rich strand, not yet known for plants, might impact the epigenetic telomere chromatin modification. © 2015 The Authors The Plant Journal © 2015 John Wiley & Sons Ltd.

The circumstellar environments of dusty main sequence stars

NASA Astrophysics Data System (ADS)

Gebrim, Antonio S. Hales

Our current understanding of the formation of planetary systems is strongly linked to astronomical observations of gas and dust around young stars. This thesis is dedicated to studying the physical conditions acting in the circumstellar environments of pre-main sequence and early main sequence dusty stars. These early stellar ages correspond to the timescales over which planets are thought to be formed. The first part of this work is dedicated to a search for dusty early A-type stars in the northern galactic plane. Data from the IPHAS Ha survey is first used to select a sample of galactic A-type stars. This sample is then correlated with data from the Spitzer Space Telescope in order to search for 8 microns and 24 microns excesses associated with warm dust orbiting the stars. The improved photometric sensitivities of these new galactic surveys allow the list of known galactic 'Vega-like' sources to be extended to unexplored optical magnitude ranges (13.5 < r < 18.5 mags). Only 1.1% of a sample of 3062 A-type stars with available optical to mid-infrared spectral energy distributions showed detectable excesses at 8 microns. Searching over 1860 stars observed at 24 microns yielded similar statistical results (1.2%). Only 10 stars have both 8 and 24 micron excesses. These results support the idea that warm dust located relatively close to the stars is rare in main sequence systems. Follow-up observations of this new sample of dust-excess stars will provide better insights into the properties of the systems. Resolved images are crucial for understanding the dynamics and evolution of proto-planetary disks. Observing the detailed disk structure requires high-contrast, high-spatial resolution imaging very close to the bright central star. As a consequence, only a handful of these systems have yet been resolved. The second part of this work shows how near-infrared Polarimetric Imaging on the 3.8 meter United Kingdom Infrared Telescope can be used to obtain reflected-light images of dust-disks around dust excess stars. This technique allows one to automatically suppress the unpolarised light from the central star, increasing the dynamic range for detecting polarised light scattered by the dust present in circumstellar discs. The detections of extended disks around the classical T Tauri star TW Hya and the Herbig Ac star HD 169142 are reported, as well as the strong but spatially unresolved polarization signals measured toward two other Herbig Ae stars. Monte Carlo scattering simulations are used to fit the J-, H- and K-band polarization images of the disk around TW Hya, providing new constraints on the geometry of TW Hya's disk. The third part of this thesis is dedicated to studying the gas content and dynamics around dust-excess stars. The evolution of circumstellar gas is thought to be strongly linked to the formation of gaseous giant planets similar to Jupiter, Saturn and most currently known extra-solar planets. However, the timescales over which circumstellar gas discs dissipate remains poorly constrained, mainly due to the observational difficulties associated with detecting small amounts of circumstellar gas. An analysis of high-resolution (R 50 000) optical spectroscopic data of a sample of 'Vega-like' candidates from the catalogue of Mannings & Barlow (1998) is presented. Analysis of the stellar spectra allows one to search for narrow absorption features due to circumstellar gas and possible Falling Evaporating Bodies, similar to the ones seen in the (3 Pictoris system. None of the stars from this sample show emission line activity in either Ha, Ca II or Na I, indicating that accretion of material onto the stars has ceased and suggesting they are true main sequence Vega-like stars. Four stars were found to exhibit narrow absorption features near the cores of the photospheric Ca II and Na I D lines, with HD 110058 being the strongest candidate to host a (3 Pictoris-like gas disk. If confirmed, HD 110058 would represent the Vega-like star with the lowest Lir/L* value (3.7 x 10"4) around which a CS gas disk has been detected.

Phylogeny and evolution of the auks (subfamily Alcinae) based on mitochondrial DNA sequences

USGS Publications Warehouse

Moum, Truls; Johansen, Steinar; Erikstad, Kjell Einar; Piatt, John F.

1994-01-01

The genetic divergence and phylogeny of the auks was assessed by mitochondrial DNA sequence comparisons in a study using 19 of the 22 auk species and two outgroup representatives. We compared more than 500 nucleotides from each of two mitochondrial genes encoding 12S rRNA and the NADH dehydrogenase subunit 6. Divergence times were estimated from transversional substitutions. The dovekie (Alle alle) is related to the razorbill (Alca torda) and the murres (Uria spp). Furthermore, the Xantus's murrelet (Synthliboramphus hypoleucus) and the ancient (Synthliboramphus antiquus) and Japanese murrelets (Synthliboramphus wumizusume) are genetically distinct members of the same main lineage, whereas brachyramphine and synthliboramphine murrelets are not closely related. An early adaptive radiation of six main species groups of auks seems to trace back to Middle Miocene. Later speciation probably involved ecological differentiations and geographical isolations.

A search for T Tauri stars and related objects: Archival photometry of candidate variables in V733 Cep field

NASA Astrophysics Data System (ADS)

Jurdana-Šepić, R.; Poljančić Beljan, I.

Searching for T Tauri stars or related early type variables we carried out a BVRI photometric measurements of five candidates with positions within the field of the pre-main sequence object V733 Cephei (Persson's star) located in the dark cloud L1216 near to Cepheus OB3 Association: VES 946, VES 950, NSV 14333, NSV 25966 and V385 Cep. Their magnitudes are determined on the plates from Asiago Observatory historical photographic archive exposed 1971 - 1978. We provide finding charts for program stars and comparison sequence stars, magnitude estimations, magnitude mean values and BVR_cI_c light curves of program stars.

Pre-supernova models for massive stars produced with large nuclear reaction network by MESA

NASA Astrophysics Data System (ADS)

Park, Byeongchan; Kwak, Kyujin

2018-04-01

Core-collapsed Supernova (CCSN) is one of violent phenomena in the universe. CCSN generates heavy elements and leaves a neutron star behind. It has been known that the physical properties of CCSN depend on those of pre-supernova such as mass, metallicities including distribution of elements, and the density and temperature profile which are obtained from the stellar evolution calculation. In particular, the production of heavy elements in CCSN is sensitive to the abundance profiles in the pre-supernova models. In this study, we evolve a massive main sequence star with 15Msun and solar metallicity to the pre-supernova stage by using two different networks, small and large. The large nuclear reaction network includes more than four times isotopes than the small network. Our calculations were done by MESA (Modules for Experiments in Stellar Astrophysics) which allowed us to use the large network containing about a hundred isotopes. We compare the results obtained with two networks.

The Intermediate Stellar Population in R136 Determined from Hubble Space Telescope Images

NASA Astrophysics Data System (ADS)

Hunter, D. A.; WFPC1 IDT; WFPC2 IDT

1994-12-01

We have analyzed Hubble Space Telescope (HST) images of the compact, luminous star cluster R136 in the LMC that were taken with the refurbished HST and new Wide Field/Planetary Camera. These images allow us to examine the stellar population in a region of unusually intense star formation at a scale of 0.01 pc. We have detected stars to 23.5 in F555W and have quantified the stellar population to an M_{555,o} of 0.9 or a mass of 2.8 cal Msolar . Comparisons of HR diagrams with isochrones that were constructed for the HST flight filter system from theoretical stellar evolutionary tracks reveal massive stars, a main sequence to at least 2.8 cal Msolar , and stars with M_{555,o}>=0.5 still on pre-main sequence tracks. The average stellar population is fit with a 3--4 Myr isochrone. Contrary to expectations from star formation models, however, the formation period for the massive stars and lower mass stars appear to largely overlap. We have measured the IMF for stars 2.8--15 cal Msolar in three annuli from 0.5--4.7 pc from the center of the cluster. The slopes of the IMF in all three annuli are the same within the uncertainties, thus, showing no evidence for mass segregation beyond 0.5 pc. Furthermore, the combined IMF slope, -1.2+/-0.1, is close to a normal Salpeter IMF. The lower mass limit must be lower than the limits of our measurements: <=2.8 cal Msolar beyond 0.5 pc and <=7 cal Msolar within 0.1 pc. This is contrary to some predictions that the lower mass limit could be as high as 10 cal Msolar in regions of intense massive star formation. Integrated properties of R136 are consistent with its being comparable to a rather small globular cluster when such clusters were the same age as R136.

A STELLAR-MASS-DEPENDENT DROP IN PLANET OCCURRENCE RATES

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mulders, Gijs D.; Pascucci, Ilaria; Apai, Dániel

2015-01-10

The Kepler spacecraft has discovered a large number of planets with up to one-year periods and down to terrestrial sizes. While the majority of the target stars are main-sequence dwarfs of spectral type F, G, and K, Kepler covers stars with effective temperatures as low as 2500 K, which corresponds to M stars. These cooler stars allow characterization of small planets near the habitable zone, yet it is not clear if this population is representative of that around FGK stars. In this paper, we calculate the occurrence of planets around stars of different spectral types as a function of planetmore » radius and distance from the star and show that they are significantly different from each other. We further identify two trends. First, the occurrence of Earth- to Neptune-sized planets (1-4 R {sub ⊕}) is successively higher toward later spectral types at all orbital periods probed by Kepler; planets around M stars occur twice as frequently as around G stars, and thrice as frequently as around F stars. Second, a drop in planet occurrence is evident at all spectral types inward of a ∼10 day orbital period, with a plateau further out. By assigning to each spectral type a median stellar mass, we show that the distance from the star where this drop occurs is stellar mass dependent, and scales with semi-major axis as the cube root of stellar mass. By comparing different mechanisms of planet formation, trapping, and destruction, we find that this scaling best matches the location of the pre-main-sequence co-rotation radius, indicating efficient trapping of migrating planets or planetary building blocks close to the star. These results demonstrate the stellar-mass dependence of the planet population, both in terms of occurrence rate and of orbital distribution. The prominent stellar-mass dependence of the inner boundary of the planet population shows that the formation or migration of planets is sensitive to the stellar parameters.« less

So close, so different: geothermal flux shapes divergent soil microbial communities at neighbouring sites.

PubMed

Gagliano, A L; Tagliavia, M; D'Alessandro, W; Franzetti, A; Parello, F; Quatrini, P

2016-03-01

This study is focused on the (micro)biogeochemical features of two close geothermal sites (FAV1 and FAV2), both selected at the main exhalative area of Pantelleria Island, Italy. A previous biogeochemical survey revealed high CH4 consumption and the presence of a diverse community of methanotrophs at FAV2 site, whereas the close site FAV1 was apparently devoid of methanotrophs and recorded no CH4 consumption. Next-Generation Sequencing (NGS) techniques were applied to describe the bacterial and archaeal communities which have been linked to the physicochemical conditions and the geothermal sources of energy available at the two sites. Both sites are dominated by Bacteria and host a negligible component of ammonia-oxidizing Archaea (phylum Thaumarchaeota). The FAV2 bacterial community is characterized by an extraordinary diversity of methanotrophs, with 40% of the sequences assigned to Methylocaldum, Methylobacter (Gammaproteobacteria) and Bejerickia (Alphaproteobacteria); conversely, a community of thermo-acidophilic chemolithotrophs (Acidithiobacillus, Nitrosococcus) or putative chemolithotrophs (Ktedonobacter) dominates the FAV1 community, in the absence of methanotrophs. Since physical andchemical factors of FAV1, such as temperature and pH, cannot be considered limiting for methanotrophy, it is hypothesized that the main limiting factor for methanotrophs could be high NH4(+) concentration. At the same time, abundant availability of NH4(+) and other high energy electron donors and acceptors determined by the hydrothermal flux in this site create more energetically favourable conditions for chemolithotrophs that outcompete methanotrophs in non-nitrogen-limited soils. © 2015 John Wiley & Sons Ltd.

Understanding young stars - A history

DOE Office of Scientific and Technical Information (OSTI.GOV)

Stahler, S.W.

1988-12-01

The history of pre-main-sequence theory is briefly reviewed. The paper of Henyey et al. (1955) is seen as an important transitional work, one which abandoned previous simplifying assumptions yet failed to incorporate newer insights into the surface structure of late-type stars. The subsequent work of Hayashi and his contemporaries is outlined, with an emphasis on the underlying physical principles. Finally, the recent impact of protostar theory is discussed, and speculations are offered on future developments. 56 references.

Spitzer Spectroscopy of the Transition Object TW Hya

DTIC Science & Technology

2010-02-24

results bear on our understanding of the evolutionary state of the TW Hya disk . Subject headings: (stars:) circumstellar matter — (stars:) planetary systems... protoplanetary disks — stars: pre-main sequence — (stars: individual) TW Hya 1. Introduction Spectroscopy with the Spitzer Space Telescope has...region of the disk . (2) If a planet has formed with a mass sufficient to open a gap (∼ 1MJ), gas will be cleared in the vicinity of its orbit, but gap

Deciphering the X-ray Emission of the Nearest Herbig Ae Star

NASA Technical Reports Server (NTRS)

Skinner, Stephen L.

2004-01-01

In this research program, we obtained and analyzed an X-ray observation of the young nearby intermediate mass pre-main sequence star HD 104237 using the XMM-Newton space-based observatory. The observation was obtained on 17 Feb. 2002. This observation yielded high-quality X-ray images, spectra, and timing data which provided valuable information on the physical processes responsible for the X-ray emission. This star is a member of the group of so-called Herbig Ae/Be stars, which are young intermediate mass (approx. 2 - 4 solar masses) pre-main sequence (PMS) stars a few million years old that have not yet begun core hydrogen burning. The objective of the XMM-Newton observation was to obtain higher quality data than previously available in order to constrain possible X-ray emission mechanisms. The origin of the X-ray emission from Herbig Ae/Be stars is not yet known. These intermediate mass PMS stars lie on radiative tracks and are not expected to emit X-rays via solar-like magnetic processes, nor are their winds powerful enough to produce X-rays by radiative wind shocks as in more massive O-type stars. The emission could originate in unseen low-mass companions, or it may be intrinsic to the Herbig stars themselves if they still have primordial magnetic fields or can sustain magnetic activity via a nonsolar dynamo.

Astrophysical Impact of the Updated 9Be(p,α)6Li and 10B(p,α)7Be Reaction Rates As Deduced By THM

NASA Astrophysics Data System (ADS)

Lamia, L.; Spitaleri, C.; Tognelli, E.; Degl'Innocenti, S.; Pizzone, R. G.; Prada Moroni, P. G.

2015-10-01

The complete understanding of the stellar abundances of lithium, beryllium, and boron represents one of the most interesting open problems in astrophysics. These elements are largely used to probe stellar structure and mixing phenomena in different astrophysical scenarios, such as pre-main-sequence or main-sequence stars. Their different fragility against (p,α) burning reactions allows one to investigate different depths of the stellar interior. Such fusion mechanisms are triggered at temperatures between T ≈ (2-5) × {10}6 K, thus defining a corresponding Gamow energy between ≈ 3-10 keV, where S(E)-factor measurements need to be performed to get reliable reaction rate evaluations. The Trojan Horse Method is a well defined procedure to measure cross sections at Gamow energies overcoming the uncertainties due to low-energy S(E)-factor extrapolation as well as electron screening effects. Taking advantage of the {\\mathtt{THM}} measure of the 9Be(p,α)6Li and 10B(p,α)7Be cross sections, the corresponding reaction rates have been calculated and compared with the evaluations by the NACRE collaboration, widely used in the literature. The impact on surface abundances of the updated 9Be and 10B (p,α) burning rates is discussed for pre-MS stars.

Gradient waveform pre-emphasis based on the gradient system transfer function.

PubMed

Stich, Manuel; Wech, Tobias; Slawig, Anne; Ringler, Ralf; Dewdney, Andrew; Greiser, Andreas; Ruyters, Gudrun; Bley, Thorsten A; Köstler, Herbert

2018-02-25

The gradient system transfer function (GSTF) has been used to describe the distorted k-space trajectory for image reconstruction. The purpose of this work was to use the GSTF to determine the pre-emphasis for an undistorted gradient output and intended k-space trajectory. The GSTF of the MR system was determined using only standard MR hardware without special equipment such as field probes or a field camera. The GSTF was used for trajectory prediction in image reconstruction and for a gradient waveform pre-emphasis. As test sequences, a gradient-echo sequence with phase-encoding gradient modulation and a gradient-echo sequence with a spiral read-out trajectory were implemented and subsequently applied on a structural phantom and in vivo head measurements. Image artifacts were successfully suppressed by applying the GSTF-based pre-emphasis. Equivalent results are achieved with images acquired using GSTF-based post-correction of the trajectory as a part of image reconstruction. In contrast, the pre-emphasis approach allows reconstruction using the initially intended trajectory. The artifact suppression shown for two sequences demonstrates that the GSTF can serve for a novel pre-emphasis. A pre-emphasis based on the GSTF information can be applied to any arbitrary sequence type. © 2018 International Society for Magnetic Resonance in Medicine.

Crystal Structure of the HEAT Domain from the Pre-mRNA Processing Factor Symplekin

PubMed Central

Kennedy, Sarah A.; Frazier, Monica L.; Steiniger, Mindy; Mast, Ann M.; Marzluff, William F.; Redinbo, Matthew R.

2009-01-01

The majority of eukaryotic pre-mRNAs are processed by 3′-end cleavage and polyadenylation, although in metazoa the replication-dependant histone mRNAs are processed by 3′-end cleavage but not polyadenylation. The macromolecular complex responsible for processing both canonical and histone pre-mRNAs contains the ~1,160-residue protein Symplekin. Secondary structural prediction algorithms identified putative HEAT domains in the 300 N-terminal residues of all Symplekins of known sequence. The structure and dynamics of this domain were investigated to begin elucidating the role Symplekin plays in mRNA maturation. The crystal structure of the Drosophila melanogaster Symplekin HEAT domain was determined to 2.4 Å resolution using SAD phasing methods. The structure exhibits 5 canonical HEAT repeats along with an extended 31 amino acid loop (loop 8) between the fourth and fifth repeat that is conserved within closely related Symplekin sequences. Molecular dynamics simulations of this domain show that the presence of loop 8 dampens correlated and anticorrelated motion in the HEAT domain, therefore providing a neutral surface for potential protein-protein interactions. HEAT domains are often employed for such macromolecular contacts. The Symplekin HEAT region not only structurally aligns with several established scaffolding proteins, but also has been reported to contact proteins essential for regulating 3′-end processing. Taken together, these data support the conclusion that the Symplekin HEAT domain serves as a scaffold for protein-protein interactions essential to the mRNA maturation process. PMID:19576221

An Observational Study of Accretion Dynamics in Short-Period Pre-Main Sequence Binaries

NASA Astrophysics Data System (ADS)

Tofflemire, Benjamin; Mathieu, Robert; Herczeg, Greg; Johns-Krull, Christopher; Akeson, Rachel; Ciardi, David

2018-01-01

Over the past thirty years, a detailed picture of star formation has emerged that highlights the importance of the interaction between a pre-main sequence (pre-MS) star and its protoplanetary disk. The properties of an emergent star, the lifetime of a protoplanetary disk, and the formation of planets are all, in part, determined by this star-disk interaction. Many stars, however, form in binary or higher-order systems where orbital dynamics are capable of fundamentally altering this star-disk interaction. Orbital resonances, especially in short-period systems, are capable of clearing the central region of a protoplanetary disk, leaving the possibility for three stable accretion disks: a circumstellar disk around each star and a circumbinary disk. In this model, accretion onto the stars is predicted to proceed in periodic streams that form at the inner edge of the circumbinary disk, cross the dynamically cleared gap, and feed circumstellar disks or accrete directly onto the stars themselves. This pulsed-accretion paradigm predicts bursts of accretion that are periodic with the orbital period, where the duration, amplitude, location in orbital phase, and which star if preferentially fed, all depend on the orbital parameters. To test these predictions, we have carried out intensive observational campaigns combining time-series, optical and near-infrared photometry with time-series, optical spectroscopy. These data are capable of monitoring the stellar accretion rate, the properties of warm circumstellar dust, and the kinematics of accretion flows, all as a function of orbital phase. In our sample of 9 pre-MS binaries with diverse orbital parameters, we search for evidence of periodic accretion events and seek to determine the role orbital parameters have on the characteristics of accretion events. Two results from our campaign will be highlighted: 1) the detection of periodic pulsed accretion events in DQ Tau and TWA 3A, and 2) evidence that the TWA 3A primary is the dominant accretor in the system. We compare these findings to the results of numerical simulations and comment on the role of magnetospheric accretion in pre-MS binaries.

Reinflating Giant Planets

NASA Astrophysics Data System (ADS)

Kohler, Susanna

2017-01-01

Two new, large gas-giant exoplanets have been discovered orbiting close to their host stars. A recent study examining these planets and others like them may help us to better understand what happens to close-in hot Jupiters as their host stars reach the end of their main-sequence lives.OversizedGiantsUnbinned transit light curves for HAT-P-65b. [Adapted from Hartman et al. 2016]The discovery of HAT-P-65b and HAT-P-66b, two new transiting hot Jupiters, is intriguing. These planets have periods of just under 3 days and masses of roughly 0.5 and 0.8 times that of Jupiter, but their sizes are whats really interesting: they have inflated radii of 1.89 and 1.59 times that of Jupiter.These two planets, discovered using the Hungarian-made Automated Telescope Network (HATNet) in Arizona and Hawaii, mark the latest in an ever-growing sample of gas-giant exoplanets with radii larger than expected based on theoretical planetary structure models.What causes this discrepancy? Did the planets just fail to contract to the expected size when they were initially formed, or were they reinflated later in their lifetimes? If the latter, how? These are questions that scientists are only now starting to be able to address using statistics of the sample of close-in, transiting planets.Unbinned transit light curves for HAT-P-66b. [Hartman et al. 2016]Exploring Other PlanetsLed by Joel Hartman (Princeton University), the team that discovered HAT-P-65b and HAT-P-66b has examined these planets observed parameters and those of dozens of other known close-in, transiting exoplanets discovered with a variety of transiting exoplanet missions: HAT, WASP, Kepler, TrES, and KELT. Hartman and collaborators used this sample to draw conclusions about what causes some of these planets to have such large radii.The team found that there is a statistically significant correlation between the radii of close-in giant planets and the fractional ages of their host stars (i.e., the stars age divided by its full expected lifetime). The two newly discovered hot Jupiters with inflated radii, for instance, are orbiting stars that are roughly 84% and 83% through their life spans and are approaching the main-sequence turnoff point.Late-Life ReinflationFractional age of the host stars of close-in transiting exoplanets vs. the planets radius. There is a statistically significant correlation between age and planet radius. [Adapted from Hartman et al. 2016]Hartman and collaborators propose that the data support the following scenario: as host stars evolve and become more luminous toward the ends of their main-sequence lifetimes, they deposit more energy deep into the interiors of the planets closely orbiting them. These close-in planets then increase their equilibrium temperatures and their radii reinflate as a result.Based on these results, we would expect to continue to find hot Jupiters with inflated radii primarily orbiting closely around older stars. Conversely, close-in giant planets around younger stars should primarily have non-inflated radii. As we continue to build our observational sample of transiting hot Jupiters in the future, we will be able to see how this model holds up.CitationJ. D. Hartman et al 2016 AJ 152 182. doi:10.3847/0004-6256/152/6/182

Microbial diversity in an Armenian geothermal spring assessed by molecular and culture-based methods.

PubMed

Panosyan, Hovik; Birkeland, Nils-Kåre

2014-11-01

The phylogenetic diversity of the prokaryotic community thriving in the Arzakan hot spring in Armenia was studied using molecular and culture-based methods. A sequence analysis of 16S rRNA gene clone libraries demonstrated the presence of a diversity of microorganisms belonging to the Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Epsilonproteobacteria, Firmicutes, Bacteroidetes phyla, and Cyanobacteria. Proteobacteria was the dominant group, representing 52% of the bacterial clones. Denaturing gradient gel electrophoresis profiles of the bacterial 16S rRNA gene fragments also indicated the abundance of Proteobacteria, Bacteroidetes, and Cyanobacteria populations. Most of the sequences were most closely related to uncultivated microorganisms and shared less than 96% similarity with their closest matches in GenBank, indicating that this spring harbors a unique community of novel microbial species or genera. The majority of the sequences of an archaeal 16S rRNA gene library, generated from a methanogenic enrichment, were close relatives of members of the genus Methanoculleus. Aerobic endospore-forming bacteria mainly belonging to Bacillus and Geobacillus were detected only by culture-dependent methods. Three isolates were successfully obtained having 99, 96, and 96% 16S rRNA gene sequence similarities to Arcobacter sp., Methylocaldum sp., and Methanoculleus sp., respectively. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Cognitive and neural foundations of discrete sequence skill: a TMS study.

PubMed

Ruitenberg, Marit F L; Verwey, Willem B; Schutter, Dennis J L G; Abrahamse, Elger L

2014-04-01

Executing discrete movement sequences typically involves a shift with practice from a relatively slow, stimulus-based mode to a fast mode in which performance is based on retrieving and executing entire motor chunks. The dual processor model explains the performance of (skilled) discrete key-press sequences in terms of an interplay between a cognitive processor and a motor system. In the present study, we tested and confirmed the core assumptions of this model at the behavioral level. In addition, we explored the involvement of the pre-supplementary motor area (pre-SMA) in discrete sequence skill by applying inhibitory 20 min 1-Hz off-line repetitive transcranial magnetic stimulation (rTMS). Based on previous work, we predicted pre-SMA involvement in the selection/initiation of motor chunks, and this was confirmed by our results. The pre-SMA was further observed to be more involved in more complex than in simpler sequences, while no evidence was found for pre-SMA involvement in direct stimulus-response translations or associative learning processes. In conclusion, support is provided for the dual processor model, and for pre-SMA involvement in the initiation of motor chunks. Copyright © 2014 Elsevier Ltd. All rights reserved.

Human action classification using procrustes shape theory

NASA Astrophysics Data System (ADS)

Cho, Wanhyun; Kim, Sangkyoon; Park, Soonyoung; Lee, Myungeun

2015-02-01

In this paper, we propose new method that can classify a human action using Procrustes shape theory. First, we extract a pre-shape configuration vector of landmarks from each frame of an image sequence representing an arbitrary human action, and then we have derived the Procrustes fit vector for pre-shape configuration vector. Second, we extract a set of pre-shape vectors from tanning sample stored at database, and we compute a Procrustes mean shape vector for these preshape vectors. Third, we extract a sequence of the pre-shape vectors from input video, and we project this sequence of pre-shape vectors on the tangent space with respect to the pole taking as a sequence of mean shape vectors corresponding with a target video. And we calculate the Procrustes distance between two sequences of the projection pre-shape vectors on the tangent space and the mean shape vectors. Finally, we classify the input video into the human action class with minimum Procrustes distance. We assess a performance of the proposed method using one public dataset, namely Weizmann human action dataset. Experimental results reveal that the proposed method performs very good on this dataset.

Cross-Specificities between cII-like Proteins and pRE-like Promoters of Lambdoid Bacteriophages

PubMed Central

Wulff, Daniel L.; Mahoney, Michael E.

1987-01-01

We have investigated the activation of transcription from the pRE promoters of phages λ, 21 and P22 by the λ and 21 cII proteins and the P22 c1 (cII-like) protein, using an in vivo system in which cII protein from a derepressed prophage activates transcription from a pRE DNA fragment on a multicopy plasmid. We find that each protein is highly specific for its own cognate pRE promoter, although measureable cross-reactions are observed. The primary recognition sequence for cII protein on λ pRE is a pair of TTGC repeat sequences in the sequence 5'-TTGCN 6TTGC-3' at the -35 region of the promoter. This same sequence is found in 21 pRE, while P22 pRE has the sequence 5'-TTGCN6TTGT-3', which is the same as that of λctr1, a pRE+ variant of λ. λctr1 pRE is half as active as λ + pRE when assayed with either the λ cII or the P22 c1 proteins. Therefore, the single base change in the P22 repeat sequence cannot explain why the P22 c1 protein is much more active with P22 pRE than λ p RE. The dya5 mutation, a G→A change at position -43 of pRE, makes pRE a stronger promoter when assayed with either the λ or 21 cII proteins or the P22 c1 protein. We conclude that efficient activation of a cII-dependent promoter by a cII protein requires sequence information in addition to the TTGC repeat sequences. We do not know the characteristics of the proteins which are responsible for the specificity of each protein for its own cognate promoter. However, λdya8, which has a Glu27→Lys alteration in the λ cII protein and a cII+ phenotype, results in a mutant cII protein that is much more highly specific than wild-type cII protein for its own cognate λ p RE promoter. This is especially remarkable because the dya8 amino acid alteration makes the helix-2 region (the region of the protein predicted to make contact with the phosphodiester backbone of the DNA) of λ cII protein conform exactly with the helix-2 region of the P22 c1 protein in both charge and charge distribution. PMID:2953649

Discovery and characterization of 3000+ main-sequence binaries from APOGEE spectra

NASA Astrophysics Data System (ADS)

El-Badry, Kareem; Ting, Yuan-Sen; Rix, Hans-Walter; Quataert, Eliot; Weisz, Daniel R.; Cargile, Phillip; Conroy, Charlie; Hogg, David W.; Bergemann, Maria; Liu, Chao

2018-05-01

We develop a data-driven spectral model for identifying and characterizing spatially unresolved multiple-star systems and apply it to APOGEE DR13 spectra of main-sequence stars. Binaries and triples are identified as targets whose spectra can be significantly better fit by a superposition of two or three model spectra, drawn from the same isochrone, than any single-star model. From an initial sample of ˜20 000 main-sequence targets, we identify ˜2500 binaries in which both the primary and secondary stars contribute detectably to the spectrum, simultaneously fitting for the velocities and stellar parameters of both components. We additionally identify and fit ˜200 triple systems, as well as ˜700 velocity-variable systems in which the secondary does not contribute detectably to the spectrum. Our model simplifies the process of simultaneously fitting single- or multi-epoch spectra with composite models and does not depend on a velocity offset between the two components of a binary, making it sensitive to traditionally undetectable systems with periods of hundreds or thousands of years. In agreement with conventional expectations, almost all the spectrally identified binaries with measured parallaxes fall above the main sequence in the colour-magnitude diagram. We find excellent agreement between spectrally and dynamically inferred mass ratios for the ˜600 binaries in which a dynamical mass ratio can be measured from multi-epoch radial velocities. We obtain full orbital solutions for 64 systems, including 14 close binaries within hierarchical triples. We make available catalogues of stellar parameters, abundances, mass ratios, and orbital parameters.

Fast selection of miRNA candidates based on large-scale pre-computed MFE sets of randomized sequences.

PubMed

Warris, Sven; Boymans, Sander; Muiser, Iwe; Noback, Michiel; Krijnen, Wim; Nap, Jan-Peter

2014-01-13

Small RNAs are important regulators of genome function, yet their prediction in genomes is still a major computational challenge. Statistical analyses of pre-miRNA sequences indicated that their 2D structure tends to have a minimal free energy (MFE) significantly lower than MFE values of equivalently randomized sequences with the same nucleotide composition, in contrast to other classes of non-coding RNA. The computation of many MFEs is, however, too intensive to allow for genome-wide screenings. Using a local grid infrastructure, MFE distributions of random sequences were pre-calculated on a large scale. These distributions follow a normal distribution and can be used to determine the MFE distribution for any given sequence composition by interpolation. It allows on-the-fly calculation of the normal distribution for any candidate sequence composition. The speedup achieved makes genome-wide screening with this characteristic of a pre-miRNA sequence practical. Although this particular property alone will not be able to distinguish miRNAs from other sequences sufficiently discriminative, the MFE-based P-value should be added to the parameters of choice to be included in the selection of potential miRNA candidates for experimental verification.

Modelling the 2013 North Aegean (Greece) seismic sequence: geometrical and frictional constraints, and aftershock probabilities

NASA Astrophysics Data System (ADS)

Karakostas, Vassilis; Papadimitriou, Eleftheria; Gospodinov, Dragomir

2014-04-01

The 2013 January 8 Mw 5.8 North Aegean earthquake sequence took place on one of the ENE-WSW trending parallel dextral strike slip fault branches in this area, in the continuation of 1968 large (M = 7.5) rupture. The source mechanism of the main event indicates predominantly strike slip faulting in agreement with what is expected from regional seismotectonics. It was the largest event to have occurred in the area since the establishment of the Hellenic Unified Seismological Network (HUSN), with an adequate number of stations in close distances and full azimuthal coverage, thus providing the chance of an exhaustive analysis of its aftershock sequence. The main shock was followed by a handful of aftershocks with M ≥ 4.0 and tens with M ≥ 3.0. Relocation was performed by using the recordings from HUSN and a proper crustal model for the area, along with time corrections in each station relative to the model used. Investigation of the spatial and temporal behaviour of seismicity revealed possible triggering of adjacent fault segments. Theoretical static stress changes from the main shock give a preliminary explanation for the aftershock distribution aside from the main rupture. The off-fault seismicity is perfectly explained if μ > 0.5 and B = 0.0, evidencing high fault friction. In an attempt to forecast occurrence probabilities of the strong events (Mw ≥ 5.0), estimations were performed following the Restricted Epidemic Type Aftershock Sequence (RETAS) model. The identified best-fitting MOF model was used to execute 1-d forecasts for such aftershocks and follow the probability evolution in time during the sequence. Forecasting was also implemented on the base of a temporal model of aftershock occurrence, different from the modified Omori formula (the ETAS model), which resulted in probability gain (though small) in strong aftershock forecasting for the beginning of the sequence.

Ground penetrating radar documents short-term near-surface hydrological changes around Old Faithful Geyser, Yellowstone National Park, USA

NASA Astrophysics Data System (ADS)

Lynne, Bridget Y.; Heasler, Henry; Jaworowski, Cheryl; Smith, Gary J.; Smith, Isaac J.; Foley, Duncan

2018-04-01

In April 2015, Ground Penetrating Radar (GPR) was used to characterize the shallow subsurface (< 5 m depth) of the western sinter slope immediately adjacent to Old Faithful Geyser and near the north side of an inferred geyser cavity. A series of time-sequence images were collected between two eruptions of Old Faithful Geyser. Each set of time-sequence GPR recordings consisted of four transects aligned to provide coverage near the potential location of the inferred 15 m deep geyser chamber. However, the deepest penetration we could achieve with a 200 MHz GPR antennae was 5 m. Seven time-sequence events were collected over a 48-minute interval to image changes in the near-surface, during pre- and post-eruptive cycles. Time-sequence GPR images revealed a series of possible micro-fractures in a highly porous siliceous sinter in the near-surface that fill and drain repetitively, immediately after an eruption and during the recharge period prior to the next main eruptive event.

Binaries among low-mass stars in nearby young moving groups

NASA Astrophysics Data System (ADS)

Janson, Markus; Durkan, Stephen; Hippler, Stefan; Dai, Xiaolin; Brandner, Wolfgang; Schlieder, Joshua; Bonnefoy, Mickaël; Henning, Thomas

2017-03-01

The solar galactic neighborhood contains a number of young co-moving associations of stars (known as young moving groups) with ages of 10-150 Myr, which are prime targets for a range of scientific studies, including direct imaging planet searches. The late-type stellar populations of such groups still remain in their pre-main sequence phase, and are thus well suited for purposes such as isochronal dating. Close binaries are particularly useful in this regard since they allow for a model-independent dynamical mass determination. Here we present a dedicated effort to identify new close binaries in nearby young moving groups, through high-resolution imaging with the AstraLux Sur Lucky Imaging camera. We surveyed 181 targets, resulting in the detection of 61 companions or candidates, of which 38 are new discoveries. An interesting example of such a case is 2MASS J00302572-6236015 AB, which is a high-probability member of the Tucana-Horologium moving group, and has an estimated orbital period of less than 10 yr. Among the previously known objects is a serendipitous detection of the deuterium burning boundary circumbinary companion 2MASS J01033563-5515561 (AB)b in the z' band, thereby extending the spectral coverage for this object down to near-visible wavelengths. Based on observations collected at the European Southern Observatory, Chile (Programs 096.C-0243 and 097.C-0135).Tables 1-3 are only available at the CDS via anonymous ftp to http://cdsarc.u-strasbg.fr (http://130.79.128.5) or via http://cdsarc.u-strasbg.fr/viz-bin/qcat?J/A+A/599/A70

40 CFR 92.124 - Test sequence; general requirements.

Code of Federal Regulations, 2012 CFR

2012-07-01

.... (e) Pre-test engine measurements (e.g., idle and throttle notch speeds, fuel flows, etc.), pre-test engine performance checks (e.g., verification of engine power, etc.) and pre-test system calibrations (e... 40 Protection of Environment 21 2012-07-01 2012-07-01 false Test sequence; general requirements...

40 CFR 92.124 - Test sequence; general requirements.

Code of Federal Regulations, 2014 CFR

2014-07-01

.... (e) Pre-test engine measurements (e.g., idle and throttle notch speeds, fuel flows, etc.), pre-test engine performance checks (e.g., verification of engine power, etc.) and pre-test system calibrations (e... 40 Protection of Environment 20 2014-07-01 2013-07-01 true Test sequence; general requirements. 92...

40 CFR 92.124 - Test sequence; general requirements.

Code of Federal Regulations, 2010 CFR

2010-07-01

.... (e) Pre-test engine measurements (e.g., idle and throttle notch speeds, fuel flows, etc.), pre-test engine performance checks (e.g., verification of engine power, etc.) and pre-test system calibrations (e... 40 Protection of Environment 20 2010-07-01 2010-07-01 false Test sequence; general requirements...

40 CFR 92.124 - Test sequence; general requirements.

Code of Federal Regulations, 2013 CFR

2013-07-01

.... (e) Pre-test engine measurements (e.g., idle and throttle notch speeds, fuel flows, etc.), pre-test engine performance checks (e.g., verification of engine power, etc.) and pre-test system calibrations (e... 40 Protection of Environment 21 2013-07-01 2013-07-01 false Test sequence; general requirements...

40 CFR 92.124 - Test sequence; general requirements.

Code of Federal Regulations, 2011 CFR

2011-07-01

.... (e) Pre-test engine measurements (e.g., idle and throttle notch speeds, fuel flows, etc.), pre-test engine performance checks (e.g., verification of engine power, etc.) and pre-test system calibrations (e... 40 Protection of Environment 20 2011-07-01 2011-07-01 false Test sequence; general requirements...

Spectroscopic observations of the optical counterpart of Centaurus X-4

NASA Technical Reports Server (NTRS)

Van Paradijs, J.; Verbunt, F.; Van Der Linden, T.; Pedersen, H.; Wamsteker, W.

1980-01-01

The optical spectrum of the transient X-ray burst source Centaurus X-4 was observed about 5 weeks after the source reached its maximum. The brightness of the optical counterpart had decreased to V = 18.2, and the star had become appreciably redder (B - V = 0.7) compared to its color at maximum. The spectrum of Centaurus X-4 is similar to that of cataclysmic variables showing strong emission lines of H-1 and weaker lines of He-1 and He-2. The N03 lambda 4640 line is not visible. The continuum energy distribution of Centaurus X-4 shows the presence of a main-sequence star in the system, with spectral type between K3 and K7. This is consistent with the orbital period of 8.2 hr proposed by Kaluzienski et al (1980), if the main-sequence star is close to filling its Roche lobe.

From protein sequence to dynamics and disorder with DynaMine.

PubMed

Cilia, Elisa; Pancsa, Rita; Tompa, Peter; Lenaerts, Tom; Vranken, Wim F

2013-01-01

Protein function and dynamics are closely related; however, accurate dynamics information is difficult to obtain. Here based on a carefully assembled data set derived from experimental data for proteins in solution, we quantify backbone dynamics properties on the amino-acid level and develop DynaMine--a fast, high-quality predictor of protein backbone dynamics. DynaMine uses only protein sequence information as input and shows great potential in distinguishing regions of different structural organization, such as folded domains, disordered linkers, molten globules and pre-structured binding motifs of different sizes. It also identifies disordered regions within proteins with an accuracy comparable to the most sophisticated existing predictors, without depending on prior disorder knowledge or three-dimensional structural information. DynaMine provides molecular biologists with an important new method that grasps the dynamical characteristics of any protein of interest, as we show here for human p53 and E1A from human adenovirus 5.

The Age-Related Properties of the HD 98800 System

NASA Technical Reports Server (NTRS)

Soderblom, David R.; Henry, Todd J.; Shetrone, Matthew D.; Jones, Burton F.; Saar, Steven H.

1996-01-01

We present optical spectroscopy of the field K star system HD 98800, which has been found to have significant infrared emission from circumstellar material. The lithium abundances of the stars in HD 98800 are well above those of Pleiades of similar color, but activity levels and rotation in these stars are at or below Pleiades level. Thus, it is not yet possible to say whether HD 98800 is or is not a pre-main-sequence system, and it is possible that its components are on or near the zero-age main sequence. However, the two visible objects that make up HD 98800 both have high levels of lithium and activity, strongly suggesting that they are physically related to one another. As shown by Torres and coworkers, having these stars physically tied implies that their relative orbit is highly eccentric and highly inclined to our line of sight, and it also means that we are viewing the HD 98800 system at an unusual time in its orbit.

Stress and Strain Rates from Faults Reconstructed by Earthquakes Relocalization

NASA Astrophysics Data System (ADS)

Morra, G.; Chiaraluce, L.; Di Stefano, R.; Michele, M.; Cambiotti, G.; Yuen, D. A.; Brunsvik, B.

2017-12-01

Recurrence of main earthquakes on the same fault depends on kinematic setting, hosting lithologies and fault geometry and population. Northern and central Italy transitioned from convergence to post-orogenic extension. This has produced a unique and very complex tectonic setting characterized by superimposed normal faults, crossing different geologic domains, that allows to investigate a variety of seismic manifestations. In the past twenty years three seismic sequences (1997 Colfiorito, 2009 L'Aquila and 2016-17 Amatrice-Norcia-Visso) activated a 150km long normal fault system located between the central and northern apennines and allowing the recordings of thousands of seismic events. Both the 1997 and the 2009 main shocks were preceded by a series of small pre-shocks occurring in proximity to the future largest events. It has been proposed and modelled that the seismicity pattern of the two foreshocks sequences was caused by active dilatancy phenomenon, due to fluid flow in the source area. Seismic activity has continued intensively until three events with 6.0

Stability of operational taxonomic units: an important but neglected property for analyzing microbial diversity.

PubMed

He, Yan; Caporaso, J Gregory; Jiang, Xiao-Tao; Sheng, Hua-Fang; Huse, Susan M; Rideout, Jai Ram; Edgar, Robert C; Kopylova, Evguenia; Walters, William A; Knight, Rob; Zhou, Hong-Wei

2015-01-01

The operational taxonomic unit (OTU) is widely used in microbial ecology. Reproducibility in microbial ecology research depends on the reliability of OTU-based 16S ribosomal subunit RNA (rRNA) analyses. Here, we report that many hierarchical and greedy clustering methods produce unstable OTUs, with membership that depends on the number of sequences clustered. If OTUs are regenerated with additional sequences or samples, sequences originally assigned to a given OTU can be split into different OTUs. Alternatively, sequences assigned to different OTUs can be merged into a single OTU. This OTU instability affects alpha-diversity analyses such as rarefaction curves, beta-diversity analyses such as distance-based ordination (for example, Principal Coordinate Analysis (PCoA)), and the identification of differentially represented OTUs. Our results show that the proportion of unstable OTUs varies for different clustering methods. We found that the closed-reference method is the only one that produces completely stable OTUs, with the caveat that sequences that do not match a pre-existing reference sequence collection are discarded. As a compromise to the factors listed above, we propose using an open-reference method to enhance OTU stability. This type of method clusters sequences against a database and includes unmatched sequences by clustering them via a relatively stable de novo clustering method. OTU stability is an important consideration when analyzing microbial diversity and is a feature that should be taken into account during the development of novel OTU clustering methods.

Formation of Bipolar Lobes by Jets

NASA Astrophysics Data System (ADS)

Soker, Noam

2002-04-01

I conduct an analytical study of the interaction of jets, or a collimated fast wind (CFW), with a previously blown asymptotic giant branch (AGB) slow wind. Such jets (or CFWs) are supposedly formed when a compact companion, a main-sequence star, or a white dwarf accretes mass from the AGB star, forms an accretion disk, and blows two jets. This type of flow, which I think shapes bipolar planetary nebulae (PNs), requires three-dimensional gasdynamical simulations, which are limited in the parameter space they can cover. By imposing several simplifying assumptions, I derive simple expressions which reproduce some basic properties of lobes in bipolar PNs and which can be used to guide future numerical simulations. I quantitatively apply the results to two proto-PNs. I show that the jet interaction with the slow wind can form lobes which are narrow close to, and far away from, the central binary system, and which are wider somewhere in between. Jets that are recollimated and have constant cross section can form cylindrical lobes with constant diameter, as observed in several bipolar PNs. Close to their source, jets blown by main-sequence companions are radiative; only further out they become adiabatic, i.e., they form high-temperature, low-density bubbles that inflate the lobes.

NMR-based diffusion pore imaging by double wave vector measurements.

PubMed

Kuder, Tristan Anselm; Laun, Frederik Bernd

2013-09-01

One main interest of nuclear magnetic resonance (NMR) diffusion experiments is the investigation of boundaries such as cell membranes hindering the diffusion process. NMR diffusion measurements allow collecting the signal from the whole sample. This mainly eliminates the problem of vanishing signal at increasing resolution. It has been a longstanding question if, in principle, the exact shape of closed pores can be determined by NMR diffusion measurements. In this work, we present a method using short diffusion gradient pulses only, which is able to reveal the shape of arbitrary closed pores without relying on a priori knowledge. In comparison to former approaches, the method has reduced demands on relaxation times due to faster convergence to the diffusion long-time limit and allows for a more flexible NMR sequence design, because, e.g., stimulated echoes can be used. Copyright © 2012 Wiley Periodicals, Inc.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mello, M.R.; Soldan, A.L.; Maxwell, J.R.

A geochemical and biological marker investigation of a variety of oils from offshore Brazil and west Africa, ranging in age from Lower Cretaceous to Tertiary, has been done, with the following aims: (1) assessing the depositional environment of source rocks, (2) correlating the reservoired oils, (3) comparing the Brazilian oils with their west African counterparts. The approach was based in stable isotope data; bulk, elemental, and hydrous pyrolysis results; and molecular studies involving quantitative geological marker investigations of alkanes using GC-MS and GC-MS-MS. The results reveal similarities between groups of oils from each side of the Atlantic and suggest anmore » origin from source rocks deposited in five types of depositional environment: lacustrine fresh water, lacustrine saline water, marine evaporitic/carbonate, restricted marine anoxic, and marine deltaic. In west Africa, the Upper Cretaceous marine anoxic succession (Cenomanian-Santonian) appears to be a major oil producer, but in Brazil it is generally immature. The Brazilian offshore oils have arisen mainly from the pre-salt sequence, whereas the African oils show a balance between origins from the pre-salt and marine sequences. The integration of the geochemical and geological data indicate that new frontiers of hydrocarbon exploration in the west African basins must consider the Tertiary reservoirs in the offshore area of Niger Delta, the reservoirs of the rift sequences in the shallow-water areas of south Gabon, Congo, and Cuanza basins, and the reservoirs from the drift sequences (post-salt) in the deep-water areas of Gabon, Congo Cabinda, and Cuanza basins.« less

Software for pre-processing Illumina next-generation sequencing short read sequences

PubMed Central

2014-01-01

Background When compared to Sanger sequencing technology, next-generation sequencing (NGS) technologies are hindered by shorter sequence read length, higher base-call error rate, non-uniform coverage, and platform-specific sequencing artifacts. These characteristics lower the quality of their downstream analyses, e.g. de novo and reference-based assembly, by introducing sequencing artifacts and errors that may contribute to incorrect interpretation of data. Although many tools have been developed for quality control and pre-processing of NGS data, none of them provide flexible and comprehensive trimming options in conjunction with parallel processing to expedite pre-processing of large NGS datasets. Methods We developed ngsShoRT (next-generation sequencing Short Reads Trimmer), a flexible and comprehensive open-source software package written in Perl that provides a set of algorithms commonly used for pre-processing NGS short read sequences. We compared the features and performance of ngsShoRT with existing tools: CutAdapt, NGS QC Toolkit and Trimmomatic. We also compared the effects of using pre-processed short read sequences generated by different algorithms on de novo and reference-based assembly for three different genomes: Caenorhabditis elegans, Saccharomyces cerevisiae S288c, and Escherichia coli O157 H7. Results Several combinations of ngsShoRT algorithms were tested on publicly available Illumina GA II, HiSeq 2000, and MiSeq eukaryotic and bacteria genomic short read sequences with the focus on removing sequencing artifacts and low-quality reads and/or bases. Our results show that across three organisms and three sequencing platforms, trimming improved the mean quality scores of trimmed sequences. Using trimmed sequences for de novo and reference-based assembly improved assembly quality as well as assembler performance. In general, ngsShoRT outperformed comparable trimming tools in terms of trimming speed and improvement of de novo and reference-based assembly as measured by assembly contiguity and correctness. Conclusions Trimming of short read sequences can improve the quality of de novo and reference-based assembly and assembler performance. The parallel processing capability of ngsShoRT reduces trimming time and improves the memory efficiency when dealing with large datasets. We recommend combining sequencing artifacts removal, and quality score based read filtering and base trimming as the most consistent method for improving sequence quality and downstream assemblies. ngsShoRT source code, user guide and tutorial are available at http://research.bioinformatics.udel.edu/genomics/ngsShoRT/. ngsShoRT can be incorporated as a pre-processing step in genome and transcriptome assembly projects. PMID:24955109

Analysis of the complete genome of subgroup A' hepatitis B virus isolates from South Africa.

PubMed

Kramvis, Anna; Weitzmann, Louise; Owiredu, William K B A; Kew, Michael C

2002-04-01

A phylogenetic analysis is presented of six complete and seven pre-S1/S2/S gene sequences of hepatitis B virus (HBV) isolates from South Africa. Five of the full-length sequences and all of the pre-S2/S sequences have been previously reported. Four of the six complete genomes and three of the five incomplete sequences clustered with subgroup A', a unique segment of genotype A of HBV previously identified in 60% of South African isolates using analysis of the pre-S2/S region alone. This separation was also evident when the polymerase open reading frame was analysed, but not on analysis of either the X or pre-core/core genes. Amino acids were identified in the pre-S1 and polymerase regions specific to subgroup A'. In common with genotype D, 10 of 11 genotype A South African isolates had an 11 amino acid deletion in the amino end of the pre-S1 region. This deletion is also found in hepadnaviruses from non-human primates.

3D Model of the San Emidio Geothermal Area

DOE Data Explorer

James E. Faulds

2013-12-31

The San Emidio geothermal system is characterized by a left-step in a west-dipping normal fault system that bounds the western side of the Lake Range. The 3D geologic model consists of 5 geologic units and 55 faults. Overlying Jurrassic-Triassic metasedimentary basement is a ~500 m-1000 m thick section of the Miocene lower Pyramid sequence, pre- syn-extensional Quaternary sedimentary rocks and post-extensional Quaternary rocks. 15-30º eastward dip of the stratigraphy is controlled by the predominant west-dipping fault set. Both geothermal production and injection are concentrated north of the step over in an area of closely spaced west dipping normal faults.

Structure-from-motion for MAV image sequence analysis with photogrammetric applications

NASA Astrophysics Data System (ADS)

Schönberger, J. L.; Fraundorfer, F.; Frahm, J.-M.

2014-08-01

MAV systems have found increased attention in the photogrammetric community as an (autonomous) image acquisition platform for accurate 3D reconstruction. For an accurate reconstruction in feasible time, the acquired imagery requires specialized SfM software. Current systems typically use high-resolution sensors in pre-planned flight missions from far distance. We describe and evaluate a new SfM pipeline specifically designed for sequential, close-distance, and low-resolution imagery from mobile cameras with relatively high frame-rate and high overlap. Experiments demonstrate reduced computational complexity by leveraging the temporal consistency, comparable accuracy and point density with respect to state-of-the-art systems.

Enhancing Protein Disulfide Bond Cleavage by UV Excitation and Electron Capture Dissociation for Top-Down Mass Spectrometry.

PubMed

Wongkongkathep, Piriya; Li, Huilin; Zhang, Xing; Loo, Rachel R Ogorzalek; Julian, Ryan R; Loo, Joseph A

2015-11-15

The application of ion pre-activation with 266 nm ultraviolet (UV) laser irradiation combined with electron capture dissociation (ECD) is demonstrated to enhance top-down mass spectrometry sequence coverage of disulfide bond containing proteins. UV-based activation can homolytically cleave a disulfide bond to yield two separated thiol radicals. Activated ECD experiments of insulin and ribonuclease A containing three and four disulfide bonds, respectively, were performed. UV-activation in combination with ECD allowed the three disulfide bonds of insulin to be cleaved and the overall sequence coverage to be increased. For the larger sized ribonuclease A with four disulfide bonds, irradiation from an infrared laser (10.6 µm) to disrupt non-covalent interactions was combined with UV-activation to facilitate the cleavage of up to three disulfide bonds. Preferences for disulfide bond cleavage are dependent on protein structure and sequence. Disulfide bonds can reform if the generated radicals remain in close proximity. By varying the time delay between the UV-activation and the ECD events, it was determined that disulfide bonds reform within 10-100 msec after their UV-homolytic cleavage.

Fast selection of miRNA candidates based on large-scale pre-computed MFE sets of randomized sequences

PubMed Central

2014-01-01

Background Small RNAs are important regulators of genome function, yet their prediction in genomes is still a major computational challenge. Statistical analyses of pre-miRNA sequences indicated that their 2D structure tends to have a minimal free energy (MFE) significantly lower than MFE values of equivalently randomized sequences with the same nucleotide composition, in contrast to other classes of non-coding RNA. The computation of many MFEs is, however, too intensive to allow for genome-wide screenings. Results Using a local grid infrastructure, MFE distributions of random sequences were pre-calculated on a large scale. These distributions follow a normal distribution and can be used to determine the MFE distribution for any given sequence composition by interpolation. It allows on-the-fly calculation of the normal distribution for any candidate sequence composition. Conclusion The speedup achieved makes genome-wide screening with this characteristic of a pre-miRNA sequence practical. Although this particular property alone will not be able to distinguish miRNAs from other sequences sufficiently discriminative, the MFE-based P-value should be added to the parameters of choice to be included in the selection of potential miRNA candidates for experimental verification. PMID:24418292

Mycobacterium tuberculosis and whole-genome sequencing: how close are we to unleashing its full potential?

PubMed

Satta, G; Lipman, M; Smith, G P; Arnold, C; Kon, O M; McHugh, T D

2018-06-01

Nearly two decades after completion of the genome sequence of Mycobacterium tuberculosis (MTB), and with the advent of next generation sequencing technologies (NGS), whole-genome sequencing (WGS) has been applied to a wide range of clinical scenarios. Starting in 2017, England is the first country in the world to pioneer its use on a national scale for the diagnosis of tuberculosis, detection of drug resistance, and typing of MTB. This narrative review critically analyses the current applications of WGS for MTB and explains how close we are to realizing its full potential as a diagnostic, epidemiologic, and research tool. We searched for reports (both original articles and reviews) published in English up to 31 May 2017, with combinations of the following keywords: whole-genome sequencing, Mycobacterium, and tuberculosis. MEDLINE, Embase, and Scopus were used as search engines. We included articles that covered different aspects of whole-genome sequencing in relation to MTB. This review focuses on three main themes: the role of WGS for the prediction of drug susceptibility, MTB outbreak investigation and genetic diversity, and research applications of NGS. Many of the original expectations have been accomplished, and we believe that with its unprecedented sensitivity and power, WGS has the potential to address many unanswered questions in the near future. However, caution is still needed when interpreting WGS data as there are some important limitations to be aware of, from correct interpretation of drug susceptibilities to the bioinformatic support needed. Copyright © 2017 European Society of Clinical Microbiology and Infectious Diseases. Published by Elsevier Ltd. All rights reserved.

GyrB sequence analysis and MALDI-TOF MS as identification tools for plant pathogenic Clavibacter.

PubMed

Zaluga, Joanna; Heylen, Kim; Van Hoorde, Koenraad; Hoste, Bart; Van Vaerenbergh, Johan; Maes, Martine; De Vos, Paul

2011-09-01

The bacterial genus Clavibacter has only one species, Clavibacter michiganensis, containing five subspecies. All five are plant pathogens, among which three are recognized as quarantine pests (mentioned on the EPPO A2 list). Prevention of their introduction and epidemic outbreaks requires a reliable and accurate identification. Currently, identification of these bacteria is time consuming and often problematic, mainly because of cross-reactions with other plant-associated bacteria in immunological tests and false-negative results in PCR detection methods. Furthermore, distinguishing closely related subspecies is not straightforward. This study aimed at evaluating the use of matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) and a fragment of the gyrB sequence for the reliable and fast identification of the Clavibacter subspecies. Amplification and sequencing of gyrB using a single primer set had sufficient resolution and specificity to identify each subspecies based on both sequence similarities in cluster analyses and specific signatures within the sequences. All five subspecies also generated distinct and reproducible MALDI-TOF MS profiles, with unique and specific ion peaks for each subspecies, which could be used as biomarkers for identification. Results from both methods were in agreement and were able to distinguish the five Clavibacter subspecies from each other and from representatives of closely related Rathayibacter, Leifsonia or Curtobacterium species. Our study suggests that proteomic analysis using MALDI-TOF MS and gyrB sequence are powerful diagnostic tools for the accurate identification of Clavibacter plant pathogens. Copyright © 2011 Elsevier GmbH. All rights reserved.

Australian wild rice reveals pre-domestication origin of polymorphism deserts in rice genome.

PubMed

Krishnan S, Gopala; Waters, Daniel L E; Henry, Robert J

2014-01-01

Rice is a major source of human food with a predominantly Asian production base. Domestication involved selection of traits that are desirable for agriculture and to human consumers. Wild relatives of crop plants are a source of useful variation which is of immense value for crop improvement. Australian wild rices have been isolated from the impacts of domestication in Asia and represents a source of novel diversity for global rice improvement. Oryza rufipogon is a perennial wild progenitor of cultivated rice. Oryza meridionalis is a related annual species in Australia. We have examined the sequence of the genomes of AA genome wild rices from Australia that are close relatives of cultivated rice through whole genome re-sequencing. Assembly of the resequencing data to the O. sativa ssp. japonica cv. Nipponbare shows that Australian wild rices possess 2.5 times more single nucleotide polymorphisms than in the Asian wild rice and cultivated O. sativa ssp. indica. Analysis of the genome of domesticated rice reveals regions of low diversity that show very little variation (polymorphism deserts). Both the perennial and annual wild rice from Australia show a high degree of conservation of sequence with that found in cultivated rice in the same 4.58 Mbp region on chromosome 5, which suggests that some of the 'polymorphism deserts' in this and other parts of the rice genome may have originated prior to domestication due to natural selection. Analysis of genes in the 'polymorphism deserts' indicates that this selection may have been due to biotic or abiotic stress in the environment of early rice relatives. Despite having closely related sequences in these genome regions, the Australian wild populations represent an invaluable source of diversity supporting rice food security.

AN OBJECTIVE DEFINITION FOR THE MAIN SEQUENCE OF STAR-FORMING GALAXIES

DOE Office of Scientific and Technical Information (OSTI.GOV)

Renzini, Alvio; Peng, Ying-jie, E-mail: alvio.renzini@oapd.inaf.it, E-mail: y.peng@mrao.cam.ac.uk

The main sequence (MS) of star-forming (SF) galaxies plays a fundamental role in driving galaxy evolution and our efforts to understand it. However, different studies find significant differences in the normalization, slope, and shape of the MS. These discrepancies arise mainly from the different selection criteria adopted to isolate SF galaxies, which may include or exclude galaxies with a specific star formation rate (SFR) substantially below the MS value. To obviate this limitation of all current criteria, we propose an objective definition of the MS that does not rely at all on a pre-selection of SF galaxies. Constructing the 3Dmore » SFR–mass–number plot, the MS is then defined as the ridge line of the SF peak, as illustrated with various figures. The advantages of such a definition are manifold. If generally adopted, it will facilitate the inter-comparison of results from different groups using the same SFR and stellar mass diagnostics, or it will highlight the relative systematics of different diagnostics. All of this could help to understand MS galaxies as systems in a quasi-steady state equilibrium and would also provide a more objective criterion for identifying quenching galaxies.« less

BP Piscium: its flaring disc imaged with SPHERE/ZIMPOL★

NASA Astrophysics Data System (ADS)

de Boer, J.; Girard, J. H.; Canovas, H.; Min, M.; Sitko, M.; Ginski, C.; Jeffers, S. V.; Mawet, D.; Milli, J.; Rodenhuis, M.; Snik, F.; Keller, C. U.

2017-03-01

Whether BP Piscium (BP Psc) is either a pre-main sequence T Tauri star at d ≈ 80 pc, or a post-main sequence G giant at d ≈ 300 pc is still not clear. As a first-ascent giant, it is the first to be observed with a molecular and dust disc. Alternatively, BP Psc would be among the nearest T Tauri stars with a protoplanetary disc (PPD). We investigate whether the disc geometry resembles typical PPDs, by comparing polarimetric images with radiative transfer models. Our Very Large Telescope/Spectro-Polarimetric High-contrast Exoplanet REsearch (SPHERE)/Zurich IMaging Polarimeter (ZIMPOL) observations allow us to perform polarimetric differential imaging, reference star differential imaging, and Richardson-Lucy deconvolution. We present the first visible light polarization and intensity images of the disc of BP Psc. Our deconvolution confirms the disc shape as detected before, mainly showing the southern side of the disc. In polarized intensity the disc is imaged at larger detail and also shows the northern side, giving it the typical shape of high-inclination flared discs. We explain the observed disc features by retrieving the large-scale geometry with MCMAX radiative transfer modelling, which yields a strongly flared model, atypical for discs of T Tauri stars.

Dust in circumstellar disks

NASA Astrophysics Data System (ADS)

Rodmann, Jens

2006-02-01

This thesis presents observational and theoretical studies of the size and spatial distribution of dust particles in circumstellar disks. Using millimetre interferometric observations of optically thick disks around T Tauri stars, I provide conclusive evidence for the presence of millimetre- to centimetre-sized dust aggregates. These findings demonstrate that dust grain growth to pebble-sized dust particles is completed within less than 1 Myr in the outer disks around low-mass pre-main-sequence stars. The modelling of the infrared spectral energy distributions of several solar-type main-sequence stars and their associated circumstellar debris disks reveals the ubiquity of inner gaps devoid of substantial amounts of dust among Vega-type infrared excess sources. It is argued that the absence of circumstellar material in the inner disks is most likely the result of the gravitational influence of a large planet and/or a lack of dust-producing minor bodies in the dust-free region. Finally, I describe a numerical model to simulate the dynamical evolution of dust particles in debris disks, taking into account the gravitational perturbations by planets, photon radiation pressure, and dissipative drag forces due to the Poynting-Robertson effect and stellar wind. The validity of the code it established by several tests and comparison to semi-analytic approximations. The debris disk model is applied to simulate the main structural features of a ring of circumstellar material around the main-sequence star HD 181327. The best agreement between model and observation is achieved for dust grains a few tens of microns in size locked in the 1:1 resonance with a Jupiter-mass planet (or above) on a circular orbit.

Design and implementation of a synthetic pre-miR switch for controlling miRNA biogenesis in mammals

PubMed Central

Atanasov, Janina; Groher, Florian

2017-01-01

Abstract Synthetic RNA-based systems have increasingly been used for the regulation of eukaryotic gene expression. Due to their structural properties, riboregulators provide a convenient basis for the development of ligand-dependent controllable systems. Here, we demonstrate reversible conditional control of miRNA biogenesis with an aptamer domain as a sensing unit connected to a natural miRNA precursor for the first time. For the design of the pre-miR switch, we replaced the natural terminal loop with the TetR aptamer. Thus, the TetR aptamer was positioned close to the Dicer cleavage sites, which allowed sterical control over pre-miR processing by Dicer. Our design proved to be highly versatile, allowing us to regulate the biogenesis of three structurally different miRNAs: miR-126, -34a and -199a. Dicer cleavage was inhibited up to 143-fold via co-expression of the TetR protein, yet could be completely restored upon addition of doxycycline. Moreover, we showed the functionality of the pre-miR switches for gene regulation through the interaction of the respective miRNA with its specific target sequence. Our designed device is capable of robust and reversible control of miRNA abundance. Thus, we offer a novel investigational tool for functional miRNA analysis. PMID:29036355

Mapping sequence performed during the STS-121 R-Bar Pitch Maneuver

NASA Image and Video Library

2006-07-06

ISS013-E-47629 (6 July 2006) --- A close-up view of Space Shuttle Discovery's tail section is featured in this image photographed by an Expedition 13 crewmember on the International Space Station during STS-121 R-Pitch Maneuver survey on Flight Day 3. Visible are the shuttle's main engines, vertical stabilizer, orbital maneuvering system (OMS) pods, reaction control system (RCS) jets and a portion of payload bay door radiator and wings.

AGN contribution to the total IR luminosity in Herschel selected galaxies out to z~1.5

NASA Astrophysics Data System (ADS)

Baronchelli, Ivano; Scarlata, Claudia; Rodighiero, Giulia; Berta, Stefano; Sedgwick, Christopher; Vaccari, Mattia; Franceschini, Alberto; Urrutia, Tanya; Malkan, Matthew Arnold; Salvato, Mara; Bonato, Matteo; Serjeant, Stephen; Pearson, Chris; Marchetti, Lucia

2016-01-01

In the past decade, a growing amount of evidence suggests a tight link between the growth of Active Galactic Nuclei (AGN) and that of their host galaxies. X-ray studies on the Super Massive Black Holes (SMBHs) activity indicate the existence of a Black Hole Accretion Rate (BHAR) "main sequence", similar to the "main sequence" observed in star-forming galaxies, between the star-formation rate (SFR) and stellar mass (M*). We use the multi wavelength data from the SIMES survey to study the optical to sub-mm spectral energy distribution (SED) of galaxies identified at 250 μm by the Herschel Space Observatory. In particular, for galaxies in the 0.2-1.5 redshift range, we explore the relations among galaxy's stellar mass, SFR, and SMBH accretion rate. The deep Spitzer-IRAC/MIPS (3.6, 4.5 and 24 μm) together with the deep AKARI-IRC observations (7, 11 and 15 μm) allow us to constrain the critical spectral region where the dusty torus emission of AGNs is more prominent. Thanks to the Herschel-SPIRE observations, we can also precisely measure the SFR from the bolometric (i.e. 8-1000 μm) far-IR emission. Using this multi-wavelength approach we confirm the existence, at z<0.5, of the M*-BHAR "main sequence". The measured average ratio between BHAR and SFR is close to the value required to maintain the SMBH-to-M* ratio of ˜103 and decreases at higher specific SFRs (SSFR=SFR/M*). Finally, combining our observations with literature results, we show that the slope of the BHAR main sequence is evolving with redshift between z~0 and z~2.

ASTEROSEISMIC ANALYSIS OF THE PRE-MAIN-SEQUENCE STARS IN NGC 2264

DOE Office of Scientific and Technical Information (OSTI.GOV)

Guenther, D. B.; Casey, M. P.; Kallinger, T.

2009-10-20

NGC 2264 is a young open cluster lying above the Galactic plane in which six variable stars have previously been identified as possible pre-main-sequence (PMS) pulsators. Their oscillation spectra are relatively sparse with each star having from 2 to 12 unambiguous frequency identifications based on Microvariability and Oscillations of Stars satellite and multi-site ground-based photometry. We describe our efforts to find classical PMS stellar models (i.e., models evolved from the Hayashi track) whose oscillation spectra match the observed frequencies. We find model eigenspectra that match the observed frequencies and are consistent with the stars' locations in the HR diagram formore » the three faintest of the six stars. Not all the frequencies found in spectra of the three brightest stars can be matched to classical PMS model spectra possibly because of effects not included in our PMS models such as chemical and angular momentum stratification in the outer layers of the star. All the oscillation spectra contain both radial and nonradial p-modes. We argue that the PMS pulsating stars divide into two groups depending on whether or not they have undergone complete mixing (i.e., have gone through a Hayashi phase). Lower mass stars that do evolve through a Hayashi phase have oscillation spectra predicted by classical PMS models, whereas more massive stars that do not, retain mass infall effects in their surface layers and are not well modeled by classical PMS models.« less

Photometric and spectroscopic study of low mass embedded star clusters in reflection nebulae

NASA Astrophysics Data System (ADS)

Soares, J. B.; Bica, E.; Ahumada, A. V.; Clariá, J. J.

2005-02-01

An analysis of the candidate embedded stellar systems in the reflection nebulae vdBH-RN 26, vdBH-RN} 38, vdBH-RN} 53a, GGD 20, ESO 95-RN 18 and NGC 6595 is presented. Optical spectroscopic data from CASLEO (Argentina) in conjunction with near infrared photometry from the 2MASS Point Source Catalogue were employed. The analysis is based on source surface density, colour-colour and colour-magnitude diagrams together with theoretical pre-main sequence isochrones. We take into account the field population affecting the analysis by carrying out a statistical subtraction. The fundamental parameters for the stellar systems were derived. The resulting ages are in the range 1-4 Myr and the objects are dominated by pre-main sequence stars. The observed masses locked in the clusters are less than 25 M⊙. The studied systems have no stars of spectral types earlier than B, indicating that star clusters do not necessarily evolve through an HII region phase. The relatively small locked mass combined with the fact that they are not numerous in catalogues suggests that these low mass clusters are not important donors of stars to the field populations. Based on observations made at Complejo Astronómico El Leoncito, which is operated under agreement between the Consejo Nacional de Investigaciones Científicas y Técnicas de la República Argentina and the National Universities of La Plata, Córdoba and San Juan, Argentina.

X-ray Emission from Pre-Main-Sequence Stars - Testing the Solar Analogy

NASA Technical Reports Server (NTRS)

Skinner, Stephen L.

2000-01-01

This LTSA award funded my research on the origin of stellar X-ray emission and the validity of the solar-stellar analogy. This research broadly addresses the relevance of our current understanding of solar X-ray physics to the interpretation of X-ray emission from stars in general. During the past five years the emphasis has been on space-based X-ray observations of very young stars in star-forming regions (T Tauri stars and protostars), cool solar-like G stars, and evolved high-mass Wolf-Rayet (WR) stars. These observations were carried out primarily with the ASCA and ROSAT space-based observatories (and most recently with Chandra), supplemented by ground-based observations. This research has focused on the identification of physical processes that are responsible for the high levels of X-ray emission seen in pre-main-sequence (PMS) stars, active cool stars, and WR stars. A related issue is how the X-ray emission of such stars changes over time, both on short timescales of days to years and on evolutionary timescales of millions of years. In the case of the Sun it is known that magnetic fields play a key role in the production of X-rays by confining the coronal plasma in loop-like structures where it is heated to temperatures of several million K. The extent to which the magnetically-confined corona interpretation can be applied to other X-ray emitting stars is the key issue that drives the research summarized here.

Effects of disc mid-plane evolution on CO snowline location

NASA Astrophysics Data System (ADS)

Panić, O.; Min, M.

2017-05-01

Temperature changes in the planet forming disc mid-planes carry important physico-chemical consequences, such as the effect on the locations of the condensation fronts of molecules - the snowlines. Snowlines impose major chemical gradients and possibly foster grain growth. The aim of this paper is to understand how disc mid-plane temperature changes with gas and dust evolution, and identify trends that may influence planet formation or allow to constrain disc evolution observationally. We calculate disc temperature, hydrostatic equilibrium and dust settling in a mutually consistent way from a grid of disc models at different stages of gas loss, grain growth and hole opening. We find that the CO snowline location depends very strongly on disc properties. The CO snowline location migrates closer to the star for increasing degrees of gas dispersal and dust growth. Around a typical A-type star, the snowline can be anywhere between several tens and a few hundred au, depending on the disc properties such as gas mass and grain size. In fact, gas loss is as efficient as dust evolution in settling discs, and flat discs may be gas-poor counterparts of flared discs. Our results, in the context of different pre-main-sequence evolution of the luminosity in low- and intermediate-mass stars suggest very different thermal (and hence chemical) histories in these two types of discs. Discs of T Tauri stars settle and cool down, while discs of Herbig Ae stars may remain rather warm throughout the pre-main sequence.

Assembling in Sequence: A Saleable Work Skill. Occupation Simulation Packet. Grades 3rd-4th.

ERIC Educational Resources Information Center

Hueston, Jean

This teacher's guide for grades 3 and 4 contains simulated work experiences for students using the isolated skill concept - assembling in sequence. Teacher instructions include objectives, evaluation, and sequence of activities. The guide contains pre-tests and post-tests with instructions and answer keys. Three pre-skill activities are suggested,…

CombAlign: a code for generating a one-to-many sequence alignment from a set of pairwise structure-based sequence alignments.

PubMed

Zhou, Carol L Ecale

2015-01-01

In order to better define regions of similarity among related protein structures, it is useful to identify the residue-residue correspondences among proteins. Few codes exist for constructing a one-to-many multiple sequence alignment derived from a set of structure or sequence alignments, and a need was evident for creating such a tool for combining pairwise structure alignments that would allow for insertion of gaps in the reference structure. This report describes a new Python code, CombAlign, which takes as input a set of pairwise sequence alignments (which may be structure based) and generates a one-to-many, gapped, multiple structure- or sequence-based sequence alignment (MSSA). The use and utility of CombAlign was demonstrated by generating gapped MSSAs using sets of pairwise structure-based sequence alignments between structure models of the matrix protein (VP40) and pre-small/secreted glycoprotein (sGP) of Reston Ebolavirus and the corresponding proteins of several other filoviruses. The gapped MSSAs revealed structure-based residue-residue correspondences, which enabled identification of structurally similar versus differing regions in the Reston proteins compared to each of the other corresponding proteins. CombAlign is a new Python code that generates a one-to-many, gapped, multiple structure- or sequence-based sequence alignment (MSSA) given a set of pairwise sequence alignments (which may be structure based). CombAlign has utility in assisting the user in distinguishing structurally conserved versus divergent regions on a reference protein structure relative to other closely related proteins. CombAlign was developed in Python 2.6, and the source code is available for download from the GitHub code repository.

Insights into the genome evolution of Yersinia pestis through whole genome comparison with Yersinia pseudotuberculosis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Souza, B; Stoutland, P; Derbise, A

2004-01-24

Yersinia pestis, the causative agent of plague, is a highly uniform clone that diverged recently from the enteric pathogen Yersinia pseudotuberculosis. Despite their close genetic relationship, they differ radically in their pathogenicity and transmission. Here we report the complete genomic sequence of Y. pseudotuberculosis IP32953 and its use for detailed genome comparisons to available Y. pestis sequences. Analyses of identified differences across a panel of Yersinia isolates from around the world reveals 32 Y. pestis chromosomal genes that, together with the two Y. pestis-specific plasmids, represent the only new genetic material in Y. pestis acquired since the divergence from Y.more » pseudotuberculosis. In contrast, 149 new pseudogenes (doubling the previous estimate) and 317 genes absent from Y. pestis were detected, indicating that as many as 13% of Y. pseudotuberculosis genes no longer function in Y. pestis. Extensive IS-mediated genome rearrangements and reductive evolution through massive gene loss, resulting in elimination and modification of pre-existing gene expression pathways appear to be more important than acquisition of new genes in the evolution of Y. pestis. These results provide a sobering example of how a highly virulent epidemic clone can suddenly emerge from a less virulent, closely related progenitor.« less

Evolutionary distance from human homologs reflects allergenicity of animal food proteins.

PubMed

Jenkins, John A; Breiteneder, Heimo; Mills, E N Clare

2007-12-01

In silico analysis of allergens can identify putative relationships among protein sequence, structure, and allergenic properties. Such systematic analysis reveals that most plant food allergens belong to a restricted number of protein superfamilies, with pollen allergens behaving similarly. We have investigated the structural relationships of animal food allergens and their evolutionary relatedness to human homologs to define how closely a protein must resemble a human counterpart to lose its allergenic potential. Profile-based sequence homology methods were used to classify animal food allergens into Pfam families, and in silico analyses of their evolutionary and structural relationships were performed. Animal food allergens could be classified into 3 main families--tropomyosins, EF-hand proteins, and caseins--along with 14 minor families each composed of 1 to 3 allergens. The evolutionary relationships of each of these allergen superfamilies showed that in general, proteins with a sequence identity to a human homolog above approximately 62% were rarely allergenic. Single substitutions in otherwise highly conserved regions containing IgE epitopes in EF-hand parvalbumins may modulate allergenicity. These data support the premise that certain protein structures are more allergenic than others. Contrasting with plant food allergens, animal allergens, such as the highly conserved tropomyosins, challenge the capability of the human immune system to discriminate between foreign and self-proteins. Such immune responses run close to becoming autoimmune responses. Exploiting the closeness between animal allergens and their human homologs in the development of recombinant allergens for immunotherapy will need to consider the potential for developing unanticipated autoimmune responses.

Rotational evolution of slow-rotator sequence stars

NASA Astrophysics Data System (ADS)

Lanzafame, A. C.; Spada, F.

2015-12-01

Context. The observed relationship between mass, age and rotation in open clusters shows the progressive development of a slow-rotator sequence among stars possessing a radiative interior and a convective envelope during their pre-main sequence and main-sequence evolution. After 0.6 Gyr, most cluster members of this type have settled on this sequence. Aims: The observed clustering on this sequence suggests that it corresponds to some equilibrium or asymptotic condition that still lacks a complete theoretical interpretation, and which is crucial to our understanding of the stellar angular momentum evolution. Methods: We couple a rotational evolution model, which takes internal differential rotation into account, with classical and new proposals for the wind braking law, and fit models to the data using a Monte Carlo Markov chain (MCMC) method tailored to the problem at hand. We explore to what extent these models are able to reproduce the mass and time dependence of the stellar rotational evolution on the slow-rotator sequence. Results: The description of the evolution of the slow-rotator sequence requires taking the transfer of angular momentum from the radiative core to the convective envelope into account. We find that, in the mass range 0.85-1.10 M⊙, the core-envelope coupling timescale for stars in the slow-rotator sequence scales as M-7.28. Quasi-solid body rotation is achieved only after 1-2 Gyr, depending on stellar mass, which implies that observing small deviations from the Skumanich law (P ∝ √{t}) would require period data of older open clusters than is available to date. The observed evolution in the 0.1-2.5 Gyr age range and in the 0.85-1.10 M⊙ mass range is best reproduced by assuming an empirical mass dependence of the wind angular momentum loss proportional to the convective turnover timescale and to the stellar moment of inertia. Period isochrones based on our MCMC fit provide a tool for inferring stellar ages of solar-like main-sequence stars from their mass and rotation period that is largely independent of the wind braking model adopted. These effectively represent gyro-chronology relationships that take the physics of the two-zone model for the stellar angular momentum evolution into account.

High-precision Radio and Infrared Astrometry of LSPM J1314+1320AB. II. Testing Pre-main-sequence Models at the Lithium Depletion Boundary with Dynamical Masses

NASA Astrophysics Data System (ADS)

Dupuy, Trent J.; Forbrich, Jan; Rizzuto, Aaron; Mann, Andrew W.; Aller, Kimberly; Liu, Michael C.; Kraus, Adam L.; Berger, Edo

2016-08-01

We present novel tests of pre-main-sequence models based on individual dynamical masses for the M7 binary LSPM J1314+1320AB. Joint analysis of Keck adaptive optics astrometric monitoring along with Very Long Baseline Array radio data from a companion paper yield component masses of 92.8 ± 0.6 M Jup (0.0885 ± 0.0006 M ⊙) and 91.7 ± 1.0 M Jup (0.0875 ± 0.0010 M ⊙) and a parallactic distance of 17.249 ± 0.013 pc. We find component luminosities consistent with the system being coeval at 80.8 ± 2.5 Myr, according to BHAC15 evolutionary models. The presence of lithium is consistent with model predictions, marking the first test of the theoretical lithium depletion boundary using ultracool dwarfs of known mass. However, we find that the evolutionary model-derived average effective temperature (2950 ± 5 K) is 180 K hotter than that given by a spectral type-{T}{eff} relation based on BT-Settl models (2770 ± 100 K). We suggest that the dominant source of this discrepancy is model radii being too small by ≈13%. In a test mimicking the typical application of models by observers, we derive masses on the H-R diagram using luminosity and BT-Settl temperature. The estimated masses are lower by {46}-19+16 % (2.0σ) than we measure dynamically and would imply that this is a system of ≈50 M Jup brown dwarfs, highlighting the large systematic errors possible in H-R diagram properties. This is the first time masses have been measured for ultracool (≥M6) dwarfs displaying spectral signatures of low gravity. Based on features in the infrared, LSPM J1314+1320AB appears to have higher gravity than typical Pleiades and AB Dor members, opposite the expectation given its younger age. The components of LSPM J1314+1320AB are now the nearest, lowest mass pre-main-sequence stars with direct mass measurements. Data presented herein were obtained at the W. M. Keck Observatory, which is operated as a scientific partnership among the California Institute of Technology, the University of California, and the National Aeronautics and Space Administration. The Observatory was made possible by the generous financial support of the W. M. Keck Foundation.

The strange hot horizontal-branch binary star in NGC 6752

NASA Astrophysics Data System (ADS)

Bidin, Christian Moni

2018-05-01

M5865 is the only so-far confirmed close binary found in the extreme horizontal branch (EHB) of a globular cluster. A detailed study has recently proposed that this object could be a close system (period P=1.61 days) comprising a EHB and a main-sequence star of mass M≈0.6 Mʘ. Such a system has never been found among hundreds of known EHB binaries in the field, and it results in a very interesting, unique object. In this contribution, we resume the previous literature results on M5865, we discuss the reasons of interest on it, and we present some very preliminary results obtained from new observations.

Contrasting dynamics of leaf potential and gas exchange during progressive drought cycles and recovery in Amorpha fruticosa and Robinia pseudoacacia.

PubMed

Yan, Weiming; Zheng, Shuxia; Zhong, Yangquanwei; Shangguan, Zhouping

2017-06-30

Leaf gas exchange is closely associated with water relations; however, less attention has been given to this relationship over successive drought events. Dynamic changes in gas exchange and water potential in the seedlings of two woody species, Amorpha fruticosa and Robinia pseudoacacia, were monitored during recurrent drought. The pre-dawn leaf water potential declined in parallel with gas exchange in both species, and sharp declines in gas exchange occurred with decreasing water potential. A significant correlation between pre-dawn water potential and gas exchange was observed in both species and showed a right shift in R. pseudoacacia in the second drought. The results suggested that stomatal closure in early drought was mediated mainly by elevated foliar abscisic acid (ABA) in R. pseudoacacia, while a shift from ABA-regulated to leaf-water-potential-driven stomatal closure was observed in A. fruticosa. After re-watering, the pre-dawn water potential recovered quickly, whereas stomatal conductance did not fully recover from drought in R. pseudoacacia, which affected the ability to tightly control transpiration post-drought. The dynamics of recovery from drought suggest that stomatal behavior post-drought may be restricted mainly by hydraulic factors, but non-hydraulic factors may also be involved in R. pseudoacacia.

Sequence stratigraphy and high-frequency cycles: New aspects for a quantitative evaluation of the Gulf of Suez basin, Egypt

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nio, S.D.; Yang, C.S.; Tewfik, N.

1993-09-01

A new development in the application of sequence stratigraphic concepts in marine as well as continental basins is the recognition of high-frequency cyclic patterns in rock successions in the subsurface. Studies of six wells from the northern, central, and southern parts of the Gulf of Suez show the presence of well-preserved, high-frequency cycles with periodicities similar to the orbitally forced Malankovitch parameters. Subsurface rock successions, third-order sequences, and high-frequency cycles were compared with outcrops. After establishing the biostratigraphic framework for the above-mentioned wells, a sequence analysis was performed. Sequence boundaries and maximum flooding positions in each well were calibrated withmore » the occurrences and evaluation of the high-frequency cycles. It became obvious that there is an intimate relationship between these high-frequency Milankovitch cycles and sequence organization. In addition, a close relationship can be observed in the subsurface as well as in outcrops between high-frequency climatic changes (connected to the Milankovitch cycles) and (litho)facies variability. Quantitative evaluations of each sequence and/or systems tract can be computed with the International Geoservices' cyclicity analysis tool (MILABAR). The results are summarized in a well composite chart, rate (NAR), and ratio of preserved time. In correlations between the wells, an accuracy of 500-100 Ka can be obtained. The quantitative evaluation of the sequence and high-frequency cycle analysis gave some new aspects concerning the (litho)facies and geodynamic development during the pre- as well as the synrift stages of the Gulf of Suez Basin.« less

40 CFR 98.437 - Records that must be retained.

Code of Federal Regulations, 2011 CFR

2011-07-01

... Contained in Pre-Charged Equipment or Closed-Cell Foams § 98.437 Records that must be retained. (a) In... closed-cell foams must retain the following records substantiating each of the imports that they report... entry form. (4) Ports of entry through which the pre-charged equipment or closed-cell foams passed. (5...

40 CFR 98.437 - Records that must be retained.

Code of Federal Regulations, 2013 CFR

2013-07-01

... Contained in Pre-Charged Equipment or Closed-Cell Foams § 98.437 Records that must be retained. (a) In... closed-cell foams must retain the following records substantiating each of the imports that they report... entry form. (4) Ports of entry through which the pre-charged equipment or closed-cell foams passed. (5...

40 CFR 98.437 - Records that must be retained.

Code of Federal Regulations, 2014 CFR

2014-07-01

... Contained in Pre-Charged Equipment or Closed-Cell Foams § 98.437 Records that must be retained. (a) In... closed-cell foams must retain the following records substantiating each of the imports that they report... entry form. (4) Ports of entry through which the pre-charged equipment or closed-cell foams passed. (5...

CAN WE PREDICT THE GLOBAL MAGNETIC TOPOLOGY OF A PRE-MAIN-SEQUENCE STAR FROM ITS POSITION IN THE HERTZSPRUNG-RUSSELL DIAGRAM?

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gregory, S. G.; Hillenbrand, L. A.; Donati, J.-F.

2012-08-20

Zeeman-Doppler imaging studies have shown that the magnetic fields of T Tauri stars can be significantly more complex than a simple dipole and can vary markedly between sources. We collect and summarize the magnetic field topology information obtained to date and present Hertzsprung-Russell (H-R) diagrams for the stars in the sample. Intriguingly, the large-scale field topology of a given pre-main-sequence (PMS) star is strongly dependent upon the stellar internal structure, with the strength of the dipole component of its multipolar magnetic field decaying rapidly with the development of a radiative core. Using the observational data as a basis, we arguemore » that the general characteristics of the global magnetic field of a PMS star can be determined from its position in the H-R diagram. Moving from hotter and more luminous to cooler and less luminous stars across the PMS of the H-R diagram, we present evidence for four distinct magnetic topology regimes. Stars with large radiative cores, empirically estimated to be those with a core mass in excess of {approx}40% of the stellar mass, host highly complex and dominantly non-axisymmetric magnetic fields, while those with smaller radiative cores host axisymmetric fields with field modes of higher order than the dipole dominant (typically, but not always, the octupole). Fully convective stars above {approx}> 0.5 M{sub Sun} appear to host dominantly axisymmetric fields with strong (kilo-Gauss) dipole components. Based on similarities between the magnetic properties of PMS stars and main-sequence M-dwarfs with similar internal structures, we speculate that a bistable dynamo process operates for lower mass stars ({approx}< 0.5 M{sub Sun} at an age of a few Myr) and that they will be found to host a variety of magnetic field topologies. If the magnetic topology trends across the H-R diagram are confirmed, they may provide a new method of constraining PMS stellar evolution models.« less

Sequence variation in the env gene of simian immunodeficiency virus recovered from immunized macaques is predominantly in the V1 region.

PubMed

Almond, N; Jenkins, A; Heath, A B; Kitchin, P

1993-05-01

Three cynomolgus macaques were immunized with recombinant envelope protein preparations derived from simian immunodeficiency virus (SIV). Although humoral and cellular responses were elicited by the immunization regime, all macaques became infected upon challenge with 10 MID50 of the 11/88 virus challenge stock of SIVmac251-32H. The polymerase chain reaction was used to amplify proviral SIV gp120 sequences present in the blood of both immunized and control macaques at 2 months post-infection. A comparison of the predominant sequences found in the region from V2 to V5 of gp120 failed to differentiate provirus recovered from either immunized or control animals. A detailed investigation of sequences obtained from the hypervariable V1 region identified a mixture of sequences in both immunized and control macaques. Some sequences were identical to those previously detected in the virus challenge stock, whereas others had not been detected previously. Phenogram analysis of the new V1 sequences found in immunized animals revealed that they were quite distinct from those from the virus challenge stock and that they included alterations to potential N-linked glycosylation sites. In contrast, new sequence variants recovered from the control animals were closely related to sequences from the virus challenge stock. The difference in diversity of new V1 sequences recovered from immunized and control macaques was highly significant (P < 0.001). Thus, the presence of pre-existing immune responses to SIV envelope protein is associated with greater genetic change in the V1 region of gp120. These data are discussed in relation to the epitopes of SIV gp120 that may confer protection from in vivo challenge.

Evidence of the evolved nature of the B[e] star MWC 137

DOE Office of Scientific and Technical Information (OSTI.GOV)

Muratore, M. F.; Arias, M. L.; Cidale, L.

2015-01-01

The evolutionary phase of B[e] stars is difficult to establish due to the uncertainties in their fundamental parameters. For instance, possible classifications for the Galactic B[e] star MWC 137 include pre-main-sequence and post-main-sequence phases, with a large range in luminosity. Our goal is to clarify the evolutionary stage of this peculiar object, and to study the CO molecular component of its circumstellar medium. To this purpose, we modeled the CO molecular bands using high-resolution K-band spectra. We find that MWC 137 is surrounded by a detached cool (T=1900±100 K) and dense (N=(3±1)×10{sup 21} cm{sup −2}) ring of CO gas orbitingmore » the star with a rotational velocity, projected to the line of sight, of 84 ± 2 km s{sup −1}. We also find that the molecular gas is enriched in the isotope {sup 13}C, excluding the classification of the star as a Herbig Be. The observed isotopic abundance ratio ({sup 12}C/{sup 13}C = 25 ± 2) derived from our modeling is compatible with a proto-planetary nebula, main-sequence, or supergiant evolutionary phase. However, based on some observable characteristics of MWC 137, we propose that the supergiant scenario seems to be the most plausible. Hence, we suggest that MWC 137 could be in an extremely short-lived phase, evolving from a B[e] supergiant to a blue supergiant with a bipolar ring nebula.« less

Direct deposition of silver nanoplates on quartz surface by sequence pre-treatment hydroxylation and silanisation.

PubMed

Abu Bakar, Norhayati; Mat Salleh, Muhamad; Ali Umar, Akrajas; Shapter, Joseph George

2017-01-01

Silver nanoparticles deposited on quartz substrates are widely used as SERS substrates. The nanoparticles can be deposited directly from colloidal solution by dipping technique. However, the adhesion of the particles on the quartz surface is very poor. Normally the substrate is pre-treated with hydroxylation or silanisation process. In this paper, we have demonstrated that the application of the sequence pre-treatment hydroxylation and silanisation have improved the density of silver nanoplates desposited on the quartz surface. •Sequence hydroxylation and silanisation pre-treatment assists the deposition of the nanoplate on the surface.•Various immersion times of the quartz surface into the colloidal nanoplates determined size distributions and density surface of the nanoplates on the surface.

A mass-wasting dominated Quaternary mountain range, the Coastal Range in eastern Taiwan

NASA Astrophysics Data System (ADS)

Hsieh, Meng-Long; Hogg, Alan; Song, Sheng-Rong; Kang, Su-Chen; Chou, Chun-Yen

2017-12-01

Fluvial bedrock incision, which creates topographic relief and controls hillslope development, has been considered the key medium linking denudation and tectonic uplift of unglaciated mountains. This article, however, shows a different scenario from the Coastal Range in eastern Taiwan. This range, with the steepness inherited from pre-orogenic volcanoes, has been subject to mass wasting even before its emergence above sea level no earlier than Middle Pleistocene. Numerous terraced alluvial fans/fan deltas record the ancient mass movements of the range, including rock avalanches. Multiple radiocarbon dates <16 ka cal BP reveal the recurrence intervals of these movements of over several thousand years. The largest event is dated ∼15 ka cal BP, and the two second largest, 9-8 ka cal BP. These mass movements were sourced from ridges with minimum heights of 350-400 m, have sequences not clearly related to the known climate-change events, and are believed to have been triggered mainly by severe rainfall events, large earthquakes, or their combinations. The resulting fluctuation of sediment yield has episodically changed river behavior, forming river terraces in catchments >1 km2. Alluvial terraces are typically exhibited close to the source ridges of mass movements, and strath terraces along the downstream parts of rivers. Both were created when enormous sediment supply had exceeded or matched the prevailing river transport capacity. This process, along with the protection by giant boulders from mass movement, disturbed the long-term incision trend of rivers in response to tectonic uplift. As a result, the observed Holocene bedrock incision at most sites has not kept pace with the tectonic uplift. The spatial contrast in mass-wasting histories further accounts for the great diversity of the terrace sequences, even in areas with similar tectonic and base-level conditions.

The structural evolution of the Ghadames and Illizi basins during the Paleozoic, Mesozoic and Cenozoic: Petroleum implications

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gauthier, F.J.; Boudjema, A.; Lounis, R.

1995-08-01

The Ghadames and Illizi basins cover the majority of the eastern Sahara of Algeria. Geologicaly, this part of the Central Saharan platform has been influenced by a series of structural arches and {open_quotes}moles{close_quotes} (continental highs) which controlled sedimentation and structure through geologic time. These features, resulting from and having been affected by nine major tectonic phases ranging from pre-Cambrian to Tertiary, completely bound the Ghadames and Illizi Basins. During the Paleozoic both basins formed one continuous depositional entity with the Ghadames basin being the distal portion of the continental sag basin where facies and thickness variations are observed over largemore » distances. It is during the Mesozoic-Cenozoic that the Ghadames basin starts to evolve differently from the Illizi Basin. Eustatic low-stand periods resulted in continental deposition yielding the major petroleum-bearing reservoir horizons (Cambrian, Ordovician, Siluro-Devonian and Carboniferous). High-stand periods corresponds to the major marine transgressions covering the majority of the Saharan platform. These transgressions deposited the principal source rock intervals of the Silurian and Middle to Upper Devonian. The main reservoirs of the Mesozoic and Cenozoic are Triassic sandstone sequences which are covered by a thick evaporite succession forming a super-seal. Structurally, the principal phases affecting this sequence are the extensional events related to the breakup of Pangea and the Alpine compressional events. The Ghadames and Illizi basins, therefore, have been controlled by a polphase tectonic history influenced by Pan African brittle basement fracturing which resulted in complex structures localized along the major basin bounding trends as well as several subsidiary trends within the basin. These trends, as demonstrated with key seismic data, have been found to contain the majority of hydrocarbons trapped.« less

Variable stars around selected open clusters in the VVV area: Young Stellar Objects

NASA Astrophysics Data System (ADS)

Medina, Nicolas; Borissova, Jura; Bayo, Amelia; Kurtev, Radostin; Lucas, Philip

2017-09-01

Time-varying phenomena are one of the most substantial sources of astrophysical information, and led to many fundamental discoveries in modern astronomy. We have developed an automated tool to search and analyze variable sources in the near infrared Ks band, using the data from the Vista Variables in the Vía Láctea (VVV) ESO Public Survey ([5, 8]). One of our main goals is to investigate the Young Stellar Objects (YSOs) in the Galactic star forming regions, looking for: •Variability. •New pre-main sequence star clusters. Here we present the newly discovered YSOs within some selected stellar clusters in our Galaxy.

Dynamical masses of pms stars in the taurus star formation region

NASA Astrophysics Data System (ADS)

Simon, M.

2013-02-01

Our preliminary orbital parameters for DF Tau, T Tau Sa-Sb, ZZ Tau and the Pleaides binary are presented in the paper Orbital Motion in Pre-Main Sequence Binaries by G.H. Schaefer, L. Prato, M. Simon, & J. Patience (2013, in prep. for AJ). In the few pages available here I present an overview of our motivation for this work and of our results. The slides and complete references for my talk at the Leuven conference are available at http://www.astro.sunysb.edu/msimon/public.

VizieR Online Data Catalog: Photometric observations of PMS objects (Fernandez, 1995)

NASA Astrophysics Data System (ADS)

Fernandez, M.

1995-05-01

We present the observational data of a photometric monitoring of 24 pre-main sequence objects: T Tauri stars, Ae/Be Herbig stars and some unclassified objects. Observations were carried out from July 1988 to August 1992, using the UBV(RI)_c system. Variability with time scales from days to years and amplitudes in the V band larger than 0.1 mag is found for a part of this sample. The analysis of the possible causes of this variability are discussed in separate papers (Fernandez & Eiroa 1995a,b). (24 data files).

Studies of Circumstellar Disk Evolution

NASA Technical Reports Server (NTRS)

Hartmann, Lee W.

2005-01-01

The aim of this project is to develop a comprehensive global picture of the physical conditions in, and evolutionary timescales of, pre-main sequence accretion disks. The results of this work will help constrain the initial conditions for planet formation. To this end we are developing much larger samples of 3-10 Myr-old stars to provide better empirical constraints on protoplanetary disk evolution; measuring disk accretion rates in these systems; and constructing detailed model disk structures consistent with observations to infer physical conditions such as grain growth in protoplanetary disks.

Four-channel asymmetric Real-Time PCR hybridization probe assay: a rapid pre-screening method for critical BCR-ABL kinase domain mutations.

PubMed

Martinez-Serra, Jordi; Gutiérrez, Antonio; Marcús, Toni F; Soverini, Simona; Amat, Juan Carlos; Navarro-Palou, María; Ros, Teresa; Bex, Teresa; Ballester, Carmen; Bauça, Josep Miquel; SanFelix, Sara; Novo, Andrés; Vidal, Carmen; Santos, Carmen; Besalduch, Joan

2012-03-01

Within the laboratory protocols, used for the study of BCR-ABL resistance mutations in chronic myeloid leukemia patients treated with Imatinib, direct sequencing remains the reference method. Since the incidence of patients with a mutation-related loss of response is not very high, it is very useful in the routine laboratory to perform a fast pre-screening method. With this in mind, we have designed a new technique, based on a single Real-Time FRET-based PCR, followed by a study of melting peaks. This new tool, developed in a LightCycler 2.0, combines four different fluorescence channels for the simultaneous detection, in a single close tube, of critical mutations within the ABL kinase domain. Assay evaluation performed on 33 samples, previously genotyped by sequentiation, resulted in full concordance of results. This new methodology detects in a few steps the presence of critical mutations associated to Imatinib resistance. Copyright © 2012 Elsevier Inc. All rights reserved.

Introduced T cell receptor variable region gene segments recombine in pre-B cells: evidence that B and T cells use a common recombinase.

PubMed

Yancopoulos, G D; Blackwell, T K; Suh, H; Hood, L; Alt, F W

1986-01-31

We have recently proposed that a common recombinase performs all of the many variable region gene assembly events in B and T cells, and that the specificity of these joining events is mediated by regulating the "accessibility" of the involved gene segments. To test this possibility, we have introduced "accessible" T cell receptor (TCR) variable region gene segments into a pre-B cell line capable of recombining endogenous and transfected immunoglobulin (Ig) variable region gene segments. Although the corresponding "inaccessible" endogenous TCR gene segments do not rearrange in this line or in B cells in general, the introduced TCR gene segments join very frequently and, in fact, closely resemble introduced Ig gene segments in their recombination characteristics. These observations suggest a new role for conventional Ig transcriptional enhancers--recombinational enhancement. Our studies provide insight into additional aspects of the joining mechanism such as N region insertion, aberrant joining, and recombination-recognition sequence requirements for joining.

Separating endogenous ancient DNA from modern day contamination in a Siberian Neandertal

PubMed Central

Skoglund, Pontus; Northoff, Bernd H.; Shunkov, Michael V.; Derevianko, Anatoli P.; Pääbo, Svante; Krause, Johannes; Jakobsson, Mattias

2014-01-01

One of the main impediments for obtaining DNA sequences from ancient human skeletons is the presence of contaminating modern human DNA molecules in many fossil samples and laboratory reagents. However, DNA fragments isolated from ancient specimens show a characteristic DNA damage pattern caused by miscoding lesions that differs from present day DNA sequences. Here, we develop a framework for evaluating the likelihood of a sequence originating from a model with postmortem degradation—summarized in a postmortem degradation score—which allows the identification of DNA fragments that are unlikely to originate from present day sources. We apply this approach to a contaminated Neandertal specimen from Okladnikov Cave in Siberia to isolate its endogenous DNA from modern human contaminants and show that the reconstructed mitochondrial genome sequence is more closely related to the variation of Western Neandertals than what was discernible from previous analyses. Our method opens up the potential for genomic analysis of contaminated fossil material. PMID:24469802

MESA models for the evolutionary status of the epsilon Aurigae disk-eclipsed binary system

NASA Astrophysics Data System (ADS)

Stencel, Robert E.; Gibson, Justus

2018-06-01

The brightest member of the class of disk-eclipsed binary stars is the Algol-like long-period binary, epsilon Aurigae (HD 31964, F0Iap + disk, http://adsabs.harvard.edu/abs/2016SPIE.9907E..17S ). Using MESA (Modules for Experiments in Stellar Astrophysics, version 9575), we have made an evaluation of its evolutionary state. We sought to satisfy several observational constraints, including: (1) requiring evolutionary tracks to pass close to the current temperature and luminosity of the primary star; (2) obtaining a period near the observed value of 27.1 years; (3) matching a mass function of 3.0; (4) concurrent Roche lobe overflow and mass transfer; (5) an isotopic ratio 12C / 13C = 5 and, (6) matching the interferometrically determined angular diameter. A MESA model starting with binary masses of 9.85 + 4.5 solar masses, with a 100 day initial period, produces a 1.2 + 10.6 solar masses result having a 547 day period, plus a single digit 12C / 13C ratio. These values were reached near an age of 20 Myr, when the donor star comes close to the observed luminosity and temperature for epsilon Aurigae A, as a post-RGB/pre-AGB star. Contemporaneously, the accretor then appears as an upper main sequence, early B-type star. This benchmark model can provide a basis for further exploration of this interacting binary, and other long period binary stars. This report has been submitted to MNRAS, along with a parallel investigation of mass transfer stream and disk sub-structure. The authors are grateful to the estate of William Herschel Womble for the support of astronomy at the University of Denver.

Young Cluster Berkeley 59: Properties, Evolution, and Star Formation

NASA Astrophysics Data System (ADS)

Panwar, Neelam; Pandey, A. K.; Samal, Manash R.; Battinelli, Paolo; Ogura, K.; Ojha, D. K.; Chen, W. P.; Singh, H. P.

2018-01-01

Berkeley 59 is a nearby (∼1 kpc) young cluster associated with the Sh2-171 H II region. We present deep optical observations of the central ∼2.5 × 2.5 pc2 area of the cluster, obtained with the 3.58 m Telescopio Nazionale Galileo. The V/(V–I) color–magnitude diagram manifests a clear pre-main-sequence (PMS) population down to ∼0.2 M ⊙. Using the near-infrared and optical colors of the low-mass PMS members, we derive a global extinction of A V = 4 mag and a mean age of ∼1.8 Myr, respectively, for the cluster. We constructed the initial mass function and found that its global slopes in the mass ranges of 0.2–28 M ⊙ and 0.2–1.5 M ⊙ are ‑1.33 and ‑1.23, respectively, in good agreement with the Salpeter value in the solar neighborhood. We looked for the radial variation of the mass function and found that the slope is flatter in the inner region than in the outer region, indicating mass segregation. The dynamical status of the cluster suggests that the mass segregation is likely primordial. The age distribution of the PMS sources reveals that the younger sources appear to concentrate close to the inner region compared to the outer region of the cluster, a phenomenon possibly linked to the time evolution of star-forming clouds. Within the observed area, we derive a total mass of ∼103 M ⊙ for the cluster. Comparing the properties of Berkeley 59 with other young clusters, we suggest it resembles more closely the Trapezium cluster.

Orbital Monitoring of the AstraLux Large M-dwarf Multiplicity Sample

NASA Astrophysics Data System (ADS)

Janson, Markus; Bergfors, Carolina; Brandner, Wolfgang; Bonnefoy, Mickaël; Schlieder, Joshua; Köhler, Rainer; Hormuth, Felix; Henning, Thomas; Hippler, Stefan

2014-10-01

Orbital monitoring of M-type binaries is essential for constraining their fundamental properties. This is particularly useful in young systems, where the extended pre-main-sequence evolution can allow for precise isochronal dating. Here, we present the continued astrometric monitoring of the more than 200 binaries of the AstraLux Large Multiplicity Survey, building both on our previous work, archival data, and new astrometric data spanning the range of 2010-2012. The sample is very young overall—all included stars have known X-ray emission, and a significant fraction (18%) of them have recently also been identified as members of young moving groups in the solar neighborhood. We identify ~30 targets that both have indications of being young and for which an orbit either has been closed or appears possible to close in a reasonable time frame (a few years to a few decades). One of these cases, GJ 4326, is, however, identified as probably being substantially older than has been implied from its apparent moving group membership, based on astrometric and isochronal arguments. With further astrometric monitoring, these targets will provide a set of empirical isochrones, against which theoretical isochrones can be calibrated, and which can be used to evaluate the precise ages of nearby young moving groups. Based on observations collected at the European Southern Observatory, Chile, under observing programs 081.C-0314(A), 082.C-0053(A), and 084.C-0812(A), and on observations collected at the Centro Astronómico Hispano Alemán (CAHA) at Calar Alto, operated jointly by the Max-Planck Institute for Astronomy and the Instituto de Astrofísica de Andalucía (CSIC).

Stellar Evolution with Rotation: Mixing Processes in AGB Stars

NASA Astrophysics Data System (ADS)

Driebe, T.; Blöcker, T.

We included diffusive angular momentum transport and rotationally induced mixing processes in our stellar evolution code and studied the influence of rotation on the evolution of intermediate mass stars (M*=2dots6 Msolar) towards and along the asymptotic giant branch (AGB). The calculations start in the fully convective pre-main sequence phase and the initial angular momentu m was adjusted such that on the zero-age main sequence vrot=200 km/ s is achieved. The diffusion coefficients for the five rotational instabilities considered (dynamical shear, secular shear, Eddington-Sweet (ES) circulation, Solberg-Høiland-instability and Goldreich-Schubert-Fricke (GSF) instability) were adopted from Heger et al. (2000, ApJ 528, 368). Mixing efficiency and sensitivity of these processes against molecular weight gradients have been determined by calibration of the main sequence width. In this study we focus on the abundance evolution of carbon. On the one hand, the surface abundance ratios of 12C/13C a nd 12C/16O at the base of the AGB were found to be ≈ 7dots 10 and ≈ 0.1, resp., being a factor of two lower than in non-rotating models. This results from the slow but continuously operating rotationally induced mixing due to the ES-circulation and the GSF-instability during the long main sequence phase. On the other hand, 13C serves as neutron source for interior s-process nucleosynthesis in AGB stars vi a 13C(α,n)16O. Herwig et al. (1997, A&A 324, L81) found that a 13C pocket is forme d in the intershell region of 3 Msolar AGB star if diffusive overshoot is considered. Our calculations show, that mixing processes due to rotation open an alternative channel for the formation of a 13C pocket as found by Langer et al. (1999, A&A 346, L37). Again, ES-circulation and GSF-instability are the predominant rotational mixing processes.

Understanding Low-cycle Fatigue Life Improvement Mechanisms in a Pre-twinned Magnesium Alloy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wu, Wei; An, Ke

The mechanisms of fatigue life improvement by pre-twinning process in a commercial rolled magnesium (Mg) alloy have been investigated using real-time in situ neutron diffraction under a continuous-loading condition. It is found that by introducing the excess twinned grains through pre-compression along the rolling direction the fatigue life was enhanced approximately 50%, mainly resulting from the prolonged detwinning process and inhibited dislocation slip during reverse tension. Moreover, after pre-twinning process, the removal of the rapid strain hardening during reverse tension leads to a compressive mean stress value and more symmetric shape of stress-strain hysteresis loop. The pre-twinning has significant impactsmore » on the twinning-detwinning characteristics and deformation modes during cyclic loading and greatly facilitates the twinning-detwinning activities in plastic deformation. The cyclic straining leads to the increase of contribution of tensile twinning deformation in overall plastic deformation in both the as-received and pre-deformed sample. The mechanisms of load partitioning in different groups of grains are closely related to the deformation modes in each deformation stage, while the fatigue cycling has little influence on the load sharing. The pre-twinning process provides an easy and cost-effective route to improve the low-cycle fatigue life through manufacturing and processing, which would advance the wide application of light-weight wrought Mg alloys as structural materials.« less

Understanding Low-cycle Fatigue Life Improvement Mechanisms in a Pre-twinned Magnesium Alloy

DOE PAGES

Wu, Wei; An, Ke

2015-10-03

The mechanisms of fatigue life improvement by pre-twinning process in a commercial rolled magnesium (Mg) alloy have been investigated using real-time in situ neutron diffraction under a continuous-loading condition. It is found that by introducing the excess twinned grains through pre-compression along the rolling direction the fatigue life was enhanced approximately 50%, mainly resulting from the prolonged detwinning process and inhibited dislocation slip during reverse tension. Moreover, after pre-twinning process, the removal of the rapid strain hardening during reverse tension leads to a compressive mean stress value and more symmetric shape of stress-strain hysteresis loop. The pre-twinning has significant impactsmore » on the twinning-detwinning characteristics and deformation modes during cyclic loading and greatly facilitates the twinning-detwinning activities in plastic deformation. The cyclic straining leads to the increase of contribution of tensile twinning deformation in overall plastic deformation in both the as-received and pre-deformed sample. The mechanisms of load partitioning in different groups of grains are closely related to the deformation modes in each deformation stage, while the fatigue cycling has little influence on the load sharing. The pre-twinning process provides an easy and cost-effective route to improve the low-cycle fatigue life through manufacturing and processing, which would advance the wide application of light-weight wrought Mg alloys as structural materials.« less

HABITABLE ZONES OF POST-MAIN SEQUENCE STARS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ramirez, Ramses M.; Kaltenegger, Lisa

Once a star leaves the main sequence and becomes a red giant, its Habitable Zone (HZ) moves outward, promoting detectable habitable conditions at larger orbital distances. We use a one-dimensional radiative-convective climate and stellar evolutionary models to calculate post-MS HZ distances for a grid of stars from 3700 to 10,000 K (∼M1 to A5 stellar types) for different stellar metallicities. The post-MS HZ limits are comparable to the distances of known directly imaged planets. We model the stellar as well as planetary atmospheric mass loss during the Red Giant Branch (RGB) and Asymptotic Giant Branch (AGB) phases for super-Moons tomore » super-Earths. A planet can stay between 200 million years up to 9 Gyr in the post-MS HZ for our hottest and coldest grid stars, respectively, assuming solar metallicity. These numbers increase for increased stellar metallicity. Total atmospheric erosion only occurs for planets in close-in orbits. The post-MS HZ orbital distances are within detection capabilities of direct imaging techniques.« less

On the non-variability of HR 7653 (15 Vul) based on BRITE data

NASA Astrophysics Data System (ADS)

Smalley, B.; Paunzen, E.; Lüftinger, T.; Moffat, A. F. J.; Pigulski, A.; Rucinski, S.; Sikora, J.; Wade, G. A.; Weiss, W.; BEST

2018-02-01

We present space-based BRITE photometric observations of the metallic line (CP1) star HR 7653 (15 Vul). This chemically peculiar star of the upper main sequence was suspected to show variability due to rotation and a magnetic field. Such a variability is quite unusual among the, in general, non-magnetic CP1 stars. We investigated the astrophysical parameters of HR 7653 placing it close to the terminal age main sequence or even in the subgiant phase. The longest BRITE data set has a time base of 18.01 d from which we conclude that there are no coherent long-period variations (>1 d) visible above 2.1 mmag in the red and 6.6 mmag in the blue. Furthermore, we searched for δ Scuti type pulsations. On the basis of a discrete Fourier analysis method, we find no peaks in the Fourier spectra above 0.5 mmag and 8.6 mmag, for the red and blue filters, respectively.

Morphology of the UV aurorae Jupiter during Juno's first perijove observations

NASA Astrophysics Data System (ADS)

Bonfond, B.; Gladstone, G. R.; Grodent, D.; Greathouse, T. K.; Versteeg, M. H.; Hue, V.; Davis, M. W.; Vogt, M. F.; Gérard, J.-C.; Radioti, A.; Bolton, S.; Levin, S. M.; Connerney, J. E. P.; Mauk, B. H.; Valek, P.; Adriani, A.; Kurth, W. S.

2017-05-01

On 27 August 2016, the NASA Juno spacecraft performed its first close-up observations of Jupiter during its perijove. Here we present the UV images and color ratio maps from the Juno-UVS UV imaging spectrograph acquired at that time. Data were acquired during four sequences (three in the north, one in the south) from 5:00 UT to 13:00 UT. From these observations, we produced complete maps of the Jovian aurorae, including the nightside. The sequence shows the development of intense outer emission outside the main oval, first in a localized region (255°-295° System III longitude) and then all around the pole, followed by a large nightside protrusion of auroral emissions from the main emission into the polar region. Some localized features show signs of differential drift with energy, typical of plasma injections in the middle magnetosphere. Finally, the color-ratio map in the north shows a well-defined area in the polar region possibly linked to the polar cap.

Absolute dimensions and masses of eclipsing binaries. V. IQ Persei

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lacy, C.H.; Frueh, M.L.

1985-08-01

New photometric and spectroscopic observations of the 1.7 day eclipsing binary IQ Persei (B8 + A6) have been analyzed to yield very accurate fundamental properties of the system. Reticon spectroscopic observations obtained at McDonald Observatory were used to determine accurate radial velocities of both stars in this slightly eccentric large light-ratio binary. A new set of VR light curves obtained at McDonald Observatory were analyzed by synthesis techniques, and previously published UBV light curves were reanalyzed to yield accurate photometric orbits. Orbital parameters derived from both sets of photometric observations are in excellent agreement. The absolute dimensions, masses, luminosities, andmore » apsidal motion period (140 yr) derived from these observations agree well with the predictions of theoretical stellar evolution models. The A6 secondary is still very close to the zero-age main sequence. The B8 primary is about one-third of the way through its main-sequence evolution. 27 references.« less

Complementary DNA cloning and molecular evolution of opine dehydrogenases in some marine invertebrates.

PubMed

Kimura, Tomohiro; Nakano, Toshiki; Yamaguchi, Toshiyasu; Sato, Minoru; Ogawa, Tomohisa; Muramoto, Koji; Yokoyama, Takehiko; Kan-No, Nobuhiro; Nagahisa, Eizou; Janssen, Frank; Grieshaber, Manfred K

2004-01-01

The complete complementary DNA sequences of genes presumably coding for opine dehydrogenases from Arabella iricolor (sandworm), Haliotis discus hannai (abalone), and Patinopecten yessoensis (scallop) were determined, and partial cDNA sequences were derived for Meretrix lusoria (Japanese hard clam) and Spisula sachalinensis (Sakhalin surf clam). The primers ODH-9F and ODH-11R proved useful for amplifying the sequences for opine dehydrogenases from the 4 mollusk species investigated in this study. The sequence of the sandworm was obtained using primers constructed from the amino acid sequence of tauropine dehydrogenase, the main opine dehydrogenase in A. iricolor. The complete cDNA sequence of A. iricolor, H. discus hannai, and P. yessoensis encode 397, 400, and 405 amino acids, respectively. All sequences were aligned and compared with published databank sequences of Loligo opalescens, Loligo vulgaris (squid), Sepia officinalis (cuttlefish), and Pecten maximus (scallop). As expected, a high level of homology was observed for the cDNA from closely related species, such as for cephalopods or scallops, whereas cDNA from the other species showed lower-level homologies. A similar trend was observed when the deduced amino acid sequences were compared. Furthermore, alignment of these sequences revealed some structural motifs that are possibly related to the binding sites of the substrates. The phylogenetic trees derived from the nucleotide and amino acid sequences were consistent with the classification of species resulting from classical taxonomic analyses.

The 2016 Central Italy "reverse" seismic sequence

NASA Astrophysics Data System (ADS)

Chiaraluce, Lauro; Di Stefano, Raffaele; Tinti, Elisa; Scognamiglio, Laura; Michele, Maddalena; Cattaneo, Marco; De Gori, Pasquale; Chiarabba, Claudio; Monachesi, Giancarlo; Lombardi, Annamaria; Valoroso, Luisa; Latorre, Diana; Marzorati, Simone

2017-04-01

The 2016 seismic sequence consists so far of a series of moderate to large earthquakes that within three month's time activated a 60 km long segmented normal fault system located in the Central Italy and almost contiguous to the 1997 Colfiorito and 2009 L'Aquila normal fault systems. The first mainshock of the sequence occurred with MW6.0 on the 24th of August at 01:36 UTC close to the Accumoli and Amatrice villages producing evidence for centimetres' surface ruptures along the Mt. Vettore normal fault outcrop. Two months later on the 26th of October at 19:18 UTC another mainshock with MW5.9 occurred 25 km to the north activating another normal fault segment approximately on the along strike continuation of the first structure. Then, four days later on the 30th of October at 06:40 UTC the largest shock of the sequence with MW6.5 close to Norcia, in the middle part of the fault system activated two months before. We reconstruct the first order anatomy of the activated normal faults system, by analysing the spatial and temporal distribution of 25,354 aftershocks with 0.1

Einstein X-ray survey of the Pleiades - The dependence of X-ray emission on stellar age

NASA Technical Reports Server (NTRS)

Micela, G.; Sciortino, S.; Serio, S.; Vaiana, G. S.; Bookbinder, J.; Golub, L.; Harnden, F. R., Jr.; Rosner, R.

1985-01-01

The data obtained with two pointed observations of 1 deg by 1 deg fields of the Pleiades region have been analyzed, and the results are presented. The maximum-likelihood X-ray luminosity functions for the Pleiades G and K stars in the cluster are derived, and it is shown that, for the G stars, the Pleiades X-ray luminosity function is significantly brighter than the corresponding function for Hyades G dwarf stars. This finding indicates a dependence of X-ray luminosity on stellar age, which is confirmed by comparison of the same data with median X-ray luminosities of pre-main sequence and local disk population dwarf G stars. It is suggested that the significantly larger number of bright X-ray sources associated with G stars than with K stars, the lack of detection of M stars, and the relatively rapid rotation of the Pleiades K stars can be explained in terms of the onset of internal differential rotation near the convective envelope-radidative core interface after the spin-up phase during evolution to the main sequence.

Dynamical Asteroseismology: towards improving the theories of stellar structure and (tidal) evolution

NASA Astrophysics Data System (ADS)

Tkachenko, Andrew

2017-10-01

The potential of the dynamical asteroseismology, the research area that builds upon the synergies between the asteroseismology and binary stars research fields, is discussed in this manuscript. We touch upon the following topics: i) the mass discrepancy observed in intermediate-to high-mass main-sequence and evolved binaries as well as in the low mass systems that are still in the pre-main sequence phase of their evolution; ii) the rotationally induced mixing in high-mass stars, in particular how the most recent theoretical predictions and spectroscopic findings compare to the results of asteroseismic investigations; iii) internal gravity waves and their potential role in the evolution of binary star systems and surface nitrogen enrichment in high-mass stars; iv) the tidal evolution theory, in particular how its predictions of spin-orbit synchronisation and orbital circularisation compare to the present-day high-quality observations; v) the tidally-induced pulsations and their role in the angular momentum transport within binary star systems; vi) the scaling relations between fundamental and seismic properties of stars across the entire HR-diagram.

Description of HIV-1 Group M Molecular Epidemiology and Drug Resistance Prevalence in Equatorial Guinea from Migrants in Spain

PubMed Central

Yebra, Gonzalo; de Mulder, Miguel; Holguín, África

2013-01-01

Background The HIV epidemic is increasing in Equatorial Guinea (GQ), West Central Africa, but few studies have reported its HIV molecular epidemiology. We aimed to describe the HIV-1 group M (HIV-1M) variants and drug-resistance mutations in GQ using sequences sampled in this country and in Spain, a frequent destination of Equatoguinean migrants. Methods We collected 195 HIV-1M pol sequences from Equatoguinean subjects attending Spanish clinics during 1997-2011, and 83 additional sequences sampled in GQ in 1997 and 2008 from GenBank. All (n = 278) were re-classified using phylogeny and tested for drug-resistance mutations. To evaluate the origin of CRF02_AG in GQ, we analyzed 2,562 CRF02_AG sequences and applied Bayesian MCMC inference (BEAST program). Results Most Equatoguinean patients recruited in Spain were women (61.1%) or heterosexuals (87.7%). In the 278 sequences, the variants found were CRF02_AG (47.8%), A (13.7%), B (7.2%), C (5.8%), G (5.4%) and others (20.1%). We found 6 CRF02_AG clusters emerged from 1983.9 to 2002.5 with origin in GQ (5.5 sequences/cluster). Transmitted drug-resistance (TDR) rate among naïve patients attended in Spain (n = 144) was 4.7%: 3.4% for PI (all with M46IL), 1.8% for NRTI (all with M184V) and 0.9% for NNRTI (Y188L). Among pre-treated patients, 9/31 (29%) presented any resistance, mainly affecting NNRTI (27.8%). Conclusions We report a low (<5%) TDR rate among naïve, with PI as the most affected class. Pre-treated patients also showed a low drug-resistance prevalence (29%) maybe related to the insufficient treatment coverage in GQ. CRF02_AG was the prevalent HIV-1M variant and entered GQ through independent introductions at least since the early 1980s. PMID:23717585

Human intron-encoded Alu RNAs are processed and packaged into Wdr79-associated nucleoplasmic box H/ACA RNPs

PubMed Central

Jády, Beáta E.; Ketele, Amandine; Kiss, Tamás

2012-01-01

Alu repetitive sequences are the most abundant short interspersed DNA elements in the human genome. Full-length Alu elements are composed of two tandem sequence monomers, the left and right Alu arms, both derived from the 7SL signal recognition particle RNA. Since Alu elements are common in protein-coding genes, they are frequently transcribed into pre-mRNAs. Here, we demonstrate that the right arms of nascent Alu transcripts synthesized within pre-mRNA introns are processed into metabolically stable small RNAs. The intron-encoded Alu RNAs, termed AluACA RNAs, are structurally highly reminiscent of box H/ACA small Cajal body (CB) RNAs (scaRNAs). They are composed of two hairpin units followed by the essential H (AnAnnA) and ACA box motifs. The mature AluACA RNAs associate with the four H/ACA core proteins: dyskerin, Nop10, Nhp2, and Gar1. Moreover, the 3′ hairpin of AluACA RNAs carries two closely spaced CB localization motifs, CAB boxes (UGAG), which bind Wdr79 in a cumulative fashion. In contrast to canonical H/ACA scaRNPs, which concentrate in CBs, the AluACA RNPs accumulate in the nucleoplasm. Identification of 348 human AluACA RNAs demonstrates that intron-encoded AluACA RNAs represent a novel, large subgroup of H/ACA RNAs, which are apparently confined to human or primate cells. PMID:22892240

Exploring bacterial diversity in hospital environments by GS-FLX Titanium pyrosequencing.

PubMed

Poza, Margarita; Gayoso, Carmen; Gómez, Manuel J; Rumbo-Feal, Soraya; Tomás, María; Aranda, Jesús; Fernández, Ana; Bou, Germán

2012-01-01

Understanding microbial populations in hospital environments is crucial for improving human health. Hospital-acquired infections are an increasing problem in intensive care units (ICU). In this work we present an exploration of bacterial diversity at inanimate surfaces of the ICU wards of the University Hospital A Coruña (Spain), as an example of confined hospital environment subjected to selective pressure, taking the entrance hall of the hospital, an open and crowded environment, as reference. Surface swab samples were collected from both locations and recovered DNA used as template to amplify a hypervariable region of the bacterial 16S rRNA gene. Sequencing of the amplicons was performed at the Roche 454 Sequencing Center using GS-FLX Titanium procedures. Reads were pre-processed and clustered into OTUs (operational taxonomic units), which were further classified. A total of 16 canonical bacterial phyla were detected in both locations. Members of the phyla Firmicutes (mainly Staphylococcus and Streptococcus) and Actinobacteria (mainly Micrococcaceae, Corynebacteriaceae and Brevibacteriaceae) were over-represented in the ICU with respect to the Hall. The phyllum Proteobacteria was also well represented in the ICU, mainly by members of the families Enterobacteriaceae, Methylobacteriaceae and Sphingomonadaceae. In the Hall sample, the phyla Proteobacteria, Bacteroidetes, Deinococcus-Thermus and Cyanobacteria were over-represented with respect to the ICU. Over-representation of Proteobacteria was mainly due to the high abundance of Enterobacteriaceae members. The presented results demonstrate that bacterial diversity differs at the ICU and entrance hall locations. Reduced diversity detected at ICU, relative to the entrance hall, can be explained by its confined character and by the existence of antimicrobial selective pressure. This is the first study using deep sequencing techniques made in hospital wards showing substantial hospital microbial diversity.

An eye movement pre-training fosters the comprehension of processes and functions in technical systems.

PubMed

Skuballa, Irene T; Fortunski, Caroline; Renkl, Alexander

2015-01-01

The main research goal of the present study was to investigate in how far pre-training eye movements can facilitate knowledge acquisition in multimedia (pre-training principle). We combined considerations from research on eye movement modeling and pre-training to design and test a non-verbal eye movement-based pre-training. Participants in the experimental condition watched an animated circle moving in close spatial resemblance to a static visualization of a solar plant accompanied by a narration in a subsequently presented learning environment. This training was expected to foster top-down processes as reflected in gaze behavior during the learning process and enhance knowledge acquisition. We compared two groups (N = 45): participants in the experimental condition received pre-training in a first step and processed the learning material in a second step, whereas the control group underwent the second step without any pre-training. The pre-training group outperformed the control group in their learning outcomes, particularly in knowledge about processes and functions of the solar plant. However, the superior learning outcomes in the pre-training group could not be explained by eye-movement patterns. Furthermore, the pre-training moderated the relationship between experienced stress and learning outcomes. In the control group, high stress levels hindered learning, which was not found for the pre-training group. On a delayed posttest participants were requested to draw a picture of the learning content. Despite a non-significant effect of training on the quality of drawings, the pre-training showed associations between learning outcomes at the first testing time and process-related aspects in the quality of their drawings. Overall, non-verbal pre-training is a successful instructional intervention to promote learning processes in novices although these processes did not directly reflect in learners' eye movement behavior during learning.

DIRECT N-BODY MODELING OF THE OLD OPEN CLUSTER NGC 188: A DETAILED COMPARISON OF THEORETICAL AND OBSERVED BINARY STAR AND BLUE STRAGGLER POPULATIONS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Geller, Aaron M.; Hurley, Jarrod R.; Mathieu, Robert D., E-mail: a-geller@northwestern.edu, E-mail: mathieu@astro.wisc.edu, E-mail: jhurley@astro.swin.edu.au

2013-01-01

Following on from a recently completed radial-velocity survey of the old (7 Gyr) open cluster NGC 188 in which we studied in detail the solar-type hard binaries and blue stragglers of the cluster, here we investigate the dynamical evolution of NGC 188 through a sophisticated N-body model. Importantly, we employ the observed binary properties of the young (180 Myr) open cluster M35, where possible, to guide our choices for parameters of the initial binary population. We apply pre-main-sequence tidal circularization and a substantial increase to the main-sequence tidal circularization rate, both of which are necessary to match the observed tidalmore » circularization periods in the literature, including that of NGC 188. At 7 Gyr the main-sequence solar-type hard-binary population in the model matches that of NGC 188 in both binary frequency and distributions of orbital parameters. This agreement between the model and observations is in a large part due to the similarities between the NGC 188 and M35 solar-type binaries. Indeed, among the 7 Gyr main-sequence binaries in the model, only those with P {approx}> 1000 days begin to show potentially observable evidence for modifications by dynamical encounters, even after 7 Gyr of evolution within the star cluster. This emphasizes the importance of defining accurate initial conditions for star cluster models, which we propose is best accomplished through comparisons with observations of young open clusters like M35. Furthermore, this finding suggests that observations of the present-day binaries in even old open clusters can provide valuable information on their primordial binary populations. However, despite the model's success at matching the observed solar-type main-sequence population, the model underproduces blue stragglers and produces an overabundance of long-period circular main-sequence-white-dwarf binaries as compared with the true cluster. We explore several potential solutions to the paucity of blue stragglers and conclude that the model dramatically underproduces blue stragglers through mass-transfer processes. We suggest that common-envelope evolution may have been incorrectly imposed on the progenitors of the spurious long-period circular main-sequence-white-dwarf binaries, which perhaps instead should have gone through stable mass transfer to create blue stragglers, thereby bringing both the number and binary frequency of the blue straggler population in the model into agreement with the true blue stragglers in NGC 188. Thus, improvements in the physics of mass transfer and common-envelope evolution employed in the model may in fact solve both discrepancies with the observations. This project highlights the unique accessibility of open clusters to both comprehensive observational surveys and full-scale N-body simulations, both of which have only recently matured sufficiently to enable such a project, and underscores the importance of open clusters to the study of star cluster dynamics.« less

Sequences downstream of AAUAAA signals affect pre-mRNA cleavage and polyadenylation in vitro both directly and indirectly.

PubMed Central

Ryner, L C; Takagaki, Y; Manley, J L

1989-01-01

To investigate the role of sequences lying downstream of the conserved AAUAAA hexanucleotide in pre-mRNA cleavage and polyadenylation, deletions or substitutions were constructed in polyadenylation signals from simian virus 40 and adenovirus, and their effects were assayed in both crude and fractionated HeLa cell nuclear extracts. As expected, these sequences influenced the efficiency of both cleavage and polyadenylation as well as the accuracy of the cleavage reaction. Sequences near or upstream of the actual site of poly(A) addition appeared to specify a unique cleavage site, since their deletion resulted, in some cases, in heterogeneous cleavage. Furthermore, the sequences that allowed the simian virus 40 late pre-RNA to be cleaved preferentially by partially purified cleavage activity were also those at the cleavage site itself. Interestingly, sequences downstream of the cleavage site interacted with factors not directly involved in catalyzing cleavage and polyadenylation, since the effects of deletions were substantially diminished when partially purified components were used in assays. In addition, these sequences contained elements that could affect 3'-end formation both positively and negatively. Images PMID:2566911

Generalizations of γ-open set in topological spaces

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bhattacharya, Baby, E-mail: babybhatt75@gmail.com; Paul, Arnab, E-mail: mrarnabpaul87@gmail.com

The main aim of this work is to study three generalized forms of γ-open set due to D. Andrijevic (D. Andrijevic, On the Topology Generated by pre-open sets, Presented at the Sixth Prague Topological Symposium, 39 (1987), 367-376)in a topological space. Out of which the dual appearance of one is the stronger form of b-locally closed set in the sense of Arafa A. Nasef (A. A Nasef,On b-locally closed sets and related topics, CHAOS SOLITONS & FRACTALS 12(2001) 1909-1915). Also, we introduce the concept of different types of continuity and study their basic properties by using these newly defined sets.more » Finally, we establish the interrelationships among themselves together with some already existing generalized forms of continuity.« less

Circular RNAs: Unexpected outputs of many protein-coding genes

PubMed Central

Wilusz, Jeremy E.

2017-01-01

ABSTRACT Pre-mRNAs from thousands of eukaryotic genes can be non-canonically spliced to generate circular RNAs, some of which accumulate to higher levels than their associated linear mRNA. Recent work has revealed widespread mechanisms that dictate whether the spliceosome generates a linear or circular RNA. For most genes, circular RNA biogenesis via backsplicing is far less efficient than canonical splicing, but circular RNAs can accumulate due to their long half-lives. Backsplicing is often initiated when complementary sequences from different introns base pair and bring the intervening splice sites close together. This process is further regulated by the combinatorial action of RNA binding proteins, which allow circular RNAs to be expressed in unique patterns. Some genes do not require complementary sequences to generate RNA circles and instead take advantage of exon skipping events. It is still unclear what most mature circular RNAs do, but future investigations into their functions will be facilitated by recently described methods to modulate circular RNA levels. PMID:27571848

Developing the personal narratives of children with complex communication needs associated with intellectual disabilities: What is the potential of Storysharing® ?

PubMed

Bunning, Karen; Gooch, Lynsey; Johnson, Miranda

2017-07-01

Sharing personal experience in narrative is challenging for individuals with intellectual disabilities. The aim was to investigate the potential of Storysharing ® (Storysharing is an innovative communication method based on personal narrative, which has been developed to support conversations with people who have severe difficulties in communication) intervention. The study involved eleven pupil-educational supporter dyads at a special school. Storysharing ® was implemented over a 15-week period. Personal narratives were captured on video pre- and post-intervention. The data were analysed for discourse and narrative. Significant differences revealed a decline in 'query-answer' sequences and an increase in supporter use of 'prompts'. After intervention, there were fewer story episodes. Narrative structure showed gains in action sequences leading to climax, and in closing elements, indicating a more complete narrative. The Storysharing ® intervention appears to be associated with changes to the dyadic, personal narratives illustrating its potential. © 2016 John Wiley & Sons Ltd.

The first whole transcriptomic exploration of pre-oviposited early chicken embryos using single and bulked embryonic RNA-sequencing.

PubMed

Hwang, Young Sun; Seo, Minseok; Choi, Hee Jung; Kim, Sang Kyung; Kim, Heebal; Han, Jae Yong

2018-04-01

The chicken is a valuable model organism, especially in evolutionary and embryology research because its embryonic development occurs in the egg. However, despite its scientific importance, no transcriptome data have been generated for deciphering the early developmental stages of the chicken because of practical and technical constraints in accessing pre-oviposited embryos. Here, we determine the entire transcriptome of pre-oviposited avian embryos, including oocyte, zygote, and intrauterine embryos from Eyal-giladi and Kochav stage I (EGK.I) to EGK.X collected using a noninvasive approach for the first time. We also compare RNA-sequencing data obtained using a bulked embryo sequencing and single embryo/cell sequencing technique. The raw sequencing data were preprocessed with two genome builds, Galgal4 and Galgal5, and the expression of 17,108 and 26,102 genes was quantified in the respective builds. There were some differences between the two techniques, as well as between the two genome builds, and these were affected by the emergence of long intergenic noncoding RNA annotations. The first transcriptome datasets of pre-oviposited early chicken embryos based on bulked and single embryo sequencing techniques will serve as a valuable resource for investigating early avian embryogenesis, for comparative studies among vertebrates, and for novel gene annotation in the chicken genome.

Formation of close binary black holes merging due to gravitational-wave radiation

NASA Astrophysics Data System (ADS)

Tutukov, A. V.; Cherepashchuk, A. M.

2017-10-01

The conditions for the formation of close-binary black-hole systems merging over the Hubble time due to gravitational-wave radiation are considered in the framework of current ideas about the evolution of massive close-binary systems. The original systems whose mergers were detected by LIGO consisted of main-sequence stars with masses of 30-100 M ⊙. The preservation of the compactness of a binary black hole during the evolution of its components requires either the formation of a common envelope, probably also with a low initial abundance of metals, or the presence of a "kick"—a velocity obtained during a supernova explosion accompanied by the formation of a black hole. In principle, such a kick can explain the relatively low frequency of mergers of the components of close-binary stellar black holes, if the characteristic speed of the kick exceeds the orbital velocities of the system components during the supernova explosion. Another opportunity for the components of close-binary systems to approach each other is related to their possible motion in a dense molecular cloud.

Common features and peculiarities of the seismic activity at Phlegraean Fields, Long Valley, and Vesuvius

USGS Publications Warehouse

Marzocchi, W.; Vilardo, G.; Hill, D.P.; Ricciardi, G.P.; Ricco, C.

2001-01-01

We analyzed and compared the seismic activity that has occurred in the last two to three decades in three distinct volcanic areas: Phlegraean Fields, Italy; Vesuvius, Italy; and Long Valley, California. Our main goal is to identify and discuss common features and peculiarities in the temporal evolution of earthquake sequences that may reflect similarities and differences in the generating processes between these volcanic systems. In particular, we tried to characterize the time series of the number of events and of the seismic energy release in terms of stochastic, deterministic, and chaotic components. The time sequences from each area consist of thousands of earthquakes that allow a detailed quantitative analysis and comparison. The results obtained showed no evidence for either deterministic or chaotic components in the earthquake sequences in Long Valley caldera, which appears to be dominated by stochastic behavior. In contrast, earthquake sequences at Phlegrean Fields and Mount Vesuvius show a deterministic signal mainly consisting of a 24-hour periodicity. Our analysis suggests that the modulation in seismicity is in some way related to thermal diurnal processes, rather than luni-solar tidal effects. Independently from the process that generates these periodicities on the seismicity., it is suggested that the lack (or presence) of diurnal cycles is seismic swarms of volcanic areas could be closely linked to the presence (or lack) of magma motion.

Detection and genotyping of torque teno virus (TTV) in healthy blood donors and patients infected with HBV or HCV in Qatar.

PubMed

AbuOdeh, Raed; Al-Mawlawi, Naema; Al-Qahtani, Ahmed A; Bohol, Marie Fe F; Al-Ahdal, Mohammed N; Hasan, Haydar A; AbuOdeh, Lamees; Nasrallah, Gheyath K

2015-07-01

Torque Teno virus (TTV) has been associated with non A-G hepatitis. The goal of this study was to estimate the infection rates and genotypic characteristics of TTV in the State of Qatar. A total of 644 blood samples representing different nationalities: (i) Qatari (118) and (ii) non-Qatari (526) nationals (mostly from Arab and South Eeast Asia countries) were tested for the presence of TTV DNA by nested PCR. The majority (573) of the blood samples belonged to healthy blood donors, whereas 54 and 53 of the blood samples belonged to patients infected with hepatitis B virus (HBV) and hepatitis C virus (HCV), respectively. The results obtained showed that the TTV infection rates in the healthy blood donors, and those infected with HBV or HCV patients were 81.4, 90.75 and 84.9%, respectively. Significant association between TTV viremia and age, or nationality was observed. Sequence analysis of PCR fragments amplified from the 5'-untranslated region (5'-UTR) of all (531) TTV positive samples showed that 65.5% (348/531) of the PCR fragment sequences were classified into main genogroup 3, followed by main genogroups 5 (24%), 2 (5.8%), and 1 (4.7%). Genogroup 4 was not detected among the our studied subjects. Phylogenetic and pairwise analyses using sequences from TTV viremic samples also showed an overall close similarity to the main genogroup 3. In conclusion, there was no significant difference in the rates of TTV detection among Qataris and non-Qataris and several genotypes, mainly genotype 3, were isolated. © 2015 Wiley Periodicals, Inc.

Detection and characterisation of coronaviruses in migratory and non-migratory Australian wild birds.

PubMed

Chamings, Anthony; Nelson, Tiffanie M; Vibin, Jessy; Wille, Michelle; Klaassen, Marcel; Alexandersen, Soren

2018-04-13

We evaluated the presence of coronaviruses by PCR in 918 Australian wild bird samples collected during 2016-17. Coronaviruses were detected in 141 samples (15.3%) from species of ducks, shorebirds and herons and from multiple sampling locations. Sequencing of selected positive samples found mainly gammacoronaviruses, but also some deltacoronaviruses. The detection rate of coronaviruses was improved by using multiple PCR assays, as no single assay could detect all coronavirus positive samples. Sequencing of the relatively conserved Orf1 PCR amplicons found that Australian duck gammacoronaviruses were similar to duck gammacoronaviruses around the world. Some sequenced shorebird gammacoronaviruses belonged to Charadriiformes lineages, but others were more closely related to duck gammacoronaviruses. Australian duck and heron deltacoronaviruses belonged to lineages with other duck and heron deltacoronaviruses, but were almost 20% different in nucleotide sequence to other deltacoronavirus sequences available. Deltacoronavirus sequences from shorebirds formed a lineage with a deltacoronavirus from a ruddy turnstone detected in the United States. Given that Australian duck gammacoronaviruses are highly similar to those found in other regions, and Australian ducks rarely come into contact with migratory Palearctic duck species, we hypothesise that migratory shorebirds are the important vector for moving wild bird coronaviruses into and out of Australia.

Short intronic repeat sequences facilitate circular RNA production

PubMed Central

Liang, Dongming

2014-01-01

Recent deep sequencing studies have revealed thousands of circular noncoding RNAs generated from protein-coding genes. These RNAs are produced when the precursor messenger RNA (pre-mRNA) splicing machinery “backsplices” and covalently joins, for example, the two ends of a single exon. However, the mechanism by which the spliceosome selects only certain exons to circularize is largely unknown. Using extensive mutagenesis of expression plasmids, we show that miniature introns containing the splice sites along with short (∼30- to 40-nucleotide) inverted repeats, such as Alu elements, are sufficient to allow the intervening exons to circularize in cells. The intronic repeats must base-pair to one another, thereby bringing the splice sites into close proximity to each other. More than simple thermodynamics is clearly at play, however, as not all repeats support circularization, and increasing the stability of the hairpin between the repeats can sometimes inhibit circular RNA biogenesis. The intronic repeats and exonic sequences must collaborate with one another, and a functional 3′ end processing signal is required, suggesting that circularization may occur post-transcriptionally. These results suggest detailed and generalizable models that explain how the splicing machinery determines whether to produce a circular noncoding RNA or a linear mRNA. PMID:25281217

Isothermal folding of a light-up bio-orthogonal RNA origami nanoribbon.

PubMed

Torelli, Emanuela; Kozyra, Jerzy Wieslaw; Gu, Jing-Ying; Stimming, Ulrich; Piantanida, Luca; Voïtchovsky, Kislon; Krasnogor, Natalio

2018-05-03

RNA presents intringuing roles in many cellular processes and its versatility underpins many different applications in synthetic biology. Nonetheless, RNA origami as a method for nanofabrication is not yet fully explored and the majority of RNA nanostructures are based on natural pre-folded RNA. Here we describe a biologically inert and uniquely addressable RNA origami scaffold that self-assembles into a nanoribbon by seven staple strands. An algorithm is applied to generate a synthetic De Bruijn scaffold sequence that is characterized by the lack of biologically active sites and repetitions larger than a predetermined design parameter. This RNA scaffold and the complementary staples fold in a physiologically compatible isothermal condition. In order to monitor the folding, we designed a new split Broccoli aptamer system. The aptamer is divided into two nonfunctional sequences each of which is integrated into the 5' or 3' end of two staple strands complementary to the RNA scaffold. Using fluorescence measurements and in-gel imaging, we demonstrate that once RNA origami assembly occurs, the split aptamer sequences are brought into close proximity forming the aptamer and turning on the fluorescence. This light-up 'bio-orthogonal' RNA origami provides a prototype that can have potential for in vivo origami applications.

rVISTA 2.0: Evolutionary Analysis of Transcription Factor Binding Sites

DOE Office of Scientific and Technical Information (OSTI.GOV)

Loots, G G; Ovcharenko, I

2004-01-28

Identifying and characterizing the patterns of DNA cis-regulatory modules represents a challenge that has the potential to reveal the regulatory language the genome uses to dictate transcriptional dynamics. Several studies have demonstrated that regulatory modules are under positive selection and therefore are often conserved between related species. Using this evolutionary principle we have created a comparative tool, rVISTA, for analyzing the regulatory potential of noncoding sequences. The rVISTA tool combines transcription factor binding site (TFBS) predictions, sequence comparisons and cluster analysis to identify noncoding DNA regions that are highly conserved and present in a specific configuration within an alignment. Heremore » we present the newly developed version 2.0 of the rVISTA tool that can process alignments generated by both zPicture and PipMaker alignment programs or use pre-computed pairwise alignments of seven vertebrate genomes available from the ECR Browser. The rVISTA web server is closely interconnected with the TRANSFAC database, allowing users to either search for matrices present in the TRANSFAC library collection or search for user-defined consensus sequences. rVISTA tool is publicly available at http://rvista.dcode.org/.« less

Detection of Pasteuria penetrans infection in Meloidogyne arenaria race 1 in planta by polymerase chain reaction.

PubMed

Schmidt, L M; Preston, J F; Nong, G; Dickson, D W; Aldrich, H C

2004-06-01

We report on the development of a PCR-based assay to detect Pasteuria penetrans infection of Meloidogyne arenaria in planta using specific primers for recently sequenced sigE, spoIIAB and atpF genes of P. penetrans biotype P20. Amplification of these genes in crude DNA extracts of ground tomato root galls using real-time kinetic PCR distinguished infected from uninfected M. arenaria race 1 by analysis of consensus thresholds for single copy genes. Fluorescent in situ hybridization (FISH) using the sigE primer sequence as a probe shows hybridization to P. penetrans cells in various stages of vegetative (pre-endospore) development. Ratios of gene copies for sigE and 16S rDNA were obtained for P. penetrans and compared to Bacillus subtilis as a genomic paradigm of endospore-forming bacteria. Phylogenetic analysis of the sigE gene from Gram-positive, endospore-forming bacteria finds P. penetrans most closely related Paenbacillus polymyxa. The sporulation genes (spo genes), particularly sigE, have sequence diversity that recommends them for species and biotype differentiation of the numerous Pasteuria isolates that infect a large number of plant-parasitic nematodes.

Superposed orogenic collision and core-complex formation at the present contact between the Dinarides and the Pannonian basin: The Bukulja and Cer Mountains in central and western Serbia

NASA Astrophysics Data System (ADS)

Matenco, Liviu; Toljic, Marinko; Ducea, Mihai; Stojadinovic, Uros

2010-05-01

Formation of large extensional detachments during orogenic collapse can follow inherited weakness zones such as major asymmetries given by pre-existing subduction zones active during mountain building processes. This is valid in particular in low-topography foreland coupling orogens of Mediterranean type where large amounts of deformation is concentrated in their lower plates, favoring weakness zones activated during a subsequent phase of extensional collapse. One good place to study the orogenic collapse post-dating major collision is the NE margin of the Dinarides in central and western Serbia, where Cretaceous-Eocene shortening and collision was recorded in the Alpine Tethys Sava zone between the European-derived Dacia and Tisza mega-units and the lower Adriatic plate. This is the same place where the Pannonian basin formed as a Miocene back-arc basin in response to a different subduction and roll-back taking place along the external Carpathians. A lineament of Paleogene and Miocene plutons is observed at the northern and eastern margin of the Dinarides, interpreted to be the product of both syn- to post-orogenic subduction magmatism and of decompressional melting during the Pannonian extension. Two of these plutons, Cer and Bukulja, located in western and respectively central Serbia, are intruded in the Jadar-Kopaonik composite thrust sheet, part of the lower Adriatic plate, near the contact with the main suture formed during the Cretaceous-Eocene subduction of the Sava zone. The Lower Miocene age (19-17Ma) Bukulja intrusion is a S-type granite with rare aplitic veins (Cvetkovic et al., 2007). The Cer intrusive complex is a S type two mica granite of around 16Ma in age with an older I-type quartz monzonite component (Koroneos et al. in press). Both granitoids are intruded into the Jadar-Kopaonik metamorphic series, which are in direct contact along the northern, eastern and southern flank with non-metamorphosed, mainly clastic sediments of Cretaceous-Miocene in age and, in the case of Bukulja, with serpentinized ophiolites. The metamorphic sequences are generally characterized by a Paleozoic age meta-sedimentary basement and a meta-sedimentary and meta-volcanic sequence. In the case of Bukulja, a succession of contrasting metamorphosed lithologies has been observed such as sandstones, black limestones, shallow water white limestones, basic volcanic sequences, deep nodular limestones and turbiditic sequences. The lower part of the sequence represents a metamorphosed Triassic sequence similar to what has been defined as the Kopaonik and Studenica series in southern Serbia. This part of the sequence is characterized by at least 3 successive stages of folding, asymmetric folds with WSW-ward vergence and NNE-SSW upright folds being affected by vertical flattening folds associated with extension (see also Marovic et al., 2007). The upper part of the sequence, which is the only part outcropping along the eastern flank of the Cer granitoid, is made up by metamorphosed distal turbidites which have been palinologically dated in Bukulja as Upper Cretaceous in age. This is the metamorphosed equivalent of the Upper Cretaceous - Eocene "flysch"-type of deposits commonly observed elsewhere in the main Sava subduction zone. These rocks are overprinted with a pervasive and strong extensional milonitic foliation indicating top-100 movement of the hanging-wall and are in direct contact with non-metamorphosed, but similar Upper Cretaceous distal turbidites. This suggests a large-scale tectonic omission along the eastern flanks of the Bukulja and Cer detachment. In the case of Bukulja, the extension was associated with the formation of the Early Miocene Morava basin in the detachment hanging-wall, which is an endemic lacustrine precursor of the much larger Middle-Late Miocene Pannonian basin. These finding points towards a bi-modal evolution of the internal Dinarides in central and western Serbia near the present-day contact with the Pannonian basin. An Upper Cretaceous-Eocene phase of top-WSW shortening and metamorphism in the Sava zone and its subducting lower Adriatic plate was subsequently followed by massive core-complex exhumation and top-E directed extension during initiation of the Carpathians back-arc extension. Interestingly, the newly defined extensional detachments accompanying the Pannonian extension closely follow the pre-existing subduction zone and its associated duplications in the lower orogenic plate. This conclusion is compatible with observations in other areas of the Dinarides, such as the Prosara-Motajica in Bosnia/Croatia or Kopaonik-Studenica in southern Serbia (Schefer et al., 2008; Ustaszewski et al., 2009).

Using He I λ10830 to Diagnose Mass Flows Around Herbig Ae/Be Stars

NASA Astrophysics Data System (ADS)

Cauley, Paul W.; Johns-Krull, Christopher M.

2015-01-01

The pre-main sequence Herbig Ae/Be stars (HAEBES) are the intermediate mass cousins of the low mass T Tauri stars (TTSs). However, it is not clear that the same accretion and mass outflow mechanisms operate identically in both mass regimes. Classical TTSs (CTTSs) accrete material from their disks along stellar magnetic field lines in a scenario called magnetospheric accretion. Magnetospheric accretion requires a strong stellar dipole field in order to truncate the inner gas disk. These fields are either absent or very weak on a large majority of HAEBES, challenging the view that magnetospheric accretion is the dominant accretion mechanism. If magnetospheric accretion does not operate similarly around HAEBES as it does around CTTSs, then strong magnetocentrifugal outflows, which are directly linked to accretion and are ubiquitous around CTTSs, may be driven less efficiently from HAEBE systems. Here we present high resolution spectroscopic observations of the He I λ10830 line in a sample of 48 HAEBES. He I λ10830 is an excellent tracer of both mass infall and outflow which is directly manifested as red and blue-shifted absorption in the profile morphologies. These features, among others, are common in our sample. The occurrence of both red and blue-shifted absorption profiles is less frequent, however, than is found in CTTSs. Statistical contingency tests confirm this difference at a significant level. In addition, we find strong evidence for smaller disk truncation radii in the objects displaying red-shifted absorption profiles. This is expected for HAEBES experiencing magnetospheric accretion based on their large rotation rates and weak magnetic field strengths. Finally, the low incidence of blue-shifted absorption in our sample compared to CTTSs and the complete lack of simultaneous red and blue-shifted absorption features suggests that magnetospheric accretion in HAEBES is less efficient at driving strong outflows. The stellar wind-like outflows that are observed are likely driven, at least in part, by boundary layer accretion. The smaller (or absent) disk truncation radii in HAEBES may have consequences for the frequency of planets in close orbits around main sequence B and A stars.

A Constraint on the Formation Timescale of the Young Open Cluster NGC 2264: Lithium Abundance of Pre-main Sequence Stars

NASA Astrophysics Data System (ADS)

Lim, Beomdu; Sung, Hwankyung; Kim, Jinyoung S.; Bessell, Michael S.; Hwang, Narae; Park, Byeong-Gon

2016-11-01

The timescale of cluster formation is an essential parameter in order to understand the formation process of star clusters. Pre-main sequence (PMS) stars in nearby young open clusters reveal a large spread in brightness. If the spread were considered to be a result of a real spread in age, the corresponding cluster formation timescale would be about 5-20 Myr. Hence it could be interpreted that star formation in an open cluster is prolonged for up to a few tens of Myr. However, difficulties in reddening correction, observational errors, and systematic uncertainties introduced by imperfect evolutionary models for PMS stars can result in an artificial age spread. Alternatively, we can utilize Li abundance as a relative age indicator of PMS star to determine the cluster formation timescale. The optical spectra of 134 PMS stars in NGC 2264 have been obtained with MMT/Hectochelle. The equivalent widths have been measured for 86 PMS stars with a detectable Li line (3500\\lt {T}{eff}[{{K}}]≤slant 6500). Li abundance under the condition of local thermodynamic equilibrium (LTE) was derived using the conventional curve of growth method. After correction for non-LTE effects, we find that the initial Li abundance of NGC 2264 is A({Li})=3.2+/- 0.2. From the distribution of the Li abundances, the underlying age spread of the visible PMS stars is estimated to be about 3-4 Myr and this, together with the presence of embedded populations in NGC 2264, suggests that the cluster formed on a timescale shorter than 5 Myr.

Binary progenitors of supernovae

NASA Astrophysics Data System (ADS)

Trimble, V.

1984-12-01

Among the massive stars that are expected to produce Type II, hydrogen-rich supernovae, the presence of a close companion can increase the main sequence mass needed to yield a collapsing core. In addition, due to mass transfer from the primary to the secondary, the companion enhances the stripping of the stellar hydrogen envelope produced by single star winds and thereby makes it harder for the star to give rise to a typical SN II light curve. Among the less massive stars that may be the basis for Type I, hydrogen-free supernovae, a close companion could be an innocent bystander to carbon detonation/deflagration in the primary. It may alternatively be a vital participant which transfers material to a white dwarf primary and drives it to explosive conditions.

SIMAP--a comprehensive database of pre-calculated protein sequence similarities, domains, annotations and clusters.

PubMed

Rattei, Thomas; Tischler, Patrick; Götz, Stefan; Jehl, Marc-André; Hoser, Jonathan; Arnold, Roland; Conesa, Ana; Mewes, Hans-Werner

2010-01-01

The prediction of protein function as well as the reconstruction of evolutionary genesis employing sequence comparison at large is still the most powerful tool in sequence analysis. Due to the exponential growth of the number of known protein sequences and the subsequent quadratic growth of the similarity matrix, the computation of the Similarity Matrix of Proteins (SIMAP) becomes a computational intensive task. The SIMAP database provides a comprehensive and up-to-date pre-calculation of the protein sequence similarity matrix, sequence-based features and sequence clusters. As of September 2009, SIMAP covers 48 million proteins and more than 23 million non-redundant sequences. Novel features of SIMAP include the expansion of the sequence space by including databases such as ENSEMBL as well as the integration of metagenomes based on their consistent processing and annotation. Furthermore, protein function predictions by Blast2GO are pre-calculated for all sequences in SIMAP and the data access and query functions have been improved. SIMAP assists biologists to query the up-to-date sequence space systematically and facilitates large-scale downstream projects in computational biology. Access to SIMAP is freely provided through the web portal for individuals (http://mips.gsf.de/simap/) and for programmatic access through DAS (http://webclu.bio.wzw.tum.de/das/) and Web-Service (http://mips.gsf.de/webservices/services/SimapService2.0?wsdl).

An ultra-sparse code underliesthe generation of neural sequences in a songbird

NASA Astrophysics Data System (ADS)

Hahnloser, Richard H. R.; Kozhevnikov, Alexay A.; Fee, Michale S.

2002-09-01

Sequences of motor activity are encoded in many vertebrate brains by complex spatio-temporal patterns of neural activity; however, the neural circuit mechanisms underlying the generation of these pre-motor patterns are poorly understood. In songbirds, one prominent site of pre-motor activity is the forebrain robust nucleus of the archistriatum (RA), which generates stereotyped sequences of spike bursts during song and recapitulates these sequences during sleep. We show that the stereotyped sequences in RA are driven from nucleus HVC (high vocal centre), the principal pre-motor input to RA. Recordings of identified HVC neurons in sleeping and singing birds show that individual HVC neurons projecting onto RA neurons produce bursts sparsely, at a single, precise time during the RA sequence. These HVC neurons burst sequentially with respect to one another. We suggest that at each time in the RA sequence, the ensemble of active RA neurons is driven by a subpopulation of RA-projecting HVC neurons that is active only at that time. As a population, these HVC neurons may form an explicit representation of time in the sequence. Such a sparse representation, a temporal analogue of the `grandmother cell' concept for object recognition, eliminates the problem of temporal interference during sequence generation and learning attributed to more distributed representations.

Hybrid channel flow-type mechanisms in the Greater Himalayan Sequence (West Nepal): new constraints from vorticity of flow and quartz petrofabric analyses.

NASA Astrophysics Data System (ADS)

Frassi, Chiara

2016-04-01

Three main tectono-metamorphic units are classically recognized along the Himalayan belt: the Lesser Himalayan (LH), the Greater Himalayan sequence (GHS) and the Tibetan Sedimentary sequence (TSS). The GHS may be interpreted as a low-viscosity tabular body of mid-crustal rocks extruded southward in Miocene times beneath the Tibetan plateau between two parallel and opposite-sense crustal-scale shear zones: the Main Central thrust at the base, and the South Tibetan Detachment system at the top. The pre-/syn-shearing mineral assemblage documented within these crustal-scale shear zones indicates that the metamorphic grade increases toward the core of the GHS producing an inverted and a normal thermal gradient respectively on the top and on the bottom of the slab. In addition, thermal profiles estimated using both petrology- and microstructures/fabrics-based thermometers indicate that the metamorphic isograds are condensed. Although horizontal extension and vorticity estimates collected across the GHS could be strongly biased by the criteria used to define the map position of the MCT, published vorticity data document general shear flow (1>Wk>0) within the slab with a pure-shear component of flow slightly predominant within the core of the GHS whereas the simple-shear component seems to dominate at the top of the slab. The lower boundary of the GHS records a general shear flow with a comparable contribution of simple and pure shearing. The associated crustal extrusion is compatible with Couette - Poiseuille velocity flow profile as assumed in crustal-scale channel flow-type models In this study, the quartz c-axis petrofabrics, vorticity and deformation-temperature studies are integrated with microstructures and metamorphic studies to individuate the location of the MCT and to document the spatial distribution of ductile deformation patterns across the lower portion of the GHS exposed in the Chaudabise river valley in western Nepal. My results indicate that the Main Central Thrust is located ˜5 km structurally below the previous mapped locations. Deformation temperature increases up structural section from ˜450°C to ˜650°C and overlaps with peak metamorphic temperature indicating that penetrative shearing was responsible for the exhumation of the GHS occurred at "close" to peak metamorphic conditions. I interpreted the telescoping and the inversion of the paleo-isotherms at the base of the GHS as produced mainly by a sub-simple shearing (Wm = 0.88-1) pervasively distributed through the lower portion of the GHS. The results are consistent with hybrid channel flow-type models where the boundary between lower and upper portions of the GHS, broadly corresponding to the tectono-metamorphic discontinuity recently documented in west Nepal, represents the limit between buried material, affected by dominant simple shearing, and exhumed material affected by a general flow dominates by pure shearing. This interpretation is consistent with the recent models suggesting the simultaneous operation of channel flow- and critical wedge-type processes at different structural depth.

Benthic foraminifera baseline assemblages from a coastal nearshore reef complex on the central Great Barrier Reef

NASA Astrophysics Data System (ADS)

Johnson, Jamie; Perry, Chris; Smithers, Scott; Morgan, Kyle

2016-04-01

Declining water quality due to river catchment modification since European settlement (c. 1850 A.D.) represents a major threat to the health of coral reefs on Australia's Great Barrier Reef (GBR), particularly for those located in the coastal waters of the GBR's inner-shelf. These nearshore reefs are widely perceived to be most susceptible to declining water quality owing to their close proximity to river point sources. Despite this, nearshore reefs have been relatively poorly studied with the impacts and magnitudes of environmental degradation still remaining unclear. This is largely due to ongoing debates concerning the significance of increased sediment yields against naturally high background sedimentary regimes. Benthic foraminifera are increasingly used as tools for monitoring environmental and ecological change on coral reefs. On the GBR, the majority of studies have focussed on the spatial distributions of contemporary benthic foraminiferal assemblages. While baseline assemblages from other environments (e.g. inshore reefs and mangroves) have been described, very few records exist for nearshore reefs. Here, we present preliminary results from the first palaeoecological study of foraminiferal assemblages of nearshore reefs on the central GBR. Cores were recovered from the nearshore reef complex at Paluma Shoals using percussion techniques. Recovery was 100%, capturing the entire Holocene reef sequence of the selected reef structures. Radiocarbon dating and subsequent age-depth modelling techniques were used to identify reef sequences pre-dating European settlement. Benthic foraminifera assemblages were reconstructed from the identified sequences to establish pre-European ecological baselines with the aim of providing a record of foraminiferal distribution during vertical reef accretion and against which contemporary ecological change may be assessed.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hachisu, Izumi; Kato, Mariko, E-mail: hachisu@ea.c.u-tokyo.ac.jp, E-mail: mariko@educ.cc.keio.ac.jp

We identified a general course of classical nova outbursts in the B – V versus U – B color-color diagram. It is reported that novae show spectra similar to those of A-F supergiants near optical light maximum. However, they do not follow the supergiant sequence in the color-color diagram, neither the blackbody nor the main-sequence sequence. Instead, we found that novae evolve along a new sequence in the pre-maximum and near-maximum phases, which we call 'the nova-giant sequence'. This sequence is parallel to but Δ(U – B) ≈ –0.2 mag bluer than the supergiant sequence. This is because the massmore » of a nova envelope is much (∼10{sup –4} times) less than that of a normal supergiant. After optical maximum, its color quickly evolves back blueward along the same nova-giant sequence and reaches the point of free-free emission (B – V = –0.03, U – B = –0.97), which coincides with the intersection of the blackbody sequence and the nova-giant sequence, and remains there for a while. Then the color evolves leftward (blueward in B – V but almost constant in U – B), owing mainly to the development of strong emission lines. This is the general course of nova outbursts in the color-color diagram, which was deduced from eight well-observed novae in various speed classes. For a nova with unknown extinction, we can determine a reliable value of the color excess by matching the observed track of the target nova with this general course. This is a new and convenient method for obtaining the color excesses of classical novae. Using this method, we redetermined the color excesses of 20 well-observed novae. The obtained color excesses are in reasonable agreement with the previous results, which in turn support the idea of our general track of nova outbursts. Additionally, we estimated the absolute V magnitudes of about 30 novae using a method for time-stretching nova light curves to analyze the distance-reddening relations of the novae.« less

Humanoid assessing rehabilitative exercises.

PubMed

Simonov, M; Delconte, G

2015-01-01

This article is part of the Focus Theme of Methods of Information in Medicine on "New Methodologies for Patients Rehabilitation". The article presents the approach in which the rehabilitative exercise prepared by healthcare professional is encoded as formal knowledge and used by humanoid robot to assist patients without involving other care actors. The main objective is the use of humanoids in rehabilitative care. An example is pulmonary rehabilitation in COPD patients. Another goal is the automated judgment functionality to determine how the rehabilitation exercise matches the pre-programmed correct sequence. We use the Aldebaran Robotics' NAO humanoid to set up artificial cognitive application. Pre-programmed NAO induces elderly patient to undertake humanoid-driven rehabilitation exercise, but needs to evaluate the human actions against the correct template. Patient is observed using NAO's eyes. We use the Microsoft Kinect SDK to extract motion path from the humanoid's recorded video. We compare human- and humanoid-operated process sequences by using the Dynamic Time Warping (DTW) and test the prototype. This artificial cognitive software showcases the use of DTW algorithm to enable humanoids to judge in near real-time about the correctness of rehabilitative exercises performed by patients following the robot's indications. One could enable better sustainable rehabilitative care services in remote residential settings by combining intelligent applications piloting humanoids with the DTW pattern matching algorithm applied at run time to compare humanoid- and human-operated process sequences. In turn, it will lower the need of human care.

The evolution of angular momentum among zero-age main-sequence solar-type stars

NASA Technical Reports Server (NTRS)

Soderblom, David R.; Stauffer, John R.; Macgregor, Keith B.; Jones, Burton F.

1993-01-01

We consider a survey of rotation among F, G, and K dwarfs of the Pleiades in the context of other young clusters (Alpha Persei and the Hyades) and pre-main-sequence (PMS) stars (in Taurus-Auriga and Orion) in order to examine how the angular momentum of a star like the sun evolves during its early life on the main sequence. The rotation of PMS stars can be evolved into distributions like those seen in the young clusters if there is only modest, rotation-independent angular momentum loss prior to the ZAMS. Even then, the ultrafast rotators (UFRs, or ZAMS G and K dwarfs with v sin i equal to or greater than 30 km/s) must owe their extra angular momentum to their conditions of formation and to different angular momentum loss rates above a threshold velocity, for it is unlikely that these stars had angular momentum added as they neared the ZAMS, nor can a spread in ages within a cluster account for the range of rotation seen. Only a fraction of solar-type stars are thus capable of becoming UFRs, and it is not a phase that all stars experience. Simple scaling relations (like the Skumanich relation) applied to the observed surface rotation rates of young solar-type stars cannot reproduce the way in which the Pleiades evolve into the Hyades. We argue that invoking internal differential rotation in these ZAMS stars can explain several aspects of the observations and thus can provide a consistent picture of ZAMS angular momentum evolution.

On the determination of age and mass functions of stars in young open star clusters from the analysis of their luminosity functions

NASA Astrophysics Data System (ADS)

Piskunov, A. E.; Belikov, A. N.; Kharchenko, N. V.; Sagar, R.; Subramaniam, A.

2004-04-01

We construct the observed luminosity functions of the remote young open clusters NGC 2383, 2384, 4103, 4755, 7510 and Hogg 15 from CCD observations of them. The observed LFs are corrected for field star contamination determined with the help of a Galactic star count model. In the case of Hogg 15 and NGC 2383 we also consider the additional contamination from neighbouring clusters NGC 4609 and 2384, respectively. These corrections provide a realistic pattern of cluster LF in the vicinity of the main-sequence (MS) turn-on point and at fainter magnitudes reveal the so-called H-feature arising as a result of the transition of the pre-MS phase to the MS, which is dependent on the cluster age. The theoretical LFs are constructed representing a cluster population model with continuous star formation for a short time-scale and a power-law initial mass function (IMF), and these are fitted to the observed LF. As a result, we are able to determine for each cluster a set of parameters describing the cluster population (the age, duration of star formation, IMF slope and percentage of field star contamination). It is found that in spite of the non-monotonic behaviour of observed LFs, cluster IMFs can be described as power-law functions with slopes similar to Salpeter's value. The present main-sequence turn-on cluster ages are several times lower than those derived from the fitting of theoretical isochrones to the turn-off region of the upper main sequences.

The provenance of Archean clastic metasediments in the Narryer Gneiss Complex, western Australia: Trace element geochemistry, Nd isotopes, and U-Pb ages for detrital zircons

DOE Office of Scientific and Technical Information (OSTI.GOV)

Maas, R.; McCulloch, M.T.

1991-07-01

Clastic metasedimentary rocks of mid-Archean age from the Mt. Narryer and Jack Hills metasedimentary belts have REE patterns resembling those of mid- to late-Archean pelitic-quartzitic cratonic sequences elsewhere, and post-Archean continental rocks in general. Detrital zircons in the metasediments range in age from ca. 3,000 to 3,700 Ma. This indicates a provenance from mature cratonic sources controlled by K-rich granitic rocks. Additional minor sediment sources were identified as older, mainly chemical sedimentary sequences, ultramafic rocks, and felsic rocks characterized by low HREE contents, perhaps of tonalitic affinity. Differences between sedimentary REE patterns and those in the surrounding 3.73-3.0 Ga orthogneissmore » terrain, and between detrital zircon ages and the age distribution in the gneisses, suggest that the present association of the metasedimentary belts with the orthogneiss terrain is of tectonic origin. The occurrence of detrital zircons with U-Pb ages > 4 Ga in certain quartzites and conglomerates of the Jack Hills and Mt. Narryer metasedimentary sequences indicates a further, most likely granitic, source. {epsilon}{sub Nd}(T{sub Dep}) values in Jack Hills metasediments vary widely (+5 to {minus}12) but have a smaller range in the Mt. Narryer belt ({minus}5 to {minus}9). The lowest {epsilon}{sub Nd} values of both sequences are interpreted to reflect the presence of detritus derived from 4.1-4.2 Ga old LREE-enriched continental crust in proportions considerably larger ({ge} 10%) than estimated previously from the abundance of pre-4 Ga detrital zircons ({approx}3%). This would imply the former existence of significant volumes of pre-4 Ga continental crust in the provenance of the Mt. Narryer and Jack Hills metasediments.« less

Reprocessing of Archival Direct Imaging Data of Herbig Ae/Be Stars

NASA Astrophysics Data System (ADS)

Safsten, Emily; Stephens, Denise C.

2017-01-01

Herbig Ae/Be (HAeBe) stars are intermediate mass (2-10 solar mass) pre-main sequence stars with circumstellar disks. They are the higher mass analogs of the better-known T Tauri stars. Observing planets within these young disks would greatly aid in understanding planet formation processes and timescales, particularly around massive stars. So far, only one planet, HD 100546b, has been confirmed to orbit a HAeBe star. With over 250 HAeBe stars known, and several observed to have disks with structures thought to be related to planet formation, it seems likely that there are as yet undiscovered planetary companions within the circumstellar disks of some of these young stars.Direct detection of a low-luminosity companion near a star requires high contrast imaging, often with the use of a coronagraph, and the subtraction of the central star's point spread function (PSF). Several processing algorithms have been developed in recent years to improve PSF subtraction and enhance the signal-to-noise of sources close to the central star. However, many HAeBe stars were observed via direct imaging before these algorithms came out. We present here current work with the PSF subtraction program PynPoint, which employs a method of principal component analysis, to reprocess archival images of HAeBe stars to increase the likelihood of detecting a planet in their disks.

3D architecture modeling of reservoir compartments in a Shingled Turbidite Reservoir using high-resolution seismic data and sparse well control, example from Mars {open_quotes}Pink{close_quotes} reservoir, Mississippi Canyon Area, Gulf of Mexico

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chapin, M.A.; Mahaffie, M.J.; Tiller, G.M.

1996-12-31

Economics of most deep-water development projects require large reservoir volumes to be drained with relatively few wells. The presence of reservoir compartments must therefore be detected and planned for in a pre-development stage. We have used 3-D seismic data to constrain large-scale, deterministic reservoir bodies in a 3-D architecture model of Pliocene-turbidite sands of the {open_quotes}E{close_quotes} or {open_quotes}Pink{close_quotes} reservoir, Prospect Mars, Mississippi Canyon Areas 763 and 807, Gulf of Mexico. Reservoir compartmentalization is influenced by stratigraphic shingling, which in turn is caused by low accommodation space predentin the upper portion of a ponded seismic sequence within a salt withdrawal mini-basin.more » The accumulation is limited by updip onlap onto a condensed section marl, and by lateral truncation by a large scale submarine erosion surface. Compartments were suggested by RFT pressure variations and by geochemical analysis of RFT fluid samples. A geological interpretation derived from high-resolution 3-D seismic and three wells was linked to 3-D architecture models through seismic inversion, resulting in a reservoir all available data. Distinguishing subtle stratigraphical shingles from faults was accomplished by detailed, loop-level mapping, and was important to characterize the different types of reservoir compartments. Seismic inversion was used to detune the seismic amplitude, adjust sandbody thickness, and update the rock properties. Recent development wells confirm the architectural style identified. This modeling project illustrates how high-quality seismic data and architecture models can be combined in a pre-development phase of a prospect, in order to optimize well placement.« less

3D architecture modeling of reservoir compartments in a Shingled Turbidite Reservoir using high-resolution seismic data and sparse well control, example from Mars [open quotes]Pink[close quotes] reservoir, Mississippi Canyon Area, Gulf of Mexico

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chapin, M.A.; Mahaffie, M.J.; Tiller, G.M.

1996-01-01

Economics of most deep-water development projects require large reservoir volumes to be drained with relatively few wells. The presence of reservoir compartments must therefore be detected and planned for in a pre-development stage. We have used 3-D seismic data to constrain large-scale, deterministic reservoir bodies in a 3-D architecture model of Pliocene-turbidite sands of the [open quotes]E[close quotes] or [open quotes]Pink[close quotes] reservoir, Prospect Mars, Mississippi Canyon Areas 763 and 807, Gulf of Mexico. Reservoir compartmentalization is influenced by stratigraphic shingling, which in turn is caused by low accommodation space predentin the upper portion of a ponded seismic sequence withinmore » a salt withdrawal mini-basin. The accumulation is limited by updip onlap onto a condensed section marl, and by lateral truncation by a large scale submarine erosion surface. Compartments were suggested by RFT pressure variations and by geochemical analysis of RFT fluid samples. A geological interpretation derived from high-resolution 3-D seismic and three wells was linked to 3-D architecture models through seismic inversion, resulting in a reservoir all available data. Distinguishing subtle stratigraphical shingles from faults was accomplished by detailed, loop-level mapping, and was important to characterize the different types of reservoir compartments. Seismic inversion was used to detune the seismic amplitude, adjust sandbody thickness, and update the rock properties. Recent development wells confirm the architectural style identified. This modeling project illustrates how high-quality seismic data and architecture models can be combined in a pre-development phase of a prospect, in order to optimize well placement.« less

Molecular epidemiology of hepatitis B virus in Misiones, Argentina.

PubMed

Mojsiejczuk, Laura Noelia; Torres, Carolina; Sevic, Ina; Badano, Inés; Malan, Richard; Flichman, Diego Martin; Liotta, Domingo Javier; Campos, Rodolfo Hector

2016-10-01

Hepatitis B virus (HBV) infection is a major public health problem worldwide. The aims of this study were to describe the molecular epidemiology of HBV in the Province of Misiones, Argentina and estimate the phylodynamic of the main groups in a Bayesian coalescent framework. To this end, partial or complete genome sequences were obtained from 52 blood donor candidates. The phylogenetic analysis based on partial sequences of S/P region showed a predominance of genotype D (65.4%), followed by genotype F (30.8%) and genotype A as a minority (3.8%). At subgenotype level, the circulation of subgenotypes D3 (42.3%), D2 (13.5%), F1b (11.5%) and F4 (9.6%) was mainly identified. The Bayesian coalescent analysis of 29 complete genome sequences for the main groups revealed that the subgenotypes D2 and D3 had several introductions to the region, with ancestors dating back from 1921 to 1969 and diversification events until the late '70s. The genotype F in Misiones has a more recent history; subgenotype F4 isolates were intermixed with sequences from Argentina and neighboring countries and only one significant cluster dated back in 1994 was observed. Subgenotype F1b isolates exhibited low genetic distance and formed a closely related monophyletic cluster, suggesting a very recent introduction. In conclusion, the phylogenetic and coalescent analyses showed that the European genotype D has a higher circulation, a longer history of diversification and may be responsible for the largest proportion of chronic HBV infections in the Province of Misiones. Genotype F, especially subgenotype F1b, had a more recent introduction and its diversification in the last 20years might be related to its involvement in new transmission events. Copyright © 2016 Elsevier B.V. All rights reserved.

GapFiller: a de novo assembly approach to fill the gap within paired reads

PubMed Central

2012-01-01

Background Next Generation Sequencing technologies are able to provide high genome coverages at a relatively low cost. However, due to limited reads' length (from 30 bp up to 200 bp), specific bioinformatics problems have become even more difficult to solve. De novo assembly with short reads, for example, is more complicated at least for two reasons: first, the overall amount of "noisy" data to cope with increased and, second, as the reads' length decreases the number of unsolvable repeats grows. Our work's aim is to go at the root of the problem by providing a pre-processing tool capable to produce (in-silico) longer and highly accurate sequences from a collection of Next Generation Sequencing reads. Results In this paper a seed-and-extend local assembler is presented. The kernel algorithm is a loop that, starting from a read used as seed, keeps extending it using heuristics whose main goal is to produce a collection of error-free and longer sequences. In particular, GapFiller carefully detects reliable overlaps and operates clustering similar reads in order to reconstruct the missing part between the two ends of the same insert. Our tool's output has been validated on 24 experiments using both simulated and real paired reads datasets. The output sequences are declared correct when the seed-mate is found. In the experiments performed, GapFiller was able to extend high percentages of the processed seeds and find their mates, with a false positives rate that turned out to be nearly negligible. Conclusions GapFiller, starting from a sufficiently high short reads coverage, is able to produce high coverages of accurate longer sequences (from 300 bp up to 3500 bp). The procedure to perform safe extensions, together with the mate-found check, turned out to be a powerful criterion to guarantee contigs' correctness. GapFiller has further potential, as it could be applied in a number of different scenarios, including the post-processing validation of insertions/deletions detection pipelines, pre-processing routines on datasets for de novo assembly pipelines, or in any hierarchical approach designed to assemble, analyse or validate pools of sequences. PMID:23095524

Longitudinal Detection and Persistence of Minority Drug-Resistant Populations and Their Effect on Salvage Therapy

PubMed Central

Nishizawa, Masako; Matsuda, Masakazu; Hattori, Junko; Shiino, Teiichiro; Matano, Tetsuro; Heneine, Walid; Johnson, Jeffrey A.; Sugiura, Wataru

2015-01-01

Background Drug-resistant HIV are more prevalent and persist longer than previously demonstrated by bulk sequencing due to the ability to detect low-frequency variants. To clarify a clinical benefit to monitoring minority-level drug resistance populations as a guide to select active drugs for salvage therapy, we retrospectively analyzed the dynamics of low-frequency drug-resistant population in antiretroviral (ARV)-exposed drug resistant individuals. Materials and Methods Six HIV-infected individuals treated with ARV for more than five years were analyzed. These individuals had difficulty in controlling viremia, and treatment regimens were switched multiple times guided by standard drug resistance testing using bulk sequencing. To detect minority variant populations with drug resistance, we used a highly sensitive allele-specific PCR (AS-PCR) with detection thresholds of 0.3–2%. According to ARV used in these individuals, we focused on the following seven reverse transcriptase inhibitor-resistant mutations: M41L, K65R, K70R, K103N, Y181C, M184V, and T215F/Y. Results of AS-PCR were compared with bulk sequencing data for concordance and presence of additional mutations. To clarify the genetic relationship between low-frequency and high-frequency populations, AS-PCR amplicon sequences were compared with bulk sequences in phylogenetic analysis. Results The use of AS-PCR enabled detection of the drug-resistant mutations, M41L, K103N, Y181C, M184V and T215Y, present as low-frequency populations in five of the six individuals. These drug resistant variants persisted for several years without ARV pressure. Phylogenetic analysis indicated that pre-existing K103N and T215I variants had close genetic relationships with high-frequency K103N and T215I observed during treatment. Discussion and Conclusion Our results demonstrate the long-term persistence of drug-resistant viruses in the absence of drug pressure. The rapid virologic failures with pre-existing mutant viruses detectable by AS-PCR highlight the clinical importance of low-frequency drug-resistant viruses. Thus, our results highlight the usefulness of AS-PCR and support its expanded evaluation in ART clinical management. PMID:26360259

Microplates in liquid chromatography--new solution in clinical research? A review.

PubMed

Krcmova, Lenka; Solichova, Dagmar; Solich, Petr

2013-10-15

Microplates are routinely used in Radio- or Immuno-assays. Recently, microplates have found use not only in analytical but also in the pre-analytical phase in bioanalyses (sample storage, sample preparation). New connection of this technology to liquid chromatography could be economical, fast and simple solution for many routine laboratories handling large sequences of biological samples. This review summarises the application of microplates in bioanalytical laboratories. Different types of sorbents, materials and shapes of microplates are discussed, and the main advantages and disadvantages of microplates used in clinical research are presented. Copyright © 2013 Elsevier B.V. All rights reserved.

Stellar and Circumstellar Properties of the Pre-Main-Sequence Binary GV Tau From Infrared Spectroscopy

DTIC Science & Technology

2008-09-20

surface gravity . With ourL-band spectra in order 25 (3.0450Y3.0865m;Fig. 1e), we detect strong HCN absorption (10% deep) and weaker C2H2 absorption in...Doppmann et al. 2005). The absorption lines of Na i and Mg i are particularly gravity and temperature sensitive, but in the opposite sense from each...other. For example, at cool effective temperatures (3200Y4500 K) and subdwarf surface gravities (3:5 log g 4:5) Na andMg lines both grow stronger as

Lithium and age of pre-main sequence stars: the case of Parenago 1802

NASA Astrophysics Data System (ADS)

Giarrusso, M.; Tognelli, E.; Catanzaro, G.; Degl'Innocenti, S.; Dell'Omodarme, M.; Lamia, L.; Leone, F.; Pizzone, R. G.; Prada Moroni, P. G.; Romano, S.; Spitaleri, C.

2016-04-01

With the aim to test the present capability of the stellar surface lithium abundance in providing an estimation for the age of PMS stars, we analyze the case of the detached, double-lined, eclipsing binary system PAR 1802. For this system, the lithium age has been compared with the theoretical one, as estimated by applying a Bayesian analysis method on a large grid of stellar evolutionary models. The models have been computed for several values of chemical composition and mixing length, by means of the code FRANEC updated with the Trojan Horse reaction rates involving lithium burning.

Theoretical Modeling and Computer Simulations for the Origins and Evolution of Reproducing Molecular Systems and Complex Systems with Many Interactive Parts

NASA Technical Reports Server (NTRS)

Liang, Shoudan

2000-01-01

Our research effort has produced nine publications in peer-reviewed journals listed at the end of this report. The work reported here are in the following areas: (1) genetic network modeling; (2) autocatalytic model of pre-biotic evolution; (3) theoretical and computational studies of strongly correlated electron systems; (4) reducing thermal oscillations in atomic force microscope; (5) transcription termination mechanism in prokaryotic cells; and (6) the low glutamine usage in thennophiles obtained by studying completely sequenced genomes. We discuss the main accomplishments of these publications.

Nature vs. Nurture: The influence of OB star environments on proto-planetary disk evolution

NASA Astrophysics Data System (ADS)

Bouwman, Jeroen

2006-09-01

We propose a combined IRAC/IRS study of a large, well-defined and unbiased X-ray selected sample of pre-main-sequence stars in three OB associations: Pismis 24 in NGC 6357, NGC 2244 in the Rosette Nebula, and IC 1795 in the W3 complex. The samples are based on recent Chandra X-ray Observatory studies which reliably identify hundreds of cluster members and were carefully chosen to avoid high infrared nebular background. A new Chandra exposure of IC 1795 is requested, and an optical followup to characterise the host stars is planned.

Phlebotomus (Paraphlebotomus) chabaudi and Phlebotomus riouxi: closely related species or synonyms?

PubMed Central

Lehrter, Véronique; Bañuls, Anne-Laure; Léger, Nicole; Rioux, Jean-Antoine; Depaquit, Jérôme

2017-01-01

Phlebotomus riouxi Depaquit, Killick-Kendrick & Léger 1998 was described as a species closely related to Phlebotomus chabaudi Croset, Abonnenc & Rioux 1970, differing mainly by the size and number of setae of the coxite basal lobe. Molecular studies carried out on several populations from Algeria and Tunisia and based on mitochondrial genes cytochrome b (Cytb) and cytochrome oxidase I (COI) supported the typological validity of these two species. Recently, specimens from a single population in southern Tunisia were morphologically identified as Ph. riouxi, Ph. chabaudi and intermediates, but were clustered in the same clade according to their Cytb and nuclear gene elongation factor-1 α (EF-1α) sequences. These species were thus synonymized. To further explore this synonymy, we carried out a molecular study on specimens from Algeria and Tunisia using the same molecular markers and a part of 28S rDNA. We did not find any morphologically intermediate specimens in our sampling. We highlighted differences between the genetic divergence rates within and between the two species for the three markers and we identified new haplotypes. The sequence analysis did not reveal any signature of introgression in allopatric nor in sympatric populations such as in the Ghomrassen population. Phylogenetic analyses based on our specimens revealed that the two main clades are Ph. chabaudi and Ph. riouxi, in agreement with the morphological identification. These results support the validity of Ph. riouxi and Ph. chabaudi as typological species. PMID:29194032

Phlebotomus (Paraphlebotomus) chabaudi and Phlebotomus riouxi: closely related species or synonyms?

PubMed

Lehrter, Véronique; Bañuls, Anne-Laure; Léger, Nicole; Rioux, Jean-Antoine; Depaquit, Jérôme

2017-01-01

Phlebotomus riouxi Depaquit, Killick-Kendrick & Léger 1998 was described as a species closely related to Phlebotomus chabaudi Croset, Abonnenc & Rioux 1970, differing mainly by the size and number of setae of the coxite basal lobe. Molecular studies carried out on several populations from Algeria and Tunisia and based on mitochondrial genes cytochrome b (Cytb) and cytochrome oxidase I (COI) supported the typological validity of these two species. Recently, specimens from a single population in southern Tunisia were morphologically identified as Ph. riouxi, Ph. chabaudi and intermediates, but were clustered in the same clade according to their Cytb and nuclear gene elongation factor-1 α (EF-1α) sequences. These species were thus synonymized. To further explore this synonymy, we carried out a molecular study on specimens from Algeria and Tunisia using the same molecular markers and a part of 28S rDNA. We did not find any morphologically intermediate specimens in our sampling. We highlighted differences between the genetic divergence rates within and between the two species for the three markers and we identified new haplotypes. The sequence analysis did not reveal any signature of introgression in allopatric nor in sympatric populations such as in the Ghomrassen population. Phylogenetic analyses based on our specimens revealed that the two main clades are Ph. chabaudi and Ph. riouxi, in agreement with the morphological identification. These results support the validity of Ph. riouxi and Ph. chabaudi as typological species. © V. Lehrter et al., published by EDP Sciences, 2017.

Variability and genetic structure of the population of watermelon mosaic virus infecting melon in Spain.

PubMed

Moreno, I M; Malpica, J M; Díaz-Pendón, J A; Moriones, E; Fraile, A; García-Arenal, F

2004-01-05

The genetic structure of the population of Watermelon mosaic virus (WMV) in Spain was analysed by the biological and molecular characterisation of isolates sampled from its main host plant, melon. The population was a highly homogeneous one, built of a single pathotype, and comprising isolates closely related genetically. There was indication of temporal replacement of genotypes, but not of spatial structure of the population. Analyses of nucleotide sequences in three genomic regions, that is, in the cistrons for the P1, cylindrical inclusion (CI) and capsid (CP) proteins, showed lower similar values of nucleotide diversity for the P1 than for the CI or CP cistrons. The CI protein and the CP were under tighter evolutionary constraints than the P1 protein. Also, for the CI and CP cistrons, but not for the P1 cistron, two groups of sequences, defining two genetic strains, were apparent. Thus, different genomic regions of WMV show different evolutionary dynamics. Interestingly, for the CI and CP cistrons, sequences were clustered into two regions of the sequence space, defining the two strains above, and no intermediary sequences were identified. Recombinant isolates were found, accounting for at least 7% of the population. These recombinants presented two interesting features: (i) crossover points were detected between the analysed regions in the CI and CP cistrons, but not between those in the P1 and CI cistrons, (ii) crossover points were not observed within the analysed coding regions for the P1, CI or CP proteins. This indicates strong selection against isolates with recombinant proteins, even when originated from closely related strains. Hence, data indicate that genotypes of WMV, generated by mutation or recombination, outside of acceptable, discrete, regions in the evolutionary space, are eliminated from the virus population by negative selection.

Pre-capture multiplexing improves efficiency and cost-effectiveness of targeted genomic enrichment.

PubMed

Shearer, A Eliot; Hildebrand, Michael S; Ravi, Harini; Joshi, Swati; Guiffre, Angelica C; Novak, Barbara; Happe, Scott; LeProust, Emily M; Smith, Richard J H

2012-11-14

Targeted genomic enrichment (TGE) is a widely used method for isolating and enriching specific genomic regions prior to massively parallel sequencing. To make effective use of sequencer output, barcoding and sample pooling (multiplexing) after TGE and prior to sequencing (post-capture multiplexing) has become routine. While previous reports have indicated that multiplexing prior to capture (pre-capture multiplexing) is feasible, no thorough examination of the effect of this method has been completed on a large number of samples. Here we compare standard post-capture TGE to two levels of pre-capture multiplexing: 12 or 16 samples per pool. We evaluated these methods using standard TGE metrics and determined the ability to identify several classes of genetic mutations in three sets of 96 samples, including 48 controls. Our overall goal was to maximize cost reduction and minimize experimental time while maintaining a high percentage of reads on target and a high depth of coverage at thresholds required for variant detection. We adapted the standard post-capture TGE method for pre-capture TGE with several protocol modifications, including redesign of blocking oligonucleotides and optimization of enzymatic and amplification steps. Pre-capture multiplexing reduced costs for TGE by at least 38% and significantly reduced hands-on time during the TGE protocol. We found that pre-capture multiplexing reduced capture efficiency by 23 or 31% for pre-capture pools of 12 and 16, respectively. However efficiency losses at this step can be compensated by reducing the number of simultaneously sequenced samples. Pre-capture multiplexing and post-capture TGE performed similarly with respect to variant detection of positive control mutations. In addition, we detected no instances of sample switching due to aberrant barcode identification. Pre-capture multiplexing improves efficiency of TGE experiments with respect to hands-on time and reagent use compared to standard post-capture TGE. A decrease in capture efficiency is observed when using pre-capture multiplexing; however, it does not negatively impact variant detection and can be accommodated by the experimental design.

Characterization of microbial compositions in a thermophilic chemostat of mixed culture fermentation.

PubMed

Zhang, Fang; Yang, Jing-Hua; Dai, Kun; Chen, Yun; Li, Qiu-Rong; Gao, Fa-Ming; Zeng, Raymond J

2016-02-01

The microbial community compositions of a chemostat enriched in a thermophilic (55 °C) mixed culture fermentation (MCF) for hydrogen production under different operational conditions were revealed in this work by integrating denaturing gradient gel electrophoresis (DGGE), Illumina Miseq high-throughput sequencing, and 16S rRNA clone library sequencing. The results showed that the community structure of the enriched cultures was relatively simple. Clones close to the genera of Thermoanaerobacter and/or Bacillus mainly dominated the bacteria. And homoacetogens and archaea were washed out and not detected even by Illumina Miseq high-throughput sequencing which supported the benefit for hydrogen production. On the other hand, the results revealed that the metabolic shift was clearly associated with the change of dominated bacterial groups. The effects of hydrogen partial pressure (PH2) and pH from 4.0 to 5.5 on the microbial compositions were not notable and Thermoanaerobacter was dominant, thus, the metabolites were also not changed. While Bacillus, Thermoanaerobacter and Propionispora hippei dominated the bacteria communities at neutral pH, or Bacillus and Thermoanaerobacter dominated at high influent glucose concentrations, consequently the main metabolites shifted to acetate, ethanol, propionate, or lactate. Thereby, the effect of microbial composition on the metabolite distribution and shift shall be considered when modeling thermophilic MCF in the future.

Comparison of whole-genome bisulfite sequencing library preparation strategies identifies sources of biases affecting DNA methylation data.

PubMed

Olova, Nelly; Krueger, Felix; Andrews, Simon; Oxley, David; Berrens, Rebecca V; Branco, Miguel R; Reik, Wolf

2018-03-15

Whole-genome bisulfite sequencing (WGBS) is becoming an increasingly accessible technique, used widely for both fundamental and disease-oriented research. Library preparation methods benefit from a variety of available kits, polymerases and bisulfite conversion protocols. Although some steps in the procedure, such as PCR amplification, are known to introduce biases, a systematic evaluation of biases in WGBS strategies is missing. We perform a comparative analysis of several commonly used pre- and post-bisulfite WGBS library preparation protocols for their performance and quality of sequencing outputs. Our results show that bisulfite conversion per se is the main trigger of pronounced sequencing biases, and PCR amplification builds on these underlying artefacts. The majority of standard library preparation methods yield a significantly biased sequence output and overestimate global methylation. Importantly, both absolute and relative methylation levels at specific genomic regions vary substantially between methods, with clear implications for DNA methylation studies. We show that amplification-free library preparation is the least biased approach for WGBS. In protocols with amplification, the choice of bisulfite conversion protocol or polymerase can significantly minimize artefacts. To aid with the quality assessment of existing WGBS datasets, we have integrated a bias diagnostic tool in the Bismark package and offer several approaches for consideration during the preparation and analysis of WGBS datasets.

A new model for approximating RNA folding trajectories and population kinetics

NASA Astrophysics Data System (ADS)

Kirkpatrick, Bonnie; Hajiaghayi, Monir; Condon, Anne

2013-01-01

RNA participates both in functional aspects of the cell and in gene regulation. The interactions of these molecules are mediated by their secondary structure which can be viewed as a planar circle graph with arcs for all the chemical bonds between pairs of bases in the RNA sequence. The problem of predicting RNA secondary structure, specifically the chemically most probable structure, has many useful and efficient algorithms. This leaves RNA folding, the problem of predicting the dynamic behavior of RNA structure over time, as the main open problem. RNA folding is important for functional understanding because some RNA molecules change secondary structure in response to interactions with the environment. The full RNA folding model on at most O(3n) secondary structures is the gold standard. We present a new subset approximation model for the full model, give methods to analyze its accuracy and discuss the relative merits of our model as compared with a pre-existing subset approximation. The main advantage of our model is that it generates Monte Carlo folding pathways with the same probabilities with which they are generated under the full model. The pre-existing subset approximation does not have this property.

Origin-Dependent Inverted-Repeat Amplification: Tests of a Model for Inverted DNA Amplification.

PubMed

Brewer, Bonita J; Payen, Celia; Di Rienzi, Sara C; Higgins, Megan M; Ong, Giang; Dunham, Maitreya J; Raghuraman, M K

2015-12-01

DNA replication errors are a major driver of evolution--from single nucleotide polymorphisms to large-scale copy number variations (CNVs). Here we test a specific replication-based model to explain the generation of interstitial, inverted triplications. While no genetic information is lost, the novel inversion junctions and increased copy number of the included sequences create the potential for adaptive phenotypes. The model--Origin-Dependent Inverted-Repeat Amplification (ODIRA)-proposes that a replication error at pre-existing short, interrupted, inverted repeats in genomic sequences generates an extrachromosomal, inverted dimeric, autonomously replicating intermediate; subsequent genomic integration of the dimer yields this class of CNV without loss of distal chromosomal sequences. We used a combination of in vitro and in vivo approaches to test the feasibility of the proposed replication error and its downstream consequences on chromosome structure in the yeast Saccharomyces cerevisiae. We show that the proposed replication error-the ligation of leading and lagging nascent strands to create "closed" forks-can occur in vitro at short, interrupted inverted repeats. The removal of molecules with two closed forks results in a hairpin-capped linear duplex that we show replicates in vivo to create an inverted, dimeric plasmid that subsequently integrates into the genome by homologous recombination, creating an inverted triplication. While other models have been proposed to explain inverted triplications and their derivatives, our model can also explain the generation of human, de novo, inverted amplicons that have a 2:1 mixture of sequences from both homologues of a single parent--a feature readily explained by a plasmid intermediate that arises from one homologue and integrates into the other homologue prior to meiosis. Our tests of key features of ODIRA lend support to this mechanism and suggest further avenues of enquiry to unravel the origins of interstitial, inverted CNVs pivotal in human health and evolution.

Sequencing a piece of history: complete genome sequence of the original Escherichia coli strain

PubMed Central

Dunne, Karl A; Chaudhuri, Roy R; Rossiter, Amanda E; Beriotto, Irene; Browning, Douglas F; Squire, Derrick; Cunningham, Adam F; Cole, Jeffrey A; Loman, Nicholas

2017-01-01

In 1885, Theodor Escherich first described the Bacillus coli commune, which was subsequently renamed Escherichia coli. We report the complete genome sequence of this original strain (NCTC 86). The 5 144 392 bp circular chromosome encodes the genes for 4805 proteins, which include antigens, virulence factors, antimicrobial-resistance factors and secretion systems, of a commensal organism from the pre-antibiotic era. It is located in the E. coli A subgroup and is closely related to E. coli K-12 MG1655. E. coli strain NCTC 86 and the non-pathogenic K-12, C, B and HS strains share a common backbone that is largely co-linear. The exception is a large 2 803 932 bp inversion that spans the replication terminus from gmhB to clpB. Comparison with E. coli K-12 reveals 41 regions of difference (577 351 bp) distributed across the chromosome. For example, and contrary to current dogma, E. coli NCTC 86 includes a nine gene sil locus that encodes a silver-resistance efflux pump acquired before the current widespread use of silver nanoparticles as an antibacterial agent, possibly resulting from the widespread use of silver utensils and currency in Germany in the 1800s. In summary, phylogenetic comparisons with other E. coli strains confirmed that the original strain isolated by Escherich is most closely related to the non-pathogenic commensal strains. It is more distant from the root than the pathogenic organisms E. coli 042 and O157 : H7; therefore, it is not an ancestral state for the species. PMID:28663823

Short genome report of cellulose-producing commensal Escherichia coli 1094.

PubMed

Bernal-Bayard, Joaquin; Gomez-Valero, Laura; Wessel, Aimee; Khanna, Varun; Bouchier, Christiane; Ghigo, Jean-Marc

2018-01-01

Bacterial surface colonization and biofilm formation often rely on the production of an extracellular polymeric matrix that mediates cell-cell and cell-surface contacts. In Escherichia coli and many Betaproteobacteria and Gammaproteobacteria cellulose is often the main component of the extracellular matrix. Here we report the complete genome sequence of the cellulose producing strain E. coli 1094 and compare it with five other closely related genomes within E. coli phylogenetic group A. We present a comparative analysis of the regions encoding genes responsible for cellulose biosynthesis and discuss the changes that could have led to the loss of this important adaptive advantage in several E. coli strains. Data deposition: The annotated genome sequence has been deposited at the European Nucleotide Archive under the accession number PRJEB21000.

DNA sequence templates adjacent nucleosome and ORC sites at gene amplification origins in Drosophila

PubMed Central

Liu, Jun; Zimmer, Kurt; Rusch, Douglas B.; Paranjape, Neha; Podicheti, Ram; Tang, Haixu; Calvi, Brian R.

2015-01-01

Eukaryotic origins of DNA replication are bound by the origin recognition complex (ORC), which scaffolds assembly of a pre-replicative complex (pre-RC) that is then activated to initiate replication. Both pre-RC assembly and activation are strongly influenced by developmental changes to the epigenome, but molecular mechanisms remain incompletely defined. We have been examining the activation of origins responsible for developmental gene amplification in Drosophila. At a specific time in oogenesis, somatic follicle cells transition from genomic replication to a locus-specific replication from six amplicon origins. Previous evidence indicated that these amplicon origins are activated by nucleosome acetylation, but how this affects origin chromatin is unknown. Here, we examine nucleosome position in follicle cells using micrococcal nuclease digestion with Ilumina sequencing. The results indicate that ORC binding sites and other essential origin sequences are nucleosome-depleted regions (NDRs). Nucleosome position at the amplicons was highly similar among developmental stages during which ORC is or is not bound, indicating that being an NDR is not sufficient to specify ORC binding. Importantly, the data suggest that nucleosomes and ORC have opposite preferences for DNA sequence and structure. We propose that nucleosome hyperacetylation promotes pre-RC assembly onto adjacent DNA sequences that are disfavored by nucleosomes but favored by ORC. PMID:26227968

Rate of gestational weight gain, pre-pregnancy body mass index and preterm birth subtypes: a retrospective cohort study from Peru

PubMed Central

Carnero, AM; Mejía, CR; García, PJ

2014-01-01

Objective To examine the shape (functional form) of the association between the rate of gestational weight gain, pre-pregnancy body mass index (BMI), and preterm birth and its subtypes. Design Retrospective cohort study. Setting National reference obstetric centre in Lima, Peru. Population Pregnant women who delivered singleton babies during the period 2006–2009, resident in Lima, and beginning prenatal care at ≤12 weeks of gestation (n = 8964). Methods Data were collected from the centre database. The main analyses consisted of logistic regression with fractional polynomial modelling. Main outcome measures Preterm birth and its subtypes. Results Preterm birth occurred in 12.2% of women, being mostly idiopathic (85.7%). The rate of gestational weight gain was independently associated with preterm birth, and the shape of this association varied by pre-pregnancy BMI. In women who were underweight, the association was linear (per 0.1 kg/week increase) and protective (OR 0.88; 95% CI 0.82–1.00). In women of normal weight or who were overweight, the association was U-shaped: the odds of delivering preterm increased exponentially with rates <0.10 or >0.66 kg/week, and <0.04 or >0.50 kg/week, respectively. In women who were obese, the association was linear, but nonsignificant (OR 1.01; 95% CI 0.95–1.06). The association described for preterm birth closely resembled that of idiopathic preterm birth, although the latter was stronger. The rate of gestational weight gain was not associated with indicated preterm birth or preterm prelabour rupture of membranes. Conclusions In Peruvian pregnant women starting prenatal care at ≤12 weeks of gestation, the rate of gestational weight gain is independently associated with preterm birth, mainly because of its association with idiopathic preterm birth, and the shape of both associations varies by pre-pregnancy BMI. PMID:22607522

The provenance of Archean clastic metasediments in the Narryer Gneiss Complex, Western Australia: Trace element geochemistry, Nd isotopes, and U-Pb ages for detrital zircons

NASA Astrophysics Data System (ADS)

Maas, Roland; McCulloch, Malcolm T.

1991-07-01

Clastic metasedimentary rocks of mid-Archean age from the Mt. Narryer and Jack Hills metasedimentary belts have REE patterns resembling those of mid- to late-Archean pelitic-quartzitic cratonic sequences elsewhere, and post-Archean continental rocks in general. Detrital zircons in the metasediments range in age from ca. 3000 to 3700 Ma. This indicates a provenance from mature cratonic sources controlled by K-rich granitic rocks. Additional minor sediment sources were identified as older, mainly chemical sedimentary sequences, ultramafic rocks, and felsic rocks characterized by low HREE contents, perhaps of tonalitic affinity. The association of the near-shore/fluviatile clastic association studied here with extensive turbiditic and chemical sedimentary sequences indicates these sources formed part of a (rifted ?) cratonic margin ca. 3 Ga ago. Differences between sedimentary REE patterns and those in the surrounding 3.73-3.0 Ga orthogneiss terrain, and between detrital zircon ages and the age distribution in the gneisses, suggest that the present association of the metasedimentary belts with the orthogneiss terrain is of tectonic origin. The occurrence of detrital zircons with U-Pb ages > 4 Ga in certain quartzites and conglomerates of the Jack Hills and Mt. Narryer metasedimentary sequences indicates a further, most likely granitic, source. ɛNd( TDep) values in Jack Hills metasediments vary widely (+5 to -12) but have a smaller range in the Mt. Narryer belt (-5 to -9). The lowest ɛNd values of both sequences are interpreted to reflect the presence of detritus derived from 4.1-4.2 Ga old LREE-enriched continental crust in proportions considerably larger (≥ 10%) than estimated previously from the abundance of pre-4 Ga detrital zircons (≈3%). This would imply the former existence of significant volumes of pre-4 Ga continental crust in the provenance of the Mt. Narryer and Jack Hills metasediments.

Analysis of the ergosterol biosynthesis pathway cloning, molecular characterization and phylogeny of lanosterol 14 α-demethylase (ERG11) gene of Moniliophthora perniciosa.

PubMed

de Oliveira Ceita, Geruza; Vilas-Boas, Laurival Antônio; Castilho, Marcelo Santos; Carazzolle, Marcelo Falsarella; Pirovani, Carlos Priminho; Selbach-Schnadelbach, Alessandra; Gramacho, Karina Peres; Ramos, Pablo Ivan Pereira; Barbosa, Luciana Veiga; Pereira, Gonçalo Amarante Guimarães; Góes-Neto, Aristóteles

2014-10-01

The phytopathogenic fungus Moniliophthora perniciosa (Stahel) Aime & Philips-Mora, causal agent of witches' broom disease of cocoa, causes countless damage to cocoa production in Brazil. Molecular studies have attempted to identify genes that play important roles in fungal survival and virulence. In this study, sequences deposited in the M. perniciosa Genome Sequencing Project database were analyzed to identify potential biological targets. For the first time, the ergosterol biosynthetic pathway in M. perniciosa was studied and the lanosterol 14α-demethylase gene (ERG11) that encodes the main enzyme of this pathway and is a target for fungicides was cloned, characterized molecularly and its phylogeny analyzed. ERG11 genomic DNA and cDNA were characterized and sequence analysis of the ERG11 protein identified highly conserved domains typical of this enzyme, such as SRS1, SRS4, EXXR and the heme-binding region (HBR). Comparison of the protein sequences and phylogenetic analysis revealed that the M. perniciosa enzyme was most closely related to that of Coprinopsis cinerea.

Analysis of the ergosterol biosynthesis pathway cloning, molecular characterization and phylogeny of lanosterol 14 α-demethylase (ERG11) gene of Moniliophthora perniciosa

PubMed Central

de Oliveira Ceita, Geruza; Vilas-Boas, Laurival Antônio; Castilho, Marcelo Santos; Carazzolle, Marcelo Falsarella; Pirovani, Carlos Priminho; Selbach-Schnadelbach, Alessandra; Gramacho, Karina Peres; Ramos, Pablo Ivan Pereira; Barbosa, Luciana Veiga; Pereira, Gonçalo Amarante Guimarães; Góes-Neto, Aristóteles

2014-01-01

The phytopathogenic fungus Moniliophthora perniciosa (Stahel) Aime & Philips-Mora, causal agent of witches’ broom disease of cocoa, causes countless damage to cocoa production in Brazil. Molecular studies have attempted to identify genes that play important roles in fungal survival and virulence. In this study, sequences deposited in the M. perniciosa Genome Sequencing Project database were analyzed to identify potential biological targets. For the first time, the ergosterol biosynthetic pathway in M. perniciosa was studied and the lanosterol 14α-demethylase gene (ERG11) that encodes the main enzyme of this pathway and is a target for fungicides was cloned, characterized molecularly and its phylogeny analyzed. ERG11 genomic DNA and cDNA were characterized and sequence analysis of the ERG11 protein identified highly conserved domains typical of this enzyme, such as SRS1, SRS4, EXXR and the heme-binding region (HBR). Comparison of the protein sequences and phylogenetic analysis revealed that the M. perniciosa enzyme was most closely related to that of Coprinopsis cinerea. PMID:25505843

Young Binaries and Early Stellar Evolution

NASA Astrophysics Data System (ADS)

Brandner, Wolfgang

1996-07-01

Most main-sequence stars are members of binary or multiple systems. The same is true for pre-main-sequence (PMS) stars, as recent surveys have shown. Therefore studying star formation means to a large extent studying the formation of binary systems. Similarly, studying early stellar evolution primarily involves PMS binary systems. In this thesis I have studied the binary frequency among ROSAT selected T Tauri stars in the Chamaeleon T association and the Scorpius-Centaurus OB association, and the evolutionary status of Hα-selected PMS binaries in the T associations of Chamaeleon, Lupus, and ρ Ophiuchi. The direct imaging and spectroscopic observations in the optical have been carried out under subarcsec seeing conditions at the ESO New Technology Telescope (NTT) at La Silla. Furthermore, high-spatial resolution images of selected PMS stars in the near infrared were obtained with the ESO adaptive optics system COME-ON+/ADONIS. Among 195 T Tauri stars observed using direct imaging 31 binaries could be identified, 12 of them with subarcsec separation. Based on statistical arguments alone I conclude that almost all of them are indeed physical (i.e. gravitationally bound) binary or multiple systems. Using astrometric measurements of some binaries I showed that the components of these binaries are common proper motion pairs, very likely in a gravitationally bound orbit around each other. The overall binary frequency among T Tauri stars with a range of separations between 120 and 1800 AU is in agreement with the binary frequency observed among main-sequence stars in the solar neighbourhood. However, within individual regions the spatial distribution of binaries is non-uniform. In particular, in Upper Scorpius, weak-line T Tauri stars in the vicinity of early type stars seem to be almost devoid of multiple systems, whereas in another area in Upper Scorpius half of all weak-line T Tauri stars have a companion in a range of separation between 0.''7 and 3.''0. For a sample of 14 spatially resolved PMS binaries (separations 0.''6 to 1.prime'7) located in the above mentioned T associations both photometric and spectroscopic information has been analyzed. All binaries (originally unresolved) were identified as PMS stars based on their strong Hα emission and their association with dark clouds. Using the spectral A index, which measures the strength of the CaH band at 697.5nm relative to the nearby continuum as a luminosity class indicator, I showed that the classical T Tauri stars in the sample tend to be close to luminosity class V. Eight out of the 14 pairs could be placed on an H--R diagram. When comparing with theoretical PMS evolutionary tracks the individual components of all pairs appear to be coeval within the observational errors. This result is similar to Hartigan et al. (1994) who found two thirds of the wider pairs with separations from 400 AU to 6000 AU to be coeval. However, unlike Hartigan et al.'s finding for the wider pairs, I find no non-coeval pairs. One of the presumed binaries in our sample (ESO Hα 281) turned out to be a likely chance projection with the ``primary'' showing neither Hα emission nor Li absorption. Finally, using adaptive optics at the ESO 3.6m telescope, diffraction-limited JHK images of the region around the Herbig AeBe star NX Pup were obtained. The close companion (sep. 0.''128) to NX Pup -- originally discovered by HST -- was clearly resolved and its JHK magnitudes were determined. A third object at a separation of 7.''0 from NX Pup was identified as a classical T Tauri star so that NX Pup may in fact form a hierarchical triple system. I discuss the evolutionary status of these stars and derive estimates for their spectral types, luminosities, masses, and ages. My conclusions are that binarity is established very early in stellar evolution, that the orbital parameters of wide binaries (a >= 120AU) remain virtually unchanged during their PMS evolution, and that the components of the wide binaries were formed at the same time --- perhaps either through collisional fragmentation or fragmentation of rotating filaments. (Copies of the thesis (written in German) and related pre-/reprints are available from the author upon request.)

IDENTIFICATION OF THE LITHIUM DEPLETION BOUNDARY AND AGE OF THE SOUTHERN OPEN CLUSTER BLANCO 1

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cargile, P. A.; James, D. J.; Jeffries, R. D., E-mail: p.cargile@vanderbilt.ed

2010-12-20

We present results from a spectroscopic study of the very low mass members of the Southern open cluster Blanco 1 using the Gemini-N telescope. We obtained intermediate resolution (R {approx} 4400) GMOS spectra for 15 cluster candidate members with I {approx} 14-20 mag, and employed a series of membership criteria-proximity to the cluster's sequence in an I/I - K{sub s} color-magnitude diagram (CMD), kinematics agreeing with the cluster systemic motion, magnetic activity as a youth indicator-to classify 10 of these objects as probable cluster members. For these objects, we searched for the presence of the Li I 6708 A featuremore » to identify the lithium depletion boundary (LDB) in Blanco 1. The I/I - K{sub s} CMD shows a clear mass segregation in the Li distribution along the cluster sequence; namely, all higher mass stars are found to be Li poor, while lower mass stars are found to be Li rich. The division between Li-poor and Li-rich (i.e., the LDB) in Blanco 1 is found at I = 18.78 {+-} 0.24 and I - K{sub s} = 3.05 {+-} 0.10. Using current pre-main-sequence evolutionary models, we determine an LDB age of 132 {+-} 24 Myr. Comparing our derived LDB age to upper-main-sequence isochrone ages for Blanco 1, as well as for other open clusters with identified LDBs, we find good chronometric consistency when using stellar evolution models that incorporate a moderate degree of convective core overshoot.« less

Genomic Sequences of Australian Bluetongue Virus Prototype Serotypes Reveal Global Relationships and Possible Routes of Entry into Australia

PubMed Central

Bulach, Dieter M.; Amos-Ritchie, Rachel; Adams, Mathew M.; Walker, Peter J.; Weir, Richard

2012-01-01

Bluetongue virus (BTV) is transmitted by biting midges (Culicoides spp.). It causes disease mainly in sheep and occasionally in cattle and other species. BTV has spread into northern Europe, causing disease in sheep and cattle. The introduction of new serotypes, changes in vector species, and climate change have contributed to these changes. Ten BTV serotypes have been isolated in Australia without apparent associated disease. Simplified methods for preferential isolation of double-stranded RNA (dsRNA) and template preparation enabled high-throughput sequencing of the 10 genome segments of all Australian BTV prototype serotypes. Phylogenetic analysis reinforced the Western and Eastern topotypes previously characterized but revealed unique features of several Australian BTVs. Many of the Australian BTV genome segments (Seg-) were closely related, clustering together within the Eastern topotypes. A novel Australian topotype for Seg-5 (NS1) was identified, with taxa spread across several serotypes and over time. Seg-1, -2, -3, -4, -6, -7, -9, and -10 of BTV_2_AUS_2008 were most closely related to the cognate segments of viruses from Taiwan and Asia and not other Australian viruses, supporting the conclusion that BTV_2 entered Australia recently. The Australian BTV_15_AUS_1982 prototype was revealed to be unusual among the Australian BTV isolates, with Seg-3 and -8 distantly related to other BTV sequences from all serotypes. PMID:22514341

Pre-stack depth Migration imaging of the Hellenic Subduction Zone

NASA Astrophysics Data System (ADS)

Hussni, S. G.; Becel, A.; Schenini, L.; Laigle, M.; Dessa, J. X.; Galve, A.; Vitard, C.

2017-12-01

In 365 AD, a major M>8-tsunamignic earthquake occurred along the southwestern segment of the Hellenic subduction zone. Although this is the largest seismic event ever reported in Europe, some fundamental questions remain regarding the deep geometry of the interplate megathrust, as well as other faults within the overriding plate potentially connected to it. The main objective here is to image those deep structures, whose depths range between 15 and 45 km, using leading edge seismic reflection equipment. To this end, a 210-km-long multichannel seismic profile was acquired with the 8 km-long streamer and the 6600 cu.in source of R/V Marcus Langseth. This was realized at the end of 2015, during the SISMED cruise. This survey was made possible through a collective effort gathering labs (Géoazur, LDEO, ISTEP, ENS-Paris, EOST, LDO, Dpt. Geosciences of Pau Univ). A preliminary processing sequence has first been applied using Geovation software of CGG, which yielded a post-stack time migration of collected data, as well as pre-stack time migration obtained with a model derived from velocity analyses. Using Paradigm software, a pre-stack depth migration was subsequently carried out. This step required some tuning in the pre-processing sequence in order to improve multiple removal, noise suppression and to better reveal the true geometry of reflectors in depth. This iteration of pre-processing included, the use of parabolic Radon transform, FK filtering and time variant band pass filtering. An initial velocity model was built using depth-converted RMS velocities obtained from SISMED data for the sedimentary layer, complemented at depth with a smooth version of the tomographic velocities derived from coincident wide-angle data acquired during the 2012-ULYSSE survey. Then, we performed a Kirchhoff Pre-stack depth migration with traveltimes calculated using the Eikonal equation. Velocity model were then tuned through residual velocity analyses to flatten reflections in common reflection point gathers. These new results improve the imaging of deep reflectors and even reveal some new features. We will present this work, a comparison with our previously obtained post-stack time migration, as well as some insights into the new geological structures revealed by the depth imaging.

Investigation of New Morpholino Oligomers to Increase Survival Motor Neuron Protein Levels in Spinal Muscular Atrophy

PubMed Central

Ramirez, Agnese; Crisafulli, Sebastiano G.; Rizzuti, Mafalda; Bresolin, Nereo; Comi, Giacomo P.; Corti, Stefania

2018-01-01

Spinal muscular atrophy (SMA) is an autosomal-recessive childhood motor neuron disease and the main genetic cause of infant mortality. SMA is caused by deletions or mutations in the survival motor neuron 1 (SMN1) gene, which results in SMN protein deficiency. Only one approved drug has recently become available and allows for the correction of aberrant splicing of the paralogous SMN2 gene by antisense oligonucleotides (ASOs), leading to production of full-length SMN protein. We have already demonstrated that a sequence of an ASO variant, Morpholino (MO), is particularly suitable because of its safety and efficacy profile and is both able to increase SMN levels and rescue the murine SMA phenotype. Here, we optimized this strategy by testing the efficacy of four new MO sequences targeting SMN2. Two out of the four new MO sequences showed better efficacy in terms of SMN protein production both in SMA induced pluripotent stem cells (iPSCs) and SMAΔ7 mice. Further, the effect was enhanced when different MO sequences were administered in combination. Our data provide an important insight for MO-based treatment for SMA. Optimization of the target sequence and validation of a treatment based on a combination of different MO sequences could support further pre-clinical studies and the progression toward future clinical trials. PMID:29316633

Investigation of New Morpholino Oligomers to Increase Survival Motor Neuron Protein Levels in Spinal Muscular Atrophy.

PubMed

Ramirez, Agnese; Crisafulli, Sebastiano G; Rizzuti, Mafalda; Bresolin, Nereo; Comi, Giacomo P; Corti, Stefania; Nizzardo, Monica

2018-01-06

Spinal muscular atrophy (SMA) is an autosomal-recessive childhood motor neuron disease and the main genetic cause of infant mortality. SMA is caused by deletions or mutations in the survival motor neuron 1 ( SMN1 ) gene, which results in SMN protein deficiency. Only one approved drug has recently become available and allows for the correction of aberrant splicing of the paralogous SMN2 gene by antisense oligonucleotides (ASOs), leading to production of full-length SMN protein. We have already demonstrated that a sequence of an ASO variant, Morpholino (MO), is particularly suitable because of its safety and efficacy profile and is both able to increase SMN levels and rescue the murine SMA phenotype. Here, we optimized this strategy by testing the efficacy of four new MO sequences targeting SMN2 . Two out of the four new MO sequences showed better efficacy in terms of SMN protein production both in SMA induced pluripotent stem cells (iPSCs) and SMAΔ7 mice. Further, the effect was enhanced when different MO sequences were administered in combination. Our data provide an important insight for MO-based treatment for SMA. Optimization of the target sequence and validation of a treatment based on a combination of different MO sequences could support further pre-clinical studies and the progression toward future clinical trials.

Prevalence of precore-defective mutant of hepatitis B virus in HBV carriers.

PubMed

Niitsuma, H; Ishii, M; Saito, Y; Miura, M; Kobayashi, K; Ohori, H; Toyota, T

1995-08-01

Two hundred and seventy-three serum specimens from hepatitis B virus (HBV) carriers were examined for the presence of a characteristic one point mutation at nucleotide (nt) 1896 from the EcoRI site of the HBV genome in the precore region (the preC mutant) using restriction fragment length polymorphism (RFLP) analysis. This assay approach could detect preC mutants or wild-type sequences when either form constituted more than 10% of the total sample. Overall, 65.5% (76/116) of HBeAg-positive carriers had only the preC wild-type. All HBeAg-positive asymptomatic carriers (n = 14) had only the preC wild-type. In patients with chronic hepatitis B and in anti-HBe-positive asymptomatic carriers, increased prevalence of the preC mutant was associated with the development of anti-HBe antibodies and normalization of the serum alanine aminotransferase concentration. Furthermore, 27 (29.0%) of 93 HBeAg-negative carriers had unexpectedly preC wild-type sequences only. Direct sequencing of the HBV precore region of HBV specimens from 24 patients revealed no mutation at nt 1896, supporting the specificity of the RFLP analysis. These results suggest that RFLP analysis was accurate for the detection of the preC mutation and that the absence of serum HBeAg cannot be explained solely by the dominance of the preC mutant.

Phylogenetic characterization of Canine Parvovirus VP2 partial sequences from symptomatic dogs samples.

PubMed

Zienius, D; Lelešius, R; Kavaliauskis, H; Stankevičius, A; Šalomskas, A

2016-01-01

The aim of the present study was to detect canine parvovirus (CPV) from faecal samples of clinically ill domestic dogs by polymerase chain reaction (PCR) followed by VP2 gene partial sequencing and molecular characterization of circulating strains in Lithuania. Eleven clinically and antigen-tested positive dog faecal samples, collected during the period of 2014-2015, were investigated by using PCR. The phylogenetic investigations indicated that the Lithuanian CPV VP2 partial sequences (3025-3706 cds) were closely related and showed 99.0-99.9% identity. All Lithuanian sequences were associated with one phylogroup, but grouped in different clusters. Ten of investigated Lithuanian CPV VP2 sequences were closely associated with CPV 2a antigenic variant (99.4% nt identity). Five CPV VP2 sequences from Lithuania were related to CPV-2a, but were rather divergent (6.8 nt differences). Only one CPV VP2 sequence from Lithuania was associated (99.3% nt identity) with CPV-2b VP2 sequences from France, Italy, USA and Korea. The four of eleven investigated Lithuanian dogs with CPV infection symptoms were vaccinated with CPV-2 vaccine, but their VP2 sequences were phylogenetically distantly associated with CPV vaccine strains VP2 sequences (11.5-15.8 nt differences). Ten Lithuanian CPV VP2 sequences had monophyletic relations among the close geographically associated samples, but five of them were rather divergent (1.0% less sequence similarity). The one Lithuanian CPV VP2 sequence was closely related with CPV-2b antigenic variant. All the Lithuanian CPV VP2 partial sequences were conservative and phylogenetically low associated with most commonly used CPV vaccine strains.

Characterization of the Lower Cambrian sandstone aquifer in the Swedish Baltic Sea area - assessment regarding its potential suitability for storage of CO2

NASA Astrophysics Data System (ADS)

Erlström, M.; Sivhed, U.

2012-04-01

In the Baltic region the Cambrian sandstone is considered to have great economic value concerning its aquifer and reservoir properties. Its potential as petroleum reservoir is well known, especially from the Polish, Lithuanian and Russian sectors of the Baltic Sea where oil and gas has been found in anticline traps in the sandstone sequence. Offshore exploration in the Swedish sector has so far not encountered any significant findings of oil and gas. However, the extensive exploration has generated data, which is now being used for assessing the overall properties regarding suitability for storage of CO2. The Swedish primary industry has a great interest in finding potential sites for storage of CO2. A suitable site in the Baltic Sea would be a most favourable alternative in comparison to more remote alternatives such as deep saline aquifers in the North Sea. The Lower Cambrian is in the Swedish sector of the Baltic Sea composed of three main sandstone units varying in thickness between 5 and 50 m occurring within an up to 250 m thick Cambrian sequence dominated by fine-grained terriclastic sediments. The limit of Lower Palaeozoic sequence in the Baltic area is today defined by erosional truncation because of the gently dipping Lower Palaeozoic sequence. To the north and northwest, the limit is found in the Pre-Quaternary, whereas the erosional limit is deeply buried beneath Permian and Mesozoic sediments to the south. Here the Lower Palaeozoic limit is buried to depths reaching more than 2 km. The Cambrian sequence in the distal parts of the Swedish sector occurs at depths of c. 1300 m while it constitutes the bedrock surface in a narrow zone trending from Öland to the north of of Gotland. Sandstone beds constitute 40-60% of the total Cambrian sequence. The main sandstone units have a regional distribution of several thousands of square kilometres. The up to 50 m thick Faludden sandstone member exhibits the best reservoir properties including porosities in the range of 10-16% and permeabilities of 200-400 mD. Wire line logs indicate uniform physical properties of the member. The Faludden sandstone is in addition interpreted as a closed aquifer since it wedges out updip and is overlain by alum shale and several hundred metres of Ordovician-Silurian argillaceous limestone with bentonite clays acting as a significant seal. The regional distribution in combination with the satisfactory physical properties makes it an interesting candidate for CO2 storage. Investigations of the hydraulic properties of the aquifer as well as properties of the seal, in combination with numeric modelling have to be performed as to achieve a reliable assessment of the storage capacity. Research projects regarding this are now being launched by the Geological Survey of Sweden, Uppsala University, Lund University and the industry. Existing data regarding the Lower Cambrian sandstone in the Baltic Sea will also be included in the Nordic CCS GIS Atlas and data base within the recently launched Nordiccs-project.

Equilibrium, stability, and orbital evolution of close binary systems

NASA Technical Reports Server (NTRS)

Lai, Dong; Rasio, Frederic A.; Shapiro, Stuart L.

1994-01-01

We present a new analytic study of the equilibrium and stability properties of close binary systems containing polytropic components. Our method is based on the use of ellipsoidal trial functions in an energy variational principle. We consider both synchronized and nonsynchronized systems, constructing the compressible generalizations of the classical Darwin and Darwin-Riemann configurations. Our method can be applied to a wide variety of binary models where the stellar masses, radii, spins, entropies, and polytropic indices are all allowed to vary over wide ranges and independently for each component. We find that both secular and dynamical instabilities can develop before a Roche limit or contact is reached along a sequence of models with decreasing binary separation. High incompressibility always makes a given binary system more susceptible to these instabilities, but the dependence on the mass ratio is more complicated. As simple applications, we construct models of double degenerate systems and of low-mass main-sequence star binaries. We also discuss the orbital evoltuion of close binary systems under the combined influence of fluid viscosity and secular angular momentum losses from processes like gravitational radiation. We show that the existence of global fluid instabilities can have a profound effect on the terminal evolution of coalescing binaries. The validity of our analytic solutions is examined by means of detailed comparisons with the results of recent numerical fluid calculations in three dimensions.

The conserved CAAGAAAGA spacer sequence is an essential element for the formation of 3' termini of the sea urchin H3 histone mRNA by RNA processing.

PubMed Central

Georgiev, O; Birnstiel, M L

1985-01-01

Analysis of cDNA sequences obtained from the small nuclear RNA U7 has previously suggested specific contacts, by base pairing, between the conserved stem-loop structure and CAAGAAAGA sequence of the histone pre-mRNA and the 5'-terminal sequence of the U7 RNA during RNA processing. In order to test some aspects of the model we have created a series of linker scan, deletion and insertion mutants of the 3' terminus of a sea urchin H3 histone gene and have injected mutant DNAs or in vitro synthesized precursors into frog oocyte nuclei for interpretation. We find that, in addition to the stem-loop structure of the mRNA, the CAAGAAAGA spacer transcript within the histone pre-mRNA is required absolutely for RNA processing, as predicted from our model. Spacer sequences immediately downstream of the CAAGAAAGA motif are not complementary to U7 RNA. Nevertheless, they are necessary for obtaining a maximal rate of RNA processing, as is the ACCA sequence coding for the 3' terminus of the mature mRNA. An increase of distance between the mRNA palindrome and the CAAGAAAGA by as little as six nucleotides abolishes all processing. It may, therefore, be useful to regard both these sequence motifs as part of one and the same RNA processing signal with narrowly defined topologies. Interestingly, U7 RNA-dependent 3' processing of histone pre-mRNA can occur in RNA injection experiments only when the in vitro synthesized pre-mRNA contains sequence extensions well beyond the region of sequence complementarities to the U7 RNA. In addition to directing 3' processing the terminal mRNA sequences may have a role in histone mRNA stabilization in the cytoplasmic compartment. Images Fig. 3. Fig. 4. Fig. 5. Fig. 6. Fig. 7. PMID:2410259

Aftershock decay, productivity, and stress rates in Hawaii: Indicators of temperature and stress from magma sources

USGS Publications Warehouse

Klein, Fred W.; Wright, Tom; Nakata, Jennifer

2006-01-01

We examined dozens of aftershock sequences in Hawaii in terms of Gutenberg-Richter and modified Omori law parameters. We studied p, the rate of aftershock decay; Ap, the aftershock productivity, defined as the observed divided by the expected number of aftershocks; and c, the time delay when aftershock rates begin to fall. We found that for earthquakes shallower than 20 km, p values >1.2 are near active magma centers. We associate this high decay rate with higher temperatures and faster stress relaxation near magma reservoirs. Deep earthquakes near Kilauea's inferred magma transport path show a range of p values, suggesting the absence of a large, deep magma reservoir. Aftershock productivity is >4.0 for flank earthquakes known to be triggered by intrusions but is normal (0.25 to 4.0) for isolated main shocks. We infer that continuing, post-main shock stress from the intrusion adds to the main shock's stress step and causes higher Ap. High Ap in other zones suggests less obvious intrusions and pulsing magma pressure near Kilauea's feeding conduit. We calculate stress rates and stress rate changes from pre-main shock and aftershock rates. Stress rate increased after many intrusions but decreased after large M7–8 earthquakes. Stress rates are highest in the seismically active volcano flanks and lowest in areas far from volcanic centers. We found sequences triggered by intrusions tend to have high Ap, high (>0.10 day) c values, a stress rate increase, and sometimes a peak in aftershock rate hours after the main shock. We interpret these values as indicating continuing intrusive stress after the main shock.

Pre-Service Teachers' Approaches to a Historical Problem in Mechanics

ERIC Educational Resources Information Center

Malgieri, Massimiliano; Onorato, Pasquale; Mascheretti, Paolo; De Ambrosis, Anna

2014-01-01

In this paper we report on an activity sequence with a group of 29 pre-service physics teachers based on the reconstruction and analysis of a thought experiment that was crucial for Huygens' derivation of the formula for the centre of oscillation of a physical pendulum. The sequence starts with student teachers approaching the historical…

Mapping contacts between gRNA and mRNA in trypanosome RNA editing.

PubMed

Leung, S S; Koslowsky, D J

1999-02-01

All guide RNAs (gRNAs) identified to date have defined 5' anchor sequences, guiding sequences and a non-encoded 3' uridylate tail. The 5' anchor is required for in vitro editing and is thought to be responsible for selection and binding to the pre-edited mRNA. Little is known, however, about how the gRNAs are used to direct RNA editing. Utilizing the photo-reactive crosslinking agent, azidophenacyl (APA), attached to the 5'- or 3'-terminus of the gRNA, we have begun to map the structural relationships between the different defined regions of the gRNA with the pre-edited mRNA. Analyses of crosslinked conjugates produced with a 5'-terminal APA group confirm that the anchor of the gRNA is correctly positioning the interacting molecules. 3' Crosslinks (X-linker placed at the 3'-end of a U10tail) have also been mapped for three different gRNA/mRNA pairs. In all cases, analyses indicate that the U-tail can interact with a range of nucleotides located upstream of the first edited site. It appears that the U-tail prefers purine-rich sites, close to the first few editing sites. These results suggest that the U-tail may act in concert with the anchor to melt out secondary structure in the mRNA in the immediate editing domain, possibly increasing the accessibility of the editing complex to the proper editing sites.

DNA analysis of ancient dogs of the Americas: identifying possible founding haplotypes and reconstructing population histories.

PubMed

Witt, Kelsey E; Judd, Kathleen; Kitchen, Andrew; Grier, Colin; Kohler, Timothy A; Ortman, Scott G; Kemp, Brian M; Malhi, Ripan S

2015-02-01

As dogs have traveled with humans to every continent, they can potentially serve as an excellent proxy when studying human migration history. Past genetic studies into the origins of Native American dogs have used portions of the hypervariable region (HVR) of mitochondrial DNA (mtDNA) to indicate that prior to European contact the dogs of Native Americans originated in Eurasia. In this study, we summarize past DNA studies of both humans and dogs to discuss their population histories in the Americas. We then sequenced a portion of the mtDNA HVR of 42 pre-Columbian dogs from three sites located in Illinois, coastal British Columbia, and Colorado, and identify four novel dog mtDNA haplotypes. Next, we analyzed a dataset comprised of all available ancient dog sequences from the Americas to infer the pre-Columbian population history of dogs in the Americas. Interestingly, we found low levels of genetic diversity for some populations consistent with the possibility of deliberate breeding practices. Furthermore, we identified multiple putative founding haplotypes in addition to dog haplotypes that closely resemble those of wolves, suggesting admixture with North American wolves or perhaps a second domestication of canids in the Americas. Notably, initial effective population size estimates suggest at least 1000 female dogs likely existed in the Americas at the time of the first known canid burial, and that population size increased gradually over time before stabilizing roughly 1200 years before present. Copyright © 2014 Elsevier Ltd. All rights reserved.

Reassessment of the source of the 1976 Friuli, NE Italy, earthquake sequence from the joint inversion of high-precision levelling and triangulation data

NASA Astrophysics Data System (ADS)

Cheloni, D.; D'Agostino, N.; D'Anastasio, E.; Selvaggi, G.

2012-08-01

In this study, we revisit the mechanism of the 1976 Friuli (NE Italy) earthquake sequence (main shocks Mw 6.4, 5.9 and 6.0). We present a new source model that simultaneously fits all the available geodetic measurements of the observed deformation. We integrate triangulation measurements, which have never been previously used in the source modelling of this sequence, with high-precision levelling that covers the epicentral area. We adopt a mixed linear/non-linear optimization scheme, in which we iteratively search for the best-fitting solution by performing several linear slip inversions while varying fault location using a grid search method. Our preferred solution consists of a shallow north-dipping fault plane with assumed azimuth of 282° and accommodating a reverse dextral slip of about 1 m. The estimated geodetic moment is 6.6 × 1018 Nm (Mw 6.5), in agreement with seismological estimates. Yet, our preferred model shows that the geodetic solution is consistent with the activation of a single fault system during the entire sequence, the surface expression of which could be associated with the Buia blind thrust, supporting the hypothesis that the main activity of the Eastern Alps occurs close to the relief margin, as observed in other mountain belts. The retrieved slip pattern consists of a main coseismic patch located 3-5 km depth, in good agreement with the distribution of the main shocks. Additional slip is required in the shallower portions of the fault to reproduce the local uplift observed in the region characterized by Quaternary active folding. We tentatively interpret this patch as postseismic deformation (afterslip) occurring at the edge of the main coseismic patch. Finally, our rupture plane spatially correlates with the area of the locked fault determined from interseismic measurements, supporting the hypothesis that interseismic slip on the creeping dislocation causes strain to accumulate on the shallow (above ˜10 km depth) locked section. Assuming that all the long-term accommodation between Adria and Eurasia is seismically released, a time span of 500-700 years of strain-accumulating plate motion would result in a 1976-like earthquake.

Interpretation of the BRITE oscillation data of the hybrid pulsator ν Eridani: a call for the modification of stellar opacities

DOE Office of Scientific and Technical Information (OSTI.GOV)

Daszyńska-Daszkiewicz, J.; Pamyatnykh, A. A.; Walczak, P.

The analysis of the BRIght Target Explorer (BRITE) oscillation spectrum of the main-sequence early B-type star ν Eridani is presented in this paper. Only models with the modified mean opacity profile can account for the observed frequency ranges as well as for the values of some individual frequencies. The number of the κ-modified seismic models is constrained by the non-adiabatic parameter f, which is very sensitive to the opacity changes in the subphotospheric layers, where the pulsations are driven. We present an example of the model that satisfies all the above conditions. It seems that the OPLIB opacities are preferredmore » over those from the OPAL and OP projects. Finally and moreover, we discuss additional consequences of the opacity modification, namely, an enhancement of the efficiency of convection in the Z bump as well as an occurrence of close radial modes which is a kind of avoided-crossing phenomenon common for non-radial modes in standard main-sequence models.« less

Interpretation of the BRITE oscillation data of the hybrid pulsator ν Eridani: a call for the modification of stellar opacities

DOE PAGES

Daszyńska-Daszkiewicz, J.; Pamyatnykh, A. A.; Walczak, P.; ...

2016-12-22

The analysis of the BRIght Target Explorer (BRITE) oscillation spectrum of the main-sequence early B-type star ν Eridani is presented in this paper. Only models with the modified mean opacity profile can account for the observed frequency ranges as well as for the values of some individual frequencies. The number of the κ-modified seismic models is constrained by the non-adiabatic parameter f, which is very sensitive to the opacity changes in the subphotospheric layers, where the pulsations are driven. We present an example of the model that satisfies all the above conditions. It seems that the OPLIB opacities are preferredmore » over those from the OPAL and OP projects. Finally and moreover, we discuss additional consequences of the opacity modification, namely, an enhancement of the efficiency of convection in the Z bump as well as an occurrence of close radial modes which is a kind of avoided-crossing phenomenon common for non-radial modes in standard main-sequence models.« less

The unstable fate of the planet orbiting the A star in the HD 131399 triple stellar system

NASA Astrophysics Data System (ADS)

Veras, Dimitri; Mustill, Alexander J.; Gänsicke, Boris T.

2017-02-01

Validated planet candidates need not lie on long-term stable orbits, and instability triggered by post-main-sequence stellar evolution can generate architectures which transport rocky material to white dwarfs, hence polluting them. The giant planet HD 131399Ab orbits its parent A star at a projected separation of about 50-100 au. The host star, HD 131399A, is part of a hierarchical triple with HD 131399BC being a close binary separated by a few hundred au from the A star. Here, we determine the fate of this system, and find the following: (I) Stability along the main sequence is achieved only for a favourable choice of parameters within the errors. (II) Even for this choice, in almost every instance, the planet is ejected during the transition between the giant branch and white dwarf phases of HD 131399A. This result provides an example of both how the free-floating planet population may be enhanced by similar systems and how instability can manifest in the polluted white dwarf progenitor population.

a Fast Segmentation Algorithm for C-V Model Based on Exponential Image Sequence Generation

NASA Astrophysics Data System (ADS)

Hu, J.; Lu, L.; Xu, J.; Zhang, J.

2017-09-01

For the island coastline segmentation, a fast segmentation algorithm for C-V model method based on exponential image sequence generation is proposed in this paper. The exponential multi-scale C-V model with level set inheritance and boundary inheritance is developed. The main research contributions are as follows: 1) the problems of the "holes" and "gaps" are solved when extraction coastline through the small scale shrinkage, low-pass filtering and area sorting of region. 2) the initial value of SDF (Signal Distance Function) and the level set are given by Otsu segmentation based on the difference of reflection SAR on land and sea, which are finely close to the coastline. 3) the computational complexity of continuous transition are successfully reduced between the different scales by the SDF and of level set inheritance. Experiment results show that the method accelerates the acquisition of initial level set formation, shortens the time of the extraction of coastline, at the same time, removes the non-coastline body part and improves the identification precision of the main body coastline, which automates the process of coastline segmentation.

The Fate of Exoplanets and the Red Giant Rapid Rotator Connection

NASA Astrophysics Data System (ADS)

Carlberg, Joleen K.; Majewski, Steven R.; Arras, Phil; Smith, Verne V.; Cunha, Katia; Bizyaev, Dmitry

2011-03-01

We have computed the fate of exoplanet companions around main sequence stars to explore the frequency of planet ingestion by their host stars during the red giant branch evolution. Using published properties of exoplanetary systems combined with stellar evolution models and Zahn's theory of tidal friction, we modeled the tidal decay of the planets' orbits as their host stars evolve. Most planets currently orbiting within 2 AU of their star are expected to be ingested by the end of their stars' red giant branch ascent. Our models confirm that many transiting planets are sufficiently close to their parent star that they will be accreted during the main sequence lifetime of the star. We also find that planet accretion may play an important role in explaining the mysterious red giant rapid rotators, although appropriate planetary systems do not seem to be plentiful enough to account for all such rapid rotators. We compare our modeled rapid rotators and surviving planetary systems to their real-life counterparts and discuss the implications of this work to the broader field of exoplanets.

STELLAR BORON ABUNDANCES NEAR THE MAIN-SEQUENCE TURNOFF OF THE OPEN CLUSTER NGC 3293 AND IMPLICATIONS FOR THE EFFICIENCY OF ROTATIONALLY DRIVEN MIXING IN STELLAR ENVELOPES

DOE Office of Scientific and Technical Information (OSTI.GOV)

Proffitt, Charles R.; Lennon, Daniel J.; Langer, Norbert

2016-06-10

Spectra from the Hubble Space Telescope Cosmic Origins Spectrograph and the Space Telescope Imaging Spectrograph covering the B iii resonance line have been obtained for 10 early-B stars near the turnoff of the young Galactic open cluster NGC 3293. This is the first sample of boron abundance determinations in a single, clearly defined population of early-B stars that also covers a substantial range of projected rotational velocities. In most of these stars we detect partial depletion of boron at a level consistent with that expected for rotational mixing in single stars, but inconsistent with expectations for depletion from close binarymore » evolution. However, our results do suggest that the efficiency of rotational mixing is at or slightly below the low end of the range predicted by the available theoretical calculations. The two most luminous targets observed have a very large boron depletion and may be the products of either binary interactions or post-main-sequence evolution.« less

Membership and Coronal Activity in the NGC 2232 and Cr 140 Open Clusters

NASA Technical Reports Server (NTRS)

Oliversen, Ronald J. (Technical Monitor); Patten, Brian M.

2004-01-01

Making use of eight archival ROSAT HRI images in the regions of the NGC 2232 and Cr 140, this project's primary focus is to identify X-ray sources and to extract net source counts for these sources in these two open clusters. These X-ray data would be combined with ground-based photometry and spectroscopy in order to identify G, K, and early-M type cluster members. Such membership data are important because, at present, no members later than spectral type approx. F5 are currently known for either cluster. With ages estimated to be approx. 25 Myr and at distances of just approx. 350 pc, the combined late-type membership of the NGC 2232 and Cr 140 clusters would yield an almost unique sample of solar-type stars in the post-T Tauri/pre-main sequence phase of evolution. These stars could be used to assess the level and dispersion of coronal activity levels, as a part of a probe of the importance of magnetic braking and the level of magnetic dynamo activity, for solar-type stars just before they reach the zero-age main sequence.

International Ultraviolet Explorer (IUE) ultraviolet spectral atlas of selected astronomical objects

NASA Technical Reports Server (NTRS)

Wu, Chi-Chao; Reichert, Gail A.; Ake, Thomas B.; Boggess, Albert; Holm, Albert V.; Imhoff, Catherine L.; Kondo, Yoji; Mead, Jaylee M.; Shore, Steven N.

1992-01-01

The IUE Ultraviolet Spectral Atlas of Selected Astronomical Objects (or 'the Atlas'), is based on the data that were available in the IUE archive in 1986, and is intended to be a quick reference for the ultraviolet spectra of many categories of astronomical objects. It shows reflected sunlight from the Moon, planets, and asteroids, and also shows emission from comets. Comprehensive compilations of UV spectra for main sequence, subgiant, giant, bright giant, and supergiant stars are published elsewhere. This Atlas contains the spectra for objects occupying other areas of the Hertzsprung-Russell diagram: pre-main sequence stars, chemically peculiar stars, pulsating variables, subluminous stars, and Wolf-Rayet stars. This Atlas also presents phenomena such as the chromospheric and transition region emissions from late-type stars; composite spectra of stars, gas streams, accretion disks and gas envelopes of binary systems; the behavior of gas ejecta shortly after the outburst of novac and supernovac; and the H II regions, planetary nebulae, and supernova remnants. Population 2 stars, globular clusters, and luminous stars in the Magellanic Clouds, M31, and M33, are also included in this publication. Finally, the Atlas gives the ultraviolet spectra of galaxies of different Hubble types and of active galaxies.

On the barn owl's visual pre-attack behavior: I. Structure of head movements and motion patterns.

PubMed

Ohayon, Shay; van der Willigen, Robert F; Wagner, Hermann; Katsman, Igor; Rivlin, Ehud

2006-09-01

Barn owls exhibit a rich repertoire of head movements before taking off for prey capture. These movements occur mainly at light levels that allow for the visual detection of prey. To investigate these movements and their functional relevance, we filmed the pre-attack behavior of barn owls. Off-line image analysis enabled reconstruction of all six degrees of freedom of head movements. Three categories of head movements were observed: fixations, head translations and head rotations. The observed rotations contained a translational component. Head rotations did not follow Listing's law, but could be well described by a second-order surface, which indicated that they are in close agreement with Donder's law. Head translations did not contain any significant rotational components. Translations were further segmented into straight-line and curved paths. Translations along an axis perpendicular to the line of sight were similar to peering movements observed in other animals. We suggest that these basic motion elements (fixations, head rotations, translations along a straight line, and translation along a curved trajectory) may be combined to form longer and more complex behavior. We speculate that these head movements mainly underlie estimation of distance during prey capture.

Pulsed electric field assisted assembly of polyaniline

NASA Astrophysics Data System (ADS)

Kumar, Arun; Kazmer, David O.; Barry, Carol M. F.; Mead, Joey L.

2012-08-01

Assembling conducting polyaniline (PANi) on pre-patterned nano-structures by a high rate, commercially viable route offers an opportunity for manufacturing devices with nanoscale features. In this work we report for the first time the use of pulsed electric field to assist electrophoresis for the assembly of conducting polyaniline on gold nanowire interdigitated templates. This technique offers dynamic control over heat build-up, which has been a main drawback in the DC electrophoresis and AC dielectrophoresis as well as the main cause of nanowire template damage. The use of this technique allowed higher voltages to be applied, resulting in shorter assembly times (e.g., 17.4 s, assembly resolution of 100 nm). Moreover, the area coverage increases with the increase in number of pulses. A similar trend was observed with the deposition height and the increase in deposition height followed a linear trend with a correlation coefficient of 0.95. When the experimental mass deposited was compared with Hamaker’s theoretical model, the two were found to be very close. The pre-patterned templates with PANi deposition were subsequently used to transfer the nanoscale assembled PANi from the rigid templates to thermoplastic polyurethane using the thermoforming process.

Massive star formation by accretion. II. Rotation: how to circumvent the angular momentum barrier?

NASA Astrophysics Data System (ADS)

Haemmerlé, L.; Eggenberger, P.; Meynet, G.; Maeder, A.; Charbonnel, C.; Klessen, R. S.

2017-06-01

Context. Rotation plays a key role in the star-formation process, from pre-stellar cores to pre-main-sequence (PMS) objects. Understanding the formation of massive stars requires taking into account the accretion of angular momentum during their PMS phase. Aims: We study the PMS evolution of objects destined to become massive stars by accretion, focusing on the links between the physical conditions of the environment and the rotational properties of young stars. In particular, we look at the physical conditions that allow the production of massive stars by accretion. Methods: We present PMS models computed with a new version of the Geneva Stellar Evolution code self-consistently including accretion and rotation according to various accretion scenarios for mass and angular momentum. We describe the internal distribution of angular momentum in PMS stars accreting at high rates and we show how the various physical conditions impact their internal structures, evolutionary tracks, and rotation velocities during the PMS and the early main sequence. Results: We find that the smooth angular momentum accretion considered in previous studies leads to an angular momentum barrier and does not allow the formation of massive stars by accretion. A braking mechanism is needed in order to circumvent this angular momentum barrier. This mechanism has to be efficient enough to remove more than two thirds of the angular momentum from the inner accretion disc. Due to the weak efficiency of angular momentum transport by shear instability and meridional circulation during the accretion phase, the internal rotation profiles of accreting stars reflect essentially the angular momentum accretion history. As a consequence, careful choice of the angular momentum accretion history allows circumvention of any limitation in mass and velocity, and production of stars of any mass and velocity compatible with structure equations.

The Structure of the Star-forming Cluster RCW 38

NASA Astrophysics Data System (ADS)

Winston, E.; Wolk, S. J.; Bourke, T. L.; Megeath, S. T.; Gutermuth, R.; Spitzbart, B.

2011-12-01

We present a study of the structure of the high-mass star-forming region RCW 38 and the spatial distribution of its young stellar population. Spitzer Infrared Array Camera (IRAC) photometry (3-8 μm) is combined with Two Micron All Sky Survey near-IR data to identify young stellar objects (YSOs) by IR-excess emission from their circumstellar material. Chandra X-ray data are used to identify class III pre-main-sequence stars lacking circumstellar material. We identify 624 YSOs: 23 class 0/I and 90 flat spectrum protostars, 437 class II stars, and 74 class III stars. We also identify 29 (27 new) O star candidates over the IRAC field. Seventy-two stars exhibit IR-variability, including 7 class 0/I and 12 flat spectrum YSOs. A further 177 tentative candidates are identified by their location in the IRAC [3.6] versus [3.6]-[5.8] color-magnitude diagram. We find strong evidence of subclustering in the region. Three subclusters were identified surrounding the central cluster, with massive and variable stars in each subcluster. The central region shows evidence of distinct spatial distributions of the protostars and pre-main-sequence stars. A previously detected IR cluster, DB2001_Obj36, has been established as a subcluster of RCW 38. This suggests that star formation in RCW 38 occurs over a more extended area than previously thought. The gas-to-dust ratio is examined using the X-ray derived hydrogen column density, N H and the K-band extinction, and found to be consistent with the diffuse interstellar medium, in contrast with Serpens and NGC 1333. We posit that the high photoionizing flux of massive stars in RCW 38 affects the agglomeration of the dust grains.

DETECTION OF A COOL, ACCRETION-SHOCK-GENERATED X-RAY PLASMA IN EX LUPI DURING THE 2008 OPTICAL ERUPTION

DOE Office of Scientific and Technical Information (OSTI.GOV)

Teets, William K.; Weintraub, David A.; Kastner, Joel H.

2012-11-20

EX Lupi is the prototype for a class of young, pre-main-sequence stars which are observed to undergo irregular, presumably accretion-generated, optical outbursts that result in a several magnitude rise of the optical flux. EX Lupi was observed to optically erupt in 2008 January, triggering Chandra ACIS Target of Opportunity observations shortly thereafter. We find very strong evidence that most of the X-ray emission in the first few months after the optical outburst is generated by accretion of circumstellar material onto the stellar photosphere. Specifically, we find a strong correlation between the decreasing optical and X-ray fluxes following the peak ofmore » the outburst in the optical, which suggests that these observed declines in both the optical and X-ray fluxes are the result of declining accretion rate. In addition, in our models of the X-ray spectrum, we find strong evidence for a {approx}0.4 keV plasma component, as expected for accretion shocks on low-mass, pre-main-sequence stars. From 2008 March through October, this cool plasma component appeared to fade as EX Lupi returned to its quiescent level in the optical, consistent with a decrease in the overall emission measure of accretion-shock-generated plasma. The overall small increase of the X-ray flux during the optical outburst of EX Lupi is similar to what was observed in previous X-ray observations of the 2005 optical outburst of the EX Lupi-type star V1118 Ori but contrasts with the large increase of the X-ray flux from the erupting young star V1647 Ori during its 2003 and 2008 optical outbursts.« less

The antenna transcriptome changes in mosquito Anopheles sinensis, pre- and post- blood meal.

PubMed

Chen, Qian; Pei, Di; Li, Jianyong; Jing, Chengyu; Wu, Wenjian; Man, Yahui

2017-01-01

Antenna is the main chemosensory organ in mosquitoes. Characterization of the transcriptional changes after blood meal, especially those related to chemoreception, may help to explain mosquito blood sucking behavior and to identify novel targets for mosquito control. Anopheles sinensis is an Asiatic mosquito species which transmits malaria and lymphatic filariasis. However, studies on chemosensory biology in female An. sinensis are quite lacking. Here we report a transcriptome analysis of An. sinensis female antennae pre- and post- blood meal. We created six An. sinensis antenna RNA-seq libraries, three from females without blood meal and three from females five hours after a blood meal. Illumina sequencing was conducted to analyze the transcriptome differences between the two groups. In total, the sequenced fragments created 21,643 genes, 1,828 of them were novel. 12,861 of these genes were considered to be expressed (FPKM >1.0) in at least one of the two groups, with 12,159 genes expressed in both groups. 548 genes were differentially expressed in the blood-fed group, with 331 genes up-regulated and 217 genes down-regulated. GO enrichment analysis of the differentially expressed genes suggested that there were no statistically over represented GO terms among down-regulated genes in blood-fed mosquitoes, while the enriched GO terms of the up-regulated genes occurred mainly in metabolic process. For the chemosensory gene families, a subtle distinction in the expression levels can be observed according to our statistical analysis. However, the firstly comprehensive identification of these chemosensory gene families in An. sinensis antennae will help to characterize the precise function of these proteins in odor recognition in mosquitoes. This study provides a first global view in the changes of transcript accumulation elicited by blood meal in An. sinensis female antennae.

Time Variability of the Dust Sublimation Zones in Pre-Main Sequence Disk Systems

NASA Technical Reports Server (NTRS)

Sitko, Michael L.; Carpenter, W. J.; Grady, C. A.; Russel, R. W.; Lynch, D. K.; Rudy, R. J.; Mazuk, S. M.; Venturini, C. C.; Kimes, R. L.; Beerman, L. C.;

Detection of a Cool, Accretion-Shock-Generated X-Ray Plasma in EX Lupi During the 2008 Optical Eruption

NASA Technical Reports Server (NTRS)

Teets, William K.; Weintraub, David A.; Kastner, Joel H.; Grosso, Nicholas; Hamaguchi, Kenji; Richmond, Michael

2012-01-01

EX Lupi is the prototype for a class of young, pre-main-sequence stars which are observed to undergo irregular, presumably accretion-generated, optical outbursts that result in a several magnitude rise of the optical flux. EX Lupi was observed to optically erupt in 2008 January, triggering Chandra ACIS Target of Opportunity observations shortly thereafter. We find very strong evidence that most of the X-ray emission in the first few months after the optical outburst is generated by accretion of circumstellar material onto the stellar photosphere. Specifically, we find a strong correlation between the decreasing optical and X-ray fluxes following the peak of the outburst in the optical, which suggests that these observed declines in both the optical and X-ray fluxes are the result of declining accretion rate. In addition, in our models of the X-ray spectrum, we find strong evidence for an approx 0.4 keV plasma component, as expected for accretion shocks on low-mass, pre-main-sequence stars. From 2008 March through October, this cool plasma component appeared to fade as EX Lupi returned to its quiescent level in the optical, consistent with a decrease in the overall emission measure of accretion-shock-generated plasma. The overall small increase of the X-ray flux during the optical outburst of EX Lupi is similar to what was observed in previous X-ray observations of the 2005 optical outburst of the EX Lupi-type star V1118 Ori but contrasts with the large increase of the X-ray flux from the erupting young star V1647 Ori during its 2003 and 2008 optical outbursts.

A Multi-Fiber Spectroscopic Search for Low-mass Young Stars in Orion OB1

NASA Astrophysics Data System (ADS)

Loerincs, Jacqueline; Briceno, Cesar; Calvet, Nuria; Mateo, Mario L.; Hernandez, Jesus

2017-01-01

We present here results of a low resolution spectroscopic followup of candidate low-mass pre-main sequence stars in the Orion OB1 association. Our targets were selected from the CIDA Variability Survey of Orion (CVSO), and we used the Michigan/Magellan Fiber Spectrograph (M2FS) on the Magellan Clay 6.5m telescope to obtain spectra of 500 candidate T Tauri stars distributed in seven 0.5 deg diameter fields, adding to a total area of ~5.5 deg2. We identify young stars by looking at the distinctive Hα 6563 Å emission and Lithium Li I 6707 Å absorption features characteristic of young low mass pre-main sequence stars. Furthermore, by measuring the strength of their Hα emission lines, confirmed T Tauri stars can be classified as either Classical T Tauris (CTTS) or Weak-line T Tauris (WTTS), which give indication of whether the star is actively accreting material from a gas and dust disk surrounding the star, which may be the precursor of a planetary system. We confirm a total of 90 T Tauri stars, of which 50% are newly identified young members of Orion; out of the 49 new detections,15 are accreting CTTS, and of these all but one are found in the OB1b sub-region. This result is in line with our previous findings that this region is much younger than the more extended Orion OB1a sub-association. The M2FS results add to our growing census of young stars in Orion, that is allowing us to characterize in a systematic and consistent way the distribution of stellar ages across the entire complex, in order to building a complete picture of star formation in this, one of nearest most active sites of star birth.

High Dispersion Line Profile Studies of TW HYA and Other Pre-Main Sequence Stars

NASA Astrophysics Data System (ADS)

Linsky, Jeffrey L.

1984-07-01

We propose to extend our study of line profiles in T Tauri stars by obtaining a 16 hour SWP-HI spectrum of TW Hya and 6-8 hour LWP-HI spectra of TW Hya, AK Sco, CoD -35 10525 and CoD -33 10685. High dispersion spectra of pre-main sequence (PMS) stars provide unique information on line widths, shifts, and asymmetries, as well as evidence for mass outflow, circumstellar absorption, and diagnostics for the temperature structure of the outer atmosphere layers of these complex yet incredibly important objects. We have previously obtained and studied line profiles in RU Lupi and the prototype star T Tau. RU Lupi has line profiles that are dominated by the wind expansion, for example the MgII and FeII multiplet UV1 profiles are unique in that they have a classical P Cygni shape, whereas T Tau has more symmetric emission profiles indicative of a chromosphere and hotter layers not dominated by expansion. TW Hya is different from these two previously studied stars in that it may be the brightest known example of a post-T Tauri star, and hence less active and older than the other PMS stars. We intend to compare its line profiles with those of RU Lupi and T Tauri in order to understand the differences in the non-thermal mass motions, wind expansion, and thermal structures of these three very different T Tau stars. The requested LWPHI spectra are to obtain MgII and FeII multiplet UV1. profiles of 4 different T Tauri objects so as to infer the expansion and thermal structure in their chromospheric layers.

Closed Genome Sequence of Chryseobacterium piperi Strain CTMT/ATCC BAA-1782, a Gram-Negative Bacterium with Clostridial Neurotoxin-Like Coding Sequences

PubMed Central

Wentz, Travis G.; Muruvanda, Tim; Thirunavukkarasu, Nagarajan; Hoffmann, Maria; Allard, Marc W.; Hodge, David R.; Pillai, Segaran P.; Hammack, Thomas S.; Brown, Eric W.

2017-01-01

ABSTRACT Clostridial neurotoxins, including botulinum and tetanus neurotoxins, are among the deadliest known bacterial toxins. Until recently, the horizontal mobility of this toxin gene family appeared to be limited to the genus Clostridium. We report here the closed genome sequence of Chryseobacterium piperi, a Gram-negative bacterium containing coding sequences with homology to clostridial neurotoxin family proteins. PMID:29192076

Molecular prevalence and genetic diversity of bovine Theileria orientalis in Myanmar.

PubMed

Bawm, Saw; Shimizu, Kohei; Hirota, Jun-Ichi; Tosa, Yusuke; Htun, Lat Lat; Maw, Ni Ni; Thein, Myint; Kato, Hirotomo; Sakurai, Tatsuya; Katakura, Ken

2014-08-01

Theileria orientalis is a causative agent of benign theileriosis in cattle and distributed in mainly Asian countries. In the present study, we examined the prevalence of T. orientalis infection by PCR based on the major piroplasm surface protein gene (MPSP) sequences in cattle in Myanmar, followed by phylogenetic analysis of the MPSP genes. The MPSP gene was amplified in 258 of 713 (36.2%) cattle blood DNA samples collected from five cities in different geographical regions of Myanmar. Phylogenetic analysis of MPSP sequences from 54 T. orientalis-positive DNA samples revealed the presence of six allelic genotypes, including Types 1, 3, 4, 5, 7, and N-3. Types 5 and 7 were the predominant types detected. Sequences of the MPSP genes detected in Myanmar were closely related to those from Thailand, Vietnam or Mongolia. These findings suggest that movement of animals carrying T. orientalis parasites between Southeast Asian countries could be a reason for the similar genotype distribution of the parasites in Myanmar. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Diversity of partial RNA-dependent RNA polymerase gene sequences of soybean blotchy mosaic virus isolates from different host-, geographical- and temporal origins.

PubMed

Strydom, Elrea; Pietersen, Gerhard

2018-05-01

Infection of soybean by the plant cytorhabdovirus soybean blotchy mosaic virus (SbBMV) results in significant yield losses in the temperate, lower-lying soybean production regions of South Africa. A 277 bp portion of the RNA-dependent RNA polymerase gene of 66 SbBMV isolates from different: hosts, geographical locations in South Africa, and times of collection (spanning 16 years) were amplified by RT-PCR and sequenced to investigate the genetic diversity of isolates. Phylogenetic reconstruction revealed three main lineages, designated Groups A, B and C, with isolates grouping primarily according to geographic origin. Pairwise nucleotide identities ranged between 85.7% and 100% among all isolates, with isolates in Group A exhibiting the highest degree of sequence identity, and isolates of Groups A and B being more closely related to each other than to those in Group C. This is the first study investigating the genetic diversity of SbBMV.

Evaluation of recovery in lip closing pressure and occlusal force and contact area after orthognathic surgery.

PubMed

Ueki, Koichiro; Moroi, Akinori; Sotobori, Megumi; Ishihara, Yuri; Marukawa, Kohei; Iguchi, Ran; Kosaka, Akihiko; Ikawa, Hiroumi; Nakazawa, Ryuichi; Higuchi, Masatoshi

2014-10-01

The purpose of this study was to evaluate the relationship between lip closing force, occlusal contact area and occlusal force after orthognathic surgery in skeletal Class III patients. The subjects consisted of 54 patients (28 female and 26 male) diagnosed with mandibular prognathism who underwent sagittal split ramus osteotomy with and without Le Fort I osteotomy. Maximum and minimum lip closing forces, occlusal contact area and occlusal force were measured pre-operatively, 6 months and 1 year post-operative. Maximum and minimum lip closing forces, occlusal contact area and occlusal force increased with time after surgery, however a significant increase was not found in the occlusal contact area in women. In increased ratio (6 months/pre-operative and 1 year/pre-operative), the maximum lip closing force was significantly correlated with the occlusal contact area (P < 0.0001). This study suggested that orthognathic surgery could improve the occlusal force, contact area and lip closing force, and an increase ratio in maximum lip closing force was associated with an increased ratio in occlusal contact area. Copyright © 2014 European Association for Cranio-Maxillo-Facial Surgery. Published by Elsevier Ltd. All rights reserved.

Interferometric capability for the Magellan Project

NASA Astrophysics Data System (ADS)

Carleton, Nathaniel P.; Traub, Wesley A.; Angel, J. Roger P.

1998-07-01

The Magellan Project is building two 6.5-m telescopes, 60 m apart, at the Las Campanas Observatory in Chile. There are on-going plans to combine the beams of the two main telescopes, and of smaller auxiliary telescopes, for interferometric measurements. In this paper we consider the array of auxiliary telescopes as a stand-alone instrument, recognizing that it will operate as such for some large fraction of the time. Our interest is sharpened by the availability of six 1.8-m optical systems, retired from the Smithsonian-Arizona Multiple-Mirror Telescope in preparation for the installation of a single-mirror 6.5-m system. We have completed a design for a 1.8-m telescope, in which the MMT components are supported on a proven tripod mount. The optics-support uses steel for stiffness, and low-thermal- expansion rods for passive stability. This array will be a powerful tool for the investigation of stellar limb darkening, surface features, and changes of diameter in pulsations, as well as dust disks, shells, and binary companions. The 1.8-m telescopes on good sites such as Magellan's should be able to operate at full aperture for interferometry at 2.2 micrometers . They should therefore be able to reach to magnitude K equals 10 or so, and thus to cover substantial samples of both main-sequence and pre-main- sequence stars, and of fully evolved stars as well.

Closed Circular Chains

ERIC Educational Resources Information Center

Caglayan, Günhan

2016-01-01

A Steiner chain is defined as the sequence of n circles that are all tangent to two given non-intersecting circles. A closed chain, in particular, is one in which every circle in the sequence is tangent to the previous and next circles of the chain. In a closed Steiner chain the first and the "n"th circles of the chain are also tangent…

ASCA Observations of the T Tauri Star SU Aurigae and the Surrounding L1517 Dark Cloud

NASA Technical Reports Server (NTRS)

Skinner, Stephen L.; Walter, Frederick M.

1998-01-01

We present the results of a approximately equals 40 ks pointed Advanced Satellite for Cosmology and Astrophysics (ASCA) observation of the L1517 star-forming region, centered on the X-ray-bright T Tauri star SU Aurigae. This star has the highest X-ray luminosity of any classical T Tauri star in the Taurus-Auriga region, and its optical spectra show evidence for both mass inflow and outflow. Strong X-ray emission was detected from SU Aur (L(sub x) = 10(exp 30.9) ergs s(exp -1)) as well as weaker emission from five other pre-main-sequence stars. Although no large-amplitude flares were detected, the X-ray emission of SU Aur showed clear variability in the form of a slow decline in count rate during the 1.3 day observation. We provide the first direct comparison of the coronal differential emission measure (DEM) distribution of a classical T Tauri star with that of a young main-sequence star of similar spectral type. The DEM distributions of SU Aur (G2; age 3 Myr) and the young solar-like star EK Draconis (GO V; age 70 Myr) are qualitatively similar, with both showing a bimodal temperature distribution characterized by a cool plasma component peaking at approximately 8-9 MK and a hot component peaking at approximately 20-21 MK. However, there is a striking difference in the relative proportion of plasma at high temperatures in the two stars, with hot plasma (>20 MK) accounting for approximately equals 80% of the volume emission measure of SU Aur, compared to only approximately equals 40% in EK Dra. These results provide new insight into the changes that will occur in the corona of a T Tauri star as it descends onto the main sequence. A sharp decline in the fraction of coronal plasma at flarelike temperatures will occur during the late-T Tauri and post-T Tauri phases, and other recent X-ray studies have shown that this decline will continue after the young solar-like star reaches the main sequence.

CSI 2264: Simultaneous optical and X-ray variability in pre-main sequence stars. I. Time resolved X-ray spectral analysis during optical dips and accretion bursts in stars with disks

NASA Astrophysics Data System (ADS)

Guarcello, M. G.; Flaccomio, E.; Micela, G.; Argiroffi, C.; Sciortino, S.; Venuti, L.; Stauffer, J.; Rebull, L.; Cody, A. M.

2017-06-01

Context. Pre-main sequence stars are variable sources. The main mechanisms responsible for their variability are variable extinction, unsteady accretion, and rotational modulation of both hot and dark photospheric spots and X-ray-active regions. In stars with disks, this variability is related to the morphology of the inner circumstellar region (≤0.1 AU) and that of the photosphere and corona, all impossible to be spatially resolved with present-day techniques. This has been the main motivation for the Coordinated Synoptic Investigation of NGC 2264, a set of simultaneous observations of NGC 2264 with 15 different telescopes. Aims: In this paper, we focus on the stars with disks. We analyze the X-ray spectral properties extracted during optical bursts and dips in order to unveil the nature of these phenomena. Stars without disks are studied in a companion paper. Methods: We analyze simultaneous CoRoT and Chandra/ACIS-I observations to search for coherent optical and X-ray flux variability in stars with disks. Then, stars are analyzed in two different samples. In stars with variable extinction, we look for a simultaneous increase of optical extinction and X-ray absorption during the optical dips; in stars with accretion bursts, we search for soft X-ray emission and increasing X-ray absorption during the bursts. Results: We find evidence for coherent optical and X-ray flux variability among the stars with variable extinction. In 9 of the 24 stars with optical dips, we observe a simultaneous increase of X-ray absorption and optical extinction. In seven dips, it is possible to calculate the NH/AV ratio in order to infer the composition of the obscuring material. In 5 of the 20 stars with optical accretion bursts, we observe increasing soft X-ray emission during the bursts that we associate to the emission of accreting gas. It is not surprising that these properties are not observed in all the stars with dips and bursts, since favorable geometric configurations are required. Conclusions: The observed variable absorption during the dips is mainly due to dust-free material in accretion streams. In stars with accretion bursts, we observe, on average, a larger soft X-ray spectral component not observed in non-accreting stars.

40 CFR 98.430 - Definition of the source category.

Code of Federal Regulations, 2011 CFR

2011-07-01

... Contained in Pre-Charged Equipment or Closed-Cell Foams § 98.430 Definition of the source category. (a) The...-cell foams, consists of any entity that imports or exports pre-charged equipment that contains a fluorinated GHG, and any entity that imports or exports closed-cell foams that contain a fluorinated GHG. ...

40 CFR 98.430 - Definition of the source category.

Code of Federal Regulations, 2013 CFR

2013-07-01

... Contained in Pre-Charged Equipment or Closed-Cell Foams § 98.430 Definition of the source category. (a) The...-cell foams, consists of any entity that imports or exports pre-charged equipment that contains a fluorinated GHG, and any entity that imports or exports closed-cell foams that contain a fluorinated GHG. ...

40 CFR 98.430 - Definition of the source category.

Code of Federal Regulations, 2014 CFR

2014-07-01

... Contained in Pre-Charged Equipment or Closed-Cell Foams § 98.430 Definition of the source category. (a) The...-cell foams, consists of any entity that imports or exports pre-charged equipment that contains a fluorinated GHG, and any entity that imports or exports closed-cell foams that contain a fluorinated GHG. ...

40 CFR 98.430 - Definition of the source category.

Code of Federal Regulations, 2012 CFR

2012-07-01

... Contained in Pre-Charged Equipment or Closed-Cell Foams § 98.430 Definition of the source category. (a) The...-cell foams, consists of any entity that imports or exports pre-charged equipment that contains a fluorinated GHG, and any entity that imports or exports closed-cell foams that contain a fluorinated GHG. ...

Analysis of Pre-Analytic Factors Affecting the Success of Clinical Next-Generation Sequencing of Solid Organ Malignancies.

PubMed

Chen, Hui; Luthra, Rajyalakshmi; Goswami, Rashmi S; Singh, Rajesh R; Roy-Chowdhuri, Sinchita

2015-08-28

Application of next-generation sequencing (NGS) technology to routine clinical practice has enabled characterization of personalized cancer genomes to identify patients likely to have a response to targeted therapy. The proper selection of tumor sample for downstream NGS based mutational analysis is critical to generate accurate results and to guide therapeutic intervention. However, multiple pre-analytic factors come into play in determining the success of NGS testing. In this review, we discuss pre-analytic requirements for AmpliSeq PCR-based sequencing using Ion Torrent Personal Genome Machine (PGM) (Life Technologies), a NGS sequencing platform that is often used by clinical laboratories for sequencing solid tumors because of its low input DNA requirement from formalin fixed and paraffin embedded tissue. The success of NGS mutational analysis is affected not only by the input DNA quantity but also by several other factors, including the specimen type, the DNA quality, and the tumor cellularity. Here, we review tissue requirements for solid tumor NGS based mutational analysis, including procedure types, tissue types, tumor volume and fraction, decalcification, and treatment effects.

An eye movement pre-training fosters the comprehension of processes and functions in technical systems

PubMed Central

Skuballa, Irene T.; Fortunski, Caroline; Renkl, Alexander

2015-01-01

The main research goal of the present study was to investigate in how far pre-training eye movements can facilitate knowledge acquisition in multimedia (pre-training principle). We combined considerations from research on eye movement modeling and pre-training to design and test a non-verbal eye movement-based pre-training. Participants in the experimental condition watched an animated circle moving in close spatial resemblance to a static visualization of a solar plant accompanied by a narration in a subsequently presented learning environment. This training was expected to foster top-down processes as reflected in gaze behavior during the learning process and enhance knowledge acquisition. We compared two groups (N = 45): participants in the experimental condition received pre-training in a first step and processed the learning material in a second step, whereas the control group underwent the second step without any pre-training. The pre-training group outperformed the control group in their learning outcomes, particularly in knowledge about processes and functions of the solar plant. However, the superior learning outcomes in the pre-training group could not be explained by eye-movement patterns. Furthermore, the pre-training moderated the relationship between experienced stress and learning outcomes. In the control group, high stress levels hindered learning, which was not found for the pre-training group. On a delayed posttest participants were requested to draw a picture of the learning content. Despite a non-significant effect of training on the quality of drawings, the pre-training showed associations between learning outcomes at the first testing time and process-related aspects in the quality of their drawings. Overall, non-verbal pre-training is a successful instructional intervention to promote learning processes in novices although these processes did not directly reflect in learners' eye movement behavior during learning. PMID:26029138

Numerical investigation on pressure fluctuations in centrifugal compressor with different inlet guide vanes pre-whirl angles

NASA Astrophysics Data System (ADS)

Wang, Y. C.; Shi, M.; Cao, S. L.; Li, Z. H.

2013-12-01

The pressure fluctuations in a centrifugal compressor with different inlet guide vanes (IGV) pre-whirl angles were investigated numerically, as well as the pre-stress model and static structural of blade. The natural frequency was evaluated by pre-stress model analysis. The results show that, the aero-dynamic pressure acting on blade surface is smaller than rotation pre-stress, which wouldn't result in large deformation of blade. The natural frequencies with rotation pre-stress are slightly higher than without rotation pre-stress. The leading mechanism of pressure fluctuations for normal conditions is the rotor-stator (IGVs) interaction, while is serious flow separations for conditions that are close to surge line. A few frequency components in spectra are close to natural frequency, which possibly result in resonant vibration if amplitude is large enough, which is dangerous for compressor working, and should be avoided.

Implementing and Evaluating a Sequence of Instruction on Gaseous Pressure with Pre-Service Primary School Student Teachers.

ERIC Educational Resources Information Center

Taylor, Neil; Lucas, Keith B.

2000-01-01

Describes a teaching sequence on gaseous pressure implemented in a group of pre-service primary teachers in Fiji that provides subjects with a strong visual model of particle behavior which they then applied to a series of collaborative science activities for which they attempted to construct explanations. Suggests that this teaching sequence…

Petroleum source-rock potentials of the cretaceous transgressive-regressive sedimentary sequences of the Cauvery Basin

NASA Astrophysics Data System (ADS)

Chandra, Kuldeep; Philip, P. C.; Sridharan, P.; Chopra, V. S.; Rao, Brahmaji; Saha, P. K.

The present work is an attempt to contribute to knowledge on the petroleum source-rock potentials of the marine claystones and shales of basins associated with passive continental margins where the source-rock developments are known to have been associated with the anoxic events in the Mesozoic era. Data on three key exploratory wells from three major depressions Ariyallur-Pondicherry, Thanjavur and Nagapattinam of the Cauvery Basin are described and discussed. The average total organic carbon contents of the transgressive Pre-Albian-Cinomanian and Coniacian/Santonian claystones/shales range from 1.44 and 1.16%, respectively. The transgressive/regressive Campanian/Maastrichtian claystones contain average total organic carbon varying from 0.62 to 1.19%. The kerogens in all the studied stratigraphic sequences are classified as type-III with Rock-Eval hydrogen indices varying from 30 to 275. The nearness of land masses to the depositional basin and the mainly clastic sedimentation resulted in accumulation and preservation of dominantly type-III kerogens. The Pre-Albian to Cinomanian sequences of peak transgressive zone deposited in deep marine environments have kerogens with a relatively greater proportion of type-II components with likely greater contribution of planktonic organic matters. The global anoxic event associated with the Albian-Cinomanian marine transgression, like in many other parts of the world, has pervaded the Cauvery Basin and favoured development of good source-rocks with type-III kerogens. The Coniacian-Campanian-Maastrichtian transgressive/regressive phase is identified to be relatively of lesser significance for development of good quality source-rocks.

Short intronic repeat sequences facilitate circular RNA production.

PubMed

Liang, Dongming; Wilusz, Jeremy E

2014-10-15

Recent deep sequencing studies have revealed thousands of circular noncoding RNAs generated from protein-coding genes. These RNAs are produced when the precursor messenger RNA (pre-mRNA) splicing machinery "backsplices" and covalently joins, for example, the two ends of a single exon. However, the mechanism by which the spliceosome selects only certain exons to circularize is largely unknown. Using extensive mutagenesis of expression plasmids, we show that miniature introns containing the splice sites along with short (∼ 30- to 40-nucleotide) inverted repeats, such as Alu elements, are sufficient to allow the intervening exons to circularize in cells. The intronic repeats must base-pair to one another, thereby bringing the splice sites into close proximity to each other. More than simple thermodynamics is clearly at play, however, as not all repeats support circularization, and increasing the stability of the hairpin between the repeats can sometimes inhibit circular RNA biogenesis. The intronic repeats and exonic sequences must collaborate with one another, and a functional 3' end processing signal is required, suggesting that circularization may occur post-transcriptionally. These results suggest detailed and generalizable models that explain how the splicing machinery determines whether to produce a circular noncoding RNA or a linear mRNA. © 2014 Liang and Wilusz; Published by Cold Spring Harbor Laboratory Press.

Cloning and sequence analysis of Galleria mellonella juvenile hormone binding protein--a search for ancestors and relatives.

PubMed

Rodriguez Parkitna, Jan M; Ozyhar, Andrzej; Wiśniewski, Jacek R; Kochman, Marian

2002-09-01

Juvenile hormone binding proteins (JHBPs) serve as specific carriers of juvenile hormone (JH) in insect hemolymph. As shown in this report, Galleria mellonella JHBP is encoded by a cDNA of 1063 nucleotides. The pre-protein consists of 245 amino acids with a 20 amino acid leader sequence. The concentration of the JHBP mRNA reaches a maximum on the third day of the last larval instar, and decreases five-fold towards pupation. Comparison of amino acid sequences of JHBPs from Bombyx mori, Heliothis virescens, Manduca sexta and G. mellonella shows that 57 positions out of 226 are occupied by identical amino acids. A phylogeny tree was constructed from 32 proteins, which function could be associated to JH. It has three major branches: (i) ligand binding domains of nuclear receptors, (ii) JHBPs and JH esterases (JHEs), and (iii) hypothetical proteins found in Drosophila melanogaster genome. Despite the close positioning of JHEs and JHBPs on the tree, which probably arises from the presence of a common JH binding motif, these proteins are unlikely to belong to the same family. Detailed analysis of the secondary structure modeling shows that JHBPs may contain a beta-barrel motif flanked by alpha-helices and thus be evolutionary related to the same superfamily as calycins.

Effect of the rotation and tidal dissipation history of stars on the evolution of close-in planets

NASA Astrophysics Data System (ADS)

Bolmont, Emeline; Mathis, Stéphane

2016-11-01

Since 20 years, a large population of close-in planets orbiting various classes of low-mass stars (from M-type to A-type stars) has been discovered. In such systems, the dissipation of the kinetic energy of tidal flows in the host star may modify its rotational evolution and shape the orbital architecture of the surrounding planetary system. In this context, recent observational and theoretical works demonstrated that the amplitude of this dissipation can vary over several orders of magnitude as a function of stellar mass, age and rotation. In addition, stellar spin-up occurring during the Pre-Main-Sequence (PMS) phase because of the contraction of stars and their spin-down because of the torque applied by magnetized stellar winds strongly impact angular momentum exchanges within star-planet systems. Therefore, it is now necessary to take into account the structural and rotational evolution of stars when studying the orbital evolution of close-in planets. At the same time, the presence of planets may modify the rotational dynamics of the host stars and as a consequence their evolution, magnetic activity and mixing. In this work, we present the first study of the dynamics of close-in planets of various masses orbiting low-mass stars (from 0.6~M_⊙ to 1.2~M_⊙) where we compute the simultaneous evolution of the star's structure, rotation and tidal dissipation in its external convective envelope. We demonstrate that tidal friction due to the stellar dynamical tide, i.e. tidal inertial waves excited in the convection zone, can be larger by several orders of magnitude than the one of the equilibrium tide currently used in Celestial Mechanics, especially during the PMS phase. Moreover, because of this stronger tidal friction in the star, the orbital migration of the planet is now more pronounced and depends more on the stellar mass, rotation and age. This would very weakly affect the planets in the habitable zone because they are located at orbital distances such that stellar tide-induced migration happens on very long timescales. We also demonstrate that the rotational evolution of host stars is only weakly affected by the presence of planets except for massive companions.

THE FORMATION AND EVOLUTION OF YOUNG LOW-MASS STARS WITHIN HALOS WITH HIGH CONCENTRATION OF DARK MATTER PARTICLES

DOE Office of Scientific and Technical Information (OSTI.GOV)

Casanellas, Jordi; Lopes, IlIDio, E-mail: jordicasanellas@ist.utl.p, E-mail: ilidio.lopes@ist.utl.p

2009-11-01

The formation and evolution of low-mass stars within dense halos of dark matter (DM) leads to evolution scenarios quite different from the classical stellar evolution. As a result of our detailed numerical work, we describe these new scenarios for a range of DM densities on the host halo, for a range of scattering cross sections of the DM particles considered, and for stellar masses from 0.7 to 3 M {sub sun}. For the first time, we also computed the evolution of young low-mass stars in their Hayashi track in the pre-main-sequence phase and found that, for high DM densities, thesemore » stars stop their gravitational collapse before reaching the main sequence, in agreement with similar studies on first stars. Such stars remain indefinitely in an equilibrium state with lower effective temperatures (|DELTAT{sub eff}|>10{sup 3} K for a star of one solar mass), the annihilation of captured DM particles in their core being the only source of energy. In the case of lower DM densities, these protostars continue their collapse and progress through the main-sequence burning hydrogen at a lower rate. A star of 1 M{sub sun} will spend a time period greater than the current age of the universe consuming all the hydrogen in its core if it evolves in a halo with DM density rho{sub c}hi = 10{sup 9} GeV cm{sup -3}. We also show the strong dependence of the effective temperature and luminosity of these stars on the characteristics of the DM particles and how this can be used as an alternative method for DM research.« less

Chromospherically Active Stars in the RAVE Survey. II. Young Dwarfs in the Solar Neighborhood

NASA Astrophysics Data System (ADS)

Žerjal, M.; Zwitter, T.; Matijevič, G.; Grebel, E. K.; Kordopatis, G.; Munari, U.; Seabroke, G.; Steinmetz, M.; Wojno, J.; Bienaymé, O.; Bland-Hawthorn, J.; Conrad, C.; Freeman, K. C.; Gibson, B. K.; Gilmore, G.; Kunder, A.; Navarro, J.; Parker, Q. A.; Reid, W.; Siviero, A.; Watson, F. G.; Wyse, R. F. G.

2017-01-01

A large sample of over 38,000 chromospherically active candidate solar-like stars and cooler dwarfs from the RAVE survey is addressed in this paper. An improved activity identification with respect to the previous study was introduced to build a catalog of field stars in the solar neighborhood with an excess emission flux in the calcium infrared triplet wavelength region. The central result of this work is the calibration of the age-activity relation for main-sequence dwarfs in a range from a few 10 {Myr} up to a few Gyr. It enabled an order of magnitude age estimation of the entire active sample. Almost 15,000 stars are shown to be younger than 1 {Gyr} and ˜2000 younger than 100 {Myr}. The young age of the most active stars is confirmed by their position off the main sequence in the J - K versus {N}{UV}-V diagram showing strong ultraviolet excess, mid-infrared excess in the J - K versus {W}1-{W}2 diagram, and very cool temperatures (J-K> 0.7). They overlap with the reference pre-main-sequence RAVE stars often displaying X-ray emission. The activity level increasing with the color reveals their different nature from the solar-like stars and probably represents an underlying dynamo-generating magnetic fields in cool stars. Of the RAVE objects from DR5, 50% are found in the TGAS catalog and supplemented with accurate parallaxes and proper motions by Gaia. This makes the database of a large number of young stars in a combination with RAVE’s radial velocities directly useful as a tracer of the very recent large-scale star formation history in the solar neighborhood. The data are available online in the Vizier database.

The evolution of surface magnetic fields in young solar-type stars II: the early main sequence (250-650 Myr)

NASA Astrophysics Data System (ADS)

Folsom, C. P.; Bouvier, J.; Petit, P.; Lèbre, A.; Amard, L.; Palacios, A.; Morin, J.; Donati, J.-F.; Vidotto, A. A.

2018-03-01

There is a large change in surface rotation rates of sun-like stars on the pre-main sequence and early main sequence. Since these stars have dynamo-driven magnetic fields, this implies a strong evolution of their magnetic properties over this time period. The spin-down of these stars is controlled by interactions between stellar and magnetic fields, thus magnetic evolution in turn plays an important role in rotational evolution. We present here the second part of a study investigating the evolution of large-scale surface magnetic fields in this critical time period. We observed stars in open clusters and stellar associations with known ages between 120 and 650 Myr, and used spectropolarimetry and Zeeman Doppler Imaging to characterize their large-scale magnetic field strength and geometry. We report 15 stars with magnetic detections here. These stars have masses from 0.8 to 0.95 M⊙, rotation periods from 0.326 to 10.6 d, and we find large-scale magnetic field strengths from 8.5 to 195 G with a wide range of geometries. We find a clear trend towards decreasing magnetic field strength with age, and a power law decrease in magnetic field strength with Rossby number. There is some tentative evidence for saturation of the large-scale magnetic field strength at Rossby numbers below 0.1, although the saturation point is not yet well defined. Comparing to younger classical T Tauri stars, we support the hypothesis that differences in internal structure produce large differences in observed magnetic fields, however for weak-lined T Tauri stars this is less clear.

On the nature of phase attraction in sensorimotor synchronization with interleaved auditory sequences.

PubMed

Repp, Bruno H

2004-10-01

In a task that requires in-phase synchronization of finger taps with an isochronous sequence of target tones that is interleaved with a sequence of distractor tones at various fixed phase relationships, the taps tend to be attracted to the distractor tones, especially when the distractor tones closely precede the target tones [Repp, B. H. (2003a). Phase attraction in sensorimotor synchronization with auditory sequences: Effects of single and periodic distractors on synchronization accuracy. Journal of Experimental Psychology: Human Perception and Performance, 29, 290-309]. The present research addressed two related questions about this distractor effect: (1) Is it a function of the absolute temporal separation or of the relative phase of the two stimulus sequences? (2) Is it the result of perceptual grouping (integration) of target and distractor tones or of simultaneous attraction to two independent sequences? In three experiments, distractor effects were compared across two different sequence rates. The results suggest that absolute temporal separation, not relative phase, is the critical variable. Experiment 3 also included an anti-phase tapping task that addressed the second question directly. The results suggest that the attraction of taps to distractor tones is caused mainly by temporal integration of target and distractor tones within a fixed window of 100-150 ms duration, with the earlier-occurring tone being weighted more strongly than the later-occurring one.

The seismic stratigraphy of Okanagan Lake, British Columbia; a record of rapid deglaciation in a deep 'fiord-lake' basin

NASA Astrophysics Data System (ADS)

Eyles, Nicholas; Mullins, Henry T.; Hine, Albert C.

1991-09-01

This paper presents the first detailed data regarding the newly discovered deep infill of Okanagan Lake. Okanagan Lake (50°00'N, 119°30'W) is 120 km long, ˜ 3-5 km wide and occupies a glacially overdeepened bedrock basin in the southern interior of British Columbia. This basin, and other elongate lakes of the region (e.g. Shuswap, Kootenay, Kalamalka, Canim and Mahood lakes), mark the site of westward flowing ice streams within successive Cordilleran ice sheets. An air gun seismic survey of Okanagan Lake shows that the bedrock floor is nearly 650 m below sea-level, more than 2000 m below the rim of the surrounding plateau. The maximum thickness of Pleistocene sediment in Okanagan Lake basin approaches 800 m. Forty-six seismic reflection traverses and an axial profile show a relatively simple stratigraphy composed of three seismic sequences argued to be no older than the last glacial cycle (< 30 ka). A discontinuous basal unit (sequence I) characterized by large-scale diffractions, and up to 460 m thick, infills the narrow, V-shaped bedrock floor of the basin and is interpreted as a boulder gravel deposited by subglacial meltwaters. Overlying seismic sequence II is composed of two sub-sequences. Sub-sequence IIa is a chaotic to massive facies up to 736 m thick. Lakeshore exposures close to where this unit reaches lake level show deformed and chaotically-bedded glaciolacustrine silts containing gravel lens and large ice-rafted boulders. The surface topography of this sub-sequence is irregular and in general mimics the form of the underlying bedrock as a result of compaction. This sequence passes laterally into stratified facies (sub-sequence IIb) at the northern end of the basin. Seismic sequence II appears to record rapid ice-proximal dumping of glaciolacustrine silt as the Okanagan glacier backwasted upvalley in a deep lake. A thin (60 m max.) laminated seismic sequence (III) drapes the hummocky surface of sequence II and represents postglacial sedimentation from fan-deltas. The extreme thickness of sequences I and II in Okanagan Lake reflects the focussing of large volumes of meltwater and sediment into the basin during deglaciation; pre-existing sediments that pre-date the last glacial cycle appear to have been completely eroded. Glaciological conditions during sedimentation may have been similar to marine-based outlet glaciers calving in deep water in fiord basins. In contrast to marine settings where ice bergs are free to disperse, large volumes of dead ice were trapped within the basin; structural evidence for sedimentation around dead ice blocks has been previously used to argue that the Cordilleran Ice Sheet downwasted in situ. We emphasize in contrast, the trapping of dead ice left behind by rapidly calving lake-based outlet glaciers.

Convert a low-cost sensor to a colorimeter using an improved regression method

NASA Astrophysics Data System (ADS)

Wu, Yifeng

2008-01-01

Closed loop color calibration is a process to maintain consistent color reproduction for color printers. To perform closed loop color calibration, a pre-designed color target should be printed, and automatically measured by a color measuring instrument. A low cost sensor has been embedded to the printer to perform the color measurement. A series of sensor calibration and color conversion methods have been developed. The purpose is to get accurate colorimetric measurement from the data measured by the low cost sensor. In order to get high accuracy colorimetric measurement, we need carefully calibrate the sensor, and minimize all possible errors during the color conversion. After comparing several classical color conversion methods, a regression based color conversion method has been selected. The regression is a powerful method to estimate the color conversion functions. But the main difficulty to use this method is to find an appropriate function to describe the relationship between the input and the output data. In this paper, we propose to use 1D pre-linearization tables to improve the linearity between the input sensor measuring data and the output colorimetric data. Using this method, we can increase the accuracy of the regression method, so as to improve the accuracy of the color conversion.

Tidal Interaction among Red Giants Close Binary Systems in APOGEE Database

NASA Astrophysics Data System (ADS)

Sun, Meng; Arras, Phil; Majewski, Steven R.; Troup, Nicholas William; Weinberg, Nevin N.

2017-01-01

Motivated by the newly discovered close binary systems in the Apache Point Observatory Galactic Evolution Experiment (APOGEE-1), the tidal evolution of binaries containing a red giant branch (RGB) star with a stellar or substellar companion was investigated. The tide raised by the companion in the RGB star leads to exchange of angular momentum between the orbit and the stellar spin, causing the orbit to contract. The tidal dissipation rate is computed using turbulent viscosity acting on the equilibrium tidal flow, where careful attention is paid to the effects of reduced viscosity for close-in companions. Evolutionary models for the RGB stars, from the zero-age main sequence to the present, were acquired from the MESA code. "Standard" turbulent viscosity gives rise to such a large orbital decay that many observed systems have decay times much shorter than the RGB evolution time. Several theories for "reduced" turbulent viscosity are investigated, and reduce the number of systems with uncomfortably short decay times.

Complete Genome Sequence of a Street Rabies Virus Isolated from a Dog in Nigeria

PubMed Central

Zhou, Ming; Zhou, Zutao; Kia, Grace S. N.; Gnanadurai, Clement W.; Leyson, Christina M.; Umoh, Jarlath U.; Kwaga, Jacob P.; Kazeem, Haruna M.

2013-01-01

A canine rabies virus (RABV) was isolated from a trade dog in Nigeria. Its entire genome was sequenced and found to be closely related to canine RABVs circulating in Africa. Sequence comparison indicates that the virus is closely related to the Africa 2 RABV lineage. The virus is now termed DRV-NG11. PMID:23469344

Mutations That Improve the pRE Promoter of Coliphage Lambda

PubMed Central

Mahoney, Michael E.; Wulff, Daniel L.

1987-01-01

The dya5 mutation, a C→T change at position -43 of the λ pRE promoter, results in a twofold increase in pRE activity in vivo. Smaller increases in pRE activity are found for the dya2 mutation, a T→C change at position -1 of pRE, and the dya3 mutation, an A→G change at +5 of pRE. The mutant p RE promoters retain complete dependence on cII protein for activity. These observations argue, at least for pRE-like promoters, that promoter activities are influenced by nucleotide sequences at least eight nucleotides to the 5'-side of the conventional -35 region consensus sequence, and by nucleotide sequences near the start-site of transcription. Although Hawley and McClure (1983) found A·T pairs more frequently than G·TC pairs in the region of -40 to -45 of prokaryotic promoters, other mutations that change a G·TC pair to an A·T pair at positions -41, -44 and -45 of pRE do not result in increased promoter activity. We also found that a T→C change at position -42 results in a mild decrease in promoter activity. These observations argue that Ts at positions -42 and -43 of pRE are required for maximum promoter activity, but do not support the hypothesis that As and Ts in the -40 to -45 region generally lead to higher promoter activities. PMID:2953648

Timing of terrane accretion in eastern and east-central Maine

NASA Astrophysics Data System (ADS)

Ludman, Allan

1986-05-01

The Norumbega fault zone is often cited as a post-Acadian suture between exotic blocks, even though stratigraphic, structural, and metamorphic data indicate that there is little offset of the Silurian-Devonian strata that the zone cuts in eastern Maine. Similarly, the Kingman fault zone has been shown by gravity and geochemical studies to separate distinct crustal blocks, whereas mapping shows that it lies entirely within a Silurian turbidite package. These conflicts are resolved if the two fault zones represent boundaries between Ordovician or older crustal blocks that had accreted to form a composite terrane prior to deposition of the cover sequences. The faults now mapped within these younger rocks formed by reactivation of the pre-Silurian boundaries during late Acadian time; movement continued until the late Carboniferous. Most of the accretionary history of Maine had thus ended before the Silurian. A complex composite terrane may have formed during Cambrian-Ordovician time that (1) interacted with cratonic North America during the Taconian orogeny and (2) became the “basement” upon which the Silurian and Lower Devonian strata of eastern Maine were deposited.

An optimal open/closed-loop control method with application to a pre-stressed thin duralumin plate

NASA Astrophysics Data System (ADS)

Nadimpalli, Sruthi Raju

The excessive vibrations of a pre-stressed duralumin plate, suppressed by a combination of open-loop and closed-loop controls, also known as open/closed-loop control, is studied in this thesis. The two primary steps involved in this process are: Step (I) with an assumption that the closed-loop control law is proportional, obtain the optimal open-loop control by direct minimization of the performance measure consisting of energy at terminal time and a penalty on open-loop control force via calculus of variations. If the performance measure also involves a penalty on closed-loop control effort then a Fourier based method is utilized. Step (II) the energy at terminal time is minimized numerically to obtain optimal values of feedback gains. The optimal closed-loop control gains obtained are used to describe the displacement and the velocity of open-loop, closed-loop and open/closed-loop controlled duralumin plate.

Biogas production enhancement using semi-aerobic pre-aeration in a hybrid bioreactor landfill.

PubMed

Cossu, Raffaello; Morello, Luca; Raga, Roberto; Cerminara, Giulia

2016-09-01

Landfilling continues to be one of the main methods used in managing Municipal Solid Waste (MSW) worldwide, particularly in developing countries. Although in many countries national legislation aims to reduce this practice as much as possible, landfill is a necessary and unavoidable step in closing the material cycle. The need for innovative waste management techniques to improve landfill management and minimize the adverse environmental impact produced has resulted in an increasing interest in innovative systems capable of accelerating waste stabilization. Landfill bioreactors allow decomposition kinetics to be increased and post-operational phase to be shortened; in particular, hybrid bioreactors combine the benefits afforded by both aerobic and anaerobic processes. Six bioreactor simulators were used in the present study: four managed as hybrid, with an initial semi-aerobic phase and a second anaerobic phase, and two as anaerobic control bioreactors. The main goal of the first aerated phase is to reduce Volatile Fatty Acids (VFA) in order to increase pH and enhance methane production during the anaerobic phase; for this reason, air injection was stopped only when these parameters reached the optimum range for methanogenic bacteria. Biogas and leachate were constantly monitored throughout the entire methanogenic phase with the aim of calibrating a Gompertz Model and evaluating the effects of pre-aeration on subsequent methane production. The results showed that moderate and intermittent pre-aeration produces a positive effect both on methane potential and in the kinetics of reaction. Copyright © 2015 Elsevier Ltd. All rights reserved.

[Deregulation of pre-messenger RNA splicing and rare diseases].

PubMed

de la Grange, Pierre

2016-12-01

Most of protein-coding human genes are subjected to alternative pre-mRNA splicing. This mechanism is highly regulated to precisely modulate detection of specific splice sites. This regulation is under control of the spliceosome and several splicing factors are also required to modulate the alternative usage of splice sites. Splicing factors and spliceosome components recognize splicing signals and regulatory sequences of the pre-mRNAs. These splicing sequences make splicing susceptible to polymorphisms and mutations. Examples of associations between human rare diseases and defects in pre-messenger RNA splicing are accumulating. Although many alterations are caused by mutations in splicing sequence (i.e., cis acting mutations), recent studies described the disruptive impact of mutations within spliceosome components or splicing factors (i.e., trans acting mutations). Following growing of knowledge regarding splicing regulation, several approaches have been developed to compensate for the effect of deleterious mutations and to restore sufficient amounts of functional protein. © 2016 médecine/sciences – Inserm.

Model for Codon Position Bias in RNA Editing

NASA Astrophysics Data System (ADS)

Liu, Tsunglin; Bundschuh, Ralf

2005-08-01

RNA editing can be crucial for the expression of genetic information via inserting, deleting, or substituting a few nucleotides at specific positions in an RNA sequence. Within coding regions in an RNA sequence, editing usually occurs with a certain bias in choosing the positions of the editing sites. In the mitochondrial genes of Physarum polycephalum, many more editing events have been observed at the third codon position than at the first and second, while in some plant mitochondria the second codon position dominates. Here we propose an evolutionary model that explains this bias as the basis of selection at the protein level. The model predicts a distribution of the three positions rather close to the experimental observation in Physarum. This suggests that the codon position bias in Physarum is mainly a consequence of selection at the protein level.

A model for codon position bias in RNA editing

NASA Astrophysics Data System (ADS)

Bundschuh, Ralf; Liu, Tsunglin

2006-03-01

RNA editing can be crucial for the expression of genetic information via inserting, deleting, or substituting a few nucleotides at specific positions in an RNA sequence. Within coding regions in an RNA sequence, editing usually occurs with a certain bias in choosing the positions of the editing sites. In the mitochondrial genes of Physarum polycephalum, many more editing events have been observed at the third codon position than at the first and second, while in some plant mitochondria the second codon position dominates. Here we propose an evolutionary model that explains this bias as the basis of selection at the protein level. The model predicts a distribution of the three positions rather close to the experimental observation in Physarum. This suggests that the codon position bias in Physarum is mainly a consequence of selection at the protein level.

The main challenges that remain in applying high-throughput sequencing to clinical diagnostics.

PubMed

Loeffelholz, Michael; Fofanov, Yuriy

2015-01-01

Over the last 10 years, the quality, price and availability of high-throughput sequencing instruments have improved to the point that this technology may be close to becoming a routine tool in the diagnostic microbiology laboratory. Two groups of challenges, however, have to be resolved in order to move this powerful research technology into routine use in the clinical microbiology laboratory. The computational/bioinformatics challenges include data storage cost and privacy concerns, requiring analysis to be performed without access to cloud storage or expensive computational infrastructure. The logistical challenges include interpretation of complex results and acceptance and understanding of the advantages and limitations of this technology by the medical community. This article focuses on the approaches to address these challenges, such as file formats, algorithms, data collection, reporting and good laboratory practices.

The 2016 Kumamoto earthquake sequence.

PubMed

Kato, Aitaro; Nakamura, Kouji; Hiyama, Yohei

2016-01-01

Beginning in April 2016, a series of shallow, moderate to large earthquakes with associated strong aftershocks struck the Kumamoto area of Kyushu, SW Japan. An M j 7.3 mainshock occurred on 16 April 2016, close to the epicenter of an M j 6.5 foreshock that occurred about 28 hours earlier. The intense seismicity released the accumulated elastic energy by right-lateral strike slip, mainly along two known, active faults. The mainshock rupture propagated along multiple fault segments with different geometries. The faulting style is reasonably consistent with regional deformation observed on geologic timescales and with the stress field estimated from seismic observations. One striking feature of this sequence is intense seismic activity, including a dynamically triggered earthquake in the Oita region. Following the mainshock rupture, postseismic deformation has been observed, as well as expansion of the seismicity front toward the southwest and northwest.

The 2016 Kumamoto earthquake sequence

PubMed Central

KATO, Aitaro; NAKAMURA, Kouji; HIYAMA, Yohei

2016-01-01

Beginning in April 2016, a series of shallow, moderate to large earthquakes with associated strong aftershocks struck the Kumamoto area of Kyushu, SW Japan. An Mj 7.3 mainshock occurred on 16 April 2016, close to the epicenter of an Mj 6.5 foreshock that occurred about 28 hours earlier. The intense seismicity released the accumulated elastic energy by right-lateral strike slip, mainly along two known, active faults. The mainshock rupture propagated along multiple fault segments with different geometries. The faulting style is reasonably consistent with regional deformation observed on geologic timescales and with the stress field estimated from seismic observations. One striking feature of this sequence is intense seismic activity, including a dynamically triggered earthquake in the Oita region. Following the mainshock rupture, postseismic deformation has been observed, as well as expansion of the seismicity front toward the southwest and northwest. PMID:27725474

Optimizing exoplanet transit searches

NASA Astrophysics Data System (ADS)

Herrero, E.; Ribas, I.; Jordi, C.

2013-05-01

Exoplanet searches using the transit technique are nowadays providing a great number of findings. Most exoplanet transit detection programs that are currently underway are focused on large catalogs of stars with no pre-selection. This necessarily makes such surveys quite inefficient, because huge amounts of data are processed for a relatively low transiting planet yield. In this work we investigate a method to increase the efficiency of a targeted exoplanet search with the transit technique by preselecting a subset of candidates from large catalogs of stars. Assuming spin-orbit alignment, this can be done by considering stars that have higher probability to be oriented nearly equator-on (inclination close to 90°). We use activity-rotation velocity relations for low-mass stars to study the dependence of the position in the activity - v sin(i) diagram on the stellar axis inclination. We compose a catalog of G-, K-, M-type main sequence simulated stars using isochrones, an isotropic inclination distribution and empirical relations to obtain their rotation periods and activity indexes. Then the activity-vsini diagram is filled and statistics are applied to trace the areas containing the higher ratio of stars with inclinations above 80°. A similar statistics is applied to stars from real catalogs with log(R'_{HK}) and v sin(i) data to find their probability of being equator-on. We present the method used to generate the simulated star catalog and the subsequent statistics to find the highly inclined stars from real catalogs using the activity-v sin(i) diagram. Several catalogs from the literature are analysed and a subsample of stars with the highest probability of being equator-on is presented. Assuming spin-orbit alignment, the efficiency of an exoplanet transit search in the resulting subsample of probably highly inclined stars is estimated to be two to three times higher than with a global search with no pre-selection.

Environmental DNA sequencing primers for eutardigrades and bdelloid rotifers

PubMed Central

2009-01-01

Background The time it takes to isolate individuals from environmental samples and then extract DNA from each individual is one of the problems with generating molecular data from meiofauna such as eutardigrades and bdelloid rotifers. The lack of consistent morphological information and the extreme abundance of these classes makes morphological identification of rare, or even common cryptic taxa a large and unwieldy task. This limits the ability to perform large-scale surveys of the diversity of these organisms. Here we demonstrate a culture-independent molecular survey approach that enables the generation of large amounts of eutardigrade and bdelloid rotifer sequence data directly from soil. Our PCR primers, specific to the 18s small-subunit rRNA gene, were developed for both eutardigrades and bdelloid rotifers. Results The developed primers successfully amplified DNA of their target organism from various soil DNA extracts. This was confirmed by both the BLAST similarity searches and phylogenetic analyses. Tardigrades showed much better phylogenetic resolution than bdelloids. Both groups of organisms exhibited varying levels of endemism. Conclusion The development of clade-specific primers for characterizing eutardigrades and bdelloid rotifers from environmental samples should greatly increase our ability to characterize the composition of these taxa in environmental samples. Environmental sequencing as shown here differs from other molecular survey methods in that there is no need to pre-isolate the organisms of interest from soil in order to amplify their DNA. The DNA sequences obtained from methods that do not require culturing can be identified post-hoc and placed phylogenetically as additional closely related sequences are obtained from morphologically identified conspecifics. Our non-cultured environmental sequence based approach will be able to provide a rapid and large-scale screening of the presence, absence and diversity of Bdelloidea and Eutardigrada in a variety of soils. PMID:20003362

X-ray and Optical Observations of NGC 1788

NASA Astrophysics Data System (ADS)

Alcalá, J. M.; Covino, E.; Wachter, S.; Hoard, D. W.; Sterzik, M. F.; Durisen, R. H.; Freyberg, M.; Cooksey, K.

We report on the results of ROSAT High Resolution Imager (HRI) X-ray observations and optical wide-field spectroscopy and imaging in the star forming region NGC 1788. Several new low mass pre-main sequence (PMS) stars have been found based on intermediate resolution spectroscopy. Many new PMS candidate members of NGC 1788 are selected using the spectroscopically confirmed PMS stars to define the PMS locus in color-magnitude diagrams. Some objects with very red colors detected just above the limiting magnitude of our images, are good candidates for young Brown Dwarfs (BDs). The BD nature of these objects need to be confirmed with subsequent IR observations.

The W Serpentis binaries with a few words on epsilon Aurigae

NASA Technical Reports Server (NTRS)

Plavec, M. J.

1982-01-01

The Algol systems, U-Cephei and V356 Sagittarii, which should be included among the W Serpentis stars, characterized by strong ultraviolet emission lines are discussed. The spectra of the W-Ser stars are similar to those of the T-Tauri stars, and a similarity of physical conditions is indicated. A model of W-Serpentis, a B-star embedded in a thick disk, may be relevant to other exotic eclipsing systems, possibly even to obliquity of ecliptic Aurigae. The obliquity of ecliptic and the relationship to Aur, BM Orionis is reviewed; the system probably contains a pre main sequence star highly flattened by differential rotation.

Base Pairing between U3 Small Nucleolar RNA and the 5′ End of 18S rRNA Is Required for Pre-rRNA Processing

PubMed Central

Sharma, Kishor; Tollervey, David

1999-01-01

The loop of a stem structure close to the 5′ end of the 18S rRNA is complementary to the box A region of the U3 small nucleolar RNA (snoRNA). Substitution of the 18S loop nucleotides inhibited pre-rRNA cleavage at site A1, the 5′ end of the 18S rRNA, and at site A2, located 1.9 kb away in internal transcribed spacer 1. This inhibition was largely suppressed by a compensatory mutation in U3, demonstrating functional base pairing. The U3–pre-rRNA base pairing is incompatible with the structure that forms in the mature 18S rRNA and may prevent premature folding of the pre-rRNA. In the Escherichia coli pre-rRNA the homologous region of the 16S rRNA is also sequestered, in that case by base pairing to the 5′ external transcribed spacer (5′ ETS). Cleavage at site A0 in the yeast 5′ ETS strictly requires base pairing between U3 and a sequence within the 5′ ETS. In contrast, the U3-18S interaction is not required for A0 cleavage. U3 therefore carries out at least two functionally distinct base pair interactions with the pre-rRNA. The nucleotide at the site of A1 cleavage was shown to be specified by two distinct signals; one of these is the stem-loop structure within the 18S rRNA. However, in contrast to the efficiency of cleavage, the position of A1 cleavage is not dependent on the U3-loop interaction. We conclude that the 18S stem-loop structure is recognized at least twice during pre-rRNA processing. PMID:10454548

Fine Dissection of Human Mitochondrial DNA Haplogroup HV Lineages Reveals Paleolithic Signatures from European Glacial Refugia

PubMed Central

Sarno, Stefania; Sevini, Federica; Vianello, Dario; Tamm, Erika; Metspalu, Ene; van Oven, Mannis; Hübner, Alexander; Sazzini, Marco; Franceschi, Claudio; Pettener, Davide; Luiselli, Donata

2015-01-01

Genetic signatures from the Paleolithic inhabitants of Eurasia can be traced from the early divergent mitochondrial DNA lineages still present in contemporary human populations. Previous studies already suggested a pre-Neolithic diffusion of mitochondrial haplogroup HV*(xH,V) lineages, a relatively rare class of mtDNA types that includes parallel branches mainly distributed across Europe and West Asia with a certain degree of structure. Up till now, variation within haplogroup HV was addressed mainly by analyzing sequence data from the mtDNA control region, except for specific sub-branches, such as HV4 or the widely distributed haplogroups H and V. In this study, we present a revised HV topology based on full mtDNA genome data, and we include a comprehensive dataset consisting of 316 complete mtDNA sequences including 60 new samples from the Italian peninsula, a previously underrepresented geographic area. We highlight points of instability in the particular topology of this haplogroup, reconstructed with BEAST-generated trees and networks. We also confirm a major lineage expansion that probably followed the Late Glacial Maximum and preceded Neolithic population movements. We finally observe that Italy harbors a reservoir of mtDNA diversity, with deep-rooting HV lineages often related to sequences present in the Caucasus and the Middle East. The resulting hypothesis of a glacial refugium in Southern Italy has implications for the understanding of late Paleolithic population movements and is discussed within the archaeological cultural shifts occurred over the entire continent. PMID:26640946

Burial of thermally perturbed Lesser Himalayan mid-crust: Evidence from petrochemistry and P-T estimation of the western Arunachal Himalaya, India

NASA Astrophysics Data System (ADS)

Goswami-Banerjee, Sriparna; Bhowmik, Santanu Kumar; Dasgupta, Somnath; Pant, Naresh Chandra

2014-11-01

In this work, we establish a dual prograde P-T path of the Lesser Himalayan Sequence (LHS) rocks from the western Arunachal Himalaya (WAH). The investigated metagranites, garnet- and kyanite-zone metapelites of the LHS are part of an inverted metamorphic sequence (IMS) that is exposed on the footwall side of the Main Central Thrust (MCT). Integrated petrographic, mineral chemistry, geothermobarometric (conventional and isopleth intersection methods) and P-T pseudosection modeling studies reveal a near isobaric (at P ~ 8-9 kbar) peak Barrovian metamorphism with increase in TMax from ~ 560 °C in the metagranite through ~ 590-600 °C in the lower and middle garnet-zone to ~ 600-630 °C in the upper garnet- and kyanite-zone rocks. The metamorphic sequence of the LHS additionally records a pre-Barrovian near isobaric thermal gradient in the mid crust (at ~ 6 kbar) from ~ 515 °C (in the middle garnet zone) to ~ 560-580 °C (in the upper garnet- and kyanite zone, adjoining the Main Central Thrust). Further burial (along steep dP/dT gradient) to a uniform depth corresponding to ~ 8-9 kbar and prograde heating of the differentially heated LHS rocks led to the formation of near isobaric metamorphic field gradient in the Barrovian metamorphic zones of the WAH. A combined critical taper and channel flow model is presented to explain the inverted metamorphic zonation of the rocks of the WAH.

New FeFe-hydrogenase genes identified in a metagenomic fosmid library from a municipal wastewater treatment plant as revealed by high-throughput sequencing.

PubMed

Tomazetto, Geizecler; Wibberg, Daniel; Schlüter, Andreas; Oliveira, Valéria M

2015-01-01

A fosmid metagenomic library was constructed with total community DNA obtained from a municipal wastewater treatment plant (MWWTP), with the aim of identifying new FeFe-hydrogenase genes encoding the enzymes most important for hydrogen metabolism. The dataset generated by pyrosequencing of a fosmid library was mined to identify environmental gene tags (EGTs) assigned to FeFe-hydrogenase. The majority of EGTs representing FeFe-hydrogenase genes were affiliated with the class Clostridia, suggesting that this group is the main hydrogen producer in the MWWTP analyzed. Based on assembled sequences, three FeFe-hydrogenase genes were predicted based on detection of the L2 motif (MPCxxKxxE) in the encoded gene product, confirming true FeFe-hydrogenase sequences. These sequences were used to design specific primers to detect fosmids encoding FeFe-hydrogenase genes predicted from the dataset. Three identified fosmids were completely sequenced. The cloned genomic fragments within these fosmids are closely related to members of the Spirochaetaceae, Bacteroidales and Firmicutes, and their FeFe-hydrogenase sequences are characterized by the structure type M3, which is common to clostridial enzymes. FeFe-hydrogenase sequences found in this study represent hitherto undetected sequences, indicating the high genetic diversity regarding these enzymes in MWWTP. Results suggest that MWWTP have to be considered as reservoirs for new FeFe-hydrogenase genes. Copyright © 2014 Institut Pasteur. Published by Elsevier Masson SAS. All rights reserved.

High Class-Imbalance in pre-miRNA Prediction: A Novel Approach Based on deepSOM.

PubMed

Stegmayer, Georgina; Yones, Cristian; Kamenetzky, Laura; Milone, Diego H

2017-01-01

The computational prediction of novel microRNA within a full genome involves identifying sequences having the highest chance of being a miRNA precursor (pre-miRNA). These sequences are usually named candidates to miRNA. The well-known pre-miRNAs are usually only a few in comparison to the hundreds of thousands of potential candidates to miRNA that have to be analyzed, which makes this task a high class-imbalance classification problem. The classical way of approaching it has been training a binary classifier in a supervised manner, using well-known pre-miRNAs as positive class and artificially defining the negative class. However, although the selection of positive labeled examples is straightforward, it is very difficult to build a set of negative examples in order to obtain a good set of training samples for a supervised method. In this work, we propose a novel and effective way of approaching this problem using machine learning, without the definition of negative examples. The proposal is based on clustering unlabeled sequences of a genome together with well-known miRNA precursors for the organism under study, which allows for the quick identification of the best candidates to miRNA as those sequences clustered with known precursors. Furthermore, we propose a deep model to overcome the problem of having very few positive class labels. They are always maintained in the deep levels as positive class while less likely pre-miRNA sequences are filtered level after level. Our approach has been compared with other methods for pre-miRNAs prediction in several species, showing effective predictivity of novel miRNAs. Additionally, we will show that our approach has a lower training time and allows for a better graphical navegability and interpretation of the results. A web-demo interface to try deepSOM is available at http://fich.unl.edu.ar/sinc/web-demo/deepsom/.

Evidence for feedback and stellar-dynamically regulated bursty star cluster formation: the case of the Orion Nebula Cluster

NASA Astrophysics Data System (ADS)

Kroupa, Pavel; Jeřábková, Tereza; Dinnbier, František; Beccari, Giacomo; Yan, Zhiqiang

2018-04-01

A scenario for the formation of multiple co-eval populations separated in age by about 1 Myr in very young clusters (VYCs, ages less than 10 Myr) and with masses in the range 600-20 000 M⊙ is outlined. It rests upon a converging inflow of molecular gas building up a first population of pre-main sequence stars. The associated just-formed O stars ionise the inflow and suppress star formation in the embedded cluster. However, they typically eject each other out of the embedded cluster within 106 yr, that is before the molecular cloud filament can be ionised entirely. The inflow of molecular gas can then resume forming a second population. This sequence of events can be repeated maximally over the life-time of the molecular cloud (about 10 Myr), but is not likely to be possible in VYCs with mass <300 M⊙, because such populations are not likely to contain an O star. Stellar populations heavier than about 2000 M⊙ are likely to have too many O stars for all of these to eject each other from the embedded cluster before they disperse their natal cloud. VYCs with masses in the range 600-2000 M⊙ are likely to have such multi-age populations, while VYCs with masses in the range 2000-20 000 M⊙ can also be composed solely of co-eval, mono-age populations. More massive VYCs are not likely to host sub-populations with age differences of about 1 Myr. This model is applied to the Orion Nebula Cluster (ONC), in which three well-separated pre-main sequences in the colour-magnitude diagram of the cluster have recently been discovered. The mass-inflow history is constrained using this model and the number of OB stars ejected from each population are estimated for verification using Gaia data. As a further consequence of the proposed model, the three runaway O star systems, AE Aur, μ Col and ι Ori, are considered as significant observational evidence for stellar-dynamical ejections of massive stars from the oldest population in the ONC. Evidence for stellar-dynamical ejections of massive stars in the currently forming population is also discussed.

Chandra and HST Observations of the High Energy (X-ray/UV) Radiation Fields for an Evolutionary Sequence of Pre-Main-Sequence Stars

NASA Astrophysics Data System (ADS)

Brown, Alexander; Herczeg, G. J.; Brown, J. M.; Walter, F. M.; Valenti, J.; Ardila, D.; Hillenbrand, L. A.; Edwards, S.; Johns-Krull, C. M.; Alexander, R.; Bergin, E. A.; Calvet, N.; Bethell, T. J.; Ingleby, L.; Bary, J. S.; Audard, M.; Baldovin, C.; Roueff, E.; Abgrall, H.; Gregory, S. G.; Ayres, T. R.; Linsky, J. L.

2010-03-01

Pre-main-sequence (PMS) stars are strong X-ray and UV emitters and the high energy radiation from the central stars directly influences the physical and chemical processes in their protoplanetary disks. Gas and dust in protoplanetary systems are excited by these photons, which are the dominant ionization source for hundreds of AU around the star. X-rays penetrate deep into disks and power complex chemistry on grain surfaces. ``Transitional disks'' are an important short-lived evolutionary stage for PMS stars and protoplanetary systems. These disks have transformed most of the dust and gas in their inner regions into planetesimals or larger solid bodies. As dust disks disappear after ages of roughly 5 Myr high levels of stellar magnetic activity persist and continue to bathe the newly-forming protoplanetary systems with intense high energy radiation. We present new X-ray and UV spectra for a sample of PMS stars at a variety of evolutionary stages, including the classical T Tauri stars DE Tau and DK Tau, the transitional disk stars GM Aur and HD135344B, the Herbig Ae star HD104237, and the weak-lined T Tauri star LkCa4, the Eta Cha cluster [age 7 Myr] members RECX1, RECX-11, and RECX-15, and TW Hya association [age 8 Myr] member TWA-2. These include the first results from our 111 orbit HST Large project and associated X-ray data. New and archival Chandra, XMM, and Swift X-ray spectra and HST COS+STIS FUV spectra are being used to reconstruct the full high energy (X-ray/EUV/FUV/NUV) spectra of these stars, thus allowing detailed modeling of the physics and chemistry of their circumstellar environments. The UV spectra provide improved emission line profiles revealing details of the magnetically-heated plasma and accretion and outflow processes. This work is supported by Chandra grants GO8-9024X, GO9-0015X and GO9-0020B and proposal 11200754 and HST GO grants 11336, 11616, and 11828.

High quality de novo sequencing and assembly of the Saccharomyces arboricolus genome

PubMed Central

2013-01-01

Background Comparative genomics is a formidable tool to identify functional elements throughout a genome. In the past ten years, studies in the budding yeast Saccharomyces cerevisiae and a set of closely related species have been instrumental in showing the benefit of analyzing patterns of sequence conservation. Increasing the number of closely related genome sequences makes the comparative genomics approach more powerful and accurate. Results Here, we report the genome sequence and analysis of Saccharomyces arboricolus, a yeast species recently isolated in China, that is closely related to S. cerevisiae. We obtained high quality de novo sequence and assemblies using a combination of next generation sequencing technologies, established the phylogenetic position of this species and considered its phenotypic profile under multiple environmental conditions in the light of its gene content and phylogeny. Conclusions We suggest that the genome of S. arboricolus will be useful in future comparative genomics analysis of the Saccharomyces sensu stricto yeasts. PMID:23368932

PreCisIon: PREdiction of CIS-regulatory elements improved by gene's positION.

PubMed

Elati, Mohamed; Nicolle, Rémy; Junier, Ivan; Fernández, David; Fekih, Rim; Font, Julio; Képès, François

2013-02-01

Conventional approaches to predict transcriptional regulatory interactions usually rely on the definition of a shared motif sequence on the target genes of a transcription factor (TF). These efforts have been frustrated by the limited availability and accuracy of TF binding site motifs, usually represented as position-specific scoring matrices, which may match large numbers of sites and produce an unreliable list of target genes. To improve the prediction of binding sites, we propose to additionally use the unrelated knowledge of the genome layout. Indeed, it has been shown that co-regulated genes tend to be either neighbors or periodically spaced along the whole chromosome. This study demonstrates that respective gene positioning carries significant information. This novel type of information is combined with traditional sequence information by a machine learning algorithm called PreCisIon. To optimize this combination, PreCisIon builds a strong gene target classifier by adaptively combining weak classifiers based on either local binding sequence or global gene position. This strategy generically paves the way to the optimized incorporation of any future advances in gene target prediction based on local sequence, genome layout or on novel criteria. With the current state of the art, PreCisIon consistently improves methods based on sequence information only. This is shown by implementing a cross-validation analysis of the 20 major TFs from two phylogenetically remote model organisms. For Bacillus subtilis and Escherichia coli, respectively, PreCisIon achieves on average an area under the receiver operating characteristic curve of 70 and 60%, a sensitivity of 80 and 70% and a specificity of 60 and 56%. The newly predicted gene targets are demonstrated to be functionally consistent with previously known targets, as assessed by analysis of Gene Ontology enrichment or of the relevant literature and databases.

A two-stage stochastic rule-based model to determine pre-assembly buffer content

NASA Astrophysics Data System (ADS)

Gunay, Elif Elcin; Kula, Ufuk

2018-01-01

This study considers instant decision-making needs of the automobile manufactures for resequencing vehicles before final assembly (FA). We propose a rule-based two-stage stochastic model to determine the number of spare vehicles that should be kept in the pre-assembly buffer to restore the altered sequence due to paint defects and upstream department constraints. First stage of the model decides the spare vehicle quantities, where the second stage model recovers the scrambled sequence respect to pre-defined rules. The problem is solved by sample average approximation (SAA) algorithm. We conduct a numerical study to compare the solutions of heuristic model with optimal ones and provide following insights: (i) as the mismatch between paint entrance and scheduled sequence decreases, the rule-based heuristic model recovers the scrambled sequence as good as the optimal resequencing model, (ii) the rule-based model is more sensitive to the mismatch between the paint entrance and scheduled sequences for recovering the scrambled sequence, (iii) as the defect rate increases, the difference in recovery effectiveness between rule-based heuristic and optimal solutions increases, (iv) as buffer capacity increases, the recovery effectiveness of the optimization model outperforms heuristic model, (v) as expected the rule-based model holds more inventory than the optimization model.

How close is close: 16S rRNA sequence identity may not be sufficient to guarantee species identity

NASA Technical Reports Server (NTRS)

Fox, G. E.; Wisotzkey, J. D.; Jurtshuk, P. Jr

1992-01-01

16S rRNA (genes coding for rRNA) sequence comparisons were conducted with the following three psychrophilic strains: Bacillus globisporus W25T (T = type strain) and Bacillus psychrophilus W16AT, and W5. These strains exhibited more than 99.5% sequence identity and within experimental uncertainty could be regarded as identical. Their close taxonomic relationship was further documented by phenotypic similarities. In contrast, previously published DNA-DNA hybridization results have convincingly established that these strains do not belong to the same species if current standards are used. These results emphasize the important point that effective identity of 16S rRNA sequences is not necessarily a sufficient criterion to guarantee species identity. Thus, although 16S rRNA sequences can be used routinely to distinguish and establish relationships between genera and well-resolved species, very recently diverged species may not be recognizable.

Genome Sequencing of Steroid Producing Bacteria Using Ion Torrent Technology and a Reference Genome.

PubMed

Sola-Landa, Alberto; Rodríguez-García, Antonio; Barreiro, Carlos; Pérez-Redondo, Rosario

2017-01-01

The Next-Generation Sequencing technology has enormously eased the bacterial genome sequencing and several tens of thousands of genomes have been sequenced during the last 10 years. Most of the genome projects are published as draft version, however, for certain applications the complete genome sequence is required.In this chapter, we describe the strategy that allowed the complete genome sequencing of Mycobacterium neoaurum NRRL B-3805, an industrial strain exploited for steroid production, using Ion Torrent sequencing reads and the genome of a close strain as the reference. This protocol can be applied to analyze the genetic variations between closely related strains; for example, to elucidate the point mutations between a parental strain and a random mutagenesis-derived mutant.

AmericaPlex26: A SNaPshot Multiplex System for Genotyping the Main Human Mitochondrial Founder Lineages of the Americas

PubMed Central

Coutinho, Alexandra; Valverde, Guido; Fehren-Schmitz, Lars; Cooper, Alan; Barreto Romero, Maria Inés; Espinoza, Isabel Flores; Llamas, Bastien; Haak, Wolfgang

2014-01-01

Phylogeographic studies have described a reduced genetic diversity in Native American populations, indicative of one or more bottleneck events during the peopling and prehistory of the Americas. Classical sequencing approaches targeting the mitochondrial diversity have reported the presence of five major haplogroups, namely A, B, C, D and X, whereas the advent of complete mitochondrial genome sequencing has recently refined the number of founder lineages within the given diversity to 15 sub-haplogroups. We developed and optimized a SNaPshot assay to study the mitochondrial diversity in pre-Columbian Native American populations by simultaneous typing of 26 single nucleotide polymorphisms (SNPs) characterising Native American sub-haplogroups. Our assay proved to be highly sensitive with respect to starting concentrations of target DNA and could be applied successfully to a range of ancient human skeletal material from South America from various time periods. The AmericaPlex26 is a powerful assay with enhanced phylogenetic resolution that allows time- and cost-efficient mitochondrial DNA sub-typing from valuable ancient specimens. It can be applied in addition or alternative to standard sequencing of the D-loop region in forensics, ancestry testing, and population studies, or where full-resolution mitochondrial genome sequencing is not feasible. PMID:24671218

AmericaPlex26: a SNaPshot multiplex system for genotyping the main human mitochondrial founder lineages of the Americas.

PubMed

Coutinho, Alexandra; Valverde, Guido; Fehren-Schmitz, Lars; Cooper, Alan; Barreto Romero, Maria Inés; Espinoza, Isabel Flores; Llamas, Bastien; Haak, Wolfgang

2014-01-01

Phylogeographic studies have described a reduced genetic diversity in Native American populations, indicative of one or more bottleneck events during the peopling and prehistory of the Americas. Classical sequencing approaches targeting the mitochondrial diversity have reported the presence of five major haplogroups, namely A, B, C, D and X, whereas the advent of complete mitochondrial genome sequencing has recently refined the number of founder lineages within the given diversity to 15 sub-haplogroups. We developed and optimized a SNaPshot assay to study the mitochondrial diversity in pre-Columbian Native American populations by simultaneous typing of 26 single nucleotide polymorphisms (SNPs) characterising Native American sub-haplogroups. Our assay proved to be highly sensitive with respect to starting concentrations of target DNA and could be applied successfully to a range of ancient human skeletal material from South America from various time periods. The AmericaPlex26 is a powerful assay with enhanced phylogenetic resolution that allows time- and cost-efficient mitochondrial DNA sub-typing from valuable ancient specimens. It can be applied in addition or alternative to standard sequencing of the D-loop region in forensics, ancestry testing, and population studies, or where full-resolution mitochondrial genome sequencing is not feasible.

Does the sequence of data collection influence participants' responses to closed and open-ended questions? A methodological study.

PubMed

Covell, Christine L; Sidani, Souraya; Ritchie, Judith A

2012-06-01

The sequence used for collecting quantitative and qualitative data in concurrent mixed-methods research may influence participants' responses. Empirical evidence is needed to determine if the order of data collection in concurrent mixed methods research biases participants' responses to closed and open-ended questions. To examine the influence of the quantitative-qualitative sequence on responses to closed and open-ended questions when assessing the same variables or aspects of a phenomenon simultaneously within the same study phase. A descriptive cross-sectional, concurrent mixed-methods design was used to collect quantitative (survey) and qualitative (interview) data. The setting was a large multi-site health care centre in Canada. A convenience sample of 50 registered nurses was selected and participated in the study. Participants were randomly assigned to one of two sequences for data collection, quantitative-qualitative or qualitative-quantitative. Independent t-tests were performed to compare the two groups' responses to the survey items. Directed content analysis was used to compare the participants' responses to the interview questions. The sequence of data collection did not greatly affect the participants' responses to the closed-ended questions (survey items) or the open-ended questions (interview questions). The sequencing of data collection, when using both survey and semi-structured interviews, may not bias participants' responses to closed or open-ended questions. Additional research is required to confirm these findings. Copyright © 2011 Elsevier Ltd. All rights reserved.

Genetic structure and diversity of coffee (Coffea) across Africa and the Indian Ocean islands revealed using microsatellites

PubMed Central

Razafinarivo, Norosoa J.; Guyot, Romain; Davis, Aaron P.; Couturon, Emmanuel; Hamon, Serge; Crouzillat, Dominique; Rigoreau, Michel; Dubreuil-Tranchant, Christine; Poncet, Valerie; De Kochko, Alexandre; Rakotomalala, Jean-Jacques; Hamon, Perla

2013-01-01

Background and Aims The coffee genus (Coffea) comprises 124 species, and is indigenous to the Old World Tropics. Due to its immense economic importance, Coffea has been the focus of numerous genetic diversity studies, but despite this effort it remains insufficiently studied. In this study the genetic diversity and genetic structure of Coffea across Africa and the Indian Ocean islands is investigated. Methods Genetic data were produced using 13 polymorphic nuclear microsatellite markers (simple sequence repeats, SSRs), including seven expressed sequence tag-SSRs, and the data were analysed using model- and non-model-based methods. The study includes a total of 728 individuals from 60 species. Key Results Across Africa and the Indian Ocean islands Coffea comprises a closely related group of species with an overall pattern of genotypes running from west to east. Genetic structure was identified in accordance with pre-determined geographical regions and phylogenetic groups. There is a good relationship between morpho-taxonomic species delimitations and genetic units. Genetic diversity in African and Indian Ocean Coffea is high in terms of number of alleles detected, and Madagascar appears to represent a place of significant diversification in terms of allelic richness and species diversity. Conclusions Cross-species SSR transferability in African and Indian Ocean islands Coffea was very efficient. On the basis of the number of private alleles, diversification in East Africa and the Indian Ocean islands appears to be more recent than in West and West-Central Africa, although this general trend is complicated in Africa by the position of species belonging to lineages connecting the main geographical regions. The general pattern of phylogeography is not in agreement with an overall east to west (Mascarene, Madagascar, East Africa, West Africa) increase in genome size, the high proportion of shared alleles between the four regions or the high numbers of exclusive shared alleles between pairs or triplets of regions. PMID:23275631

Transcriptome Analysis and Discovery of Genes Relevant to Development in Bradysia odoriphaga at Three Developmental Stages.

PubMed

Gao, Huanhuan; Zhai, Yifan; Wang, Wenbo; Chen, Hao; Zhou, Xianhong; Zhuang, Qianying; Yu, Yi; Li, Rumei

2016-01-01

Bradysia odoriphaga (Diptera: Sciaridae) is the most important pest of Chinese chive (Allium tuberosum) in Asia; however, the molecular genetics are poorly understood. To explore the molecular biological mechanism of development, Illumina sequencing and de novo assembly were performed in the third-instar, fourth-instar, and pupal B. odoriphaga. The study resulted in 16.2 Gb of clean data and 47,578 unigenes (≥125 bp) contained in 7,632,430 contigs, 46.21% of which were annotated from non-redundant protein (NR), Gene Ontology (GO), Clusters of Orthologous Groups (COG), Eukaryotic Orthologous Groups (KOG), and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. It was found that 19.67% of unigenes matched the homologous species mainly, including Aedes aegypti, Culex quinquefasciatus, Ceratitis capitata, and Anopheles gambiae. According to differentially expressed gene (DEG) analysis, 143, 490, and 309 DEGs were annotated as involved in the developmental process in the GO database respectively, in the comparisons of third-instar and fourth-instar larvae, third-instar larvae and pupae, and fourth-instar larvae and pupae. Twenty-five genes were closely related to these processes, including developmental process, reproduction process, and reproductive organs development and programmed cell death (PCD). The information of unigenes assembled in B. odoriphaga through transcriptome and DEG analyses could provide a detailed genetic basis and regulated information for elaborating the developmental mechanism from the larval, pre-pupal to pupal stages of B. odoriphaga.

On the orbit calculation of visual binaries with a very short arc: application to the PMS binary system, FW Tau AB

NASA Astrophysics Data System (ADS)

Docobo, J. A.; Tamazian, V. S.; Campo, P. P.

2018-05-01

In the vast majority of cases when available astrometric measurements of a visual binary cover a very short orbital arc, it is practically impossible to calculate a good quality orbit. It is especially important for systems with pre-main-sequence components where standard mass-spectrum calibrations cannot be applied nor can a dynamical parallax be calculated. We have shown that the analytical method of Docobo allows us to put certain constraints on the most likely orbital solutions, using an available realistic estimate of the global mass of the system. As an example, we studied the interesting PMS binary, FW Tau AB, located in the Taurus-Auriga as well as investigated a range of its possible orbital solutions combined with an assumed distance between 120 and 160 pc. To maintain the total mass of FW Tau AB in a realistic range between 0.2 and 0.6M_{⊙}, minimal orbital periods should begin at 105, 150, 335, and 2300 yr for distances of 120, 130, 140, and 150 pc, respectively (no plausible orbits were found assuming a distance of 160 pc). An original criterion to establish the upper limit of the orbital period is applied. When the position angle in some astrometric measurements was flipped by 180°, orbits with periods close to 45 yr are also plausible. Three example orbits with periods of 44.6, 180, and 310 yr are presented.

High-contrast imaging of HD 163296 with the Keck/NIRC2 L΄-band vortex coronograph

NASA Astrophysics Data System (ADS)

Guidi, G.; Ruane, G.; Williams, J. P.; Mawet, D.; Testi, L.; Zurlo, A.; Absil, O.; Bottom, M.; Choquet, É.; Christiaens, V.; Castellá, B. Femenía; Huby, E.; Isella, A.; Kastner, J.; Meshkat, T.; Reggiani, M.; Riggs, A.; Serabyn, E.; Wallack, N.

2018-06-01

We present observations of the nearby (D˜100 pc) Herbig star HD 163296 taken with the vortex coronograph at Keck/NIRC2 in the L' band (3.7 μm), to search for planetary mass companions in the ringed disc surrounding this pre-main sequence star. The images reveal an arc-like region of scattered light from the disc surface layers that is likely associated with the first bright ring detected with ALMA in the λ=1.3mm dust continuum at ˜65 au. We also detect a point-like source at ˜0{^''.}5 projected separation in the North-East direction, close to the inner edge of the second gap in the millimetre images. Comparing the point source photometry with the atmospheric emission models of non-accreting giant planets, we obtain a mass of 6-7 MJ for a putative protoplanet, assuming a system age of 5 Myr. Based on the contrast at a 95% level of completeness calculated on the emission-free regions of our images, we set upper limits for the masses of giant planets of 8-15 MJ, 4.5-6.5 MJ and 2.5-4.0 MJ at the locations of the first, second and third gap in the millimetre dust continuum, respectively. Further deep, high resolution thermal IR imaging of the HD 163296 system are warranted, to confirm the presence and nature of the point source and to better understand the structure of the dust disc.

Prediction of plant pre-microRNAs and their microRNAs in genome-scale sequences using structure-sequence features and support vector machine.

PubMed

Meng, Jun; Liu, Dong; Sun, Chao; Luan, Yushi

2014-12-30

MicroRNAs (miRNAs) are a family of non-coding RNAs approximately 21 nucleotides in length that play pivotal roles at the post-transcriptional level in animals, plants and viruses. These molecules silence their target genes by degrading transcription or suppressing translation. Studies have shown that miRNAs are involved in biological responses to a variety of biotic and abiotic stresses. Identification of these molecules and their targets can aid the understanding of regulatory processes. Recently, prediction methods based on machine learning have been widely used for miRNA prediction. However, most of these methods were designed for mammalian miRNA prediction, and few are available for predicting miRNAs in the pre-miRNAs of specific plant species. Although the complete Solanum lycopersicum genome has been published, only 77 Solanum lycopersicum miRNAs have been identified, far less than the estimated number. Therefore, it is essential to develop a prediction method based on machine learning to identify new plant miRNAs. A novel classification model based on a support vector machine (SVM) was trained to identify real and pseudo plant pre-miRNAs together with their miRNAs. An initial set of 152 novel features related to sequential structures was used to train the model. By applying feature selection, we obtained the best subset of 47 features for use with the Back Support Vector Machine-Recursive Feature Elimination (B-SVM-RFE) method for the classification of plant pre-miRNAs. Using this method, 63 features were obtained for plant miRNA classification. We then developed an integrated classification model, miPlantPreMat, which comprises MiPlantPre and MiPlantMat, to identify plant pre-miRNAs and their miRNAs. This model achieved approximately 90% accuracy using plant datasets from nine plant species, including Arabidopsis thaliana, Glycine max, Oryza sativa, Physcomitrella patens, Medicago truncatula, Sorghum bicolor, Arabidopsis lyrata, Zea mays and Solanum lycopersicum. Using miPlantPreMat, 522 Solanum lycopersicum miRNAs were identified in the Solanum lycopersicum genome sequence. We developed an integrated classification model, miPlantPreMat, based on structure-sequence features and SVM. MiPlantPreMat was used to identify both plant pre-miRNAs and the corresponding mature miRNAs. An improved feature selection method was proposed, resulting in high classification accuracy, sensitivity and specificity.

eShadow: A tool for comparing closely related sequences

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ovcharenko, Ivan; Boffelli, Dario; Loots, Gabriela G.

2004-01-15

Primate sequence comparisons are difficult to interpret due to the high degree of sequence similarity shared between such closely related species. Recently, a novel method, phylogenetic shadowing, has been pioneered for predicting functional elements in the human genome through the analysis of multiple primate sequence alignments. We have expanded this theoretical approach to create a computational tool, eShadow, for the identification of elements under selective pressure in multiple sequence alignments of closely related genomes, such as in comparisons of human to primate or mouse to rat DNA. This tool integrates two different statistical methods and allows for the dynamic visualizationmore » of the resulting conservation profile. eShadow also includes a versatile optimization module capable of training the underlying Hidden Markov Model to differentially predict functional sequences. This module grants the tool high flexibility in the analysis of multiple sequence alignments and in comparing sequences with different divergence rates. Here, we describe the eShadow comparative tool and its potential uses for analyzing both multiple nucleotide and protein alignments to predict putative functional elements. The eShadow tool is publicly available at http://eshadow.dcode.org/« less

Zygosaccharomyces favi sp. nov., an obligate osmophilic yeast species from bee bread and honey.

PubMed

Čadež, Neža; Fülöp, László; Dlauchy, Dénes; Péter, Gábor

2015-03-01

Five yeast strains representing a hitherto undescribed yeast species were isolated from bee bread and honey in Hungary. They are obligate osmophilic, i.e. they are unable to grow in/on high water activity culture media. Following isogamous conjugation, they form 1-4 spheroid or subspheroid ascospores in persistent asci. The analysis of the sequences of their large subunit rRNA gene D1/D2 domain placed the new species in the Zygosaccharomyces clade. In terms of pairwise sequence similarity, Zygosaccharomyces gambellarensis is the most closely related species. Comparisons of D1/D2, internal transcribed spacer and translation elongation factor-1α (EF-1α) gene sequences of the five strains with that of the type strain of Z. gambellarensis revealed that they represent a new yeast species. The name Zygosaccharomyces favi sp. nov. (type strain: NCAIM Y.01994(T) = CBS 13653(T) = NRRL Y-63719(T) = ZIM 2551(T)) is proposed for this new yeast species, which based on phenotype can be distinguished from related Zygosaccharomyces species by its obligate osmophilic nature. Some intragenomic sequence variability, mainly indels, was detected among the ITS copies of the strains of the new species.

A pre-protective strategy for precise tumor targeting and efficient photodynamic therapy with a switchable DNA/upconversion nanocomposite.

PubMed

Yu, Zhengze; Ge, Yegang; Sun, Qiaoqiao; Pan, Wei; Wan, Xiuyan; Li, Na; Tang, Bo

2018-04-14

Tumor-specific targeting based on folic acid (FA) is one of the most common and significant approaches in cancer therapy. However, the expression of folate receptors (FRs) in normal tissues will lead to unexpected targeting and unsatisfactory therapeutic effect. To address this issue, we develop a pre-protective strategy for precise tumor targeting and efficient photodynamic therapy (PDT) using a switchable DNA/upconversion nanocomposite, which can be triggered in the acidic tumor microenvironment. The DNA/upconversion nanocomposite is composed of polyacrylic acid (PAA) coated upconversion nanoparticles (UCNPs), the surface of which is modified using FA and chlorin e6 (Ce6) functionalized DNA sequences with different lengths. Initially, FA on the shorter DNA was protected by a longer DNA to prevent the bonding to FRs on normal cells. Once reaching the acidic tumor microenvironment, C base-rich longer DNA forms a C-quadruplex, resulting in the exposure of the FA groups and the bonding of FA and FRs on cancer cell membranes to achieve precise targeting. Simultaneously, the photosensitizer chlorin e6 (Ce6) gets close to the surface of UCNPs, enabling the excitation of Ce6 to generate singlet oxygen ( 1 O 2 ) under near infrared light via Förster resonance energy transfer (FRET). In vivo experiments indicated that higher tumor targeting efficiency was achieved and the tumor growth was greatly inhibited through the pre-protective strategy.

Eruptive history of Mount Katmai, Alaska

USGS Publications Warehouse

Hildreth, Edward; Fierstein, Judith

2012-01-01

Compositionally, products of Mount Katmai represent an ordinary medium-K arc array, both tholeiitic and calcalkaline, that extends from 51.6% to 72.3% SiO2. Values of 87Sr/86Sr range from 0.70335 to 0.70372, correlating loosely with fractionation indices. The 5–6 km3 of continuously zoned andesite-dacite magma (58%–68% SiO2) that erupted at Novarupta in 1912 was withdrawn from beneath Mount Katmai and bears close compositional affinity with products of that edifice, not with pre-1912 products of the adjacent Trident cluster. Evidence is presented that the 7–8 km3 of high-silica rhyolite (77% SiO2) released in 1912 is unlikely to have been stored under Novarupta or Trident. Pre-eruptive contiguity with the andesite-dacite reservoir is suggested by (1) eruption of ∼3 km3 of rhyolite magma first, followed by mutual mingling in fluctuating proportions; (2) thermal and redox continuity of the whole zoned sequence despite the wide compositional gap; (3) Nd, Sr, O isotopic, and rare earth element (REE) affinities of the whole array; (4) compositional continuity of the nearly aphyric rhyolite with the glass (melt) phase of the phenocryst-rich dacite; and (5) phase-equilibrium experiments that indicate similar shallow pre-eruptive storage depths (3–6 km) for rhyolite, dacite, and andesite.

Meteoroid mayhem in Ole Virginny: Source of the North American tektite strewn field

USGS Publications Warehouse

Poag, C. Wylie; Powars, David S.; Poppe, Lawrence J.; Mixon, Robert B.

1994-01-01

New seismic reflection data from Chesapeake Bay reveal a buried, 85-km-wide, 1.5-2.0-km-deep, peak-ring impact crater, carved through upper Eocene to Lower Cretaceous sedimentary strata and into underlying pre-Mesozoic crystalline basement rocks. A polymictic, late Eocene impact breccia, composed mainly of locally derived sedimentary debris (determined from four continuous cores), surrounds and partly fills the crater. Structural and sedimentary characteristics of the Chesapeake Bay crater closely resemble those of the Miocene Ries peakring crater in southern Germany. We speculate that the Chesapeake Bay crater is the source of the North American tektite strewn field.

Meteoroid mayhem in Ole Virginny: source of the North American tektite strewn field

USGS Publications Warehouse

Poag, C.W.; Powars, D.S.; Poppe, L.J.; Mixon, R.B.

1994-01-01

New seismic reflection data from Chesapeake Bay reveal a buried, 85-km-wide, 1.5-2.0-km-deep, peak-ring impact crater, carved through upper Eocene to Lower Cretaceous sedimentary strata and into underlying pre-Mesozoic crystalline basement rocks. A polymictic, late Eocene impact breccia, composed mainly of locally derived sedimentary debris (determined from four continuous cores), surrounds and partly fills the crater. Structural and sedimentary characteristics of the Chesapeake Bay crater closely resemble those of the Miocene Ries peak-ring crater in southern Germany. It is speculated that the Chesapeake Bay crater is the source of the North American tektite strewn field. -Authors

[Phylogenetic analysis of closely related Leuconostoc citreum species based on partial housekeeping genes].

PubMed

Lv, Qiang; Chen, Ming; Xu, Haiyan; Song, Yuqin; Sun, Zhihong; Dan, Tong; Sun, Tiansong

2013-07-04

Using the 16S rRNA, dnaA, murC and pyrG gene sequences, we identified the phylogenetic relationship among closely related Leuconostoc citreum species. Seven Leu. citreum strains originally isolated from sourdough were characterized by PCR methods to amplify the dnaA, murC and pyrG gene sequences, which were determined to assess the suitability as phylogenetic markers. Then, we estimated the genetic distance and constructed the phylogenetic trees including 16S rRNA and above mentioned three housekeeping genes combining with published corresponding sequences. By comparing the phylogenetic trees, the topology of three housekeeping genes trees were consistent with that of 16S rRNA gene. The homology of closely related Leu. citreum species among dnaA, murC, pyrG and 16S rRNA gene sequences were different, ranged from75.5% to 97.2%, 50.2% to 99.7%, 65.0% to 99.8% and 98.5% 100%, respectively. The phylogenetic relationship of three housekeeping genes sequences were highly consistent with the results of 16S rRNA gene sequence, while the genetic distance of these housekeeping genes were extremely high than 16S rRNA gene. Consequently, the dnaA, murC and pyrG gene are suitable for classification and identification closely related Leu. citreum species.

The genome sequence of the model ascomycete fungus Podospora anserina.

PubMed

Espagne, Eric; Lespinet, Olivier; Malagnac, Fabienne; Da Silva, Corinne; Jaillon, Olivier; Porcel, Betina M; Couloux, Arnaud; Aury, Jean-Marc; Ségurens, Béatrice; Poulain, Julie; Anthouard, Véronique; Grossetete, Sandrine; Khalili, Hamid; Coppin, Evelyne; Déquard-Chablat, Michelle; Picard, Marguerite; Contamine, Véronique; Arnaise, Sylvie; Bourdais, Anne; Berteaux-Lecellier, Véronique; Gautheret, Daniel; de Vries, Ronald P; Battaglia, Evy; Coutinho, Pedro M; Danchin, Etienne Gj; Henrissat, Bernard; Khoury, Riyad El; Sainsard-Chanet, Annie; Boivin, Antoine; Pinan-Lucarré, Bérangère; Sellem, Carole H; Debuchy, Robert; Wincker, Patrick; Weissenbach, Jean; Silar, Philippe

2008-01-01

The dung-inhabiting ascomycete fungus Podospora anserina is a model used to study various aspects of eukaryotic and fungal biology, such as ageing, prions and sexual development. We present a 10X draft sequence of P. anserina genome, linked to the sequences of a large expressed sequence tag collection. Similar to higher eukaryotes, the P. anserina transcription/splicing machinery generates numerous non-conventional transcripts. Comparison of the P. anserina genome and orthologous gene set with the one of its close relatives, Neurospora crassa, shows that synteny is poorly conserved, the main result of evolution being gene shuffling in the same chromosome. The P. anserina genome contains fewer repeated sequences and has evolved new genes by duplication since its separation from N. crassa, despite the presence of the repeat induced point mutation mechanism that mutates duplicated sequences. We also provide evidence that frequent gene loss took place in the lineages leading to P. anserina and N. crassa. P. anserina contains a large and highly specialized set of genes involved in utilization of natural carbon sources commonly found in its natural biotope. It includes genes potentially involved in lignin degradation and efficient cellulose breakdown. The features of the P. anserina genome indicate a highly dynamic evolution since the divergence of P. anserina and N. crassa, leading to the ability of the former to use specific complex carbon sources that match its needs in its natural biotope.

Molecular delineation of the Agave Red Worm Comadia redtenbacheri  (Lepidoptera: Cossidae).

PubMed

CÁrdenas-Aquino, MarÍa Del Rosario; AlarcÓn-rodrÍguez, Norma Marina; Rivas-Medrano, Mario; GonzÁlez-hernÁndez, HÉctor; Vargas-hernÁndez, Mateo; SÁnchez-Arroyo, Hussein; Llanderal-cÁzares, Celina

2018-01-25

Comadia redtenbacheri (Hammerschmidt) (Agave Red Worm) is the only member of the family Cossidae that has been described as a phytophagous specialist of the plant genus Agave, which is mainly distributed in México. A new extraction protocol adapted from Stewart Via (1993) has been implemented for sequencing the COI gene from samples collected in five states of the North Central (Querétaro and Zacatecas), South Central (Estado de México) and East Central (Hidalgo and Tlaxcala) regions of México with the purpose of contributing to delineation of the species. A Maximum Likelihood (ML) tree based on these COI sequences as well as COI sequences from other Cossinae species was developed to complement the existing morphological and taxonomic approaches to delineation of this species. As expected, our Comadia samples cluster together within a monophyletic clade that includes four C. redtenbacheri sequences previously reported. This group seems to be consistent with our reconstruction, which is supported by a bootstrap value of over 99%. The closely related branches associated with the latter group include organisms known to be the plant and tree borers of the Cossinae subfamily. The COI sequences from our samples were analyzed to determine the percentage of identity among the C. redtenbacheri in a first attempt to detect differences in the sequence that matches a particular region of México.

Potential Links between Hepadnavirus and Bornavirus Sequences in the Host Genome and Cancer.

PubMed

Honda, Tomoyuki

2017-01-01

Various viruses leave their sequences in the host genomes during infection. Such events occur mainly in retrovirus infection but also sometimes in DNA and non-retroviral RNA virus infections. If viral sequences are integrated into the genomes of germ line cells, the sequences can become inherited as endogenous viral elements (EVEs). The integration events of viral sequences may have oncogenic potential. Because proviral integrations of some retroviruses and/or reactivation of endogenous retroviruses are closely linked to cancers, viral insertions related to non-retroviral viruses also possibly contribute to cancer development. This article focuses on genomic viral sequences derived from two non-retroviral viruses, whose endogenization is already reported, and discusses their possible contributions to cancer. Viral insertions of hepatitis B virus play roles in the development of hepatocellular carcinoma. Endogenous bornavirus-like elements, the only non-retroviral RNA virus-related EVEs found in the human genome, may also be involved in cancer formation. In addition, the possible contribution of the interactions between viruses and retrotransposons, which seem to be a major driving force for generating EVEs related to non-retroviral RNA viruses, to cancers will be discussed. Future studies regarding the possible links described here may open a new avenue for the development of novel therapeutics for tumor virus-related cancers and/or provide novel insights into EVE functions.

Magnetospheric Accretion in Close Pre-main-sequence Binaries

NASA Astrophysics Data System (ADS)

Ardila, David R.; Jonhs-Krull, Christopher; Herczeg, Gregory J.; Mathieu, Robert D.; Quijano-Vodniza, Alberto

2015-10-01

The transfer of matter between a circumbinary disk and a young binary system remains poorly understood, obscuring the interpretation of accretion indicators. To explore the behavior of these indicators in multiple systems, we have performed the first systematic time-domain study of young binaries in the ultraviolet. We obtained far- and near-ultraviolet HST/COS spectra of the young spectroscopic binaries DQ Tau and UZ Tau E. Here we focus on the continuum from 2800 to 3200 Å and on the C iv doublet (λλ1548.19, 1550.77 Å) as accretion diagnostics. Each system was observed over three or four consecutive binary orbits, at phases ∼0, 0.2, 0.5, and 0.7. Those observations are complemented by ground-based U-band measurements. Contrary to model predictions, we do not detect any clear correlation between accretion luminosity and phase. Further, we do not detect any correlation between C iv flux and phase. For both stars the appearance of the C iv line is similar to that of single Classical T Tauri Stars (CTTSs), despite the lack of stable long-lived circumstellar disks. However, unlike the case in single CTTSs, the narrow and broad components of the C iv lines are uncorrelated, and we argue that the narrow component is powered by processes other than accretion, such as flares in the stellar magnetospheres and/or enhanced activity in the upper atmosphere. We find that both stars contribute equally to the narrow component C iv flux in DQ Tau, but the primary dominates the narrow component C iv emission in UZ Tau E. The C iv broad component flux is correlated with other accretion indicators, suggesting an accretion origin. However, the line is blueshifted, which is inconsistent with its origin in an infall flow close to the star. It is possible that the complicated geometry of the region, as well as turbulence in the shock region, are responsible for the blueshifted line profiles.

USE OF COMPETITIVE DNA HYBRIDIZATION TO IDENTIFY DIFFERENCES IN THE GENOMES OF TWO CLOSELY RELATED FECAL INDICATOR BACTERIA

EPA Science Inventory

Although recent technological advances in DNA sequencing and computational biology now allow scientists to compare entire microbial genomes, comparisons of closely related bacterial species and individual isolates by whole-genome sequencing approaches remains prohibitively expens...

ADIABATIC MASS LOSS IN BINARY STARS. II. FROM ZERO-AGE MAIN SEQUENCE TO THE BASE OF THE GIANT BRANCH

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ge, Hongwei; Chen, Xuefei; Han, Zhanwen

2015-10-10

In the limit of extremely rapid mass transfer, the response of a donor star in an interacting binary becomes asymptotically one of adiabatic expansion. We survey here adiabatic mass loss from Population I stars (Z = 0.02) of mass 0.10 M{sub ⊙}–100 M{sub ⊙} from the zero-age main sequence to the base of the giant branch, or to central hydrogen exhaustion for lower main sequence stars. The logarithmic derivatives of radius with respect to mass along adiabatic mass-loss sequences translate into critical mass ratios for runaway (dynamical timescale) mass transfer, evaluated here under the assumption of conservative mass transfer. Formore » intermediate- and high-mass stars, dynamical mass transfer is preceded by an extended phase of thermal timescale mass transfer as the star is stripped of most of its envelope mass. The critical mass ratio q{sub ad} (throughout this paper, we follow the convention of defining the binary mass ratio as q ≡ M{sub donor}/M{sub accretor}) above which this delayed dynamical instability occurs increases with advancing evolutionary age of the donor star, by ever-increasing factors for more massive donors. Most intermediate- or high-mass binaries with nondegenerate accretors probably evolve into contact before manifesting this instability. As they approach the base of the giant branch, however, and begin developing a convective envelope, q{sub ad} plummets dramatically among intermediate-mass stars, to values of order unity, and a prompt dynamical instability occurs. Among low-mass stars, the prompt instability prevails throughout main sequence evolution, with q{sub ad} declining with decreasing mass, and asymptotically approaching q{sub ad} = 2/3, appropriate to a classical isentropic n = 3/2 polytrope. Our calculated q{sub ad} values agree well with the behavior of time-dependent models by Chen and Han of intermediate-mass stars initiating mass transfer in the Hertzsprung gap. Application of our results to cataclysmic variables, as systems that must be stable against rapid mass transfer, nicely circumscribes the range in q{sub ad} as a function of the orbital period in which they are found. These results are intended to advance the verisimilitude of population synthesis models of close binary evolution.« less

Performance of aerobic nitrite granules treating an anaerobic pre-treated wastewater originating from the potato industry.

PubMed

Dobbeleers, Thomas; Daens, Dominique; Miele, Solange; D'aes, Jolien; Caluwé, Michel; Geuens, Luc; Dries, Jan

2017-02-01

In this study nitrogen removal via nitrite >80% was achieved after approximately 80days in a sequencing batch reactor (SBR) treating pre-treated industrial wastewater originating from the potato industry. Thereafter, SBR performance was investigated during the formation of aerobic nitrite granules (ANG). The first granules appeared after 26days leading to full granulation after 64days. ANG showed excellent settling properties, as the Sludge Volume Index (SVI) went down to 16mL/g and a SVI 10 /SVI 30 =1 was obtained. qPCR analysis showed that slow growing organisms, especially polyphosphate accumulating organisms (PAO) were stimulated by an anaerobic feeding strategy. The average nitrogen removal was 95.3% over the entire operational period, and it mainly followed the "nitrite-route". Moreover, with ANG also phosphorus removal efficiencies up to 65.7% could be achieved. However, it has to be mentioned that nitrous oxide was an important denitrification product, which implies some environmental concerns. Copyright © 2016 Elsevier Ltd. All rights reserved.

Cloning, characterization and comparative analysis of pig plasma apolipoprotein A-IV.

PubMed

Navarro, María A; Acín, Sergio; Iturralde, María; Calleja, Lucía; Carnicer, Ricardo; Guzmán-García, Mario A; González-Ramón, Nieves; Mata, Pedro; Isabel, Beatriz; López-Bote, Clemente J; Lampreave, Fermín; Piñeiro, Andrés; Osada, Jesús

2004-01-21

Pig apolipoprotein (apo) A-IV cDNA was cloned, characterized and compared to the human ortholog. Mature porcine apo A-IV consists of 362 amino acids and displays a 75.6% sequence identity with human protein. Pig apo A-IV is the smallest reported mammalian apo A-IV because it lacks the repeated motifs of glutamine and glutamic acid at the carboxyl terminus. A phylogenic tree of apo A-IV mammalian proteins reveals that porcine apo A-IV is more closely related to humans and primates than to rodents. This protein is highly hydrophobic and is mainly associated with lipoproteins.

Translational initiation in Leishmania tarentolae and Phytomonas serpens (Kinetoplastida) is strongly influenced by pre-ATG triplet and its 5' sequence context.

PubMed

Lukes, Julius; Paris, Zdenek; Regmi, Sandesh; Breitling, Reinhard; Mureev, Sergey; Kushnir, Susanna; Pyatkov, Konstantin; Jirků, Milan; Alexandrov, Kirill A

2006-08-01

To investigate the influence of sequence context of translation initiation codon on translation efficiency in Kinetoplastida, we constructed a library of expression plasmids randomized in the three nucleotides prefacing ATG of a reporter gene encoding enhanced green fluorescent protein (EGFP). All 64 possible combinations of pre-ATG triplets were individually stably integrated into the rDNA locus of Leishmania tarentolae and the resulting cell lines were assessed for EGFP expression. The expression levels were quantified directly by measuring the fluorescence of EGFP protein in living cells and confirmed by Western blotting. We observed a strong influence of the pre-ATG triplet on the level of protein expression over a 20-fold range. To understand the degree of evolutionary conservation of the observed effect, we transformed Phytomonas serpens, a trypanosomatid parasite of plants, with a subset of the constructs. The pattern of translational efficiency mediated by individual pre-ATG triplets in this species was similar to that observed in L. tarentolae. However, the pattern of translational efficiency of two other proteins (red fluorescent protein and tetracycline repressor) containing selected pre-ATG triplets did not correlate with either EGFP or each other. Thus, we conclude that a conserved mechanism of translation initiation site selection exists in kinetoplastids that is strongly influenced not only by the pre-ATG sequences but also by the coding region of the gene.

Close encounters of the third-body kind. [intruding bodies in binary star systems

NASA Technical Reports Server (NTRS)

Davies, M. B.; Benz, W.; Hills, J. G.

1994-01-01

We simulated encounters involving binaries of two eccentricities: e = 0 (i.e., circular binaries) and e = 0.5. In both cases the binary contained a point mass of 1.4 solar masses (i.e., a neutron star) and a 0.8 solar masses main-sequence star modeled as a polytrope. The semimajor axes of both binaries were set to 60 solar radii (0.28 AU). We considered intruders of three masses: 1.4 solar masses (a neutron star), 0.8 solar masses (a main-sequence star or a higher mass white dwarf), and 0.64 solar masses (a more typical mass white dwarf). Our strategy was to perform a large number (40,000) of encounters using a three-body code, then to rerun a small number of cases with a three-dimensional smoothed particle hydrodynamics (SPH) code to determine the importance of hydrodynamical effects. Using the results of the three-body runs, we computed the exchange across sections, sigma(sub ex). From the results of the SPH runs, we computed the cross sections for clean exchange, denoted by sigma(sub cx); the formation of a triple system, denoted by sigma(sub trp); and the formation of a merged binary with an object formed from the merger of two of the stars left in orbit around the third star, denoted by sigma(sub mb). For encounters between either binary and a 1.4 solar masses neutron star, sigma(sub cx) approx. 0.7 sigma(sub ex) and sigma(sub mb) + sigma(sub trp) approx. 0.3 sigma(sub ex). For encounters between either binary and the 0.8 solar masses main-sequence star, sigma(sub cx) approx. 0.50 sigma(sub ex) and sigma(sub mb) + sigma(sub trp) approx. 1.0 sigma(sub ex). If the main sequence star is replaced by a main-sequence star of the same mass, we have sigma(sub cx) approx. 0.5 sigma(sub ex) and sigma(sub mb) + sigma(sub trp) approx. 1.6 sigma(sub ex). Although the exchange cross section is a sensitive function of intruder mass, we see that the cross section to produce merged binaries is roughly independent of intruder mass. The merged binaries produced have semi-major axes much larger than either those of the original binaries or those of binaries produced in clean exchanges. Coupled with their lower kick velocities, received from the encounters, their larger size will enhance their cross section, shortening the waiting time to a subsequent encounter with another single star.

125. Pre1911. Crew on main deck, starboard side at main ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

125. Pre-1911. Crew on main deck, starboard side at main hatch, looking aft. Note dark object in center of photo that may be original main deck capstan. Fred Heick collection. (K9.9571) - Ship BALCLUTHA, 2905 Hyde Street Pier, San Francisco, San Francisco County, CA

De novo transcriptome sequencing and analysis of the cereal cyst nematode, Heterodera avenae.

PubMed

Kumar, Mukesh; Gantasala, Nagavara Prasad; Roychowdhury, Tanmoy; Thakur, Prasoon Kumar; Banakar, Prakash; Shukla, Rohit N; Jones, Michael G K; Rao, Uma

2014-01-01

The cereal cyst nematode (CCN, Heterodera avenae) is a major pest of wheat (Triticum spp) that reduces crop yields in many countries. Cyst nematodes are obligate sedentary endoparasites that reproduce by amphimixis. Here, we report the first transcriptome analysis of two stages of H. avenae. After sequencing extracted RNA from pre parasitic infective juvenile and adult stages of the life cycle, 131 million Illumina high quality paired end reads were obtained which generated 27,765 contigs with N50 of 1,028 base pairs, of which 10,452 were annotated. Comparative analyses were undertaken to evaluate H. avenae sequences with those of other plant, animal and free living nematodes to identify differences in expressed genes. There were 4,431 transcripts common to H. avenae and the free living nematode Caenorhabditis elegans, and 9,462 in common with more closely related potato cyst nematode, Globodera pallida. Annotation of H. avenae carbohydrate active enzymes (CAZy) revealed fewer glycoside hydrolases (GHs) but more glycosyl transferases (GTs) and carbohydrate esterases (CEs) when compared to M. incognita. 1,280 transcripts were found to have secretory signature, presence of signal peptide and absence of transmembrane. In a comparison of genes expressed in the pre-parasitic juvenile and feeding female stages, expression levels of 30 genes with high RPKM (reads per base per kilo million) value, were analysed by qRT-PCR which confirmed the observed differences in their levels of expression levels. In addition, we have also developed a user-friendly resource, Heterodera transcriptome database (HATdb) for public access of the data generated in this study. The new data provided on the transcriptome of H. avenae adds to the genetic resources available to study plant parasitic nematodes and provides an opportunity to seek new effectors that are specifically involved in the H. avenae-cereal host interaction.

De Novo Transcriptome Sequencing and Analysis of the Cereal Cyst Nematode, Heterodera avenae

PubMed Central

Kumar, Mukesh; Gantasala, Nagavara Prasad; Roychowdhury, Tanmoy; Thakur, Prasoon Kumar; Banakar, Prakash; Shukla, Rohit N.; Jones, Michael G. K.; Rao, Uma

2014-01-01

The cereal cyst nematode (CCN, Heterodera avenae) is a major pest of wheat (Triticum spp) that reduces crop yields in many countries. Cyst nematodes are obligate sedentary endoparasites that reproduce by amphimixis. Here, we report the first transcriptome analysis of two stages of H. avenae. After sequencing extracted RNA from pre parasitic infective juvenile and adult stages of the life cycle, 131 million Illumina high quality paired end reads were obtained which generated 27,765 contigs with N50 of 1,028 base pairs, of which 10,452 were annotated. Comparative analyses were undertaken to evaluate H. avenae sequences with those of other plant, animal and free living nematodes to identify differences in expressed genes. There were 4,431 transcripts common to H. avenae and the free living nematode Caenorhabditis elegans, and 9,462 in common with more closely related potato cyst nematode, Globodera pallida. Annotation of H. avenae carbohydrate active enzymes (CAZy) revealed fewer glycoside hydrolases (GHs) but more glycosyl transferases (GTs) and carbohydrate esterases (CEs) when compared to M. incognita. 1,280 transcripts were found to have secretory signature, presence of signal peptide and absence of transmembrane. In a comparison of genes expressed in the pre-parasitic juvenile and feeding female stages, expression levels of 30 genes with high RPKM (reads per base per kilo million) value, were analysed by qRT-PCR which confirmed the observed differences in their levels of expression levels. In addition, we have also developed a user-friendly resource, Heterodera transcriptome database (HATdb) for public access of the data generated in this study. The new data provided on the transcriptome of H. avenae adds to the genetic resources available to study plant parasitic nematodes and provides an opportunity to seek new effectors that are specifically involved in the H. avenae-cereal host interaction. PMID:24802510

The anatomy of a major late-stage thrust and implications for models of late-stage collisional orogenesis in the Caledonian crust of northern Scandinavia

NASA Astrophysics Data System (ADS)

Anderson, Mark; Hames, Willis; Stokes, Alison

2010-05-01

Within the stack of Caledonian crystalline thrust sheets of northern Scandinavia, a single amphibolite facies lithotectonic unit, the Småtinden nappe, is identified as a major, basement-coupled ("stretching") shear zone. This dominantly pelitic unit achieved peak metamorphic conditions of 535-550°C and 8-9kbars, and the stretching geometry suggests that this most likely occurred in response to overthrusting of a hot, pre-assembled Caledonian thrust stack. Along-strike variations in microstructural geometries and patterns of mineral zoning in widely developed porphyroblast phases suggest, however, subsequent strain partitioning within the zone during late-stage decoupling of the thrust stack from the basement along major out-of-sequence thrusts. Large parts of the nappe are characterised by relatively late, static growth preserving concordant Si-Se relationships, and typically symmetrical external fabrics consistent with formation under dominantly pure shear conditions. In the Salangen area, however, the nappe is characterised by early garnet growth, with discordant Si-Se relationships and asymmetric external fabric geometries consistent with formation during ESE-directed simple shear. Remarkably consistent thermometric estimates from chlorites in both regimes (post- and syn-shearing) suggest that out-of-sequence ramping occurred at temperatures in the range 370-400 ̊C, within the typical range of blocking temperatures for argon retention in muscovite. 40Ar-39Ar dating of muscovites from S-C fabrics in the out-of-sequence shear zone suggest that late-stage thrusting occurred during the middle-late Devonian (ca. 395-375 Ma). Hanging-wall and footwall geometries coupled with these radiometric dates indicate that the development of these late thrusts closely relates to reactivation of pre-Caledonian Baltic basement during the Devonian (400-370 Ma). East-west contraction during the upper end of this time frame is peculiar considering that this was the period of large magnitude and rapid extension in western Norway.

Multicenter validation of cancer gene panel-based next-generation sequencing for translational research and molecular diagnostics.

PubMed

Hirsch, B; Endris, V; Lassmann, S; Weichert, W; Pfarr, N; Schirmacher, P; Kovaleva, V; Werner, M; Bonzheim, I; Fend, F; Sperveslage, J; Kaulich, K; Zacher, A; Reifenberger, G; Köhrer, K; Stepanow, S; Lerke, S; Mayr, T; Aust, D E; Baretton, G; Weidner, S; Jung, A; Kirchner, T; Hansmann, M L; Burbat, L; von der Wall, E; Dietel, M; Hummel, M

2018-04-01

The simultaneous detection of multiple somatic mutations in the context of molecular diagnostics of cancer is frequently performed by means of amplicon-based targeted next-generation sequencing (NGS). However, only few studies are available comparing multicenter testing of different NGS platforms and gene panels. Therefore, seven partner sites of the German Cancer Consortium (DKTK) performed a multicenter interlaboratory trial for targeted NGS using the same formalin-fixed, paraffin-embedded (FFPE) specimen of molecularly pre-characterized tumors (n = 15; each n = 5 cases of Breast, Lung, and Colon carcinoma) and a colorectal cancer cell line DNA dilution series. Detailed information regarding pre-characterized mutations was not disclosed to the partners. Commercially available and custom-designed cancer gene panels were used for library preparation and subsequent sequencing on several devices of two NGS different platforms. For every case, centrally extracted DNA and FFPE tissue sections for local processing were delivered to each partner site to be sequenced with the commercial gene panel and local bioinformatics. For cancer-specific panel-based sequencing, only centrally extracted DNA was analyzed at seven sequencing sites. Subsequently, local data were compiled and bioinformatics was performed centrally. We were able to demonstrate that all pre-characterized mutations were re-identified correctly, irrespective of NGS platform or gene panel used. However, locally processed FFPE tissue sections disclosed that the DNA extraction method can affect the detection of mutations with a trend in favor of magnetic bead-based DNA extraction methods. In conclusion, targeted NGS is a very robust method for simultaneous detection of various mutations in FFPE tissue specimens if certain pre-analytical conditions are carefully considered.

Molecular Basis of Substrate Recognition and Degradation by Human Presequence Protease

PubMed Central

King, John V.; Liang, Wenguang G.; Scherpelz, Kathryn P.; Schilling, Alexander B.; Meredith, Stephen C.; Tang, Wei-Jen

2014-01-01

Summary Human Presequence Protease (hPreP) is an M16 metalloprotease localized in mitochondria. There, hPreP facilitates proteostasis by utilizing a ∼13,300Å3 catalytic chamber to degrade a diverse array of potentially toxic peptides, including mitochondrial presequences and amyloid-β (Aβ), the latter of which contributes to Alzheimer's disease pathogenesis. Here we report crystal structures for hPreP alone and in complex with Aβ, which show that hPreP uses size-exclusion and charge complementation for substrate recognition. These structures also reveal hPreP-specific features that permit a diverse array of peptides, with distinct distributions of charged and hydrophobic residues, to be specifically captured, cleaved, and their amyloidogenic features destroyed. SAXS analysis demonstrates that hPreP in solution exists in dynamic equilibrium between closed and open states, with the former being preferred. Furthermore, Aβ binding induces the closed state and hPreP dimerization. Together, these data reveal the molecular basis for flexible yet specific substrate recognition and degradation by hPreP. PMID:24931469

Influence of the capillary on the ignition of the transient spark discharge

NASA Astrophysics Data System (ADS)

Gerling, T.; Hoder, T.; Brandenburg, R.; Bussiahn, R.; Weltmann, K.-D.

2013-04-01

A self-pulsing negative dc discharge in argon generated in a needle-to-plane geometry at open atmosphere is investigated. Additionally, the needle electrode can be surrounded by a quartz capillary. It is shown that the relative position of the capillary end to the needle tip strongly influences the discharge inception and its spatio-temporal dynamics. Without the capillary for the selected working parameters a streamer corona is ignited, but when the capillary surrounds the needle, the transient spark (TS) discharge is ignited after a pre-streamer (PS) occurs. The time between PS and TS discharge depends on the relative capillary end position. The existence of the PS is confirmed by electro-optical characterization. Furthermore, spectrally and spatio-temporally resolved cross-correlation spectroscopy is applied to show the most active region of pre-phase emission activity as indicators for high local electric field strength. The results indicate that with a capillary in place, the necessary energy input of the pre-phase into the system is mainly reduced by additional electrical fields at the capillary edge. Even such a small change as a shift of dielectric surface close to the plasma largely changes the energy balance in the system.

Using White Dwarf Companions of Blue Stragglers to Constrain Mass Transfer Physics

NASA Astrophysics Data System (ADS)

Gosnell, Natalie M.; Leiner, Emily; Geller, Aaron M.; Knigge, Christian; Mathieu, Robert D.; Sills, Alison; Leigh, Nathan

2018-06-01

Complete membership studies of old open clusters reveal that 25% of the evolved stars follow pathways in stellar evolution that are impacted by binary evolution. Recent studies show that the majority of blue straggler stars, traditionally defined to be stars brighter and bluer than the corresponding main sequence turnoff, are formed through mass transfer from a giant star onto a main sequence companion, resulting in a white dwarf in a binary system with a blue straggler. We will present constraints on the histories and mass transfer efficiencies for two blue straggler-white dwarf binaries in open cluster NGC 188. The constraints are a result of measuring white dwarf cooling temperatures and surface gravities with HST COS far-ultraviolet spectroscopy. This information sets both the timeline for mass transfer and the stellar masses in the pre-mass transfer binary, allowing us to constrain aspects of the mass transfer physics. One system is formed through Case C mass transfer, leaving a CO-core white dwarf, and provides an interesting test case for mass transfer from an asymptotic giant branch star in an eccentric system. The other system formed through Case B mass transfer, leaving a He-core white dwarf, and challenges our current understanding of the expected regimes for stable mass transfer from red giant branch stars.

The great escape - III. Placing post-main-sequence evolution of planetary and binary systems in a Galactic context

NASA Astrophysics Data System (ADS)

Veras, Dimitri; Evans, N. Wyn; Wyatt, Mark C.; Tout, Christopher A.

2014-01-01

Our improving understanding of the life cycle of planetary systems prompts investigations of the role of the Galenvironment before, during and after asymptotic giant branch (AGB) stellar evolution. Here, we investigate the interplay between stellar mass-loss, Galactic tidal perturbations and stellar flybys for evolving stars which host one planet, smaller body or stellar binary companion and reside in the Milky Way's bulge or disc. We find that the potential evolutionary pathways from a main sequence (MS) to a white dwarf (WD) planetary system are a strong function of Galactocentric distance only with respect to the prevalence of stellar flybys. Planetary ejection and collision with the parent star should be more common towards the bulge. At a given location anywhere in the Galaxy, if the mass-loss is adiabatic, then the secondary is likely to avoid close flybys during AGB evolution, and cannot eventually escape the resulting WD because of Galactic tides alone. Partly because AGB mass-loss will shrink a planetary system's Hill ellipsoid axes by about 20 to 40 per cent, Oort clouds orbiting WDs are likely to be more depleted and dynamically excited than on the MS.

Pre-load on oral implants after screw tightening fixed full prostheses: an in vivo study.

PubMed

Duyck, J; Van Oosterwyck, H; Vander Sloten, J; De Cooman, M; Puers, R; Naert, I

2001-03-01

The fit of implant supported fixed prostheses is said to be of clinical concern because of the rigid fixation of an oral implant in its surrounding bone. The influence of the torque sequence of the set screws during fixation of implant supported fixed full prostheses on the final pre-load was investigated in vitro. No significant effect of the torque sequence of the set screws on the final pre-load was observed. The main objective of this study was to quantify and qualify the pre-load in vivo on implants supporting a fixed full prosthesis. This was performed when the prostheses were supported by all five or six implants and was repeated when the prostheses were supported by only four and three implants. A total of 13 patients with a fixed full implant supported prosthesis were selected. The existing abutments were changed for strain gauged abutments. After tightening the set screws with a torque of 10 N cm, the pre-load conditions were registered. The average (SEM) axial forces and bending moments in case of five or six, four and three supporting implants were 323 N (43 N), 346 N (59 N), 307 N (60 N) 21 N cm (3 N cm) and 21 N cm (2 N cm), 23 N cm (5 N cm), respectively. In addition, the pre-load was registered after fixation of a machined gold cylinder, as delivered by the manufacturer, on each of the supporting implants, representing the 'optimal fit' situation. The corresponding average (SEM) axial forces and bending moments in case of five or six, four and three supporting implants were 426 N (36 N), 405 N (40 N), 413 N (46 N) and 8 N cm (1 N cm), 8 N cm (1 N cm), 8 N cm (1 N cm), respectively. The induced axial forces after tightening the prostheses were significantly lower then after tightening the gold cylinder in case of five or six supporting implants (P < 0.02). The induced bending moments after tightening the prostheses were statistically significantly higher (P < 0.0001) then after tightening the gold cylinder in all test conditions (five or six, four or three supporting implants). This study underlines the static load present after screw tightening implant supported fixed full prostheses.

Sequence-specific bias correction for RNA-seq data using recurrent neural networks.

PubMed

Zhang, Yao-Zhong; Yamaguchi, Rui; Imoto, Seiya; Miyano, Satoru

2017-01-25

The recent success of deep learning techniques in machine learning and artificial intelligence has stimulated a great deal of interest among bioinformaticians, who now wish to bring the power of deep learning to bare on a host of bioinformatical problems. Deep learning is ideally suited for biological problems that require automatic or hierarchical feature representation for biological data when prior knowledge is limited. In this work, we address the sequence-specific bias correction problem for RNA-seq data redusing Recurrent Neural Networks (RNNs) to model nucleotide sequences without pre-determining sequence structures. The sequence-specific bias of a read is then calculated based on the sequence probabilities estimated by RNNs, and used in the estimation of gene abundance. We explore the application of two popular RNN recurrent units for this task and demonstrate that RNN-based approaches provide a flexible way to model nucleotide sequences without knowledge of predetermined sequence structures. Our experiments show that training a RNN-based nucleotide sequence model is efficient and RNN-based bias correction methods compare well with the-state-of-the-art sequence-specific bias correction method on the commonly used MAQC-III data set. RNNs provides an alternative and flexible way to calculate sequence-specific bias without explicitly pre-determining sequence structures.

Whistle sequences in wild killer whales (Orcinus orca).

PubMed

Riesch, Rüdiger; Ford, John K B; Thomsen, Frank

2008-09-01

Combining different stereotyped vocal signals into specific sequences increases the range of information that can be transferred between individuals. The temporal emission pattern and the behavioral context of vocal sequences have been described in detail for a variety of birds and mammals. Yet, in cetaceans, the study of vocal sequences is just in its infancy. Here, we provide a detailed analysis of sequences of stereotyped whistles in killer whales off Vancouver Island, British Columbia. A total of 1140 whistle transitions in 192 whistle sequences recorded from resident killer whales were analyzed using common spectrographic analysis techniques. In addition to the stereotyped whistles described by Riesch et al., [(2006). "Stability and group specificity of stereotyped whistles in resident killer whales, Orcinus orca, off British Columbia," Anim. Behav. 71, 79-91.] We found a new and rare stereotyped whistle (W7) as well as two whistle elements, which are closely linked to whistle sequences: (1) stammers and (2) bridge elements. Furthermore, the frequency of occurrence of 12 different stereotyped whistle types within the sequences was not randomly distributed and the transition patterns between whistles were also nonrandom. Finally, whistle sequences were closely tied to close-range behavioral interactions (in particular among males). Hence, we conclude that whistle sequences in wild killer whales are complex signal series and propose that they are most likely emitted by single individuals.