Discovery of Extended Main-sequence Turnoffs in Four Young Massive Clusters in the Magellanic Clouds

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

Li, Chengyuan; De Grijs, Richard; Deng, Licai

An increasing number of young massive clusters (YMCs) in the Magellanic Clouds have been found to exhibit bimodal or extended main sequences (MSs) in their color–magnitude diagrams (CMDs). These features are usually interpreted in terms of a coeval stellar population with different stellar rotational rates, where the blue and red MS stars are populated by non- (or slowly) and rapidly rotating stellar populations, respectively. However, some studies have shown that an age spread of several million years is required to reproduce the observed wide turnoff regions in some YMCs. Here we present the ultraviolet–visual CMDs of four Large and Smallmore » Magellanic Cloud YMCs, NGC 330, NGC 1805, NGC 1818, and NGC 2164, based on high-precision Hubble Space Telescope photometry. We show that they all exhibit extended main-sequence turnoffs (MSTOs). The importance of age spreads and stellar rotation in reproducing the observations is investigated. The observed extended MSTOs cannot be explained by stellar rotation alone. Adopting an age spread of 35–50 Myr can alleviate this difficulty. We conclude that stars in these clusters are characterized by ranges in both their ages and rotation properties, but the origin of the age spread in these clusters remains unknown.« less

IRAS 18153-1651: an H II region with a possible wind bubble blown by a young main-sequence B star

NASA Astrophysics Data System (ADS)

Gvaramadze, V. V.; Mackey, J.; Kniazev, A. Y.; Langer, N.; Chené, A.-N.; Castro, N.; Haworth, T. J.; Grebel, E. K.

2017-04-01

We report the results of spectroscopic observations and numerical modelling of the H II region IRAS 18153-1651. Our study was motivated by the discovery of an optical arc and two main-sequence stars of spectral type B1 and B3 near the centre of IRAS 18153-1651. We interpret the arc as the edge of the wind bubble (blown by the B1 star), whose brightness is enhanced by the interaction with a photoevaporation flow from a nearby molecular cloud. This interpretation implies that we deal with a unique case of a young massive star (the most massive member of a recently formed low-mass star cluster) caught just tens of thousands of years after its stellar wind has begun to blow a bubble into the surrounding dense medium. Our 2D, radiation-hydrodynamics simulations of the wind bubble and the H II region around the B1 star provide a reasonable match to observations, both in terms of morphology and absolute brightness of the optical and mid-infrared emission, and verify the young age of IRAS 18153-1651. Taken together our results strongly suggest that we have revealed the first example of a wind bubble blown by a main-sequence B star.

The Role Of Rejuvenation In Shaping The High-Mass End Of The Main Sequence

NASA Astrophysics Data System (ADS)

Mancini, Chiara

2017-06-01

We investigate the nature of star forming galaxies with reduced specific SFRs and high stellar masses, those that seemingly cause the so-called bending of the main sequence. The fact that such objects host large bulges recently lead some to suggest that the internal formation of the bulges, via compaction or disk instabilities, was the late event that induced sSFRs of massive galaxies to drop in a slow downfall and thus the main sequence to bend. We have studied in detail a sample of 16 galaxies at 0.5

Massive Stars

NASA Astrophysics Data System (ADS)

Livio, Mario; Villaver, Eva

2009-11-01

Participants; Preface Mario Livio and Eva Villaver; 1. High-mass star formation by gravitational collapse of massive cores M. R. Krumholz; 2. Observations of massive star formation N. A. Patel; 3. Massive star formation in the Galactic center D. F. Figer; 4. An X-ray tour of massive star-forming regions with Chandra L. K. Townsley; 5. Massive stars: feedback effects in the local universe M. S. Oey and C. J. Clarke; 6. The initial mass function in clusters B. G. Elmegreen; 7. Massive stars and star clusters in the Antennae galaxies B. C. Whitmore; 8. On the binarity of Eta Carinae T. R. Gull; 9. Parameters and winds of hot massive stars R. P. Kudritzki and M. A. Urbaneja; 10. Unraveling the Galaxy to find the first stars J. Tumlinson; 11. Optically observable zero-age main-sequence O stars N. R. Walborn; 12. Metallicity-dependent Wolf-Raynet winds P. A. Crowther; 13. Eruptive mass loss in very massive stars and Population III stars N. Smith; 14. From progenitor to afterlife R. A. Chevalier; 15. Pair-production supernovae: theory and observation E. Scannapieco; 16. Cosmic infrared background and Population III: an overview A. Kashlinsky.

Constraining the weak-wind problem: an XMM-HST campaign for the magnetic O9.7 V star HD 54879

NASA Astrophysics Data System (ADS)

Shenar, T.; Oskinova, L. M.; Järvinen, S. P.; Luckas, P.; Hainich, R.; Todt, H.; Hubrig, S.; Sander, A. A. C.; Ilyin, I.; Hamann, W.-R.

2018-01-01

Mass-loss rates of massive, late type main sequence stars are much weaker than currently predicted, but their true values are very difficult to measure. We suggest that confined stellar winds of magnetic stars can be exploited to constrain the true mass-loss rates Ṁ of massive main sequence stars. We acquired UV, X-ray, and optical amateur data of HD 54879 (O9.7 V), one of a few O-type stars with a detected atmospheric magnetic field (Bd ≳ 2 kG). We analyze these data with the Potsdam Wolf-Rayet (PoWR) and XSPEC codes. We can roughly estimate the mass-loss rate the star would have in the absence of a magnetic field as log ṀB = 0 ≈ -9.0 M⊙yr-1. Since the wind is partially trapped within the Alfvén radius rA ≳ 12 R*, the true mass-loss rate of HD 54879 is log Ṁ ≲ -10.2 M⊙yr-1. Moreover, we find that the microturbulent, macroturbulent, and projected rotational velocities are lower than previously suggested (< 4 km s-1). An initial mass of 16 M⊙ and an age of 5 Myr are inferred. We derive a mean X-ray emitting temperature of log TX = 6.7 K and an X-ray luminosity of log LX = 32 erg s-1. The latter implies a significant X-ray excess (log LX/LBol ≈ -6.0), most likely stemming from collisions at the magnetic equator. A tentative period of P ≈ 5 yr is derived from variability of the Hα line. Our study confirms that strongly magnetized stars lose little or no mass, and supplies important constraints on the weak-wind problem of massive main sequence stars.

Extended Star Formation or a Range of Stellar Rotation Velocities? The Nature of Extended Main Sequence Turnoffs in Intermediate-Age Star Clusters

NASA Astrophysics Data System (ADS)

Goudfrooij, Paul

2016-10-01

Recently, deep color-magnitude diagrams (CMDs) from HST data revealed that several massive intermediate-age star clusters in the Magellanic Clouds exhibit extended main-sequence turn-offs (eMSTOs), and in some cases also dual red clumps. This poses serious questions regarding the mechanisms responsible for the formation of massive star clusters and their well-known light-element abundance variations. The nature of eMSTOs is currently a hotly debated topic of study. Several recent studies indicate that the eMSTOs are caused by an age spread of about 100-500 Myr among cluster stars, while other studies indicate that eMSTOs can be caused by a coeval population in which the relevant stars span a range of rotation velocities. Formal evidence to (dis-)prove either scenario still remains at large, mainly because the available stellar tracks that incorporate the effects of rotation are only available for masses > 1.7 Msun whereas the stars in the known eMSTOs of intermediate-age clusters are less massive. To circumvent this issue, we identified a massive star cluster in the Large Magellanic Cloud (LMC) that has the right dynamical properties to host an eMSTO along with an age at which the effects of age spreads to CMD morphology are substantially different from those of spreads of rotation rates: the 600 Myr old cluster NGC 1831. We propose to obtain deep WFC3/UVIS imaging with filters F336W and F814W to analyze the morphologies of the MSTO and upper MS regions of NGC 1831 at high precision and compare with model predictions. This will have a lasting impact on our understanding of the eMSTO phenomenon and of star cluster formation in general.

Age Spread in W3 Main: Large Binocular Telescope/LUCI Near-infrared Spectroscopy of the Massive Stellar Content

NASA Astrophysics Data System (ADS)

Bik, A.; Henning, Th.; Stolte, A.; Brandner, W.; Gouliermis, D. A.; Gennaro, M.; Pasquali, A.; Rochau, B.; Beuther, H.; Ageorges, N.; Seifert, W.; Wang, Y.; Kudryavtseva, N.

2012-01-01

We present near-infrared multi-object spectroscopy and JHK s imaging of the massive stellar content of the Galactic star-forming region W3 Main, obtained with LUCI at the Large Binocular Telescope. We confirm 15 OB stars in W3 Main and derive spectral types between O5V and B4V from their absorption line spectra. Three massive young stellar objects are identified by their emission line spectra and near-infrared excess. The color-color diagram of the detected sources allows a detailed investigation of the slope of the near-infrared extinction law toward W3 Main. Analysis of the Hertzsprung-Russell diagram suggests that the Nishiyama extinction law fits the stellar population of W3 Main best (E(J - H)/E(H - K s) = 1.76 and R_{{K_s}} = 1.44). From our spectrophotometric analysis of the massive stars and the nature of their surrounding H II regions, we derive the evolutionary sequence of W3 Main and we find evidence of an age spread of at least 2-3 Myr. While the most massive star (IRS2) is already evolved, indications for high-mass pre-main-sequence evolution are found for another star (IRS N1), deeply embedded in an ultracompact H II (UCH II) region, in line with the different evolutionary phases observed in the corresponding H II regions. We derive a stellar mass of W3 Main of (4 ± 1) × 103 M ⊙ by extrapolating from the number of OB stars using a Kroupa initial mass function and correcting for our spectroscopic incompleteness. We have detected the photospheres of OB stars from the more evolved diffuse H II region to the much younger UCH II regions, suggesting that these stars have finished their formation and cleared away their circumstellar disks very fast. Only in the hyper-compact H II region (IRS5) do the early-type stars seem to be still surrounded by circumstellar material. Based on data acquired using the Large Binocular Telescope (LBT). The LBT is an international collaboration among institutions in Germany, Italy, and the United States. LBT Corporation partners are LBT Beteiligungsgesellschaft, Germany, representing the Max Planck Society, the Astrophysical Institute Potsdam, and Heidelberg University; Istituto Nazionale di Astrofisica, Italy; The University of Arizona on behalf of the Arizona university system; The Ohio State University, and The Research Corporation, on behalf of the University of Notre Dame, University of Minnesota, and University of Virginia.

T-ReX Spies the Stars of 30 Doradus

NASA Astrophysics Data System (ADS)

Broos, Patrick; Townsley, Leisa K.; Pollock, Andrew; Crowther, Paul

2017-08-01

30 Doradus (the Tarantula Nebula) is the Local Group's most massive young star-forming complex. At its heart is R136, the most massive resolved stellar cluster; R136 contains, in turn, the most massive stars known. The Chandra X-ray Observatory has recently observed 30 Dor for the 2-megasecond X-ray Visionary Project ``The Tarantula -- Revealed by X-rays'' (T-ReX). This deep observation exploits Chandra's fine spatial resolution to study the full complement of massive stars and the brightest pre-main sequence stars that trace 25 Myrs of star formation in this incomparable nearby starburst. Here we give preliminary results from the ongoing analyses of the data, focusing on the massive stars. While many remain undetected even in this deep ACIS-I observation, a few show dramatic X-ray lightcurves and/or high luminosities befitting this amazing starburst cluster.

The efficiency of seismic attributes to differentiate between massive and non-massive carbonate successions for hydrocarbon exploration activity

NASA Astrophysics Data System (ADS)

Sarhan, Mohammad Abdelfattah

2017-12-01

The present work investigates the efficiency of applying volume seismic attributes to differentiate between massive and non-massive carbonate sedimentary successions on using seismic data. The main objective of this work is to provide a pre-drilling technique to recognize the porous carbonate section (probable hydrocarbon reservoirs) based on seismic data. A case study from the Upper Cretaceous - Eocene carbonate successions of Abu Gharadig Basin, northern Western Desert of Egypt has been tested in this work. The qualitative interpretations of the well-log data of four available wells distributed in the study area, namely; AG-2, AG-5, AG-6 and AG-15 wells, has confirmed that the Upper Cretaceous Khoman A Member represents the massive carbonate section whereas the Eocene Apollonia Formation represents the non-massive carbonate unit. The present work have proved that the most promising seismic attributes capable of differentiating between massive and non-massive carbonate sequences are; Root Mean Square (RMS) Amplitude, Envelope (Reflection Strength), Instantaneous Frequency, Chaos, Local Flatness and Relative Acoustic Impedance.

Presupernova Evolution of Differentially Rotating Massive Stars Including Magnetic Fields

NASA Astrophysics Data System (ADS)

Heger, A.; Woosley, S. E.; Spruit, H. C.

2005-06-01

As a massive star evolves through multiple stages of nuclear burning on its way to becoming a supernova, a complex, differentially rotating structure is set up. Angular momentum is transported by a variety of classic instabilities and also by magnetic torques from fields generated by the differential rotation. We present the first stellar evolution calculations to follow the evolution of rotating massive stars including, at least approximately, all these effects, magnetic and nonmagnetic, from the zero-age main sequence until the onset of iron-core collapse. The evolution and action of the magnetic fields is as described by Spruit in 2002, and a range of uncertain parameters is explored. In general, we find that magnetic torques decrease the final rotation rate of the collapsing iron core by about a factor of 30-50 when compared with the nonmagnetic counterparts. Angular momentum in that part of the presupernova star destined to become a neutron star is an increasing function of main-sequence mass. That is, pulsars derived from more massive stars rotate faster and rotation plays a more important role in the star's explosion. The final angular momentum of the core has been determined-to within a factor of 2-by the time the star ignites carbon burning. For the lighter stars studied, around 15 Msolar, we predict pulsar periods at birth near 15 ms, though a factor of 2 range is easily tolerated by the uncertainties. Several mechanisms for additional braking in a young neutron star, especially by fallback, are explored.

Modeling the early evolution of massive OB stars with an experimental wind routine. The first bi-stability jump and the angular momentum loss problem

NASA Astrophysics Data System (ADS)

Keszthelyi, Z.; Puls, J.; Wade, G. A.

2017-02-01

Context. Stellar evolution models of massive stars are very sensitive to the adopted mass-loss scheme. The magnitude and evolution of mass-loss rates significantly affect the main sequence evolution, and the properties of post-main sequence objects, including their rotational velocities. Aims: Driven by potential discrepancies between theoretically predicted and observationally derived mass-loss rates in the OB star range, we aim in particular to investigate the response to mass-loss rates that are lower than currently adopted, in parallel with the mass-loss behavior at the "first" bi-stability jump. Methods: We performed 1D hydrodynamical model calculations of single 20-60 M⊙ Galactic (Z = 0.014) stars where the effects of stellar winds are already significant in the main sequence phase. We have developed an experimental wind routine to examine the behavior and response of the models under the influence of different mass-loss rates. This observationally guided, simple and flexible wind routine is not a new mass-loss description but a useful tool based on the wind-momentum luminosity relation and other scaling relations, and provides a meaningful base for various tests and comparisons. Results: The main result of this study indicates a dichotomy between solutions of currently debated problems regarding mass-loss rates of hot massive stars. In a fully diffusive approach, and for commonly adopted initial rotational velocities, lower mass-loss rates than theoretically predicted require to invoke an additional source of angular momentum loss (either due to bi-stability braking, or yet unidentified) to brake down surface rotational velocities. On the other hand, a large jump in the mass-loss rates due to the bi-stability mechanism (a factor of 5-7 predicted by Vink et al. (2000, A&A, 362, 295), but a factor of 10-20 in modern models of massive stars) is challenged by observational results, and might be avoided if the early mass-loss rates agreed with the theoretically predicted values. Conclusions: We conclude that simultaneously adopting lower mass-loss rates and a significantly smaller jump in the mass-loss rates over the bi-stability region (both compared to presently used prescriptions) would require an additional mechanism for angular momentum loss to be present in massive stars. Otherwise, the observed rotational velocities of a large population of B supergiants, that are thought to be the evolutionary descendants of O stars, would remain unexplained.

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 zero age main sequence of WIMP burners

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

Fairbairn, Malcolm; Scott, Pat; Edsjoe, Joakim

2008-02-15

We modify a stellar structure code to estimate the effect upon the main sequence of the accretion of weakly-interacting dark matter onto stars and its subsequent annihilation. The effect upon the stars depends upon whether the energy generation rate from dark matter annihilation is large enough to shut off the nuclear burning in the star. Main sequence weakly-interacting massive particles (WIMP) burners look much like proto-stars moving on the Hayashi track, although they are in principle completely stable. We make some brief comments about where such stars could be found, how they might be observed and more detailed simulations whichmore » are currently in progress. Finally we comment on whether or not it is possible to link the paradoxically hot, young stars found at the galactic center with WIMP burners.« less

High-Mass Stars in the Centers of Young Dense Clusters: Mass Segregation, Binary Mergers and Gamma-Ray Bursts

NASA Astrophysics Data System (ADS)

Zinnecker, H.

We start by discussing dense, young star-clusters, particularly the 30 Doradus cluster with its core R136. The question of mass segregation and core collapse of the massive stars is addressed. Analytical estimates of relaxation times and collision times predict that the central N=10 subsystem of massive stars in the R136 core will evolve dynamically in such a way and fast enough (i.e. within their main-sequence lifetime of a few Myr) that a dominant massive binary system is formed whose orbit will shrink to a point where merging of the components appears inevitable. The merger product will be spinning rapidly, and we put forward the idea that this rare and very massive object might be the perfect precursor of a gamma-ray burst (collapsar).

Opportunities and challenges for the integration of massively parallel genomic sequencing into clinical practice: lessons from the ClinSeq project.

PubMed

Biesecker, Leslie G

2012-04-01

The debate surrounding the return of results from high-throughput genomic interrogation encompasses many important issues including ethics, law, economics, and social policy. As well, the debate is also informed by the molecular, genetic, and clinical foundations of the emerging field of clinical genomics, which is based on this new technology. This article outlines the main biomedical considerations of sequencing technologies and demonstrates some of the early clinical experiences with the technology to enable the debate to stay focused on real-world practicalities. These experiences are based on early data from the ClinSeq project, which is a project to pilot the use of massively parallel sequencing in a clinical research context with a major aim to develop modes of returning results to individual subjects. The study has enrolled >900 subjects and generated exome sequence data on 572 subjects. These data are beginning to be interpreted and returned to the subjects, which provides examples of the potential usefulness and pitfalls of clinical genomics. There are numerous genetic results that can be readily derived from a genome including rare, high-penetrance traits, and carrier states. However, much work needs to be done to develop the tools and resources for genomic interpretation. The main lesson learned is that a genome sequence may be better considered as a health-care resource, rather than a test, one that can be interpreted and used over the lifetime of the patient.

Convective overshooting in the evolution of very massive stars

NASA Technical Reports Server (NTRS)

Stothers, R.; Chin, C.-W.

1981-01-01

Possible convective overshooting in stars of 30-120 solar masses are considered, including a merger between the convective core and the intermediate zone, and penetration by the outer convection zone into the hydrogen-shell region when the star is a supergiant. Convective mixing between the core and inner envelopes is found to lead to a brief renewal of hydrogen burning in the core, and a moderate widening of the main sequence bond in the H-R diagram. Deep penetration by the outer convection zone is found to force the star out of the red supergiant configuration and into a configuration near the main sequence. This would account for the apparent spread of the uppermost part of the main sequence and the concentration of luminous supergiants towards earlier spectral types. In addition, heavy mass loss need not be assumed to achieve the points of agreement, and are tentatively considered unimportant from an evolutionary point of view.

The Secrets of the Nearest Starburst Cluster. I. Very Large Telescope/ISAAC Photometry of NGC 3603

NASA Astrophysics Data System (ADS)

Stolte, Andrea; Brandner, Wolfgang; Brandl, Bernhard; Zinnecker, Hans; Grebel, Eva K.

2004-08-01

VLT/ISAAC JHKL photometry with subarcsecond resolution of the dense, massive starburst cluster NGC 3603 YC forming the core of the NGC 3603 giant molecular cloud is analyzed to reveal characteristics of the stellar population in unprecedented detail. The color-magnitude plane features a strong pre-main-sequence/main-sequence (PMS/MS) transition region, including the PMS/MS transition point, and reveals a secondary sequence for the first time in a nearby young starburst cluster. Arguments for a possible binary nature of this sequence are given. The resolved PMS/MS transition region allows isochrone fitting below the hydrogen-burning turn-on in NGC 3603 YC, yielding an independent estimate of global cluster parameters. A distance modulus of 13.9 mag, equivalent to d=6.0+/-0.3 kpc, is derived, as well as a line-of-sight extinction of AV=4.5+/-0.6 toward PMS stars in the cluster center. The interpretation of a binary candidate sequence suggests a single age of 1 Myr for NGC 3603 YC, providing evidence for a single burst of star formation without the need to employ an age spread in the PMS population, as argued for in earlier studies. Disk fractions are derived from L-band excesses, indicating a radial increase in the disk frequency from 20% to 40% from the core to the cluster outskirts. The low disk fraction in the cluster core, as compared to the 42% L-band excess fraction found for massive stars in the Trapezium cluster of a comparably young age, indicates strong photoevaporation in the cluster center. The estimated binary fraction of 30%, as well as the low disk fraction, suggest strong impacts on low-mass star formation due to stellar interactions in the dense starburst. The significant differences between NGC 3603 YC and less dense and massive young star clusters in the Milky Way reveal the importance of using local starbursts as templates for massive extragalactic star formation. Based on observations obtained at the ESO VLT on Paranal, Chile, under programs 63.I-0015 and 65.I-0135, and data from the public VLT archive provided by ESO, as well as observations made with the NASA/ESA Hubble Space Telescope, obtained at the Space Telescope Science Institute, which is operated by the Association of Universities for Research in Astronomy, Inc. under NASA contract NAS5-26555.

FOC Imaging of the Dusty Envelopes of Mass-Losing Supergiants

NASA Astrophysics Data System (ADS)

Kastner, Joel

1996-07-01

Stars more massive than 10 M_odot are destined to explode as supernovae {SN}. Pre-SN mass loss can prolong core buildup, and the rate and duration of mass loss therefore largely determines a massive star's post-main sequence evolution and its position in the H-R diagram prior to SN detonation. The envelope ejected by a mass-losing supergiant also plays an important role in the formation and evolution of a SN remnant. We propose to investigate these processes with HST. We will use the FOC to image two massive stars that are in different stages of post-main sequence evolution: VY CMa, the prototype for a class of heavily mass-losing OH/IR supergiants, and HD 179821, a post-red supergiant that is likely in transition to the Wolf-Rayet phase. Both are known to possess compact reflection nebulae, but ground-based techniques are unable to separate the inner nebulosities from the PSF of the central stars. We will use the unparalleled resolution of the FOC to probe the structure of these nebulae at subarcsecond scales. These data will yield the mass loss histories of the central stars and will demonstrate the presence or absence of axisymmetric mass loss and circumstellar disks. In so doing, our HST/FOC program will define the role of mass loss in determining the fates of SN progenitors and SN remnants.

WR and LBV stars

NASA Astrophysics Data System (ADS)

Kochiashvili, Nino; Beradze, Sophie; Kochiashvili, Ia; Natsvlishvili, Rezo; Vardosanidze, Manana

Evolutionary scenarios of massive stars were revised in recent decades, after finding "unusual", blue progenitor of SN 1987A and after detecting the more massive stars than the accepted 120 M ⊙ maximum limit of stellar masses. A very important relation exists between WR and LBV stars. They represent the earlier, pre-SN evolutionary states of massive stars. WR and LBV stars and "classic" evolutionary scheme of the relation between the different type massive stars are discussed in this article. There also exist the newest evolutionary scenarios for low metallicity massive stars, which give us a different picture of their post main-sequence evolution. There is a rather good tradition of observations and investigations of massive stars at Abastumani Astrophysical Observatory. The authors discuss the new findings on the fate of P Cygni, the LBV star. These results on the reddening of the star and about its next possible outburst in the near future were obtained on the basis of UBV long-term electrophotometric observations of P Cygni by Eugene Kharadze and Nino Magalashvili. The observations were held in 1951-1983 at Abastumani Observatory using 33-cm and 48-cm reflectors.

A massive parallel sequencing workflow for diagnostic genetic testing of mismatch repair genes

PubMed Central

Hansen, Maren F; Neckmann, Ulrike; Lavik, Liss A S; Vold, Trine; Gilde, Bodil; Toft, Ragnhild K; Sjursen, Wenche

2014-01-01

The purpose of this study was to develop a massive parallel sequencing (MPS) workflow for diagnostic analysis of mismatch repair (MMR) genes using the GS Junior system (Roche). A pathogenic variant in one of four MMR genes, (MLH1, PMS2, MSH6, and MSH2), is the cause of Lynch Syndrome (LS), which mainly predispose to colorectal cancer. We used an amplicon-based sequencing method allowing specific and preferential amplification of the MMR genes including PMS2, of which several pseudogenes exist. The amplicons were pooled at different ratios to obtain coverage uniformity and maximize the throughput of a single-GS Junior run. In total, 60 previously identified and distinct variants (substitutions and indels), were sequenced by MPS and successfully detected. The heterozygote detection range was from 19% to 63% and dependent on sequence context and coverage. We were able to distinguish between false-positive and true-positive calls in homopolymeric regions by cross-sample comparison and evaluation of flow signal distributions. In addition, we filtered variants according to a predefined status, which facilitated variant annotation. Our study shows that implementation of MPS in routine diagnostics of LS can accelerate sample throughput and reduce costs without compromising sensitivity, compared to Sanger sequencing. PMID:24689082

Low-mass White Dwarfs with Hydrogen Envelopes as a Missing Link in the Tidal Disruption Menu

NASA Astrophysics Data System (ADS)

Law-Smith, Jamie; MacLeod, Morgan; Guillochon, James; Macias, Phillip; Ramirez-Ruiz, Enrico

2017-06-01

We construct a menu of objects that can give rise to bright flares when disrupted by massive black holes (BHs), ranging from planets to evolved stars. Through their tidal disruption, main sequence and evolved stars can effectively probe the existence of otherwise quiescent supermassive BHs, and white dwarfs can probe intermediate mass BHs. Many low-mass white dwarfs possess extended hydrogen envelopes, which allow for the production of prompt flares in disruptive encounters with moderately massive BHs of 105-{10}7 {M}⊙ —masses that may constitute the majority of massive BHs by number. These objects are a missing link in two ways: (1) for probing moderately massive BHs and (2) for understanding the hydrodynamics of the disruption of objects with tenuous envelopes. A flare arising from the tidal disruption of a 0.17 {M}⊙ white dwarf by a {10}5 {M}⊙ {BH} reaches a maximum between 0.6 and 11 days, with a peak fallback rate that is usually super-Eddington and results in a flare that is likely brighter than a typical tidal disruption event. Encounters stripping only the envelope can provide hydrogen-only fallback, while encounters disrupting the core evolve from H- to He-rich fallback. While most tidal disruption candidates observed thus far are consistent with the disruptions of main sequence stars, the rapid timescales of nuclear transients such as Dougie and PTF10iya are naturally explained by the disruption of low-mass white dwarfs. As the number of observed flares continues to increase, the menu presented here will be essential for characterizing nuclear BHs and their environments through tidal disruptions.

Main sequence models for massive zero-metal stars

NASA Technical Reports Server (NTRS)

Cary, N.

1974-01-01

Zero-age main-sequence models for stars of 20, 10, 5, and 2 solar masses with no heavy elements are constructed for three different possible primordial helium abundances: Y=0.00, Y=0.23, and Y=0.30. The latter two values of Y bracket the range of primordial helium abundances cited by Wagoner. With the exceptions of the two 20 solar mass models that contain helium, these models are found to be self-consistent in the sense that the formation of carbon through the triple-alpha process during premain sequence contraction is not sufficient to bring the CN cycle into competition with the proton-proton chain on the ZAMS. The zero-metal models of the present study have higher surface and central temperatures, higher central densities, smaller radii, and smaller convective cores than do the population I models with the same masses.

End of the Line for a Star like Ours

ERIC Educational Resources Information Center

Riddle, Bob

2010-01-01

Stars of different masses have varying life spans, with the more massive stars "burning out" more quickly than stars of lower masses. How or what they do when they burn out also varies, depending on the mass of the star. All stars are called "main sequence stars" as they continue fusing hydrogen and staying in a state of equilibrium--a balance…

Reconstructing evolutionary trees in parallel for massive sequences.

PubMed

Zou, Quan; Wan, Shixiang; Zeng, Xiangxiang; Ma, Zhanshan Sam

2017-12-14

Building the evolutionary trees for massive unaligned DNA sequences is challenging and crucial. However, reconstructing evolutionary tree for ultra-large sequences is hard. Massive multiple sequence alignment is also challenging and time/space consuming. Hadoop and Spark are developed recently, which bring spring light for the classical computational biology problems. In this paper, we tried to solve the multiple sequence alignment and evolutionary reconstruction in parallel. HPTree, which is developed in this paper, can deal with big DNA sequence files quickly. It works well on the >1GB files, and gets better performance than other evolutionary reconstruction tools. Users could use HPTree for reonstructing evolutioanry trees on the computer clusters or cloud platform (eg. Amazon Cloud). HPTree could help on population evolution research and metagenomics analysis. In this paper, we employ the Hadoop and Spark platform and design an evolutionary tree reconstruction software tool for unaligned massive DNA sequences. Clustering and multiple sequence alignment are done in parallel. Neighbour-joining model was employed for the evolutionary tree building. We opened our software together with source codes via http://lab.malab.cn/soft/HPtree/ .

Forensic Loci Allele Database (FLAD): Automatically generated, permanent identifiers for sequenced forensic alleles.

PubMed

Van Neste, Christophe; Van Criekinge, Wim; Deforce, Dieter; Van Nieuwerburgh, Filip

2016-01-01

It is difficult to predict if and when massively parallel sequencing of forensic STR loci will replace capillary electrophoresis as the new standard technology in forensic genetics. The main benefits of sequencing are increased multiplexing scales and SNP detection. There is not yet a consensus on how sequenced profiles should be reported. We present the Forensic Loci Allele Database (FLAD) service, made freely available on http://forensic.ugent.be/FLAD/. It offers permanent identifiers for sequenced forensic alleles (STR or SNP) and their microvariants for use in forensic allele nomenclature. Analogous to Genbank, its aim is to provide permanent identifiers for forensically relevant allele sequences. Researchers that are developing forensic sequencing kits or are performing population studies, can register on http://forensic.ugent.be/FLAD/ and add loci and allele sequences with a short and simple application interface (API). Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Mass functions for globular cluster main sequences based on CCD photometry and stellar models

NASA Astrophysics Data System (ADS)

McClure, Robert D.; Vandenberg, Don A.; Smith, Graeme H.; Fahlman, Gregory G.; Richer, Harvey B.; Hesser, James E.; Harris, William E.; Stetson, Peter B.; Bell, R. A.

1986-08-01

Main-sequence luminosity functions constructed from CCD observations of globular clusters reveal a strong trend in slope with metal abundance. Theoretical luminosity functions constructed from VandenBerg and Bell's (1985) isochrones have been fitted to the observations and reveal a trend between x, the power-law index of the mass function, and metal abundance. The most metal-poor clusters require an index of about x = 2.5, whereas the most metal-rich clusters exhibit an index of x of roughly -0.5. The luminosity functions for two sparse clusters, E3 and Pal 5, are distinct from those of the more massive clusters, in that they show a turndown which is possibly a result of mass loss or tidal disruption.

The environmental impacts on the star formation main sequence: An Hα study of the newly discovered rich cluster at z = 1.52

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

Koyama, Yusei; Kodama, Tadayuki; Tadaki, Ken-ichi

2014-07-01

We report the discovery of a strong over-density of galaxies in the field of a radio galaxy at z = 1.52 (4C 65.22) based on our broadband and narrow-band (Hα) photometry with the Subaru Telescope. We find that Hα emitters are located in the outskirts of the density peak (cluster core) dominated by passive red-sequence galaxies. This resembles the situation in lower-redshift clusters, suggesting that the newly discovered structure is a well-evolved rich galaxy cluster at z = 1.5. Our data suggest that the color-density and stellar mass-density relations are already in place at z ∼ 1.5, mostly driven bymore » the passive red massive galaxies residing within r{sub c} ≲ 200 kpc from the cluster core. These environmental trends almost disappear when we consider only star-forming (SF) galaxies. We do not find SFR-density or SSFR-density relations amongst SF galaxies, and the location of the SF main sequence does not significantly change with environment. Nevertheless, we find a tentative hint that star-bursting galaxies (up-scattered objects from the main sequence) are preferentially located in a small group at ∼1 Mpc away from the main body of the cluster. We also argue that the scatter of the SF main sequence could be dependent on the distance to the nearest neighboring galaxy.« less

The Effects of Rotation on the Main-sequence Turnoff of Intermediate-age Massive Star Clusters

NASA Astrophysics Data System (ADS)

Yang, Wuming; Bi, Shaolan; Meng, Xiangcun; Liu, Zhie

2013-10-01

The double or extended main-sequence turnoffs (MSTOs) in the color-magnitude diagram (CMD) of intermediate-age massive star clusters in the Large Magellanic Cloud are generally interpreted as age spreads of a few hundred Myr. However, such age spreads do not exist in younger clusters (i.e., 40-300 Myr), which challenges this interpretation. The effects of rotation on the MSTOs of star clusters have been studied in previous works, but the results obtained are conflicting. Compared with previous works, we consider the effects of rotation on the main-sequence lifetime of stars. Our calculations show that rotating models have a fainter and redder MSTO with respect to non-rotating counterparts with ages between about 0.8 and 2.2 Gyr, but have a brighter and bluer MSTO when age is larger than 2.4 Gyr. The spread of the MSTO caused by a typical rotation rate is equivalent to the effect of an age spread of about 200 Myr. Rotation could lead to the double or extended MSTOs in the CMD of the star clusters with ages between about 0.8 and 2.2 Gyr. However, the extension is not significant, and it does not even exist in younger clusters. If the efficiency of the mixing were high enough, the effects of the mixing would counteract the effect of the centrifugal support in the late stage of evolution, and the rotationally induced extension would disappear in the old intermediate-age star clusters, but younger clusters would have an extended MSTO. Moreover, the effects of rotation might aid in understanding the formation of some "multiple populations" in globular clusters.

Formation of the black-hole binary M33 X-7 through mass exchange in a tight massive system.

PubMed

Valsecchi, Francesca; Glebbeek, Evert; Farr, Will M; Fragos, Tassos; Willems, Bart; Orosz, Jerome A; Liu, Jifeng; Kalogera, Vassiliki

2010-11-04

The X-ray source M33 X-7 in the nearby galaxy Messier 33 is among the most massive X-ray binary stellar systems known, hosting a rapidly spinning, 15.65M(⊙) black hole orbiting an underluminous, 70M(⊙) main-sequence companion in a slightly eccentric 3.45-day orbit (M(⊙), solar mass). Although post-main-sequence mass transfer explains the masses and tight orbit, it leaves unexplained the observed X-ray luminosity, the star's underluminosity, the black hole's spin and the orbital eccentricity. A common envelope phase, or rotational mixing, could explain the orbit, but the former would lead to a merger and the latter to an overluminous companion. A merger would also ensue if mass transfer to the black hole were invoked for its spin-up. Here we report simulations of evolutionary tracks which reveal that if M33 X-7 started as a primary body of 85M(⊙)-99M(⊙) and a secondary body of 28M(⊙)-32M(⊙), in a 2.8-3.1-d orbit, its observed properties can be consistently explained. In this model, the main-sequence primary transfers part of its envelope to the secondary and loses the rest in a wind; it ends its life as a ∼16M(⊙) helium star with an iron-nickel core that collapses to a black hole (with or without an accompanying supernova). The release of binding energy, and possibly collapse asymmetries, 'kick' the nascent black hole into an eccentric orbit. Wind accretion explains the X-ray luminosity, and the black-hole spin can be natal.

Revising the Evolutionary Stage of HD 163899: The Effects of Convective Overshooting and Rotation

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

Ostrowski, Jakub; Daszyńska-Daszkiewicz, Jadwiga; Cugier, Henryk, E-mail: ostrowski@astro.uni.wroc.pl

We revise the evolutionary status of the B-type supergiant HD 163899 based on the new determinations of the mass–luminosity ratio, effective temperature, and rotational velocity, as well as on the interpretation of the oscillation spectrum of the star. The observed value of the nitrogen-to-carbon abundance fixes the value of the rotation rate of the star. Now, more massive models are strongly preferred than those previously considered, and it is very likely that the star is still in the main-sequence stage. The rotationally induced mixing manifests as the nitrogen overabundance in the atmosphere, which agrees with our analysis of the HARPSmore » spectra. Thus, HD 163899 probably belongs to a group of evolved nitrogen-rich main-sequence stars.« less

Theory of Bipolar Outflows from Accreting Hot Stars

NASA Astrophysics Data System (ADS)

Konigl, A.

1996-05-01

There is a growing number of observational indicators for the presence of bipolar outflows in massive, young stellar objects that are still accreting mass as part of their formation process. In particular, there is evidence that the outflows from these objects can attain higher velocities and kinetic luminosities than their lower-mass counterparts. Furthermore, the higher-mass objects appear to smoothly continue the correlation found in T Tauri stars between outflow and accretion signatures, and in several cases there are direct clues to the existence of a disk from optical and infrared spectroscopy. These results suggest that the disk--outflow connection found in low-mass pre--main-sequence stars extends to more massive objects, and that a similar physical mechanism may drive the outflows in both cases. In this presentation, I first critically examine the observational basis for this hypothesis, considering, among other things, the possibility that several low-luminosity outflows might occasionally masquerade as a single flow from a luminous object, and the effects that the radiation field of a hot star could have on the spectroscopic diagnostics of an accretion-driven outflow. I then go on to consider how the commonly invoked centrifugally driven wind models of bipolar outflows in low-mass stars would be affected by the various physical processes (such as photoionization, photoevaporation, radiation pressure, and stellar wind ram pressure) that operate in higher-mass stars. I conclude by mentioning some of the tantalizing questions that one could hope to address as this young field of research continues to develop (for example: is there a high-mass analog of the FU Orionis outburst phenomenon? Could one use observations of progressively more massive, and hence less convective, stars to elucidate the role of stellar magnetic fields in the accretion and outflow processes? Would it be possible to observationally identify massive stars that have reached the main sequence while they were still accreting? Does the evolution of protostellar disks differ in low-mass and high-mass objects?).

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.

A new Böhm-Vitense gap in the temperature range 5560 to 5610 K in the main sequence hm-Vitense gap in the main sequence

NASA Astrophysics Data System (ADS)

Kovtyukh, V. V.; Soubiran, C.; Belik, S. I.

2004-12-01

Highly precise temperatures (σ = 10-15 K) have been determined from line depth ratios for a set of 248 F-K field dwarfs of about solar metallicity (-0.5 < [Fe/H] < +0.4), based on high resolution (R=42 000), high S/N echelle spectra. A new gap has been discovered in the distribution of stars on the Main Sequence in the temperature range 5560 to 5610 K. This gap coincides with a jump in the microturbulent velocity Vt and the well-known Li depression near 5600 K in field dwarfs and open clusters. As the principal cause of the observed discontinuities in stellar properties we propose the penetration of the convective zone into the inner layers of stars slightly less massive than the Sun and related to it, a change in the temperature gradient. Based on spectra collected with the ELODIE spectrograph at the 1.93-m telescope of the Observatoire de Haute-Provence (France). Full Table 1 is only available in electronic form at http://www.edpsciences.org

Superluminous Spiral Galaxies

NASA Astrophysics Data System (ADS)

Ogle, Patrick M.; Lanz, Lauranne; Nader, Cyril; Helou, George

2016-02-01

We report the discovery of spiral galaxies that are as optically luminous as elliptical brightest cluster galaxies, with r-band monochromatic luminosity Lr = 8-14L* (4.3-7.5 × 1044 erg s-1). These super spiral galaxies are also giant and massive, with diameter D = 57-134 kpc and stellar mass Mstars = 0.3-3.4 × 1011M⊙. We find 53 super spirals out of a complete sample of 1616 SDSS galaxies with redshift z < 0.3 and Lr > 8L*. The closest example is found at z = 0.089. We use existing photometry to estimate their stellar masses and star formation rates (SFRs). The SDSS and Wide-field Infrared Survey Explorer colors are consistent with normal star-forming spirals on the blue sequence. However, the extreme masses and rapid SFRs of 5-65 M⊙ yr-1 place super spirals in a sparsely populated region of parameter space, above the star-forming main sequence of disk galaxies. Super spirals occupy a diverse range of environments, from isolation to cluster centers. We find four super spiral galaxy systems that are late-stage major mergers—a possible clue to their formation. We suggest that super spirals are a remnant population of unquenched, massive disk galaxies. They may eventually become massive lenticular galaxies after they are cut off from their gas supply and their disks fade.

Geology, ore facies and sulfur isotopes geochemistry of the Nudeh Besshi-type volcanogenic massive sulfide deposit, southwest Sabzevar basin, Iran

NASA Astrophysics Data System (ADS)

Maghfouri, Sajjad; Rastad, Ebrahim; Mousivand, Fardin; Lin, Ye; Zaw, Khin

2016-08-01

The southwest Sabzevar basin is placed in the southwestern part of a crustal domain known as the Sabzevar zone, at the north of Central Iranian microcontinent. This basin hosts abundant mineral deposits; particularly of the Mn exhalative and Cu-Zn volcanogenic massive sulfide (VMS) types. The evolution of this basin is governed by the Neo-tethys oceanic crust subduction beneath the Central Iranian microcontinent and by the resulting continental arc (Sanandaj-Sirjan) and back-arc (Sabzevar-Naien). This evolution followed two major sequences: (I) Lower Late Cretaceous Volcano-Sedimentary Sequence (LLCVSS), which is indicated by fine-grained siliciclastic sediments, gray basic coarse-grained different pyroclastic rocks and bimodal volcanism. During this stage, tuff-hosted stratiform, exhalative Mn deposits (Nudeh, Benesbourd, Ferizy and Goft), oxide Cu deposits (Garab and Ferizy) and Cu-Zn VMS (Nudeh, Chun and Lala) deposits formed. (II) Upper Late Cretaceous Sedimentary Dominated Sequence (ULCSS), including pelagic limestone, marly tuff, silty limestone and marl with minor andesitic tuff rocks. The economically most important Mn (Zakeri and Cheshmeh-sefid) deposits of Sabzevar zone occur within the marly tuff of this sequence. The Nudeh Cu-Zn volcanogenic massive sulfide (VMS) deposit is situated in the LLCVSS. The host-rock of deposits consists of alkali olivine basalt flow and tuffaceous silty sandstone. Mineralization occurs as stratiform blanket-like and tabular orebodies. Based on ore body structure, mineralogy, and ore fabric, we recognize three different ore facies in the Nudeh deposit: (1) a stringer zone, consisting of a discordant mineralization of sulfides forming a stockwork of sulfide-bearing quartz veins cutting the footwall volcano-sedimentary rocks; (2) a massive ore, consisting of massive replacement pyrite, chalcopyrite, sphalerite and Friedrichite with magnetite; (3) bedded ore, with laminated to disseminated pyrite, and chalcopyrite. Chloritization, silicification, sericitization and epidotization are the main wall-rock alterations; alteration intensity increases towards the stringer zone. The δ34S composition of the sulfides ranges from -1.5‰ to +3.69‰ with a general increase of δ34S ratios of massive ore facies to stockwork zone. The heavier values indicate that some of the sulfur was derived from seawater sulfate that was ultimately thermochemically reduced in deep hydrothermal reaction zones. Sulfur isotopes, along with sedimentological, textural, petrological, mineralogical, and geochemical evidences, suggest that this deposit should be classified as a Besshi-type VMS ore deposit.

The Formation and Gravitational-wave Detection of Massive Stellar Black Hole Binaries

NASA Astrophysics Data System (ADS)

Belczynski, Krzysztof; Buonanno, Alessandra; Cantiello, Matteo; Fryer, Chris L.; Holz, Daniel E.; Mandel, Ilya; Miller, M. Coleman; Walczak, Marek

2014-07-01

If binaries consisting of two ~100 M ⊙ black holes exist, they would serve as extraordinarily powerful gravitational-wave sources, detectable to redshifts of z ~ 2 with the advanced LIGO/Virgo ground-based detectors. Large uncertainties about the evolution of massive stars preclude definitive rate predictions for mergers of these massive black holes. We show that rates as high as hundreds of detections per year, or as low as no detections whatsoever, are both possible. It was thought that the only way to produce these massive binaries was via dynamical interactions in dense stellar systems. This view has been challenged by the recent discovery of several >~ 150 M ⊙ stars in the R136 region of the Large Magellanic Cloud. Current models predict that when stars of this mass leave the main sequence, their expansion is insufficient to allow common envelope evolution to efficiently reduce the orbital separation. The resulting black hole-black hole binary remains too wide to be able to coalesce within a Hubble time. If this assessment is correct, isolated very massive binaries do not evolve to be gravitational-wave sources. However, other formation channels exist. For example, the high multiplicity of massive stars, and their common formation in relatively dense stellar associations, opens up dynamical channels for massive black hole mergers (e.g., via Kozai cycles or repeated binary-single interactions). We identify key physical factors that shape the population of very massive black hole-black hole binaries. Advanced gravitational-wave detectors will provide important constraints on the formation and evolution of very massive stars.

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).

Statistical method to compare massive parallel sequencing pipelines.

PubMed

Elsensohn, M H; Leblay, N; Dimassi, S; Campan-Fournier, A; Labalme, A; Roucher-Boulez, F; Sanlaville, D; Lesca, G; Bardel, C; Roy, P

2017-03-01

Today, sequencing is frequently carried out by Massive Parallel Sequencing (MPS) that cuts drastically sequencing time and expenses. Nevertheless, Sanger sequencing remains the main validation method to confirm the presence of variants. The analysis of MPS data involves the development of several bioinformatic tools, academic or commercial. We present here a statistical method to compare MPS pipelines and test it in a comparison between an academic (BWA-GATK) and a commercial pipeline (TMAP-NextGENe®), with and without reference to a gold standard (here, Sanger sequencing), on a panel of 41 genes in 43 epileptic patients. This method used the number of variants to fit log-linear models for pairwise agreements between pipelines. To assess the heterogeneity of the margins and the odds ratios of agreement, four log-linear models were used: a full model, a homogeneous-margin model, a model with single odds ratio for all patients, and a model with single intercept. Then a log-linear mixed model was fitted considering the biological variability as a random effect. Among the 390,339 base-pairs sequenced, TMAP-NextGENe® and BWA-GATK found, on average, 2253.49 and 1857.14 variants (single nucleotide variants and indels), respectively. Against the gold standard, the pipelines had similar sensitivities (63.47% vs. 63.42%) and close but significantly different specificities (99.57% vs. 99.65%; p < 0.001). Same-trend results were obtained when only single nucleotide variants were considered (99.98% specificity and 76.81% sensitivity for both pipelines). The method allows thus pipeline comparison and selection. It is generalizable to all types of MPS data and all pipelines.

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.

The tidal disruption of a star by a massive black hole

NASA Technical Reports Server (NTRS)

Evans, Charles R.; Kochanek, Christopher S.

1989-01-01

Results are reported from a three-dimensional numerical calculation of the tidal disruption of a low-mass main-sequence star on a parabolic orbit around a massive black hole (Mh = 10 to the 6th stellar mass). The postdisruption evolution is followed until hydrodynamic forces becomes negligible and the liberated gas becomes ballistic. Also given is the rate at which bound mass returns to pericenter after orbiting the hole once. The processes that determine the time scale to circularize the debris orbits and allow an accretion torus to form are discussed. This time scale and the time scales for radiative cooling and accretion inflow determine the onset and duration of the subsequent flare in the AGN luminosity.

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.

The volcanic-sedimentary sequence of the Lousal deposit, Iberian Pyrite Belt (Portugal)

NASA Astrophysics Data System (ADS)

Rosa, Carlos; Rosa, Diogo; Matos, Joao; Relvas, Jorge

2010-05-01

The Iberian Pyrite Belt (IPB) is a massive sulfide province that is located in the south of Portugal and Spain, and hosts more than 90 massive sulfide deposits that amount to more than 1850 million metric tonnes of sulfide ore (Tornos, 2006). The ore deposits size, vary from ~1Mt to >100Mt (e.g. Neves Corvo and Aljustrel in Portugal, and Rio Tinto and Tharsis in Spain). The ore deposits are hosted by a submarine sedimentary and volcanic, felsic dominated, succession that constitutes the Upper Devonian to Lower Carboniferous Volcanic and Sedimentary Complex (VSC). The VSC ranges in thickness from approximately 600 to 1300 m (Tornos 2006). The VSC overlies the Phyllite-Quartzite Group (PQ) (Upper Devonian, base unknown) and is overlain by the Baixo Alentejo Flysch Group (Lower to Upper Carboniferous). The Lousal massive sulfide deposit is located in the western part of the IPB and occurs mostly interbedded with black mudstone. The VSC sequence at Lousal mine consists of a mudstone and quartzite sequence (PQ Group) in the lower part of the succession, over which a thick sequence of rhyolitic lavas (>300 m) occurs. Above the rhyolitic lavas there is a thick sequence of black and grey mudstone that hosts the massive sulfide ore bodies, and a rhyolitic sill. The upper part of the VSC sequence consists of a thick mudstone interval that hosts two thick basaltic units, locally with pillows. The rhyolites have small coherent cores, locally with flow bands, that grade to surrounding massive clastic intervals, with large lateral extent. The clasts show jigsaw-fit arrangement in many places and have planar or curviplanar margins and locally are perlitic at the margin. The top contact of these units is in most locations not exposed, which makes difficult to interpret the mode of emplacement. However, the thick clastic intervals, above described, are in accordance with quenching of volcanic glass with abundant water and therefore indicate that quenching of the rhyolites was the dominant fragmentation mechanism. Unlike many locations of the IPB, fiamme-rich pyroclastic units were not identified at Lousal. The ore deposits occur in close proximity with this volcanic centre that may have driven hydrothermal circulation that led to ore formation. The volcanic rocks show intense chloritic alteration, indicating that the mineralizing event occurred after most of the rhyolitic units have emplaced. The massive sulfides show abundant sedimentary structures which is not typical in the massive sulfide deposits of the IPB. The Lousal 50 Mt massive sulfide deposit consists of at least 11 ore bodies and was exploited until 1988 mainly for pyrite. The ores mined averaged 0.7% Cu, 0.8%Pb e 1.4%Zn (Strauss, 1971). These relatively low base metal grades led to an evaluation of the contents and distribution of high-tech element in the ore bodies, which would improve the economic viability of mining the deposit. This evaluation is currently focusing on the distribution and mineralogy of selenium, as ores mined in the past were known to be rich in this element. This work benefits from research projects INCA (PTDC/CTE-GIN/67027/2006; Characterization of crucial mineral resources for the development of renewable energy technologies: The Iberian Pyrite Belt ores as a source of indium and other high-technology elements) and project ARCHYMEDES II (POCTI/CTA/45873/2002), both funded by the Fundação para a Ciência e Tecnologia. REFERENCES Strauss, G.K., 1970. Sobre la geologia de la provincia piritifera del Suroeste de la Peninsula Iberica y sus yacimientos, en especial sobre la mina de pirita de Lousal (Portugal): Memoria del IGME 77, 1-266. Tornos, F., 2006. Environment of formation and styles of volcanogenic massive sulfides: The Iberian Pyrite Belt. Ore Geology Reviews 28, 259-307.

Increasing the reach of forensic genetics with massively parallel sequencing.

PubMed

Budowle, Bruce; Schmedes, Sarah E; Wendt, Frank R

2017-09-01

The field of forensic genetics has made great strides in the analysis of biological evidence related to criminal and civil matters. More so, the discipline has set a standard of performance and quality in the forensic sciences. The advent of massively parallel sequencing will allow the field to expand its capabilities substantially. This review describes the salient features of massively parallel sequencing and how it can impact forensic genetics. The features of this technology offer increased number and types of genetic markers that can be analyzed, higher throughput of samples, and the capability of targeting different organisms, all by one unifying methodology. While there are many applications, three are described where massively parallel sequencing will have immediate impact: molecular autopsy, microbial forensics and differentiation of monozygotic twins. The intent of this review is to expose the forensic science community to the potential enhancements that have or are soon to arrive and demonstrate the continued expansion the field of forensic genetics and its service in the investigation of legal matters.

Wolf-Rayet stars as starting points or as endpoints of the evolution of massive stars?

NASA Technical Reports Server (NTRS)

Lamers, H. J. G. L. M.; Maeder, A.; Schmutz, W.; Cassinelli, J. P.

1991-01-01

The paper investigates the evidence for the two interpretations of Wolf-Rayet stars suggested in the literature: (1) massive premain-sequence stars with disks and (2) massive stars which have lost most of their H-rich layers in a stellar wind is investigated. The abundance determinations which are done in two different ways and which lead to different conclusions are discussed. The composition is solar, which would suggest interpretation (1), or the CNO abundances are strongly anomalous, which would suggest interpretation (2). Results from evolutionary calculations, stellar statistics, the existence of Ofpe/WN9 transition stars and W-R stars with evolved companions show overwhelming evidence that W-R stars are not premain-sequence stars but that they are in a late stage of evolution. Moreover, the fact that W-R stars are usually in clear regions of space, whereas massive premain-sequence stars are embedded in ultracompact H II regions also shows that W-R stars are not young premain-sequence stars.

The formation and gravitational-wave detection of massive stellar black hole binaries

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

Belczynski, Krzysztof; Walczak, Marek; Buonanno, Alessandra

2014-07-10

If binaries consisting of two ∼100 M{sub ☉} black holes exist, they would serve as extraordinarily powerful gravitational-wave sources, detectable to redshifts of z ∼ 2 with the advanced LIGO/Virgo ground-based detectors. Large uncertainties about the evolution of massive stars preclude definitive rate predictions for mergers of these massive black holes. We show that rates as high as hundreds of detections per year, or as low as no detections whatsoever, are both possible. It was thought that the only way to produce these massive binaries was via dynamical interactions in dense stellar systems. This view has been challenged by themore » recent discovery of several ≳ 150 M{sub ☉} stars in the R136 region of the Large Magellanic Cloud. Current models predict that when stars of this mass leave the main sequence, their expansion is insufficient to allow common envelope evolution to efficiently reduce the orbital separation. The resulting black hole-black hole binary remains too wide to be able to coalesce within a Hubble time. If this assessment is correct, isolated very massive binaries do not evolve to be gravitational-wave sources. However, other formation channels exist. For example, the high multiplicity of massive stars, and their common formation in relatively dense stellar associations, opens up dynamical channels for massive black hole mergers (e.g., via Kozai cycles or repeated binary-single interactions). We identify key physical factors that shape the population of very massive black hole-black hole binaries. Advanced gravitational-wave detectors will provide important constraints on the formation and evolution of very massive stars.« less

Hα3: an Hα imaging survey of HI selected galaxies from ALFALFA. VI. The role of bars in quenching star formation from z = 3 to the present epoch

NASA Astrophysics Data System (ADS)

Gavazzi, G.; Consolandi, G.; Dotti, M.; Fanali, R.; Fossati, M.; Fumagalli, M.; Viscardi, E.; Savorgnan, G.; Boselli, A.; Gutiérrez, L.; Hernández Toledo, H.; Giovanelli, R.; Haynes, M. P.

2015-08-01

A growing body of evidence indicates that the star formation rate per unit stellar mass (sSFR) decreases with increasing mass in normal main-sequence star-forming galaxies. Many processes have been advocated as being responsible for this trend (also known as mass quenching), e.g., feedback from active galactic nuclei (AGNs), and the formation of classical bulges. In order to improve our insight into the mechanisms regulating the star formation in normal star-forming galaxies across cosmic epochs, we determine a refined star formation versus stellar mass relation in the local Universe. To this end we use the Hα narrow-band imaging follow-up survey (Hα3) of field galaxies selected from the HI Arecibo Legacy Fast ALFA Survey (ALFALFA) in the Coma and Local superclusters. By complementing this local determination with high-redshift measurements from the literature, we reconstruct the star formation history of main-sequence galaxies as a function of stellar mass from the present epoch up to z = 3. In agreement with previous studies, our analysis shows that quenching mechanisms occur above a threshold stellar mass Mknee that evolves with redshift as ∝ (1 + z)2. Moreover, visual morphological classification of individual objects in our local sample reveals a sharp increase in the fraction of visually classified strong bars with mass, hinting that strong bars may contribute to the observed downturn in the sSFR above Mknee. We test this hypothesis using a simple but physically motivated numerical model for bar formation, finding that strong bars can rapidly quench star formation in the central few kpc of field galaxies. We conclude that strong bars contribute significantly to the red colors observed in the inner parts of massive galaxies, although additional mechanisms are likely required to quench the star formation in the outer regions of massive spiral galaxies. Intriguingly, when we extrapolate our model to higher redshifts, we successfully recover the observed redshift evolution for Mknee. Our study highlights how the formation of strong bars in massive galaxies is an important mechanism in regulating the redshift evolution of the sSFR for field main-sequence galaxies. Based on observations taken at the observatory of San Pedro Martir (Baja California, Mexico), belonging to the Mexican Observatorio Astronómico Nacional.

Massively parallel whole genome amplification for single-cell sequencing using droplet microfluidics.

PubMed

Hosokawa, Masahito; Nishikawa, Yohei; Kogawa, Masato; Takeyama, Haruko

2017-07-12

Massively parallel single-cell genome sequencing is required to further understand genetic diversities in complex biological systems. Whole genome amplification (WGA) is the first step for single-cell sequencing, but its throughput and accuracy are insufficient in conventional reaction platforms. Here, we introduce single droplet multiple displacement amplification (sd-MDA), a method that enables massively parallel amplification of single cell genomes while maintaining sequence accuracy and specificity. Tens of thousands of single cells are compartmentalized in millions of picoliter droplets and then subjected to lysis and WGA by passive droplet fusion in microfluidic channels. Because single cells are isolated in compartments, their genomes are amplified to saturation without contamination. This enables the high-throughput acquisition of contamination-free and cell specific sequence reads from single cells (21,000 single-cells/h), resulting in enhancement of the sequence data quality compared to conventional methods. This method allowed WGA of both single bacterial cells and human cancer cells. The obtained sequencing coverage rivals those of conventional techniques with superior sequence quality. In addition, we also demonstrate de novo assembly of uncultured soil bacteria and obtain draft genomes from single cell sequencing. This sd-MDA is promising for flexible and scalable use in single-cell sequencing.

Genotypic tropism testing by massively parallel sequencing: qualitative and quantitative analysis.

PubMed

Däumer, Martin; Kaiser, Rolf; Klein, Rolf; Lengauer, Thomas; Thiele, Bernhard; Thielen, Alexander

2011-05-13

Inferring viral tropism from genotype is a fast and inexpensive alternative to phenotypic testing. While being highly predictive when performed on clonal samples, sensitivity of predicting CXCR4-using (X4) variants drops substantially in clinical isolates. This is mainly attributed to minor variants not detected by standard bulk-sequencing. Massively parallel sequencing (MPS) detects single clones thereby being much more sensitive. Using this technology we wanted to improve genotypic prediction of coreceptor usage. Plasma samples from 55 antiretroviral-treated patients tested for coreceptor usage with the Monogram Trofile Assay were sequenced with standard population-based approaches. Fourteen of these samples were selected for further analysis with MPS. Tropism was predicted from each sequence with geno2pheno[coreceptor]. Prediction based on bulk-sequencing yielded 59.1% sensitivity and 90.9% specificity compared to the trofile assay. With MPS, 7600 reads were generated on average per isolate. Minorities of sequences with high confidence in CXCR4-usage were found in all samples, irrespective of phenotype. When using the default false-positive-rate of geno2pheno[coreceptor] (10%), and defining a minority cutoff of 5%, the results were concordant in all but one isolate. The combination of MPS and coreceptor usage prediction results in a fast and accurate alternative to phenotypic assays. The detection of X4-viruses in all isolates suggests that coreceptor usage as well as fitness of minorities is important for therapy outcome. The high sensitivity of this technology in combination with a quantitative description of the viral population may allow implementing meaningful cutoffs for predicting response to CCR5-antagonists in the presence of X4-minorities.

WNL Stars - the Most Massive Stars in the Universe?

NASA Astrophysics Data System (ADS)

Schnurr, Olivier; Moffat, Anthony F. J.; St-Louis, Nicole; Skalkowski, Gwenael; Niemela, Virpi; Shara, Michael M.

2001-08-01

We propose to carry out an intensive and complete time-dependent spectroscopic study of all 47 known WNL stars in the LMC, an ideal laboratory to study the effect of lower ambient metallicity, Z, on stellar evolution. WNL stars are luminous, cooler WR stars of the nitrogen sequence. This will allow us to: 1) determine the binary frequency. The Roche-lobe overflow (RLOF) mechanism in close binaries is predicted to be responsible for the formation of a significant fraction of WR stars in low Z environments such as the LMC. 2) determine the masses. Since some of these stars (denoted WNL(h) or WNLh) are supposed to be hydrogen-burning and thus main-sequence stellar objects of the highest luminosity, they may be the most massive stars known. 3) study wind-wind collision (WWC) effects in WR+O binaries involving very luminous WNL stars with strong winds. Interesting in itself as a high-energy phenomenon, WWC is in competition with conservative RLOF (i.e. mass transfer to the secondary star), and therefore has to be taken into account in this context.

WNLh Stars - The Most Massive Stars in the Universe?

NASA Astrophysics Data System (ADS)

Schnurr, Olivier; St-Louis, Nicole; Moffat, Anthony F. J.; Foellmi, Cedric

2002-08-01

We propose to conclude our intensive and complete time-dependent spectroscopic study of all 47 known WNL stars in the LMC, an ideal laboratory to study the effect of lower ambient metallicity, Z, on stellar evolution. WNL stars are luminous, cooler WR stars of the nitrogen sequence. This will allow us to: 1) determine the binary frequency. The Roche-lobe overflow (RLOF) mechanism in close binaries is predicted to be responsible for the formation of a significant fraction of WR stars in low Z environments such as the LMC. 2) determine the masses. Since some of these stars (denoted WNL(h) or WNLh) are supposed to be hydrogen-burning and thus main-sequence stellar objects of the highest luminosity, they may be the most massive stars known. 3) study wind-wind collision (WWC) effects in WR+O binaries involving very luminous WNL stars with strong winds. Interesting in itself as a high-energy phenomenon, WWC is in competition with conservative RLOF (i.e. mass transfer to the secondary star), and therefore has to be taken into account in this context.

Talks also presented at the Symposium

NASA Astrophysics Data System (ADS)

Eldridge, J. J.; Bray, J. C.; McClelland, L. A. S.; Xiao, L.

2017-11-01

Internal rotation and magnetism are key ingredients that largely affect explosive stellar deaths (Supernovae and Gamma Ray Bursts) and the properties of stellar remnants (White Dwarfs, Neutron Stars and Black Holes). However, the study of these subtle internal stellar properties has been limited to very indirect proxies. In the last couple of years, exciting asteroseismic results have been obtained by the Kepler satellite. Among these results are 1) The direct measure of the degree of radial differential rotation in many evolved low-mass stars and in a few massive stars, and 2) The detection of strong (>105 G) internal magnetic fields in thousands of red giant stars that had convective cores during their main sequence. I will discuss the impact of these important findings for our understanding of massive star evolution.

A Statistical Study of Brown Dwarf Companions from the SDSS-III MARVELS Survey

NASA Astrophysics Data System (ADS)

Grieves, Nolan; Ge, Jian; Thomas, Neil; Ma, Bo; De Lee, Nathan M.; Lee, Brian L.; Fleming, Scott W.; Sithajan, Sirinrat; Varosi, Frank; Liu, Jian; Zhao, Bo; Li, Rui; Agol, Eric; MARVELS Team

2016-01-01

We present 23 new Brown Dwarf (BD) candidates from the Multi-object APO Radial-Velocity Exoplanet Large-Area Survey (MARVELS) of the Sloan Digital Sky Survey III (SDSS-III). The BD candidates were selected from the processed MARVELS data using the latest University of Florida 2D pipeline, which shows significant improvement and reduction of systematic errors over the 1D pipeline results included in the SDSS Data Release 12. This sample is the largest BD yield from a single radial velocity survey. Of the 23 candidates, 18 are around main sequence stars and 5 are around giant stars. Given a giant contamination rate of ~24% for the MARVELS survey, we find a BD occurrence rate around main sequence stars of ~0.7%, which agrees with previous studies and confirms the BD desert, while the BD occurrence rate around the MARVELS giant stars is ~0.6%. Preliminary results show that our new candidates around solar type stars support a two population hypothesis, where BDs are divided at a mass of ~42.5 MJup. BDs less massive than 42.5 MJup have eccentricity distributions consistent with planet-planet scattering models, where BDs more massive than 42.5 MJup have both period and eccentricity distributions similar to that of stellar binaries. Special Brown Dwarf systems such as multiple BD systems and highly eccentric BDs will also be presented.

Stability of metal-rich very massive stars

NASA Astrophysics Data System (ADS)

Goodman, J.; White, Christopher J.

2016-02-01

We revisit the stability of very massive non-rotating main-sequence stars at solar metallicity, with the goal of understanding whether radial pulsations set a physical upper limit to stellar mass. Models of up to 938 solar masses are constructed with the MESA code, and their linear stability in the fundamental mode, assumed to be the most dangerous, is analysed with a fully non-adiabatic method. Models above 100 M⊙ have extended tenuous atmospheres (`shelves') that affect the stability of the fundamental. Even when positive, this growth rate is small, in agreement with previous results. We argue that small growth rates lead to saturation at small amplitudes that are not dangerous to the star. A mechanism for saturation is demonstrated involving non-linear parametric coupling to short-wavelength g-modes and the damping of the latter by radiative diffusion. The shelves are subject to much more rapidly growing strange modes. This also agrees with previous results but is extended here to higher masses. The strange modes probably saturate via shocks rather than mode coupling but have very small amplitudes in the core, where almost all of the stellar mass resides. Although our stellar models are hydrostatic, the structure of their outer parts suggests that optically thick winds, driven by some combination of radiation pressure, transonic convection, and strange modes, are more likely than pulsation in the fundamental mode to limit the main-sequence lifetime.

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

The Role of Rotation in the Evolution of Massive Stars

NASA Technical Reports Server (NTRS)

Heap, Sara R.; Lanz, Thierry M.

2002-01-01

Recent evolutionary models of massive stars predict important effects of rotation including: increasing the rate of mass-loss; lowering the effective gravity; altering the evolutionary track on the HRD; extending the main-sequence phase (both on the HR diagram and in time); and mixing of CNO-processed elements up to the stellar surface. Observations suggest that rotation is a more important factor at lower metallicities because of higher initial rotational velocities and weaker winds. This makes the SMC, a low-metallicity galaxy (Z= 0.2 solar Z), an excellent environment for discerning the role of rotation in massive stars. We report on a FUSE + STIS + optical spectral analysis of 17 O-type stars in the SMC, where we found an enormous range in N abundances. Three stars in the sample have the same (low) CN abundances as the nebular material out of which they formed, namely C = 0.085 solar C and N = 0.034 solar N. However, more than half show N approx. solar N, an enrichment factor of 30X! Such unexpectedly high levels of N have ramifications for the evolution of massive stars including precursors to supernovae. They also raise questions about the sources of nitrogen in the early universe.

EXTENDED STAR FORMATION IN THE INTERMEDIATE-AGE LARGE MAGELLANIC CLOUD STAR CLUSTER NGC 2209

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

Keller, Stefan C.; Mackey, A. Dougal; Da Costa, Gary S.

2012-12-10

We present observations of the 1 Gyr old star cluster NGC 2209 in the Large Magellanic Cloud made with the GMOS imager on the Gemini South Telescope. These observations show that the cluster exhibits a main-sequence turnoff that spans a broader range in luminosity than can be explained by a single-aged stellar population. This places NGC 2209 amongst a growing list of intermediate-age (1-3 Gyr) clusters that show evidence for extended or multiple epochs of star formation of between 50 and 460 Myr in extent. The extended main-sequence turnoff observed in NGC 2209 is a confirmation of the prediction inmore » Keller et al. made on the basis of the cluster's large core radius. We propose that secondary star formation is a defining feature of the evolution of massive star clusters. Dissolution of lower mass clusters through evaporation results in only clusters that have experienced secondary star formation surviving for a Hubble time, thus providing a natural connection between the extended main-sequence turnoff phenomenon and the ubiquitous light-element abundance ranges seen in the ancient Galactic globular clusters.« less

Domains of pulsational instability of low-frequency modes in rotating upper main sequence stars

NASA Astrophysics Data System (ADS)

Szewczuk, Wojciech; Daszyńska-Daszkiewicz, Jadwiga

2017-07-01

We determine instability domains on the Hertzsprung-Russell diagram for rotating main sequence stars with masses of 2-20 M⊙. The effects of the Coriolis force are treated wihin the traditional approximation. High-order g modes with harmonic degrees ℓ up to 4 and mixed gravity-Rossby modes with |m| up to 4 are considered. We include the effects of rotation in wider instability strips for a given ℓ compared to the non-rotating case and in an extension of the pulsational instability to hotter and more massive models. We present results for a fixed value of the initial rotation velocity as well as for a fixed ratio of the angular rotation frequency to its critical value. Moreover, we check how the initial hydrogen abundance, metallicity, overshooting from the convective core and opacity affect the pulsational instability domains. The effect of rotation on the period spacing is also discussed.

A slightly more massive young Sun as an explanation for warm temperatures on early Mars.

PubMed

Whitmire, D P; Doyle, L R; Reynolds, R T; Matese, J J

1995-03-25

The valley network channels on the heavily cratered ancient surface of Mars suggest the presence of liquid water approximately 3.8 Gyr ago. However, the implied warm climate is difficult to explain in the context of the standard solar model, even allowing for the maximum CO2 greenhouse heating. In this paper we investigate the astronomical and planetary implications of a nonstandard solar model in which the zero-age, main-sequence Sun had a mass of 1.05 +/- 0.02 M solar. The excess mass was subsequently lost in a solar wind during the first 1.2(-0.2, +0.4) Gyr of the Sun's main sequence phase. The implied mass-loss rate of 4(+3, -2) x 10(-11) M solar yr-1, or about 10(3)x that of the current Sun, may be detectable in several nearby young solar type stars.

Massively Parallel Sequencing Detected a Mutation in the MFN2 Gene Missed by Sanger Sequencing Due to a Primer Mismatch on an SNP Site.

PubMed

Neupauerová, Jana; Grečmalová, Dagmar; Seeman, Pavel; Laššuthová, Petra

2016-05-01

We describe a patient with early onset severe axonal Charcot-Marie-Tooth disease (CMT2) with dominant inheritance, in whom Sanger sequencing failed to detect a mutation in the mitofusin 2 (MFN2) gene because of a single nucleotide polymorphism (rs2236057) under the PCR primer sequence. The severe early onset phenotype and the family history with severely affected mother (died after delivery) was very suggestive of CMT2A and this suspicion was finally confirmed by a MFN2 mutation. The mutation p.His361Tyr was later detected in the patient by massively parallel sequencing with a gene panel for hereditary neuropathies. According to this information, new primers for amplification and sequencing were designed which bind away from the polymorphic sites of the patient's DNA. Sanger sequencing with these new primers then confirmed the heterozygous mutation in the MFN2 gene in this patient. This case report shows that massively parallel sequencing may in some rare cases be more sensitive than Sanger sequencing and highlights the importance of accurate primer design which requires special attention. © 2016 John Wiley & Sons Ltd/University College London.

Increasing phylogenetic resolution at low taxonomic levels using massively parallel sequencing of chloroplast genomes

Treesearch

Matthew Parks; Richard Cronn; Aaron Liston

2009-01-01

We reconstruct the infrageneric phylogeny of Pinus from 37 nearly-complete chloroplast genomes (average 109 kilobases each of an approximately 120 kilobase genome) generated using multiplexed massively parallel sequencing. We found that 30/33 ingroup nodes resolved wlth > 95-percent bootstrap support; this is a substantial improvement relative...

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.

Discovery of magnetic A supergiants: the descendants of magnetic main-sequence B stars

NASA Astrophysics Data System (ADS)

Neiner, Coralie; Oksala, Mary E.; Georgy, Cyril; Przybilla, Norbert; Mathis, Stéphane; Wade, Gregg; Kondrak, Matthias; Fossati, Luca; Blazère, Aurore; Buysschaert, Bram; Grunhut, Jason

2017-10-01

In the context of the high resolution, high signal-to-noise ratio, high sensitivity, spectropolarimetric survey BritePol, which complements observations by the BRITE constellation of nanosatellites for asteroseismology, we are looking for and measuring the magnetic field of all stars brighter than V = 4. In this paper, we present circularly polarized spectra obtained with HarpsPol at ESO in La Silla (Chile) and ESPaDOnS at CFHT (Hawaii) for three hot evolved stars: ι Car, HR 3890 and ɛ CMa. We detected a magnetic field in all three stars. Each star has been observed several times to confirm the magnetic detections and check for variability. The stellar parameters of the three objects were determined and their evolutionary status was ascertained employing evolution models computed with the Geneva code. ɛ CMa was already known and is confirmed to be magnetic, but our modelling indicates that it is located near the end of the main sequence, I.e. it is still in a core hydrogen burning phase. ι Car and HR 3890 are the first discoveries of magnetic hot supergiants located well after the end of the main sequence on the Hertzsprung-Russell diagram. These stars are probably the descendants of main-sequence magnetic massive stars. Their current field strength (a few G) is compatible with magnetic flux conservation during stellar evolution. These results provide observational constraints for the development of future evolutionary models of hot stars including a fossil magnetic field.

VizieR Online Data Catalog: Evolution of rotating very massive LC stars (Kohler, 2015)

NASA Astrophysics Data System (ADS)

Kohler, K.; Langer, N.; de Koter, A.; de Mink, S. E.; Crowther, P. A.; Evans, C. J.; Grafener, G.; Sana, H.; Sanyal, D.; Schneider, F. R. N.; Vink, J. S.

2014-11-01

A dense model grid with chemical composition appropriate for the Large Magellanic Cloud is presented. A one-dimensional hydrodynamic stellar evolution code was used to compute our models on the main sequence, taking into account rotation, transport of angular momentum by magnetic fields and stellar wind mass loss. We present stellar evolution models with initial masses of 70-500M⊙ and with initial surface rotational velocities of 0-550km/s. (2 data files).

Spectroscopic and physical parameters of Galactic O-type stars. III. Mass discrepancy and rotational mixing

NASA Astrophysics Data System (ADS)

Markova, N.; Puls, J.; Langer, N.

2018-05-01

Context. Massive stars play a key role in the evolution of galaxies and our Universe. Aims: Our goal is to compare observed and predicted properties of single Galactic O stars to identify and constrain uncertain physical parameters and processes in stellar evolution and atmosphere models. Methods: We used a sample of 53 objects of all luminosity classes and with spectral types from O3 to O9.7. For 30 of these, we determined the main photospheric and wind parameters, including projected rotational rates accounting for macroturbulence, and He and N surface abundances, using optical spectroscopy and applying the model atmosphere code FASTWIND. For the remaining objects, similar data from the literature, based on analyses by means of the CMFGEN code, were used instead. The properties of our sample were then compared to published predictions based on two grids of single massive star evolution models that include rotationally induced mixing. Results: Any of the considered model grids face problem in simultaneously reproducing the stellar masses, equatorial gravities, surface abundances, and rotation rates of our sample stars. The spectroscopic masses derived for objects below 30 M⊙ tend to be smaller than the evolutionary ones, no matter which of the two grids have been used as a reference. While this result may indicate the need to improve the model atmosphere calculations (e.g. regarding the treatment of turbulent pressure), our analysis shows that the established mass problem cannot be fully explained in terms of inaccurate parameters obtained by quantitative spectroscopy or inadequate model values of Vrot on the zero age main sequence. Within each luminosity class, we find a close correlation of N surface abundance and luminosity, and a stronger N enrichment in more massive and evolved O stars. Additionally, we also find a correlation of the surface nitrogen and helium abundances. The large number of nitrogen-enriched stars above 30 M⊙ argues for rotationally induced mixing as the most likely explanation. However, none of the considered models can match the observed trends correctly, especially in the high mass regime. Conclusions: We confirm mass discrepancy for objects in the low mass O-star regime. We conclude that the rotationally induced mixing of helium to the stellar surface is too strong in some of the models. We also suggest that present inadequacies of the models to represent the N enrichment in more massive stars with relatively slow rotation might be related (among other issues) to problematic efficiencies of rotational mixing. We are left with a picture in which invoking binarity and magnetic fields is required to achieve a more complete agreement of the observed surface properties of a population of massive main-sequence stars with corresponding evolutionary models.

De novo assembly of human genomes with massively parallel short read sequencing.

PubMed

Li, Ruiqiang; Zhu, Hongmei; Ruan, Jue; Qian, Wubin; Fang, Xiaodong; Shi, Zhongbin; Li, Yingrui; Li, Shengting; Shan, Gao; Kristiansen, Karsten; Li, Songgang; Yang, Huanming; Wang, Jian; Wang, Jun

2010-02-01

Next-generation massively parallel DNA sequencing technologies provide ultrahigh throughput at a substantially lower unit data cost; however, the data are very short read length sequences, making de novo assembly extremely challenging. Here, we describe a novel method for de novo assembly of large genomes from short read sequences. We successfully assembled both the Asian and African human genome sequences, achieving an N50 contig size of 7.4 and 5.9 kilobases (kb) and scaffold of 446.3 and 61.9 kb, respectively. The development of this de novo short read assembly method creates new opportunities for building reference sequences and carrying out accurate analyses of unexplored genomes in a cost-effective way.

Models of the circumstellar medium of evolving, massive runaway stars moving through the Galactic plane

NASA Astrophysics Data System (ADS)

Meyer, D. M.-A.; Mackey, J.; Langer, N.; Gvaramadze, V. V.; Mignone, A.; Izzard, R. G.; Kaper, L.

2014-11-01

At least 5 per cent of the massive stars are moving supersonically through the interstellar medium (ISM) and are expected to produce a stellar wind bow shock. We explore how the mass-loss and space velocity of massive runaway stars affect the morphology of their bow shocks. We run two-dimensional axisymmetric hydrodynamical simulations following the evolution of the circumstellar medium of these stars in the Galactic plane from the main sequence to the red supergiant phase. We find that thermal conduction is an important process governing the shape, size and structure of the bow shocks around hot stars, and that they have an optical luminosity mainly produced by forbidden lines, e.g. [O III]. The Hα emission of the bow shocks around hot stars originates from near their contact discontinuity. The Hα emission of bow shocks around cool stars originates from their forward shock, and is too faint to be observed for the bow shocks that we simulate. The emission of optically thin radiation mainly comes from the shocked ISM material. All bow shock models are brighter in the infrared, i.e. the infrared is the most appropriate waveband to search for bow shocks. Our study suggests that the infrared emission comes from near the contact discontinuity for bow shocks of hot stars and from the inner region of shocked wind for bow shocks around cool stars. We predict that, in the Galactic plane, the brightest, i.e. the most easily detectable bow shocks are produced by high-mass stars moving with small space velocities.

Massive star evolution and SN 1987A

NASA Technical Reports Server (NTRS)

Arnett, David

1991-01-01

The evolution of massive stars through hydrogen and helium burning is addressed. A set of stellar evolutionary sequences for mass/solar mass of 15, 20, and 25, and metallicity of 0.002, 0.005, 0.007, 0.010, and 0.20 are presented; semiconvection is restricted to operating slower than the local thermal time scale. Using these sequences, simple models of the massive star content of the LMC are found to agree moderately well with the new observational data of Fitzpatrick and Garmany (1990). LMC supergiants were detected only in their postmain-sequence phases, so that 5-10 times more massive stars are there but not identified as such. It is argued that SN 1987A exhibits the normal evolution of a single star of about 20 solar mases having LMC abundances. Despite the variety of envelope behavior, the structure of the core at collapse is rather similar for the stars of a given mass. Variations due to different rates of mass loss are likely to be larger than those due to composition.

CLAST: CUDA implemented large-scale alignment search tool.

PubMed

Yano, Masahiro; Mori, Hiroshi; Akiyama, Yutaka; Yamada, Takuji; Kurokawa, Ken

2014-12-11

Metagenomics is a powerful methodology to study microbial communities, but it is highly dependent on nucleotide sequence similarity searching against sequence databases. Metagenomic analyses with next-generation sequencing technologies produce enormous numbers of reads from microbial communities, and many reads are derived from microbes whose genomes have not yet been sequenced, limiting the usefulness of existing sequence similarity search tools. Therefore, there is a clear need for a sequence similarity search tool that can rapidly detect weak similarity in large datasets. We developed a tool, which we named CLAST (CUDA implemented large-scale alignment search tool), that enables analyses of millions of reads and thousands of reference genome sequences, and runs on NVIDIA Fermi architecture graphics processing units. CLAST has four main advantages over existing alignment tools. First, CLAST was capable of identifying sequence similarities ~80.8 times faster than BLAST and 9.6 times faster than BLAT. Second, CLAST executes global alignment as the default (local alignment is also an option), enabling CLAST to assign reads to taxonomic and functional groups based on evolutionarily distant nucleotide sequences with high accuracy. Third, CLAST does not need a preprocessed sequence database like Burrows-Wheeler Transform-based tools, and this enables CLAST to incorporate large, frequently updated sequence databases. Fourth, CLAST requires <2 GB of main memory, making it possible to run CLAST on a standard desktop computer or server node. CLAST achieved very high speed (similar to the Burrows-Wheeler Transform-based Bowtie 2 for long reads) and sensitivity (equal to BLAST, BLAT, and FR-HIT) without the need for extensive database preprocessing or a specialized computing platform. Our results demonstrate that CLAST has the potential to be one of the most powerful and realistic approaches to analyze the massive amount of sequence data from next-generation sequencing technologies.

Tracking the roots of cellulase hyperproduction by the fungus Trichoderma reesei using massively parallel DNA sequencing

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

Le Crom, Stphane; Schackwitz, Wendy; Pennacchiod, Len

2009-09-22

Trichoderma reesei (teleomorph Hypocrea jecorina) is the main industrial source of cellulases and hemicellulases harnessed for the hydrolysis of biomass to simple sugars, which can then be converted to biofuels, such as ethanol, and other chemicals. The highly productive strains in use today were generated by classical mutagenesis. To learn how cellulase production was improved by these techniques, we performed massively parallel sequencing to identify mutations in the genomes of two hyperproducing strains (NG14, and its direct improved descendant, RUT C30). We detected a surprisingly high number of mutagenic events: 223 single nucleotides variants, 15 small deletions or insertions andmore » 18 larger deletions leading to the loss of more than 100 kb of genomic DNA. From these events we report previously undocumented non-synonymous mutations in 43 genes that are mainly involved in nuclear transport, mRNA stability, transcription, secretion/vacuolar targeting, and metabolism. This homogeneity of functional categories suggests that multiple changes are necessary to improve cellulase production and not simply a few clear-cut mutagenic events. Phenotype microarrays show that some of these mutations result in strong changes in the carbon assimilation pattern of the two mutants with respect to the wild type strain QM6a. Our analysis provides the first genome-wide insights into the changes induced by classical mutagenesis in a filamentous fungus, and suggests new areas for the generation of enhanced T. reesei strains for industrial applications such as biofuel production.« less

Modelling the multiwavelength emission of Ultraluminous X-ray sources accreting above Eddington

NASA Astrophysics Data System (ADS)

Ambrosi, E.; Zampieri, L.

2017-10-01

Understanding ULXs requires a comprehensive modelling of their multiwavelength emission properties. We compute the optical-through-X-ray emission of ULXs assuming that they are binary systems with stellar-mass or massive-stellar Black Holes and considering the possibility that a non-standard disc sets in when the mass transfer rate (\\dot{M}) becomes highly super-Eddington. The emission model is applied to self-consistent simulations of ULX binaries. We compare our color-magnitude diagrams (CMDs) with those in the literature and find significant differences in the post main sequence evolution. When the donor is on the main-sequence and \\dot{M} is mildly super-Eddington, the behaviour of the system is similar to that found in previous investigations. However, when the donor star leaves the main-sequence and \\dot{M} becomes highly super-Eddington, the optical luminosity of the system is systematically larger and the colours show a markedly different evolution. The emission properties depend on the variable shielding of the outer disc and donor induced by the changing inner disc structure. We determine also the effects caused by the onset of a strong optically thick outflow. CMDs in various photometric systems are compared to the observed properties of the optical counterparts of several ULXs, obtaining updated constraints on their donor mass and accretion rate.

JUPITER WILL BECOME A HOT JUPITER: CONSEQUENCES OF POST-MAIN-SEQUENCE STELLAR EVOLUTION ON GAS GIANT PLANETS

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

Spiegel, David S.; Madhusudhan, Nikku, E-mail: dave@ias.edu, E-mail: Nikku.Madhusudhan@yale.edu

When the Sun ascends the red giant branch (RGB), its luminosity will increase and all the planets will receive much greater irradiation than they do now. Jupiter, in particular, might end up more highly irradiated than the hot Neptune GJ 436b and, hence, could appropriately be termed a 'hot Jupiter'. When their stars go through the RGB or asymptotic giant branch stages, many of the currently known Jupiter-mass planets in several-AU orbits will receive levels of irradiation comparable to the hot Jupiters, which will transiently increase their atmospheric temperatures to {approx}1000 K or more. Furthermore, massive planets around post-main-sequence starsmore » could accrete a non-negligible amount of material from the enhanced stellar winds, thereby significantly altering their atmospheric chemistry as well as causing a significant accretion luminosity during the epochs of most intense stellar mass loss. Future generations of infrared observatories might be able to probe the thermal and chemical structure of such hot Jupiters' atmospheres. Finally, we argue that, unlike their main-sequence analogs (whose zonal winds are thought to be organized in only a few broad, planetary-scale jets), red-giant hot Jupiters should have multiple, narrow jets of zonal winds and efficient day-night redistribution.« less

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.

Stellar populations dominated by massive stars in dusty starburst galaxies across cosmic time

NASA Astrophysics Data System (ADS)

Zhang, Zhi-Yu; Romano, D.; Ivison, R. J.; Papadopoulos, Padelis P.; Matteucci, F.

2018-06-01

All measurements of cosmic star formation must assume an initial distribution of stellar masses—the stellar initial mass function—in order to extrapolate from the star-formation rate measured for typically rare, massive stars (of more than eight solar masses) to the total star-formation rate across the full stellar mass spectrum1. The shape of the stellar initial mass function in various galaxy populations underpins our understanding of the formation and evolution of galaxies across cosmic time2. Classical determinations of the stellar initial mass function in local galaxies are traditionally made at ultraviolet, optical and near-infrared wavelengths, which cannot be probed in dust-obscured galaxies2,3, especially distant starbursts, whose apparent star-formation rates are hundreds to thousands of times higher than in the Milky Way, selected at submillimetre (rest-frame far-infrared) wavelengths4,5. The 13C/18O isotope abundance ratio in the cold molecular gas—which can be probed via the rotational transitions of the 13CO and C18O isotopologues—is a very sensitive index of the stellar initial mass function, with its determination immune to the pernicious effects of dust. Here we report observations of 13CO and C18O emission for a sample of four dust-enshrouded starbursts at redshifts of approximately two to three, and find unambiguous evidence for a top-heavy stellar initial mass function in all of them. A low 13CO/C18O ratio for all our targets—alongside a well tested, detailed chemical evolution model benchmarked on the Milky Way6—implies that there are considerably more massive stars in starburst events than in ordinary star-forming spiral galaxies. This can bring these extraordinary starbursts closer to the `main sequence' of star-forming galaxies7, although such main-sequence galaxies may not be immune to changes in initial stellar mass function, depending on their star-formation densities.

Stellar populations dominated by massive stars in dusty starburst galaxies across cosmic time.

PubMed

Zhang, Zhi-Yu; Romano, D; Ivison, R J; Papadopoulos, Padelis P; Matteucci, F

2018-06-01

All measurements of cosmic star formation must assume an initial distribution of stellar masses-the stellar initial mass function-in order to extrapolate from the star-formation rate measured for typically rare, massive stars (of more than eight solar masses) to the total star-formation rate across the full stellar mass spectrum 1 . The shape of the stellar initial mass function in various galaxy populations underpins our understanding of the formation and evolution of galaxies across cosmic time 2 . Classical determinations of the stellar initial mass function in local galaxies are traditionally made at ultraviolet, optical and near-infrared wavelengths, which cannot be probed in dust-obscured galaxies 2,3 , especially distant starbursts, whose apparent star-formation rates are hundreds to thousands of times higher than in the Milky Way, selected at submillimetre (rest-frame far-infrared) wavelengths 4,5 . The 13 C/ 18 O isotope abundance ratio in the cold molecular gas-which can be probed via the rotational transitions of the 13 CO and C 18 O isotopologues-is a very sensitive index of the stellar initial mass function, with its determination immune to the pernicious effects of dust. Here we report observations of 13 CO and C 18 O emission for a sample of four dust-enshrouded starbursts at redshifts of approximately two to three, and find unambiguous evidence for a top-heavy stellar initial mass function in all of them. A low 13 CO/C 18 O ratio for all our targets-alongside a well tested, detailed chemical evolution model benchmarked on the Milky Way 6 -implies that there are considerably more massive stars in starburst events than in ordinary star-forming spiral galaxies. This can bring these extraordinary starbursts closer to the 'main sequence' of star-forming galaxies 7 , although such main-sequence galaxies may not be immune to changes in initial stellar mass function, depending on their star-formation densities.

Classification and sedimentary characteristics of lacustrine hyperpycnal channels: Triassic outcrops in the south Ordos Basin, central China

NASA Astrophysics Data System (ADS)

Xian, Benzhong; Wang, Junhui; Gong, Chenglin; Yin, Yu; Chao, Chuzhi; Liu, Jianping; Zhang, Guodong; Yan, Qi

2018-06-01

Subaquatic channels are known as active conduits for the delivery of terrigenous sediments into related marine and lacustrine basins, as well as important targets for hydrocarbon exploration. Compared to submarine channels, lacustrine subaqueous channels created by hyperpycnal flows are understudied. Using well-exposed outcrops collected from three different locations in the southern Ordos Basin, central China, morphologies and architecture of a channelized hyperpycnal system were studied and classified. Six facies associations represent sedimentary processes from strong erosion by bedload dominated hyperpycnal flows, to transitional deposition jointly controlled by bedload and suspended-load dominated hyperpycnal flows, finally to deposition from suspended-load dominated hyperpycnal flows. On the basis of channel morphologies, infilling sediments and sedimentary processes, the documented channels can be classified into four main categories, which are erosional, bedload dominated, suspended-load dominated, and depositional channels. In very proximal and very distal locations, erosional channels and depositional channels serve as two end-members, while in middle areas, bedload-dominated channels and suspended-load dominated channels are transitional types. Erosional channels, as a response to strong erosion from bedload dominated hyperpycnal flows on upper slope, were mainly filled by mud interbedded with thin sand beds. As flow energy decreases, bedload dominated channels develop on middle slopes, which are characterized mainly by under- to balanced sediment infillings with cross-bedded sandstones and/or minor massive sandstones. Compared to bedload dominated channels, suspended-load dominated channels mainly develop in deeper water, and were filled mainly by massive or planar-laminated sandstones. Depositional channels, as a response to suspended-load dominated hyperpycnal flows in deep-water areas, are characterized by thin-medium bed classical turbidites with Bouma sequences and thin- to thick massive sandstones. Such evolution patterns of hyperpycnal channel systems are ascribed to the progressive decrease in flow capacity of hyperpycnal flows, and provide an adequate explanation for the basinward channelization behavior of hyperpycnal systems.

Observational studies of regions of massive star formation

NASA Astrophysics Data System (ADS)

Cooper, Heather Danielle Blythe

2013-03-01

Massive stars have a profound influence on their surroundings. However, relatively little is known about their formation. The study of massive star formation is hindered by a lack of observational evidence, primarily due to difficulties observing massive stars at early stages in their development. The Red MSX Source survey (RMS survey) is a valuable tool with which to address these issues. Near-infrared H- and K-band spectra were taken for 247 candidate massive young stellar objects (MYSOs), selected from the RMS survey. 195 (∼80%) of the targets are YSOs, of which 131 are massive YSOs (LBOL>5E3L⊙, M>8 M⊙). This is the largest spectroscopic study of massive YSOs to date. This study covers minimally obscured objects right through to very red, dusty sources. Almost all YSOs show some evidence for emission lines, though there is a wide variety of observed properties, with HI, H2 Fe II, and CO among the most commonly observed lines. Evidence for disks and outflows was frequently seen. Comparisons of Brγ and H2 emission with low mass YSOs suggest that the emission mechanism for these lines is the same for low-, intermediate-, and high-mass YSOs, i.e. high-mass YSOs appear to resemble scaled-up versions of low-mass YSOs. It was found that the YSOs form an evolutionary sequence, based on their spectra, consistent with the existing theoretical models. Type I YSOs have strong H2 emission, no ionized lines, and are redder than the other two subtypes. As such, these are considered to be the youngest sources. The Type III sources are bluest, and therefore considered to be the oldest subtype. They have strong H I lines and fluorescent Fe II 1.6878 μm emission. They may also have weak H2 emission. Type III sources may even be beginning to form a mini-H II region. XSHOOTER data from 10 Herbig Be stars were analysed. The evidence suggests that winds and disks are common among Herbig stars, as they are among their main sequence classical Be star counterparts. Line broadening was seen in many of the sources, though it was not possible to identify whether this was due to Stark broadening or electron scattering. The observations and analysis presented in this thesis are an important step forward for the field of massive star formation. They also have the potential to be a starting block for future work.

Combining stress transfer and source directivity: the case of the 2012 Emilia seismic sequence

PubMed Central

Convertito, Vincenzo; Catalli, Flaminia; Emolo, Antonio

2013-01-01

The Emilia seismic sequence (Northern Italy) started on May 2012 and caused 17 casualties, severe damage to dwellings and forced the closure of several factories. The total number of events recorded in one month was about 2100, with local magnitude ranging between 1.0 and 5.9. We investigate potential mechanisms (static and dynamic triggering) that may describe the evolution of the sequence. We consider rupture directivity in the dynamic strain field and observe that, for each main earthquake, its aftershocks and the subsequent large event occurred in an area characterized by higher dynamic strains and corresponding to the dominant rupture direction. We find that static stress redistribution alone is not capable of explaining the locations of subsequent events. We conclude that dynamic triggering played a significant role in driving the sequence. This triggering was also associated with a variation in permeability and a pore pressure increase in an area characterized by a massive presence of fluids. PMID:24177982

Supernova 1987A - the evolution from blue to red

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

Tuchman, Y.; Wheeler, J.C.

1989-09-01

The evolution of stars with mass comparable to that of the progenitor of SN 1987A from the main sequence to the Hayashi track is critically examined to determine why some models evolve to the red on nuclear time scales, some on thermal time scales, and some not at all. Thermal equilibrium solutions to a parametrized series of structural models with active hydrogen burning shells have two stable solutions with different T(eff) for the same helium core M(He) mass and a minimum M(He) below which no blue thermal equlibrium solution is possible. The dependence of the equilibrium solutions on stellar mass,more » envelope composition, and mass loss are investigated. The solutions quantitatively account for the 'gap' in the HR diagrams of massive stars in the Galaxy and LMC and suggest that the outer envelopes are not substantially enriched in helium during the first passage from the main sequence to the Hayashi track. 23 refs.« less

Theoretical studies of massive stars. I - Evolution of a 15-solar-mass star from the zero-age main sequence to neon ignition

NASA Technical Reports Server (NTRS)

Endal, A. S.

1975-01-01

The evolution of a star with mass 15 times that of the sun from the zero-age main sequence to neon ignition has been computed by the Henyey method. The hydrogen-rich envelope and all shell sources were explicitly included in the models. An algorithm has been developed for approximating the results of carbon burning, including the branching ratio for the C-12 + C-12 reaction and taking some secondary reactions into account. Penetration of the convective envelope into the core is found to be unimportant during the stages covered by the models. Energy transfer from the carbon-burning shell to the core by degenerate electron conduction becomes important after the core carbon-burning stage. Neon ignition will occur in a semidegenerate core and will lead to a mild 'flash.' Detailed numerical results are given in an appendix. Continuation of the calculations into later stages and variations with the total mass of the star will be discussed in later papers.

Role of APOE Isoforms in the Pathogenesis of TBI induced Alzheimer’s Disease

DTIC Science & Technology

2016-10-01

deletion, APOE targeted replacement, complex breeding, CCI model optimization, mRNA library generation, high throughput massive parallel sequencing...demonstrate that the lack of Abca1 increases amyloid plaques and decreased APOE protein levels in AD-model mice. In this proposal we will test the hypothesis...injury, inflammatory reaction, transcriptome, high throughput massive parallel sequencing, mRNA-seq., behavioral testing, memory impairment, recovery 3

High-Resolution Functional Mapping of the Venezuelan Equine Encephalitis Virus Genome by Insertional Mutagenesis and Massively Parallel Sequencing

DTIC Science & Technology

2010-10-14

High-Resolution Functional Mapping of the Venezuelan Equine Encephalitis Virus Genome by Insertional Mutagenesis and Massively Parallel Sequencing...Venezuelan equine encephalitis virus (VEEV) genome. We initially used a capillary electrophoresis method to gain insight into the role of the VEEV...Smith JM, Schmaljohn CS (2010) High-Resolution Functional Mapping of the Venezuelan Equine Encephalitis Virus Genome by Insertional Mutagenesis and

Massively Parallel DNA Sequencing Facilitates Diagnosis of Patients with Usher Syndrome Type 1

PubMed Central

Yoshimura, Hidekane; Iwasaki, Satoshi; Nishio, Shin-ya; Kumakawa, Kozo; Tono, Tetsuya; Kobayashi, Yumiko; Sato, Hiroaki; Nagai, Kyoko; Ishikawa, Kotaro; Ikezono, Tetsuo; Naito, Yasushi; Fukushima, Kunihiro; Oshikawa, Chie; Kimitsuki, Takashi; Nakanishi, Hiroshi; Usami, Shin-ichi

2014-01-01

Usher syndrome is an autosomal recessive disorder manifesting hearing loss, retinitis pigmentosa and vestibular dysfunction, and having three clinical subtypes. Usher syndrome type 1 is the most severe subtype due to its profound hearing loss, lack of vestibular responses, and retinitis pigmentosa that appears in prepuberty. Six of the corresponding genes have been identified, making early diagnosis through DNA testing possible, with many immediate and several long-term advantages for patients and their families. However, the conventional genetic techniques, such as direct sequence analysis, are both time-consuming and expensive. Targeted exon sequencing of selected genes using the massively parallel DNA sequencing technology will potentially enable us to systematically tackle previously intractable monogenic disorders and improve molecular diagnosis. Using this technique combined with direct sequence analysis, we screened 17 unrelated Usher syndrome type 1 patients and detected probable pathogenic variants in the 16 of them (94.1%) who carried at least one mutation. Seven patients had the MYO7A mutation (41.2%), which is the most common type in Japanese. Most of the mutations were detected by only the massively parallel DNA sequencing. We report here four patients, who had probable pathogenic mutations in two different Usher syndrome type 1 genes, and one case of MYO7A/PCDH15 digenic inheritance. This is the first report of Usher syndrome mutation analysis using massively parallel DNA sequencing and the frequency of Usher syndrome type 1 genes in Japanese. Mutation screening using this technique has the power to quickly identify mutations of many causative genes while maintaining cost-benefit performance. In addition, the simultaneous mutation analysis of large numbers of genes is useful for detecting mutations in different genes that are possibly disease modifiers or of digenic inheritance. PMID:24618850

Massively parallel DNA sequencing facilitates diagnosis of patients with Usher syndrome type 1.

PubMed

Yoshimura, Hidekane; Iwasaki, Satoshi; Nishio, Shin-Ya; Kumakawa, Kozo; Tono, Tetsuya; Kobayashi, Yumiko; Sato, Hiroaki; Nagai, Kyoko; Ishikawa, Kotaro; Ikezono, Tetsuo; Naito, Yasushi; Fukushima, Kunihiro; Oshikawa, Chie; Kimitsuki, Takashi; Nakanishi, Hiroshi; Usami, Shin-Ichi

2014-01-01

Usher syndrome is an autosomal recessive disorder manifesting hearing loss, retinitis pigmentosa and vestibular dysfunction, and having three clinical subtypes. Usher syndrome type 1 is the most severe subtype due to its profound hearing loss, lack of vestibular responses, and retinitis pigmentosa that appears in prepuberty. Six of the corresponding genes have been identified, making early diagnosis through DNA testing possible, with many immediate and several long-term advantages for patients and their families. However, the conventional genetic techniques, such as direct sequence analysis, are both time-consuming and expensive. Targeted exon sequencing of selected genes using the massively parallel DNA sequencing technology will potentially enable us to systematically tackle previously intractable monogenic disorders and improve molecular diagnosis. Using this technique combined with direct sequence analysis, we screened 17 unrelated Usher syndrome type 1 patients and detected probable pathogenic variants in the 16 of them (94.1%) who carried at least one mutation. Seven patients had the MYO7A mutation (41.2%), which is the most common type in Japanese. Most of the mutations were detected by only the massively parallel DNA sequencing. We report here four patients, who had probable pathogenic mutations in two different Usher syndrome type 1 genes, and one case of MYO7A/PCDH15 digenic inheritance. This is the first report of Usher syndrome mutation analysis using massively parallel DNA sequencing and the frequency of Usher syndrome type 1 genes in Japanese. Mutation screening using this technique has the power to quickly identify mutations of many causative genes while maintaining cost-benefit performance. In addition, the simultaneous mutation analysis of large numbers of genes is useful for detecting mutations in different genes that are possibly disease modifiers or of digenic inheritance.

Star Formation in the Orion Nebula Cluster

NASA Astrophysics Data System (ADS)

Palla, Francesco; Stahler, Steven W.

1999-11-01

We study the record of star formation activity within the dense cluster associated with the Orion Nebula. The bolometric luminosity function of 900 visible members is well matched by a simplified theoretical model for cluster formation. This model assumes that stars are produced at a constant rate and distributed according to the field-star initial mass function. Our best-fit age for the system, within this framework, is 2×106 yr. To undertake a more detailed analysis, we present a new set of theoretical pre-main-sequence tracks. These cover all masses from 0.1 to 6.0 Msolar, and start from a realistic stellar birthline. The tracks end along a zero-age main-sequence that is in excellent agreement with the empirical one. As a further aid to cluster studies, we offer an heuristic procedure for the correction of pre-main-sequence luminosities and ages to account for the effects of unresolved binary companions. The Orion Nebula stars fall neatly between our birthline and zero-age main-sequence in the H-R diagram. All those more massive than about 8 Msolar lie close to the main sequence, as also predicted by theory. After accounting for the finite sensitivity of the underlying observations, we confirm that the population between 0.4 and 6.0 Msolar roughly follows a standard initial mass function. We see no evidence for a turnover at lower masses. We next use our tracks to compile stellar ages, also between 0.4 and 6.0 Msolar. Our age histogram reveals that star formation began at a low level some 107 yr ago and has gradually accelerated to the present epoch. The period of most active formation is indeed confined to a few×106 yr, and has recently ended with gas dispersal from the Trapezium. We argue that the acceleration in stellar births, which extends over a wide range in mass, reflects the gravitational contraction of the parent cloud spawning this cluster.

The Stellar Population Associated with the IRAS Source 16132-5039

NASA Astrophysics Data System (ADS)

Roman-Lopes, A.; Abraham, Z.

2004-05-01

We report the discovery of a young massive stellar cluster and infrared nebula in the direction of the CS molecular cloud associated with the IRAS point source 16132-5039. Analysis of mid-infrared images from the more accurate Midcourse Space Experiment catalog reveals that there are two independent components associated with the IRAS source. The integral of the spectral energy distribution for these components between 8.28 and 100 μm gives lower limits for the bolometric luminosity of the embedded objects of 8.7×104 and 9×103 Lsolar, which correspond to zero-age main-sequence O8 and B0.5 stars, respectively. The number of Lyman continuum photons expected from the stars that lie along the reddening line for early-type stars is about 1.7×1049 s-1, enough to produce the detected flux densities at 5 GHz. The near-infrared spectrum of the nebula increases with frequency, implying that free-free emission cannot be the main source of the extended luminosity, from which we conclude that the observed emission must be mainly dust-scattered light. A comparison of the cluster described in this paper with the young stellar cluster associated with the IRAS source 16177-5018, which is located at the same distance and in the same direction, shows that the mean visual absorption of the newly discovered cluster is about 10 mag smaller and that it contains less massive stars, suggesting that it was formed from a less massive molecular cloud. Based on observations made at the Laboratório Nacional de Astrofisica, Ministério da Ciência e Tecnologia, Brazil.

The rapid evolution of molecular genetic diagnostics in neuromuscular diseases.

PubMed

Volk, Alexander E; Kubisch, Christian

2017-10-01

The development of massively parallel sequencing (MPS) has revolutionized molecular genetic diagnostics in monogenic disorders. The present review gives a brief overview of different MPS-based approaches used in clinical diagnostics of neuromuscular disorders (NMDs) and highlights their advantages and limitations. MPS-based approaches like gene panel sequencing, (whole) exome sequencing, (whole) genome sequencing, and RNA sequencing have been used to identify the genetic cause in NMDs. Although gene panel sequencing has evolved as a standard test for heterogeneous diseases, it is still debated, mainly because of financial issues and unsolved problems of variant interpretation, whether genome sequencing (and to a lesser extent also exome sequencing) of single patients can already be regarded as routine diagnostics. However, it has been shown that the inclusion of parents and additional family members often leads to a substantial increase in the diagnostic yield in exome-wide/genome-wide MPS approaches. In addition, MPS-based RNA sequencing just enters the research and diagnostic scene. Next-generation sequencing increasingly enables the detection of the genetic cause in highly heterogeneous diseases like NMDs in an efficient and affordable way. Gene panel sequencing and family-based exome sequencing have been proven as potent and cost-efficient diagnostic tools. Although clinical validation and interpretation of genome sequencing is still challenging, diagnostic RNA sequencing represents a promising tool to bypass some hurdles of diagnostics using genomic DNA.

CANDELS+3D-HST: Compact SFGs at z ∼ 2-3, the progenitors of the first quiescent galaxies

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

Barro, G.; Faber, S. M.; Koo, D. C.

We analyze the star-forming and structural properties of 45 massive (log(M/M{sub ☉}) >10) compact star-forming galaxies (SFGs) at 2 < z < 3 to explore whether they are progenitors of compact quiescent galaxies at z ∼ 2. The optical/NIR and far-IR Spitzer/Herschel colors indicate that most compact SFGs are heavily obscured. Nearly half (47%) host an X-ray-bright active galactic nucleus (AGN). In contrast, only about 10% of other massive galaxies at that time host AGNs. Compact SFGs have centrally concentrated light profiles and spheroidal morphologies similar to quiescent galaxies and are thus strikingly different from other SFGs, which typically aremore » disk-like and sometimes clumpy or irregular. Most compact SFGs lie either within the star formation rate (SFR)-mass main sequence (65%) or below it (30%), on the expected evolutionary path toward quiescent galaxies. These results show conclusively that galaxies become more compact before they lose their gas and dust, quenching star formation. Using extensive HST photometry from CANDELS and grism spectroscopy from the 3D-HST survey, we model their stellar populations with either exponentially declining (τ) star formation histories (SFHs) or physically motivated SFHs drawn from semianalytic models (SAMs). SAMs predict longer formation timescales and older ages ∼2 Gyr, which are nearly twice as old as the estimates of the τ models. Both models yield good spectral energy distribution fits, indicating that the systematic uncertainty in the age due to degeneracies in the SFH is of that order of magnitude. However, SAM SFHs better match the observed slope and zero point of the SFR-mass main sequence. Contrary to expectations, some low-mass compact SFGs (log(M/M{sub ☉}) =10-10.6) have younger ages but lower specific SFRs than that of more massive galaxies, suggesting that the low-mass galaxies reach the red sequence faster. If the progenitors of compact SFGs are extended SFGs, state-of-the-art SAMs show that mergers and disk instabilities (DIs) are both able to shrink galaxies, but DIs are more frequent (60% versus 40%) and form more concentrated galaxies. We confirm this result via high-resolution hydrodynamic simulations.« less

Tidal dissipation in rotating low-mass stars and implications for the orbital evolution of close-in planets. I. From the PMS to the RGB at solar metallicity

NASA Astrophysics Data System (ADS)

Gallet, F.; Bolmont, E.; Mathis, S.; Charbonnel, C.; Amard, L.

2017-08-01

Context. Star-planet interactions must be taken into account in stellar models to understand the dynamical evolution of close-in planets. The dependence of the tidal interactions on the structural and rotational evolution of the star is of particular importance and should be correctly treated. Aims: We quantify how tidal dissipation in the convective envelope of rotating low-mass stars evolves from the pre-main sequence up to the red-giant branch depending on the initial stellar mass. We investigate the consequences of this evolution on planetary orbital evolution. Methods: We couple the tidal dissipation formalism previously described to the stellar evolution code STAREVOL and apply this coupling to rotating stars with masses between 0.3 and 1.4 M⊙. As a first step, this formalism assumes a simplified bi-layer stellar structure with corresponding averaged densities for the radiative core and the convective envelope. We use a frequency-averaged treatment of the dissipation of tidal inertial waves in the convection zone (but neglect the dissipation of tidal gravity waves in the radiation zone). In addition, we generalize a recent work by following the orbital evolution of close-in planets using the new tidal dissipation predictions for advanced phases of stellar evolution. Results: On the pre-main sequence the evolution of tidal dissipation is controlled by the evolution of the internal structure of the contracting star. On the main sequence it is strongly driven by the variation of surface rotation that is impacted by magnetized stellar winds braking. The main effect of taking into account the rotational evolution of the stars is to lower the tidal dissipation strength by about four orders of magnitude on the main sequence, compared to a normalized dissipation rate that only takes into account structural changes. Conclusions: The evolution of the dissipation strongly depends on the evolution of the internal structure and rotation of the star. From the pre-main sequence up to the tip of the red-giant branch, it varies by several orders of magnitude, with strong consequences for the orbital evolution of close-in massive planets. These effects are the strongest during the pre-main sequence, implying that the planets are mainly sensitive to the star's early history.

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

Ogle, Patrick M.; Lanz, Lauranne; Nader, Cyril

We report the discovery of spiral galaxies that are as optically luminous as elliptical brightest cluster galaxies, with r-band monochromatic luminosity L{sub r} = 8–14L* (4.3–7.5 × 10{sup 44} erg s{sup −1}). These super spiral galaxies are also giant and massive, with diameter D = 57–134 kpc and stellar mass M{sub stars} = 0.3–3.4 × 10{sup 11}M{sub ⊙}. We find 53 super spirals out of a complete sample of 1616 SDSS galaxies with redshift z < 0.3 and L{sub r} > 8L*. The closest example is found at z = 0.089. We use existing photometry to estimate their stellar masses and star formation rates (SFRs). The SDSS and Wide-field Infrared Survey Explorer colors aremore » consistent with normal star-forming spirals on the blue sequence. However, the extreme masses and rapid SFRs of 5–65 M{sub ⊙} yr{sup −1} place super spirals in a sparsely populated region of parameter space, above the star-forming main sequence of disk galaxies. Super spirals occupy a diverse range of environments, from isolation to cluster centers. We find four super spiral galaxy systems that are late-stage major mergers—a possible clue to their formation. We suggest that super spirals are a remnant population of unquenched, massive disk galaxies. They may eventually become massive lenticular galaxies after they are cut off from their gas supply and their disks fade.« less

Evaluation of massively parallel sequencing for forensic DNA methylation profiling.

PubMed

Richards, Rebecca; Patel, Jayshree; Stevenson, Kate; Harbison, SallyAnn

2018-05-11

Epigenetics is an emerging area of interest in forensic science. DNA methylation, a type of epigenetic modification, can be applied to chronological age estimation, identical twin differentiation and body fluid identification. However, there is not yet an agreed, established methodology for targeted detection and analysis of DNA methylation markers in forensic research. Recently a massively parallel sequencing-based approach has been suggested. The use of massively parallel sequencing is well established in clinical epigenetics and is emerging as a new technology in the forensic field. This review investigates the potential benefits, limitations and considerations of this technique for the analysis of DNA methylation in a forensic context. The importance of a robust protocol, regardless of the methodology used, that minimises potential sources of bias is highlighted. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

BINARY ASTROMETRIC MICROLENSING WITH GAIA

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

Sajadian, Sedighe, E-mail: sajadian@ipm.ir; Department of Physics, Sharif University of Technology, P.O. Box 11155-9161, Tehran

2015-04-15

We investigate whether or not Gaia can specify the binary fractions of massive stellar populations in the Galactic disk through astrometric microlensing. Furthermore, we study whether or not some information about their mass distributions can be inferred via this method. In this regard, we simulate the binary astrometric microlensing events due to massive stellar populations according to the Gaia observing strategy by considering (i) stellar-mass black holes, (ii) neutron stars, (iii) white dwarfs, and (iv) main-sequence stars as microlenses. The Gaia efficiency for detecting the binary signatures in binary astrometric microlensing events is ∼10%–20%. By calculating the optical depth duemore » to the mentioned stellar populations, the numbers of the binary astrometric microlensing events being observed with Gaia with detectable binary signatures, for the binary fraction of about 0.1, are estimated to be 6, 11, 77, and 1316, respectively. Consequently, Gaia can potentially specify the binary fractions of these massive stellar populations. However, the binary fraction of black holes measured with this method has a large uncertainty owing to a low number of the estimated events. Knowing the binary fractions in massive stellar populations helps with studying the gravitational waves. Moreover, we investigate the number of massive microlenses for which Gaia specifies masses through astrometric microlensing of single lenses toward the Galactic bulge. The resulting efficiencies of measuring the mass of mentioned populations are 9.8%, 2.9%, 1.2%, and 0.8%, respectively. The numbers of their astrometric microlensing events being observed in the Gaia era in which the lens mass can be inferred with the relative error less than 0.5 toward the Galactic bulge are estimated as 45, 34, 76, and 786, respectively. Hence, Gaia potentially gives us some information about the mass distribution of these massive stellar populations.« less

X-ray Properties of the Young Open Clusters HM1 and IC 2944-2948

NASA Technical Reports Server (NTRS)

Naze, Y.; Rauw, G.; Sana, H.; Corcoran, Michael F.

2013-01-01

Using XMM-Newton data, we study for the first time the X-ray emission of HM1 and IC 2944/2948. Low-mass, pre-main-sequence objects with an age of a few Myr are detected, as well as a few background or foreground objects. Most massive stars in both clusters display the usual high-energy properties of that type of objects, though with log [L(sub X)/L(sub BOL)] apparently lower in HM1 than in IC2944/2948. Compared with studies of other clusters, it seems that a low signal-to-noise ratio at soft energies, due to the high extinction, may be the main cause of this difference. In HM1, the two Wolf-Rayet stars show contrasting behaviors:WR89 is extremely bright, but much softer than WR87. It remains to be seen whether wind-wind collisions or magnetically confined winds can explain these emissions. In IC 2944/2948, the X-ray sources concentrate around HD 101205; a group of massive stars to the north of this object is isolated, suggesting that there exist two subclusters in the field-of-view.

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

Van Dyk, Schuyler D.; De Mink, Selma E.; Zapartas, Emmanouil

Core-collapse supernovae (SNe), which mark the deaths of massive stars, are among the most powerful explosions in the universe and are responsible, e.g., for a predominant synthesis of chemical elements in their host galaxies. The majority of massive stars are thought to be born in close binary systems. To date, putative binary companions to the progenitors of SNe may have been detected in only two cases, SNe 1993J and 2011dh. We report on the search for a companion of the progenitor of the Type Ic SN 1994I, long considered to have been the result of binary interaction. Twenty years aftermore » explosion, we used the Hubble Space Telescope to observe the SN site in the ultraviolet (F275W and F336W bands), resulting in deep upper limits on the expected companion: F275W > 26.1 mag and F336W > 24.7 mag. These allow us to exclude the presence of a main sequence companion with a mass ≳10 M{sub ⊙}. Through comparison with theoretical simulations of possible progenitor populations, we show that the upper limits to a companion detection exclude interacting binaries with semi-conservative (late Case A or early Case B) mass transfer. These limits tend to favor systems with non-conservative, late Case B mass transfer with intermediate initial orbital periods and mass ratios. The most likely mass range for a putative main sequence companion would be ∼5–12 M{sub ⊙}, the upper end of which corresponds to the inferred upper detection limit.« less

New Observational Evidence of Flash Mixing on the White Dwarf Cooling Curve

NASA Technical Reports Server (NTRS)

Brown, T. M.; Lanz, T.; Sweigart, A. V.; Cracraft, Misty; Hubeny, Ivan; Landsman, W. B.

2011-01-01

Blue hook stars are a class of subluminous extreme horizontal branch stars that were discovered in UV images of the massive globular clusters w Cen and NGC 2808. These stars occupy a region of the HR diagram that is unexplained by canonical stellar evolution theory. Using new theoretical evolutionary and atmospheric models, we have shown that the blue hook stars are very likely the progeny of stars that undergo extensive internal mixing during a late helium-core flash on the white dwarf cooling curve. This "flash mixing" produces hotter-than-normal EHB stars with atmospheres significantly enhanced in helium and carbon. The larger bolometric correction, combined with the decrease in hydrogen opacity, makes these stars appear sub luminous in the optical and UV. Flash mixing is more likely to occur in stars born with a high helium abundance, due to their lower mass at the main sequence turnoff. For this reason, the phenomenon is more common in those massive globular clusters that show evidence for secondary populations enhanced in helium. However, a high helium abundance does not, by itself, explain the presence of blue hook stars in massive globular clusters. Here, we present new observational evidence for flash mixing, using recent HST observations. These include UV color-magnitude diagrams of six massive globular clusters and far-UV spectroscopy of hot subdwarfs in one of these clusters (NGC 2808).

The Role of Rotation in the Evolution of Massive Stars

NASA Technical Reports Server (NTRS)

Heap, Sara R.; Lanz, Thierry M.

2003-01-01

Recent evolutionary models of massive stars predict important effects of rotation including: increasing the rate of mass loss; lowering the effective gravity; altering the evolutionary track on the Hertzsprung-Russel Diagram (HRD); extending the main-sequence phase (both on the HR diagram and in time); and mixing of CNO-processed elements up to the stellar surface. Observations suggest that rotation is a more important factor at lower metallicities because of higher initial rotational velocities and weaker winds. This makes the Small Magellanic Cloud (SMC), a low-metallicity galaxy (Z=0.2 solar Z), an excellent environment for discerning the role of rotation in massive stars. We report on a FUSE+STIS+optical spectral analysis of 17 O-type stars in the SMC, where we found an enormous range in N abundances. Three stars in the sample have the same (low) CN abundances as the nebular material out of which they formed, namely C=0.085 solar C and N=0.034 solar N. However, more than half show N approx. solar N, an enrichment factor of 30X! Such unexpectedly high levels of N have ramifications for the evolution of massive stars including precursors to supernovae. They also raise questions about the sources of nitrogen in the early universe. This study was supported in part by grants from NASA's ADP, HST GO-7437, and FUSE B134.

High Resolution Studies of Mass Loss from Massive Binary Stars

NASA Astrophysics Data System (ADS)

Corcoran, Michael F.; Gull, Theodore R.; Hamaguchi, Kenji; Richardson, Noel; Madura, Thomas; Post Russell, Christopher Michael; Teodoro, Mairan; Nichols, Joy S.; Moffat, Anthony F. J.; Shenar, Tomer; Pablo, Herbert

2017-01-01

Mass loss from hot luminous single and binary stars has a significant, perhaps decisive, effect on their evolution. The combination of X-ray observations of hot shocked gas embedded in the stellar winds and high-resolution optical/UV spectra of the cooler mass in the outflow provides unique ways to study the unstable process by which massive stars lose mass both through continuous stellar winds and rare, impulsive, large-scale mass ejections. The ability to obtain coordinated observations with the Hubble Space Telescope Imaging Spectrograph (HST/STIS) and the Chandra High-Energy Transmission Grating Spectrometer (HETGS) and other X-ray observatories has allowed, for the first time, studies of resolved line emisssion over the temperature range of 104- 108K, and has provided observations to confront numerical dynamical models in three dimensions. Such observations advance our knowledge of mass-loss asymmetries, spatial and temporal variabilities, and the fundamental underlying physics of the hot shocked outflow, providing more realistic constraints on the amount of mass lost by different luminous stars in a variety of evolutionary stages. We discuss the impact that these joint observational studies have had on our understanding of dynamical mass outflows from massive stars, with particular emphasis on two important massive binaries, Delta Ori Aa, a linchpin of the mass luminosity relation for upper HRD main sequence stars, and the supermassive colliding wind binary Eta Carinae.

Formation of Thorne-Żytkow objects in close binaries

NASA Astrophysics Data System (ADS)

Hutilukejiang, Bumareyamu; Zhu, Chunhua; Wang, Zhaojun; Lü, Guoliang

2018-04-01

Thorne-Żytkow objects (TŻOs), originally proposed by Thorne and Żytkow, may form as a result of unstable mass transfer in a massive X-ray binary after a neutron star (NS) is engulfed in the envelope of its companion star. Using a rapid binary evolution program and the Monte Carlo method, we simulated the formation of TŻOs in close binary stars. The Galactic birth rate of TŻOs is about 1.5× 10^{-4} yr^{-1}. Their progenitors may be composed of a NS and a main-sequence star, a star in the Hertzsprung gap or a core-helium burning, or a naked helium star. The birth rates of TŻOs via the above different progenitors are 1.7× 10^{-5}, 1.2× 10^{-4}, 0.7× 10^{-5}, 0.6× 10^{-5} yr^{-1}, respectively. These progenitors may be massive X-ray binaries. We found that the observational properties of three massive X-ray binaries (SMC X-1, Cen X-3 and LMC X-4) in which the companions of NSs may fill their Roche robes were consistent with those of their progenitors.

Probabilistic HR Diagrams: A New Infrared and X-ray Chronometer for Very Young, Massive Stellar Clusters and Associations

NASA Astrophysics Data System (ADS)

Maldonado, Jessica; Povich, Matthew S.

2016-01-01

We present a novel method for constraining the duration of star formation in very young, massive star-forming regions. Constraints on stellar population ages are derived from probabilistic HR diagrams (pHRDs) generated by fitting stellar model spectra to the infrared (IR) spectral energy distributions (SEDs) of Herbig Ae/Be stars and their less-evolved, pre-main sequence progenitors. Stellar samples for the pHRDs are selected based on the detection of X-ray emission associated with the IR source, and the lack of detectible IR excess emission at wavelengths ≤4.5 µm. The SED model fits were used to create two-dimensional probability distributions of the stellar parameters, specifically bolometric luminosity versus temperature and mass versus evolutionary age. We present first results from the pHRD analysis of the relatively evolved Carina Nebula and the unevolved M17 SWex infrared dark cloud, which reveal the expected, strikingly different star formation durations between these two regions. In the future, we will apply this method to analyze available X-ray and IR data from the MYStIX project on other Galactic massive star forming regions within 3 kpc of the Sun.

ENHANCED STAR FORMATION OF LESS MASSIVE GALAXIES IN A PROTOCLUSTER AT z = 2.5

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

Hayashi, Masao; Kodama, Tadayuki; Tanaka, Ichi

2016-08-01

We investigate a correlation between star formation rate (SFR) and stellar mass for H α emission-line galaxies (HAEs) in one of the richest protoclusters ever known at z∼2.5, the USS 1558-003 protocluster. This study is based on a 9.7 hr narrowband imaging data with MOIRCS on the Subaru telescope. We are able to construct a sample in combination with additional H -band data taken with WFC3 on the Hubble Space Telescope , of 100 HAEs reaching the dust-corrected SFRs down to 3 M {sub ⊙} yr{sup −1} and the stellar masses down to 10{sup 8.0} M {sub ⊙}. We findmore » that while the star-forming galaxies with ≳10{sup 9.3} M {sub ⊙} are located on the universal SFR-mass main sequence (MS) irrespective of the environment, less massive star-forming galaxies with ≲10{sup 9.3} M {sub ⊙} show a significant upward scatter from the MS in this protocluster. This suggests that some less massive galaxies are in a starburst phase, although we do not know yet if this is due to environmental effects.« less

Meeting the challenges of non-referenced genome assembly from short-read sequence data

Treesearch

M. Parks; A. Liston; R. Cronn

2010-01-01

Massively parallel sequencing technologies (MPST) offer unprecedented opportunities for novel sequencing projects. MPST, while offering tremendous sequencing capacity, are typically most effective in resequencing projects (as opposed to the sequencing of novel genomes) due to the fact that sequence is returned in relatively short reads. Nonetheless, there is great...

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.

The dark nemesis of galaxy formation: why hot haloes trigger black hole growth and bring star formation to an end

NASA Astrophysics Data System (ADS)

Bower, Richard G.; Schaye, Joop; Frenk, Carlos S.; Theuns, Tom; Schaller, Matthieu; Crain, Robert A.; McAlpine, Stuart

2017-02-01

Galaxies fall into two clearly distinct types: `blue-sequence' galaxies which are rapidly forming young stars, and `red-sequence' galaxies in which star formation has almost completely ceased. Most galaxies more massive than 3 × 1010 M⊙ follow the red sequence, while less massive central galaxies lie on the blue sequence. We show that these sequences are created by a competition between star formation-driven outflows and gas accretion on to the supermassive black hole at the galaxy's centre. We develop a simple analytic model for this interaction. In galaxies less massive than 3 × 1010 M⊙, young stars and supernovae drive a high-entropy outflow which is more buoyant than any tenuous corona. The outflow balances the rate of gas inflow, preventing high gas densities building up in the central regions. More massive galaxies, however, are surrounded by an increasingly hot corona. Above a halo mass of ˜1012 M⊙, the outflow ceases to be buoyant and star formation is unable to prevent the build-up of gas in the central regions. This triggers a strongly non-linear response from the black hole. Its accretion rate rises rapidly, heating the galaxy's corona, disrupting the incoming supply of cool gas and starving the galaxy of the fuel for star formation. The host galaxy makes a transition to the red sequence, and further growth predominantly occurs through galaxy mergers. We show that the analytic model provides a good description of galaxy evolution in the EAGLE hydrodynamic simulations. So long as star formation-driven outflows are present, the transition mass scale is almost independent of subgrid parameter choice.

THE ROLE OF THE MAGNETOROTATIONAL INSTABILITY IN MASSIVE STARS

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

Wheeler, J. Craig; Kagan, Daniel; Chatzopoulos, Emmanouil, E-mail: wheel@astro.as.utexas.edu

2015-01-20

The magnetorotational instability (MRI) is key to physics in accretion disks and is widely considered to play some role in massive star core collapse. Models of rotating massive stars naturally develop very strong shear at composition boundaries, a necessary condition for MRI instability, and the MRI is subject to triply diffusive destabilizing effects in radiative regions. We have used the MESA stellar evolution code to compute magnetic effects due to the Spruit-Tayler (ST) mechanism and the MRI, separately and together, in a sample of massive star models. We find that the MRI can be active in the later stages ofmore » massive star evolution, leading to mixing effects that are not captured in models that neglect the MRI. The MRI and related magnetorotational effects can move models of given zero-age main sequence mass across ''boundaries'' from degenerate CO cores to degenerate O/Ne/Mg cores and from degenerate O/Ne/Mg cores to iron cores, thus affecting the final evolution and the physics of core collapse. The MRI acting alone can slow the rotation of the inner core in general agreement with the observed ''initial'' rotation rates of pulsars. The MRI analysis suggests that localized fields ∼10{sup 12} G may exist at the boundary of the iron core. With both the ST and MRI mechanisms active in the 20 M {sub ☉} model, we find that the helium shell mixes entirely out into the envelope. Enhanced mixing could yield a population of yellow or even blue supergiant supernova progenitors that would not be standard SN IIP.« less

The origin of ultra-compact binaries

NASA Technical Reports Server (NTRS)

Hachisu, Izumi; Miyaji, Shigeki; Saio, Hideyuki

1987-01-01

The origin of ultra-compact binaries composed of a neutron star and a low-mass (about 0.06 solar mass) white dwarf is considered. Taking account of the systemic losses of mass and angular momentum, it was found that a serious difficulty exists in the scenarios which involve tidal captures of a normal star (a main sequence star or a red giant) by a neutron star. This difficulty can be avoided if a red giant star is captured by a massive white dwarf (M is approx. greater than 1.2 solar masses), which becomes a neutron star through the accretion induced collapse.

Next generation sequencing (NGS): a golden tool in forensic toolkit.

PubMed

Aly, S M; Sabri, D M

The DNA analysis is a cornerstone in contemporary forensic sciences. DNA sequencing technologies are powerful tools that enrich molecular sciences in the past based on Sanger sequencing and continue to glowing these sciences based on Next generation sequencing (NGS). Next generation sequencing has excellent potential to flourish and increase the molecular applications in forensic sciences by jumping over the pitfalls of the conventional method of sequencing. The main advantages of NGS compared to conventional method that it utilizes simultaneously a large number of genetic markers with high-resolution of genetic data. These advantages will help in solving several challenges such as mixture analysis and dealing with minute degraded samples. Based on these new technologies, many markers could be examined to get important biological data such as age, geographical origins, tissue type determination, external visible traits and monozygotic twins identification. It also could get data related to microbes, insects, plants and soil which are of great medico-legal importance. Despite the dozens of forensic research involving NGS, there are requirements before using this technology routinely in forensic cases. Thus, there is a great need to more studies that address robustness of these techniques. Therefore, this work highlights the applications of forensic sciences in the era of massively parallel sequencing.

A streamlined method for analysing genome-wide DNA methylation patterns from low amounts of FFPE DNA.

PubMed

Ludgate, Jackie L; Wright, James; Stockwell, Peter A; Morison, Ian M; Eccles, Michael R; Chatterjee, Aniruddha

2017-08-31

Formalin fixed paraffin embedded (FFPE) tumor samples are a major source of DNA from patients in cancer research. However, FFPE is a challenging material to work with due to macromolecular fragmentation and nucleic acid crosslinking. FFPE tissue particularly possesses challenges for methylation analysis and for preparing sequencing-based libraries relying on bisulfite conversion. Successful bisulfite conversion is a key requirement for sequencing-based methylation analysis. Here we describe a complete and streamlined workflow for preparing next generation sequencing libraries for methylation analysis from FFPE tissues. This includes, counting cells from FFPE blocks and extracting DNA from FFPE slides, testing bisulfite conversion efficiency with a polymerase chain reaction (PCR) based test, preparing reduced representation bisulfite sequencing libraries and massively parallel sequencing. The main features and advantages of this protocol are: An optimized method for extracting good quality DNA from FFPE tissues. An efficient bisulfite conversion and next generation sequencing library preparation protocol that uses 50 ng DNA from FFPE tissue. Incorporation of a PCR-based test to assess bisulfite conversion efficiency prior to sequencing. We provide a complete workflow and an integrated protocol for performing DNA methylation analysis at the genome-scale and we believe this will facilitate clinical epigenetic research that involves the use of FFPE tissue.

Flow cytometry for enrichment and titration in massively parallel DNA sequencing

PubMed Central

Sandberg, Julia; Ståhl, Patrik L.; Ahmadian, Afshin; Bjursell, Magnus K.; Lundeberg, Joakim

2009-01-01

Massively parallel DNA sequencing is revolutionizing genomics research throughout the life sciences. However, the reagent costs and labor requirements in current sequencing protocols are still substantial, although improvements are continuously being made. Here, we demonstrate an effective alternative to existing sample titration protocols for the Roche/454 system using Fluorescence Activated Cell Sorting (FACS) technology to determine the optimal DNA-to-bead ratio prior to large-scale sequencing. Our method, which eliminates the need for the costly pilot sequencing of samples during titration is capable of rapidly providing accurate DNA-to-bead ratios that are not biased by the quantification and sedimentation steps included in current protocols. Moreover, we demonstrate that FACS sorting can be readily used to highly enrich fractions of beads carrying template DNA, with near total elimination of empty beads and no downstream sacrifice of DNA sequencing quality. Automated enrichment by FACS is a simple approach to obtain pure samples for bead-based sequencing systems, and offers an efficient, low-cost alternative to current enrichment protocols. PMID:19304748

Learning Quantitative Sequence-Function Relationships from Massively Parallel Experiments

NASA Astrophysics Data System (ADS)

Atwal, Gurinder S.; Kinney, Justin B.

2016-03-01

A fundamental aspect of biological information processing is the ubiquity of sequence-function relationships—functions that map the sequence of DNA, RNA, or protein to a biochemically relevant activity. Most sequence-function relationships in biology are quantitative, but only recently have experimental techniques for effectively measuring these relationships been developed. The advent of such "massively parallel" experiments presents an exciting opportunity for the concepts and methods of statistical physics to inform the study of biological systems. After reviewing these recent experimental advances, we focus on the problem of how to infer parametric models of sequence-function relationships from the data produced by these experiments. Specifically, we retrace and extend recent theoretical work showing that inference based on mutual information, not the standard likelihood-based approach, is often necessary for accurately learning the parameters of these models. Closely connected with this result is the emergence of "diffeomorphic modes"—directions in parameter space that are far less constrained by data than likelihood-based inference would suggest. Analogous to Goldstone modes in physics, diffeomorphic modes arise from an arbitrarily broken symmetry of the inference problem. An analytically tractable model of a massively parallel experiment is then described, providing an explicit demonstration of these fundamental aspects of statistical inference. This paper concludes with an outlook on the theoretical and computational challenges currently facing studies of quantitative sequence-function relationships.

The G305 star-forming complex: the central star clusters Danks 1 and Danks 2

NASA Astrophysics Data System (ADS)

Davies, Ben; Clark, J. S.; Trombley, Christine; Figer, Donald F.; Najarro, Francisco; Crowther, Paul A.; Kudritzki, Rolf-Peter; Thompson, Mark; Urquhart, James S.; Hindson, Luke

2012-01-01

The G305 H II complex (G305.4+0.1) is one of the most massive star-forming structures yet identified within the Galaxy. It is host to many massive stars at all stages of formation and evolution, from embedded molecular cores to post-main-sequence stars. Here, we present a detailed near-infrared analysis of the two central star clusters Danks 1 and Danks 2, using Hubble Space Telescope+NICMOS imaging and Very Large Telescope+ISAAC spectroscopy. We find that the spectrophotometric distance to the clusters is consistent with the kinematic distance to the G305 complex, an average of all measurements giving a distance of 3.8 ± 0.6 kpc. From analysis of the stellar populations and the pre-main-sequence stars, we find that Danks 2 is the elder of the two clusters, with an age of 3+3- 1 Myr. Danks 1 is clearly younger with an age of 1.5+1.5- 0.5 Myr, and is dominated by three very luminous H-rich Wolf-Rayet stars which may have masses ≳100 M⊙. The two clusters have mass functions consistent with the Salpeter slope, and total cluster masses of 8000 ± 1500 and 3000 ± 800 M⊙ for Danks 1 and Danks 2, respectively. Danks 1 is significantly the more compact cluster of the two, and is one of the densest clusters in the Galaxy with log (ρ/M⊙ pc-3) = 5.5+0.5- 0.4. In addition to the clusters, there is a population of apparently isolated Wolf-Rayet stars within the molecular cloud's cavity. Our results suggest that the star-forming history of G305 began with the formation of Danks 2, and subsequently Danks 1, with the origin of the diffuse evolved population currently uncertain. Together, the massive stars at the centre of the G305 region appear to be clearing away what is left of the natal cloud, triggering a further generation of star formation at the cloud's periphery.

Conservation of the C-type lectin fold for massive sequence variation in a Treponema diversity-generating retroelement

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

Le Coq, Johanne; Ghosh, Partho

2012-06-19

Anticipatory ligand binding through massive protein sequence variation is rare in biological systems, having been observed only in the vertebrate adaptive immune response and in a phage diversity-generating retroelement (DGR). Earlier work has demonstrated that the prototypical DGR variable protein, major tropism determinant (Mtd), meets the demands of anticipatory ligand binding by novel means through the C-type lectin (CLec) fold. However, because of the low sequence identity among DGR variable proteins, it has remained unclear whether the CLec fold is a general solution for DGRs. We have addressed this problem by determining the structure of a second DGR variable protein,more » TvpA, from the pathogenic oral spirochete Treponema denticola. Despite its weak sequence identity to Mtd ({approx}16%), TvpA was found to also have a CLec fold, with predicted variable residues exposed in a ligand-binding site. However, this site in TvpA was markedly more variable than the one in Mtd, reflecting the unprecedented approximate 10{sup 20} potential variability of TvpA. In addition, similarity between TvpA and Mtd with formylglycine-generating enzymes was detected. These results provide strong evidence for the conservation of the formylglycine-generating enzyme-type CLec fold among DGRs as a means of accommodating massive sequence variation.« less

Conservation of the C-type lectin fold for massive sequence variation in a Treponema diversity-generating retroelement

PubMed Central

Le Coq, Johanne; Ghosh, Partho

2011-01-01

Anticipatory ligand binding through massive protein sequence variation is rare in biological systems, having been observed only in the vertebrate adaptive immune response and in a phage diversity-generating retroelement (DGR). Earlier work has demonstrated that the prototypical DGR variable protein, major tropism determinant (Mtd), meets the demands of anticipatory ligand binding by novel means through the C-type lectin (CLec) fold. However, because of the low sequence identity among DGR variable proteins, it has remained unclear whether the CLec fold is a general solution for DGRs. We have addressed this problem by determining the structure of a second DGR variable protein, TvpA, from the pathogenic oral spirochete Treponema denticola. Despite its weak sequence identity to Mtd (∼16%), TvpA was found to also have a CLec fold, with predicted variable residues exposed in a ligand-binding site. However, this site in TvpA was markedly more variable than the one in Mtd, reflecting the unprecedented approximate 1020 potential variability of TvpA. In addition, similarity between TvpA and Mtd with formylglycine-generating enzymes was detected. These results provide strong evidence for the conservation of the formylglycine-generating enzyme-type CLec fold among DGRs as a means of accommodating massive sequence variation. PMID:21873231

Conservation of the C-type lectin fold for massive sequence variation in a Treponema diversity-generating retroelement.

PubMed

Le Coq, Johanne; Ghosh, Partho

2011-08-30

Anticipatory ligand binding through massive protein sequence variation is rare in biological systems, having been observed only in the vertebrate adaptive immune response and in a phage diversity-generating retroelement (DGR). Earlier work has demonstrated that the prototypical DGR variable protein, major tropism determinant (Mtd), meets the demands of anticipatory ligand binding by novel means through the C-type lectin (CLec) fold. However, because of the low sequence identity among DGR variable proteins, it has remained unclear whether the CLec fold is a general solution for DGRs. We have addressed this problem by determining the structure of a second DGR variable protein, TvpA, from the pathogenic oral spirochete Treponema denticola. Despite its weak sequence identity to Mtd (∼16%), TvpA was found to also have a CLec fold, with predicted variable residues exposed in a ligand-binding site. However, this site in TvpA was markedly more variable than the one in Mtd, reflecting the unprecedented approximate 10(20) potential variability of TvpA. In addition, similarity between TvpA and Mtd with formylglycine-generating enzymes was detected. These results provide strong evidence for the conservation of the formylglycine-generating enzyme-type CLec fold among DGRs as a means of accommodating massive sequence variation.

Simultaneous mutation and copy number variation (CNV) detection by multiplex PCR-based GS-FLX sequencing.

PubMed

Goossens, Dirk; Moens, Lotte N; Nelis, Eva; Lenaerts, An-Sofie; Glassee, Wim; Kalbe, Andreas; Frey, Bruno; Kopal, Guido; De Jonghe, Peter; De Rijk, Peter; Del-Favero, Jurgen

2009-03-01

We evaluated multiplex PCR amplification as a front-end for high-throughput sequencing, to widen the applicability of massive parallel sequencers for the detailed analysis of complex genomes. Using multiplex PCR reactions, we sequenced the complete coding regions of seven genes implicated in peripheral neuropathies in 40 individuals on a GS-FLX genome sequencer (Roche). The resulting dataset showed highly specific and uniform amplification. Comparison of the GS-FLX sequencing data with the dataset generated by Sanger sequencing confirmed the detection of all variants present and proved the sensitivity of the method for mutation detection. In addition, we showed that we could exploit the multiplexed PCR amplicons to determine individual copy number variation (CNV), increasing the spectrum of detected variations to both genetic and genomic variants. We conclude that our straightforward procedure substantially expands the applicability of the massive parallel sequencers for sequencing projects of a moderate number of amplicons (50-500) with typical applications in resequencing exons in positional or functional candidate regions and molecular genetic diagnostics. 2008 Wiley-Liss, Inc.

The Discovery of an Eccentric Millisecond Pulsar in the Galactic Plane

NASA Astrophysics Data System (ADS)

Champion, David J.; Ransom, Scott M.; Lazarus, Patrick; Camilo, Fernando; Kaspi, Victoria M.; Nice, David J.; Freire, Paulo C. C.; Cordes, James M.; Hessels, Jason W. T.; Bassa, Cees; Lorimer, Duncan R.; Stairs, Ingrid H.; van Leeuwen, Joeri; Arzoumnian, Zaven; Backer, Don C.; Bhat, N. D. Ramesh; Chatterjee, Shami; Crawford, Fronefield; Deneva, Julia S.; Faucher-Giguère, Claude-André; Gaensler, B. M.; Han, Jinlin; Jenet, Fredrick A.; Kasian, Laura; Kondratiev, Vlad I.; Kramer, Michael; Lazio, Joseph; McLaughlin, Maura A.; Stappers, Ben W.; Venkataraman, Arun; Vlemmings, Wouter

2008-02-01

The evolution of binary systems is governed by their orbital properties and the stellar density of the local environment. Studies of neutron stars in binary star systems offer unique insights into both these issues. In an Arecibo survey of the Galactic disk, we have found PSR J1903+0327, a radio emitting neutron star (a ``pulsar'') with a 2.15 ms rotation period, in a 95-day orbit around a massive companion. Observations in the infra-red suggests that the companion may be a main-sequence star. Theories requiring an origin in the Galactic disk cannot account for the extraordinarily high orbital eccentricity observed (0.44) or a main-sequence companion of a pulsar that has spin properties suggesting a prolonged accretion history. The most likely formation mechanism is an exchange interaction in a globular star cluster. This requires that the binary was either ejected from its parent globular cluster as a result of a three-body interaction, or that that cluster was disrupted by repeated passages through the disk of the Milky Way.

Young massive star clusters in the era of HST and integral field spectroscopy

NASA Astrophysics Data System (ADS)

Zeidler, Peter; Nota, Antonella; Sabbi, Elena; Grebel, Eva K.; Pasquali, Anna

2018-01-01

With an age of 1 – 2 Myr at a distance of 4 kpc and a total stellar mass of 3.7×104 M⊙, Westerlund 2 (Wd2) is one of the most massive young star clusters in the Milky Way. We present a detailed analysis of its prominent pre-main-sequence population using the data of a high-resolution multi-band survey in the optical and near-infrared with the Hubble Space Telescope (HST), in combination with our spectroscopic survey, observed with the VLT/MUSE integral field unit. With our derived high-resolution extinction map of the region, which is absolutely essential giving the dominating presences of the gas and dust, we derived the spatial dependence of the mass function and quantify the degree of mass segregation down to 0.65 M⊙ with a completeness level better than 50%. Studying the radial dependence of the mass function of Wd2 and quantifying the degree of mass segregation in this young massive star cluster showed that it consists of two sub-clumps, namely the main cluster and the northern clump. From the MUSE data, we can extract individual stellar spectra and spectral energy distributions of the stars, based on the astrometry, provided by our high-resolution HST photometric catalog. This data will provide us with an almost complete spectral classification of a young massive star cluster down to 1.0 M⊙. The combination of the MUSE data, together with 3 more years of approved HST data will allow us to obtain, for the first time, the 3D motions of the stars with an accuracy of 1-2 km s-2 to determine the stellar velocity dispersion in order to study the fate of Wd2. This information is of great importance to adjust the initial conditions in cluster evolution models in order to connect these young massive star clusters and the old globular cluster population. Additionally, the combination of the photometric and spectroscopic datasets allows us to study the stars and their feedback onto the surrounding HII region simultaneously, as well as peculiar objects such as the massive, eclipsing Wolf-Rayet binary, WR20a or a possible Herbig-Haro object in the northern clump.

Globular cluster photometry with the Hubble Space Telescope. I - Description of the method and analysis of the core of 47 Tuc

NASA Technical Reports Server (NTRS)

Guhathakurta, Puragra; Yanny, Brian; Schneider, Donald P.; Bahcall, John N.

1992-01-01

Accurate photometry for individual post-main-sequence stars in the core of the Galactic globular cluster 47 Tuc is presented and analyzed using an empirical point spread function model and Monte Carlo simulations. A V vs. V-I color-magnitude diagrams is constructed which shows several distinct stellar types, including RGB and HB stars. Twenty-four blue straggler stars are detected in 47 Tuc, more concentrated toward the center of the cluster than the giants. This supports the hypothesis is that the stragglers are either coalesced stars or members of binary systems that are more massive than single stars. The radial profile of the projected stellar density is flat in the central region of 47 Tuc with a core radius of 23 +/- 2 arcsec. No signature of a collapsed core is evident. The observed radial cumulative distribution of stars rules out the presence of a massive compact object in the center.

Genomics pipelines and data integration: challenges and opportunities in the research setting

PubMed Central

Davis-Turak, Jeremy; Courtney, Sean M.; Hazard, E. Starr; Glen, W. Bailey; da Silveira, Willian; Wesselman, Timothy; Harbin, Larry P.; Wolf, Bethany J.; Chung, Dongjun; Hardiman, Gary

2017-01-01

Introduction The emergence and mass utilization of high-throughput (HT) technologies, including sequencing technologies (genomics) and mass spectrometry (proteomics, metabolomics, lipids), has allowed geneticists, biologists, and biostatisticians to bridge the gap between genotype and phenotype on a massive scale. These new technologies have brought rapid advances in our understanding of cell biology, evolutionary history, microbial environments, and are increasingly providing new insights and applications towards clinical care and personalized medicine. Areas covered The very success of this industry also translates into daunting big data challenges for researchers and institutions that extend beyond the traditional academic focus of algorithms and tools. The main obstacles revolve around analysis provenance, data management of massive datasets, ease of use of software, interpretability and reproducibility of results. Expert Commentary The authors review the challenges associated with implementing bioinformatics best practices in a large-scale setting, and highlight the opportunity for establishing bioinformatics pipelines that incorporate data tracking and auditing, enabling greater consistency and reproducibility for basic research, translational or clinical settings. PMID:28092471

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.

Genomics pipelines and data integration: challenges and opportunities in the research setting.

PubMed

Davis-Turak, Jeremy; Courtney, Sean M; Hazard, E Starr; Glen, W Bailey; da Silveira, Willian A; Wesselman, Timothy; Harbin, Larry P; Wolf, Bethany J; Chung, Dongjun; Hardiman, Gary

2017-03-01

The emergence and mass utilization of high-throughput (HT) technologies, including sequencing technologies (genomics) and mass spectrometry (proteomics, metabolomics, lipids), has allowed geneticists, biologists, and biostatisticians to bridge the gap between genotype and phenotype on a massive scale. These new technologies have brought rapid advances in our understanding of cell biology, evolutionary history, microbial environments, and are increasingly providing new insights and applications towards clinical care and personalized medicine. Areas covered: The very success of this industry also translates into daunting big data challenges for researchers and institutions that extend beyond the traditional academic focus of algorithms and tools. The main obstacles revolve around analysis provenance, data management of massive datasets, ease of use of software, interpretability and reproducibility of results. Expert commentary: The authors review the challenges associated with implementing bioinformatics best practices in a large-scale setting, and highlight the opportunity for establishing bioinformatics pipelines that incorporate data tracking and auditing, enabling greater consistency and reproducibility for basic research, translational or clinical settings.

The nature of donors in ultraluminous X-ray binaries powered by neutron stars

NASA Astrophysics Data System (ADS)

Karino, Shigeyuki

2018-03-01

This study examines the properties of the donor stars of three recently discovered ultraluminous X-ray sources (ULXs) powered by rotating neutron stars. In order to do this, a theoretical relationship was constructed between the X-ray luminosity (LX) and the orbital period (Porb) suitable for ULXs with neutron stars. Using this new LX-Porb relationship, we attempted to determine the currently unknown nature of donor stars in ULXs associated with neutron stars. In particular, from a comparison between the observed properties and the stellar evolution tracks, we suggest that the donor star in the NGC5907 ULX-1 system is a moderately massive star of 6-12 M⊙, just departing from the main sequence phase. The results of our models for the other two ULX systems (M82 X-2 and NGC7793 P-13) are consistent with those in previous studies. Although there are only a few samples, observed ULX systems with neutron stars seem to involve relatively massive donors.

Integration of targeted sequencing and NIPT into clinical practice in a Chinese family with maple syrup urine disease.

PubMed

You, Yanqin; Sun, Yan; Li, Xuchao; Li, Yali; Wei, Xiaoming; Chen, Fang; Ge, Huijuan; Lan, Zhangzhang; Zhu, Qian; Tang, Ying; Wang, Shujuan; Gao, Ya; Jiang, Fuman; Song, Jiaping; Shi, Quan; Zhu, Xuan; Mu, Feng; Dong, Wei; Gao, Vince; Jiang, Hui; Yi, Xin; Wang, Wei; Gao, Zhiying

2014-08-01

This article demonstrates a prominent noninvasive prenatal approach to assist the clinical diagnosis of a single-gene disorder disease, maple syrup urine disease, using targeted sequencing knowledge from the affected family. The method reported here combines novel mutant discovery in known genes by targeted massively parallel sequencing with noninvasive prenatal testing. By applying this new strategy, we successfully revealed novel mutations in the gene BCKDHA (Ex2_4dup and c.392A>G) in this Chinese family and developed a prenatal haplotype-assisted approach to noninvasively detect the genotype of the fetus (transmitted from both parents). This is the first report of integration of targeted sequencing and noninvasive prenatal testing into clinical practice. Our study has demonstrated that this massively parallel sequencing-based strategy can potentially be used for single-gene disorder diagnosis in the future.

Simultaneous digital quantification and fluorescence-based size characterization of massively parallel sequencing libraries.

PubMed

Laurie, Matthew T; Bertout, Jessica A; Taylor, Sean D; Burton, Joshua N; Shendure, Jay A; Bielas, Jason H

2013-08-01

Due to the high cost of failed runs and suboptimal data yields, quantification and determination of fragment size range are crucial steps in the library preparation process for massively parallel sequencing (or next-generation sequencing). Current library quality control methods commonly involve quantification using real-time quantitative PCR and size determination using gel or capillary electrophoresis. These methods are laborious and subject to a number of significant limitations that can make library calibration unreliable. Herein, we propose and test an alternative method for quality control of sequencing libraries using droplet digital PCR (ddPCR). By exploiting a correlation we have discovered between droplet fluorescence and amplicon size, we achieve the joint quantification and size determination of target DNA with a single ddPCR assay. We demonstrate the accuracy and precision of applying this method to the preparation of sequencing libraries.

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.

Evolution of black holes in the galaxy

NASA Astrophysics Data System (ADS)

Brown, G. E.; Lee, C.-H.; Wijers, R. A. M. J.; Bethe, H. A.

2000-08-01

In this article we consider the formation and evolution of black holes, especially those in binary stars where radiation from the matter falling on them can be seen. We consider a number of effects introduced by some of us, which are not traditionally included in binary evolution of massive stars. These are (i) hypercritical accretion, which allows neutron stars to accrete enough matter to collapse to a black hole during their spiral-in into another star. (ii) The strong mass loss of helium stars, which causes their evolution to differ from that of the helium core of a massive star. (iii) The direct formation of low-mass black holes (M~2Msolar) from single stars, a consequence of a significant strange-matter content of the nuclear-matter equation of state at high density. We discuss these processes here, and then review how they affect various populations of binaries with black holes and neutron stars. We have found that hypercritical accretion changes the standard scenario for the evolution of binary neutron stars: it now usually gives a black-hole, neutron-star (BH-NS) binary, because the first-born neutron star collapses to a low-mass black hole in the course of the evolution. A less probable double helium star scenario has to be introduced in order to form neutron-star binaries. The result is that low-mass black-hole, neutron star (LBH-NS) binaries dominate the rate of detectable gravity-wave events, say, by LIGO, by a factor /~20 over the binary neutron stars. The formation of high-mass black holes is suppressed somewhat due to the influence of mass loss on the cores of massive stars, raising the minimum mass for a star to form a massive BH to perhaps 80Msolar. Still, inclusion of high-mass black-hole, neutron-star (HBH-NS) binaries increases the predicted LIGO detection rate by another /~30% lowering of the mass loss rates of Wolf-Rayet stars may lower the HBH mass limit, and thereby further increase the merger rate. We predict that /~33 mergers per year will be observed with LIGO once the advanced detectors planned to begin in 2004 are in place. Black holes are also considered as progenitors for gamma ray bursters (GRB). Due to their rapid spin, potentially high magnetic fields, and relatively clean environment, mergers of black-hole, neutron-star binaries may be especially suitable. Combined with their 10 times greater formation rate than binary neutron stars this makes them attractive candidates for GRB progenitors, although the strong concentration of GRBs towards host galaxies may favor massive star progenitors or helium-star, black-hole mergers. We also consider binaries with a low-mass companion, and study the evolution of the very large number of black-hole transients, consisting of a black hole of mass ~7Msolar accompanied by a K or M main-sequence star (except for two cases with a somewhat more massive subgiant donor). We show that common envelope evolution must take place in the supergiant stage of the massive progenitor of the black hole, giving an explanation of why the donor masses are so small. We predict that there are about 22 times more binaries than observed, in which the main-sequence star, somewhat more massive than a K- or M-star, sits quietly inside its Roche Lobe, and will only become an X-ray source when the companion evolves off the main sequence. We briefly discuss the evolution of low-mass X-ray binaries into millisecond pulsars. We point out that in the usual scenario for forming millisecond pulsars with He white-dwarf companions, the long period of stable mass transfer will usually lead to the collapse of the neutron star into a black hole. We then discuss Van den Heuvel's ``Hercules X-1 scenario'' for forming low-mass X-ray binaries, commenting on the differences in accretion onto the compact object by radiative or semiconvective donors, rather than the deeply convective donors used in the earlier part of our review. In Appendix /A we describe the evolution of Cyg X-3, finding the compact object to be a black hole of ~3Msolar, together with an ~10Msolar He star. In Appendix /B we do the accounting for gravitational mergers and in Appendix /C we show low-mass black-hole, neutron-star binaries to be good progenitors for gamma ray bursters.

Understanding the scatter in the spatially resolved star formation main sequence of local massive spiral galaxies

NASA Astrophysics Data System (ADS)

Abdurro'uf; Akiyama, Masayuki

2017-08-01

We investigate the relation between star formation rate (SFR) and stellar mass (M*) at the sub-galactic scale (˜1 kpc) of 93 local (0.01 < z < 0.02) massive (M* > 1010.5 M⊙) spiral galaxies. To derive a spatially resolved SFR and stellar mass, we perform the so-called pixel-to-pixel spectral energy distribution (SED) fitting, which fits an observed spatially resolved multiband SED with a library of model SEDs using Bayesian statistics. We use two bands (far-ultraviolet or FUV and near-ultraviolet or NUV) and five bands (u, g, r, I and z) of imaging data from Galaxy Evolution Explorer (GALEX) and Sloan Digital Sky Survey (SDSS), respectively. We find a tight nearly linear relation between the local surface density of SFR (ΣSFR) and stellar mass (Σ*), which is flattened at high Σ*. The near linear relation between Σ* and ΣSFR suggests a constant specific SFR (sSFR) throughout the galaxies, and the scatter of the relation is directly related to that of the sSFR. Therefore, we analyse the variation of the sSFR in various scales. More massive galaxies on average have lower sSFR throughout them than less massive galaxies. We also find that barred galaxies have a lower sSFR in the core region than non-barred galaxies. However, in the outer region, the sSFRs of barred and non-barred galaxies are similar and lead to a similar total sSFR.

A safe an easy method for building consensus HIV sequences from 454 massively parallel sequencing data.

PubMed

Fernández-Caballero Rico, Jose Ángel; Chueca Porcuna, Natalia; Álvarez Estévez, Marta; Mosquera Gutiérrez, María Del Mar; Marcos Maeso, María Ángeles; García, Federico

2018-02-01

To show how to generate a consensus sequence from the information of massive parallel sequences data obtained from routine HIV anti-retroviral resistance studies, and that may be suitable for molecular epidemiology studies. Paired Sanger (Trugene-Siemens) and next-generation sequencing (NGS) (454 GSJunior-Roche) HIV RT and protease sequences from 62 patients were studied. NGS consensus sequences were generated using Mesquite, using 10%, 15%, and 20% thresholds. Molecular evolutionary genetics analysis (MEGA) was used for phylogenetic studies. At a 10% threshold, NGS-Sanger sequences from 17/62 patients were phylogenetically related, with a median bootstrap-value of 88% (IQR83.5-95.5). Association increased to 36/62 sequences, median bootstrap 94% (IQR85.5-98)], using a 15% threshold. Maximum association was at the 20% threshold, with 61/62 sequences associated, and a median bootstrap value of 99% (IQR98-100). A safe method is presented to generate consensus sequences from HIV-NGS data at 20% threshold, which will prove useful for molecular epidemiological studies. Copyright © 2016 Elsevier España, S.L.U. and Sociedad Española de Enfermedades Infecciosas y Microbiología Clínica. All rights reserved.

Covariance Matrix Estimation for Massive MIMO

NASA Astrophysics Data System (ADS)

Upadhya, Karthik; Vorobyov, Sergiy A.

2018-04-01

We propose a novel pilot structure for covariance matrix estimation in massive multiple-input multiple-output (MIMO) systems in which each user transmits two pilot sequences, with the second pilot sequence multiplied by a random phase-shift. The covariance matrix of a particular user is obtained by computing the sample cross-correlation of the channel estimates obtained from the two pilot sequences. This approach relaxes the requirement that all the users transmit their uplink pilots over the same set of symbols. We derive expressions for the achievable rate and the mean-squared error of the covariance matrix estimate when the proposed method is used with staggered pilots. The performance of the proposed method is compared with existing methods through simulations.

The 13Carbon footprint of B[e] supergiants

NASA Astrophysics Data System (ADS)

Liermann, A.; Kraus, M.; Schnurr, O.; Fernandes, M. Borges

2010-10-01

We report on the first detection of 13C enhancement in two B[e] supergiants (B[e]SGs) in the Large Magellanic Cloud. Stellar evolution models predict the surface abundance in 13C to strongly increase during main-sequence and post-main-sequence evolution of massive stars. However, direct identification of chemically processed material on the surface of B[e]SGs is hampered by their dense, disc-forming winds, hiding the stars. Recent theoretical computations predict the detectability of enhanced 13C via the molecular emission in 13CO arising in the circumstellar discs of B[e]SGs. To test this potential method and to unambiguously identify a post-main-sequence B[e] SG by its 13CO emission, we have obtained high-quality K-band spectra of two known B[e] SGs in the Large Magellanic Cloud, using the Very Large Telescope's Spectrograph for INtegral Field Observation in the Near-Infrared (VLT/SINFONI). Both stars clearly show the 13CO band emission, whose strength implies a strong enhancement of 13C, in agreement with theoretical predictions. This first ever direct confirmation of the evolved nature of B[e]SGs thus paves the way to the first identification of a Galactic B[e]SG. Based on observations collected with the ESO VLT Paranal Observatory under programme 384.D-1078(A). E-mail: liermann@mpifr-bonn.mpg.de (AL); kraus@sunstel.asu.cas.cz (MK); oschnurr@aip.de (OS); borges@on.br (MBF)

Properties of six short-period massive binaries: A study of the effects of binarity on surface chemical abundances

NASA Astrophysics Data System (ADS)

Martins, F.; Mahy, L.; Hervé, A.

2017-11-01

Context. A significant percentage of massive stars are found in multiple systems. The effect of binarity on stellar evolution is poorly constrained. In particular, the role of tides and mass transfer on surface chemical abundances is not constrained observationally. Aims: The aim of this study is to investigate the effect of binarity on the stellar properties and surface abundances of massive binaries. Methods: We performed a spectroscopic analysis of six Galactic massive binaries. We obtained the spectra of individual components via a spectral disentangling method and subsequently analyzed these spectra by means of atmosphere models. The stellar parameters and CNO surface abundances were determined. Results: Most of these six systems are comprised of main-sequence stars. Three systems are detached, two are in contact, and no information is available for the sixth system. For 11 out of the 12 stars studied, the surface abundances are only mildly affected by stellar evolution and mixing. The surface abundances are not different from those of single stars within the uncertainties. The secondary of XZ Cep is strongly chemically enriched. Considering previous determinations of surface abundances in massive binary systems suggests that the effect of tides on chemical mixing is limited, whereas the mass transfer and removal of outer layers of the mass donor leads to the appearance of chemically processed material at the surface, although this is not systematic. The evolutionary masses of the components of our six systems are on average 16.5% higher than the dynamical masses. Some systems seem to have reached synchronization, while others may still be in a transitory phase. Based on observations made with the SOPHIE spectrograph on the 1.93 m telescope at Observatoire de Haute-Provence (OHP, CNRS/AMU), France.

Identifying Massive Runaway Stars by Detecting Infrared Bowshock Nebula: Four OB Stars and a New Massive Early-B Binary System

NASA Astrophysics Data System (ADS)

Sorber, Rebecca L.; Rebecca L. Sorber, Henry A. Kobulnicky, Daniel A. Dale, Matthew S. Povich, William T. Chick, Heather N. Wernke, Julian E. Andrews, Stephan Munari, Grace M. Olivier, Danielle Schurhammer

2016-01-01

Though the main sequence evolution of OB type stars is relatively well known, the mass loss rates for these stars are still highly uncertain. Some OB stars are gravitationally ejected from their birth sites, traveling at speeds of 30 km/s or more which results in a prominent bowshock nebulae. We identified OB bowshock candidates at low Galactic latitudes by visual inspection of the Wide-field Infrared Survey Explorer (WISE) 22-micron images. Each candidate was observed using the Longslit Spectrograph at the Wyoming Infrared Observatory (WIRO) 2.3 meter telescope. We present here the results from observing four such candidates, and all four are confirmed as early type stars: GO92.3191+0.0591 (B1V) (aka ALS11826), GO86.551014-1.0873935 (B2V; a probable short-period binary), G076.6921-2.4071 (B5V), and G075.5711-0.2558 (B0V) (aka HD 194303). These results enlarge the sample of candidate runaway massive stars hosting bowshocks and provide a promising sample of such objects for studying stellar mass loss. This work is supported by the National Science Foundation Grants AST-1063146 (REU), AST-1411851 (RUI), and AST-1412845.

Sequence investigation of 34 forensic autosomal STRs with massively parallel sequencing.

PubMed

Zhang, Suhua; Niu, Yong; Bian, Yingnan; Dong, Rixia; Liu, Xiling; Bao, Yun; Jin, Chao; Zheng, Hancheng; Li, Chengtao

2018-05-01

STRs vary not only in the length of the repeat units and the number of repeats but also in the region with which they conform to an incremental repeat pattern. Massively parallel sequencing (MPS) offers new possibilities in the analysis of STRs since they can simultaneously sequence multiple targets in a single reaction and capture potential internal sequence variations. Here, we sequenced 34 STRs applied in the forensic community of China with a custom-designed panel. MPS performance were evaluated from sequencing reads analysis, concordance study and sensitivity testing. High coverage sequencing data were obtained to determine the constitute ratios and heterozygous balance. No actual inconsistent genotypes were observed between capillary electrophoresis (CE) and MPS, demonstrating the reliability of the panel and the MPS technology. With the sequencing data from the 200 investigated individuals, 346 and 418 alleles were obtained via CE and MPS technologies at the 34 STRs, indicating MPS technology provides higher discrimination than CE detection. The whole study demonstrated that STR genotyping with the custom panel and MPS technology has the potential not only to reveal length and sequence variations but also to satisfy the demands of high throughput and high multiplexing with acceptable sensitivity.

Dubinett - Targeted Sequencing 2012 — EDRN Public Portal

Cancer.gov

we propose to use targeted massively parallel DNA sequencing to identify somatic alterations within mutational hotspots in matched sets of primary lung tumors, premalignant lesions, and adjacent,histologically normal lung tissue.

Les galaxies

NASA Astrophysics Data System (ADS)

Combes, Francoise

2016-08-01

Considerable progress has been made on galaxy formation and evolution in recent years, and new issues. The old Hubble classification according to the tuning fork of spirals, lenticulars and ellipticals, is still useful but has given place to the red sequence, the blue cloud and the green valley, showing a real bimodality of types between star forming galaxies (blue) and quenched ones (red). Large surveys have shown that stellar mass and environment density are the two main factors of the evolution from blue to red sequences. Evolution is followed directly with redshift through a look-back time of more than 12 billion years. The most distant galaxy at z=11. has already a stellar mass of a billion suns. In an apparent anti-hierarchical scenario, the most massive galaxies form stars early on, while essentially dwarf galaxies are actively star-formers now. This downsizing feature also applies to the growth of super-massive black holes at the heart of each bulgy galaxy. The feedback from active nuclei is essential to explain the distribution of mass in galaxies, and in particular to explain why the fraction of baryonic matter is so low, lower by more than a factor 5 than the baryonic fraction of the Universe. New instruments just entering in operation, like MUSE and ALMA, provide a new and rich data flow, which is developed in this series of articles.

Yet Another Model for the Gamma-Ray Bursts

NASA Astrophysics Data System (ADS)

Leonard, P. J. T.

2000-05-01

We consider whether a gamma-ray burst can result from a merger between a neutron star and a massive main-sequence star in a binary system following a supernova explosion. The scenario for how this can happen is outlined in Leonard, Hills & Dewey 1994, ApJ, 423, L19-L22. The initially more massive star in a massive binary system evolves and undergoes core collapse to produce a neutron star and supernova. Since the outer layers of the originally more massive star have been transferred to the other star, then the supernova may be hydrogen deficient. The newly-formed neutron star receives a random kick during the explosion. In a small fraction of the cases, the kick has the appropriate direction and amplitude to remove most of the orbital angular momentum of the post-supernova binary system. The result is an orbit with a pericenter smaller than the radius of the non-exploding star. The neutron star rather quickly becomes embedded in the other star, and sinks to its center, giving the envelope of the merged object a lot of rotational angular momentum in the process. Leonard, Hills & Dewey estimate the rate of this process in the Galaxy to be 0.06 per square kpc per Myr for secondaries more massive than 15 solar masses. The fate of the merged object has been the source of much speculation, and we shall assume that a collapsar-like scenario results. That is, the neutron star experiences runaway accretion, collapses into a black hole, which continues to accrete, and produces a pair of jets that bore their way out of the merged object. Observers who lie in the direction of either jet will see a gamma-ray burst. Roughly 1% of supernovae in massive binary systems result in neutron stars quickly becoming embedded in the secondaries, and of those which produce black holes, only 1% would be observable as gamma-ray bursts, if the jets are beamed into 1% of the sky.

Evaluation of targeted exome sequencing for 28 protein-based blood group systems, including the homologous gene systems, for blood group genotyping.

PubMed

Schoeman, Elizna M; Lopez, Genghis H; McGowan, Eunike C; Millard, Glenda M; O'Brien, Helen; Roulis, Eileen V; Liew, Yew-Wah; Martin, Jacqueline R; McGrath, Kelli A; Powley, Tanya; Flower, Robert L; Hyland, Catherine A

2017-04-01

Blood group single nucleotide polymorphism genotyping probes for a limited range of polymorphisms. This study investigated whether massively parallel sequencing (also known as next-generation sequencing), with a targeted exome strategy, provides an extended blood group genotype and the extent to which massively parallel sequencing correctly genotypes in homologous gene systems, such as RH and MNS. Donor samples (n = 28) that were extensively phenotyped and genotyped using single nucleotide polymorphism typing, were analyzed using the TruSight One Sequencing Panel and MiSeq platform. Genes for 28 protein-based blood group systems, GATA1, and KLF1 were analyzed. Copy number variation analysis was used to characterize complex structural variants in the GYPC and RH systems. The average sequencing depth per target region was 66.2 ± 39.8. Each sample harbored on average 43 ± 9 variants, of which 10 ± 3 were used for genotyping. For the 28 samples, massively parallel sequencing variant sequences correctly matched expected sequences based on single nucleotide polymorphism genotyping data. Copy number variation analysis defined the Rh C/c alleles and complex RHD hybrids. Hybrid RHD*D-CE-D variants were correctly identified, but copy number variation analysis did not confidently distinguish between D and CE exon deletion versus rearrangement. The targeted exome sequencing strategy employed extended the range of blood group genotypes detected compared with single nucleotide polymorphism typing. This single-test format included detection of complex MNS hybrid cases and, with copy number variation analysis, defined RH hybrid genes along with the RHCE*C allele hitherto difficult to resolve by variant detection. The approach is economical compared with whole-genome sequencing and is suitable for a red blood cell reference laboratory setting. © 2017 AABB.

Quantitative ultrashort echo time imaging for assessment of massive iron overload at 1.5 and 3 Tesla.

PubMed

Krafft, Axel J; Loeffler, Ralf B; Song, Ruitian; Tipirneni-Sajja, Aaryani; McCarville, M Beth; Robson, Matthew D; Hankins, Jane S; Hillenbrand, Claudia M

2017-11-01

Hepatic iron content (HIC) quantification via transverse relaxation rate (R2*)-MRI using multi-gradient echo (mGRE) imaging is compromised toward high HIC or at higher fields due to the rapid signal decay. Our study aims at presenting an optimized 2D ultrashort echo time (UTE) sequence for R2* quantification to overcome these limitations. Two-dimensional UTE imaging was realized via half-pulse excitation and radial center-out sampling. The sequence includes chemically selective saturation pulses to reduce streaking artifacts from subcutaneous fat, and spatial saturation (sSAT) bands to suppress out-of-slice signals. The sequence employs interleaved multi-echo readout trains to achieve dense temporal sampling of rapid signal decays. Evaluation was done at 1.5 Tesla (T) and 3T in phantoms, and clinical applicability was demonstrated in five patients with biopsy-confirmed massively high HIC levels (>25 mg Fe/g dry weight liver tissue). In phantoms, the sSAT pulses were found to remove out-of-slice contamination, and R2* results were in excellent agreement to reference mGRE R2* results (slope of linear regression: 1.02/1.00 for 1.5/3T). UTE-based R2* quantification in patients with massive iron overload proved successful at both field strengths and was consistent with biopsy HIC values. The UTE sequence provides a means to measure R2* in patients with massive iron overload, both at 1.5T and 3T. Magn Reson Med 78:1839-1851, 2017. © 2017 Wiley Periodicals, Inc. © 2017 International Society for Magnetic Resonance in Medicine.

Use Massive Parallel Sequencing and Exome Capture Technology to Sequence the Exome of Fanconi Anemia Children and Their Patents

ClinicalTrials.gov

2013-11-21

Fanconi Anemia; Autosomal or Sex Linked Recessive Genetic Disease; Bone Marrow Hematopoiesis Failure, Multiple Congenital Abnormalities, and Susceptibility to Neoplastic Diseases.; Hematopoiesis Maintainance.

Black Hole Growth Is Mainly Linked to Host-galaxy Stellar Mass Rather Than Star Formation Rate

NASA Astrophysics Data System (ADS)

Yang, G.; Chen, C.-T. J.; Vito, F.; Brandt, W. N.; Alexander, D. M.; Luo, B.; Sun, M. Y.; Xue, Y. Q.; Bauer, F. E.; Koekemoer, A. M.; Lehmer, B. D.; Liu, T.; Schneider, D. P.; Shemmer, O.; Trump, J. R.; Vignali, C.; Wang, J.-X.

2017-06-01

We investigate the dependence of black hole accretion rate (BHAR) on host-galaxy star formation rate (SFR) and stellar mass (M *) in the CANDELS/GOODS-South field in the redshift range of 0.5≤slant z< 2.0. Our sample consists of ≈ {{18,000}} galaxies, allowing us to probe galaxies with 0.1{M}⊙ {{yr}}-1≲ {SFR}≲ 100 {M}⊙ {{yr}}-1 and/or {10}8{M}⊙ ≲ {M}* ≲ {10}11 {M}⊙ . We use sample-mean BHAR to approximate long-term average BHAR. Our sample-mean BHARs are derived from the Chandra Deep Field-South 7 Ms observations, while the SFRs and M * have been estimated by the CANDELS team through spectral energy distribution fitting. The average BHAR is correlated positively with both SFR and M *, and the BHAR-SFR and BHAR-M * relations can both be described acceptably by linear models with a slope of unity. However, BHAR appears to be correlated more strongly with M * than SFR. This result indicates that M * is the primary host-galaxy property related to supermassive black hole (SMBH) growth, and the apparent BHAR-SFR relation is largely a secondary effect due to the star-forming main sequence. Among our sources, massive galaxies ({M}* ≳ {10}10{M}⊙ ) have significantly higher BHAR/SFR ratios than less massive galaxies, indicating that the former have higher SMBH fueling efficiency and/or higher SMBH occupation fraction than the latter. Our results can naturally explain the observed proportionality between {M}{BH} and M * for local giant ellipticals and suggest that their {M}{BH}/{M}* is higher than that of local star-forming galaxies. Among local star-forming galaxies, massive systems might have higher {M}{BH}/{M}* compared to dwarfs.

Evidence of a Volcanogenic Massive Sulfide (Znsbnd Pbsbnd Cusbnd Ag) district within the Tiébélé Birimian (Paleoproterozoic) Greenstone Belts, Southern Burkina Faso (West - Africa)

NASA Astrophysics Data System (ADS)

Ilboudo, Hermann; Lompo, Martin; Wenmenga, Urbain; Napon, Salif; Naba, Seta; Ngom, Papa Malick

2017-05-01

Twenty years after the discovery of the Perkoa Znsbnd Ag deposit, another type of Znsbnd Cusbnd Pb ± Ag Volcanogenic Massive Sulfide (VMS) subgroup of occurrences forming a district has been highlighted within the Paleoproterozoic Birimian Greenstone Belts of the West African Craton in Burkina Faso. The geology of the area is characterized by a series of dominantly mafic volcanic rocks with intercalated black shales which increase in proportion upwards in the stratigraphy. This stratigraphic package is overlain by a felsic volcanic sequence comprising reworked tuff and rhyolite. Although mineralization is locally associated with sedimentary rocks, it is more commonly found in rhyolites. The metamorphic grade is dominantly greenschist facies. The main lithologies in the mafic sequence range from basalt to andesite with associated gabbro. The felsic sequence consists of dacite to rhyolite with associated granitoids (granite-granodiorite-tonalite). The volcanic rocks are commonly tholeiitic (Zr/Y = 2-4.5) with relatively high Zr and Y content, although a limited number of samples plot in transitional (Zr/Y = 4.5-7) or calc-alkaline (Zr/Y = 7-25) fields. Rhyolites, which constitute the main mineralized rocks at Tiébélé, have similar key trace element signatures to other rhyolites-related known VMS systems worldwide. Both have low Zr/Y (<7) and low LaN/YbN (<6), which suggests low crustal residence times of magmas in extensional settings. Detailed investigations identified at least four VMS targets notably at Koubongo, Nabenia, Loubel and AVV (Aménagement de la Vallée des Voltas) extending over an area of 332 km2. Typical mineral assemblages defining VMS occurrences are mainly hosted by meta-sedimentary rocks and rhyolite but are also found as veins in tonalite. These assemblages can be grouped into four different styles: (i) Variably banded massive sulfides dominated by sphalerite over galena, pyrite, and chalcopyrite within metasediments; (ii) Pyrite-rich or pyrrhotite banded type associated with sphalerite, chalcopyrite, and galena within silicified and carbonatized units; (iii) Disseminated and finely oriented sulfides, including pyrite - pyrrhotite - magnetite ± sphalerite within quartz-phyric rhyolite; and (iv) Fracture filling pyrrhotite-rich - magnetite - sphalerite mineralization possibly within tonalite. Irrespective of the style of the mineralization, chemistry of altered and least altered rhyolite reveals a significant increase in Mg ± Fe and H2O, and a loss of K within mineralization associated alteration. This may suggest sea water leaching of underlying (?) mafic and sedimentary rocks, with Mgsbnd Fe transfer into the rhyolites concomitant with the loss of K. This paper highlights the features of new occurrences of VMS mineralization type within the Birimian system of West Africa. We think this could help for new discoveries along the belts. Exploration based upon ground mapping, geochemistry and geophysics is highly recommended.

Resolved photometry of extragalactic young massive star clusters

NASA Astrophysics Data System (ADS)

Larsen, S. S.; de Mink, S. E.; Eldridge, J. J.; Langer, N.; Bastian, N.; Seth, A.; Smith, L. J.; Brodie, J.; Efremov, Yu. N.

2011-08-01

Aims: We present colour-magnitude diagrams (CMDs) of young massive star clusters in several galaxies located well beyond the Local Group. The richness of these clusters allows us to obtain large samples of post-main sequence stars and test how well the observed CMDs are reproduced by canonical stellar isochrones. Methods: We use imaging of seven clusters in the galaxies NGC 1313, NGC 1569, NGC 1705, NGC 5236 and NGC 7793 obtained with the Advanced Camera for Surveys on board the Hubble Space Telescope and carry out PSF-fitting photometry of individual stars in the clusters. The clusters have ages in the range ~(5-50) × 106 years and masses of ~105 M⊙-106 M⊙. Although crowding prevents us from obtaining photometry in the inner regions of the clusters, we are still able to measure up to 30-100 supergiant stars in each of the richest clusters. The resulting CMDs and luminosity functions are compared with photometry of artificially generated clusters, designed to reproduce the photometric errors and completeness as realistically as possible. Results: In agreement with previous studies, our CMDs show no clear gap between the H-burning main sequence and the He-burning supergiant stars, contrary to predictions by common stellar isochrones. In general, the isochrones also fail to match the observed number ratios of red-to-blue supergiant stars, although the difficulty of separating blue supergiants from the main sequence complicates this comparison. In several cases we observe a large spread (1-2 mag) in the luminosities of the supergiant stars that cannot be accounted for by observational errors. We find that this spread can be reproduced by including an age spread of ~(10-30) × 106 years in the models. However, age spreads cannot fully account for the observed morphology of the CMDs and other processes, such as the evolution of interacting binary stars, may also play a role. Conclusions: Colour-magnitude diagrams can be successfully obtained for massive star clusters out to distances of at least 4-5 Mpc. Comparing such CMDs with models based on canonical isochrones we find several areas of disagreement. One interesting possibility is that an age spread of up to ~30 Myr may be present in some clusters. The data presented here may provide useful constraints on models for single and/or binary stellar evolution. Based on observations made with the NASA/ESA Hubble Space Telescope, obtained from the data archive at the Space Telescope Science Institute. STScI is operated by the association of Universities for Research in Astronomy, Inc. under the NASA contract NAS 5-26555Tables 4-10 are only available in electronic form at the CDS via anonymous ftp to cdsarc.u-strasbg.fr (130.79.128.5) or via http://cdsarc.u-strasbg.fr/viz-bin/qcat?J/A+A/532/A147

Identification of the Bovine Arachnomelia Mutation by Massively Parallel Sequencing Implicates Sulfite Oxidase (SUOX) in Bone Development

PubMed Central

Drögemüller, Cord; Tetens, Jens; Sigurdsson, Snaevar; Gentile, Arcangelo; Testoni, Stefania; Lindblad-Toh, Kerstin; Leeb, Tosso

2010-01-01

Arachnomelia is a monogenic recessive defect of skeletal development in cattle. The causative mutation was previously mapped to a ∼7 Mb interval on chromosome 5. Here we show that array-based sequence capture and massively parallel sequencing technology, combined with the typical family structure in livestock populations, facilitates the identification of the causative mutation. We re-sequenced the entire critical interval in a healthy partially inbred cow carrying one copy of the critical chromosome segment in its ancestral state and one copy of the same segment with the arachnomelia mutation, and we detected a single heterozygous position. The genetic makeup of several partially inbred cattle provides extremely strong support for the causality of this mutation. The mutation represents a single base insertion leading to a premature stop codon in the coding sequence of the SUOX gene and is perfectly associated with the arachnomelia phenotype. Our findings suggest an important role for sulfite oxidase in bone development. PMID:20865119

Multiplexed microsatellite recovery using massively parallel sequencing

USGS Publications Warehouse

Jennings, T.N.; Knaus, B.J.; Mullins, T.D.; Haig, S.M.; Cronn, R.C.

2011-01-01

Conservation and management of natural populations requires accurate and inexpensive genotyping methods. Traditional microsatellite, or simple sequence repeat (SSR), marker analysis remains a popular genotyping method because of the comparatively low cost of marker development, ease of analysis and high power of genotype discrimination. With the availability of massively parallel sequencing (MPS), it is now possible to sequence microsatellite-enriched genomic libraries in multiplex pools. To test this approach, we prepared seven microsatellite-enriched, barcoded genomic libraries from diverse taxa (two conifer trees, five birds) and sequenced these on one lane of the Illumina Genome Analyzer using paired-end 80-bp reads. In this experiment, we screened 6.1 million sequences and identified 356958 unique microreads that contained di- or trinucleotide microsatellites. Examination of four species shows that our conversion rate from raw sequences to polymorphic markers compares favourably to Sanger- and 454-based methods. The advantage of multiplexed MPS is that the staggering capacity of modern microread sequencing is spread across many libraries; this reduces sample preparation and sequencing costs to less than $400 (USD) per species. This price is sufficiently low that microsatellite libraries could be prepared and sequenced for all 1373 organisms listed as 'threatened' and 'endangered' in the United States for under $0.5M (USD).

MODULES FOR EXPERIMENTS IN STELLAR ASTROPHYSICS (MESA): BINARIES, PULSATIONS, AND EXPLOSIONS

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

Paxton, Bill; Bildsten, Lars; Cantiello, Matteo

We substantially update the capabilities of the open-source software instrument Modules for Experiments in Stellar Astrophysics (MESA). MESA can now simultaneously evolve an interacting pair of differentially rotating stars undergoing transfer and loss of mass and angular momentum, greatly enhancing the prior ability to model binary evolution. New MESA capabilities in fully coupled calculation of nuclear networks with hundreds of isotopes now allow MESA to accurately simulate the advanced burning stages needed to construct supernova progenitor models. Implicit hydrodynamics with shocks can now be treated with MESA, enabling modeling of the entire massive star lifecycle, from pre-main-sequence evolution to themore » onset of core collapse and nucleosynthesis from the resulting explosion. Coupling of the GYRE non-adiabatic pulsation instrument with MESA allows for new explorations of the instability strips for massive stars while also accelerating the astrophysical use of asteroseismology data. We improve the treatment of mass accretion, giving more accurate and robust near-surface profiles. A new MESA capability to calculate weak reaction rates “on-the-fly” from input nuclear data allows better simulation of accretion induced collapse of massive white dwarfs and the fate of some massive stars. We discuss the ongoing challenge of chemical diffusion in the strongly coupled plasma regime, and exhibit improvements in MESA that now allow for the simulation of radiative levitation of heavy elements in hot stars. We close by noting that the MESA software infrastructure provides bit-for-bit consistency for all results across all the supported platforms, a profound enabling capability for accelerating MESA's development.« less

The diversity of evolutionary pathways of compact elliptical galaxies in cosmological simulations

NASA Astrophysics Data System (ADS)

Wellons, Sarah

2017-01-01

Observations of the high-redshift universe have revealed a population of galaxies which are already very massive (~1e11 solar masses at z=2) and have typical sizes of < 2 kpc, much smaller than their counterparts in the local universe. How such dense, massive galaxies form, and why they appear to be less common at low redshift, have been questions of interest for both theorists and observers. I will discuss these questions in the context of the Illustris simulation, a hydrodynamical cosmological simulation in which tens of thousands of galaxies form, evolve, and interact with each other, situated within a cosmological context. I select a group of massive compact galaxies at z=2 in the simulation and trace them back and forth in time to discover both how they formed at high redshift, and what they evolve into at the present day. I find a variety of both progenitors (compact galaxies form in the simulation either via central starbursts generally brought on by mergers, or by racing out to the tip of the SF main sequence and forming very early) and descendants (many formerly-compact galaxies lurk at the core of a more massive galaxy today, others were consumed in mergers, and some evolve passively and undisturbed). I will also discuss the implications of these results for observational methods of connecting galaxy populations across redshifts - in particular, the assumption of a constant cumulative comoving number density - and suggest an improvement to this method which takes the complexity and variety of galaxies' evolutionary paths into account.

Re-Os sulfide geochronology of the Red Dog sediment-hosted Zn-Pb-Ag deposit, Brooks Range, Alaska

USGS Publications Warehouse

Morelli, R.M.; Creaser, R.A.; Selby, D.; Kelley, K.D.; Leach, D.L.; King, A.R.

2004-01-01

The Red Dog sediment-hosted deposit in the De Long Mountains of northern Alaska is the largest Zn producer in the world. Main stage mineralization is characterized by massive sulfide ore and crosscutting subvertical veins. Although the vein mineralization is clearly younger than the massive ore, the exact temporal relationship between the two is unclear. Re-Os geochronology of pyrite is used to determine the absolute age of main stage ore at Red Dog. A 10-point isochron on both massive and vein pyrite yields an age of 338.3 ?? 5.8 Ma and is interpreted to represent the age of main stage ore. The Re-Os data indicate that both massive and vein ore types are coeval within the resolution of the technique. Formation of the Red Dog deposit was associated with extension along a passive continental margin, and therefore the Re-Os age of main stage ore constrains the timing of rifting as well as the age of the host sedimentary rocks. Sphalerite from both massive and vein ore yields imprecise ages and shows a high degree of scatter compared to pyrite. We suggest that the Re-Os systematics of sphalerite can be disturbed and that this mineral is not reliable for Re-Os geochronology. ?? 2004 by Economic Geology.

Post-main-sequence Evolution of Icy Minor Planets. II. Water Retention and White Dwarf Pollution around Massive Progenitor Stars

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

Malamud, Uri; Perets, Hagai B., E-mail: uri.mal@tx.technion.ac.il, E-mail: hperets@physics.technion.ac.il

Most studies suggest that the pollution of white dwarf (WD) atmospheres arises from the accretion of minor planets, but the exact properties of polluting material, and in particular the evidence for water in some cases, are not yet understood. Here we study the water retention of small icy bodies in exo-solar planetary systems, as their respective host stars evolve through and off the main sequence and eventually become WDs. We explore, for the first time, a wide range of star masses and metallicities. We find that the mass of the WD progenitor star is of crucial importance for the retentionmore » of water, while its metallicity is relatively unimportant. We predict that minor planets around lower-mass WD progenitors would generally retain more water and would do so at closer distances from the WD than compared with high-mass progenitors. The dependence of water retention on progenitor mass and other parameters has direct implications for the origin of observed WD pollution, and we discuss how our results and predictions might be tested in the future as more observations of WDs with long cooling ages become available.« less

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.

Barium Stars: Theoretical Interpretation

NASA Astrophysics Data System (ADS)

Husti, Laura; Gallino, Roberto; Bisterzo, Sara; Straniero, Oscar; Cristallo, Sergio

2009-09-01

Barium stars are extrinsic Asymptotic Giant Branch (AGB) stars. They present the s-enhancement characteristic for AGB and post-AGB stars, but are in an earlier evolutionary stage (main sequence dwarfs, subgiants, red giants). They are believed to form in binary systems, where a more massive companion evolved faster, produced the s-elements during its AGB phase, polluted the present barium star through stellar winds and became a white dwarf. The samples of barium stars of Allen & Barbuy (2006) and of Smiljanic et al. (2007) are analysed here. Spectra of both samples were obtained at high-resolution and high S/N. We compare these observations with AGB nucleosynthesis models using different initial masses and a spread of 13C-pocket efficiencies. Once a consistent solution is found for the whole elemental distribution of abundances, a proper dilution factor is applied. This dilution is explained by the fact that the s-rich material transferred from the AGB to the nowadays observed stars is mixed with the envelope of the accretor. We also analyse the mass transfer process, and obtain the wind velocity for giants and subgiants with known orbital period. We find evidence that thermohaline mixing is acting inside main sequence dwarfs and we present a method for estimating its depth.

Can the periodic spectral modulations observed in 236 Sloan Sky Survey stars be due to dark matter effects?

NASA Astrophysics Data System (ADS)

Tamburini, Fabrizio; Licata, Ignazio

2017-09-01

The search for dark matter (DM) is one of the most active and challenging areas of current research. Possible DM candidates are ultralight fields such as axions and weak interacting massive particles (WIMPs). Axions piled up in the center of stars are supposed to generate matter/DM configurations with oscillating geometries at a very rapid frequency, which is a multiple of the axion mass m B (Brito et al (2015); Brito et al (2016)). Borra and Trottier (2016) recently found peculiar ultrafast periodic spectral modulations in 236 main sequence stars in the sample of 2.5 million spectra of galactic halo stars of the Sloan Digital Sky Survey (˜1% of main sequence stars in the F-K spectral range) that were interpreted as optical signals from extraterrestrial civilizations, suggesting them as possible candidates for the search for extraterrestrial intelligence (SETI) program. We argue, instead, that this could be the first indirect evidence of bosonic axion-like DM fields inside main sequence stars, with a stable radiative nucleus, where a stable DM core can be hosted. These oscillations were not observed in earlier stellar spectral classes probably because of the impossibility of starting a stable oscillatory regime due to the presence of chaotic motions in their convective nuclei. The axion mass values, (50< {m}B< 2.4× {10}3) μ {eV}, obtained from the frequency range observed by Borra and Trottier, (0.6070< f< 0.6077) THz, agree with the recent theoretical results from high-temperature lattice quantum chromodynamics (Borsanyi et al (2016); Borsanyi et al (2016b)).

Genetic heterogeneity of RPMI-8402, a T-acute lymphoblastic leukemia cell line

PubMed Central

STOCZYNSKA-FIDELUS, EWELINA; PIASKOWSKI, SYLWESTER; PAWLOWSKA, ROZA; SZYBKA, MALGORZATA; PECIAK, JOANNA; HULAS-BIGOSZEWSKA, KRYSTYNA; WINIECKA-KLIMEK, MARTA; RIESKE, PIOTR

2016-01-01

Thorough examination of genetic heterogeneity of cell lines is uncommon. In order to address this issue, the present study analyzed the genetic heterogeneity of RPMI-8402, a T-acute lymphoblastic leukemia (T-ALL) cell line. For this purpose, traditional techniques such as fluorescence in situ hybridization and immunocytochemistry were used, in addition to more advanced techniques, including cell sorting, Sanger sequencing and massive parallel sequencing. The results indicated that the RPMI-8402 cell line consists of several genetically different cell subpopulations. Furthermore, massive parallel sequencing of RPMI-8402 provided insight into the evolution of T-ALL carcinogenesis, since this cell line exhibited the genetic heterogeneity typical of T-ALL. Therefore, the use of cell lines for drug testing in future studies may aid the progress of anticancer drug research. PMID:26870252

Fungal diversity in grape must and wine fermentation assessed by massive sequencing, quantitative PCR and DGGE

PubMed Central

Wang, Chunxiao; García-Fernández, David; Mas, Albert; Esteve-Zarzoso, Braulio

2015-01-01

The diversity of fungi in grape must and during wine fermentation was investigated in this study by culture-dependent and culture-independent techniques. Carignan and Grenache grapes were harvested from three vineyards in the Priorat region (Spain) in 2012, and nine samples were selected from the grape must after crushing and during wine fermentation. From culture-dependent techniques, 362 isolates were randomly selected and identified by 5.8S-ITS-RFLP and 26S-D1/D2 sequencing. Meanwhile, genomic DNA was extracted directly from the nine samples and analyzed by qPCR, DGGE and massive sequencing. The results indicated that grape must after crushing harbored a high species richness of fungi with Aspergillus tubingensis, Aureobasidium pullulans, or Starmerella bacillaris as the dominant species. As fermentation proceeded, the species richness decreased, and yeasts such as Hanseniaspora uvarum, Starmerella bacillaris and Saccharomyces cerevisiae successively occupied the must samples. The “terroir” characteristics of the fungus population are more related to the location of the vineyard than to grape variety. Sulfur dioxide treatment caused a low effect on yeast diversity by similarity analysis. Because of the existence of large population of fungi on grape berries, massive sequencing was more appropriate to understand the fungal community in grape must after crushing than the other techniques used in this study. Suitable target sequences and databases were necessary for accurate evaluation of the community and the identification of species by the 454 pyrosequencing of amplicons. PMID:26557110

Massively Parallel Sequencing of Patients with Intellectual Disability, Congenital Anomalies and/or Autism Spectrum Disorders with a Targeted Gene Panel

PubMed Central

Brett, Maggie; McPherson, John; Zang, Zhi Jiang; Lai, Angeline; Tan, Ee-Shien; Ng, Ivy; Ong, Lai-Choo; Cham, Breana; Tan, Patrick; Rozen, Steve; Tan, Ene-Choo

2014-01-01

Developmental delay and/or intellectual disability (DD/ID) affects 1–3% of all children. At least half of these are thought to have a genetic etiology. Recent studies have shown that massively parallel sequencing (MPS) using a targeted gene panel is particularly suited for diagnostic testing for genetically heterogeneous conditions. We report on our experiences with using massively parallel sequencing of a targeted gene panel of 355 genes for investigating the genetic etiology of eight patients with a wide range of phenotypes including DD/ID, congenital anomalies and/or autism spectrum disorder. Targeted sequence enrichment was performed using the Agilent SureSelect Target Enrichment Kit and sequenced on the Illumina HiSeq2000 using paired-end reads. For all eight patients, 81–84% of the targeted regions achieved read depths of at least 20×, with average read depths overlapping targets ranging from 322× to 798×. Causative variants were successfully identified in two of the eight patients: a nonsense mutation in the ATRX gene and a canonical splice site mutation in the L1CAM gene. In a third patient, a canonical splice site variant in the USP9X gene could likely explain all or some of her clinical phenotypes. These results confirm the value of targeted MPS for investigating DD/ID in children for diagnostic purposes. However, targeted gene MPS was less likely to provide a genetic diagnosis for children whose phenotype includes autism. PMID:24690944

Inter-laboratory evaluation of the EUROFORGEN Global ancestry-informative SNP panel by massively parallel sequencing using the Ion PGM™.

PubMed

Eduardoff, M; Gross, T E; Santos, C; de la Puente, M; Ballard, D; Strobl, C; Børsting, C; Morling, N; Fusco, L; Hussing, C; Egyed, B; Souto, L; Uacyisrael, J; Syndercombe Court, D; Carracedo, Á; Lareu, M V; Schneider, P M; Parson, W; Phillips, C; Parson, W; Phillips, C

2016-07-01

The EUROFORGEN Global ancestry-informative SNP (AIM-SNPs) panel is a forensic multiplex of 128 markers designed to differentiate an individual's ancestry from amongst the five continental population groups of Africa, Europe, East Asia, Native America, and Oceania. A custom multiplex of AmpliSeq™ PCR primers was designed for the Global AIM-SNPs to perform massively parallel sequencing using the Ion PGM™ system. This study assessed individual SNP genotyping precision using the Ion PGM™, the forensic sensitivity of the multiplex using dilution series, degraded DNA plus simple mixtures, and the ancestry differentiation power of the final panel design, which required substitution of three original ancestry-informative SNPs with alternatives. Fourteen populations that had not been previously analyzed were genotyped using the custom multiplex and these studies allowed assessment of genotyping performance by comparison of data across five laboratories. Results indicate a low level of genotyping error can still occur from sequence misalignment caused by homopolymeric tracts close to the target SNP, despite careful scrutiny of candidate SNPs at the design stage. Such sequence misalignment required the exclusion of component SNP rs2080161 from the Global AIM-SNPs panel. However, the overall genotyping precision and sensitivity of this custom multiplex indicates the Ion PGM™ assay for the Global AIM-SNPs is highly suitable for forensic ancestry analysis with massively parallel sequencing. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Dynamical age differences among coeval star clusters as revealed by blue stragglers.

PubMed

Ferraro, F R; Lanzoni, B; Dalessandro, E; Beccari, G; Pasquato, M; Miocchi, P; Rood, R T; Sigurdsson, S; Sills, A; Vesperini, E; Mapelli, M; Contreras, R; Sanna, N; Mucciarelli, A

2012-12-20

Globular star clusters that formed at the same cosmic time may have evolved rather differently from the dynamical point of view (because that evolution depends on the internal environment) through a variety of processes that tend progressively to segregate stars more massive than the average towards the cluster centre. Therefore clusters with the same chronological age may have reached quite different stages of their dynamical history (that is, they may have different 'dynamical ages'). Blue straggler stars have masses greater than those at the turn-off point on the main sequence and therefore must be the result of either a collision or a mass-transfer event. Because they are among the most massive and luminous objects in old clusters, they can be used as test particles with which to probe dynamical evolution. Here we report that globular clusters can be grouped into a few distinct families on the basis of the radial distribution of blue stragglers. This grouping corresponds well to an effective ranking of the dynamical stage reached by stellar systems, thereby permitting a direct measure of the cluster dynamical age purely from observed properties.

The evolution of massive stars including mass loss - Presupernova models and explosion

NASA Technical Reports Server (NTRS)

Woosley, S. E.; Langer, Norbert; Weaver, Thomas A.

1993-01-01

The evolution of massive stars of 35, 40, 60, and 85 solar masses is followed through all stages of nuclear burning to the point of Fe core collapse. Critical nuclear reaction and mass-loss rates are varied. Efficient mass loss during the Wolf-Rayet (WR) stage is likely to lead to final masses as small as 4 solar masses. For a reasonable parameterization of the mass loss, there may be convergence of all WR stars, both single and in binaries, to a narrow band of small final masses. Our representative model, a 4.25 solar-mass WR presupernova derived from a 60 solar mass star, is followed through a simulated explosion, and its explosive nucleosynthesis and light curve are determined. Its properties are similar to those observed in Type Ib supernovae. The effects of the initial mass and mass loss on the presupernova structure of small mass WR models is also explored. Important properties of the presupernova star and its explosion can only be obtained by following the complete evolution starting on the main sequence.

ALMA Shows that Gas Reservoirs of Star-forming Disks over the Past 3 Billion Years Are Not Predominantly Molecular

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

Cortese, Luca; Catinella, Barbara; Janowiecki, Steven, E-mail: luca.cortese@uwa.edu.au

Cold hydrogen gas is the raw fuel for star formation in galaxies, and its partition into atomic and molecular phases is a key quantity for galaxy evolution. In this Letter, we combine Atacama Large Millimeter/submillimeter Array and Arecibo single-dish observations to estimate the molecular-to-atomic hydrogen mass ratio for massive star-forming galaxies at z ∼ 0.2 extracted from the HIGHz survey, i.e., some of the most massive gas-rich systems currently known. We show that the balance between atomic and molecular hydrogen in these galaxies is similar to that of local main-sequence disks, implying that atomic hydrogen has been dominating the coldmore » gas mass budget of star-forming galaxies for at least the past three billion years. In addition, despite harboring gas reservoirs that are more typical of objects at the cosmic noon, HIGHz galaxies host regular rotating disks with low gas velocity dispersions suggesting that high total gas fractions do not necessarily drive high turbulence in the interstellar medium.« less

Gene calling and bacterial genome annotation with BG7.

PubMed

Tobes, Raquel; Pareja-Tobes, Pablo; Manrique, Marina; Pareja-Tobes, Eduardo; Kovach, Evdokim; Alekhin, Alexey; Pareja, Eduardo

2015-01-01

New massive sequencing technologies are providing many bacterial genome sequences from diverse taxa but a refined annotation of these genomes is crucial for obtaining scientific findings and new knowledge. Thus, bacterial genome annotation has emerged as a key point to investigate in bacteria. Any efficient tool designed specifically to annotate bacterial genomes sequenced with massively parallel technologies has to consider the specific features of bacterial genomes (absence of introns and scarcity of nonprotein-coding sequence) and of next-generation sequencing (NGS) technologies (presence of errors and not perfectly assembled genomes). These features make it convenient to focus on coding regions and, hence, on protein sequences that are the elements directly related with biological functions. In this chapter we describe how to annotate bacterial genomes with BG7, an open-source tool based on a protein-centered gene calling/annotation paradigm. BG7 is specifically designed for the annotation of bacterial genomes sequenced with NGS. This tool is sequence error tolerant maintaining their capabilities for the annotation of highly fragmented genomes or for annotating mixed sequences coming from several genomes (as those obtained through metagenomics samples). BG7 has been designed with scalability as a requirement, with a computing infrastructure completely based on cloud computing (Amazon Web Services).

SNP discovery by high-throughput sequencing in soybean

PubMed Central

2010-01-01

Background With the advance of new massively parallel genotyping technologies, quantitative trait loci (QTL) fine mapping and map-based cloning become more achievable in identifying genes for important and complex traits. Development of high-density genetic markers in the QTL regions of specific mapping populations is essential for fine-mapping and map-based cloning of economically important genes. Single nucleotide polymorphisms (SNPs) are the most abundant form of genetic variation existing between any diverse genotypes that are usually used for QTL mapping studies. The massively parallel sequencing technologies (Roche GS/454, Illumina GA/Solexa, and ABI/SOLiD), have been widely applied to identify genome-wide sequence variations. However, it is still remains unclear whether sequence data at a low sequencing depth are enough to detect the variations existing in any QTL regions of interest in a crop genome, and how to prepare sequencing samples for a complex genome such as soybean. Therefore, with the aims of identifying SNP markers in a cost effective way for fine-mapping several QTL regions, and testing the validation rate of the putative SNPs predicted with Solexa short sequence reads at a low sequencing depth, we evaluated a pooled DNA fragment reduced representation library and SNP detection methods applied to short read sequences generated by Solexa high-throughput sequencing technology. Results A total of 39,022 putative SNPs were identified by the Illumina/Solexa sequencing system using a reduced representation DNA library of two parental lines of a mapping population. The validation rates of these putative SNPs predicted with low and high stringency were 72% and 85%, respectively. One hundred sixty four SNP markers resulted from the validation of putative SNPs and have been selectively chosen to target a known QTL, thereby increasing the marker density of the targeted region to one marker per 42 K bp. Conclusions We have demonstrated how to quickly identify large numbers of SNPs for fine mapping of QTL regions by applying massively parallel sequencing combined with genome complexity reduction techniques. This SNP discovery approach is more efficient for targeting multiple QTL regions in a same genetic population, which can be applied to other crops. PMID:20701770

Sanger sequencing as a first-line approach for molecular diagnosis of Andersen-Tawil syndrome.

PubMed

Totomoch-Serra, Armando; Marquez, Manlio F; Cervantes-Barragán, David E

2017-01-01

In 1977, Frederick Sanger developed a new method for DNA sequencing based on the chain termination method, now known as the Sanger sequencing method (SSM).  Recently, massive parallel sequencing, better known as next-generation sequencing (NGS),  is replacing the SSM for detecting mutations in cardiovascular diseases with a genetic background. The present opinion article wants to remark that "targeted" SSM is still effective as a first-line approach for the molecular diagnosis of some specific conditions, as is the case for Andersen-Tawil syndrome (ATS). ATS is described as a rare multisystemic autosomal dominant channelopathy syndrome caused mainly by a heterozygous mutation in the KCNJ2 gene . KCJN2 has particular characteristics that make it attractive for "directed" SSM. KCNJ2 has a sequence of 17,510 base pairs (bp), and a short coding region with two exons (exon 1=166 bp and exon 2=5220 bp), half of the mutations are located in the C-terminal cytosolic domain, a mutational hotspot has been described in residue Arg218, and this gene explains the phenotype in 60% of ATS cases that fulfill all the clinical criteria of the disease. In order to increase the diagnosis of ATS we urge cardiologists to search for facial and muscular abnormalities in subjects with frequent ventricular arrhythmias (especially bigeminy) and prominent U waves on the electrocardiogram.

Sanger sequencing as a first-line approach for molecular diagnosis of Andersen-Tawil syndrome

PubMed Central

Totomoch-Serra, Armando; Marquez, Manlio F.; Cervantes-Barragán, David E.

2017-01-01

In 1977, Frederick Sanger developed a new method for DNA sequencing based on the chain termination method, now known as the Sanger sequencing method (SSM).  Recently, massive parallel sequencing, better known as next-generation sequencing (NGS),  is replacing the SSM for detecting mutations in cardiovascular diseases with a genetic background. The present opinion article wants to remark that “targeted” SSM is still effective as a first-line approach for the molecular diagnosis of some specific conditions, as is the case for Andersen-Tawil syndrome (ATS). ATS is described as a rare multisystemic autosomal dominant channelopathy syndrome caused mainly by a heterozygous mutation in the KCNJ2 gene . KCJN2 has particular characteristics that make it attractive for “directed” SSM. KCNJ2 has a sequence of 17,510 base pairs (bp), and a short coding region with two exons (exon 1=166 bp and exon 2=5220 bp), half of the mutations are located in the C-terminal cytosolic domain, a mutational hotspot has been described in residue Arg218, and this gene explains the phenotype in 60% of ATS cases that fulfill all the clinical criteria of the disease. In order to increase the diagnosis of ATS we urge cardiologists to search for facial and muscular abnormalities in subjects with frequent ventricular arrhythmias (especially bigeminy) and prominent U waves on the electrocardiogram. PMID:29093808

CSI in Supernova Remnants

NASA Astrophysics Data System (ADS)

Chu, You-Hua

2017-02-01

Supernovae (SNe) explode in environments that have been significantly modified by the SN progenitors. For core-collapse SNe, the massive progenitors ionize the ambient interstellar medium (ISM) via UV radiation and sweep the ambient ISM via fast stellar winds during the main sequence phase, replenish the surroundings with stellar material via slow winds during the luminous blue variable (LBV) or red supergiant (RSG) phase, and sweep up the circumstellar medium (CSM) via fast winds during the Wolf-Rayet (WR) phase. If a massive progenitor was in a close binary system, the binary interaction could have caused mass ejection in certain preferred directions, such as the orbital plane, and even bipolar outflow/jet. As a massive star finally explodes, the SN ejecta interacts first with the CSM that was ejected and shaped by the star itself. As the newly formed supernova remnant (SNR) expands further, it encounters interstellar structures that were shaped by the progenitor from earlier times. Therefore, the structure and evolution of a SNR is largely dependent on the initial mass and close binarity of the SN progenitor. The Large Magellanic Cloud (LMC) has an excellent sample of over 50 confirmed SNRs that are well resolved by Hubble Space Telescope, Chandra X-ray Observatory, and Spitzer Space Telescope. These multi-wavelength observations allow us to conduct stellar forensics in SNRs and understand the wide variety of morphologies and physical properties of SNRs observed.

SNP-VISTA: An interactive SNP visualization tool

PubMed Central

Shah, Nameeta; Teplitsky, Michael V; Minovitsky, Simon; Pennacchio, Len A; Hugenholtz, Philip; Hamann, Bernd; Dubchak, Inna L

2005-01-01

Background Recent advances in sequencing technologies promise to provide a better understanding of the genetics of human disease as well as the evolution of microbial populations. Single Nucleotide Polymorphisms (SNPs) are established genetic markers that aid in the identification of loci affecting quantitative traits and/or disease in a wide variety of eukaryotic species. With today's technological capabilities, it has become possible to re-sequence a large set of appropriate candidate genes in individuals with a given disease in an attempt to identify causative mutations. In addition, SNPs have been used extensively in efforts to study the evolution of microbial populations, and the recent application of random shotgun sequencing to environmental samples enables more extensive SNP analysis of co-occurring and co-evolving microbial populations. The program is available at [1]. Results We have developed and present two modifications of an interactive visualization tool, SNP-VISTA, to aid in the analyses of the following types of data: A. Large-scale re-sequence data of disease-related genes for discovery of associated and/or causative alleles (GeneSNP-VISTA). B. Massive amounts of ecogenomics data for studying homologous recombination in microbial populations (EcoSNP-VISTA). The main features and capabilities of SNP-VISTA are: 1) mapping of SNPs to gene structure; 2) classification of SNPs, based on their location in the gene, frequency of occurrence in samples and allele composition; 3) clustering, based on user-defined subsets of SNPs, highlighting haplotypes as well as recombinant sequences; 4) integration of protein evolutionary conservation visualization; and 5) display of automatically calculated recombination points that are user-editable. Conclusion The main strength of SNP-VISTA is its graphical interface and use of visual representations, which support interactive exploration and hence better understanding of large-scale SNP data by the user. PMID:16336665

Wolf-Rayet stars in the Small Magellanic Cloud as testbed for massive star evolution

NASA Astrophysics Data System (ADS)

Schootemeijer, A.; Langer, N.

2018-03-01

Context. The majority of the Wolf-Rayet (WR) stars represent the stripped cores of evolved massive stars who lost most of their hydrogen envelope. Wind stripping in single stars is expected to be inefficient in producing WR stars in metal-poor environments such as the Small Magellanic Cloud (SMC). While binary interaction can also produce WR stars at low metallicity, it is puzzling that the fraction of WR binaries appears to be about 40%, independent of the metallicity. Aim. We aim to use the recently determined physical properties of the twelve known SMC WR stars to explore their possible formation channels through comparisons with stellar models. Methods: We used the MESA stellar evolution code to construct two grids of stellar models with SMC metallicity. One of these consists of models of rapidly rotating single stars, which evolve in part or completely chemically homogeneously. In a second grid, we analyzed core helium burning stellar models assuming constant hydrogen and helium gradients in their envelopes. Results: We find that chemically homogeneous evolution is not able to account for the majority of the WR stars in the SMC. However, in particular the apparently single WR star SMC AB12, and the double WR system SMC AB5 (HD 5980) appear consistent with this channel. We further find a dichotomy in the envelope hydrogen gradients required to explain the observed temperatures of the SMC WR stars. Shallow gradients are found for the WR stars with O star companions, while much steeper hydrogen gradients are required to understand the group of hot apparently single WR stars. Conclusions: The derived shallow hydrogen gradients in the WR component of the WR+O star binaries are consistent with predictions from binary models where mass transfer occurs early, in agreement with their binary properties. Since the hydrogen profiles in evolutionary models of massive stars become steeper with time after the main sequence, we conclude that most of the hot (Teff > 60 kK ) apparently single WR stars lost their envelope after a phase of strong expansion, e.g., as the result of common envelope evolution with a lower mass companion. The so far undetected companions, either main sequence stars or compact objects, are then expected to still be present. A corresponding search might identify the first immediate double black hole binary progenitor with masses as high as those detected in GW150914.

Bioinformatics and Microarray Data Analysis on the Cloud.

PubMed

Calabrese, Barbara; Cannataro, Mario

2016-01-01

High-throughput platforms such as microarray, mass spectrometry, and next-generation sequencing are producing an increasing volume of omics data that needs large data storage and computing power. Cloud computing offers massive scalable computing and storage, data sharing, on-demand anytime and anywhere access to resources and applications, and thus, it may represent the key technology for facing those issues. In fact, in the recent years it has been adopted for the deployment of different bioinformatics solutions and services both in academia and in the industry. Although this, cloud computing presents several issues regarding the security and privacy of data, that are particularly important when analyzing patients data, such as in personalized medicine. This chapter reviews main academic and industrial cloud-based bioinformatics solutions; with a special focus on microarray data analysis solutions and underlines main issues and problems related to the use of such platforms for the storage and analysis of patients data.

Mass loss in O-type stars - Parameters which affect it

NASA Technical Reports Server (NTRS)

Garmany, C. D.; Conti, P. S.

1984-01-01

Newly determined mass loss rates are presented for sixteen O-type stars in three open clusters. Combining the data with that already in the literature, no evidence is found that the rates are different in clusters with differing galactocentric distances and compositions, at least near the sun. There is still appreciable dispersion in the relationship between the mass loss rate and the stellar luminosity. It may be that the mass loss depends additionally on the stellar mass and/or radius, but these data cannot unequivocally indicate which physical dependence is correct. Evidence is found that a stellar wind increases as a massive star evolves from the zero-age main sequence.

On star formation in stellar systems. I - Photoionization effects in protoglobular clusters

NASA Technical Reports Server (NTRS)

Tenorio-Tagle, G.; Bodenheimer, P.; Lin, D. N. C.; Noriega-Crespo, A.

1986-01-01

The progressive ionization and subsequent dynamical evolution of nonhomogeneously distributed low-metal-abundance diffuse gas after star formation in globular clusters are investigated analytically, taking the gravitational acceleration due to the stars into account. The basic equations are derived; the underlying assumptions, input parameters, and solution methods are explained; and numerical results for three standard cases (ionization during star formation, ionization during expansion, and evolution resulting in a stable H II region at its equilibrium Stromgren radius) are presented in graphs and characterized in detail. The time scale of residual-gas loss in typical clusters is found to be about the same as the lifetime of a massive star on the main sequence.

The Kepler Mission: Search for Habitable Planets

NASA Technical Reports Server (NTRS)

Borucki, William; Likins, B.; DeVincenzi, Donald L. (Technical Monitor)

1998-01-01

Detecting extrasolar terrestrial planets orbiting main-sequence stars is of great interest and importance. Current ground-based methods are only capable of detecting objects about the size or mass of Jupiter or larger. The difficulties encountered with direct imaging of Earth-size planets from space are expected to be resolved in the next twenty years. Spacebased photometry of planetary transits is currently the only viable method for detection of terrestrial planets (30-600 times less massive than Jupiter). This method searches the extended solar neighborhood, providing a statistically large sample and the detailed characteristics of each individual case. A robust concept has been developed and proposed as a Discovery-class mission. Its capabilities and strengths are presented.

The Language of the Protein Universe

PubMed Central

Scaiewicz, Andrea; Levitt, Michael

2015-01-01

Proteins, the main cell machinery which play a major roll in nearly every cellular process, have always been a central focus in biology. We live in the post-genomic era, and inferring information from massive data sets is a steadily growing universal challenge. The increasing availability of fully sequenced genomes can be regarded as the “Rosetta Stone” of the protein universe, allowing the understanding of genomes and their evolution, just as the original Rosetta Stone allowed Champollion to decipher the ancient Egyptian hieroglyphics. In this review, we consider aspects of the protein domain architectures repertoire that are closely related to those of human languages and aim to provide some insights about the language of proteins. PMID:26451980

The"minimum information about an environmental sequence" (MIENS) specification

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

Yilmaz, P.; Kottmann, R.; Field, D.

We present the Genomic Standards Consortium's (GSC) 'Minimum Information about an ENvironmental Sequence' (MIENS) standard for describing marker genes. Adoption of MIENS will enhance our ability to analyze natural genetic diversity across the Tree of Life as it is currently being documented by massive DNA sequencing efforts from myriad ecosystems in our ever-changing biosphere.

Has Research on Collaborative Learning Technologies Addressed Massiveness? A Literature Review

ERIC Educational Resources Information Center

Manathunga, Kalpani; Hernández-Leo, Davinia

2015-01-01

There is a growing interest in understanding to what extent innovative educational technologies can be used to support massive courses. Collaboration is one of the main desired elements in massive learning actions involving large communities of participants. Accumulated research in collaborative learning technologies has proposed and evaluated…

PHIBSS: MOLECULAR GAS, EXTINCTION, STAR FORMATION, AND KINEMATICS IN THE z = 1.5 STAR-FORMING GALAXY EGS13011166

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

Genzel, R.; Tacconi, L. J.; Kurk, J.

We report matched resolution imaging spectroscopy of the CO 3-2 line (with the IRAM Plateau de Bure millimeter interferometer) and of the H{alpha} line (with LUCI at the Large Binocular Telescope) in the massive z = 1.53 main-sequence galaxy EGS 13011166, as part of the ''Plateau de Bure high-z, blue-sequence survey'' (PHIBSS: Tacconi et al.). We combine these data with Hubble Space Telescope V-I-J-H-band maps to derive spatially resolved distributions of stellar surface density, star formation rate, molecular gas surface density, optical extinction, and gas kinematics. The spatial distribution and kinematics of the ionized and molecular gas are remarkably similarmore » and are well modeled by a turbulent, globally Toomre unstable, rotating disk. The stellar surface density distribution is smoother than the clumpy rest-frame UV/optical light distribution and peaks in an obscured, star-forming massive bulge near the dynamical center. The molecular gas surface density and the effective optical screen extinction track each other and are well modeled by a ''mixed'' extinction model. The inferred slope of the spatially resolved molecular gas to star formation rate relation, N = dlog{Sigma}{sub starform}/dlog{Sigma}{sub molgas}, depends strongly on the adopted extinction model, and can vary from 0.8 to 1.7. For the preferred mixed dust-gas model, we find N = 1.14 {+-} 0.1.« less

Hidden Ice Worlds - Pleistocene glacigenic deposits in Essex, England. Application of the novel systematic approach to thin-section description.

NASA Astrophysics Data System (ADS)

Leszczynska, Karolina; Boreham, Julie; Boreham, Steve

2013-04-01

In the 'Hidden Ice Worlds' research project a novel systematic approach for thin-section description (Leszczynska et al., 2011) is applied to analyse the internal structure of 8 m thick periglacially disturbed sequence from the Royal Oak Pit - a small disused quarry in East Anglia, Essex, east of Chelmsford, near Danbury. Danbury Hill is situated on the south-eastern margin of the Elsterian (Anglian) till sheet. This area was glaciated only once, during the Pleistocene, Elsterian (Anglian) glaciation (480-420 ka BP), however two local ice-sheet margin fluctuations are envisaged (inter alia Turner, 1970 and others). The stratigraphical sequence of the Royal Oak Pit comprises: massive gravel, arranged in sheets, overlain by fine silty-clay and silty-sand with ripple marks and planar cross beds, overlain by a 50 cm thick unit of massive gravel gradually changing into periglacially disturbed silty-clayey-gravel with the bottom 50 cm of fine laminated silty clay. This sequence is situated on the lee side of Danbury Hill, at over 50 m OD. This is an atypical location for the periglacially disturbed deposits of such a substantial thickness (up to 8 m), which usually occur in the lower areas. The deposits at this site were investigated at a macro-scale using field-section logging, ground penetrating radar survey, clast lithology, clay mineralogy analysis and loss-on-ignition and at a micro-scale using thin-section analysis. There are two main aims of the project presented: • To describe the genesis and to discern the main processes associated with the formation of the unusually thick periglacially disturbed unit at the Danbury Hill slope and • To test the novel, tree-based, systematic approach as a guiding tool for thin for thin-section description of Quaternary deposits (Leszczynska et al., 2011). The results of the micromorphological analyses of the deposits from the Royal Oak Pit allow a new hypothesis for the origin of the sequence to be put forward. The main process responsible for the evolution of the deposits consist of multiple phases of freezing and thawing of the deposit and associated physical reworking, subsequent to Elsterian (Anglian). Inversion of the topography is proposed as a necessary condition for the formation and preservation of the periglacially disturbed sequence on hill slope at such elevated location. The novel systematic approach proved to be a useful tool in guiding the thin-section description, regardless of the type of the deposit and the aim of the research. Reference: Leszczynska, K., Boreham, J. and Boreham, S., 2011. A novel methodological approach for thin-section description and its application to periglacially disturbed Pleistocene deposits from Danbury, Essex, UK. Netherlands Journal of Geosciences 90: 271-291. Turner, C., 1970. Middle Pleistocene deposits at Marks Tey, Essex. Philosophical Transactions of the Royal Society of London, series B 257: 373-440.

A technique for setting analytical thresholds in massively parallel sequencing-based forensic DNA analysis

PubMed Central

2017-01-01

Amplicon (targeted) sequencing by massively parallel sequencing (PCR-MPS) is a potential method for use in forensic DNA analyses. In this application, PCR-MPS may supplement or replace other instrumental analysis methods such as capillary electrophoresis and Sanger sequencing for STR and mitochondrial DNA typing, respectively. PCR-MPS also may enable the expansion of forensic DNA analysis methods to include new marker systems such as single nucleotide polymorphisms (SNPs) and insertion/deletions (indels) that currently are assayable using various instrumental analysis methods including microarray and quantitative PCR. Acceptance of PCR-MPS as a forensic method will depend in part upon developing protocols and criteria that define the limitations of a method, including a defensible analytical threshold or method detection limit. This paper describes an approach to establish objective analytical thresholds suitable for multiplexed PCR-MPS methods. A definition is proposed for PCR-MPS method background noise, and an analytical threshold based on background noise is described. PMID:28542338

A technique for setting analytical thresholds in massively parallel sequencing-based forensic DNA analysis.

PubMed

Young, Brian; King, Jonathan L; Budowle, Bruce; Armogida, Luigi

2017-01-01

Amplicon (targeted) sequencing by massively parallel sequencing (PCR-MPS) is a potential method for use in forensic DNA analyses. In this application, PCR-MPS may supplement or replace other instrumental analysis methods such as capillary electrophoresis and Sanger sequencing for STR and mitochondrial DNA typing, respectively. PCR-MPS also may enable the expansion of forensic DNA analysis methods to include new marker systems such as single nucleotide polymorphisms (SNPs) and insertion/deletions (indels) that currently are assayable using various instrumental analysis methods including microarray and quantitative PCR. Acceptance of PCR-MPS as a forensic method will depend in part upon developing protocols and criteria that define the limitations of a method, including a defensible analytical threshold or method detection limit. This paper describes an approach to establish objective analytical thresholds suitable for multiplexed PCR-MPS methods. A definition is proposed for PCR-MPS method background noise, and an analytical threshold based on background noise is described.

The Evolution and Stability of Massive Stars

NASA Astrophysics Data System (ADS)

Shiode, Joshua Hajime

Massive stars are the ultimate source for nearly all the elements necessary for life. The first stars forge these elements from the sparse set of ingredients supplied by the Big Bang, and distribute enriched ashes throughout their galactic homes via their winds and explosive deaths. Subsequent generations follow suit, assembling from the enriched ashes of their predecessors. Over the last several decades, the astrophysics community has developed a sophisticated theoretical picture of the evolution of these stars, but it remains an incomplete accounting of the rich set of observations. Using state of the art models of massive stars, I have investigated the internal processes taking place throughout the life-cycles of stars spanning those from the first generation ("Population III") to the present-day ("Population I"). I will argue that early-generation stars were not highly unstable to perturbations, contrary to a host of past investigations, if a correct accounting is made for the viscous effect of convection. For later generations, those with near solar metallicity, I find that this very same convection may excite gravity-mode oscillations that produce observable brightness variations at the stellar surface when the stars are near the main sequence. If confirmed with modern high-precision monitoring experiments, like Kepler and CoRoT, the properties of observed gravity modes in massive stars could provide a direct probe of the poorly constrained physics of gravity mode excitation by convection. Finally, jumping forward in stellar evolutionary time, I propose and explore an entirely new mechanism to explain the giant eruptions observed and inferred to occur during the final phases of massive stellar evolution. This mechanism taps into the vast nuclear fusion luminosity, and accompanying convective luminosity, in the stellar core to excite waves capable of carrying a super-Eddington luminosity out to the stellar envelope. This energy transfer from the core to the envelope has the potential to unbind a significant amount of mass in close proximity to a star's eventual explosion as a core collapse supernova.

High Resolution Size Analysis of Fetal DNA in the Urine of Pregnant Women by Paired-End Massively Parallel Sequencing

PubMed Central

Tsui, Nancy B. Y.; Jiang, Peiyong; Chow, Katherine C. K.; Su, Xiaoxi; Leung, Tak Y.; Sun, Hao; Chan, K. C. Allen; Chiu, Rossa W. K.; Lo, Y. M. Dennis

2012-01-01

Background Fetal DNA in maternal urine, if present, would be a valuable source of fetal genetic material for noninvasive prenatal diagnosis. However, the existence of fetal DNA in maternal urine has remained controversial. The issue is due to the lack of appropriate technology to robustly detect the potentially highly degraded fetal DNA in maternal urine. Methodology We have used massively parallel paired-end sequencing to investigate cell-free DNA molecules in maternal urine. Catheterized urine samples were collected from seven pregnant women during the third trimester of pregnancies. We detected fetal DNA by identifying sequenced reads that contained fetal-specific alleles of the single nucleotide polymorphisms. The sizes of individual urinary DNA fragments were deduced from the alignment positions of the paired reads. We measured the fractional fetal DNA concentration as well as the size distributions of fetal and maternal DNA in maternal urine. Principal Findings Cell-free fetal DNA was detected in five of the seven maternal urine samples, with the fractional fetal DNA concentrations ranged from 1.92% to 4.73%. Fetal DNA became undetectable in maternal urine after delivery. The total urinary cell-free DNA molecules were less intact when compared with plasma DNA. Urinary fetal DNA fragments were very short, and the most dominant fetal sequences were between 29 bp and 45 bp in length. Conclusions With the use of massively parallel sequencing, we have confirmed the existence of transrenal fetal DNA in maternal urine, and have shown that urinary fetal DNA was heavily degraded. PMID:23118982

The minimal amount of starting DNA for Agilent’s hybrid capture-based targeted massively parallel sequencing

PubMed Central

Chung, Jongsuk; Son, Dae-Soon; Jeon, Hyo-Jeong; Kim, Kyoung-Mee; Park, Gahee; Ryu, Gyu Ha; Park, Woong-Yang; Park, Donghyun

2016-01-01

Targeted capture massively parallel sequencing is increasingly being used in clinical settings, and as costs continue to decline, use of this technology may become routine in health care. However, a limited amount of tissue has often been a challenge in meeting quality requirements. To offer a practical guideline for the minimum amount of input DNA for targeted sequencing, we optimized and evaluated the performance of targeted sequencing depending on the input DNA amount. First, using various amounts of input DNA, we compared commercially available library construction kits and selected Agilent’s SureSelect-XT and KAPA Biosystems’ Hyper Prep kits as the kits most compatible with targeted deep sequencing using Agilent’s SureSelect custom capture. Then, we optimized the adapter ligation conditions of the Hyper Prep kit to improve library construction efficiency and adapted multiplexed hybrid selection to reduce the cost of sequencing. In this study, we systematically evaluated the performance of the optimized protocol depending on the amount of input DNA, ranging from 6.25 to 200 ng, suggesting the minimal input DNA amounts based on coverage depths required for specific applications. PMID:27220682

A review of bioinformatic methods for forensic DNA analyses.

PubMed

Liu, Yao-Yuan; Harbison, SallyAnn

2018-03-01

Short tandem repeats, single nucleotide polymorphisms, and whole mitochondrial analyses are three classes of markers which will play an important role in the future of forensic DNA typing. The arrival of massively parallel sequencing platforms in forensic science reveals new information such as insights into the complexity and variability of the markers that were previously unseen, along with amounts of data too immense for analyses by manual means. Along with the sequencing chemistries employed, bioinformatic methods are required to process and interpret this new and extensive data. As more is learnt about the use of these new technologies for forensic applications, development and standardization of efficient, favourable tools for each stage of data processing is being carried out, and faster, more accurate methods that improve on the original approaches have been developed. As forensic laboratories search for the optimal pipeline of tools, sequencer manufacturers have incorporated pipelines into sequencer software to make analyses convenient. This review explores the current state of bioinformatic methods and tools used for the analyses of forensic markers sequenced on the massively parallel sequencing (MPS) platforms currently most widely used. Copyright © 2017 Elsevier B.V. All rights reserved.

Weighing the Most Massive Stars

NASA Astrophysics Data System (ADS)

Moffat, Anthony; Schnurr, Olivier; Chené, André-Nicolas; St-Louis, Nicole

2005-08-01

HR diagrams of the brightest stars in nearby galaxies indicate that there exists an upper luminosity limit to star formation. One can assign real masses of stars at that limit, although with low confidence because of uncertainties in current stellar models. Understanding the physics of massive stars is important because these stars dominate the light and ecology of the Universe, not only at the present epoch, but also and especially during the first generation of stars (pop III), expected to be dominated by stars in the range 100-1000 solar masses. The only viable way to determine (or calibrate) masses is by "weighing" them in binary systems. The most massive stars are expected to be formed in the most massive, densest young stellar clusters, like the core R136 of 30 Dor in the Large Magellanic Cloud or its much closer clone NGC 3603 in the Galaxy. Telescopes in space or adaptive-optics systems on large groundbased telescopes are needed to cleanly resolve such stars in order to obtain the necessary high-precision radial velocities and light curves to define the orbits and obtain the masses. We discuss recent progress on this topic, with emphasis on our own attempt to determine the masses of the components of the brightest star (A1, a known main-sequence eclipsing system of type WN6ha + O3: and period 3.7724 d) in the core of NGC 3603, first using HST/STIS (instrument failure) then using VLT/SINFONI (in progress). With A1 being one magnitude intrinsically brighter than the current record holder WR20a (WN6ha + WN6ha, P = 3.686 d, 83 + 82 solar mass), we expect masses for A1 of ~ 100 solar mass if L .M3, or more likely, ~200 solar mass if L . M

Millimeter observations of the disk around GW Orionis

NASA Astrophysics Data System (ADS)

Fang, M.; Sicilia-Aguilar, A.; Wilner, D.; Wang, Y.; Roccatagliata, V.; Fedele, D.; Wang, J. Z.

2017-07-01

The GW Ori system is a pre-main sequence triple system (GW Ori A/B/C) with companions (GW Ori B/C) at 1 AU and 8 AU, respectively, from the primary (GW Ori A). The primary of the system has a mass of 3.9 M⊙, but shows a spectral type of G8. Thus, GW Ori A could be a precursor of a B star, but it is still at an earlier evolutionary stage than Herbig Be stars. GW Ori provides an ideal target for experiments and observations (being a "blown-up" solar system with a very massive sun and at least two upscaled planets). We present the first spatially resolved millimeter interferometric observations of the disk around the triple pre-main sequence system GW Ori, obtained with the Submillimeter Array, both in continuum and in the 12CO J = 2-1, 13CO J = 2-1, and C18O J = 2-1 lines. These new data reveal a huge, massive, and bright disk in the GW Ori system. The dust continuum emission suggests a disk radius of around 400 AU, but the 12CO J = 2-1 emission shows a much more extended disk with a size around 1300 AU. Owing to the spatial resolution ( 1''), we cannot detect the gap in the disk that is inferred from spectral energy distribution (SED) modeling. We characterize the dust and gas properties in the disk by comparing the observations with the predictions from the disk models with various parameters calculated with a Monte Carlo radiative transfer code RADMC-3D. The disk mass is around0.12 M⊙, and the disk inclination with respect to the line of sight is around 35°. The kinematics in the disk traced by the CO line emission strongly suggest that the circumstellar material in the disk is in Keplerian rotation around GW Ori.Tentatively substantial C18O depletion in gas phase is required to explain the characteristics of the line emission from the disk.

ON THE RELIABILITY OF STELLAR AGES AND AGE SPREADS INFERRED FROM PRE-MAIN-SEQUENCE EVOLUTIONARY MODELS

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

Hosokawa, Takashi; Offner, Stella S. R.; Krumholz, Mark R., E-mail: Takashi.Hosokawa@jpl.nasa.gov, E-mail: hosokwtk@gmail.com

2011-09-10

We revisit the problem of low-mass pre-main-sequence stellar evolution and its observational consequences for where stars fall on the Hertzsprung-Russell diagram (HRD). In contrast to most previous work, our models follow stars as they grow from small masses via accretion, and we perform a systematic study of how the stars' HRD evolution is influenced by their initial radius, by the radiative properties of the accretion flow, and by the accretion history, using both simple idealized accretion histories and histories taken from numerical simulations of star cluster formation. We compare our numerical results to both non-accreting isochrones and to the positionsmore » of observed stars in the HRD, with a goal of determining whether both the absolute ages and the age dispersions inferred from non-accreting isochrones are reliable. We show that non-accreting isochrones can sometimes overestimate stellar ages for more massive stars (those with effective temperatures above {approx}3500 K), thereby explaining why non-accreting isochrones often suggest a systematic age difference between more and less massive stars in the same cluster. However, we also find the only way to produce a similar overestimate for the ages of cooler stars is if these stars grow from {approx}0.01 M{sub sun} seed protostars that are an order of magnitude smaller than predicted by current theoretical models, and if the size of the seed protostar correlates systematically with the final stellar mass at the end of accretion. We therefore conclude that, unless both of these conditions are met, inferred ages and age spreads for cool stars are reliable, at least to the extent that the observed bolometric luminosities and temperatures are accurate. Finally, we note that the time dependence of the mass accretion rate has remarkably little effect on low-mass stars' evolution on the HRD, and that such time dependence may be neglected for all stars except those with effective temperatures above {approx}4000 K.« less

Evaluation of ribosomal RNA removal protocols for Salmonella RNA-Seq projects

USDA-ARS?s Scientific Manuscript database

Next generation sequencing is a powerful technology and its application to sequencing entire RNA populations of food-borne pathogens will provide valuable insights. A problem unique to prokaryotic RNA-Seq is the massive abundance of ribosomal RNA. Unlike eukaryotic messenger RNA (mRNA), bacterial ...

Multiplexed microsatellite recovery using massively parallel sequencing

Treesearch

T.N. Jennings; B.J. Knaus; T.D. Mullins; S.M. Haig; R.C. Cronn

2011-01-01

Conservation and management of natural populations requires accurate and inexpensive genotyping methods. Traditional microsatellite, or simple sequence repeat (SSR), marker analysis remains a popular genotyping method because of the comparatively low cost of marker development, ease of analysis and high power of genotype discrimination. With the availability of...

On the Evolutionary Phase and Mass Loss of the Wolf-Rayet--like Stars in R136a

NASA Astrophysics Data System (ADS)

de Koter, Alex; Heap, Sara R.; Hubeny, Ivan

1997-03-01

We report on a systematic study of the most massive stars, in which we analyzed the spectra of four very luminous stars in the Large Magellanic Cloud. The stars lie in the 30 Doradus complex, three of which are located in the core of the compact cluster, R136a (R136a1, R136a3, and R136a5), and the fourth (Melnick 42), located about 8" north of R136a. Low-resolution spectra (<200 km s-1) of these four stars were obtained with the GHRS and FOS spectrographs on the Hubble Space Telescope. The GHRS spectra cover the spectral range from 1200 to 1750 A, and the FOS spectra from 3200 to 6700 A. We derived the fundamental parameters of these stars by fitting the observations by model spectra calculated with the "ISA-WIND" code of de Koter et al. We find that all four stars are very hot (~45 kK), luminous, and rich in hydrogen. Their positions on the HR-diagram imply that they are stars with masses in the range 60--90 M⊙ that are 2 million years old at most, and hence, they are O-type main-sequence stars still in the core H-burning phase of evolution. Nevertheless, the spectra of two of the stars (R136a1, R136a3) mimic those of Wolf-Rayet stars in showing very strong He II emission lines. According to our calculations, this emission is a natural consequence of a very high mass-loss rate. We conjecture that the most massive stars in R136a---those with initial masses of ~100 M⊙ or more---are born as WR-like stars and that the high mass loss may perhaps be connected to the actual stellar formation process. Because the observed mass-loss rates are up to 3 times higher than assumed by evolutionary models, the main-sequence and post--main-sequence tracks of these stars will be qualitatively different from current models. The mass-loss rate is 3.5--8 times that predicted by the analytical solutions for radiation-driven winds of Kudritzki et al. (1989). However, using sophisticated Monte Carlo calculations of radiative driving in unified model atmospheres, we show that---while we cannot say for sure what initiates the wind---radiation pressure is probably sufficient to accelerate the wind to its observed terminal velocity, if one accounts for the effects of multiple photon scattering in the dense winds of the investigated stars.

The Evolutionary Status of Be Stars: Results from a Photometric Study of Southern Open Clusters

NASA Astrophysics Data System (ADS)

McSwain, M. Virginia; Gies, Douglas R.

2005-11-01

Be stars are a class of rapidly rotating B stars with circumstellar disks that cause Balmer and other line emission. There are three possible reasons for the rapid rotation of Be stars: they may have been born as rapid rotators, spun up by binary mass transfer, or spun up during the main-sequence (MS) evolution of B stars. To test the various formation scenarios, we have conducted a photometric survey of 55 open clusters in the southern sky. Of these, five clusters are probably not physically associated groups and our results for two other clusters are not reliable, but we identify 52 definite Be stars and an additional 129 Be candidates in the remaining clusters. We use our results to examine the age and evolutionary dependence of the Be phenomenon. We find an overall increase in the fraction of Be stars with age until 100 Myr, and Be stars are most common among the brightest, most massive B-type stars above the zero-age main sequence (ZAMS). We show that a spin-up phase at the terminal-age main sequence (TAMS) cannot produce the observed distribution of Be stars, but up to 73% of the Be stars detected may have been spun-up by binary mass transfer. Most of the remaining Be stars were likely rapid rotators at birth. Previous studies have suggested that low metallicity and high cluster density may also favor Be star formation. Our results indicate a possible increase in the fraction of Be stars with increasing cluster distance from the Galactic center (in environments of decreasing metallicity). However, the trend is not significant and could be ruled out due to the intrinsic scatter in our data. We also find no relationship between the fraction of Be stars and cluster density.

Extended Main-sequence Turn-offs in Intermediate-age Star Clusters: Stellar Rotation Diminishes, but Does Not Eliminate, Age Spreads

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

Goudfrooij, Paul; Correnti, Matteo; Girardi, Léo, E-mail: goudfroo@stsci.edu

Extended main-sequence turn-off (eMSTO) regions are a common feature in color–magnitude diagrams of young- and intermediate-age star clusters in the Magellanic Clouds. The nature of eMSTOs remains debated in the literature. The currently most popular scenarios are extended star formation activity and ranges of stellar rotation rates. Here we study details of differences in main-sequence turn-off (MSTO) morphology expected from spreads in age versus spreads in rotation rates, using Monte Carlo simulations with the Geneva syclist isochrone models that include the effects of stellar rotation. We confirm a recent finding of Niederhofer et al. that a distribution of stellar rotationmore » velocities yields an MSTO extent that is proportional to the cluster age, as observed. However, we find that stellar rotation yields MSTO crosscut widths that are generally smaller than observed ones at a given age. We compare the simulations with high-quality Hubble Space Telescope data of NGC 1987 and NGC 2249, which are the two only relatively massive star clusters with an age of ∼1 Gyr for which such data is available. We find that the distribution of stars across the eMSTOs of these clusters cannot be explained solely by a distribution of stellar rotation velocities, unless the orientations of rapidly rotating stars are heavily biased toward an equator-on configuration. Under the assumption of random viewing angles, stellar rotation can account for ∼60% and ∼40% of the observed FWHM widths of the eMSTOs of NGC 1987 and NGC 2249, respectively. In contrast, a combination of distributions of stellar rotation velocities and stellar ages fits the observed eMSTO morphologies very well.« less

Heavy Element Abundances in Two B0-B0.5 Main Sequence Stars in the Small Magellanic Cloud

NASA Astrophysics Data System (ADS)

Peters, Geraldine J.

We propose FUSE observations of AV304 (B0.5V) and NGC346-637 B0V), two sharp-lined main-sequence stars in the Small Magellanic Cloud, to determine the abundances of heavy elements, especially those of the iron group. The FUSE spectral region contains numerous Fe III lines, including the resonance multiplet (UV 1) near 1130 Angstroms, that is excellent for abundance determinations and two strong multiplets of V III, an ion that does not produce measurable lines longward of 1200 Angstoms, in metal-deficient stars. In addition there are several measurable lines from Cr III and Mn III. A limited analyses of ground-based spectra of these stars by Dufton et al. (1990) and Rolleston et al. (1993) indicated an average underabundance of 0.7-0.8 dex for most light elements and a recent analysis of HSTSTIS data on AV304 by Peters & Grigsby (2001) suggests that the Fe group elements are depleted by the same amount relative to the sun. When combined with the HST-STIS results, this effort will represent the first attempt to measure the abundances of Fe group elements in the photospheres of early B, main sequence stars in an external galaxy. Although abundances of the Fe-peak elements are of interest because they are important for assessing opacities for stellar evolution calculations and the validity of theoretical calculations of explosive nucleosynthesis, the ground-based study did not yield this information because measurable lines from these species are found only in the UV spectral region. Abundances and abundance ratios of both heavy & light elements will be compared with the HST-STIS results from AV304, H II regions, supernova remnants, evolved massive stars in the SMC, and theoretical calculations of nucleosynthesis.

VLA and ALMA Imaging of Intense Galaxy-wide Star Formation in z ˜ 2 Galaxies

NASA Astrophysics Data System (ADS)

Rujopakarn, W.; Dunlop, J. S.; Rieke, G. H.; Ivison, R. J.; Cibinel, A.; Nyland, K.; Jagannathan, P.; Silverman, J. D.; Alexander, D. M.; Biggs, A. D.; Bhatnagar, S.; Ballantyne, D. R.; Dickinson, M.; Elbaz, D.; Geach, J. E.; Hayward, C. C.; Kirkpatrick, A.; McLure, R. J.; Michałowski, M. J.; Miller, N. A.; Narayanan, D.; Owen, F. N.; Pannella, M.; Papovich, C.; Pope, A.; Rau, U.; Robertson, B. E.; Scott, D.; Swinbank, A. M.; van der Werf, P.; van Kampen, E.; Weiner, B. J.; Windhorst, R. A.

2016-12-01

We present ≃0.″4 resolution extinction-independent distributions of star formation and dust in 11 star-forming galaxies (SFGs) at z = 1.3-3.0. These galaxies are selected from sensitive blank-field surveys of the 2‧ × 2‧ Hubble Ultra-Deep Field at λ = 5 cm and 1.3 mm using the Karl G. Jansky Very Large Array and Atacama Large Millimeter/submillimeter Array. They have star formation rates (SFRs), stellar masses, and dust properties representative of massive main-sequence SFGs at z ˜ 2. Morphological classification performed on spatially resolved stellar mass maps indicates a mixture of disk and morphologically disturbed systems; half of the sample harbor X-ray active galactic nuclei (AGNs), thereby representing a diversity of z ˜ 2 SFGs undergoing vigorous mass assembly. We find that their intense star formation most frequently occurs at the location of stellar-mass concentration and extends over an area comparable to their stellar-mass distribution, with a median diameter of 4.2 ± 1.8 kpc. This provides direct evidence of galaxy-wide star formation in distant blank-field-selected main-sequence SFGs. The typical galactic-average SFR surface density is 2.5 M ⊙ yr-1 kpc-2, sufficiently high to drive outflows. In X-ray-selected AGN where radio emission is enhanced over the level associated with star formation, the radio excess pinpoints the AGNs, which are found to be cospatial with star formation. The median extinction-independent size of main-sequence SFGs is two times larger than those of bright submillimeter galaxies, whose SFRs are 3-8 times larger, providing a constraint on the characteristic SFR (˜300 M ⊙ yr-1) above which a significant population of more compact SFGs appears to emerge.

Ordered fast Fourier transforms on a massively parallel hypercube multiprocessor

NASA Technical Reports Server (NTRS)

Tong, Charles; Swarztrauber, Paul N.

1991-01-01

The present evaluation of alternative, massively parallel hypercube processor-applicable designs for ordered radix-2 decimation-in-frequency FFT algorithms gives attention to the reduction of computation time-dominating communication. A combination of the order and computational phases of the FFT is accordingly employed, in conjunction with sequence-to-processor maps which reduce communication. Two orderings, 'standard' and 'cyclic', in which the order of the transform is the same as that of the input sequence, can be implemented with ease on the Connection Machine (where orderings are determined by geometries and priorities. A parallel method for trigonometric coefficient computation is presented which does not employ trigonometric functions or interprocessor communication.

Massively parallel polymerase cloning and genome sequencing of single cells using nanoliter microwells

PubMed Central

Gole, Jeff; Gore, Athurva; Richards, Andrew; Chiu, Yu-Jui; Fung, Ho-Lim; Bushman, Diane; Chiang, Hsin-I; Chun, Jerold; Lo, Yu-Hwa; Zhang, Kun

2013-01-01

Genome sequencing of single cells has a variety of applications, including characterizing difficult-to-culture microorganisms and identifying somatic mutations in single cells from mammalian tissues. A major hurdle in this process is the bias in amplifying the genetic material from a single cell, a procedure known as polymerase cloning. Here we describe the microwell displacement amplification system (MIDAS), a massively parallel polymerase cloning method in which single cells are randomly distributed into hundreds to thousands of nanoliter wells and simultaneously amplified for shotgun sequencing. MIDAS reduces amplification bias because polymerase cloning occurs in physically separated nanoliter-scale reactors, facilitating the de novo assembly of near-complete microbial genomes from single E. coli cells. In addition, MIDAS allowed us to detect single-copy number changes in primary human adult neurons at 1–2 Mb resolution. MIDAS will further the characterization of genomic diversity in many heterogeneous cell populations. PMID:24213699

High-throughput SNP genotyping in Cucurbita pepo for map construction and quantitative trait loci mapping

PubMed Central

2012-01-01

Background Cucurbita pepo is a member of the Cucurbitaceae family, the second- most important horticultural family in terms of economic importance after Solanaceae. The "summer squash" types, including Zucchini and Scallop, rank among the highest-valued vegetables worldwide. There are few genomic tools available for this species. The first Cucurbita transcriptome, along with a large collection of Single Nucleotide Polymorphisms (SNP), was recently generated using massive sequencing. A set of 384 SNP was selected to generate an Illumina GoldenGate assay in order to construct the first SNP-based genetic map of Cucurbita and map quantitative trait loci (QTL). Results We herein present the construction of the first SNP-based genetic map of Cucurbita pepo using a population derived from the cross of two varieties with contrasting phenotypes, representing the main cultivar groups of the species' two subspecies: Zucchini (subsp. pepo) × Scallop (subsp. ovifera). The mapping population was genotyped with 384 SNP, a set of selected EST-SNP identified in silico after massive sequencing of the transcriptomes of both parents, using the Illumina GoldenGate platform. The global success rate of the assay was higher than 85%. In total, 304 SNP were mapped, along with 11 SSR from a previous map, giving a map density of 5.56 cM/marker. This map was used to infer syntenic relationships between C. pepo and cucumber and to successfully map QTL that control plant, flowering and fruit traits that are of benefit to squash breeding. The QTL effects were validated in backcross populations. Conclusion Our results show that massive sequencing in different genotypes is an excellent tool for SNP discovery, and that the Illumina GoldenGate platform can be successfully applied to constructing genetic maps and performing QTL analysis in Cucurbita. This is the first SNP-based genetic map in the Cucurbita genus and is an invaluable new tool for biological research, especially considering that most of these markers are located in the coding regions of genes involved in different physiological processes. The platform will also be useful for future mapping and diversity studies, and will be essential in order to accelerate the process of breeding new and better-adapted squash varieties. PMID:22356647

THE GALEX/S{sup 4}G UV–IR COLOR–COLOR DIAGRAM: CATCHING SPIRAL GALAXIES AWAY FROM THE BLUE SEQUENCE

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

Bouquin, Alexandre Y. K.; Gil de Paz, Armando; Gallego, Jesús

We obtained GALEX FUV, NUV, and Spitzer/IRAC 3.6 μm photometry for >2000 galaxies, available for 90% of the S{sup 4}G sample. We find a very tight GALEX blue sequence (GBS) in the (FUV–NUV) versus (NUV–[3.6]) color–color diagram, which is populated by irregular and spiral galaxies, and is mainly driven by changes in the formation timescale (τ) and a degeneracy between τ and dust reddening. The tightness of the GBS provides an unprecedented way of identifying star-forming galaxies and objects that are just evolving to (or from) what we call the GALEX green valley (GGV). At the red end of the GBS, atmore » (NUV–[3.6]) > 5, we find a wider GALEX red sequence (GRS) mostly populated by E/S0 galaxies that has a perpendicular slope to that of the GBS and of the optical red sequence. We find no such dichotomy in terms of stellar mass (measured by M{sub [3.6]}) since both massive (M{sub ⋆}>10{sup 11}M{sub ⊙}) blue- and red-sequence galaxies are identified. The type that is proportionally more often found in the GGV is the S0-Sa’s, and most of these are located in high-density environments. We discuss evolutionary models of galaxies that show a rapid transition from the blue to the red sequence on a timescale of 10{sup 8} yr.« less

The GALEX/S4G UV-IR Color-Color Diagram: Catching Spiral Galaxies Away from the Blue Sequence

NASA Astrophysics Data System (ADS)

Bouquin, Alexandre Y. K.; Gil de Paz, Armando; Boissier, Samuel; Muñoz-Mateos, Juan-Carlos; Sheth, Kartik; Zaritsky, Dennis; Laine, Jarkko; Gallego, Jesús; Peletier, Reynier F.; Röck, Benjamin R.; Knapen, Johan H.

2015-02-01

We obtained GALEX FUV, NUV, and Spitzer/IRAC 3.6 μm photometry for \\gt 2000 galaxies, available for 90% of the S4G sample. We find a very tight GALEX blue sequence (GBS) in the (FUV-NUV) versus (NUV-[3.6]) color-color diagram, which is populated by irregular and spiral galaxies, and is mainly driven by changes in the formation timescale (τ) and a degeneracy between τ and dust reddening. The tightness of the GBS provides an unprecedented way of identifying star-forming galaxies and objects that are just evolving to (or from) what we call the GALEX green valley (GGV). At the red end of the GBS, at (NUV-[3.6]) \\gt 5, we find a wider GALEX red sequence (GRS) mostly populated by E/S0 galaxies that has a perpendicular slope to that of the GBS and of the optical red sequence. We find no such dichotomy in terms of stellar mass (measured by {{M}[3.6]}) since both massive ({{M}\\star }\\gt {{10}11}{{M}⊙ }) blue- and red-sequence galaxies are identified. The type that is proportionally more often found in the GGV is the S0-Sa’s, and most of these are located in high-density environments. We discuss evolutionary models of galaxies that show a rapid transition from the blue to the red sequence on a timescale of 108 yr.

Complete sequence and diversity of a maize-associated Polerovirus in East Africa

USDA-ARS?s Scientific Manuscript database

Since 2011-2012, Maize lethal necrosis (MLN) has emerged in East Africa, causing massive yield loss and propelling research to identify viruses and virus populations present in maize. As expected, next generation sequencing (NGS) has revealed diverse and abundant viruses from the family Potyviridae,...

Mining conifers’ mega-genome using rapid and efficient multiplexed high-throughput genotyping-by-sequencing (GBS) SNP discovery platform

USDA-ARS?s Scientific Manuscript database

Next-generation sequencing (NGS) technologies are revolutionizing both medical and biological research through generation of massive SNP data sets for identifying heritable genome variation underlying key traits, from rare human diseases to important agronomic phenotypes in crop species. We evaluate...

Molecular effects of doxycycline treatment on pterygium as revealed by massive transcriptome sequencing.

PubMed

Larráyoz, Ignacio M; de Luis, Alberto; Rúa, Oscar; Velilla, Sara; Cabello, Juan; Martínez, Alfredo

2012-01-01

Pterygium is a lesion of the eye surface which involves cell proliferation, migration, angiogenesis, fibrosis, and extracellular matrix remodelling. Surgery is the only approved method to treat this disorder, but high recurrence rates are common. Recently, it has been shown in a mouse model that treatment with doxycycline resulted in reduction of the pterygium lesions. Here we study the mechanism(s) of action by which doxycycline achieves these results, using massive sequencing techniques. Surgically removed pterygia from 10 consecutive patients were set in short term culture and exposed to 0 (control), 50, 200, and 500 µg/ml doxycycline for 24 h, their mRNA was purified, reverse transcribed and sequenced through Illumina's massive sequencing protocols. Acquired data were subjected to quantile normalization and analyzed using cytoscape plugin software to explore the pathways involved. False discovery rate (FDR) methods were used to identify 332 genes which modified their expression in a dose-dependent manner upon exposure to doxycycline. The more represented cellular pathways included all mitochondrial genes, the endoplasmic reticulum stress response, integrins and extracellular matrix components, and growth factors. A high correlation was obtained when comparing ultrasequencing data with qRT-PCR and ELISA results. Doxycycline significantly modified the expression of important cellular pathways in pterygium cells, in a way which is consistent with the observed efficacy of this antibiotic to reduce pterygium lesions in a mouse model. Clinical trials are under way to demonstrate whether there is a benefit for human patients.

A general method to eliminate laboratory induced recombinants during massive, parallel sequencing of cDNA library.

PubMed

Waugh, Caryll; Cromer, Deborah; Grimm, Andrew; Chopra, Abha; Mallal, Simon; Davenport, Miles; Mak, Johnson

2015-04-09

Massive, parallel sequencing is a potent tool for dissecting the regulation of biological processes by revealing the dynamics of the cellular RNA profile under different conditions. Similarly, massive, parallel sequencing can be used to reveal the complexity of viral quasispecies that are often found in the RNA virus infected host. However, the production of cDNA libraries for next-generation sequencing (NGS) necessitates the reverse transcription of RNA into cDNA and the amplification of the cDNA template using PCR, which may introduce artefact in the form of phantom nucleic acids species that can bias the composition and interpretation of original RNA profiles. Using HIV as a model we have characterised the major sources of error during the conversion of viral RNA to cDNA, namely excess RNA template and the RNaseH activity of the polymerase enzyme, reverse transcriptase. In addition we have analysed the effect of PCR cycle on detection of recombinants and assessed the contribution of transfection of highly similar plasmid DNA to the formation of recombinant species during the production of our control viruses. We have identified RNA template concentrations, RNaseH activity of reverse transcriptase, and PCR conditions as key parameters that must be carefully optimised to minimise chimeric artefacts. Using our optimised RT-PCR conditions, in combination with our modified PCR amplification procedure, we have developed a reliable technique for accurate determination of RNA species using NGS technology.

Characterization of the Gut Microbiome Using 16S or Shotgun Metagenomics

PubMed Central

Jovel, Juan; Patterson, Jordan; Wang, Weiwei; Hotte, Naomi; O'Keefe, Sandra; Mitchel, Troy; Perry, Troy; Kao, Dina; Mason, Andrew L.; Madsen, Karen L.; Wong, Gane K.-S.

2016-01-01

The advent of next generation sequencing (NGS) has enabled investigations of the gut microbiome with unprecedented resolution and throughput. This has stimulated the development of sophisticated bioinformatics tools to analyze the massive amounts of data generated. Researchers therefore need a clear understanding of the key concepts required for the design, execution and interpretation of NGS experiments on microbiomes. We conducted a literature review and used our own data to determine which approaches work best. The two main approaches for analyzing the microbiome, 16S ribosomal RNA (rRNA) gene amplicons and shotgun metagenomics, are illustrated with analyses of libraries designed to highlight their strengths and weaknesses. Several methods for taxonomic classification of bacterial sequences are discussed. We present simulations to assess the number of sequences that are required to perform reliable appraisals of bacterial community structure. To the extent that fluctuations in the diversity of gut bacterial populations correlate with health and disease, we emphasize various techniques for the analysis of bacterial communities within samples (α-diversity) and between samples (β-diversity). Finally, we demonstrate techniques to infer the metabolic capabilities of a bacteria community from these 16S and shotgun data. PMID:27148170

Highlights of Astronomy, Vol. 16

NASA Astrophysics Data System (ADS)

Montmerle, Thierry

2015-04-01

Part I. Invited Discourses: 1. The Herschel view of star formation; 2. Past, present and future of Chinese astronomy; 3. The zoo of galaxies; 4. Supernovae, the accelerating cosmos, and dark energy; Part II. Joint Discussion: 5. Very massive stars in the local universe; 6. 3-D views of the cycling Sun in stellar context; 7. Ultraviolet emission in early-type galaxies; 8. From meteors and meteorites to their parent bodies: current status and future developments; 9. The connection between radio properties and high-energy emission in AGNs; 10. Space-time reference systems for future research; Part III. Special Sessions: 11. Origin and complexity of massive star clusters; 12. Cosmic evolution of groups and clusters of galaxies; 13. Galaxy evolution through secular processes; 14. New era for studying interstellar and intergalactic magnetic fields; 15. The IR view of massive stars: the main sequence and beyond; 16. Science with large solar telescopes; 17. The impact hazard: current activities and future plans; 18. Calibration of star-formation rate measurements across the electromagnetic spectrum; 19. Future large scale facilities; 20. Dynamics of the star-planet relations strategic plan and the Global Office of Astronomy for Development; 21. Strategic plan and the Global Office of Astronomy for Development; 22. Modern views of the interstellar medium; 23. High-precision tests of stellar physics from high-precision photometry; 24. Communicating astronomy with the public for scientists; 25. Data intensive astronomy; 26. Unexplained spectral phenomena in the interstellar medium; 27. Light pollution: protecting astronomical sites and increasing global awareness through education.

ATLASGAL -- A molecular view of an unbiased sample of massive star forming clumps

NASA Astrophysics Data System (ADS)

Figura, Charles; Urquhart, James; Wyrowski, Friedrich; Giannetti, Andrea; Kim, Wonju

2018-01-01

Massive stars play an important role in many areas of astrophysics, from regulating star formation to driving the evolution of their host galaxy. Study of these stars is made difficult by their short evolutionary timescales, small populations and greater distances, and further complicated because they reach the main sequence while still shrouded in their natal clumps. As a result, many aspects of their formation are still poorly understood.We have assembled a large and statistically representative collection of massive star-forming environments that span all evolutionary stages of development by correlating mid-infrared and dust continnum surveys. We have conducted follow-up single-pointing observations toward a sample of approximately 600 of these clumps with the Mopra telescope using an 8 GHz bandwidth that spans some 27 molecular and mm-radio recombination line transitions. These lines trace a wide range of interstellar conditions with varying thermal, chemical, and kinematic properties. Many of these lines exhibit hyperfine structure allowing more detailed measurements of the clump environment (e.g. rotation temperatures and column densities).From these twenty-seven lines, we have identified thirteen line intensity ratios that strongly trace the evolutionary state of these clumps. We have investigated individual molecular and mm-radio recombination lines, contrasting these with radio and sub-mm continuum observations. We present a summary of the results of the statistical analysis of the sample, and compare them with previous similar studies to test their utility as chemical clocks of the evolutionary processes.

A strange dwarf scenario for the formation of the peculiar double white dwarf binary SDSS J125733.63+542850.5

NASA Astrophysics Data System (ADS)

Jiang, Long; Chen, Wen-Cong; Li, Xiang-Dong

2018-05-01

The Hubble Space Telescope observation of the double white dwarf (WD) binary SDSS J125733.63+542850.5 reveals that the massive WD has a surface gravity log g1 ˜ 8.7 (which implies a mass of M1 ˜ 1.06 M⊙) and an effective temperature T1 ˜ 13 000 K, while the effective temperature of the low-mass WD (M2 < 0.24 M⊙) is T2 ˜ 6400K. Therefore, the massive and the low-mass WDs have a cooling age τ1 ˜ 1 Gyr and τ2 ≥ 5 Gyr, respectively. This is in contradiction with traditional binary evolution theory. In this paper, we propose a strange dwarf (SD) scenario to explain the formation of this double WD binary. We assume that the massive WD is a SD originating from a phase transition (PT) in a ˜1.1 M⊙ WD, which has experienced accretion and spin-down processes. Its high effective temperature could arise from the heating process during the PT. Our simulations suggest that the progenitor of SDSS J125733.63+542850.5 can be a binary system consisting of a 0.65 M⊙ WD and a 1.5 M⊙ main-sequence star in a 1.492 d orbit. Especially, the secondary star (i.e. the progenitor of the low-mass WD) is likely to have an ultra-low metallicity of Z = 0.0001.

2D and 3D Models of Convective Turbulence and Oscillations in Intermediate-Mass Main-Sequence Stars

NASA Astrophysics Data System (ADS)

Guzik, Joyce Ann; Morgan, Taylor H.; Nelson, Nicholas J.; Lovekin, Catherine; Kitiashvili, Irina N.; Mansour, Nagi N.; Kosovichev, Alexander

2015-08-01

We present multidimensional modeling of convection and oscillations in main-sequence stars somewhat more massive than the sun, using three separate approaches: 1) Applying the spherical 3D MHD ASH (Anelastic Spherical Harmonics) code to simulate the core convection and radiative zone. Our goal is to determine whether core convection can excite low-frequency gravity modes, and thereby explain the presence of low frequencies for some hybrid gamma Dor/delta Sct variables for which the envelope convection zone is too shallow for the convective blocking mechanism to drive g modes; 2) Using the 3D planar ‘StellarBox’ radiation hydrodynamics code to model the envelope convection zone and part of the radiative zone. Our goals are to examine the interaction of stellar pulsations with turbulent convection in the envelope, excitation of acoustic modes, and the role of convective overshooting; 3) Applying the ROTORC 2D stellar evolution and dynamics code to calculate evolution with a variety of initial rotation rates and extents of core convective overshooting. The nonradial adiabatic pulsation frequencies of these nonspherical models will be calculated using the 2D pulsation code NRO of Clement. We will present new insights into gamma Dor and delta Sct pulsations gained by multidimensional modeling compared to 1D model expectations.

FIRST OBSERVATIONAL SIGNATURE OF ROTATIONAL DECELERATION IN A MASSIVE, INTERMEDIATE-AGE STAR CLUSTER IN THE MAGELLANIC CLOUDS

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

Wu, Xiaohan; Li, Chengyuan; De Grijs, Richard

While the extended main-sequence turnoffs (eMSTOs) found in almost all 1–2 Gyr old star clusters in the Magellanic Clouds are often explained by postulating extended star formation histories (SFHs), the tight subgiant branches (SGBs) seen in some clusters challenge this popular scenario. Puzzlingly, the SGB of the eMSTO cluster NGC 419 is significantly broader at bluer than at redder colors. We carefully assess and confirm the reality of this observational trend. If we would assume that the widths of the features in color–magnitude space were entirely owing to a range in stellar ages, the SFHs of the eMSTO stars andmore » the blue SGB region would be significantly more prolonged than that of the red part of the SGB. This cannot be explained by assuming an internal age spread. We show that rotational deceleration of a population of rapidly rotating stars, a currently hotly debated alternative scenario, naturally explains the observed trend along the SGB. Our analysis shows that a “converging” SGB could be produced if the cluster is mostly composed of rapidly rotating stars that slow down over time owing to the conservation of angular momentum during their evolutionary expansion from main-sequence turnoff stars to red giants.« less

The language of the protein universe.

PubMed

Scaiewicz, Andrea; Levitt, Michael

2015-12-01

Proteins, the main cell machinery which play a major role in nearly every cellular process, have always been a central focus in biology. We live in the post-genomic era, and inferring information from massive data sets is a steadily growing universal challenge. The increasing availability of fully sequenced genomes can be regarded as the 'Rosetta Stone' of the protein universe, allowing the understanding of genomes and their evolution, just as the original Rosetta Stone allowed Champollion to decipher the ancient Egyptian hieroglyphics. In this review, we consider aspects of the protein domain architectures repertoire that are closely related to those of human languages and aim to provide some insights about the language of proteins. Copyright © 2015 Elsevier Ltd. All rights reserved.

A Kepler Mission, A Search for Habitable Planets: Concept, Capabilities and Strengths

NASA Technical Reports Server (NTRS)

Koch, David; Borucki, William; Lissauer, Jack; Dunham, Edward; Jenkins, Jon; DeVincenzi, D. (Technical Monitor)

1998-01-01

The detection of extrasolar terrestrial planets orbiting main-sequence stars is of great interest and importance. Current ground-based methods are only capable of detecting objects about the size or mass of Jupiter or larger. The technological challenges of direct imaging of Earth-size planets from space are expected to be resolved over the next twenty years. Spacebased photometry of planetary transits is currently the only viable method for detection of terrestrial planets (30-600 times less massive than Jupiter). The method searches the extended solar neighborhood, providing a statistically large sample and the detailed characteristics of each individual case. A robust concept has been developed and proposed as a Discovery-class mission. The concept, its capabilities and strengths are presented.

The postcollapse core of M15 imaged with the HST planetary camera

NASA Technical Reports Server (NTRS)

Lauer, Tod R.; Holtzman, Jon A.; Faber, S. M.; Baum, William A.; Currie, Douglas G.; Ewald, S. P.; Groth, Edward J.; Hester, J. Jeff; Kelsall, T.

1991-01-01

It is shown here that, despite the severe spherical aberration present in the HST, the Wide Field/Planetary Camera (WFPC) images still present useful high-resolution information on M15, the classic candidate for a cluster with a collapsed core. The stars in M15 have been resolved down to the main-sequence turnoff and have been subtracted from the images. The remaining faint, unresolved stars form a diffuse background with a surprisingly large core with r(c) = 0.13 pc. The existence of a large core interior to the power-law cusp may imply that M15 has evolved well past maximum core collapse and may rule out the presence of a massive central black hole as well.

Star formation properties of Hickson Compact Groups based on deep Hα imaging

NASA Astrophysics Data System (ADS)

Eigenthaler, Paul; Ploeckinger, Sylvia; Verdugo, Miguel; Ziegler, Bodo

2015-08-01

We present deep Hα imaging of seven Hickson Compact Groups (HCGs) using the 4.1-m Southern Astrophysics Research (SOAR) Telescope. The high spatial resolution of the observations allows us to study both the integrated star formation properties of the main galaxies as well as the 2D distribution of star-forming knots in the faint tidal arms that form during interactions between the individual galaxies. We derive star formation rates and stellar masses for group members and discuss their position relative to the main sequence of star-forming galaxies. Despite the existence of tidal features within the galaxy groups, we do not find any indication for enhanced star formation in the selected sample of HCGs. We study azimuthally averaged Hα profiles of the galaxy discs and compare them with the g' and r' surface brightness profiles. We do not find any truncated galaxy discs but reveal that more massive galaxies show a higher light concentration in Hα than less massive ones. We also see that galaxies that show a high light concentration in r', show a systematic higher light concentration in Hα. Tidal dwarf galaxy (TDG) candidates have been previously detected in R-band images for two groups in our sample but we find that most of them are likely background objects as they do not show any emission in Hα. We present a new TDG candidate at the tip of the tidal tail in HCG 91.

ASSET: Analysis of Sequences of Synchronous Events in Massively Parallel Spike Trains

PubMed Central

Canova, Carlos; Denker, Michael; Gerstein, George; Helias, Moritz

2016-01-01

With the ability to observe the activity from large numbers of neurons simultaneously using modern recording technologies, the chance to identify sub-networks involved in coordinated processing increases. Sequences of synchronous spike events (SSEs) constitute one type of such coordinated spiking that propagates activity in a temporally precise manner. The synfire chain was proposed as one potential model for such network processing. Previous work introduced a method for visualization of SSEs in massively parallel spike trains, based on an intersection matrix that contains in each entry the degree of overlap of active neurons in two corresponding time bins. Repeated SSEs are reflected in the matrix as diagonal structures of high overlap values. The method as such, however, leaves the task of identifying these diagonal structures to visual inspection rather than to a quantitative analysis. Here we present ASSET (Analysis of Sequences of Synchronous EvenTs), an improved, fully automated method which determines diagonal structures in the intersection matrix by a robust mathematical procedure. The method consists of a sequence of steps that i) assess which entries in the matrix potentially belong to a diagonal structure, ii) cluster these entries into individual diagonal structures and iii) determine the neurons composing the associated SSEs. We employ parallel point processes generated by stochastic simulations as test data to demonstrate the performance of the method under a wide range of realistic scenarios, including different types of non-stationarity of the spiking activity and different correlation structures. Finally, the ability of the method to discover SSEs is demonstrated on complex data from large network simulations with embedded synfire chains. Thus, ASSET represents an effective and efficient tool to analyze massively parallel spike data for temporal sequences of synchronous activity. PMID:27420734

Identification of rare X-linked neuroligin variants by massively parallel sequencing in males with autism spectrum disorder.

PubMed

Steinberg, Karyn Meltz; Ramachandran, Dhanya; Patel, Viren C; Shetty, Amol C; Cutler, David J; Zwick, Michael E

2012-09-28

Autism spectrum disorder (ASD) is highly heritable, but the genetic risk factors for it remain largely unknown. Although structural variants with large effect sizes may explain up to 15% ASD, genome-wide association studies have failed to uncover common single nucleotide variants with large effects on phenotype. The focus within ASD genetics is now shifting to the examination of rare sequence variants of modest effect, which is most often achieved via exome selection and sequencing. This strategy has indeed identified some rare candidate variants; however, the approach does not capture the full spectrum of genetic variation that might contribute to the phenotype. We surveyed two loci with known rare variants that contribute to ASD, the X-linked neuroligin genes by performing massively parallel Illumina sequencing of the coding and noncoding regions from these genes in males from families with multiplex autism. We annotated all variant sites and functionally tested a subset to identify other rare mutations contributing to ASD susceptibility. We found seven rare variants at evolutionary conserved sites in our study population. Functional analyses of the three 3' UTR variants did not show statistically significant effects on the expression of NLGN3 and NLGN4X. In addition, we identified two NLGN3 intronic variants located within conserved transcription factor binding sites that could potentially affect gene regulation. These data demonstrate the power of massively parallel, targeted sequencing studies of affected individuals for identifying rare, potentially disease-contributing variation. However, they also point out the challenges and limitations of current methods of direct functional testing of rare variants and the difficulties of identifying alleles with modest effects.

Identification of rare X-linked neuroligin variants by massively parallel sequencing in males with autism spectrum disorder

PubMed Central

2012-01-01

Background Autism spectrum disorder (ASD) is highly heritable, but the genetic risk factors for it remain largely unknown. Although structural variants with large effect sizes may explain up to 15% ASD, genome-wide association studies have failed to uncover common single nucleotide variants with large effects on phenotype. The focus within ASD genetics is now shifting to the examination of rare sequence variants of modest effect, which is most often achieved via exome selection and sequencing. This strategy has indeed identified some rare candidate variants; however, the approach does not capture the full spectrum of genetic variation that might contribute to the phenotype. Methods We surveyed two loci with known rare variants that contribute to ASD, the X-linked neuroligin genes by performing massively parallel Illumina sequencing of the coding and noncoding regions from these genes in males from families with multiplex autism. We annotated all variant sites and functionally tested a subset to identify other rare mutations contributing to ASD susceptibility. Results We found seven rare variants at evolutionary conserved sites in our study population. Functional analyses of the three 3’ UTR variants did not show statistically significant effects on the expression of NLGN3 and NLGN4X. In addition, we identified two NLGN3 intronic variants located within conserved transcription factor binding sites that could potentially affect gene regulation. Conclusions These data demonstrate the power of massively parallel, targeted sequencing studies of affected individuals for identifying rare, potentially disease-contributing variation. However, they also point out the challenges and limitations of current methods of direct functional testing of rare variants and the difficulties of identifying alleles with modest effects. PMID:23020841

Family ties of WR to LBV nebulae yielding clues for stellar evolution

NASA Astrophysics Data System (ADS)

Weis, K.

Luminous Blue Variables (LBVs) are stars is a transitional phase massive stars may enter while evolving from main-sequence to Wolf-Rayet stars. The to LBVs intrinsic photometric variability is based on the modulation of the stellar spectrum. Within a few years the spectrum shifts from OB to AF type and back. During their cool phase LBVs are close to the Humphreys-Davidson (equivalent to Eddington/Omega-Gamma) limit. LBVs have a rather high mass loss rate, with stellar winds that are fast in the hot and slower in the cool phase of an LBV. These alternating wind velocities lead to the formation of LBV nebulae by wind-wind interactions. A nebula can also be formed in a spontaneous giant eruption in which larger amounts of mass are ejected. LBV nebulae are generally small (< 5 pc) mainly gaseous circumstellar nebulae, with a rather large fraction of LBV nebulae being bipolar. After the LBV phase the star will turn into a Wolf-Rayet star, but note that not all WR stars need to have passed the LBV phase. Some follow from the RSG and the most massive directly from the MS phase. In general WRs have a large mass loss and really fast stellar winds. The WR wind may interact with winds of earlier phases (MS, RSG) to form WR nebulae. As for WR with LBV progenitors the scenario might be different, here no older wind is present but an LBV nebula! The nature of WR nebulae are therefore manifold and in particular the connection (or family ties) of WR to LBV nebulae is important to understand the transition between these two phases, the evolution of massive stars, their winds, wind-wind and wind-nebula interactions. Looking at the similarities and differences of LBV and WR nebula, figuring what is a genuine LBV and WR nebula are the basic question addressed in the analysis presented here.

SN 2015ba: a Type IIP supernova with a long plateau.

NASA Astrophysics Data System (ADS)

Dastidar, Raya; Misra, Kuntal; Hosseinzadeh, G.; Pastorello, A.; Pumo, M. L.; Valenti, S.; McCully, C.; Tomasella, L.; Arcavi, I.; Elias-Rosa, N.; Singh, Mridweeka; Gangopadhyay, Anjasha; Howell, D. A.; Morales-Garoffolo, Antonia; Zampieri, L.; Kumar, Brijesh; Turatto, M.; Benetti, S.; Tartaglia, L.; Ochner, P.; Sahu, D. K.; Anupama, G. C.; Pandey, S. B.

2018-06-01

We present optical photometry and spectroscopy from about a week after explosion to ˜272 d of an atypical Type IIP supernova, SN 2015ba, which exploded in the edge-on galaxy IC 1029. SN 2015ba is a luminous event with an absolute V-band magnitude of -17.1 ± 0.2 mag at 50 d since explosion and has a long plateau lasting for ˜123 d. The distance to the SN is estimated to be 34.8 ± 0.7 Mpc using the expanding photosphere and standard candle methods. High-velocity H Balmer components constant with time are observed in the late-plateau phase spectra of SN 2015ba, which suggests a possible role of circumstellar interaction at these phases. Both hydrodynamical and analytical modelling suggest a massive progenitor of SN 2015ba with a pre-explosion mass of 24-26 M⊙. However, the nebular spectra of SN 2015ba exhibit insignificant levels of oxygen, which is otherwise expected from a massive progenitor. This might be suggestive of the non-monotonical link between O-core masses and the zero-age main-sequence mass of pre-supernova stars and/or uncertainties in the mixing scenario in the ejecta of supernovae.

Hubble Space Telescope Imaging of the Mass-losing Supergiant VY Canis Majoris

NASA Astrophysics Data System (ADS)

Kastner, Joel H.; Weintraub, David A.

1998-04-01

The highly luminous M supergiant VY CMa is a massive star that appears to be in its final death throes, losing mass at high rate en route to exploding as a supernova. Subarcsecond-resolution optical images of VY CMa, obtained with the Faint Object Camera (FOC) aboard the Hubble Space Telescope, vividly demonstrate that mass loss from VY CMa is highly anisotropic. In the FOC images, the optical ``star'' VY CMa constitutes the bright, well-resolved core of an elongated reflection nebula. The imaged nebula is ~3" (~4500 AU) in extent and is clumpy and highly asymmetric. The images indicate that the bright core, which lies near one edge of the nebula, is pure scattered starlight. We conclude that at optical wavelengths VY CMa is obscured from view along our line of sight by its own dusty envelope. The presence of the extended reflection nebula then suggests that this envelope is highly flattened and/or that the star is surrounded by a massive circumstellar disk. Such axisymmetric circumstellar density structure should have profound effects on post-red supergiant mass loss from VY CMa and, ultimately, on the shaping of the remnant of the supernova that will terminate its post-main-sequence evolution.

Asteroseismology of OB stars with CoRoT

NASA Astrophysics Data System (ADS)

Degroote, P.; Aerts, C.; Samadi, R.; Miglio, A.; Briquet, M.; Auvergne, M.; Baglin, A.; Baudin, F.; Catala, C.; Michel, E.

2010-12-01

The CoRoT satellite is revolutionizing the photometric study of massive O-type and B-type stars. During its long runs, CoRoT observed the entire main sequence B star domain, from typical hot β Cep stars, via cooler hybrid p- and g-mode pulsators to the SPB stars near the edge of the instability strip. CoRoT lowers the sensitivity barrier from the typical mmag-precision reached from the ground, to the μmag-level reached from space. Within the wealth of detected and identified pulsation modes, relations have been found in the form of multiplets, combination of frequencies, and frequency- and period spacings. This wealth of observational evidence is finally providing strong constraints to test current models of the internal structure and pulsations of hot stars. Aside from the expected opacity driven modes with infinite lifetime, other unexpected types of variability are detected in massive stars, such as modes of stochastic nature. The simultaneous observation of all these light curve characteristics implies a challenge for both observational asteroseismology and stellar modelling. The CoRoT space mission was developed and is operated by the French space agency CNES, with participation of ESA's RSSD and Science Programmes, Austria, Belgium, Brazil, Germany, and Spain.

Throwing Icebergs at White Dwarfs

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

Stephan, Alexander P.; Naoz, Smadar; Zuckerman, B., E-mail: alexpstephan@astro.ucla.edu

White dwarfs (WDs) have atmospheres that are expected to consist nearly entirely of hydrogen and helium, since heavier elements will sink out of sight on short timescales. However, observations have revealed atmospheric pollution by heavier elements in about a quarter to a half of all WDs. While most of the pollution can be accounted for with asteroidal or dwarf planetary material, recent observations indicate that larger planetary bodies, as well as icy and volatile material from Kuiper belt analog objects, are also viable sources of pollution. The commonly accepted pollution mechanisms, namely scattering interactions between planetary bodies orbiting the WDs,more » can hardly account for pollution by objects with large masses or long-period orbits. Here we report on a mechanism that naturally leads to the emergence of massive body and icy and volatile material pollution. This mechanism occurs in wide binary stellar systems, where the mass loss of the planets’ host stars during post main sequence stellar evolution can trigger the Eccentric Kozai–Lidov mechanism. This mechanism leads to large eccentricity excitations, which can bring massive and long-period objects close enough to the WDs to be accreted. We find that this mechanism readily explains and is consistent with observations.« less

Spitzer Microlens Measurement of a Massive Remnant in a Well-separated Binary

NASA Astrophysics Data System (ADS)

Shvartzvald, Y.; Udalski, A.; Gould, A.; Han, C.; Bozza, V.; Friedmann, M.; Hundertmark, M.; and; Beichman, C.; Bryden, G.; Calchi Novati, S.; Carey, S.; Fausnaugh, M.; Gaudi, B. S.; Henderson, C. B.; Kerr, T.; Pogge, R. W.; Varricatt, W.; Wibking, B.; Yee, J. C.; Zhu, W.; Spitzer Team; Poleski, R.; Pawlak, M.; Szymański, M. K.; Skowron, J.; Mróz, P.; Kozłowski, S.; Wyrzykowski, Ł.; Pietrukowicz, P.; Pietrzyński, G.; Soszyński, I.; Ulaczyk, K.; OGLE Group; Choi, J.-Y.; Park, H.; Jung, Y. K.; Shin, I.-G.; Albrow, M. D.; Park, B.-G.; Kim, S.-L.; Lee, C.-U.; Cha, S.-M.; Kim, D.-J.; Lee, Y.; KMTNet Group; Maoz, D.; Kaspi, S.; Wise Group; Street, R. A.; Tsapras, Y.; Bachelet, E.; Dominik, M.; Bramich, D. M.; Horne, Keith; Snodgrass, C.; Steele, I. A.; Menzies, J.; Figuera Jaimes, R.; Wambsganss, J.; Schmidt, R.; Cassan, A.; Ranc, C.; Mao, S.; Dong, Subo; RoboNet; D'Ago, G.; Scarpetta, G.; Verma, P.; Jørgensen, U. G.; Kerins, E.; Skottfelt, J.; MiNDSTEp

2015-12-01

We report the detection and mass measurement of a binary lens OGLE-2015-BLG-1285La,b, with the more massive component having M1 > 1.35 M⊙ (80% probability). A main-sequence star in this mass range is ruled out by limits on blue light, meaning that a primary in this mass range must be a neutron star (NS) or black hole (BH). The system has a projected separation r⊥ = 6.1 ± 0.4 AU and lies in the Galactic bulge. These measurements are based on the “microlens parallax” effect, i.e., comparing the microlensing light curve as seen from Spitzer, which lay at 1.25 AU projected from Earth, to the light curves from four ground-based surveys, three in the optical and one in the near-infrared. Future adaptive optics imaging of the companion by 30 m class telescopes will yield a much more accurate measurement of the primary mass. This discovery both opens the path and defines the challenges to detecting and characterizing BHs and NSs in wide binaries, with either dark or luminous companions. In particular, we discuss lessons that can be applied to future Spitzer and Kepler K2 microlensing parallax observations.

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

Non-invasive prenatal testing using massively parallel sequencing of maternal plasma DNA: from molecular karyotyping to fetal whole-genome sequencing.

PubMed

Lo, Y M Dennis

2013-12-01

The discovery of cell-free fetal DNA in maternal plasma in 1997 has stimulated a rapid development of non-invasive prenatal testing. The recent advent of massively parallel sequencing has allowed the analysis of circulating cell-free fetal DNA to be performed with unprecedented sensitivity and precision. Fetal trisomies 21, 18 and 13 are now robustly detectable in maternal plasma and such analyses have been available clinically since 2011. Fetal genome-wide molecular karyotyping and whole-genome sequencing have now been demonstrated in a number of proof-of-concept studies. Genome-wide and targeted sequencing of maternal plasma has been shown to allow the non-invasive prenatal testing of β-thalassaemia and can potentially be generalized to other monogenic diseases. It is thus expected that plasma DNA-based non-invasive prenatal testing will play an increasingly important role in future obstetric care. It is thus timely and important that the ethical, social and legal issues of non-invasive prenatal testing be discussed actively by all parties involved in prenatal care. Copyright © 2013 Reproductive Healthcare Ltd. Published by Elsevier Ltd. All rights reserved.

Genome Analysis of the Domestic Dog (Korean Jindo) by Massively Parallel Sequencing

PubMed Central

Kim, Ryong Nam; Kim, Dae-Soo; Choi, Sang-Haeng; Yoon, Byoung-Ha; Kang, Aram; Nam, Seong-Hyeuk; Kim, Dong-Wook; Kim, Jong-Joo; Ha, Ji-Hong; Toyoda, Atsushi; Fujiyama, Asao; Kim, Aeri; Kim, Min-Young; Park, Kun-Hyang; Lee, Kang Seon; Park, Hong-Seog

2012-01-01

Although pioneering sequencing projects have shed light on the boxer and poodle genomes, a number of challenges need to be met before the sequencing and annotation of the dog genome can be considered complete. Here, we present the DNA sequence of the Jindo dog genome, sequenced to 45-fold average coverage using Illumina massively parallel sequencing technology. A comparison of the sequence to the reference boxer genome led to the identification of 4 675 437 single nucleotide polymorphisms (SNPs, including 3 346 058 novel SNPs), 71 642 indels and 8131 structural variations. Of these, 339 non-synonymous SNPs and 3 indels are located within coding sequences (CDS). In particular, 3 non-synonymous SNPs and a 26-bp deletion occur in the TCOF1 locus, implying that the difference observed in cranial facial morphology between Jindo and boxer dogs might be influenced by those variations. Through the annotation of the Jindo olfactory receptor gene family, we found 2 unique olfactory receptor genes and 236 olfactory receptor genes harbouring non-synonymous homozygous SNPs that are likely to affect smelling capability. In addition, we determined the DNA sequence of the Jindo dog mitochondrial genome and identified Jindo dog-specific mtDNA genotypes. This Jindo genome data upgrade our understanding of dog genomic architecture and will be a very valuable resource for investigating not only dog genetics and genomics but also human and dog disease genetics and comparative genomics. PMID:22474061

Molecular diagnosis of glycogen storage disease and disorders with overlapping clinical symptoms by massive parallel sequencing.

PubMed

Vega, Ana I; Medrano, Celia; Navarrete, Rosa; Desviat, Lourdes R; Merinero, Begoña; Rodríguez-Pombo, Pilar; Vitoria, Isidro; Ugarte, Magdalena; Pérez-Cerdá, Celia; Pérez, Belen

2016-10-01

Glycogen storage disease (GSD) is an umbrella term for a group of genetic disorders that involve the abnormal metabolism of glycogen; to date, 23 types of GSD have been identified. The nonspecific clinical presentation of GSD and the lack of specific biomarkers mean that Sanger sequencing is now widely relied on for making a diagnosis. However, this gene-by-gene sequencing technique is both laborious and costly, which is a consequence of the number of genes to be sequenced and the large size of some genes. This work reports the use of massive parallel sequencing to diagnose patients at our laboratory in Spain using either a customized gene panel (targeted exome sequencing) or the Illumina Clinical-Exome TruSight One Gene Panel (clinical exome sequencing (CES)). Sequence variants were matched against biochemical and clinical hallmarks. Pathogenic mutations were detected in 23 patients. Twenty-two mutations were recognized (mostly loss-of-function mutations), including 11 that were novel in GSD-associated genes. In addition, CES detected five patients with mutations in ALDOB, LIPA, NKX2-5, CPT2, or ANO5. Although these genes are not involved in GSD, they are associated with overlapping phenotypic characteristics such as hepatic, muscular, and cardiac dysfunction. These results show that next-generation sequencing, in combination with the detection of biochemical and clinical hallmarks, provides an accurate, high-throughput means of making genetic diagnoses of GSD and related diseases.Genet Med 18 10, 1037-1043.

Targeted Capture and High-Throughput Sequencing Using Molecular Inversion Probes (MIPs).

PubMed

Cantsilieris, Stuart; Stessman, Holly A; Shendure, Jay; Eichler, Evan E

2017-01-01

Molecular inversion probes (MIPs) in combination with massively parallel DNA sequencing represent a versatile, yet economical tool for targeted sequencing of genomic DNA. Several thousand genomic targets can be selectively captured using long oligonucleotides containing unique targeting arms and universal linkers. The ability to append sequencing adaptors and sample-specific barcodes allows large-scale pooling and subsequent high-throughput sequencing at relatively low cost per sample. Here, we describe a "wet bench" protocol detailing the capture and subsequent sequencing of >2000 genomic targets from 192 samples, representative of a single lane on the Illumina HiSeq 2000 platform.

Familial retinoblastoma due to intronic LINE-1 insertion causes aberrant and noncanonical mRNA splicing of the RB1 gene.

PubMed

Rodríguez-Martín, Carlos; Cidre, Florencia; Fernández-Teijeiro, Ana; Gómez-Mariano, Gema; de la Vega, Leticia; Ramos, Patricia; Zaballos, Ángel; Monzón, Sara; Alonso, Javier

2016-05-01

Retinoblastoma (RB, MIM 180200) is the paradigm of hereditary cancer. Individuals harboring a constitutional mutation in one allele of the RB1 gene have a high predisposition to develop RB. Here, we present the first case of familial RB caused by a de novo insertion of a full-length long interspersed element-1 (LINE-1) into intron 14 of the RB1 gene that caused a highly heterogeneous splicing pattern of RB1 mRNA. LINE-1 insertion was inferred by mRNA studies and full-length sequenced by massive parallel sequencing. Some of the aberrant mRNAs were produced by noncanonical acceptor splice sites, a new finding that up to date has not been described to occur upon LINE-1 retrotransposition. Our results clearly show that RNA-based strategies have the potential to detect disease-causing transposon insertions. It also confirms that the incorporation of new genetic approaches, such as massive parallel sequencing, contributes to characterize at the sequence level these unique and exceptional genetic alterations.

IFRD1 Is a Candidate Gene for SMNA on Chromosome 7q22-q23

PubMed Central

Brkanac, Zoran; Spencer, David; Shendure, Jay; Robertson, Peggy D.; Matsushita, Mark; Vu, Tiffany; Bird, Thomas D.; Olson, Maynard V.; Raskind, Wendy H.

2009-01-01

We have established strong linkage evidence that supports mapping autosomal-dominant sensory/motor neuropathy with ataxia (SMNA) to chromosome 7q22-q32. SMNA is a rare neurological disorder whose phenotype encompasses both the central and the peripheral nervous system. In order to identify a gene responsible for SMNA, we have undertaken a comprehensive genomic evaluation of the region of linkage, including evaluation for repeat expansion and small deletions or duplications, capillary sequencing of candidate genes, and massively parallel sequencing of all coding exons. We excluded repeat expansion and small deletions or duplications as causative, and through microarray-based hybrid capture and massively parallel short-read sequencing, we identified a nonsynonymous variant in the human interferon-related developmental regulator gene 1 (IFRD1) as a disease-causing candidate. Sequence conservation, animal models, and protein structure evaluation support the involvement of IFRD1 in SMNA. Mutation analysis of IFRD1 in additional patients with similar phenotypes is needed for demonstration of causality and further evaluation of its importance in neurological diseases. PMID:19409521

Noninvasive prenatal testing of trisomies 21 and 18 by massively parallel sequencing of maternal plasma DNA in twin pregnancies.

PubMed

Huang, Xuan; Zheng, Jing; Chen, Min; Zhao, Yangyu; Zhang, Chunlei; Liu, Lifu; Xie, Weiwei; Shi, Shuqiong; Wei, Yuan; Lei, Dongzhu; Xu, Chenming; Wu, Qichang; Guo, Xiaoling; Shi, Xiaomei; Zhou, Yi; Liu, Qiufang; Gao, Ya; Jiang, Fuman; Zhang, Hongyun; Su, Fengxia; Ge, Huijuan; Li, Xuchao; Pan, Xiaoyu; Chen, Shengpei; Chen, Fang; Fang, Qun; Jiang, Hui; Lau, Tze Kin; Wang, Wei

2014-04-01

The objective of this study is to assess the performance of noninvasive prenatal testing for trisomies 21 and 18 on the basis of massively parallel sequencing of cell-free DNA from maternal plasma in twin pregnancies. A double-blind study was performed over 12 months. A total of 189 pregnant women carrying twins were recruited from seven hospitals. Maternal plasma DNA sequencing was performed to detect trisomies 21 and 18. The fetal karyotype was used as gold standard to estimate the sensitivity and specificity of sequencing-based noninvasive prenatal test. There were nine cases of trisomy 21 and two cases of trisomy 18 confirmed by karyotyping. Plasma DNA sequencing correctly identified nine cases of trisomy 21 and one case of trisomy 18. The discordant case of trisomy 18 was an unusual case of monozygotic twin with discordant fetal karyotype (one normal and the other trisomy 18). The sensitivity and specificity of maternal plasma DNA sequencing for fetal trisomy 21 were both 100% and for fetal trisomy 18 were 50% and 100%, respectively. Our study further supported that sequencing-based noninvasive prenatal testing of trisomy 21 in twin pregnancies could be achieved with a high accuracy, which could effectively avoid almost 95% of invasive prenatal diagnosis procedures. © 2013 John Wiley & Sons, Ltd.

The Intermediate Stellar Mass Population in R136 Determined from Hubble Space Telescope Planetary Camera 2 Images

NASA Astrophysics Data System (ADS)

Hunter, Deidre A.; Shaya, Edward J.; Holtzman, Jon A.; Light, Robert M.; O'Neil, Earl J., Jr.; Lynds, Roger

1995-07-01

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 M555,0 of 0.9 or a mass of 2.8 Msun. 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 Msun, and stars with M555,0 ≥ 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 Msun 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, -122±006 is close to a normal Salpeter IMF. The lower mass limit must be lower than the limits of our measurements: ≤ 2.8 Msun beyond 0.5 pc and ≤ 7 Msun within 0.1 pc. This is contrary to some predictions that the lower mass limit could be as high as 10 Msun 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. From the surface brightness profile, an upper limit for the core radius of 0.02 pc is set. Within a radius of 0.4 pc we estimate that there have been roughly 20 crossing times and relaxation should be well along. Within 0.5 pc crowding prevents us from detecting the intermediate mass population, but there is a hint of an excess of stars brighter than M555,0 = -5 and of a deficit in the highest mass stars between 0.6 pc and 1.2 pc. This would be consistent with dynamical segregation.

VizieR Online Data Catalog: HST photometry in R136 (Hunter+ 1995)

NASA Astrophysics Data System (ADS)

Hunter, D. A.; Shaya, E. J.; Holtzman, J. A.; Light, R. M.; Oneil, Earl J., Jr.

1996-01-01

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 0.01pc. We have detected stars to 23.5 in F555W and have quantified the stellar population to an M_555.0 of 0.9 or a mass of 2.8M⊙. 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 2.8M⊙, and stars with M_555.0>=0.5 still on pre-main sequence tracks. The average stellar population is fit with a 3-4Myr 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 2.8-15M⊙ in three annuli from 0.5-4.7pc 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 0.5pc. Furthermore, the combined IMF slope, -1.22+/-0.06, is close to a normal Salpeter IMF. The lower mass limit must be lower than the limits of our measurements: <=2.8M⊙ beyond 0.5pc and <=7M⊙ within 0.1pc. This is contrary to some predictions that the lower mass limit could be as high as 10M⊙ 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. From the surface brightness profile, an upper limit for core radius of 0.02pc is set. Within a radius of 0.4pc we estimate that there have been roughly 20 crossing times and relaxation should be well along. Within 0.5pc crowding prevents us from detecting the intermediate mass population, but there is a hint of an excess of stars brighter than M_555.0=-5 and of a deficit in the highest mass stars between 0.6pc and 1.2pc. This would be consistent with dynamical segregation. (1 data file).

Ultrasonic P- and S-Wave Attenuation and Petrophysical Properties of Deccan Flood Basalts, India, as Revealed by Borehole Studies

NASA Astrophysics Data System (ADS)

Vedanti, Nimisha; Malkoti, Ajay; Pandey, O. P.; Shrivastava, J. P.

2018-03-01

Petrophysical properties and ultrasonic P- and S-wave attenuation measurements on 35 Deccan basalt core specimens, recovered from Killari borehole site in western India, provide unique reference data-sets for a lesser studied Deccan Volcanic Province. These samples represent 338-m-thick basaltic column, consisting four lava flows each of Ambenali and Poladpur Formations, belonging to Wai Subgroup of the Deccan volcanic sequence. These basalt samples are found to be iron-rich (average FeOT: 13.4 wt%), but relatively poor in silica content (average SiO2: 47.8 wt%). The saturated massive basalt cores are characterized by a mean density of 2.91 g/cm3 (range 2.80-3.01 g/cm3) and mean P- and S-wave velocities of 5.89 km/s (range 5.01-6.50 km/s) and 3.43 km/s (range 2.84-3.69 km/s), respectively. In comparison, saturated vesicular basalt cores show a wide range in density (2.40-2.79 g/cm3) as well as P-wave (3.28-4.78 km/s) and S-wave (1.70-2.95 km/s) velocities. Based on the present study, the Deccan volcanic sequence can be assigned a weighted mean density of 2.74 g/cm3 and a low V p and V s of 5.00 and 3.00 km/s, respectively. Such low velocities in Deccan basalts can be attributed mainly to the presence of fine-grained glassy material, high iron contents, and hydrothermally altered secondary mineral products, besides higher porosity in vesicular samples. The measured Q values in saturated massive basalt cores vary enormously (Q p: 33-1960 and Q s: 35-506), while saturated vesicular basalt samples exhibit somewhat lesser variation in Q p (6-46) as well as Q s (5-49). In general, high-porosity rocks exhibit high attenuation, but we observed the high value of attenuation in some of the massive basalt core samples also. In such cases, energy loss is mainly due to the presence of fine-grained glassy material as well as secondary alteration products like chlorophaeite, that could contribute to intrinsic attenuation. Dominance of weekly bound secondary minerals might also be responsible for the generation of microcracks, which may generate squirt flow in saturated samples. Hence, we argue that the Deccan basalts attenuate seismic energy significantly, where its composition plays a major role.

Mineralogical, IR-spectral and geochemical monitoring of hydrothermal alteration in a deformed and metamorphosed Jurassic VMS deposit at Arroyo Rojo, Tierra del Fuego, Argentina

NASA Astrophysics Data System (ADS)

Biel, C.; Subías, I.; Acevedo, R. D.; Yusta, I.; Velasco, F.

2012-04-01

The Arroyo Rojo Zn-Pb-Cu volcanogenic massive sulfide deposit is the main deposit of the Fin del Mundo District in the Fuegian Andes, Argentina. This deposit is hosted by a Middle Jurassic volcanic and volcanoclastic sequence forming the Lemaire Formation. The latter consists, from the base up, of the following: rhyolitic and dacitic porphyritic rocks, ignimbrite, tuff, and flow. It is underlain by a pre-Jurassic basement and overlain by the hyaloclastic andesites of the Yahgán Formation. The Arroyo Rojo consists of stacked lenticular lenses that are associated with disseminated mineralization in both the footwall and the hanging wall. The internal structure of the ore lenses is marked by the occurrence of massive, semi-massive and banded facies, along with stringer and brecciated zones and minor ore disseminations. The mineral assemblage comprises mainly pyrite and sphalerite, with minor amounts of galena and chalcopyrite and rare pyrrhotite, arsenopyrite, tetrahedrite and bournonite. The ores and the volcanic host rocks have metamorphosed to greenschist facies and were overprinted by a penetrative tectonic foliation, which led to the development of mylonitic, and cataclastic textures, recrystallization and remobilization. Primary depositional characteristics and regional and hydrothermal alteration patterns were preserved despite deformation and metamorphism. Therefore, primary banding was preserved between facies boundaries. In addition, some remnants of magmatic origin are recognizable in preserved phenocrysts and volcaniclastic phenoclasts. Most of the volcanic and volcaniclastic rocks of the host sequence show a rhyolitic to rhyo-dacitic composition. Regional seafloor alteration, characterized by the presence of clinozoisite, Fe-chlorite and titanite, along with quartz and albite, is partially obliterated by hydrothermal alteration. The hydrothermal alteration is stratabound with the following assemblages, which developed from the base to top: (1) Quartz-Chlorite ± Sericite, (2) Quartz-Chlorite, (3) Chlorite ± Quartz-Sericite-Calcite, (4) Quartz-Chlorite ± Calcite and (5) Sericite + Quartz ± Chlorite ± Calcite. Magnesium-chlorite and phengitic white mica typically occur in the vicinity of the Arroyo Rojo ore lenses. To provide field criteria for exploration vectoring, the chemical composition of chlorite and the phengitic and paragonitic content of the white mica were determined and correlated with PIMA Fe-OH and Al-OH absorption wavelengths, respectively, relative to their proximity to the mineralized lenses. The results of this study can be used to help identify (1) felsic proximal facies associations, (2) ore horizons and (3) favorable hydrothermal alteration zones in other parts of the Fin del Mundo district.

Analysis of bacterial and archaeal diversity in coastal microbial mats using massive parallel 16S rRNA gene tag sequencing.

PubMed

Bolhuis, Henk; Stal, Lucas J

2011-11-01

Coastal microbial mats are small-scale and largely closed ecosystems in which a plethora of different functional groups of microorganisms are responsible for the biogeochemical cycling of the elements. Coastal microbial mats play an important role in coastal protection and morphodynamics through stabilization of the sediments and by initiating the development of salt-marshes. Little is known about the bacterial and especially archaeal diversity and how it contributes to the ecological functioning of coastal microbial mats. Here, we analyzed three different types of coastal microbial mats that are located along a tidal gradient and can be characterized as marine (ST2), brackish (ST3) and freshwater (ST3) systems. The mats were sampled during three different seasons and subjected to massive parallel tag sequencing of the V6 region of the 16S rRNA genes of Bacteria and Archaea. Sequence analysis revealed that the mats are among the most diverse marine ecosystems studied so far and consist of several novel taxonomic levels ranging from classes to species. The diversity between the different mat types was far more pronounced than the changes between the different seasons at one location. The archaeal community for these mats have not been studied before and revealed a strong reaction on a short period of draught during summer resulting in a massive increase in halobacterial sequences, whereas the bacterial community was barely affected. We concluded that the community composition and the microbial diversity were intrinsic of the mat type and depend on the location along the tidal gradient indicating a relation with salinity.

[WN] central stars of planetary nebulae

NASA Astrophysics Data System (ADS)

Todt, H.; Miszalski, B.; Toalá, J. A.; Guerrero, M. A.

2017-10-01

While most of the low-mass stars stay hydrogen-rich on their surface throughout their evolution, a considerable fraction of white dwarfs as well as central stars of planetary nebulae have a hydrogen-deficient surface composition. The majority of these H-deficient central stars exhibit spectra very similar to massive Wolf-Rayet stars of the carbon sequence, i.e. with broad emission lines of carbon, helium, and oxygen. In analogy to the massive Wolf-Rayet stars, they are classified as [WC] stars. Their formation, which is relatively well understood, is thought to be the result of a (very) late thermal pulse of the helium burning shell. It is therefore surprising that some H-deficient central stars which have been found recently, e.g. IC 4663 and Abell 48, exhibit spectra that resemble those of the massive Wolf-Rayet stars of the nitrogen sequence, i.e. with strong emission lines of nitrogen instead of carbon. This new type of central stars is therefore labelled [WN]. We present spectral analyses of these objects and discuss the status of further candidates as well as the evolutionary status and origin of the [WN] stars.

The Peculiar Landscape of Repetitive Sequences in the Olive (Olea europaea L.) Genome

PubMed Central

Barghini, Elena; Natali, Lucia; Cossu, Rosa Maria; Giordani, Tommaso; Pindo, Massimo; Cattonaro, Federica; Scalabrin, Simone; Velasco, Riccardo; Morgante, Michele; Cavallini, Andrea

2014-01-01

Analyzing genome structure in different species allows to gain an insight into the evolution of plant genome size. Olive (Olea europaea L.) has a medium-sized haploid genome of 1.4 Gb, whose structure is largely uncharacterized, despite the growing importance of this tree as oil crop. Next-generation sequencing technologies and different computational procedures have been used to study the composition of the olive genome and its repetitive fraction. A total of 2.03 and 2.3 genome equivalents of Illumina and 454 reads from genomic DNA, respectively, were assembled following different procedures, which produced more than 200,000 differently redundant contigs, with mean length higher than 1,000 nt. Mapping Illumina reads onto the assembled sequences was used to estimate their redundancy. The genome data set was subdivided into highly and medium redundant and nonredundant contigs. By combining identification and mapping of repeated sequences, it was established that tandem repeats represent a very large portion of the olive genome (∼31% of the whole genome), consisting of six main families of different length, two of which were first discovered in these experiments. The other large redundant class in the olive genome is represented by transposable elements (especially long terminal repeat-retrotransposons). On the whole, the results of our analyses show the peculiar landscape of the olive genome, related to the massive amplification of tandem repeats, more than that reported for any other sequenced plant genome. PMID:24671744

The peculiar landscape of repetitive sequences in the olive (Olea europaea L.) genome.

PubMed

Barghini, Elena; Natali, Lucia; Cossu, Rosa Maria; Giordani, Tommaso; Pindo, Massimo; Cattonaro, Federica; Scalabrin, Simone; Velasco, Riccardo; Morgante, Michele; Cavallini, Andrea

2014-04-01

Analyzing genome structure in different species allows to gain an insight into the evolution of plant genome size. Olive (Olea europaea L.) has a medium-sized haploid genome of 1.4 Gb, whose structure is largely uncharacterized, despite the growing importance of this tree as oil crop. Next-generation sequencing technologies and different computational procedures have been used to study the composition of the olive genome and its repetitive fraction. A total of 2.03 and 2.3 genome equivalents of Illumina and 454 reads from genomic DNA, respectively, were assembled following different procedures, which produced more than 200,000 differently redundant contigs, with mean length higher than 1,000 nt. Mapping Illumina reads onto the assembled sequences was used to estimate their redundancy. The genome data set was subdivided into highly and medium redundant and nonredundant contigs. By combining identification and mapping of repeated sequences, it was established that tandem repeats represent a very large portion of the olive genome (∼31% of the whole genome), consisting of six main families of different length, two of which were first discovered in these experiments. The other large redundant class in the olive genome is represented by transposable elements (especially long terminal repeat-retrotransposons). On the whole, the results of our analyses show the peculiar landscape of the olive genome, related to the massive amplification of tandem repeats, more than that reported for any other sequenced plant genome.

Luminous blue variables and the fates of very massive stars

NASA Astrophysics Data System (ADS)

Smith, Nathan

2017-09-01

Luminous blue variables (LBVs) had long been considered massive stars in transition to the Wolf-Rayet (WR) phase, so their identification as progenitors of some peculiar supernovae (SNe) was surprising. More recently, environment statistics of LBVs show that most of them cannot be in transition to the WR phase after all, because LBVs are more isolated than allowed in this scenario. Additionally, the high-mass H shells around luminous SNe IIn require that some very massive stars above 40 M⊙ die without shedding their H envelopes, and the precursor outbursts are a challenge for understanding the final burning sequences leading to core collapse. Recent evidence suggests a clear continuum in pre-SN mass loss from super-luminous SNe IIn, to regular SNe IIn, to SNe II-L and II-P, whereas most stripped-envelope SNe seem to arise from a separate channel of lower-mass binary stars rather than massive WR stars. This article is part of the themed issue 'Bridging the gap: from massive stars to supernovae'.

Chandra Observations of Associates of η Carinae. II. Spectra

NASA Astrophysics Data System (ADS)

Evans, Nancy Remage; Schlegel, Eric M.; Waldron, Wayne L.; Seward, Frederick D.; Krauss, Miriam I.; Nichols, Joy; Wolk, Scott J.

2004-09-01

The low-resolution X-ray spectra around η Car covering Trumpler 16 and part of Trumpler 14 have been extracted from a Chandra CCD ACIS image. Various analysis techniques have been applied to the spectra based on their count rates. The spectra with the greatest number of counts (HD 93162 = WR 25, HD 93129 AB, and HD 93250) have been fitted with a wind model, which uses several components with different temperatures and depths in the wind. Weaker spectra have been fitted with Raymond-Smith models. The weakest spectra are simply intercompared with strong spectra. In general, fits produce reasonable parameters based on knowledge of the extinction from optical studies and on the range of temperatures for high- and low-mass stars. Direct comparisons of spectra confirm the consistency of the fitting results and also hardness ratios for cases of unusually large extinction in the clusters. The spectra of the low-mass stars are harder than the more massive stars. Stars in the sequence evolving from the main sequence (HD 93250) through the system containing the O supergiant (HD 93129 AB) and then through the Wolf-Rayet stage (HD 93162), presumably ending in the extreme example of η Car, share the property of being unusually luminous and hard in X-rays. For these X-ray-luminous stars, their high mass and evolutionary status (from the very last stages of the main sequence and beyond) is the common feature. Their binary status is mixed, and their magnetic status is still uncertain. Based on observations made with the Chandra X-Ray Observatory.

White Dwarf Stars

NASA Astrophysics Data System (ADS)

Kepler, S. O.

2014-10-01

White dwarfs are the evolutionary endpoint for nearly 95% of all stars born in our Galaxy, the final stages of evolution of all low- and intermediate mass stars, i.e., main sequence stars with masses below (8.5± 1.5) M_{odot}, depending on metallicity of the progenitor, mass loss and core overshoot. Massive white dwarfs are intrinsically rare objects, tand produce a gap in the determination of the initial vs. final mass relation at the high mass end (e.g. Weidemann 2000 A&A, 363, 647; Kalirai et al. 2008, ApJ, 676, 594; Williams, Bolte & Koester 2009, ApJ, 693, 355). Main sequences stars with higher masses will explode as SNII (Smartt S. 2009 ARA&A, 47, 63), but the limit does depend on the metallicity of the progenitor. Massive white dwarfs are probably SNIa progenitors through accretion or merger. They are rare, being the final product of massive stars (less common) and have smaller radius (less luminous). Kepler et al. 2007 (MNRAS, 375, 1315), Kleinman et al. 2013 (ApJS, 204, 5) estimate only 1-2% white dwarfs have masses above 1 M_{odot}. The final stages of evolution after helium burning are a race between core growth and loss of the H-rich envelope in a stellar wind. When the burning shell is exposed, the star rapidly cools and burning ceases, leaving a white dwarf. As they cool down, the magnetic field freezes in, ranging from a few kilogauss to a gigagauss. Peculiar type Ia SN 2006gz, SN 2007if, SN 2009dc, SN 2003fg suggest progenitors in the range 2.4-2.8 M_{odot}, and Das U. & Mukhopadhyay B. (2012, Phys. Rev. D, 86, 042001) estimate that the Chandrasekhar limit increases to 2.3-2.6 M_{odot} for extremely high magnetic field stars, but differential rotation induced by accretion could also increase it, according to Hachisu I. et al. 2012 (ApJ, 744, 69). García-Berro et al. 2012, ApJ, 749, 25, for example, proposes double degenerate mergers are the progenitors of high-field magnetic white dwarfs. We propose magnetic fields enhance the line broadening in WDs, causing an overestimated surface gravity, and ultimately determine if these magnetic fields are likely developed through the star's own surface convection zone, or inherited from massive Ap/Bp progenitors. We discovered around 20 000 spectroscopic white dwarfs with the Sloan Digital Sky Survey (SDSS), with a corresponding increase in relatively rare varieties of white dwarfs, including the massive ones (Kleinman et al. 2013, ApJS, 204, 5, Kepler et al. 2013, MNRAS, 439, 2934). The mass distributions of the hydrogen-rich (DA) measured from fitting the spectra with model atmospheres calculated using unidimensinal mixing lenght-theory (MLT) shows the average mass (as measured by the surface gravity) increases apparently below 13 000K for DAs (e.g. Bergeron et al. 1991, ApJ, 367, 253; Tremblay et al. 2011, ApJ, 730, 128; Kleinman et al. 2013). Only with the tridimensional (3D) convection calculations of Tremblay et al. 2011 (A&A, 531, L19) and 2013 (A&A, 552, 13; A&A, 557, 7; arXiv 1309.0886) the problem has finally been solved, but the effects of magnetic fields are not included yet in the mass determinations. Pulsating white dwarf stars are used to measure their interior and envelope properties through seismology, and together with the luminosity function of white dwarf stars in clusters and around the Sun are valuable tools for the study of high density physics, and the history of stellar formation.

Quantitative analysis of RNA-protein interactions on a massively parallel array for mapping biophysical and evolutionary landscapes

PubMed Central

Buenrostro, Jason D.; Chircus, Lauren M.; Araya, Carlos L.; Layton, Curtis J.; Chang, Howard Y.; Snyder, Michael P.; Greenleaf, William J.

2015-01-01

RNA-protein interactions drive fundamental biological processes and are targets for molecular engineering, yet quantitative and comprehensive understanding of the sequence determinants of affinity remains limited. Here we repurpose a high-throughput sequencing instrument to quantitatively measure binding and dissociation of MS2 coat protein to >107 RNA targets generated on a flow-cell surface by in situ transcription and inter-molecular tethering of RNA to DNA. We decompose the binding energy contributions from primary and secondary RNA structure, finding that differences in affinity are often driven by sequence-specific changes in association rates. By analyzing the biophysical constraints and modeling mutational paths describing the molecular evolution of MS2 from low- to high-affinity hairpins, we quantify widespread molecular epistasis, and a long-hypothesized structure-dependent preference for G:U base pairs over C:A intermediates in evolutionary trajectories. Our results suggest that quantitative analysis of RNA on a massively parallel array (RNAMaP) relationships across molecular variants. PMID:24727714

The ν process in the innermost supernova ejecta

NASA Astrophysics Data System (ADS)

Sieverding, Andre; Martínez Pinedo, Gabriel; Langanke, Karlheinz; Harris, J. Austin; Hix, W. Raphael

2018-01-01

The neutrino-induced nucleosynthesis (ν process) in supernova explosions of massive stars of solar metallicity with initial main sequence masses between 13 and 30 M⊙ has been studied with an analytic explosion model using a new extensive set of neutrino-nucleus cross-sections and spectral properties that agree with modern supernova simulations. The production factors for the nuclei 7Li, 11B, 19F, 138La and 180Ta, are still significantly enhanced but do not reproduce the full solar abundances. We study the possible contribution of the innermost supernova eject to the production of the light elements 7Li and 11B with tracer particles based on a 2D supernova simulation of a 12 M⊙ progenitor and conclude, that a contribution exists but is negligible for the total yield for this explosion model.

Neutrino nucleosynthesis in core-collapse Supernova explosions

NASA Astrophysics Data System (ADS)

Sieverding, A.; Huther, L.; Martínez-Pinedo, G.; Langanke, K.; Heger, A.

2018-01-01

The neutrino-induced nucleosynthesis (v process) in supernova explosions of massive stars of solar metallicity with initial main sequence masses between 15 and 40 M⨀ has been studied. A new extensive set of neutrino-nucleus cross-sections for all the nuclei included in the reaction network is used and the average neutrino energies are reduced to agree with modern supernova simulations. Despite these changes the v process is found to contribute still significantly to the production of the nuclei 7Li, 11B, 19F, 138La and 180Ta, even though the total yields for those nuclei are reduced. Furthermore we study in detail contributions of the v process to the production of radioactive isotopes 26Al, 22Na and confirm the production of 92Nb and 98Tc.

The origin of the Crab Nebula and the electron capture supernova in 8-10 M solar mass stars

NASA Technical Reports Server (NTRS)

Nomoto, K.

1981-01-01

The chemical composition of the Crab Nebula is compared with several presupernova models. The small carbon and oxygen abundances in the helium-rich nebula are consistent with only the presupernova model of the star whose main sequence mass was MMS approximately 8-9.5 M. More massive stars contain too much carbon in the helium layer and smaller mass stars do not leave neutron stars. The progenitor star of the Crab Nebula lost appreciable part of the hydrogen-rich envelope before the hydrogen-rich and helium layers were mixed by convection. Finally it exploded as the electron capture supernova; the O+Ne+Mg core collapsed to form a neutron star and only the extended helium-rich envelope was ejected by the weak shock wave.

Mutation profiling of 19 candidate genes in acute myeloid leukemia suggests significance of DNMT3A mutations.

PubMed

Shin, Sang-Yong; Lee, Seung-Tae; Kim, Hee-Jin; Cho, Eun Hae; Kim, Jong-Won; Park, Silvia; Jung, Chul Won; Kim, Sun-Hee

2016-08-23

We selected 19 significantly-mutated genes in AMLs, including FLT3, DNMT3A, NPM1, TET2, RUNX1, CEBPA, WT1, IDH1, IDH2, NRAS, ASXL1, SETD2, PTPN11, TP53, KIT, JAK2, KRAS, BRAF and CBL, and performed massively parallel sequencing for 114 patients with acute myeloid leukemias, mainly including those with normal karyotypes (CN-AML). More than 80% of patients had at least one mutation in the genes tested. DNMT3A mutation was significantly associated with adverse outcome in addition to conventional risk stratification such as the European LeukemiaNet (ELN) classification. We observed clinical usefulness of mutation testing on multiple target genes and the association with disease subgroups, clinical features and prognosis in AMLs.

Comparative high-throughput transcriptome sequencing and development of SiESTa, the Silene EST annotation database

PubMed Central

2011-01-01

Background The genus Silene is widely used as a model system for addressing ecological and evolutionary questions in plants, but advances in using the genus as a model system are impeded by the lack of available resources for studying its genome. Massively parallel sequencing cDNA has recently developed into an efficient method for characterizing the transcriptomes of non-model organisms, generating massive amounts of data that enable the study of multiple species in a comparative framework. The sequences generated provide an excellent resource for identifying expressed genes, characterizing functional variation and developing molecular markers, thereby laying the foundations for future studies on gene sequence and gene expression divergence. Here, we report the results of a comparative transcriptome sequencing study of eight individuals representing four Silene and one Dianthus species as outgroup. All sequences and annotations have been deposited in a newly developed and publicly available database called SiESTa, the Silene EST annotation database. Results A total of 1,041,122 EST reads were generated in two runs on a Roche GS-FLX 454 pyrosequencing platform. EST reads were analyzed separately for all eight individuals sequenced and were assembled into contigs using TGICL. These were annotated with results from BLASTX searches and Gene Ontology (GO) terms, and thousands of single-nucleotide polymorphisms (SNPs) were characterized. Unassembled reads were kept as singletons and together with the contigs contributed to the unigenes characterized in each individual. The high quality of unigenes is evidenced by the proportion (49%) that have significant hits in similarity searches with the A. thaliana proteome. The SiESTa database is accessible at http://www.siesta.ethz.ch. Conclusion The sequence collections established in the present study provide an important genomic resource for four Silene and one Dianthus species and will help to further develop Silene as a plant model system. The genes characterized will be useful for future research not only in the species included in the present study, but also in related species for which no genomic resources are yet available. Our results demonstrate the efficiency of massively parallel transcriptome sequencing in a comparative framework as an approach for developing genomic resources in diverse groups of non-model organisms. PMID:21791039

TIA: algorithms for development of identity-linked SNP islands for analysis by massively parallel DNA sequencing.

PubMed

Farris, M Heath; Scott, Andrew R; Texter, Pamela A; Bartlett, Marta; Coleman, Patricia; Masters, David

2018-04-11

Single nucleotide polymorphisms (SNPs) located within the human genome have been shown to have utility as markers of identity in the differentiation of DNA from individual contributors. Massively parallel DNA sequencing (MPS) technologies and human genome SNP databases allow for the design of suites of identity-linked target regions, amenable to sequencing in a multiplexed and massively parallel manner. Therefore, tools are needed for leveraging the genotypic information found within SNP databases for the discovery of genomic targets that can be evaluated on MPS platforms. The SNP island target identification algorithm (TIA) was developed as a user-tunable system to leverage SNP information within databases. Using data within the 1000 Genomes Project SNP database, human genome regions were identified that contain globally ubiquitous identity-linked SNPs and that were responsive to targeted resequencing on MPS platforms. Algorithmic filters were used to exclude target regions that did not conform to user-tunable SNP island target characteristics. To validate the accuracy of TIA for discovering these identity-linked SNP islands within the human genome, SNP island target regions were amplified from 70 contributor genomic DNA samples using the polymerase chain reaction. Multiplexed amplicons were sequenced using the Illumina MiSeq platform, and the resulting sequences were analyzed for SNP variations. 166 putative identity-linked SNPs were targeted in the identified genomic regions. Of the 309 SNPs that provided discerning power across individual SNP profiles, 74 previously undefined SNPs were identified during evaluation of targets from individual genomes. Overall, DNA samples of 70 individuals were uniquely identified using a subset of the suite of identity-linked SNP islands. TIA offers a tunable genome search tool for the discovery of targeted genomic regions that are scalable in the population frequency and numbers of SNPs contained within the SNP island regions. It also allows the definition of sequence length and sequence variability of the target region as well as the less variable flanking regions for tailoring to MPS platforms. As shown in this study, TIA can be used to discover identity-linked SNP islands within the human genome, useful for differentiating individuals by targeted resequencing on MPS technologies.

Construction of an Ostrea edulis database from genomic and expressed sequence tags (ESTs) obtained from Bonamia ostreae infected haemocytes: Development of an immune-enriched oligo-microarray.

PubMed

Pardo, Belén G; Álvarez-Dios, José Antonio; Cao, Asunción; Ramilo, Andrea; Gómez-Tato, Antonio; Planas, Josep V; Villalba, Antonio; Martínez, Paulino

2016-12-01

The flat oyster, Ostrea edulis, is one of the main farmed oysters, not only in Europe but also in the United States and Canada. Bonamiosis due to the parasite Bonamia ostreae has been associated with high mortality episodes in this species. This parasite is an intracellular protozoan that infects haemocytes, the main cells involved in oyster defence. Due to the economical and ecological importance of flat oyster, genomic data are badly needed for genetic improvement of the species, but they are still very scarce. The objective of this study is to develop a sequence database, OedulisDB, with new genomic and transcriptomic resources, providing new data and convenient tools to improve our knowledge of the oyster's immune mechanisms. Transcriptomic and genomic sequences were obtained using 454 pyrosequencing and compiled into an O. edulis database, OedulisDB, consisting of two sets of 10,318 and 7159 unique sequences that represent the oyster's genome (WG) and de novo haemocyte transcriptome (HT), respectively. The flat oyster transcriptome was obtained from two strains (naïve and tolerant) challenged with B. ostreae, and from their corresponding non-challenged controls. Approximately 78.5% of 5619 HT unique sequences were successfully annotated by Blast search using public databases. A total of 984 sequences were identified as being related to immune response and several key immune genes were identified for the first time in flat oyster. Additionally, transcriptome information was used to design and validate the first oligo-microarray in flat oyster enriched with immune sequences from haemocytes. Our transcriptomic and genomic sequencing and subsequent annotation have largely increased the scarce resources available for this economically important species and have enabled us to develop an OedulisDB database and accompanying tools for gene expression analysis. This study represents the first attempt to characterize in depth the O. edulis haemocyte transcriptome in response to B. ostreae through massively sequencing and has aided to improve our knowledge of the immune mechanisms of flat oyster. The validated oligo-microarray and the establishment of a reference transcriptome will be useful for large-scale gene expression studies in this species. Copyright © 2016 Elsevier Ltd. All rights reserved.

Open clusters in Auriga OB2

NASA Astrophysics Data System (ADS)

Marco, Amparo; Negueruela, Ignacio

2016-06-01

We study the area around the H II region Sh 2-234, including the young open cluster Stock 8, to investigate the extent and definition of the association Aur OB2 and the possible role of triggering in massive cluster formation. We obtained Strömgren and J, H, KS photometry for Stock 8 and Strömgren photometry for two other cluster candidates in the area, which we confirm as young open clusters and name Alicante 11 and Alicante 12. We took spectroscopy of ˜33 early-type stars in the area, including the brightest cluster members. We calculate a common distance of 2.80^{+0.27}_{-0.24} kpc for the three open clusters and surrounding association. We derive an age 4-6 Ma for Stock 8, and do not find a significantly different age for the other clusters or the association. The star LS V +34°23, with spectral type O8 II(f), is likely the main source of ionization of Sh 2-234. We observe an important population of pre-main-sequence stars, some of them with discs, associated with the B-type members lying on the main sequence. We interpret the region as an area of recent star formation with some residual and very localized ongoing star formation. We do not find evidence for sequential star formation on a large scale. The classical definition of Aur OB2 has to be reconsidered, because its two main open clusters, Stock 8 and NGC 1893, are not at the same distance. Stock 8 is probably located in the Perseus arm, but other nearby H II regions whose distances also place them in this arm show quite different distances and radial velocities and, therefore, are not connected.

Timing the formation and assembly of early-type galaxies via spatially resolved stellar populations analysis

NASA Astrophysics Data System (ADS)

Martín-Navarro, Ignacio; Vazdekis, Alexandre; Falcón-Barroso, Jesús; La Barbera, Francesco; Yıldırım, Akın; van de Ven, Glenn

2018-04-01

To investigate star formation and assembly processes of massive galaxies, we present here a spatially resolved stellar population analysis of a sample of 45 elliptical galaxies (Es) selected from the Calar Alto Legacy Integral Field Area survey. We find rather flat age and [Mg/Fe] radial gradients, weakly dependent on the effective velocity dispersion of the galaxy within half-light radius. However, our analysis shows that metallicity gradients become steeper with increasing galaxy velocity dispersion. In addition, we have homogeneously compared the stellar population gradients of our sample of Es to a sample of nearby relic galaxies, i.e. local remnants of the high-z population of red nuggets. This comparison indicates that, first, the cores of present-day massive galaxies were likely formed in gas-rich, rapid star formation events at high redshift (z ≳ 2). This led to radial metallicity variations steeper than observed in the local Universe, and positive [Mg/Fe] gradients. Secondly, our analysis also suggests that a later sequence of minor dry mergers, populating the outskirts of early-type galaxies (ETGs), flattened the pristine [Mg/Fe] and metallicity gradients. Finally, we find a tight age-[Mg/Fe] relation, supporting that the duration of the star formation is the main driver of the [Mg/Fe] enhancement in massive ETGs. However, the star formation time-scale alone is not able to fully explain our [Mg/Fe] measurements. Interestingly, our results match the expected effect that a variable stellar initial mass function would have on the [Mg/Fe] ratio.

Forensic massively parallel sequencing data analysis tool: Implementation of MyFLq as a standalone web- and Illumina BaseSpace(®)-application.

PubMed

Van Neste, Christophe; Gansemans, Yannick; De Coninck, Dieter; Van Hoofstat, David; Van Criekinge, Wim; Deforce, Dieter; Van Nieuwerburgh, Filip

2015-03-01

Routine use of massively parallel sequencing (MPS) for forensic genomics is on the horizon. The last few years, several algorithms and workflows have been developed to analyze forensic MPS data. However, none have yet been tailored to the needs of the forensic analyst who does not possess an extensive bioinformatics background. We developed our previously published forensic MPS data analysis framework MyFLq (My-Forensic-Loci-queries) into an open-source, user-friendly, web-based application. It can be installed as a standalone web application, or run directly from the Illumina BaseSpace environment. In the former, laboratories can keep their data on-site, while in the latter, data from forensic samples that are sequenced on an Illumina sequencer can be uploaded to Basespace during acquisition, and can subsequently be analyzed using the published MyFLq BaseSpace application. Additional features were implemented such as an interactive graphical report of the results, an interactive threshold selection bar, and an allele length-based analysis in addition to the sequenced-based analysis. Practical use of the application is demonstrated through the analysis of four 16-plex short tandem repeat (STR) samples, showing the complementarity between the sequence- and length-based analysis of the same MPS data. Copyright © 2014 The Authors. Published by Elsevier Ireland Ltd.. All rights reserved.

Targeted next-generation sequencing in steroid-resistant nephrotic syndrome: mutations in multiple glomerular genes may influence disease severity.

PubMed

Bullich, Gemma; Trujillano, Daniel; Santín, Sheila; Ossowski, Stephan; Mendizábal, Santiago; Fraga, Gloria; Madrid, Álvaro; Ariceta, Gema; Ballarín, José; Torra, Roser; Estivill, Xavier; Ars, Elisabet

2015-09-01

Genetic diagnosis of steroid-resistant nephrotic syndrome (SRNS) using Sanger sequencing is complicated by the high genetic heterogeneity and phenotypic variability of this disease. We aimed to improve the genetic diagnosis of SRNS by simultaneously sequencing 26 glomerular genes using massive parallel sequencing and to study whether mutations in multiple genes increase disease severity. High-throughput mutation analysis was performed in 50 SRNS and/or focal segmental glomerulosclerosis (FSGS) patients, a validation cohort of 25 patients with known pathogenic mutations, and a discovery cohort of 25 uncharacterized patients with probable genetic etiology. In the validation cohort, we identified the 42 previously known pathogenic mutations across NPHS1, NPHS2, WT1, TRPC6, and INF2 genes. In the discovery cohort, disease-causing mutations in SRNS/FSGS genes were found in nine patients. We detected three patients with mutations in an SRNS/FSGS gene and COL4A3. Two of them were familial cases and presented a more severe phenotype than family members with mutation in only one gene. In conclusion, our results show that massive parallel sequencing is feasible and robust for genetic diagnosis of SRNS/FSGS. Our results indicate that patients carrying mutations in an SRNS/FSGS gene and also in COL4A3 gene have increased disease severity.

Clinical validation of the 50 gene AmpliSeq Cancer Panel V2 for use on a next generation sequencing platform using formalin fixed, paraffin embedded and fine needle aspiration tumour specimens.

PubMed

Rathi, Vivek; Wright, Gavin; Constantin, Diana; Chang, Siok; Pham, Huong; Jones, Kerryn; Palios, Atha; Mclachlan, Sue-Anne; Conron, Matthew; McKelvie, Penny; Williams, Richard

2017-01-01

The advent of massively parallel sequencing has caused a paradigm shift in the ways cancer is treated, as personalised therapy becomes a reality. More and more laboratories are looking to introduce next generation sequencing (NGS) as a tool for mutational analysis, as this technology has many advantages compared to conventional platforms like Sanger sequencing. In Australia all massively parallel sequencing platforms are still considered in-house in vitro diagnostic tools by the National Association of Testing Authorities (NATA) and a comprehensive analytical validation of all assays, and not just mere verification, is a strict requirement before accreditation can be granted for clinical testing on these platforms. Analytical validation of assays on NGS platforms can prove to be extremely challenging for pathology laboratories. Although there are many affordable and easily accessible NGS instruments available, there are no standardised guidelines as yet for clinical validation of NGS assays. We present an accreditation development procedure that was both comprehensive and applicable in a setting of hospital laboratory for NGS services. This approach may also be applied to other NGS applications in service laboratories. Copyright © 2016 Royal College of Pathologists of Australasia. Published by Elsevier B.V. All rights reserved.

Field observations of Flood Basalt structure: Implications for offshore interpretation and sub-volcanic investigation

NASA Astrophysics Data System (ADS)

Single, R.; Jerram, D.; Pearson, D.; Hobbs, R.

2003-04-01

Field investigations in Skye and Namibia have provided insight into structure and architecture of CFBs. The studies have been developed into lava sequence models in 3-D software GoCad. The understanding has been applied to interpretation of lavas in the Faeroe-Shetland trough. Volcanics hinder petroleum exploration in this play due to their complex internal geometries and velocity structure. Seismic resolution is poor beneath volcanics. Fieldwork has shown that lavas on Skye have developed from (olivine-phyric) compound basalts towards the base of the sequence, into more massive flows higher up the succession. Fieldwork in the Etendeka CFBs reveal a similar style of lava field development. The focus of the offshore study is through the area of the GFA-99 seismic data. Detailed 3-D interpretation over the central data area is 20x20km in dimensions. The lava sequence present may be sub-divided vertically and laterally into 4 zones between the following seismic picks: Base basalt/sub-basalt sills, top compound lava-dominated series, top Middle Series, top hyaloclastites, top massive basalt. Within the lava sequence, the surfaces have rugose topographies. Lower zone lavas are characterised by discontinuous, indistinct reflectors. These are interpreted to be sub-aerially effused basalts with compound-braided architecture. Middle Series basalts are considered to be a combination of compound lavas and more massive, tabular flows. Steeply dipping seismic reflectors also form part of the Middle Series and are interpreted as foreset-bedded hyaloclastites. The uppermost lavas have strong reflection characteristics and are laterally extensive. These are interpreted to be massive tabular lavas covering an area >8.4 x10^3 km^2. Such flows exist in upper parts of CFB sequences as evidenced from fieldwork. Complex stacking arrangements of lavas seen in the field, and the complexities observed in seismic, suggest that many factors need to be considered within CFBs for improved sub-volcanic imaging. Factors include understanding: The facies-zones present, changes in velocity structure and the geometries present within facies types. EU 5th Framework Project SIMBA is a collaborative research project combining industrial and academic partners in flood basalt research. SIMBA incorporates: TotalFinaElf GRC, ARK Geophysics, Norsk Hydro, Institut Français du Pétrole (IFP) and Universities of Durham, Cambridge, UC Dublin and Brest.

Massive pericardial effusion and rhabdomyolysis secondary to untreated severe hypothyroidism: the first report.

PubMed

Zare-Khormizi, M R; Rahmanian, M; Pourrajab, F; Akbarnia, S

2014-10-01

Hypothyroidism is an endocrine disease with various clinical manifestations. It is a rare cause for rhabdomyolysis and massive pericardial effusion. We describe a case of severe hypothyroidism secondary to autoimmune hashimoto thyroiditis with massive pericardial effusion and rhabdomyolysis. Improvement of mentioned complications after hypothyroidism treatment and rule out of other possible causes are supportive clues that hypothyroidism is the main cause of patient's rare presentation. With the best of our knowledge, it is the first report of rhabdomyolysis and massive pericardial effusion coincidence in a patient of adult population with primary uncontrolled hypothyroidism for years.

Next-Generation Sequencing: The Translational Medicine Approach from “Bench to Bedside to Population”

PubMed Central

Beigh, Mohammad Muzafar

2016-01-01

Humans have predicted the relationship between heredity and diseases for a long time. Only in the beginning of the last century, scientists begin to discover the connotations between different genes and disease phenotypes. Recent trends in next-generation sequencing (NGS) technologies have brought a great momentum in biomedical research that in turn has remarkably augmented our basic understanding of human biology and its associated diseases. State-of-the-art next generation biotechnologies have started making huge strides in our current understanding of mechanisms of various chronic illnesses like cancers, metabolic disorders, neurodegenerative anomalies, etc. We are experiencing a renaissance in biomedical research primarily driven by next generation biotechnologies like genomics, transcriptomics, proteomics, metabolomics, lipidomics etc. Although genomic discoveries are at the forefront of next generation omics technologies, however, their implementation into clinical arena had been painstakingly slow mainly because of high reaction costs and unavailability of requisite computational tools for large-scale data analysis. However rapid innovations and steadily lowering cost of sequence-based chemistries along with the development of advanced bioinformatics tools have lately prompted launching and implementation of large-scale massively parallel genome sequencing programs in different fields ranging from medical genetics, infectious biology, agriculture sciences etc. Recent advances in large-scale omics-technologies is bringing healthcare research beyond the traditional “bench to bedside” approach to more of a continuum that will include improvements, in public healthcare and will be primarily based on predictive, preventive, personalized, and participatory medicine approach (P4). Recent large-scale research projects in genetic and infectious disease biology have indicated that massively parallel whole-genome/whole-exome sequencing, transcriptome analysis, and other functional genomic tools can reveal large number of unique functional elements and/or markers that otherwise would be undetected by traditional sequencing methodologies. Therefore, latest trends in the biomedical research is giving birth to the new branch in medicine commonly referred to as personalized and/or precision medicine. Developments in the post-genomic era are believed to completely restructure the present clinical pattern of disease prevention and treatment as well as methods of diagnosis and prognosis. The next important step in the direction of the precision/personalized medicine approach should be its early adoption in clinics for future medical interventions. Consequently, in coming year’s next generation biotechnologies will reorient medical practice more towards disease prediction and prevention approaches rather than curing them at later stages of their development and progression, even at wider population level(s) for general public healthcare system. PMID:28930123

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.

ACS Imaging of beta Pic: Searching for the origin of rings and asymmetry in planetesimal disks

NASA Astrophysics Data System (ADS)

Kalas, Paul

2003-07-01

The emerging picture for planetesimal disks around main sequence stars is that their radial and azimuthal symmetries are significantly deformed by the dynamical effects of either planets interior to the disk, or stellar objects exterior to the disk. The cause of these structures, such as the 50 AU cutoff of our Kuiper Belt, remains mysterious. Structure in the beta Pic planetesimal disk could be due to dynamics controlled by an extrasolar planet, or by the tidal influence of a more massive object exterior to the disk. The hypothesis of an extrasolar planet causing the vertical deformation in the disk predicts a blue color to the disk perpendicular to the disk midplane. The hypothesis that a stellar perturber deforms the disk predicts a globally uniform color and the existence of ring-like structure beyond 800 AU radius. We propose to obtain deep, multi-color images of the beta Pic disk ansae in the region 15"-220" {200-4000 AU} radius with the ACS WFC. The unparalleled stability of the HST PSF means that these data are uniquely capable of delivering the color sensitivity that can distinguish between the two theories of beta Pic's disk structure. Ascertaining the cause of such structure provide a meaningful context for understanding the dynamical history of our early solar system, as well as other planetesimal systems imaged around main sequence stars.

A Portrait of the Transcriptome of the Neglected Trematode, Fasciola gigantica—Biological and Biotechnological Implications

PubMed Central

Young, Neil D.; Jex, Aaron R.; Cantacessi, Cinzia; Hall, Ross S.; Campbell, Bronwyn E.; Spithill, Terence W.; Tangkawattana, Sirikachorn; Tangkawattana, Prasarn; Laha, Thewarach; Gasser, Robin B.

2011-01-01

Fasciola gigantica (Digenea) is an important foodborne trematode that causes liver fluke disease (fascioliasis) in mammals, including ungulates and humans, mainly in tropical climatic zones of the world. Despite its socioeconomic impact, almost nothing is known about the molecular biology of this parasite, its interplay with its hosts, and the pathogenesis of fascioliasis. Modern genomic technologies now provide unique opportunities to rapidly tackle these exciting areas. The present study reports the first transcriptome representing the adult stage of F. gigantica (of bovid origin), defined using a massively parallel sequencing-coupled bioinformatic approach. From >20 million raw sequence reads, >30,000 contiguous sequences were assembled, of which most were novel. Relative levels of transcription were determined for individual molecules, which were also characterized (at the inferred amino acid level) based on homology, gene ontology, and/or pathway mapping. Comparisons of the transcriptome of F. gigantica with those of other trematodes, including F. hepatica, revealed similarities in transcription for molecules inferred to have key roles in parasite-host interactions. Overall, the present dataset should provide a solid foundation for future fundamental genomic, proteomic, and metabolomic explorations of F. gigantica, as well as a basis for applied outcomes such as the development of novel methods of intervention against this neglected parasite. PMID:21408104

Resolving quandaries: basaloid adenoid cystic carcinoma or breast cylindroma? The role of massively parallel sequencing.

PubMed

Fusco, Nicola; Colombo, Pierre-Emmanuel; Martelotto, Luciano G; De Filippo, Maria R; Piscuoglio, Salvatore; Ng, Charlotte K Y; Lim, Raymond S; Jacot, William; Vincent-Salomon, Anne; Reis-Filho, Jorge S; Weigelt, Britta

2016-01-01

The aims of this study were to perform a whole-exome sequencing analysis of a breast cylindroma and to investigate the role of molecular analyses in the differentiation between breast cylindroma, a benign tumour that displays MYB expression, and CYLD gene mutations, and its main differential diagnosis, the breast solid-basaloid adenoid cystic carcinoma, a malignant tumour that is characterized by the presence of the MYB-NFIB fusion gene and MYB overexpression. A 66-year-old female underwent quadrantectomy after an irregular dense shadow was discovered in the right breast at the screening mammogram. Histologically, the tumour displayed features suggestive of a solid-basaloid variant of adenoid cystic carcinoma with a differential diagnosis of cylindroma. Fluorescence in situ hybridization, reverse transcription-polymerase chain reaction, immunohistochemistry and whole-exome sequencing revealed absence of the MYB-NFIB fusion gene, low levels of MYB protein expression and a clonal somatic CYLD splice site mutation associated with loss of heterozygosity of the wild-type allele. The results of the histological, immunohistochemical and molecular analyses were consistent with a diagnosis of breast cylindroma, providing a proof-of-principle that the integration of histopathological and molecular approaches can help to differentiate between a low-malignant potential and a benign breast tumour of triple-negative phenotype. © 2015 John Wiley & Sons Ltd.

Fast parallel tandem mass spectral library searching using GPU hardware acceleration.

PubMed

Baumgardner, Lydia Ashleigh; Shanmugam, Avinash Kumar; Lam, Henry; Eng, Jimmy K; Martin, Daniel B

2011-06-03

Mass spectrometry-based proteomics is a maturing discipline of biologic research that is experiencing substantial growth. Instrumentation has steadily improved over time with the advent of faster and more sensitive instruments collecting ever larger data files. Consequently, the computational process of matching a peptide fragmentation pattern to its sequence, traditionally accomplished by sequence database searching and more recently also by spectral library searching, has become a bottleneck in many mass spectrometry experiments. In both of these methods, the main rate-limiting step is the comparison of an acquired spectrum with all potential matches from a spectral library or sequence database. This is a highly parallelizable process because the core computational element can be represented as a simple but arithmetically intense multiplication of two vectors. In this paper, we present a proof of concept project taking advantage of the massively parallel computing available on graphics processing units (GPUs) to distribute and accelerate the process of spectral assignment using spectral library searching. This program, which we have named FastPaSS (for Fast Parallelized Spectral Searching), is implemented in CUDA (Compute Unified Device Architecture) from NVIDIA, which allows direct access to the processors in an NVIDIA GPU. Our efforts demonstrate the feasibility of GPU computing for spectral assignment, through implementation of the validated spectral searching algorithm SpectraST in the CUDA environment.

Massively parallel sequencing-enabled mixture analysis of mitochondrial DNA samples.

PubMed

Churchill, Jennifer D; Stoljarova, Monika; King, Jonathan L; Budowle, Bruce

2018-02-22

The mitochondrial genome has a number of characteristics that provide useful information to forensic investigations. Massively parallel sequencing (MPS) technologies offer improvements to the quantitative analysis of the mitochondrial genome, specifically the interpretation of mixed mitochondrial samples. Two-person mixtures with nuclear DNA ratios of 1:1, 5:1, 10:1, and 20:1 of individuals from different and similar phylogenetic backgrounds and three-person mixtures with nuclear DNA ratios of 1:1:1 and 5:1:1 were prepared using the Precision ID mtDNA Whole Genome Panel and Ion Chef, and sequenced on the Ion PGM or Ion S5 sequencer (Thermo Fisher Scientific, Waltham, MA, USA). These data were used to evaluate whether and to what degree MPS mixtures could be deconvolved. Analysis was effective in identifying the major contributor in each instance, while SNPs from the minor contributor's haplotype only were identified in the 1:1, 5:1, and 10:1 two-person mixtures. While the major contributor was identified from the 5:1:1 mixture, analysis of the three-person mixtures was more complex, and the mixed haplotypes could not be completely parsed. These results indicate that mixed mitochondrial DNA samples may be interpreted with the use of MPS technologies.

Massively parallel rRNA gene sequencing exacerbates the potential for biased community diversity comparisons due to variable library sizes

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

Gihring, Thomas; Green, Stefan; Schadt, Christopher Warren

2011-01-01

Technologies for massively parallel sequencing are revolutionizing microbial ecology and are vastly increasing the scale of ribosomal RNA (rRNA) gene studies. Although pyrosequencing has increased the breadth and depth of possible rRNA gene sampling, one drawback is that the number of reads obtained per sample is difficult to control. Pyrosequencing libraries typically vary widely in the number of sequences per sample, even within individual studies, and there is a need to revisit the behaviour of richness estimators and diversity indices with variable gene sequence library sizes. Multiple reports and review papers have demonstrated the bias in non-parametric richness estimators (e.g.more » Chao1 and ACE) and diversity indices when using clone libraries. However, we found that biased community comparisons are accumulating in the literature. Here we demonstrate the effects of sample size on Chao1, ACE, CatchAll, Shannon, Chao-Shen and Simpson's estimations specifically using pyrosequencing libraries. The need to equalize the number of reads being compared across libraries is reiterated, and investigators are directed towards available tools for making unbiased diversity comparisons.« less

Sensitive and specific detection of EML4-ALK rearrangements in non-small cell lung cancer (NSCLC) specimens by multiplex amplicon RNA massive parallel sequencing.

PubMed

Moskalev, Evgeny A; Frohnauer, Judith; Merkelbach-Bruse, Sabine; Schildhaus, Hans-Ulrich; Dimmler, Arno; Schubert, Thomas; Boltze, Carsten; König, Helmut; Fuchs, Florian; Sirbu, Horia; Rieker, Ralf J; Agaimy, Abbas; Hartmann, Arndt; Haller, Florian

2014-06-01

Recurrent gene fusions of anaplastic lymphoma receptor tyrosine kinase (ALK) and echinoderm microtubule-associated protein-like 4 (EML4) have been recently identified in ∼5% of non-small cell lung cancers (NSCLCs) and are targets for selective tyrosine kinase inhibitors. While fluorescent in situ hybridization (FISH) is the current gold standard for detection of EML4-ALK rearrangements, several limitations exist including high costs, time-consuming evaluation and somewhat equivocal interpretation of results. In contrast, targeted massive parallel sequencing has been introduced as a powerful method for simultaneous and sensitive detection of multiple somatic mutations even in limited biopsies, and is currently evolving as the method of choice for molecular diagnostic work-up of NSCLCs. We developed a novel approach for indirect detection of EML4-ALK rearrangements based on 454 massive parallel sequencing after reverse transcription and subsequent multiplex amplification (multiplex ALK RNA-seq) which takes advantage of unbalanced expression of the 5' and 3' ALK mRNA regions. Two lung cancer cell lines and a selected series of 32 NSCLC samples including 11 cases with EML4-ALK rearrangement were analyzed with this novel approach in comparison to ALK FISH, ALK qRT-PCR and EML4-ALK RT-PCR. The H2228 cell line with known EML4-ALK rearrangement showed 171 and 729 reads for 5' and 3' ALK regions, respectively, demonstrating a clearly unbalanced expression pattern. In contrast, the H1299 cell line with ALK wildtype status displayed no reads for both ALK regions. Considering a threshold of 100 reads for 3' ALK region as indirect indicator of EML4-ALK rearrangement, there was 100% concordance between the novel multiplex ALK RNA-seq approach and ALK FISH among all 32 NSCLC samples. Multiplex ALK RNA-seq is a sensitive and specific method for indirect detection of EML4-ALK rearrangements, and can be easily implemented in panel based molecular diagnostic work-up of NSCLCs by massive parallel sequencing. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

THE STRUCTURE OF THE MERGING RCS 231953+00 SUPERCLUSTER AT z {approx} 0.9

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

Faloon, A. J.; Webb, T. M. A.; Geach, J. E.

2013-05-10

The RCS 2319+00 supercluster is a massive supercluster at z = 0.9 comprising three optically selected, spectroscopically confirmed clusters separated by <3 Mpc on the plane of the sky. This supercluster is one of a few known examples of the progenitors of present-day massive clusters (10{sup 15} M{sub Sun} by z {approx} 0.5). We present an extensive spectroscopic campaign carried out on the supercluster field resulting, in conjunction with previously published data, in 1961 high-confidence galaxy redshifts. We find 302 structure members spanning three distinct redshift walls separated from one another by {approx}65 Mpc ({Delta} z = 0.03). The componentmore » clusters have spectroscopic redshifts of 0.901, 0.905, and 0.905. The velocity dispersions are consistent with those predicted from X-ray data, giving estimated cluster masses of {approx}10{sup 14.5}-10{sup 14.9} M{sub Sun }. The Dressler-Shectman test finds evidence of substructure in the supercluster field and a friends-of-friends analysis identified five groups in the supercluster, including a filamentary structure stretching between two cluster cores previously identified in the infrared by Coppin et al. The galaxy colors further show this filamentary structure to be a unique region of activity within the supercluster, comprised mainly of blue galaxies compared to the {approx}43%-77% red-sequence galaxies present in the other groups and cluster cores. Richness estimates from stacked luminosity function fits result in average group mass estimates consistent with {approx}10{sup 13} M{sub Sun} halos. Currently, 22% of our confirmed members reside in {approx}> 10{sup 13} M{sub Sun} groups/clusters destined to merge onto the most massive cluster, in agreement with the massive halo galaxy fractions important in cluster galaxy pre-processing in N-body simulation merger tree studies.« less

A NICMOS direct imaging search for giant planets around the seven single white dwarfs in the Hyades

NASA Astrophysics Data System (ADS)

Zinnecker, Hans

2003-07-01

We propose to use the NIC1 camera on HST to search for massive giant planets around the known seven single white dwarfs in the nearby Hyades cluster at sub-arcsec separations. At an age of 625 Myr, the white dwarfs had protogenitor masses of about 3 solar masses, and massive gaseous giant planets should have formed in the massive circumstellar disks around these ex Herbig A0 stars, probably at orbital separations similar or slightly larger than that of Jupiter {5 AU} in our own solar system. Such planets would have survived the post-Main Sequence mass loss of the parent star, and would have migrated outward adiabatically by a factor 4.5, equal to the ratio of initial to final stellar mass {3Mo/0.66Mo}, due to conservation of orbital angular momentum during the mass loss {AGB and PN} phase. Thus the orbital separation NOW would be 4.5 x 5 AU = 22.5 AU, which at the distance of the Hyades {45 pc} corresponds to 0.50 arcsec. Simulations with TinyTim then show that giant planets at this separation with masses in the range 6-12 Jupiter masses and apparent J and H magnitudes in the range 20.5-23.3 mag {from Baraffe or Burrows models} can be spatially resolved around the Hyades white dwarfs. Their J and H brightnesses are known to be 15 +/- 0.5 mag, implying a median star-planet brightness ratio of 1000:1 {7.5 mag}. This combination of dynamic range and orbital separation is observable with NICMOS, by subtracting images taken at two roll angles. Therefore, the proposed near-IR diffraction-limited observations in the F110W and F160W filters promise to resolve giant planets around low-mass stars for the first time. If successful, the observations would also prove that giant planets do form around early-type stars more massive than the Sun.

Metal enrichment of the intracluster medium: SN-driven galactic winds

NASA Astrophysics Data System (ADS)

Baumgartner, V.; Breitschwerdt, D.

2009-12-01

% We investigate the role of supernova (SN)-driven galactic winds in the chemical enrichment of the intracluster medium (ICM). Such outflows on galactic scales have their origin in huge star forming regions and expel metal enriched material out of the galaxies into their surroundings as observed, for example, in the nearby starburst galaxy NGC 253. As massive stars in OB-associations explode sequentially, shock waves are driven into the interstellar medium (ISM) of a galaxy and merge, forming a superbubble (SB). These SBs expand in a direction perpendicular to the disk plane following the density gradient of the ISM. We use the 2D analytical approximation by Kompaneets (1960) to model the expansion of SBs in an exponentially stratified ISM. This is modified in order to describe the sequence of SN-explosions as a time-dependent process taking into account the main-sequence life-time of the SN-progenitors and using an initial mass function to get the number of massive stars per mass interval. The evolution of the bubble in space and time is calculated analytically, from which the onset of Rayleigh-Taylor instabilities in the shell can be determined. In its further evolution, the shell will break up and high-metallicity gas will be ejected into the halo of the galaxy and even into the ICM. We derive the number of stars needed for blow-out depending on the scale height and density of the ambient medium, as well as the fraction of alpha- and iron peak elements contained in the hot gas. Finally, the amount of metals injected by Milky Way-type galaxies to the ICM is calculated confirming the importance of this enrichment process.

Multiple stellar populations in Magellanic Cloud clusters - VI. A survey of multiple sequences and Be stars in young clusters

NASA Astrophysics Data System (ADS)

Milone, A. P.; Marino, A. F.; Di Criscienzo, M.; D'Antona, F.; Bedin, L. R.; Da Costa, G.; Piotto, G.; Tailo, M.; Dotter, A.; Angeloni, R.; Anderson, J.; Jerjen, H.; Li, C.; Dupree, A.; Granata, V.; Lagioia, E. P.; Mackey, A. D.; Nardiello, D.; Vesperini, E.

2018-06-01

The split main sequences (MSs) and extended MS turnoffs (eMSTOs) detected in a few young clusters have demonstrated that these stellar systems host multiple populations differing in a number of properties such as rotation and, possibly, age. We analyse Hubble Space Telescope photometry for 13 clusters with ages between ˜40 and ˜1000 Myr and of different masses. Our goal is to investigate for the first time the occurrence of multiple populations in a large sample of young clusters. We find that all the clusters exhibit the eMSTO phenomenon and that MS stars more massive than ˜1.6 M_{⊙} define a blue and a red MS, with the latter hosting the majority of MS stars. The comparison between the observations and isochrones suggests that the blue MSs are made of slow-rotating stars, while the red MSs host stars with rotational velocities close to the breakup value. About half of the bright MS stars in the youngest clusters are H α emitters. These Be stars populate the red MS and the reddest part of the eMSTO, thus supporting the idea that the red MS is made of fast rotators. We conclude that the split MS and the eMSTO are a common feature of young clusters in both Magellanic Clouds. The phenomena of a split MS and an eMSTO occur for stars that are more massive than a specific threshold, which is independent of the host-cluster mass. As a by-product, we report the serendipitous discovery of a young Small Magellanic Cloud cluster, GALFOR 1.

NGC 346: Looking in the Cradle of a Massive Star Cluster

NASA Astrophysics Data System (ADS)

Gouliermis, Dimitrios A.; Hony, Sacha

2017-03-01

How does a star cluster of more than few 10,000 solar masses form? We present the case of the cluster NGC 346 in the Small Magellanic Cloud, still embedded in its natal star-forming region N66, and we propose a scenario for its formation, based on observations of the rich stellar populations in the region. Young massive clusters host a high fraction of early-type stars, indicating an extremely high star formation efficiency. The Milky Way galaxy hosts several young massive clusters that fill the gap between young low-mass open clusters and old massive globular clusters. Only a handful, though, are young enough to study their formation. Moreover, the investigation of their gaseous natal environments suffers from contamination by the Galactic disk. Young massive clusters are very abundant in distant starburst and interacting galaxies, but the distance of their hosting galaxies do not also allow a detailed analysis of their formation. The Magellanic Clouds, on the other hand, host young massive clusters in a wide range of ages with the youngest being still embedded in their giant HII regions. Hubble Space Telescope imaging of such star-forming complexes provide a stellar sampling with a high dynamic range in stellar masses, allowing the detailed study of star formation at scales typical for molecular clouds. Our cluster analysis on the distribution of newly-born stars in N66 shows that star formation in the region proceeds in a clumpy hierarchical fashion, leading to the formation of both a dominant young massive cluster, hosting about half of the observed pre-main-sequence population, and a self-similar dispersed distribution of the remaining stars. We investigate the correlation between stellar surface density (and star formation rate derived from star-counts) and molecular gas surface density (derived from dust column density) in order to unravel the physical conditions that gave birth to NGC 346. A power law fit to the data yields a steep correlation between these two parameters with a considerable scatter. The fraction of stellar over the total (gas plus young stars) mass is found to be systematically higher within the central 15 pc (where the young massive cluster is located) than outside, which suggests variations in the star formation efficiency within the same star-forming complex. This trend possibly reflects a change of star formation efficiency in N66 between clustered and non-clustered star formation. Our findings suggest that the formation of NGC 346 is the combined result of star formation regulated by turbulence and of early dynamical evolution induced by the gravitational potential of the dense interstellar medium.

The VLT-FLAMES Tarantula Survey. XVII. Physical and wind properties of massive stars at the top of the main sequence

NASA Astrophysics Data System (ADS)

Bestenlehner, J. M.; Gräfener, G.; Vink, J. S.; Najarro, F.; de Koter, A.; Sana, H.; Evans, C. J.; Crowther, P. A.; Hénault-Brunet, V.; Herrero, A.; Langer, N.; Schneider, F. R. N.; Simón-Díaz, S.; Taylor, W. D.; Walborn, N. R.

2014-10-01

The evolution and fate of very massive stars (VMS) is tightly connected to their mass-loss properties. Their initial and final masses differ significantly as a result of mass loss. VMS have strong stellar winds and extremely high ionising fluxes, which are thought to be critical sources of both mechanical and radiative feedback in giant H ii regions. However, how VMS mass-loss properties change during stellar evolution is poorly understood. In the framework of the VLT-Flames Tarantula Survey (VFTS), we explore the mass-loss transition region from optically thin O star winds to denser WNh Wolf-Rayet star winds, thereby testing theoretical predictions. To this purpose we select 62 O, Of, Of/WN, and WNh stars, an unprecedented sample of stars with the highest masses and luminosities known. We perform a spectral analysis of optical VFTS as well as near-infrared VLT/SINFONI data using the non-LTE radiative transfer code CMFGEN to obtain both stellar and wind parameters. For the first time, we observationally resolve the transition between optically thin O star winds and optically thick hydrogen-rich WNh Wolf-Rayet winds. Our results suggest the existence of a "kink" between both mass-loss regimes, in agreement with recent Monte Carlo simulations. For the optically thick regime, we confirm the steep dependence on the classical Eddington factor Γe from previous theoretical and observational studies. The transition occurs on the main sequence near a luminosity of 106.1L⊙, or a mass of 80 ... 90 M⊙. Above this limit, we find that - even when accounting for moderate wind clumping (with fv = 0.1) - wind mass-loss rates are enhanced with respect to standard prescriptions currently adopted in stellar evolution calculations. We also show that this results in substantial helium surface enrichment. Finally, based on our spectroscopic analyses, we are able to provide the most accurate ionising fluxes for VMS known to date, confirming the pivotal role of VMS in ionising and shaping their environments. Appendices are available in electronic form at http://www.aanda.org

Black holes in massive gravity as heat engines

NASA Astrophysics Data System (ADS)

Hendi, S. H.; Eslam Panah, B.; Panahiyan, S.; Liu, H.; Meng, X.-H.

2018-06-01

The paper at hand studies the heat engine provided by black holes in the presence of massive gravity. The main motivation is to investigate the effects of massive gravity on different properties of the heat engine. It will be shown that massive gravity parameters modify the efficiency of engine on a significant level. Furthermore, it will be pointed out that it is possible to have a heat engine for non-spherical black holes in massive gravity, and therefore, we will study the effects of horizon topology on the properties of heat engine. Surprisingly, it will be shown that the highest efficiency for the heat engine belongs to black holes with the hyperbolic horizon, while the lowest one belongs to the spherical black holes.

Interpretation of massive sandstones in ephemeral fluvial settings: A case study from the Upper Candelária Sequence (Upper Triassic, Paraná Basin, Brazil)

NASA Astrophysics Data System (ADS)

Horn, Bruno Ludovico Dihl; Goldberg, Karin; Schultz, Cesar Leandro

2018-01-01

Ephemeral rivers display a wide range of upper- and lower-flow regime structures due to great flow-velocity changes during the floods. The development of flow structures in these setting is yet to be understood, especially in the formation of thick, massive sandstones. The Upper Triassic of Southern Gondwana was marked by a climate with great seasonal changes, yet there is no description of river systems with seasonal characteristics in Southern Gondwana. This work aims to characterize a ephemeral alluvial system of the Upper Triassic of the Paraná Basin. The characteristics of the deposits are discussed in terms of depositional processes through comparison with similar deposits from literature, flow characteristics and depositional signatures compared to flume experiments. The alluvial system is divided in four facies associations: (1) channels with wanning fill, characterized by low width/thickness ratio, tabular bodies, scour-and-fill structures with upper- and lower-flow regime bedforms; (2) channels with massive fill, characterized by low w/t ratio, sheet-like bodies, scour-and-fill structures with massive sandstones; (3) proximal sheetfloods, characterized by moderate w/t ratio, sheet-like bodies with upper- and lower-flow regime bedforms and (4) distal sheetfloods, characterized by high w/t ratio, sheet-like bodies with lower-flow regime bedforms. Evidence for the seasonal reactivation of the riverine system includes the scarcity of well-developed macroforms and presence of in-channel mudstones, thick intraformational conglomerates, and the occurrence of well- and poorly-preserved vertebrate bones in the same beds. The predominantly massive sandstones indicate deposition from a hyperconcentrated flow during abrupt changes in flow speed, caused by de-confinement or channel avulsion, whereas turbulent portions of the flow formed the upper- and lower-flow regime bedforms after the deposition of the massive layers. The upper portion of the Candelária Sequence records a good example of strongly ephemeral alluvial systems, where the predominance of massive sandstones is a particular characteristic.

Multiple outer-reef tracts along the south Florida bank margin: Outlier reefs, a new windward-margin model

USGS Publications Warehouse

Lidz, Barbara H.; Hine, A.C.; Shinn, Eugene A.; Kindinger, Jack G.

1991-01-01

High-resolution seismic-reflection profiles off the lower Florida Keys reveal a multiple outlier-reef tract system ~0.5 to 1.5 km sea-ward of the bank margin. The system is characterized by a massive, outer main reef tract of high (28 m) unburied relief that parallels the margin and at least two narrower, discontinuous reef tracts of lower relief between the main tract and the shallow bank-margin reefs. The outer tract is ~0.5 to 1 km wide and extends a distance of ~57 km. A single pass divides the outer tract into two main reefs. The outlier reefs developed on antecedent, low-gradient to horizontal offbank surfaces, interpreted to be Pleistocene beaches that formed terracelike features. Radiocarbon dates of a coral core from the outer tract confirm a pre-Holocene age. These multiple outlier reefs represent a new windward-margin model that presents a significant, unique mechanism for progradation of carbonate platforms during periods of sea-level fluctuation. Infilling of the back-reef terrace basins would create new terraced promontories and would extend or "step" the platform seaward for hundreds of metres. Subsequent outlier-reef development would produce laterally accumulating sequences.

Graben calderas of the Sierra Madre Occidental: The case of Guanajuato, central Mexico

NASA Astrophysics Data System (ADS)

Aguirre-Diaz, G. J.; Tristán-González, M.; Labarthe-Hernández, G.; Marti, J.

2013-12-01

The Sierra Madre Occidental (SMO) volcanic province is characterized by voluminous silicic ignimbrites that reach an accumulated thickness of 500 to 1500 m. A single ignimbrite can reach up to 350 m thick in its outflow facies. This ignimbrite sequence formed mostly within 38-23 Ma, building up a total estimated volume of ca. 580,000 km3 making the SMO the largest ignimbrite province of the world. We have showed that several and probably most of the SMO ignimbrites were erupted from fissures associated to Basin and Range fault systems or grabens (Geology, 2003), thus naming these volcano-tectonic structures as graben calderas (Caldera Volcanism book, Elsevier, 2008). Generally, the sequence observed in graben calderas include, from oldest to youngest, alluvial fan deposits combined with lacustrine deposits, pyroclastic surge deposits and minor volume ignimbrites, a large-volume ignimbrite that could be massive or made of successive layers, and sometimes silicic lava domes and/or mafic fissural lavas both with vents aligned with the graben trend. Fallout deposits, plinian or non-plinian, are not observed in the sequence. Thus, onset of caldera collapse represented by the major ignimbrite must occur just after deposition of continental sediments within the graben domain. A similar volcano-tectonic development is observed in pull-apart grabens. Therefore, extensional or transtensional tectonics, before and during caldera collapse, and the emplacement of a subgraben shallow silicic magma chamber are the necessary conditions for the development of graben calderas. We describe here the case of the Guanajuato graben caldera, located in the central part of Mexico and in the southeastern portion of the SMO volcanic province. The caldera is part of the economically important mining district of Guanajuato, with 28 silver mines, some active since the 16th century. The caldera structure, a rectangle of 10 x 16 km, was controlled by NW and NE regional fault systems. Most ore deposits occur along this orthogonal faulting network, but mainly along the NW fault of Veta Madre that crosses through the center of the caldera. The mid-Tertiary stratigraphy in Guanajuato follows the general sequence observed in graben calderas; i.e., from oldest to youngest includes 1) at least 1,500 m of alluvial fan deposits within a tectonic basin (Guanajuato Red Conglomerate), 2) pyroclastic flow deposits, consisting of surge deposits (Loseros Formation) that are concordant with a massive, large volume, rhyolitic ignimbrite (Bufa Rhyolite), which is covered by a layered series of pyroclastic flow deposits (Calderones Formation), and 3) effusive volcanism in the form of rhyolitic lava domes (Chichíndaro Rhyolite) and basaltic-andesite dikes and lavas (Cedros Andesite). The Guanajuato graben caldera formed at about 33 Ma, based on our new U-Pb zr age of the main ignimbrite, Bufa Rhyolite.

VizieR Online Data Catalog: Adiabatic mass loss in binary stars. II. (Ge+, 2015)

NASA Astrophysics Data System (ADS)

Ge, H.; Webbink, R. F.; Chen, X.; Han, Z.

2016-02-01

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 0.10M⊙-100M⊙ 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. For 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 qad (throughout this paper, we follow the convention of defining the binary mass ratio as q{equiv}Mdonor/Maccretor) 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, qad 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 qad declining with decreasing mass, and asymptotically approaching qad=2/3, appropriate to a classical isentropic n=3/2 polytrope. Our calculated qad values agree well with the behavior of time-dependent models by Chen & Han (2003MNRAS.341..662C) 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 qad 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. (3 data files).

Numerical simulations of downward convective overshooting in giants

NASA Astrophysics Data System (ADS)

Tian, Chun-Lin; Deng, Li-Cai; Chan, Kwing-Lam

2009-09-01

An attempt at understanding downward overshooting in the convective envelopes of post-main-sequence stars has been made on the basis of three-dimensional large-eddy simulations, using artificially modified OPAL opacity and taking into account radiation and ionization in the equation of state. Two types of star, an intermediate-mass star and a massive star, were considered. To avoid a long thermal relaxation time of the intermediate-mass star, we increased the stellar energy flux artificially while trying to maintain a structure close to the one given by a 1D stellar model. A parametric study of the flux factor was performed. For the massive star, no such process was necessary. Numerical results were analysed when the system reached the statistical steady state. It was shown that the penetration distance in pressure scaleheights is of the order of unity. The scaling relations between penetration distance, input flux and vertical velocity fluctuations studied by Singh et al. were checked. The anisotropy of the turbulent convection and the diffusion models of the third-order moments representing the non-local transport were also investigated. These models are dramatically affected by the velocity fields and no universal constant parameters seem to exist. The limitations of the numerical results were also discussed.

SPITZER MICROLENS MEASUREMENT OF A MASSIVE REMNANT IN A WELL-SEPARATED BINARY

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

Shvartzvald, Y.; Bryden, G.; Henderson, C. B.

2015-12-01

We report the detection and mass measurement of a binary lens OGLE-2015-BLG-1285La,b, with the more massive component having M{sub 1} > 1.35 M{sub ⊙} (80% probability). A main-sequence star in this mass range is ruled out by limits on blue light, meaning that a primary in this mass range must be a neutron star (NS) or black hole (BH). The system has a projected separation r{sub ⊥} = 6.1 ± 0.4 AU and lies in the Galactic bulge. These measurements are based on the “microlens parallax” effect, i.e., comparing the microlensing light curve as seen from Spitzer, which lay atmore » 1.25 AU projected from Earth, to the light curves from four ground-based surveys, three in the optical and one in the near-infrared. Future adaptive optics imaging of the companion by 30 m class telescopes will yield a much more accurate measurement of the primary mass. This discovery both opens the path and defines the challenges to detecting and characterizing BHs and NSs in wide binaries, with either dark or luminous companions. In particular, we discuss lessons that can be applied to future Spitzer and Kepler K2 microlensing parallax observations.« less

STAR FORMATION AT 4 < z < 6 FROM THE SPITZER LARGE AREA SURVEY WITH HYPER-SUPRIME-CAM (SPLASH)

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

Steinhardt, Charles L.; Capak, Peter; Masters, Dan

2014-08-20

Using the first 50% of data collected for the Spitzer Large Area Survey with Hyper-Suprime-Cam observations on the 1.8 deg{sup 2} Cosmological Evolution Survey we estimate the masses and star formation rates of 3398 M {sub *} > 10{sup 10} M {sub ☉} star-forming galaxies at 4 < z < 6 with a substantial population up to M {sub *} ≳ 10{sup 11.5} M {sub ☉}. We find that the strong correlation between stellar mass and star formation rate seen at lower redshift (the ''main sequence'' of star-forming galaxies) extends to z ∼ 6. The observed relation and scatter is consistentmore » with a continued increase in star formation rate at fixed mass in line with extrapolations from lower-redshift observations. It is difficult to explain this continued correlation, especially for the most massive systems, unless the most massive galaxies are forming stars near their Eddington-limited rate from their first collapse. Furthermore, we find no evidence for moderate quenching at higher masses, indicating quenching either has not occurred prior to z ∼ 6 or else occurs rapidly, so that few galaxies are visible in transition between star-forming and quenched.« less

The massive stellar population of W49: A spectroscopic survey

NASA Astrophysics Data System (ADS)

Wu, Shi-Wei; Bik, Arjan; Bestenlehner, Joachim M.; Henning, Thomas; Pasquali, Anna; Brandner, Wolfgang; Stolte, Andrea

2016-05-01

Context. Massive stars form on different scales that range from large, dispersed OB associations to compact, dense starburst clusters. The complex structure of regions of massive star formation and the involved short timescales provide a challenge for our understanding of their birth and early evolution. As one of the most massive and luminous star-forming region in our Galaxy, W49 is the ideal place to study the formation of the most massive stars. Aims: By classifying the massive young stars that are deeply embedded in the molecular cloud of W49, we aim to investigate and trace the star formation history of this region. Methods: We analyse near-infrared K-band spectroscopic observations of W49 from LBT/LUCI combined with JHK images obtained with NTT/SOFI and LBT/LUCI. Based on JHK-band photometry and K-band spectroscopy, the massive stars are placed in a Hertzsprung Russell diagram. By comparison with evolutionary models, their age and hence the star formation history of W49 can be investigated. Results: Fourteen O-type stars, as well as two young stellar objects (YSOs), are identified by our spectroscopic survey. Eleven O stars are main sequence stars with subtypes ranging from O3 to O9.5 and masses ranging from ~20 M⊙ to ~120 M⊙. Three of the O stars show strong wind features and are considered to be Of-type supergiants with masses beyond 100 M⊙. The two YSOs show CO emission, which is indicative of the presence of circumstellar disks in the central region of the massive cluster. The age of the cluster is estimated as ~1.5 Myr, with star formation continuing in different parts of the region. The ionising photons from the central massive stars have not yet cleared the molecular cocoon surrounding the cluster. W49 is comparable to extragalactic star-forming regions, and it provides us with a unique chance to study a starburst in detail. Based on data acquired using the Large Binocular Telescope (LBT). The LBT is an international collaboration among institutions in Germany, Italy and the United States. LBT Corporation partners are: LBT Beteiligungsgesellschaft, Germany, representing the Max Planck Society, the Astrophysical Institute Potsdam, and Heidelberg University; Istituto Nazionale di Astrofisica, Italy; The University of Arizona on behalf of the Arizona university system; The Ohio State University, and The Research Corporation, on behalf of The University of Notre Dame, University of Minnesota and University of Virginia.Based on observations made with ESO Telescopes at the La Silla Paranal Observatory under programme IDs 67.C-0514 and 073.D-0837.The reduced spectra (FITS files) are only available at the CDS via anonymous ftp to http://cdsarc.u-strasbg.fr (ftp://130.79.128.5) or via http://cdsarc.u-strasbg.fr/viz-bin/qcat?J/A+A/589/A16

The accelerated build-up of the red sequence in high-redshift galaxy clusters

NASA Astrophysics Data System (ADS)

Cerulo, P.; Couch, W. J.; Lidman, C.; Demarco, R.; Huertas-Company, M.; Mei, S.; Sánchez-Janssen, R.; Barrientos, L. F.; Muñoz, R. P.

2016-04-01

We analyse the evolution of the red sequence in a sample of galaxy clusters at redshifts 0.8 < z < 1.5 taken from the HAWK-I Cluster Survey (HCS). The comparison with the low-redshift (0.04 < z < 0.08) sample of the WIde-field Nearby Galaxy-cluster Survey (WINGS) and other literature results shows that the slope and intrinsic scatter of the cluster red sequence have undergone little evolution since z = 1.5. We find that the luminous-to-faint ratio and the slope of the faint end of the luminosity distribution of the HCS red sequence are consistent with those measured in WINGS, implying that there is no deficit of red galaxies at magnitudes fainter than M_V^{ast } at high redshifts. We find that the most massive HCS clusters host a population of bright red sequence galaxies at MV < -22.0 mag, which are not observed in low-mass clusters. Interestingly, we also note the presence of a population of very bright (MV < -23.0 mag) and massive (log (M*/M⊙) > 11.5) red sequence galaxies in the WINGS clusters, which do not include only the brightest cluster galaxies and which are not present in the HCS clusters, suggesting that they formed at epochs later than z = 0.8. The comparison with the luminosity distribution of a sample of passive red sequence galaxies drawn from the COSMOS/UltraVISTA field in the photometric redshift range 0.8 < zphot < 1.5 shows that the red sequence in clusters is more developed at the faint end, suggesting that halo mass plays an important role in setting the time-scales for the build-up of the red sequence.

Spectroscopic Confirmation of Two Massive Red-sequence-selected Galaxy Clusters at Z Approximately Equal to 1.2 in the Sparcs-North Cluster Survey

NASA Technical Reports Server (NTRS)

Muzzin, Adam; Wilson, Gillian; Yee, H.K.C.; Hoekstra, Henk; Gilbank, David; Surace, Jason; Lacy, Mark; Blindert, Kris; Majumdar, Subhabrata; Demarco, Ricardo;

VLA AND ALMA IMAGING OF INTENSE GALAXY-WIDE STAR FORMATION IN z ∼ 2 GALAXIES

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

Rujopakarn, W.; Silverman, J. D.; Dunlop, J. S.

2016-12-10

We present ≃0.″4 resolution extinction-independent distributions of star formation and dust in 11 star-forming galaxies (SFGs) at z  = 1.3–3.0. These galaxies are selected from sensitive blank-field surveys of the 2′ × 2′ Hubble Ultra-Deep Field at λ  = 5 cm and 1.3 mm using the Karl G. Jansky Very Large Array and Atacama Large Millimeter/submillimeter Array. They have star formation rates (SFRs), stellar masses, and dust properties representative of massive main-sequence SFGs at z  ∼ 2. Morphological classification performed on spatially resolved stellar mass maps indicates a mixture of disk and morphologically disturbed systems; half of the sample harbor X-ray active galactic nuclei (AGNs),more » thereby representing a diversity of z  ∼ 2 SFGs undergoing vigorous mass assembly. We find that their intense star formation most frequently occurs at the location of stellar-mass concentration and extends over an area comparable to their stellar-mass distribution, with a median diameter of 4.2 ± 1.8 kpc. This provides direct evidence of galaxy-wide star formation in distant blank-field-selected main-sequence SFGs. The typical galactic-average SFR surface density is 2.5 M {sub ⊙} yr{sup −1} kpc{sup −2}, sufficiently high to drive outflows. In X-ray-selected AGN where radio emission is enhanced over the level associated with star formation, the radio excess pinpoints the AGNs, which are found to be cospatial with star formation. The median extinction-independent size of main-sequence SFGs is two times larger than those of bright submillimeter galaxies, whose SFRs are 3–8 times larger, providing a constraint on the characteristic SFR (∼300 M {sub ⊙} yr{sup −1}) above which a significant population of more compact SFGs appears to emerge.« less

Tidal dissipation in rotating low-mass stars and implications for the orbital evolution of close-in massive planets. II. Effect of stellar metallicity

NASA Astrophysics Data System (ADS)

Bolmont, E.; Gallet, F.; Mathis, S.; Charbonnel, C.; Amard, L.; Alibert, Y.

2017-08-01

Observations of hot-Jupiter exoplanets suggest that their orbital period distribution depends on the metallicity of the host stars. We investigate here whether the impact of the stellar metallicity on the evolution of the tidal dissipation inside the convective envelope of rotating stars and its resulting effect on the planetary migration might be a possible explanation for this observed statistical trend. We use a frequency-averaged tidal dissipation formalism coupled to an orbital evolution code and to rotating stellar evolution models in order to estimate the effect of a change of stellar metallicity on the evolution of close-in planets. We consider here two different stellar masses: 0.4 M⊙ and 1.0 M⊙ evolving from the early pre-main sequence phase up to the red-giant branch. We show that the metallicity of a star has a strong effect on the stellar parameters, which in turn strongly influence the tidal dissipation in the convective region. While on the pre-main sequence, the dissipation of a metal-poor Sun-like star is higher than the dissipation of a metal-rich Sun-like star; on the main sequence it is the opposite. However, for the 0.4 M⊙ star, the dependence of the dissipation with metallicity is much less visible. Using an orbital evolution model, we show that changing the metallicity leads to different orbital evolutions (e.g., planets migrate farther out from an initially fast-rotating metal-rich star). Using this model, we qualitatively reproduced the observational trends of the population of hot Jupiters with the metallicity of their host stars. However, more steps are needed to improve our model to try to quantitatively fit our results to the observations. Specifically, we need to improve the treatment of the rotation evolution in the orbital evolution model, and ultimately we need to consistently couple the orbital model to the stellar evolution model.

Luminous blue variables and the fates of very massive stars.

PubMed

Smith, Nathan

2017-10-28

Luminous blue variables (LBVs) had long been considered massive stars in transition to the Wolf-Rayet (WR) phase, so their identification as progenitors of some peculiar supernovae (SNe) was surprising. More recently, environment statistics of LBVs show that most of them cannot be in transition to the WR phase after all, because LBVs are more isolated than allowed in this scenario. Additionally, the high-mass H shells around luminous SNe IIn require that some very massive stars above 40  M ⊙ die without shedding their H envelopes, and the precursor outbursts are a challenge for understanding the final burning sequences leading to core collapse. Recent evidence suggests a clear continuum in pre-SN mass loss from super-luminous SNe IIn, to regular SNe IIn, to SNe II-L and II-P, whereas most stripped-envelope SNe seem to arise from a separate channel of lower-mass binary stars rather than massive WR stars.This article is part of the themed issue 'Bridging the gap: from massive stars to supernovae'. © 2017 The Author(s).

Beryllium abundances along the evolutionary sequence of the open cluster IC 4651 - A new test for hydrodynamical stellar models

NASA Astrophysics Data System (ADS)

Smiljanic, R.; Pasquini, L.; Charbonnel, C.; Lagarde, N.

2010-02-01

Context. Previous analyses of lithium abundances in main sequence and red giant stars have revealed the action of mixing mechanisms other than convection in stellar interiors. Beryllium abundances in stars with Li abundance determinations can offer valuable complementary information on the nature of these mechanisms. Aims: Our aim is to derive Be abundances along the whole evolutionary sequence of an open cluster. We focus on the well-studied open cluster IC 4651. These Be abundances are used with previously determined Li abundances, in the same sample stars, to investigate the mixing mechanisms in a range of stellar masses and evolutionary stages. Methods: Atmospheric parameters were adopted from a previous abundance analysis by the same authors. New Be abundances have been determined from high-resolution, high signal-to-noise UVES spectra using spectrum synthesis and model atmospheres. The careful synthetic modeling of the Be lines region is used to calculate reliable abundances in rapidly rotating stars. The observed behavior of Be and Li is compared to theoretical predictions from stellar models including rotation-induced mixing, internal gravity waves, atomic diffusion, and thermohaline mixing. Results: Beryllium is detected in all the main sequence and turn-off sample stars, both slow- and fast-rotating stars, including the Li-dip stars, but is not detected in the red giants. Confirming previous results, we find that the Li dip is also a Be dip, although the depletion of Be is more modest than for Li in the corresponding effective temperature range. For post-main-sequence stars, the Be dilution starts earlier within the Hertzsprung gap than expected from classical predictions, as does the Li dilution. A clear dispersion in the Be abundances is also observed. Theoretical stellar models including the hydrodynamical transport processes mentioned above are able to reproduce all the observed features well. These results show a good theoretical understanding of the Li and Be behavior along the color-magnitude diagram of this intermediate-age cluster for stars more massive than 1.2 M⊙. Based on observations made with the ESO VLT, at Paranal Observatory, under programs 065.L-0427 and 067.D-0126.Current address: European Southern Observatory, Karl-Schwarzschild-Str. 2, 85748 Garching bei München, Germany.

The Evolution of Metals and Dust in the High-Redshift Universe (z greater than 6)

NASA Technical Reports Server (NTRS)

Dwek, Eliahu

2007-01-01

Dusty hyperluminous galaxies in the early universe provide unique environments for studying the role of massive stars in the formation and destruction of dust. At redshifts above approx. 6, when the universe was less than approx. 1 Gyr old, dust could have only condensed in the explosive ejecta of Type-II supernovae (SNe), since most of the progenitors of the AGB stars, the major alternative source of interstellar dust, did not have time to evolve off the main sequence. I will present analytical models for the evolution of the gas, dust, and metals in high redshift galaxies, with a special application to SDSS J1148+5251, a hyperluminous quasar at $z = 6.4$. I will also discuss possible star formation scenarios consistent with observational constraints on the dust and gas content of this object.

Collaborative observations of HDE 332077

NASA Technical Reports Server (NTRS)

Ake, Thomas B., III

1995-01-01

IUE low dispersion observations were made of the T(sub c)-deficient peculiar red giant (PRG) star, HDE 332077, to test the hypothesis that T(sub c)-poor PRG's are formed as a result of mass transfer from a binary companion rather than from internal thermal pulsing while on the asymptotic red giant branch. Previous ground-based observations of this star indicated that it is a binary, but the secondary star was too massive for an expected white dwarf. A deep, short wavelength prime (SWP) exposure was needed to search for evidence of an A-type main-sequence companion. We obtained a 120 minute LWP exposure (LWP 23479), followed by a collaborative 1230 minute SWP exposure (SWP 45113). These observations were combined with our earlier IUE and optical data on this PRG star to model the spectral energy distribution of the system.

The ν process in the innermost supernova ejecta

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

Sieverding, Andre; Martínez-Pinedo, Gabriel; Langanke, Karlheinz

2017-12-01

The neutrino-induced nucleosynthesis (ν process) in supernova explosions of massive stars of solar metallicity with initial main sequence masses between 13 and 30 M⊙ has been studied with an analytic explosion model using a new extensive set of neutrino-nucleus cross-sections and spectral properties that agree with modern supernova simulations. The production factors for the nuclei 7Li, 11B, 19F, 138La and 180Ta, are still significantly enhanced but do not reproduce the full solar abundances. We study the possible contribution of the innermost supernova eject to the production of the light elements 7Li and 11B with tracer particles based on a 2Dmore » supernova simulation of a 12 M⊙ progenitor and conclude, that a contribution exists but is negligible for the total yield for this explosion model.« less

The C and N abundances in disk stars

NASA Astrophysics Data System (ADS)

Shi, J. R.; Zhao, G.; Chen, Y. Q.

2002-01-01

Abundance analysis of carbon and nitrogen has been performed for a sample of 90 F and G type main-sequence disk stars with a metallicity range of -1.0 < [Fe/H] <+0.2 using the \\ion{C} i and N I lines. We confirm a moderate carbon excess in the most metal-poor disk dwarfs found in previous investigations. Our results suggest that carbon is enriched by superwinds of metal-rich massive stars at the beginning of the disk evolution, while a significant amount of carbon is contributed by low-mass stars in the late stage. The observed behavior of [N/Fe] is about solar in the disk stars, irrespective of the metallicity. This result suggests that nitrogen is produced mostly by intermediate-mass stars. Based on observations carried out at National Astrono- mical Observatories (Xinglong, China).

Molecular Cytogenetics Guides Massively Parallel Sequencing of a Radiation-Induced Chromosome Translocation in Human Cells.

PubMed

Cornforth, Michael N; Anur, Pavana; Wang, Nicholas; Robinson, Erin; Ray, F Andrew; Bedford, Joel S; Loucas, Bradford D; Williams, Eli S; Peto, Myron; Spellman, Paul; Kollipara, Rahul; Kittler, Ralf; Gray, Joe W; Bailey, Susan M

2018-05-11

Chromosome rearrangements are large-scale structural variants that are recognized drivers of oncogenic events in cancers of all types. Cytogenetics allows for their rapid, genome-wide detection, but does not provide gene-level resolution. Massively parallel sequencing (MPS) promises DNA sequence-level characterization of the specific breakpoints involved, but is strongly influenced by bioinformatics filters that affect detection efficiency. We sought to characterize the breakpoint junctions of chromosomal translocations and inversions in the clonal derivatives of human cells exposed to ionizing radiation. Here, we describe the first successful use of DNA paired-end analysis to locate and sequence across the breakpoint junctions of a radiation-induced reciprocal translocation. The analyses employed, with varying degrees of success, several well-known bioinformatics algorithms, a task made difficult by the involvement of repetitive DNA sequences. As for underlying mechanisms, the results of Sanger sequencing suggested that the translocation in question was likely formed via microhomology-mediated non-homologous end joining (mmNHEJ). To our knowledge, this represents the first use of MPS to characterize the breakpoint junctions of a radiation-induced chromosomal translocation in human cells. Curiously, these same approaches were unsuccessful when applied to the analysis of inversions previously identified by directional genomic hybridization (dGH). We conclude that molecular cytogenetics continues to provide critical guidance for structural variant discovery, validation and in "tuning" analysis filters to enable robust breakpoint identification at the base pair level.

Design of multiple sequence alignment algorithms on parallel, distributed memory supercomputers.

PubMed

Church, Philip C; Goscinski, Andrzej; Holt, Kathryn; Inouye, Michael; Ghoting, Amol; Makarychev, Konstantin; Reumann, Matthias

2011-01-01

The challenge of comparing two or more genomes that have undergone recombination and substantial amounts of segmental loss and gain has recently been addressed for small numbers of genomes. However, datasets of hundreds of genomes are now common and their sizes will only increase in the future. Multiple sequence alignment of hundreds of genomes remains an intractable problem due to quadratic increases in compute time and memory footprint. To date, most alignment algorithms are designed for commodity clusters without parallelism. Hence, we propose the design of a multiple sequence alignment algorithm on massively parallel, distributed memory supercomputers to enable research into comparative genomics on large data sets. Following the methodology of the sequential progressiveMauve algorithm, we design data structures including sequences and sorted k-mer lists on the IBM Blue Gene/P supercomputer (BG/P). Preliminary results show that we can reduce the memory footprint so that we can potentially align over 250 bacterial genomes on a single BG/P compute node. We verify our results on a dataset of E.coli, Shigella and S.pneumoniae genomes. Our implementation returns results matching those of the original algorithm but in 1/2 the time and with 1/4 the memory footprint for scaffold building. In this study, we have laid the basis for multiple sequence alignment of large-scale datasets on a massively parallel, distributed memory supercomputer, thus enabling comparison of hundreds instead of a few genome sequences within reasonable time.

The Spectral Energy Distribution of the Earliest Phases of Massive Star Formation from the Spizter and Herschel Archives

NASA Astrophysics Data System (ADS)

Klein, Randolf; Looney, Leslie; Henning, Thomas; Chakrabarti, Sukanya; Shenoy, Sachin

2015-08-01

Infrared Dark Clouds (IRDCs) are very good candidates for the earliest phases of massive star formation, but can only be found in regions with high infrared background. We have searched for early phases among cold and massive (M>100M⊙) cloud cores by selecting cores from millimeter continuum surveys (Faundez et al. 2004, Sridharan et al. 2005, Klein et al. 2005, Beltran et al. 2006) without associations at short wavelengths. We compared the millimeter continuum peak positions with IR and radio catalogs (2MASS, MSX, IRAS, and NVSS) and excluded cores that had sources associated with the cores' peaks. We compiled a list of 173 cores in over 117 regions that are candidates for very early phases of Massive Star Formation (MSF). Now with the Spitzer and Herschel archives, these cores can be characterized further. The GLIMPSE and MIPSGAL programs alone covered 86 of these regions. The Herschel Archive adds even longer wavelengths. We are compiling this data set to construct the complete spectral energy distribution (SED) in the mid- and far-infrared with good spatial resolution and broad spectral coverage. This allow us to disentangle the complex regions and model the SED of the deeply embedded protostars/clusters.We will be presenting the IR properties of all cores and their embedded source, attempt a characterization, and order the cores in an evolutionary sequence. The resulting properties can be compared to e.g. IRDCs, a class of objects suggested to be the earliest stages of MSF. With the relative large number of cores, we can try to answer questions like: How homogeneous or diverse are our regions in terms of their evolutionary stage? Where do our embedded sources fit in the evolutionary sequence of IRDCs, hot molecular cores, ultra-compact HII regions, etc? How is the MSF shaping the environment and vice versa? Can we extrapolate to the initial conditions of MSF using our evolutionary sequence?

Evolutionary paths among different red galaxy types at 0.3 < z < 1.5 and the build-up of massive E-S0's

NASA Astrophysics Data System (ADS)

Gallego, Jesús; Prieto, Mercedes; Eliche-Moral, M. Carmen; Balcells, Marc; Cristóbal-Hornillos, David; Erwin, Peter; Abreu, David; Domínguez-Palmero, Lilian; Hempel, Angela; López-Sanjuan, Carlos; Guzmán, Rafael; Pérez-González, Pablo G.; Barro, Guillermo; Zamorano, Jaime

2013-07-01

Some recent observations seem to disagree with hierarchical theories of galaxy formation on the role of major mergers in a late build-up of massive early-type galaxies. We re-address this question by analysing the morphology, structural distortion level, and star formation enhancement of a sample of massive galaxies (M* > 5 × 1010M⊙) lying on the Red Sequence and its surroundings at 0.3 < z < 1.5. We have used an initial sample of ~1800 sources with Ks < 20.5 mag over an area ~155 arcmin2 on the Groth Strip, combining data from the Rainbow Extragalactic Database and the GOYA Survey. Red galaxy classes that can be directly associated to intermediate stages of major mergers and to their final products have been defined. For the first time we report observationally the existence of a dominant evolutionary path among massive red galaxies at 0.6 < z < 1.5, consisting in the conversion of irregular disks into irregular spheroids, and of these ones into regular spheroids. This result points to: 1) the massive red regular galaxies at low redshifts derive from the irregular ones populating the Red Sequence and its neighbourhood at earlier epochs up to z ~ 1.5; 2) the progenitors of the bulk of present-day massive red regular galaxies have been blue disks that have migrated to the Red Sequence majoritarily through major mergers at 0.6 < z < 1.2 (these mergers thus starting at z ~ 1.5); 3) the formation of E-S0's that end up with M* > 1011M⊙ at z = 0 through gas-rich major mergers has frozen since z ~ 0.6. Our results support that major mergers have played the dominant role in the definitive build-up of present-day E-S0's with M* > 1011M⊙ at 0.6 < z < 1.2, in good agreement with the hierarchical scenario proposed in the Eliche-Moral et al. (2010a) model (see also Eliche-Moral et al. 2010b). This study is published in Prieto et al. (2012). Supported by the Spanish Ministry of Science and Innovation (MICINN) under projects AYA2009-10368, AYA2006-12955, AYA2010-21887-C04-04, and AYA2009-11137, by the Madrid Regional Government through the AstroMadrid Project (CAM S2009/ESP-1496), and by the Spanish MICINN under the Consolider-Ingenio 2010 Program grant CSD2006-00070: ``First Science with the GTC'' (http://www.iac.es/consolider-ingenio-gtc/). S. D. H. & G.

MPRAnator: a web-based tool for the design of massively parallel reporter assay experiments

PubMed Central

Georgakopoulos-Soares, Ilias; Jain, Naman; Gray, Jesse M; Hemberg, Martin

2017-01-01

Motivation: With the rapid advances in DNA synthesis and sequencing technologies and the continuing decline in the associated costs, high-throughput experiments can be performed to investigate the regulatory role of thousands of oligonucleotide sequences simultaneously. Nevertheless, designing high-throughput reporter assay experiments such as massively parallel reporter assays (MPRAs) and similar methods remains challenging. Results: We introduce MPRAnator, a set of tools that facilitate rapid design of MPRA experiments. With MPRA Motif design, a set of variables provides fine control of how motifs are placed into sequences, thereby allowing the investigation of the rules that govern transcription factor (TF) occupancy. MPRA single-nucleotide polymorphism design can be used to systematically examine the functional effects of single or combinations of single-nucleotide polymorphisms at regulatory sequences. Finally, the Transmutation tool allows for the design of negative controls by permitting scrambling, reversing, complementing or introducing multiple random mutations in the input sequences or motifs. Availability and implementation: MPRAnator tool set is implemented in Python, Perl and Javascript and is freely available at www.genomegeek.com and www.sanger.ac.uk/science/tools/mpranator. The source code is available on www.github.com/hemberg-lab/MPRAnator/ under the MIT license. The REST API allows programmatic access to MPRAnator using simple URLs. Contact: igs@sanger.ac.uk or mh26@sanger.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online. PMID:27605100

MPRAnator: a web-based tool for the design of massively parallel reporter assay experiments.

PubMed

Georgakopoulos-Soares, Ilias; Jain, Naman; Gray, Jesse M; Hemberg, Martin

2017-01-01

With the rapid advances in DNA synthesis and sequencing technologies and the continuing decline in the associated costs, high-throughput experiments can be performed to investigate the regulatory role of thousands of oligonucleotide sequences simultaneously. Nevertheless, designing high-throughput reporter assay experiments such as massively parallel reporter assays (MPRAs) and similar methods remains challenging. We introduce MPRAnator, a set of tools that facilitate rapid design of MPRA experiments. With MPRA Motif design, a set of variables provides fine control of how motifs are placed into sequences, thereby allowing the investigation of the rules that govern transcription factor (TF) occupancy. MPRA single-nucleotide polymorphism design can be used to systematically examine the functional effects of single or combinations of single-nucleotide polymorphisms at regulatory sequences. Finally, the Transmutation tool allows for the design of negative controls by permitting scrambling, reversing, complementing or introducing multiple random mutations in the input sequences or motifs. MPRAnator tool set is implemented in Python, Perl and Javascript and is freely available at www.genomegeek.com and www.sanger.ac.uk/science/tools/mpranator The source code is available on www.github.com/hemberg-lab/MPRAnator/ under the MIT license. The REST API allows programmatic access to MPRAnator using simple URLs. igs@sanger.ac.uk or mh26@sanger.ac.ukSupplementary information: Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

Molecular differentiation and phylogenetic analysis of the Egyptian foot-and-mouth disease virus SAT2.

PubMed

El-Shehawy, Laila I; Abu-Elnaga, Hany I; Rizk, Sonia A; Abd El-Kreem, Ahmed S; Mohamed, A A; Fawzy, Hossam G

2014-03-01

In February 2012, a massive new foot-and-mouth disease (FMD) outbreak struck Egypt. In this work, one-step RT-PCR assays were used for in-house detection and differentiation of foot-and-mouth disease virus (FMDV) in Egypt in this year using pan-serotypic and serotype-targeting sequence primers. FMDV SAT2 was the dominant virus in the examined isolates from the epidemic. The complete VP1 coding regions of two isolates were sequenced. The two isolates had 99.2 % sequence identity to most contemporary Egyptian SAT2 reference viruses, whereas they had 89.7-90.1 % identity to the SAT2/EGY/2/2012 isolate, which was collected from Alexandria, Egypt, and previously sequenced by WRLFMD. Phylogenetic analysis showed that Egypt had one topotype and two lineage of FMDV SAT2 in 2012. The Egyptian and the Palestinian 2012 strains were associated mainly with topotype VII, lineage SAT2/VII/Ghb-12, while the virus isolated from Alexandria Governorate belonged to the SAT2/VII/Alx-12 lineage. Topotype VII also comprised lineages that included strains isolated from Libya in 2012 and 2003. Furthermore, within the same topotype, the Egyptian SAT2/2012 isolates were related to strains from Saudi Arabia, Sudan, Eritrea, Cameroon and Nigeria. Nevertheless, more epidemiological work with neighboring countries is needed to prevent cross-border spread of disease and to reach a precise conclusion about the origin of the 2012 FMDV SAT2 emergency in the Middle East.

Dust Attenuation, Bulge Formation, and Inside-out Quenching of Star Formation in Star-forming Main Sequence Galaxies at z ∼ 2

NASA Astrophysics Data System (ADS)

Tacchella, S.; Carollo, C. M.; Förster Schreiber, N. M.; Renzini, A.; Dekel, A.; Genzel, R.; Lang, P.; Lilly, S. J.; Mancini, C.; Onodera, M.; Tacconi, L. J.; Wuyts, S.; Zamorani, G.

2018-05-01

We derive 2D dust attenuation maps at ∼1 kpc resolution from the UV continuum for 10 galaxies on the z ∼ 2 star-forming main sequence (SFMS). Comparison with IR data shows that 9 out of 10 galaxies do not require further obscuration in addition to the UV-based correction, though our sample does not include the most heavily obscured, massive galaxies. The individual rest-frame V-band dust attenuation (A V) radial profiles scatter around an average profile that gently decreases from ∼1.8 mag in the center down to ∼0.6 mag at ∼3–4 half-mass radii. We use these maps to correct UV- and Hα-based star formation rates (SFRs), which agree with each other. At masses ≲ {10}11 {M}ȯ , the dust-corrected specific SFR (sSFR) profiles are on average radially constant at a mass-doubling timescale of ∼300 Myr, pointing at a synchronous growth of bulge and disk components. At masses ≳ {10}11 {M}ȯ , the sSFR profiles are typically centrally suppressed by a factor of ∼10 relative to the galaxy outskirts. With total central obscuration disfavored, this indicates that at least a fraction of massive z ∼ 2 SFMS galaxies have started their inside-out star formation quenching that will move them to the quenched sequence. In combination with other observations, galaxies above and below the ridge of the SFMS relation have, respectively, centrally enhanced and centrally suppressed sSFRs relative to their outskirts, supporting a picture where bulges are built owing to gas “compaction” that leads to a high central SFR as galaxies move toward the upper envelope of the SFMS. Based on observations made with the NASA/ESA Hubble Space Telescope, obtained at the Space Telescope Science Institute, which is operated under NASA contract NAS 5‑26555 (programs GO9822, GO10092, GO10924, GO11694, GO12578, GO12060, GO12061, GO12062, GO12063, GO12064, GO12440, GO12442, GO12443, GO12444, GO12445, GO13669), and at the Very Large Telescope of the European Southern Observatory, Paranal, Chile (ESO Programme IDs 075.A-0466, 076.A-0527, 079.A-0341, 080.A-0330, 080.A-0339, 080.A-0635, 081.A-0672, 183.A-0781, 087.A-0081, 088.A-0202, 088.A-0209, 091.A-0126).

Tracing sources of crustal contamination using multiple S and Fe isotopes in the Hart komatiite-associated Ni-Cu-PGE sulfide deposit, Abitibi greenstone belt, Ontario, Canada

NASA Astrophysics Data System (ADS)

Hiebert, R. S.; Bekker, A.; Houlé, M. G.; Wing, B. A.; Rouxel, O. J.

2016-10-01

Assimilation by mafic to ultramafic magmas of sulfur-bearing country rocks is considered an important contributing factor to reach sulfide saturation and form magmatic Ni-Cu-platinum group element (PGE) sulfide deposits. Sulfur-bearing sedimentary rocks in the Archean are generally characterized by mass-independent fractionation of sulfur isotopes that is a result of atmospheric photochemical reactions, which produces isotopically distinct pools of sulfur. Likewise, low-temperature processing of iron, through biological and abiotic redox cycling, produces a range of Fe isotope values in Archean sedimentary rocks that is distinct from the range of the mantle and magmatic Fe isotope values. Both of these signals can be used to identify potential country rock assimilants and their contribution to magmatic sulfide deposits. We use multiple S and Fe isotopes to characterize the composition of the potential iron and sulfur sources for the sulfide liquids that formed the Hart deposit in the Shaw Dome area within the Abitibi greenstone belt in Ontario (Canada). The Hart deposit is composed of two zones with komatiite-associated Ni-Cu-PGE mineralization; the main zone consists of a massive sulfide deposit at the base of the basal flow in the komatiite sequence, whereas the eastern extension consists of a semi-massive sulfide zone located 12 to 25 m above the base of the second flow in the komatiite sequence. Low δ56Fe values and non-zero δ34S and Δ33S values of the komatiitic rocks and associated mineralization at the Hart deposit is best explained by mixing and isotope exchange with crustal materials, such as exhalite and graphitic argillite, rather than intrinsic fractionation within the komatiite. This approach allows tracing the extent of crustal contamination away from the deposit and the degree of mixing between the sulfide and komatiite melts. The exhalite and graphitic argillite were the dominant contaminants for the main zone of mineralization and the eastern extension zone of the Hart deposit, respectively. Critically, the extent of contamination, as revealed by multiple S and Fe isotope systematics, is greatest within the deposit and decreases away from it within the komatiite flow. This pattern points to a local source of crustal contamination for the mantle-derived komatiitic melt and a low degree of homogenization between the mineralization and the surrounding lava flow. Coupled S and Fe isotope patterns like those identified at the Hart deposit may provide a useful tool for assessing the potential of a komatiitic sequence to host Ni-Cu-(PGE).

First direct observation of the link between supercritical flow processes, crescent-shape bedforms and massive sand deposits

NASA Astrophysics Data System (ADS)

Hage, Sophie; Cartigny, Matthieu; Clare, Michael; Sumner, Esther; Talling, Peter; Vendettuoli, Daniela; Hughes Clarke, John; Hubbard, Stephen

2017-04-01

Massive sandstones have been studied in many outcrops worldwide as they form a building stone of good subsurface petroleum reservoirs. Massive sands are often associated with turbidites sequences in ancient sedimentary successions. Turbidites are widely known to result from the deceleration of turbidity currents, these underwater flows driven by the excess density of sediments they carry in suspension. Depositional processes that are associated with the formation of massive sands are still under debate in the literature and many theoretical mechanisms have been suggested based on outcrops interpretations, lab experiments and numerical models. Here we present the first field observations that show how massive sands are generated from flow instabilities associated with supercritical flow processes occurring in turbidity currents. We combine turbidity current measurements with seafloor topography observations on the active Squamish Delta, British Columbia (Canada). We show that supercritical flow processes shape crescent-shape bedforms on the seafloor, and how these crescent-shape bedforms are built by massive sands. This modern process-product link is then used to interpret massive sandstone successions found in ancient outcrops. We demonstrate that supercritical-flow processes can be recognised in outcrops and that these processes produce highly diachronous stratigraphic surfaces in the rock record. This has profound implications on how to interpret ancient geological successions and the Earth history they archive.

Diagenetic history of late Oligocene-early Miocene carbonates in East Sabah, Malaysia

NASA Astrophysics Data System (ADS)

Zainal Abidin, N. S.; Raymond, R. R.; Bashah, N. S. I.

2017-10-01

Limestones are particularly susceptible to drastic early diagenesis modifications, mainly cementation and dissolution. During the early Miocene, a major tectonic deformation has caused a widespread of uplift in Sabah. This has resulted change in depositional environment from deep to shallow marine, which favours the deposition of Gomantong Limestone. This study aims to investigate the diagenetic history of Gomantong Limestone in East Sabah. Thorough understanding of the diagenetic processes may provide data to unravel the tectonic activities which affected the reservoir quality of the carbonates. Combining the data from comprehensive petrographic analysis, and Scanning Electron Microscopy (SEM) of 30 samples, two main cements type were identified. These are microcrystalline cement and Mg-calcite cement of granular and blocky mosaics which are dominantly seen in all samples. The sequence of diagenesis events are determined as (1) micritization; (2) grain scale compaction; (3) cementation (pore-filling); (4) mechanical compaction and cementation infilling fractures and (5) chemical compaction. These diagenetic events are interpreted as reflection of changes in diagenetic environment from shallow marine to deep burial. The massive cementation in the Gomantong Limestone has resulted into a poor reservoir quality.

Modeling and Observations of Debris Disks

NASA Astrophysics Data System (ADS)

Moro-Martín, Amaya

2009-08-01

Debris disks are disks of dust observed around mature main sequence stars (generally A to K2 type). They are evidence that these stars harbor a reservoir of dust-producing plantesimals on spatial scales that are similar to those found for the small-body population of our solar system. Debris disks present a wide range of sizes and structural features (inner cavities, warps, offsets, rings, clumps) and there is growing evidence that, in some cases, they might be the result of the dynamical perturbations of a massive planet. Our solar system also harbors a debris disk and some of its properties resemble those of extra-solar debris disks. The study of these disks can shed light on the diversity of planetary systems and can help us place our solar system into context. This contribution is an introduction to the debris disk phenomenon, including a summary of debris disks main properties (§1-based mostly on results from extensive surveys carried out with Spitzer), and a discussion of what they can teach us about the diversity of planetary systems (§2).

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

Ferraro, F. R.; Dalessandro, E.; Lanzoni, B.

The Galactic bulge is dominated by an old, metal-rich stellar population. The possible presence and the amount of a young (a few gigayears old) minor component is one of the major issues debated in the literature. Recently, the bulge stellar system Terzan 5 was found to harbor three sub-populations with iron content varying by more than one order of magnitude (from 0.2 up to two times the solar value), with chemical abundance patterns strikingly similar to those observed in bulge field stars. Here we report on the detection of two distinct main-sequence turnoff points in Terzan 5, providing the agemore » of the two main stellar populations: 12 Gyr for the (dominant) sub-solar component and 4.5 Gyr for the component at super-solar metallicity. This discovery classifies Terzan 5 as a site in the Galactic bulge where multiple bursts of star formation occurred, thus suggesting a quite massive progenitor possibly resembling the giant clumps observed in star-forming galaxies at high redshifts. This connection opens a new route of investigation into the formation process and evolution of spheroids and their stellar content.« less

Searching for fossil fragments of the Galactic bulge formation process

NASA Astrophysics Data System (ADS)

Ferraro, Francesco

2017-08-01

We have discovered that the stellar system Terzan5 (Ter5) in the Galactic bulge harbors stellar populations with very different IRON content (delta[Fe/H] 1 dex, Ferraro+09, Nature 462, 483) and AGES (12 Gyr and 4.5 Gyr for the sub-solar and super-solar metallicity populations, respectively, Ferraro+16, ApJ,828,75). This evidence demonstrates that Ter5 is not a globular cluster, and identifies it as (1) a site in the Galactic bulge where recent star formation occurred, and (2) the remnant of a massive system able to retain the iron-enriched gas ejected by violent supernova explosions. The striking chemical similarity between Ter5 and the bulge opens the fascinating possibility that we discovered the fossil remnant of a pristine massive structure that could have contributed to the Galactic bulge assembly.Prompted by this finding, here we propose to secure deep HST optical observations for the bulge stellar system Liller1, that shows a similar complexity as Ter5, with evidence of two stellar populations with different iron content. The immediate goal is to properly explore the main sequence turnoff region of the system for unveiling possible splits due to stellar populations of different ages. As demonstrated by our experience with Ter5, the requested HST observations, in combination with the K-band diffraction limited images that we already secured with GeMS-Gemini, are essential to achieve this goal.The project will allow us to establish if other fossil remnants of the bulge formation epoch do exist, thus probing that the merging of pre-evolved massive structures has been an important channel for the formation of the Galactic bulge.

Age gradients in the stellar populations of massive star forming regions based on a new stellar chronometer

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

Getman, Konstantin V.; Feigelson, Eric D.; Kuhn, Michael A.

2014-06-01

A major impediment to understanding star formation in massive star-forming regions (MSFRs) is the absence of a reliable stellar chronometer to unravel their complex star formation histories. We present a new estimation of stellar ages using a new method that employs near-infrared (NIR) and X-ray photometry, Age {sub JX} . Stellar masses are derived from X-ray luminosities using the L{sub X} -M relation from the Taurus cloud. J-band luminosities are compared to mass-dependent pre-main-sequence (PMS) evolutionary models to estimate ages. Age {sub JX} is sensitive to a wide range of evolutionary stages, from disk-bearing stars embedded in a cloud tomore » widely dispersed older PMS stars. The Massive Young Star-Forming Complex Study in Infrared and X-ray (MYStIX) project characterizes 20 OB-dominated MSFRs using X-ray, mid-infrared, and NIR catalogs. The Age {sub JX} method has been applied to 5525 out of 31,784 MYStIX Probable Complex Members. We provide a homogeneous set of median ages for over 100 subclusters in 15 MSFRs; median subcluster ages range between 0.5 Myr and 5 Myr. The important science result is the discovery of age gradients across MYStIX regions. The wide MSFR age distribution appears as spatially segregated structures with different ages. The Age {sub JX} ages are youngest in obscured locations in molecular clouds, intermediate in revealed stellar clusters, and oldest in distributed populations. The NIR color index J – H, a surrogate measure of extinction, can serve as an approximate age predictor for young embedded clusters.« less

Predicting the Presence of Companions for Stripped-envelope Supernovae: The Case of the Broad-lined Type Ic SN 2002ap

NASA Astrophysics Data System (ADS)

Zapartas, E.; de Mink, S. E.; Van Dyk, S. D.; Fox, O. D.; Smith, N.; Bostroem, K. A.; de Koter, A.; Filippenko, A. V.; Izzard, R. G.; Kelly, P. L.; Neijssel, C. J.; Renzo, M.; Ryder, S.

2017-06-01

Many young, massive stars are found in close binaries. Using population synthesis simulations we predict the likelihood of a companion star being present when these massive stars end their lives as core-collapse supernovae (SNe). We focus on stripped-envelope SNe, whose progenitors have lost their outer hydrogen and possibly helium layers before explosion. We use these results to interpret new Hubble Space Telescope observations of the site of the broad-lined Type Ic SN 2002ap, 14 years post-explosion. For a subsolar metallicity consistent with SN 2002ap, we expect a main-sequence (MS) companion present in about two thirds of all stripped-envelope SNe and a compact companion (likely a stripped helium star or a white dwarf/neutron star/black hole) in about 5% of cases. About a quarter of progenitors are single at explosion (originating from initially single stars, mergers, or disrupted systems). All of the latter scenarios require a massive progenitor, inconsistent with earlier studies of SN 2002ap. Our new, deeper upper limits exclude the presence of an MS companion star >8-10 {M}⊙ , ruling out about 40% of all stripped-envelope SN channels. The most likely scenario for SN 2002ap includes nonconservative binary interaction of a primary star initially ≲ 23 {M}⊙ . Although unlikely (<1% of the scenarios), we also discuss the possibility of an exotic reverse merger channel for broad-lined Type Ic events. Finally, we explore how our results depend on the metallicity and the model assumptions and discuss how additional searches for companions can constrain the physics that govern the evolution of SN progenitors.

Massive black hole factories: Supermassive and quasi-star formation in primordial halos

NASA Astrophysics Data System (ADS)

Schleicher, Dominik R. G.; Palla, Francesco; Ferrara, Andrea; Galli, Daniele; Latif, Muhammad

2013-10-01

Context. Supermassive stars and quasi-stars (massive stars with a central black hole) are both considered as potential progenitors for the formation of supermassive black holes. They are expected to form from rapidly accreting protostars in massive primordial halos. Aims: We explore how long rapidly accreting protostars remain on the Hayashi track, implying large protostellar radii and weak accretion luminosity feedback. We assess the potential role of energy production in the nuclear core, and determine what regulates the evolution of such protostars into quasi-stars or supermassive stars. Methods: We followed the contraction of characteristic mass shells in rapidly accreting protostars, and inferred the timescales for them to reach nuclear densities. We compared the characteristic timescales for nuclear burning with those for which the extended protostellar envelope can be maintained. Results: We find that the extended envelope can be maintained up to protostellar masses of 3.6 × 108 ṁ3 M⊙, where ṁ denotes the accretion rate in solar masses per year. We expect the nuclear core to exhaust its hydrogen content in 7 × 106 yr. If accretion rates ṁ ≫ 0.14 can still be maintained at this point, a black hole may form within the accreting envelope, leading to a quasi-star. Alternatively, the accreting object will gravitationally contract to become a main-sequence supermassive star. Conclusions: Due to the limited gas reservoir in typical 107 M⊙ dark matter halos, the accretion rate onto the central object may drop at late times, implying the formation of supermassive stars as the typical outcome of direct collapse. However, if high accretion rates are maintained, a quasi-star with an interior black hole may form.

Looking for Photometric Signatures of Fast Rotation in Intermediate-Age Star Clusters in the Magellanic Clouds

NASA Astrophysics Data System (ADS)

Goudfrooij, Paul

2017-08-01

Recently, deep color-magnitude diagrams from HST data revealed that several massive intermediate-age star clusters in the Magellanic Clouds exhibit extended main-sequence turn-offs (eMSTOs). This discovery posed serious questions regarding the mechanisms responsible for the formation of massive globular clusters and their well-known multiple stellar populations. The nature of eMSTOs is a hotly debated topic of study. Several studies argued that the eMSTOs are caused by an age range of up to a few hundred Myr, while other studies indicate that eMSTOs can instead be caused by a coeval population in which the stars span a range of rotation velocities. Formal evidence to (dis-)prove either scenario still remains at large, in part because stellar tracks that incorporate the effects of rotation have so far only been available for masses > 1.7 Msun whereas the stars in the known eMSTOs of intermediate-age star clusters are less massive. In this proposal we aim to look for photometric signatures of fast rotators in eMSTO clusters that have been observed by HST in three passbands including (at least) F336W and F814W. We will study spreads in different stellar colors, testing against those predicted with the aid of von Zeipel's geometric study for a population of rotating stars with a significant spread in their inclination. Importantly, this spread due to the presence of rotation is predicted to occur along well-defined lines in color-color diagrams, in directions that are distinct from those in color-magnitude diagrams and distinct from the spread predicted for the age range scenario.

On The Origin Of Two-Shell Supernova Remnants

NASA Astrophysics Data System (ADS)

Gvaramadze, V. V.

2006-08-01

It is known that proper motion of massive stars causes them to explode far from the geometric centers of their wind-driven bubbles and thereby affects the symmetry of the resulting diffuse supernova remnants (SNRs). We use this fact to explain the origin of SNRs consisting of two partially overlapping shells (e.g. 3C 400.2, Cygnus Loop, Kes32, etc.), whose unusual morphology is usually treated in terms of the collision (or superposition) of two separate SNRs or breakout phenomena in a region with a density discontinuity. We propose that a SNR of this type is a natural consequence of an off-centered cavity supernova (SN) explosion of a moving massive star, which ended its evolution near the edge of the main-sequence (MS) wind-driven bubble. Our proposal implies that one of the shells is the former MS bubble reenergized by the SN blast wave. The second shell, however, could originate in two somewhat different ways, depending on the initial mass of the SN progenitor star. It could be a shell swept-up by the SN blast wave expanding through the unperturbed ambient interstellar medium if the massive star ends its evolution as a red supergiant (RSG). Or it could be the remainder of a pre-existing shell (adjacent to the MS bubble) swept-up by the fast progenitor's wind during the late evolutionary phases if after the RSG phase the star evolves through the Wolf-Rayet phase. In both cases the resulting (two-shell) SNR should be associated only with one (young) neutron star (thus one can somewhat improve the statistics of neutron star/SNR associations since the two-shell SNRs are quite numerous). We discuss several criteria to discern the SNRs formed by SN explosion after the RSG or WR phase.

ATLASGAL: Chemical evolution of star forming clumps

NASA Astrophysics Data System (ADS)

Figura, Charles C.; Urquhart, James S.; Wyrowski, Friedrich

2017-01-01

Although massive stars are few in number, they impact their host molecular clouds, clusters, and galaxies in profound ways, playing a vital role in regulating star formation in their host galaxy. Understanding the formation of these massive stars is critical to understanding this evolution, but their rapid early development causes them to reach the main sequence while still shrouded in their natal molecular cloud. Many studies have investigated these regions in a targeted manner, but a full understanding necessitates a broader view at all stages of formation across many star forming regions.We have used mid-infrared continuum surveys to guide selection of a statistically large sample of massive dust clumps from the 10,000 such clumps identified in the ATLASGAL Compact Source Catalogue (CSC), ensuring that all stages of the evolutionary process are included. A final sample of 600 fourth-quadrant sources within 1 degree of the Galactic plane were observed with the Mopra telescope with an 8 GHz bandwidth between 85.2 and 93.4 GHz.We present an overview of our results. We have identified over 30 molecular lines, seven of which with detected hyperfine structure, as well as several mm-radio recombination line transitions. Source velocities indicate that these regions trace the Crux-Scutum, Norma, and Carina Sagitarius arms. We have performed an analysis of linewidth and line intensity ratios, correlating these with star formation stages as identified by IR brightness at the 70 and 24 μm bands, and present several molecular pairs whose linewidth and intensity might serve as significant tracers of the evolutionary stage of star formation. We comment on the results of PCA analysis of the measured parameters for the overall population and the star formation stage subgroups with an eye toward characterising early stellar development through molecular line observations.

Single molecule real-time (SMRT) sequencing comes of age: applications and utilities for medical diagnostics

PubMed Central

Ardui, Simon; Ameur, Adam; Vermeesch, Joris R; Hestand, Matthew S

2018-01-01

Abstract Short read massive parallel sequencing has emerged as a standard diagnostic tool in the medical setting. However, short read technologies have inherent limitations such as GC bias, difficulties mapping to repetitive elements, trouble discriminating paralogous sequences, and difficulties in phasing alleles. Long read single molecule sequencers resolve these obstacles. Moreover, they offer higher consensus accuracies and can detect epigenetic modifications from native DNA. The first commercially available long read single molecule platform was the RS system based on PacBio's single molecule real-time (SMRT) sequencing technology, which has since evolved into their RSII and Sequel systems. Here we capsulize how SMRT sequencing is revolutionizing constitutional, reproductive, cancer, microbial and viral genetic testing. PMID:29401301

Frequency of Usher syndrome type 1 in deaf children by massively parallel DNA sequencing

PubMed Central

Yoshimura, Hidekane; Miyagawa, Maiko; Kumakawa, Kozo; Nishio, Shin-ya; Usami, Shin-ichi

2016-01-01

Usher syndrome type 1 (USH1) is the most severe of the three USH subtypes due to its profound hearing loss, absent vestibular response and retinitis pigmentosa appearing at a prepubescent age. Six causative genes have been identified for USH1, making early diagnosis and therapy possible through DNA testing. Targeted exon sequencing of selected genes using massively parallel DNA sequencing (MPS) technology enables clinicians to systematically tackle previously intractable monogenic disorders and improve molecular diagnosis. Using MPS along with direct sequence analysis, we screened 227 unrelated non-syndromic deaf children and detected recessive mutations in USH1 causative genes in five patients (2.2%): three patients harbored MYO7A mutations and one each carried CDH23 or PCDH15 mutations. As indicated by an earlier genotype–phenotype correlation study of the CDH23 and PCDH15 genes, we considered the latter two patients to have USH1. Based on clinical findings, it was also highly likely that one patient with MYO7A mutations possessed USH1 due to a late onset age of walking. This first report describing the frequency (1.3–2.2%) of USH1 among non-syndromic deaf children highlights the importance of comprehensive genetic testing for early disease diagnosis. PMID:26791358

Frequency of Usher syndrome type 1 in deaf children by massively parallel DNA sequencing.

PubMed

Yoshimura, Hidekane; Miyagawa, Maiko; Kumakawa, Kozo; Nishio, Shin-Ya; Usami, Shin-Ichi

2016-05-01

Usher syndrome type 1 (USH1) is the most severe of the three USH subtypes due to its profound hearing loss, absent vestibular response and retinitis pigmentosa appearing at a prepubescent age. Six causative genes have been identified for USH1, making early diagnosis and therapy possible through DNA testing. Targeted exon sequencing of selected genes using massively parallel DNA sequencing (MPS) technology enables clinicians to systematically tackle previously intractable monogenic disorders and improve molecular diagnosis. Using MPS along with direct sequence analysis, we screened 227 unrelated non-syndromic deaf children and detected recessive mutations in USH1 causative genes in five patients (2.2%): three patients harbored MYO7A mutations and one each carried CDH23 or PCDH15 mutations. As indicated by an earlier genotype-phenotype correlation study of the CDH23 and PCDH15 genes, we considered the latter two patients to have USH1. Based on clinical findings, it was also highly likely that one patient with MYO7A mutations possessed USH1 due to a late onset age of walking. This first report describing the frequency (1.3-2.2%) of USH1 among non-syndromic deaf children highlights the importance of comprehensive genetic testing for early disease diagnosis.

Representing and computing regular languages on massively parallel networks

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

Miller, M.I.; O'Sullivan, J.A.; Boysam, B.

1991-01-01

This paper proposes a general method for incorporating rule-based constraints corresponding to regular languages into stochastic inference problems, thereby allowing for a unified representation of stochastic and syntactic pattern constraints. The authors' approach first established the formal connection of rules to Chomsky grammars, and generalizes the original work of Shannon on the encoding of rule-based channel sequences to Markov chains of maximum entropy. This maximum entropy probabilistic view leads to Gibb's representations with potentials which have their number of minima growing at precisely the exponential rate that the language of deterministically constrained sequences grow. These representations are coupled to stochasticmore » diffusion algorithms, which sample the language-constrained sequences by visiting the energy minima according to the underlying Gibbs' probability law. The coupling to stochastic search methods yields the all-important practical result that fully parallel stochastic cellular automata may be derived to generate samples from the rule-based constraint sets. The production rules and neighborhood state structure of the language of sequences directly determines the necessary connection structures of the required parallel computing surface. Representations of this type have been mapped to the DAP-510 massively-parallel processor consisting of 1024 mesh-connected bit-serial processing elements for performing automated segmentation of electron-micrograph images.« less

Ordered fast fourier transforms on a massively parallel hypercube multiprocessor

NASA Technical Reports Server (NTRS)

Tong, Charles; Swarztrauber, Paul N.

1989-01-01

Design alternatives for ordered Fast Fourier Transformation (FFT) algorithms were examined on massively parallel hypercube multiprocessors such as the Connection Machine. Particular emphasis is placed on reducing communication which is known to dominate the overall computing time. To this end, the order and computational phases of the FFT were combined, and the sequence to processor maps that reduce communication were used. The class of ordered transforms is expanded to include any FFT in which the order of the transform is the same as that of the input sequence. Two such orderings are examined, namely, standard-order and A-order which can be implemented with equal ease on the Connection Machine where orderings are determined by geometries and priorities. If the sequence has N = 2 exp r elements and the hypercube has P = 2 exp d processors, then a standard-order FFT can be implemented with d + r/2 + 1 parallel transmissions. An A-order sequence can be transformed with 2d - r/2 parallel transmissions which is r - d + 1 fewer than the standard order. A parallel method for computing the trigonometric coefficients is presented that does not use trigonometric functions or interprocessor communication. A performance of 0.9 GFLOPS was obtained for an A-order transform on the Connection Machine.

A System Architecture for Efficient Transmission of Massive DNA Sequencing Data.

PubMed

Sağiroğlu, Mahmut Şamİl; Külekcİ, M Oğuzhan

2017-11-01

The DNA sequencing data analysis pipelines require significant computational resources. In that sense, cloud computing infrastructures appear as a natural choice for this processing. However, the first practical difficulty in reaching the cloud computing services is the transmission of the massive DNA sequencing data from where they are produced to where they will be processed. The daily practice here begins with compressing the data in FASTQ file format, and then sending these data via fast data transmission protocols. In this study, we address the weaknesses in that daily practice and present a new system architecture that incorporates the computational resources available on the client side while dynamically adapting itself to the available bandwidth. Our proposal considers the real-life scenarios, where the bandwidth of the connection between the parties may fluctuate, and also the computing power on the client side may be of any size ranging from moderate personal computers to powerful workstations. The proposed architecture aims at utilizing both the communication bandwidth and the computing resources for satisfying the ultimate goal of reaching the results as early as possible. We present a prototype implementation of the proposed architecture, and analyze several real-life cases, which provide useful insights for the sequencing centers, especially on deciding when to use a cloud service and in what conditions.

Metagenomic Sequencing of an Echovirus 30 Genome From Cerebrospinal Fluid of a Patient With Aseptic Meningitis and Orchitis.

PubMed

Piantadosi, Anne; Mukerji, Shibani S; Chitneni, Pooja; Cho, Tracey A; Cosimi, Lisa A; Hung, Deborah T; Goldberg, Marcia B; Sabeti, Pardis C; Kuritzkes, Daniel R; Grad, Yonatan H

2017-01-01

Enteroviruses cause a wide spectrum of clinical disease. In this study, we describe the case of a young man with orchitis and aseptic meningitis who was diagnosed with enterovirus infection. Using unbiased "metagenomic" massively parallel sequencing, we assembled a near-complete viral genome, the first use of this method for full-genome viral sequencing from cerebrospinal fluid. We found that the genome belonged to the subgroup echovirus 30, which is a common cause of aseptic meningitis but has not been previously reported to cause orchitis.

I/O efficient algorithms and applications in geographic information systems

NASA Astrophysics Data System (ADS)

Danner, Andrew

Modern remote sensing methods such a laser altimetry (lidar) and Interferometric Synthetic Aperture Radar (IfSAR) produce georeferenced elevation data at unprecedented rates. Many Geographic Information System (GIS) algorithms designed for terrain modelling applications cannot process these massive data sets. The primary problem is that these data sets are too large to fit in the main internal memory of modern computers and must therefore reside on larger, but considerably slower disks. In these applications, the transfer of data between disk and main memory, or I/O, becomes the primary bottleneck. Working in a theoretical model that more accurately represents this two level memory hierarchy, we can develop algorithms that are I/O-efficient and reduce the amount of disk I/O needed to solve a problem. In this thesis we aim to modernize GIS algorithms and develop a number of I/O-efficient algorithms for processing geographic data derived from massive elevation data sets. For each application, we convert a geographic question to an algorithmic question, develop an I/O-efficient algorithm that is theoretically efficient, implement our approach and verify its performance using real-world data. The applications we consider include constructing a gridded digital elevation model (DEM) from an irregularly spaced point cloud, removing topological noise from a DEM, modeling surface water flow over a terrain, extracting river networks and watershed hierarchies from the terrain, and locating polygons containing query points in a planar subdivision. We initially developed solutions to each of these applications individually. However, we also show how to combine individual solutions to form a scalable geo-processing pipeline that seamlessly solves a sequence of sub-problems with little or no manual intervention. We present experimental results that demonstrate orders of magnitude improvement over previously known algorithms.

Chemical abundances of fast-rotating massive stars . II. Interpretation and comparison with evolutionary models

NASA Astrophysics Data System (ADS)

Cazorla, Constantin; Nazé, Yaël; Morel, Thierry; Georgy, Cyril; Godart, Mélanie; Langer, Norbert

2017-08-01

Aims: Past observations of fast-rotating massive stars exhibiting normal nitrogen abundances at their surface have raised questions about the rotational mixing paradigm. We revisit this question thanks to a spectroscopic analysis of a sample of bright fast-rotating OB stars, with the goal of quantifying the efficiency of rotational mixing at high rotation rates. Methods: Our sample consists of 40 fast rotators on the main sequence, with spectral types comprised between B0.5 and O4. We compare the abundances of some key element indicators of mixing (He, CNO) with the predictions of evolutionary models for single objects and for stars in interacting binary systems. Results: The properties of half of the sample stars can be reproduced by single evolutionary models, even in the case of probable or confirmed binaries that can therefore be true single stars in a pre-interaction configuration. The main problem for the rest of the sample is a mismatch for the [N/O] abundance ratio (we confirm the existence of fast rotators with a lack of nitrogen enrichment) and/or a high helium abundance that cannot be accounted for by models. Modifying the diffusion coefficient implemented in single-star models does not solve the problem as it cannot simultaneously reproduce the helium abundances and [N/O] abundance ratios of our targets. Since part of them actually are binaries, we also compared their chemical properties with predictions for post-mass transfer systems. We found that these models can explain the abundances measured for a majority of our targets, including some of the most helium-enriched, but fail to reproduce them in other cases. Our study thus reveals that some physical ingredients are still missing in current models.

On the Formation of Massive Stars

NASA Technical Reports Server (NTRS)

Yorke, Harold W.; Sonnhalter, Cordula

2002-01-01

We calculate numerically the collapse of slowly rotating, nonmagnetic, massive molecular clumps of masses 30,60, and 120 Stellar Mass, which conceivably could lead to the formation of massive stars. Because radiative acceleration on dust grains plays a critical role in the clump's dynamical evolution, we have improved the module for continuum radiation transfer in an existing two-dimensional (axial symmetry assumed) radiation hydrodynamic code. In particular, rather than using "gray" dust opacities and "gray" radiation transfer, we calculate the dust's wavelength-dependent absorption and emission simultaneously with the radiation density at each wavelength and the equilibrium temperatures of three grain components: amorphous carbon particles. silicates, and " dirty ice " -coated silicates. Because our simulations cannot spatially resolve the innermost regions of the molecular clump, however, we cannot distinguish between the formation of a dense central cluster or a single massive object. Furthermore, we cannot exclude significant mass loss from the central object(s) that may interact with the inflow into the central grid cell. Thus, with our basic assumption that all material in the innermost grid cell accretes onto a single object. we are able to provide only an upper limit to the mass of stars that could possibly be formed. We introduce a semianalytical scheme for augmenting existing evolutionary tracks of pre-main-sequence protostars by including the effects of accretion. By considering an open outermost boundary, an arbitrary amount of material could, in principal, be accreted onto this central star. However, for the three cases considered (30, 60, and 120 Stellar Mass originally within the computation grid), radiation acceleration limited the final masses to 3 1.6, 33.6, and 42.9 Stellar Mass, respectively, for wavelength-dependent radiation transfer and to 19.1, 20.1, and 22.9 Stellar Mass. for the corresponding simulations with gray radiation transfer. Our calculations demonstrate that massive stars can in principle be formed via accretion through a disk. The accretion rate onto the central source increases rapidly after one initial free-fall time and decreases monotonically afterward. By enhancing the nonisotropic character of the radiation field, the accretion disk reduces the effects of radiative acceleration in the radial direction - a process we call the "flashlight effect." The flashlight effect is further amplified in our case by including the effects of frequency-dependent radiation transfer. We conclude with the warning that a careful treatment of radiation transfer is a mandatory requirement for realistic simulations of the formation of massive stars.

High-throughput sequencing of forensic genetic samples using punches of FTA cards with buccal swabs.

PubMed

Kampmann, Marie-Louise; Buchard, Anders; Børsting, Claus; Morling, Niels

2016-01-01

Here, we demonstrate that punches from buccal swab samples preserved on FTA cards can be used for high-throughput DNA sequencing, also known as massively parallel sequencing (MPS). We typed 44 reference samples with the HID-Ion AmpliSeq Identity Panel using washed 1.2 mm punches from FTA cards with buccal swabs and compared the results with those obtained with DNA extracted using the EZ1 DNA Investigator Kit. Concordant profiles were obtained for all samples. Our protocol includes simple punch, wash, and PCR steps, reducing cost and hands-on time in the laboratory. Furthermore, it facilitates automation of DNA sequencing.

Nanopore-CMOS Interfaces for DNA Sequencing

PubMed Central

Magierowski, Sebastian; Huang, Yiyun; Wang, Chengjie; Ghafar-Zadeh, Ebrahim

2016-01-01

DNA sequencers based on nanopore sensors present an opportunity for a significant break from the template-based incumbents of the last forty years. Key advantages ushered by nanopore technology include a simplified chemistry and the ability to interface to CMOS technology. The latter opportunity offers substantial promise for improvement in sequencing speed, size and cost. This paper reviews existing and emerging means of interfacing nanopores to CMOS technology with an emphasis on massively-arrayed structures. It presents this in the context of incumbent DNA sequencing techniques, reviews and quantifies nanopore characteristics and models and presents CMOS circuit methods for the amplification of low-current nanopore signals in such interfaces. PMID:27509529

Nanopore-CMOS Interfaces for DNA Sequencing.

PubMed

Magierowski, Sebastian; Huang, Yiyun; Wang, Chengjie; Ghafar-Zadeh, Ebrahim

2016-08-06

DNA sequencers based on nanopore sensors present an opportunity for a significant break from the template-based incumbents of the last forty years. Key advantages ushered by nanopore technology include a simplified chemistry and the ability to interface to CMOS technology. The latter opportunity offers substantial promise for improvement in sequencing speed, size and cost. This paper reviews existing and emerging means of interfacing nanopores to CMOS technology with an emphasis on massively-arrayed structures. It presents this in the context of incumbent DNA sequencing techniques, reviews and quantifies nanopore characteristics and models and presents CMOS circuit methods for the amplification of low-current nanopore signals in such interfaces.

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

Absolute properties of the eclipsing binary VV CORVI

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

Fekel, Francis C.; Henry, Gregory W.; Sowell, James R., E-mail: fekel@evans.tsuniv.edu, E-mail: gregory.w.henry@gmail.com, E-mail: jim.sowell@physics.gatech.edu

2013-12-01

We have obtained red-wavelength spectroscopy and Johnson B and V differential photoelectric photometry of the eclipsing binary VV Crv = HR 4821. The system is the secondary of the common proper motion double star ADS 8627, which has a separation of 5.''2. VV Crv has an orbital period of 3.144536 days and a low but non-zero eccentricity of 0.085. With the Wilson-Devinney program we have determined a simultaneous solution of our spectroscopic and photometric observations. Those orbital elements produce masses of M {sub 1} = 1.978 ± 0.010 M {sub ☉} and M {sub 2} = 1.513 ± 0.008 Mmore » {sub ☉}, and radii of R {sub 1} = 3.375 ± 0.010 R {sub ☉} and R {sub 2} = 1.650 ± 0.008 R {sub ☉} for the primary and secondary, respectively. The effective temperatures of the two components are 6500 K (fixed) and 6638 K, so the star we call the primary is the more massive but cooler and larger component. A comparison with evolutionary tracks indicates that the components are metal rich with [Fe/H] = 0.3, and the system has an age of 1.2 Gyr. The primary is near the end of its main-sequence lifetime and is rotating significantly faster than its pseudosynchronous velocity. The secondary is still well ensconced on the main sequence and is rotating more slowly than its pseudosynchronous rate.« less

Searching for chemical signatures of brown dwarf formation

NASA Astrophysics Data System (ADS)

Maldonado, J.; Villaver, E.

2017-06-01

Context. Recent studies have shown that close-in brown dwarfs in the mass range 35-55 MJup are almost depleted as companions to stars, suggesting that objects with masses above and below this gap might have different formation mechanisms. Aims: We aim to test whether stars harbouring massive brown dwarfs and stars with low-mass brown dwarfs show any chemical peculiarity that could be related to different formation processes. Methods: Our methodology is based on the analysis of high-resolution échelle spectra (R 57 000) from 2-3 m class telescopes. We determine the fundamental stellar parameters, as well as individual abundances of C, O, Na, Mg, Al, Si, S, Ca, Sc, Ti, V, Cr, Mn, Co, Ni, and Zn for a large sample of stars known to have a substellar companion in the brown dwarf regime. The sample is divided into stars hosting massive and low-mass brown dwarfs. Following previous works, a threshold of 42.5 MJup was considered. The metallicity and abundance trends of the two subsamples are compared and set in the context of current models of planetary and brown dwarf formation. Results: Our results confirm that stars with brown dwarf companions do not follow the well-established gas-giant planet metallicity correlation seen in main-sequence planet hosts. Stars harbouring massive brown dwarfs show similar metallicity and abundance distribution as stars without known planets or with low-mass planets. We find a tendency of stars harbouring less-massive brown dwarfs of having slightly higher metallicity, [XFe/Fe] values, and abundances of Sc II, Mn I, and Ni I than the stars having the massive brown dwarfs. The data suggest, as previously reported, that massive and low-mass brown dwarfs might present differences in period and eccentricity. Conclusions: We find evidence of a non-metallicity dependent mechanism for the formation of massive brown dwarfs. Our results agree with a scenario in which massive brown dwarfs are formed as stars. At high metallicities, the core-accretion mechanism might become efficient in the formation of low-mass brown dwarfs, while at lower metallicities low-mass brown dwarfs could form by gravitational instability in turbulent protostellar discs. Based on observations made with the Mercator Telescope; on observations made with the Nordic Optical Telescope; on data products from the SOPHIE archive; on data products from the ELODIE archive; and on data products from observations made with ESO Telescopes at the La Silla Paranal Observatory under programmes ID 072. C-0488(E), 076.C-0155(A), 076.C-0429(A), 078.C-0133(A), 079.C-0329(A), 082.C-0333(A), 083.C-0174(A), 083.C-0413(A), 085. C-0019(A), 085.C-0393(A), 087.A-9029(A), 087.C-0831(A), 090.C-0421(A), 093.C-0409(A), 094.D-0596(A), 095.A-9029(C), 178.D-0361(B), 183.C-0972(A), 184.C-0639(A), and 188.C-0779(A).

A Study on the Pedagogical Components of Massive Online Courses

ERIC Educational Resources Information Center

Raposo-Rivas, Manuela; Martínez-Figueira, Esther; Campos, Jose Antonio Sarmiento

2015-01-01

At the end of the first decade of the 21st century, the rapid growth in the MOOCs offering brought about a new educational landscape, posing new challenges to teaching and learning, mainly due to massive participation, ubiquity and free enrollment. These courses embody a confluence of technological and pedagogical mediations yet to be fully…

Fast parallel tandem mass spectral library searching using GPU hardware acceleration

PubMed Central

Baumgardner, Lydia Ashleigh; Shanmugam, Avinash Kumar; Lam, Henry; Eng, Jimmy K.; Martin, Daniel B.

2011-01-01

Mass spectrometry-based proteomics is a maturing discipline of biologic research that is experiencing substantial growth. Instrumentation has steadily improved over time with the advent of faster and more sensitive instruments collecting ever larger data files. Consequently, the computational process of matching a peptide fragmentation pattern to its sequence, traditionally accomplished by sequence database searching and more recently also by spectral library searching, has become a bottleneck in many mass spectrometry experiments. In both of these methods, the main rate limiting step is the comparison of an acquired spectrum with all potential matches from a spectral library or sequence database. This is a highly parallelizable process because the core computational element can be represented as a simple but arithmetically intense multiplication of two vectors. In this paper we present a proof of concept project taking advantage of the massively parallel computing available on graphics processing units (GPUs) to distribute and accelerate the process of spectral assignment using spectral library searching. This program, which we have named FastPaSS (for Fast Parallelized Spectral Searching) is implemented in CUDA (Compute Unified Device Architecture) from NVIDIA which allows direct access to the processors in an NVIDIA GPU. Our efforts demonstrate the feasibility of GPU computing for spectral assignment, through implementation of the validated spectral searching algorithm SpectraST in the CUDA environment. PMID:21545112

[Secondary amyloidosis of the bladder and massive hematuria].

PubMed

García-Escudero López, A; Arruza Echevarría, A; Leunda Saizar, J; Infante Riaño, R; Padilla Nieva, J; Ortiz Barredo, E

2010-01-01

To report four additional cases of secondary amyloidosis of the bladder, an extremely rare condition, as shown by the cases reported in the literature. Four clinical cases are reported, all of them occurring as hematuria, which was massive and fulminant and resulted in death in three patients. Secondary amyloidosis of the bladder is of the AA type, which is more common in females and mainly secondary to rheumatoid arthritis, but also to ankylosing spondylitis and long-standing chronic inflammatory conditions. Hematuria is the main and virtually only symptom. A pathological and immunohistochemical study confirmed diagnosis. All three patients who experienced massive, fatal hematuria had an intercurrent condition requiring urethral catheterization, which was the triggering factor. Despite its rarity, as shown by the few cases reported, secondary amyloidosis of the bladder should be considered in patients already diagnosed with systemic amyloidosis and/or the conditions reported who require simple urethral catheterization.

Large scale analysis of the mutational landscape in HT-SELEX improves aptamer discovery

PubMed Central

Hoinka, Jan; Berezhnoy, Alexey; Dao, Phuong; Sauna, Zuben E.; Gilboa, Eli; Przytycka, Teresa M.

2015-01-01

High-Throughput (HT) SELEX combines SELEX (Systematic Evolution of Ligands by EXponential Enrichment), a method for aptamer discovery, with massively parallel sequencing technologies. This emerging technology provides data for a global analysis of the selection process and for simultaneous discovery of a large number of candidates but currently lacks dedicated computational approaches for their analysis. To close this gap, we developed novel in-silico methods to analyze HT-SELEX data and utilized them to study the emergence of polymerase errors during HT-SELEX. Rather than considering these errors as a nuisance, we demonstrated their utility for guiding aptamer discovery. Our approach builds on two main advancements in aptamer analysis: AptaMut—a novel technique allowing for the identification of polymerase errors conferring an improved binding affinity relative to the ‘parent’ sequence and AptaCluster—an aptamer clustering algorithm which is to our best knowledge, the only currently available tool capable of efficiently clustering entire aptamer pools. We applied these methods to an HT-SELEX experiment developing aptamers against Interleukin 10 receptor alpha chain (IL-10RA) and experimentally confirmed our predictions thus validating our computational methods. PMID:25870409

M32 analogs? A population of massive ultra-compact dwarf and compact elliptical galaxies in intermediate-redshift clusters

DOE PAGES

Zhang, Yuanyuan; Bell, Eric F.

2017-01-13

Here, we report the discovery of relatively massive, M32-like ultra compact dwarf (UCD) and compact elliptical (CE) galaxy candidates inmore » $$0.2\\lt z\\lt 0.6$$ massive galaxy clusters imaged by the Cluster Lensing And Supernova survey with Hubble (CLASH) survey. Examining the nearly unresolved objects in the survey, we identify a sample of compact objects concentrated around the cluster central galaxies with colors similar to cluster red sequence galaxies. Their colors and magnitudes suggest stellar masses around $${10}^{9}{M}_{\\odot }$$. More than half of these galaxies have half-light radii smaller than 200 pc, falling into the category of massive UCDs and CEs, with properties similar to M32. The properties are consistent with a tidal stripping origin, but we cannot rule out the possibility that they are early-formed compact objects trapped in massive dark matter halos. The 17 CLASH clusters studied in this work on average contain 2.7 of these objects in their central 0.3 Mpc and 0.6 in their central 50 kpc. Our study demonstrates the possibility of statistically characterizing UCDs/CEs with a large set of uniform imaging survey data.« less

M32 analogs? A population of massive ultra-compact dwarf and compact elliptical galaxies in intermediate-redshift clusters

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

Zhang, Yuanyuan; Bell, Eric F.

Here, we report the discovery of relatively massive, M32-like ultra compact dwarf (UCD) and compact elliptical (CE) galaxy candidates inmore » $$0.2\\lt z\\lt 0.6$$ massive galaxy clusters imaged by the Cluster Lensing And Supernova survey with Hubble (CLASH) survey. Examining the nearly unresolved objects in the survey, we identify a sample of compact objects concentrated around the cluster central galaxies with colors similar to cluster red sequence galaxies. Their colors and magnitudes suggest stellar masses around $${10}^{9}{M}_{\\odot }$$. More than half of these galaxies have half-light radii smaller than 200 pc, falling into the category of massive UCDs and CEs, with properties similar to M32. The properties are consistent with a tidal stripping origin, but we cannot rule out the possibility that they are early-formed compact objects trapped in massive dark matter halos. The 17 CLASH clusters studied in this work on average contain 2.7 of these objects in their central 0.3 Mpc and 0.6 in their central 50 kpc. Our study demonstrates the possibility of statistically characterizing UCDs/CEs with a large set of uniform imaging survey data.« less

Individual Signatures Define Canine Skin Microbiota Composition and Variability

PubMed Central

Cuscó, Anna; Sánchez, Armand; Altet, Laura; Ferrer, Lluís; Francino, Olga

2017-01-01

Dogs present almost all their skin sites covered by hair, but canine skin disorders are more common in certain skin sites and breeds. The goal of our study is to characterize the composition and variability of the skin microbiota in healthy dogs and to evaluate the effect of the breed, the skin site, and the individual. We have analyzed eight skin sites of nine healthy dogs from three different breeds by massive sequencing of 16S rRNA gene V1–V2 hypervariable regions. The main phyla inhabiting the skin microbiota in healthy dogs are Proteobacteria, Firmicutes, Fusobacteria, Actinobacteria, and Bacteroidetes. Our results suggest that skin microbiota composition pattern is individual specific, with some dogs presenting an even representation of the main phyla and other dogs with only a major phylum. The individual is the main force driving skin microbiota composition and diversity rather than the skin site or the breed. The individual is explaining 45% of the distances among samples, whereas skin site explains 19% and breed 9%. Moreover, analysis of similarities suggests a strong dissimilarity among individuals (R = 0.79, P = 0.001) that is mainly explained by low-abundant species in each dog. Skin site also plays a role: inner pinna presents the highest diversity value, whereas perianal region presents the lowest one and the most differentiated microbiota composition. PMID:28220148

Individual Signatures Define Canine Skin Microbiota Composition and Variability.

PubMed

Cuscó, Anna; Sánchez, Armand; Altet, Laura; Ferrer, Lluís; Francino, Olga

2017-01-01

Dogs present almost all their skin sites covered by hair, but canine skin disorders are more common in certain skin sites and breeds. The goal of our study is to characterize the composition and variability of the skin microbiota in healthy dogs and to evaluate the effect of the breed, the skin site, and the individual. We have analyzed eight skin sites of nine healthy dogs from three different breeds by massive sequencing of 16S rRNA gene V1-V2 hypervariable regions. The main phyla inhabiting the skin microbiota in healthy dogs are Proteobacteria, Firmicutes, Fusobacteria, Actinobacteria, and Bacteroidetes. Our results suggest that skin microbiota composition pattern is individual specific, with some dogs presenting an even representation of the main phyla and other dogs with only a major phylum. The individual is the main force driving skin microbiota composition and diversity rather than the skin site or the breed. The individual is explaining 45% of the distances among samples, whereas skin site explains 19% and breed 9%. Moreover, analysis of similarities suggests a strong dissimilarity among individuals ( R  = 0.79, P  = 0.001) that is mainly explained by low-abundant species in each dog. Skin site also plays a role: inner pinna presents the highest diversity value, whereas perianal region presents the lowest one and the most differentiated microbiota composition.

Massively parallel sequencing of 32 forensic markers using the Precision ID GlobalFiler™ NGS STR Panel and the Ion PGM™ System.

PubMed

Wang, Zheng; Zhou, Di; Wang, Hui; Jia, Zhenjun; Liu, Jing; Qian, Xiaoqin; Li, Chengtao; Hou, Yiping

2017-11-01

Massively parallel sequencing (MPS) technologies have proved capable of sequencing the majority of the key forensic STR markers. By MPS, not only the repeat-length size but also sequence variations could be detected. Recently, Thermo Fisher Scientific has designed an advanced MPS 32-plex panel, named the Precision ID GlobalFiler™ NGS STR Panel, where the primer set has been designed specifically for the purpose of MPS technologies and the data analysis are supported by a new version HID STR Genotyper Plugin (V4.0). In this study, a series of experiments that evaluated concordance, reliability, sensitivity of detection, mixture analysis, and the ability to analyze case-type and challenged samples were conducted. In addition, 106 unrelated Han individuals were sequenced to perform genetic analyses of allelic diversity. As expected, MPS detected broader allele variations and gained higher power of discrimination and exclusion rate. MPS results were found to be concordant with current capillary electrophoresis methods, and single source complete profiles could be obtained stably using as little as 100pg of input DNA. Moreover, this MPS panel could be adapted to case-type samples and partial STR genotypes of the minor contributor could be detected up to 19:1 mixture. Aforementioned results indicate that the Precision ID GlobalFiler™ NGS STR Panel is reliable, robust and reproducible and have the potential to be used as a tool for human forensics. Copyright © 2017 Elsevier B.V. All rights reserved.

Lower Cretaceous paleo-Vertisols and sedimentary interrelationships in stacked alluvial sequences, Utah, USA

NASA Astrophysics Data System (ADS)

Joeckel, R. M.; Ludvigson, G. A.; Kirkland, J. I.

2017-11-01

The Yellow Cat Member of the Cedar Mountain Formation in Poison Strip, Utah, USA, consists of stacked, erosionally bounded alluvial sequences dominated by massive mudstones (lithofacies Fm) with paleo-Vertisols. Sediment bodies within these sequences grade vertically and laterally into each other at pedogenic boundaries, across which color, texture, and structures (sedimentary vs. pedogenic) change. Slickensides, unfilled (sealed) cracks, carbonate-filled cracks, and deeper cracks filled with sandstone; the latter features suggest thorough desiccation during aridification. Thin sandstones (Sms) in some sequences, typically as well as laminated to massive mudstones (Flm) with which they are interbedded in some cases, are interpreted as avulsion deposits. The termini of many beds of these lithofacies curve upward, parallel to nearby pedogenic slickensides, as the features we call ;turnups.; Turnups are overlain or surrounded by paleosols, but strata sheltered underneath beds with turnups retain primary sedimentary fabrics. Turnups were produced by movement along slickensides during pedogenesis, by differential compaction alongside pre-existing gilgai microhighs, or by a combination of both. Palustrine carbonates (lithofacies C) appear only in the highest or next-highest alluvial sequences, along with a deep paleo-Vertisol that exhibits partially preserved microrelief at the base of the overlying Poison Strip Member. The attributes of the Yellow Cat Member suggest comparatively low accommodation, slow accumulation, long hiatuses in clastic sedimentation, and substantial time intervals of subaerial exposure and pedogenesis; it appears to be distinct among the members of the Cedar Mountain Formation in these respects.

Massive stellar systems: observational challenges and perspectives in the E-ELT era

NASA Astrophysics Data System (ADS)

Bono, G.; Braga, V. F.; Ferraro, I.; Fiorentino, G.; Gilmozzi, R.; Iannicola, G.; Magurno, D.; Matsunaga, N.; Monelli, M.; Rastello, S.

2017-03-01

We introduce the empirical framework concerning optical and near-infrared (NIR) photometry of crowded stellar fields. In particular, we address the impact that linear detectors and analytical PSF played in improving the accuracy and the precision of multi-band color-magnitude diagrams (CMDs). We focus our attention on recent findings based on deep NIR images collected with Adaptive Optics (AO) systems at the 8-10m class telescopes and discuss pros and cons of the different approaches. We also discuss the estimate of the absolute age of globular clusters using a well defined knee along the lower main sequence. We mention the role which the current AO-assisted instruments will have in addressing longstanding astrophysical problems of the Galactic center. Finally, we outline the role of first generation of E-ELT instruments upon photometry and spectroscopy of crowded stellar fields.

Swift X-Ray Upper Limits on Type Ia Supernova Environments

NASA Technical Reports Server (NTRS)

Russell, B. R.; Immler, S.

2012-01-01

We have considered 53 Type Ia supernovae (SNe Ia) observed by the Swift X-Ray Telescope. None of the SNe Ia are individually detected at any time or in stacked images. Using these data and assuming that the SNe Ia are a homogeneous class of objects, we have calculated upper limits to the X-ray luminosity (0.2-10 keV) and mass-loss rate of L(sub 0.2-10) < 1.7 X 10(exp 38) erg/s and M(dot) < l.l X 10(exp -6) solar M/ yr x (V(sub w))/(10 km/s), respectively. The results exclude massive or evolved stars as the companion objects in SN Ia progenitor systems, but allow the possibility of main sequence or small stars, along with double degenerate systems consisting of two white dwarfs, consistent with results obtained at other wavelengths (e.g., UV, radio) in other studies.

Wolf-Rayet stars, black holes and the first detected gravitational wave source

NASA Astrophysics Data System (ADS)

Bogomazov, A. I.; Cherepashchuk, A. M.; Lipunov, V. M.; Tutukov, A. V.

2018-01-01

The recently discovered burst of gravitational waves GW150914 provides a good new chance to verify the current view on the evolution of close binary stars. Modern population synthesis codes help to study this evolution from two main sequence stars up to the formation of two final remnant degenerate dwarfs, neutron stars or black holes (Masevich and Tutukov, 1988). To study the evolution of the GW150914 predecessor we use the ;Scenario Machine; code presented by Lipunov et al. (1996). The scenario modeling conducted in this study allowed to describe the evolution of systems for which the final stage is a massive BH+BH merger. We find that the initial mass of the primary component can be 100÷140M⊙ and the initial separation of the components can be 50÷350R⊙. Our calculations show the plausibility of modern evolutionary scenarios for binary stars and the population synthesis modeling based on it.

Prospects for detecting decreasing exoplanet frequency with main-sequence age using PLATO

NASA Astrophysics Data System (ADS)

Veras, Dimitri; Brown, David J. A.; Mustill, Alexander J.; Pollacco, Don

2015-10-01

The space mission PLATO will usher in a new era of exoplanetary science by expanding our current inventory of transiting systems and constraining host star ages, which are currently highly uncertain. This capability might allow PLATO to detect changes in planetary system architecture with time, particularly because planetary scattering due to Lagrange instability may be triggered long after the system was formed. Here, we utilize previously published instability time-scale prescriptions to determine PLATO's capability to detect a trend of decreasing planet frequency with age for systems with equal-mass planets. For two-planet systems, our results demonstrate that PLATO may detect a trend for planet masses which are at least as massive as super-Earths. For systems with three or more planets, we link their initial compactness to potentially detectable frequency trends in order to aid future investigations when these populations will be better characterized.

Prospects for detecting decreasing exoplanet frequency with main-sequence age using PLATO

NASA Astrophysics Data System (ADS)

Veras, D.; Brown, D. J. A.; Mustill, A. J.; Pollacco, D.

2017-09-01

The space mission PLATO will usher in a new era of exoplanetary science by expanding our current inventory of transiting systems and constraining host star ages, which are currently highly uncertain. This capability might allow PLATO to detect changes in planetary system architecture with time, particularly because planetary scattering due to Lagrange instability may be triggered long after the system was formed. Here, we utilize previously published instability time-scale prescriptions to determine PLATO's capability to detect a trend of decreasing planet frequency with age for systems with equal- mass planets. For two-planet systems, our results demonstrate that PLATO may detect a trend for planet masses which are at least as massive as super-Earths. For systems with three or more planets, we link their initial compactness to potentially detectable frequency trends in order to aid future investigations when these populations will be better characterized.

Giant Planets: Good Neighbors for Habitable Worlds?

NASA Astrophysics Data System (ADS)

Georgakarakos, Nikolaos; Eggl, Siegfried; Dobbs-Dixon, Ian

2018-04-01

The presence of giant planets influences potentially habitable worlds in numerous ways. Massive celestial neighbors can facilitate the formation of planetary cores and modify the influx of asteroids and comets toward Earth analogs later on. Furthermore, giant planets can indirectly change the climate of terrestrial worlds by gravitationally altering their orbits. Investigating 147 well-characterized exoplanetary systems known to date that host a main-sequence star and a giant planet, we show that the presence of “giant neighbors” can reduce a terrestrial planet’s chances to remain habitable, even if both planets have stable orbits. In a small fraction of systems, however, giant planets slightly increase the extent of habitable zones provided that the terrestrial world has a high climate inertia. In providing constraints on where giant planets cease to affect the habitable zone size in a detrimental fashion, we identify prime targets in the search for habitable worlds.

Kottamia 74-inch telescope discovery of the new eclipsing binary KAO-EGYPT J225702.44+523222.1.: First CCD photometry and light curve analysis

NASA Astrophysics Data System (ADS)

Shokry, A.; Darwish, M. S.; Saad, S. M.; Eldepsy, M.; Zead, I.

2017-08-01

We present the first multicolor CCD photometry for the newly discovered binary system KAO-EGYPT J225702.44+523222.1. New times of light minimum and new ephemeris were obtained. The VR I light curves were analyzed using WD code, the difference in maximum light at phase 0.25 is modeled with a cool spot on the secondary component. The solution show that the system is A-subtype, overcontact binary with fill-out factor = 42% and low mass ratio, q = 0.275. The two components of spectral types K0 and K1 and the primary component is the massive one. The position of both components on the M-L and M-R relations revealed that the primary component is a main sequence star while the secondary is an evolved component.

A detached stellar-mass black hole candidate in the globular cluster NGC 3201

NASA Astrophysics Data System (ADS)

Giesers, Benjamin; Dreizler, Stefan; Husser, Tim-Oliver; Kamann, Sebastian; Anglada Escudé, Guillem; Brinchmann, Jarle; Carollo, C. Marcella; Roth, Martin M.; Weilbacher, Peter M.; Wisotzki, Lutz

2018-03-01

As part of our massive spectroscopic survey of 25 Galactic globular clusters with MUSE, we performed multiple epoch observations of NGC 3201 with the aim of constraining the binary fraction. In this cluster, we found one curious star at the main-sequence turn-off with radial velocity variations of the order of 100 km s- 1, indicating the membership to a binary system with an unseen component since no other variations appear in the spectra. Using an adapted variant of the generalized Lomb-Scargle periodogram, we could calculate the orbital parameters and found the companion to be a detached stellar-mass black hole with a minimum mass of 4.36 ± 0.41 M⊙. The result is an important constraint for binary and black hole evolution models in globular clusters as well as in the context of gravitational wave sources.

Blue Stragglers and Other Stars of Mass Consumption in Globular Clusters

NASA Astrophysics Data System (ADS)

Panurach, Teresa; Leigh, Nathan

2018-01-01

Simulations of globular clusters suggest that collisions between main-sequence (MS) stars happen frequently. Stellar evolution models show that these collision products can be photometrically identified, appearing off the MS locus. These collision products can appear brighter and bluer than the MS turnoff, called “blue stragglers,” or even less massive and redder than the MS. We use proper motion-cleaned photometry from the Hubble Space Telescope of 38 globular clusters to identify candidate collision products. We compare the spectral energy distributions of our candidates to theoretical templates for single and multiple star systems, to constrain the possible presence of a binary companion and test consistency with theoretical stellar evolution models for collision products. For the BSs, we also compare the observed velocities from the proper motion catalog along with mass estimates derived from isochrone-fitting to theoretical predictions for both the collision and binary mass transfer models and find better agreement with the former.

Parallel evolution of the make–accumulate–consume strategy in Saccharomyces and Dekkera yeasts

PubMed Central

Rozpędowska, Elżbieta; Hellborg, Linda; Ishchuk, Olena P.; Orhan, Furkan; Galafassi, Silvia; Merico, Annamaria; Woolfit, Megan; Compagno, Concetta; Piškur, Jure

2011-01-01

Saccharomyces yeasts degrade sugars to two-carbon components, in particular ethanol, even in the presence of excess oxygen. This characteristic is called the Crabtree effect and is the background for the 'make–accumulate–consume' life strategy, which in natural habitats helps Saccharomyces yeasts to out-compete other microorganisms. A global promoter rewiring in the Saccharomyces cerevisiae lineage, which occurred around 100 mya, was one of the main molecular events providing the background for evolution of this strategy. Here we show that the Dekkera bruxellensis lineage, which separated from the Saccharomyces yeasts more than 200 mya, also efficiently makes, accumulates and consumes ethanol and acetic acid. Analysis of promoter sequences indicates that both lineages independently underwent a massive loss of a specific cis-regulatory element from dozens of genes associated with respiration, and we show that also in D. bruxellensis this promoter rewiring contributes to the observed Crabtree effect. PMID:21556056

Two-dimensional models of early-type fast rotating stars: the ESTER project

NASA Astrophysics Data System (ADS)

Rieutord, Michel

In this talk I present the latest results of the ESTER project that has taken up the challenge of building two dimensional (axisymmetric) models of stars rotating at any rotation rate. In particular, I focus on main sequence massive and intermediate mass stars. I show what should be expected in such stars as far as the differential rotation and the associated meridional circulation are concerned, notably the emergence of a Stewartson layer along the tangent cylinder of the core. I also indicate what may be inferred about the evolution of an intermediate-mass star at constant angular momentum and how Be stars may form. I finally give some comparisons between models and observations of the gravity darkening on some nearby fast rotators as it has been derived from interferometric observations. In passing, I also discuss how 2D models can help to recover the fundamental parameters of a star.

COSMIC-LAB: Double BSS sequences as signatures of the Core Collapse phenomenon in star clusters.

NASA Astrophysics Data System (ADS)

Ferraro, Francesco

2011-10-01

Globular Clusters {GCs} are old stellar systems tracing key stages of the star formation and chemical enrichment history of the early Universe and the galaxy assembly phase. As part of a project {COSMIC-LAB} aimed at using GCs as natural laboratories to study the complex interplay between dynamics and stellar evolution, here we present a proposal dealing with the role of Blue Straggler Stars {BSS}.BSS are core-hydrogen burning stars more massive than the main-sequence turnoff population. The canonical scenarios for BSS formation are either the mass transfer between binary companions, or stellar mergers induced by collisions. We have recently discovered two distinct and parallel sequences of BSS in the core of M30 {Ferraro et al. 2009, Nature 462, 1082}. We suggested that each of the two sequences is populated by BSS formed by one of the two processes, both triggered by the cluster core collapse, that, based on the observed BSS properties, must have occurred 1-2 Gyr ago. Following this scenario, we have identified a powerful "clock" to date the occurrence of this key event in the GC history.Here we propose to secure WFC3 images of 4 post-core collapse GCs, reaching S/N=200 at the BSS magnitude level, in order to determine the ubiquity of the BSS double sequence and calibrate the "dynamical clock". This requires very high spatial resolution and very high precision photometry capabilities that are unique to the HST. The modest amount of requested time will have a deep impact on the current and future generations of dynamical evolutionary models of collisional stellar systems.

VirVarSeq: a low-frequency virus variant detection pipeline for Illumina sequencing using adaptive base-calling accuracy filtering.

PubMed

Verbist, Bie M P; Thys, Kim; Reumers, Joke; Wetzels, Yves; Van der Borght, Koen; Talloen, Willem; Aerssens, Jeroen; Clement, Lieven; Thas, Olivier

2015-01-01

In virology, massively parallel sequencing (MPS) opens many opportunities for studying viral quasi-species, e.g. in HIV-1- and HCV-infected patients. This is essential for understanding pathways to resistance, which can substantially improve treatment. Although MPS platforms allow in-depth characterization of sequence variation, their measurements still involve substantial technical noise. For Illumina sequencing, single base substitutions are the main error source and impede powerful assessment of low-frequency mutations. Fortunately, base calls are complemented with quality scores (Qs) that are useful for differentiating errors from the real low-frequency mutations. A variant calling tool, Q-cpileup, is proposed, which exploits the Qs of nucleotides in a filtering strategy to increase specificity. The tool is imbedded in an open-source pipeline, VirVarSeq, which allows variant calling starting from fastq files. Using both plasmid mixtures and clinical samples, we show that Q-cpileup is able to reduce the number of false-positive findings. The filtering strategy is adaptive and provides an optimized threshold for individual samples in each sequencing run. Additionally, linkage information is kept between single-nucleotide polymorphisms as variants are called at the codon level. This enables virologists to have an immediate biological interpretation of the reported variants with respect to their antiviral drug responses. A comparison with existing SNP caller tools reveals that calling variants at the codon level with Q-cpileup results in an outstanding sensitivity while maintaining a good specificity for variants with frequencies down to 0.5%. The VirVarSeq is available, together with a user's guide and test data, at sourceforge: http://sourceforge.net/projects/virtools/?source=directory. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Large-scale transcriptome characterization and mass discovery of SNPs in globe artichoke and its related taxa.

PubMed

Scaglione, Davide; Lanteri, Sergio; Acquadro, Alberto; Lai, Zhao; Knapp, Steven J; Rieseberg, Loren; Portis, Ezio

2012-10-01

Cynara cardunculus (2n = 2× = 34) is a member of the Asteraceae family that contributes significantly to the agricultural economy of the Mediterranean basin. The species includes two cultivated varieties, globe artichoke and cardoon, which are grown mainly for food. Cynara cardunculus is an orphan crop species whose genome/transcriptome has been relatively unexplored, especially in comparison to other Asteraceae crops. Hence, there is a significant need to improve its genomic resources through the identification of novel genes and sequence-based markers, to design new breeding schemes aimed at increasing quality and crop productivity. We report the outcome of cDNA sequencing and assembly for eleven accessions of C. cardunculus. Sequencing of three mapping parental genotypes using Roche 454-Titanium technology generated 1.7 × 10⁶ reads, which were assembled into 38,726 reference transcripts covering 32 Mbp. Putative enzyme-encoding genes were annotated using the KEGG-database. Transcription factors and candidate resistance genes were surveyed as well. Paired-end sequencing was done for cDNA libraries of eight other representative C. cardunculus accessions on an Illumina Genome Analyzer IIx, generating 46 × 10⁶ reads. Alignment of the IGA and 454 reads to reference transcripts led to the identification of 195,400 SNPs with a Bayesian probability exceeding 95%; a validation rate of 90% was obtained by Sanger-sequencing of a subset of contigs. These results demonstrate that the integration of data from different NGS platforms enables large-scale transcriptome characterization, along with massive SNP discovery. This information will contribute to the dissection of key agricultural traits in C. cardunculus and facilitate the implementation of marker-assisted selection programs. © 2012 The Authors. Plant Biotechnology Journal © 2012 Society for Experimental Biology, Association of Applied Biologists and Blackwell Publishing Ltd.

Dichotomy Boundary at Aeolis Mensae, Mars: Fretted Terrain Developed in a Sedimentary Deposit

NASA Astrophysics Data System (ADS)

Irwin, R. P., III; Watters, T. R.; Howard, A. D.; Maxwell, T. A.; Craddock, R. A.

2003-03-01

Fretted terrain in Aeolis Mensae, Mars, developed in a sedimentary deposit. A thick, massive unit with a capping layer or duricrust overlies a more durable layered sequence. Wind, collapse, and minor fluvial activity contributed to degradation.

Mycotoxins: A fungal genomics perspective

USDA-ARS?s Scientific Manuscript database

The chemical and enzymatic diversity in the fungal kingdom is staggering. Large-scale fungal genome sequencing projects are generating a massive catalog of secondary metabolite biosynthetic genes and pathways. Fungal natural products are a boon and bane to man as valuable pharmaceuticals and harmful...

Microtubule Actin Crosslinking Factor 1 Regulates the Balbiani Body and Animal-Vegetal Polarity of the Zebrafish Oocyte

PubMed Central

Gupta, Tripti; Marlow, Florence L.; Ferriola, Deborah; Mackiewicz, Katarzyna; Dapprich, Johannes; Monos, Dimitri; Mullins, Mary C.

2010-01-01

Although of fundamental importance in developmental biology, the genetic basis for the symmetry breaking events that polarize the vertebrate oocyte and egg are largely unknown. In vertebrates, the first morphological asymmetry in the oocyte is the Balbiani body, a highly conserved, transient structure found in vertebrates and invertebrates including Drosophila, Xenopus, human, and mouse. We report the identification of the zebrafish magellan (mgn) mutant, which exhibits a novel enlarged Balbiani body phenotype and a disruption of oocyte polarity. To determine the molecular identity of the mgn gene, we positionally cloned the gene, employing a novel DNA capture method to target region-specific genomic DNA of 600 kb for massively parallel sequencing. Using this technique, we were able to enrich for the genomic region linked to our mutation within one week and then identify the mutation in mgn using massively parallel sequencing. This is one of the first successful uses of genomic DNA enrichment combined with massively parallel sequencing to determine the molecular identity of a gene associated with a mutant phenotype. We anticipate that the combination of these technologies will have wide applicability for the efficient identification of mutant genes in all organisms. We identified the mutation in mgn as a deletion in the coding sequence of the zebrafish microtubule actin crosslinking factor 1 (macf1) gene. macf1 is a member of the highly conserved spectraplakin family of cytoskeletal linker proteins, which play diverse roles in polarized cells such as neurons, muscle cells, and epithelial cells. In mgn mutants, the oocyte nucleus is mislocalized; and the Balbiani body, localized mRNAs, and organelles are absent from the periphery of the oocyte, consistent with a function for macf1 in nuclear anchoring and cortical localization. These data provide the first evidence for a role for spectraplakins in polarization of the vertebrate oocyte and egg. PMID:20808893

Microtubule actin crosslinking factor 1 regulates the Balbiani body and animal-vegetal polarity of the zebrafish oocyte.

PubMed

Gupta, Tripti; Marlow, Florence L; Ferriola, Deborah; Mackiewicz, Katarzyna; Dapprich, Johannes; Monos, Dimitri; Mullins, Mary C

2010-08-19

Although of fundamental importance in developmental biology, the genetic basis for the symmetry breaking events that polarize the vertebrate oocyte and egg are largely unknown. In vertebrates, the first morphological asymmetry in the oocyte is the Balbiani body, a highly conserved, transient structure found in vertebrates and invertebrates including Drosophila, Xenopus, human, and mouse. We report the identification of the zebrafish magellan (mgn) mutant, which exhibits a novel enlarged Balbiani body phenotype and a disruption of oocyte polarity. To determine the molecular identity of the mgn gene, we positionally cloned the gene, employing a novel DNA capture method to target region-specific genomic DNA of 600 kb for massively parallel sequencing. Using this technique, we were able to enrich for the genomic region linked to our mutation within one week and then identify the mutation in mgn using massively parallel sequencing. This is one of the first successful uses of genomic DNA enrichment combined with massively parallel sequencing to determine the molecular identity of a gene associated with a mutant phenotype. We anticipate that the combination of these technologies will have wide applicability for the efficient identification of mutant genes in all organisms. We identified the mutation in mgn as a deletion in the coding sequence of the zebrafish microtubule actin crosslinking factor 1 (macf1) gene. macf1 is a member of the highly conserved spectraplakin family of cytoskeletal linker proteins, which play diverse roles in polarized cells such as neurons, muscle cells, and epithelial cells. In mgn mutants, the oocyte nucleus is mislocalized; and the Balbiani body, localized mRNAs, and organelles are absent from the periphery of the oocyte, consistent with a function for macf1 in nuclear anchoring and cortical localization. These data provide the first evidence for a role for spectraplakins in polarization of the vertebrate oocyte and egg.

The dependence of galaxy clustering on stellar mass, star-formation rate and redshift at z = 0.8-2.2, with HiZELS

NASA Astrophysics Data System (ADS)

Cochrane, R. K.; Best, P. N.; Sobral, D.; Smail, I.; Geach, J. E.; Stott, J. P.; Wake, D. A.

2018-04-01

The deep, near-infrared narrow-band survey HiZELS has yielded robust samples of H α-emitting star-forming galaxies within narrow redshift slices at z = 0.8, 1.47 and 2.23. In this paper, we distinguish the stellar mass and star-formation rate (SFR) dependence of the clustering of these galaxies. At high stellar masses (M*/M⊙ ≳ 2 × 1010), where HiZELS selects galaxies close to the so-called star-forming main sequence, the clustering strength is observed to increase strongly with stellar mass (in line with the results of previous studies of mass-selected galaxy samples) and also with SFR. These two dependencies are shown to hold independently. At lower stellar masses, however, where HiZELS probes high specific SFR galaxies, there is little or no dependence of the clustering strength on stellar mass, but the dependence on SFR remains: high-SFR low-mass galaxies are found in more massive dark matter haloes than their lower SFR counterparts. We argue that this is due to environmentally driven star formation in these systems. We apply the same selection criteria to the EAGLE cosmological hydrodynamical simulations. We find that, in EAGLE, the high-SFR low-mass galaxies are central galaxies in more massive dark matter haloes, in which the high SFRs are driven by a (halo-driven) increased gas content.

Lower Pliensbachian caldera volcanism in high-obliquity rift systems in the western North Patagonian Massif, Argentina

NASA Astrophysics Data System (ADS)

Benedini, Leonardo; Gregori, Daniel; Strazzere, Leonardo; Falco, Juan I.; Dristas, Jorge A.

2014-12-01

In the Cerro Carro Quebrado and Cerro Catri Cura area, located at the border between the Neuquén Basin and the North Patagonian Massif, the Garamilla Formation is composed of four volcanic stages: 1) andesitic lava-flows related to the beginning of the volcanic system; 2) basal massive lithic breccias that represent the caldera collapse; 3) voluminous, coarse-crystal rich massive lava-like ignimbrites related to multiple, steady eruptions that represent the principal infill of the system; and, finally 4) domes, dykes, lava flows, and lava domes of rhyolitic composition indicative of a post-collapse stage. The analysis of the regional and local structures, as well as, the architectures of the volcanic facies, indicates the existence of a highly oblique rift, with its principal extensional strain in an NNE-SSW direction (˜N10°). The analyzed rocks are mainly high-potassium dacites and rhyolites with trace and RE elements contents of an intraplate signature. The age of these rocks (189 ± 0.76 Ma) agree well with other volcanic sequences of the western North Patagonian Massif, as well as, the Neuquén Basin, indicating that Pliensbachian magmatism was widespread in both regions. The age is also coincident with phase 1 of volcanism of the eastern North Patagonia Massif (188-178 Ma) represented by ignimbrites, domes, and pyroclastic rocks of the Marifil Complex, related to intraplate magmatism.

KMOS{sup 3D} Reveals Low-level Star Formation Activity in Massive Quiescent Galaxies at 0.7 < z < 2.7

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

Belli, Sirio; Genzel, Reinhard; Förster Schreiber, Natascha M.

2017-05-20

We explore the H α emission in the massive quiescent galaxies observed by the KMOS{sup 3D} survey at 0.7 < z < 2.7. The H α line is robustly detected in 20 out of 120 UVJ -selected quiescent galaxies, and we classify the emission mechanism using the H α line width and the [N ii]/H α line ratio. We find that AGNs are likely to be responsible for the line emission in more than half of the cases. We also find robust evidence for star formation activity in nine quiescent galaxies, which we explore in detail. The H α kinematicsmore » reveal rotating disks in five of the nine galaxies. The dust-corrected H α star formation rates are low (0.2–7 M {sub ⊙} yr{sup −1}), and place these systems significantly below the main sequence. The 24 μ m-based, infrared luminosities, instead, overestimate the star formation rates. These galaxies present a lower gas-phase metallicity compared to star-forming objects with similar stellar mass, and many of them have close companions. We therefore conclude that the low-level star formation activity in these nine quiescent galaxies is likely to be fueled by inflowing gas or minor mergers, and could be a sign of rejuvenation events.« less

The fates of Solar system analogues with one additional distant planet

NASA Astrophysics Data System (ADS)

Veras, Dimitri

2016-12-01

The potential existence of a distant planet (`Planet Nine') in the Solar system has prompted a re-think about the evolution of planetary systems. As the Sun transitions from a main-sequence star into a white dwarf, Jupiter, Saturn, Uranus and Neptune are currently assumed to survive in expanded but otherwise unchanged orbits. However, a sufficiently distant and sufficiently massive extra planet would alter this quiescent end scenario through the combined effects of Solar giant branch mass-loss and Galactic tides. Here, I estimate bounds for the mass and orbit of a distant extra planet that would incite future instability in systems with a Sun-like star and giant planets with masses and orbits equivalent to those of Jupiter, Saturn, Uranus and Neptune. I find that this boundary is diffuse and strongly dependent on each of the distant planet's orbital parameters. Nevertheless, I claim that instability occurs more often than not when the planet is as massive as Jupiter and harbours a semimajor axis exceeding about 300 au, or has a mass of a super-Earth and a semimajor axis exceeding about 3000 au. These results hold for orbital pericentres ranging from 100 to at least 400 au. This instability scenario might represent a common occurrence, as potentially evidenced by the ubiquity of metal pollution in white dwarf atmospheres throughout the Galaxy.

How Planet Nine could change the fate of the Solar system

NASA Astrophysics Data System (ADS)

Veras, D.

2017-09-01

The potential existence of a distant planet ('Planet Nine') in the Solar system has prompted a re-think about the evolution of planetary systems. As the Sun transitions from a main-sequence star into a white dwarf, Jupiter, Saturn, Uranus and Neptune are currently assumed to survive in expanded but otherwise unchanged orbits. However, a sufficiently distant and sufficiently massive extra planet would alter this quiescent end scenario through the combined effects of Solar giant branch mass-loss and Galactic tides. Here I estimate bounds for the mass and orbit of a distant extra planet that would incite future instability in systems with a Sun-like star and giant planets with masses and orbits equivalent to those of Jupiter, Saturn, Uranus and Neptune. I find that this boundary is diffuse and strongly dependent on each of the distant planet's orbital parameters. Nevertheless, I claim that instability occurs more often than not when the planet is as massive as Jupiter and harbours a semimajor axis exceeding about 300 au, or has a mass of a super-Earth and a semimajor axis exceeding about 3000 au. These results hold for orbital pericentres ranging from 100 to at least 400 au. This instability scenario might represent a common occurrence, as potentially evidenced by the ubiquity of metal pollution in white dwarf atmospheres throughout the Galaxy.

Rapidly rotating second-generation progenitors for the 'blue hook' stars of ω Centauri.

PubMed

Tailo, Marco; D'Antona, Francesca; Vesperini, Enrico; Di Criscienzo, Marcella; Ventura, Paolo; Milone, Antonino P; Bellini, Andrea; Dotter, Aaron; Decressin, Thibaut; D'Ercole, Annibale; Caloi, Vittoria; Capuzzo-Dolcetta, Roberto

2015-07-16

Horizontal branch stars belong to an advanced stage in the evolution of the oldest stellar galactic population, occurring either as field halo stars or grouped in globular clusters. The discovery of multiple populations in clusters that were previously believed to have single populations gave rise to the currently accepted theory that the hottest horizontal branch members (the 'blue hook' stars, which had late helium-core flash ignition, followed by deep mixing) are the progeny of a helium-rich 'second generation' of stars. It is not known why such a supposedly rare event (a late flash followed by mixing) is so common that the blue hook of ω Centauri contains approximately 30 per cent of the horizontal branch stars in the cluster, or why the blue hook luminosity range in this massive cluster cannot be reproduced by models. Here we report that the presence of helium core masses up to about 0.04 solar masses larger than the core mass resulting from evolution is required to solve the luminosity range problem. We model this by taking into account the dispersion in rotation rates achieved by the progenitors, whose pre-main-sequence accretion disk suffered an early disruption in the dense environment of the cluster's central regions, where second-generation stars form. Rotation may also account for frequent late-flash-mixing events in massive globular clusters.

Stellar Evolutionary Effects on the Abundance of PAHS and SN-Condensed Dust in Galaxies

NASA Technical Reports Server (NTRS)

Dwek, Eli

2007-01-01

Spectral aid photometric observations of nearby galaxies show a correlation between the strength of their mid-IR aromatic features and their metal abundance, and a deficiency of these features in low-metallicity galaxies. The aromatic features are most commonly attributed to emission from PAH molecules. In this paper, we suggest that the observed correlation represents a trend of PAH abundance with galactic age, reflecting the delayed injection of PAHs and carbon dust into the ISM, by AGB stars in their final, post-AGB phase of their evolution. These AGB stars are the primary sources of PAHs and carbon dust in galaxies, and recycle their ejecta back to the interstellar medium only after a few hundred million years of evolution on the main sequence. In contrast, more massive stars that explode as Type II supernovae inject their metals and dust almost instantaneously after their formation. After determining the PAH abundances in 35 nearby galaxies, we use a chemical evolution model to show that the delayed injection of carbon dust by AGB stars provides a natural explanation to the dependence of the PAH content, in galaxies with metallicity. We also show that larger dust particles giving rise to the far-IR emission follow a distinct evolutionary trend closely related to the injection of dust by massive stars into the ISM.

SeqCompress: an algorithm for biological sequence compression.

PubMed

Sardaraz, Muhammad; Tahir, Muhammad; Ikram, Ataul Aziz; Bajwa, Hassan

2014-10-01

The growth of Next Generation Sequencing technologies presents significant research challenges, specifically to design bioinformatics tools that handle massive amount of data efficiently. Biological sequence data storage cost has become a noticeable proportion of total cost in the generation and analysis. Particularly increase in DNA sequencing rate is significantly outstripping the rate of increase in disk storage capacity, which may go beyond the limit of storage capacity. It is essential to develop algorithms that handle large data sets via better memory management. This article presents a DNA sequence compression algorithm SeqCompress that copes with the space complexity of biological sequences. The algorithm is based on lossless data compression and uses statistical model as well as arithmetic coding to compress DNA sequences. The proposed algorithm is compared with recent specialized compression tools for biological sequences. Experimental results show that proposed algorithm has better compression gain as compared to other existing algorithms. Copyright © 2014 Elsevier Inc. All rights reserved.

QUENCHING STAR FORMATION AT INTERMEDIATE REDSHIFTS: DOWNSIZING OF THE MASS FLUX DENSITY IN THE GREEN VALLEY

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

Goncalves, Thiago S.; Menendez-Delmestre, Karin; Martin, D. Christopher

2012-11-01

The bimodality in galaxy properties has been observed at low and high redshifts, with a clear distinction between star-forming galaxies in the blue cloud and passively evolving objects in the red sequence; the absence of galaxies with intermediate properties indicates that the quenching of star formation and subsequent transition between populations must happen rapidly. In this paper, we present a study of over 100 transiting galaxies in the so-called green valley at intermediate redshifts (z {approx} 0.8). By using very deep spectroscopy with the DEIMOS instrument at the Keck telescope we are able to infer the star formation histories ofmore » these objects and measure the stellar mass flux density transiting from the blue cloud to the red sequence when the universe was half its current age. Our results indicate that the process happened more rapidly and for more massive galaxies in the past, suggesting a top-down scenario in which the massive end of the red sequence is forming first. This represents another aspect of downsizing, with the mass flux density moving toward smaller galaxies in recent times.« less

Using Massive Parallel Sequencing for the Development, Validation, and Application of Population Genetics Markers in the Invasive Bivalve Zebra Mussel (Dreissena polymorpha)

PubMed Central

Peñarrubia, Luis; Sanz, Nuria; Pla, Carles; Vidal, Oriol; Viñas, Jordi

2015-01-01

The zebra mussel (Dreissena polymorpha, Pallas, 1771) is one of the most invasive species of freshwater bivalves, due to a combination of biological and anthropogenic factors. Once this species has been introduced to a new area, individuals form dense aggregations that are very difficult to remove, leading to many adverse socioeconomic and ecological consequences. In this study, we identified, tested, and validated a new set of polymorphic microsatellite loci (also known as SSRs, Single Sequence Repeats) using a Massive Parallel Sequencing (MPS) platform. After several pruning steps, 93 SSRs could potentially be amplified. Out of these SSRs, 14 were polymorphic, producing a polymorphic yield of 15.05%. These 14 polymorphic microsatellites were fully validated in a first approximation of the genetic population structure of D. polymorpha in the Iberian Peninsula. Based on this polymorphic yield, we propose a criterion for establishing the number of SSRs that require validation in similar species, depending on the final use of the markers. These results could be used to optimize MPS approaches in the development of microsatellites as genetic markers, which would reduce the cost of this process. PMID:25780924

2013 Progress Report -- DOE Joint Genome Institute

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

None

2013-11-01

In October 2012, we introduced a 10-Year Strategic Vision [http://bit.ly/JGI-Vision] for the Institute. A central focus of this Strategic Vision is to bridge the gap between sequenced genomes and an understanding of biological functions at the organism and ecosystem level. This involves the continued massive-scale generation of sequence data, complemented by orthogonal new capabilities to functionally annotate these large sequence data sets. Our Strategic Vision lays out a path to guide our decisions and ensure that the evolving set of experimental and computational capabilities available to DOE JGI users will continue to enable groundbreaking science.

Capturing the 'ome': the expanding molecular toolbox for RNA and DNA library construction.

PubMed

Boone, Morgane; De Koker, Andries; Callewaert, Nico

2018-04-06

All sequencing experiments and most functional genomics screens rely on the generation of libraries to comprehensively capture pools of targeted sequences. In the past decade especially, driven by the progress in the field of massively parallel sequencing, numerous studies have comprehensively assessed the impact of particular manipulations on library complexity and quality, and characterized the activities and specificities of several key enzymes used in library construction. Fortunately, careful protocol design and reagent choice can substantially mitigate many of these biases, and enable reliable representation of sequences in libraries. This review aims to guide the reader through the vast expanse of literature on the subject to promote informed library generation, independent of the application.

Mitochondrial DNA heteroplasmy in the emerging field of massively parallel sequencing

PubMed Central

Just, Rebecca S.; Irwin, Jodi A.; Parson, Walther

2015-01-01

Long an important and useful tool in forensic genetic investigations, mitochondrial DNA (mtDNA) typing continues to mature. Research in the last few years has demonstrated both that data from the entire molecule will have practical benefits in forensic DNA casework, and that massively parallel sequencing (MPS) methods will make full mitochondrial genome (mtGenome) sequencing of forensic specimens feasible and cost-effective. A spate of recent studies has employed these new technologies to assess intraindividual mtDNA variation. However, in several instances, contamination and other sources of mixed mtDNA data have been erroneously identified as heteroplasmy. Well vetted mtGenome datasets based on both Sanger and MPS sequences have found authentic point heteroplasmy in approximately 25% of individuals when minor component detection thresholds are in the range of 10–20%, along with positional distribution patterns in the coding region that differ from patterns of point heteroplasmy in the well-studied control region. A few recent studies that examined very low-level heteroplasmy are concordant with these observations when the data are examined at a common level of resolution. In this review we provide an overview of considerations related to the use of MPS technologies to detect mtDNA heteroplasmy. In addition, we examine published reports on point heteroplasmy to characterize features of the data that will assist in the evaluation of future mtGenome data developed by any typing method. PMID:26009256

Noninvasive prenatal detection of sex chromosomal aneuploidies by sequencing circulating cell-free DNA from maternal plasma.

PubMed

Mazloom, Amin R; Džakula, Željko; Oeth, Paul; Wang, Huiquan; Jensen, Taylor; Tynan, John; McCullough, Ron; Saldivar, Juan-Sebastian; Ehrich, Mathias; van den Boom, Dirk; Bombard, Allan T; Maeder, Margo; McLennan, Graham; Meschino, Wendy; Palomaki, Glenn E; Canick, Jacob A; Deciu, Cosmin

2013-06-01

Whole-genome sequencing of circulating cell free (ccf) DNA from maternal plasma has enabled noninvasive prenatal testing for common autosomal aneuploidies. The purpose of this study was to extend the detection to include common sex chromosome aneuploidies (SCAs): [47,XXX], [45,X], [47,XXY], and [47,XYY] syndromes. Massively parallel sequencing was performed on ccf DNA isolated from the plasma of 1564 pregnant women with known fetal karyotype. A classification algorithm for SCA detection was constructed and trained on this cohort. Another study of 411 maternal samples from women with blinded-to-laboratory fetal karyotypes was then performed to determine the accuracy of the classification algorithm. In the training cohort, the new algorithm had a detection rate (DR) of 100% (95%CI: 82.3%, 100%), a false positive rate (FPR) of 0.1% (95%CI: 0%, 0.3%), and nonreportable rate of 6% (95%CI: 4.9%, 7.4%) for SCA determination. The blinded validation yielded similar results: DR of 96.2% (95%CI: 78.4%, 99.8%), FPR of 0.3% (95%CI: 0%, 1.8%), and nonreportable rate of 5% (95%CI: 3.2%, 7.7%) for SCA determination Noninvasive prenatal identification of the most common sex chromosome aneuploidies is possible using ccf DNA and massively parallel sequencing with a high DR and a low FPR. © 2013 John Wiley & Sons, Ltd.

THE RED SEQUENCE AT BIRTH IN THE GALAXY CLUSTER Cl J1449+0856 AT z = 2

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

Strazzullo, V.; Pannella, M.; Daddi, E.

We use Hubble Space Telescope /WFC3 imaging to study the red population in the IR-selected, X-ray detected, low-mass cluster Cl J1449+0856 at z = 2, one of the few bona fide established clusters discovered at this redshift, and likely a typical progenitor of an average massive cluster today. This study explores the presence and significance of an early red sequence in the core of this structure, investigating the nature of red-sequence galaxies, highlighting environmental effects on cluster galaxy populations at high redshift, and at the same time underlining similarities and differences with other distant dense environments. Our results suggest thatmore » the red population in the core of Cl J1449+0856 is made of a mixture of quiescent and dusty star-forming galaxies, with a seedling of the future red sequence already growing in the very central cluster region, and already characterizing the inner cluster core with respect to lower-density environments. On the other hand, the color–magnitude diagram of this cluster is definitely different from that of lower-redshift z ≲ 1 clusters, as well as of some rare particularly evolved massive clusters at similar redshift, and it is suggestive of a transition phase between active star formation and passive evolution occurring in the protocluster and established lower-redshift cluster regimes.« less

Massively parallel sequencing analysis of mucinous ovarian carcinomas: genomic profiling and differential diagnoses.

PubMed

Mueller, Jennifer J; Schlappe, Brooke A; Kumar, Rahul; Olvera, Narciso; Dao, Fanny; Abu-Rustum, Nadeem; Aghajanian, Carol; DeLair, Deborah; Hussein, Yaser R; Soslow, Robert A; Levine, Douglas A; Weigelt, Britta

2018-05-21

Mucinous ovarian cancer (MOC) is a rare type of epithelial ovarian cancer resistant to standard chemotherapy regimens. We sought to characterize the repertoire of somatic mutations in MOCs and to define the contribution of massively parallel sequencing to the classification of tumors diagnosed as primary MOCs. Following gynecologic pathology and chart review, DNA samples obtained from primary MOCs and matched normal tissues/blood were subjected to whole-exome (n = 9) or massively parallel sequencing targeting 341 cancer genes (n = 15). Immunohistochemical analysis of estrogen receptor, progesterone receptor, PTEN, ARID1A/BAF250a, and the DNA mismatch (MMR) proteins MSH6 and PMS2 was performed for all cases. Mutational frequencies of MOCs were compared to those of high-grade serous ovarian cancers (HGSOCs) and mucinous tumors from other sites. MOCs were heterogeneous at the genetic level, frequently harboring TP53 (75%) mutations, KRAS (71%) mutations and/or CDKN2A/B homozygous deletions/mutations (33%). Although established criteria for diagnosis were employed, four cases harbored mutational and immunohistochemical profiles similar to those of endometrioid carcinomas, and one case for colorectal or endometrioid carcinoma. Significant differences in the frequencies of KRAS, TP53, CDKN2A, FBXW7, PIK3CA and/or APC mutations between the confirmed primary MOCs (n = 19) and HGSOCs, mucinous gastric and/or mucinous colorectal carcinomas were found, whereas no differences in the 341 genes studied between MOCs and mucinous pancreatic carcinomas were identified. Our findings suggest that the assessment of mutations affecting TP53, KRAS, PIK3CA, ARID1A and POLE, and DNA MMR protein expression may be used to further aid the diagnosis and treatment decision-making of primary MOC. Copyright © 2018 Elsevier Inc. All rights reserved.

Using Blue Stragglers to Predict Retained Black Hole Population in Globular Clusters

NASA Astrophysics Data System (ADS)

Hermanek, Keith; Chatterjee, Sourav; Rasio, Frederic

2018-01-01

Large numbers of black holes (BHs) are expected to form in massive star clusters typical of the globular clusters (GCs). Sophisticated theoretical models suggest that many of these BHs can be retained in present-day GCs. Observations have also identified several BH candidates in Galactic and extragalactic GCs (e.g., Macarone et al. 2007; Irwin et al. 2010; Strader et al. 2012; Chomiuk et al. 2013; Miller-Jones et al. 2014). It has also been shown that high-mass and high-density clusters such as GCs are efficient factories of merging binary BHs similar to those observed by the LIGO observatories (Abbott et al. 2016a,b,c,d,e; Rodriguez et al. 2016). Understanding the formation rate and properties of binary BHs are dependent on a detailed understanding of how the BHs dynamically evolve within GCs. Nevertheless, directly detecting BHs in GCs is extremely challenging; BHs only in binaries with limited configurations can be directly detected by the detection of gravitational wave, X-ray, or radio emissions. We propose an indirect of inferring the number of undetected retained BHs in a GC by investigating the dynamical effects of a large number of BHs on the production of other tracer populations such as Blue Straggler Stars (BSS). Using a large grid of detailed GC models we show that there is a clear anti-correlation between the number of BSS in a cluster and the number of retained BHs. Being the most massive species, large numbers of retained BHs will dominate the core of the cluster as a result of mass-segregation driving away other low-mass species such as main-sequence stars from central high-density regions. BSS are expected to form from physical collisions between main-sequence (MS) stars mediated by binary encounters (e.g., Chatterjee et al. 2013) in cores of GCs. Production of BSS by collisions or mass transfer channels are suppressed if a large number of retained BHs in a cluster restrict the number of MS stars in the core. Extensive observational data exist on the number and radial distribution of BSS in GCs. Thus, this anti-correlation between the number of retained BHs and the number of BSS, once carefully calibrated by theoretical models, can be used to infer the population of undetected BHs in GCs.

Apoptosis in fatal Ebola infection. Does the virus toll the bell for immune system?

PubMed

Baize, S; Leroy, E M; Mavoungou, E; Fisher-Hoch, S P

2000-02-01

In fatal Ebola virus hemorrhagic fever massive intravascular apoptosis develops rapidly following infection and progressing relentlessly until death. While data suggest that T lymphocytes are mainly deleted by apoptosis in PBMC of human fatal cases, experimental Ebola infection in animal models have shown some evidence of destruction of lymphocytes in spleen and lymph nodes probably involving both T and B cells. Nevertheless, we are able to conclude from the accumulated evidence that early interactions between Ebola virus and the immune system, probably via macrophages, main targets for viral replication, lead to massive destruction of immune cells in fatal cases.

Role of Massive Stars in the Evolution of Primitive Galaxies

NASA Technical Reports Server (NTRS)

Heap, Sara

2012-01-01

An important factor controlling galaxy evolution is feedback from massive stars. It is believed that the nature and intensity of stellar feedback changes as a function of galaxy mass and metallicity. At low mass and metallicity, feedback from massive stars is mainly in the form of photoionizing radiation. At higher mass and metallicity, it is in stellar winds. IZw 18 is a local blue, compact dwarf galaxy that meets the requirements for a primitive galaxy: low halo mass greater than 10(exp 9)Msun, strong photoionizing radiation, no galactic outflow, and very low metallicity,log(O/H)+12=7.2. We will describe the properties of massive stars and their role in the evolution of IZw 18, based on analysis of ultraviolet images and spectra obtained with HST.

Evolved stars and the origin of abundance trends in planet hosts

NASA Astrophysics Data System (ADS)

Maldonado, J.; Villaver, E.

2016-04-01

Context. Detailed chemical abundance studies have revealed different trends between samples of planet and non-planet hosts. Whether these trends are related to the presence of planets or not is strongly debated. At the same time, tentative evidence that the properties of evolved stars with planets may be different from what we know for main-sequence hosts has recently been reported. Aims: We aim to test whether evolved stars with planets show any chemical peculiarity that could be related to the planet formation process. Methods: In a consistent way, we determine the metallicity and individual abundances of a large sample of evolved (subgiants and red giants) and main-sequence stars that are with and without known planetary companions, and discuss their metallicity distribution and trends. Our methodology is based on the analysis of high-resolution échelle spectra (R ≳ 57 000) from 2-3 m class telescopes. It includes the calculation of the fundamental stellar parameters, as well as individual abundances of C, O , Na, Mg, Al, Si, S, Ca, Sc, Ti, V, Cr, Mn, Co, Ni, and Zn. Results: No differences in the ⟨[X/Fe]⟩ vs. condensation temperature (TC) slopes are found between the samples of planet and non-planet hosts when all elements are considered. However, if the analysis is restricted to only refractory elements, differences in the TC-slopes between stars with and without known planets are found. This result is found to be dependent on the stellar evolutionary stage, as it holds for main-sequence and subgiant stars, while there seems to be no difference between planet and non-planet hosts among the sample of giants. A search for correlations between the TC-slope and the stellar properties reveals significant correlations with the stellar mass and the stellar age. The data also suggest that differences in terms of mass and age between main-sequence planet and non-planet hosts may be present. Conclusions: Our results are well explained by radial mixing in the Galaxy. The sample of giants contains stars that are more massive and younger than their main-sequence counterparts. This leads to a sample of stars that are possibly less contaminated by stars that were not born in the solar neighbourhood, leading to no chemical differences between planet and non-planet hosts. The sample of main-sequence stars may contain more stars from the outer disc (specially the non-planet host sample) which might lead to the differences observed in the chemical trends. Based on observations made with the Mercator Telescope; on observations made with the Nordic Optical Telescope; on observations made with the Italian Telescopio Nazionale Galileo; on observations collected at the Centro Astronómico Hispano Alemán (CAHA) at Calar Alto; and on data products from observations made with ESO Telescopes at the La Silla Paranal Observatory under programme ID 072.C-0488(E), 080.D-0347(A), 081.D-0870(A), 087.C-0831(A), and 183.C-0972(A).Tables B.1-B.3 are only available at the CDS via anonymous ftp to http://cdsarc.u-strasbg.fr (ftp://130.79.128.5) or via http://cdsarc.u-strasbg.fr/viz-bin/qcat?J/A+A/588/A98

Rational Protein Engineering Guided by Deep Mutational Scanning

PubMed Central

Shin, HyeonSeok; Cho, Byung-Kwan

2015-01-01

Sequence–function relationship in a protein is commonly determined by the three-dimensional protein structure followed by various biochemical experiments. However, with the explosive increase in the number of genome sequences, facilitated by recent advances in sequencing technology, the gap between protein sequences available and three-dimensional structures is rapidly widening. A recently developed method termed deep mutational scanning explores the functional phenotype of thousands of mutants via massive sequencing. Coupled with a highly efficient screening system, this approach assesses the phenotypic changes made by the substitution of each amino acid sequence that constitutes a protein. Such an informational resource provides the functional role of each amino acid sequence, thereby providing sufficient rationale for selecting target residues for protein engineering. Here, we discuss the current applications of deep mutational scanning and consider experimental design. PMID:26404267

Massive sulfide metallogenesis at a late Mesozoic sediment-covered spreading axis: Evidence from the Franciscan complex and contemporary analogues

USGS Publications Warehouse

Koski, Randolph A.; Lamons, Roberta C.; Dumoulin, Julie A.; Bouse, Robin M.

1993-01-01

The Island Mountain deposit, an anomalous massive sulfide in the Central belt of the Franciscan subduction complex, northern California Coast Ranges, formed during hydrothermal activity in a sediment-dominated paleo-sea-floor environment. Although the base of the massive sulfide is juxtaposed against a 500-m-wide melange band, its gradational upper contact within a coherent sequence of sandstone, siltstone, and mudstone indicates that hydrothermal activity was concurrent with turbidite deposition. Accumulations of sulfide breccia and clastic sulfide were produced by mass wasting of the sulfide mound prior to burial by turbidites. The bulk composition of sulfide samples (pyrrhotite rich; high Cu, As, and Au contents; radiogenic Pb isotope ratios) is consistent with a hydrothermal system dominated by fluid-sediment interaction. On the basis of a comparison with possible contemporary tectonic analogues at the southern Gorda Ridge and the Chile margin triple junction, we propose that massive sulfide mineralization in the Central belt of the Franciscan complex resulted from hydrothermal activity at a late Mesozoic sediment-covered ridge axis prior to collision with the North American plate.

Massive sulfide metallogenesis at a late Mesozoic sediment-covered spreading axis: Evidence from the Franciscan complex and contemporary analogues

NASA Astrophysics Data System (ADS)

Koski, Randolph A.; Lamons, Roberta C.; Dumoulin, Julie A.; Bouse, Robin M.

1993-02-01

The Island Mountain deposit, an anomalous massive sulfide in the Central belt of the Franciscan subduction complex, northern California Coast Ranges, formed during hydrothermal activity in a sediment-dominated paleo-sea-floor environment. Although the base of the massive sulfide is juxtaposed against a 500-m-wide melange band, its gradational upper contact within a coherent sequence of sandstone, siltstone, and mudstone indicates that hydrothermal activity was concurrent with turbidite deposition. Accumulations of sulfide breccia and clastic sulfide were produced by mass wasting of the sulfide mound prior to burial by turbidites. The bulk composition of sulfide samples (pyrrhotite rich; high Cu, As, and Au contents; radiogenic Pb isotope ratios) is consistent with a hydrothermal system dominated by fluid-sediment interaction. On the basis of a comparison with possible contemporary tectonic analogues at the southern Gorda Ridge and the Chile margin triple junction, we propose that massive sulfide mineralization in the Central belt of the Franciscan complex resulted from hydrothermal activity at a late Mesozoic sediment-covered ridge axis prior to collision with the North American plate.

Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications

PubMed Central

Yilmaz, Pelin; Kottmann, Renzo; Field, Dawn; Knight, Rob; Cole, James R; Amaral-Zettler, Linda; Gilbert, Jack A; Karsch-Mizrachi, Ilene; Johnston, Anjanette; Cochrane, Guy; Vaughan, Robert; Hunter, Christopher; Park, Joonhong; Morrison, Norman; Rocca-Serra, Philippe; Sterk, Peter; Arumugam, Manimozhiyan; Bailey, Mark; Baumgartner, Laura; Birren, Bruce W; Blaser, Martin J; Bonazzi, Vivien; Booth, Tim; Bork, Peer; Bushman, Frederic D; Buttigieg, Pier Luigi; Chain, Patrick S G; Charlson, Emily; Costello, Elizabeth K; Huot-Creasy, Heather; Dawyndt, Peter; DeSantis, Todd; Fierer, Noah; Fuhrman, Jed A; Gallery, Rachel E; Gevers, Dirk; Gibbs, Richard A; Gil, Inigo San; Gonzalez, Antonio; Gordon, Jeffrey I; Guralnick, Robert; Hankeln, Wolfgang; Highlander, Sarah; Hugenholtz, Philip; Jansson, Janet; Kau, Andrew L; Kelley, Scott T; Kennedy, Jerry; Knights, Dan; Koren, Omry; Kuczynski, Justin; Kyrpides, Nikos; Larsen, Robert; Lauber, Christian L; Legg, Teresa; Ley, Ruth E; Lozupone, Catherine A; Ludwig, Wolfgang; Lyons, Donna; Maguire, Eamonn; Methé, Barbara A; Meyer, Folker; Muegge, Brian; Nakielny, Sara; Nelson, Karen E; Nemergut, Diana; Neufeld, Josh D; Newbold, Lindsay K; Oliver, Anna E; Pace, Norman R; Palanisamy, Giriprakash; Peplies, Jörg; Petrosino, Joseph; Proctor, Lita; Pruesse, Elmar; Quast, Christian; Raes, Jeroen; Ratnasingham, Sujeevan; Ravel, Jacques; Relman, David A; Assunta-Sansone, Susanna; Schloss, Patrick D; Schriml, Lynn; Sinha, Rohini; Smith, Michelle I; Sodergren, Erica; Spor, Aymé; Stombaugh, Jesse; Tiedje, James M; Ward, Doyle V; Weinstock, George M; Wendel, Doug; White, Owen; Whiteley, Andrew; Wilke, Andreas; Wortman, Jennifer R; Yatsunenko, Tanya; Glöckner, Frank Oliver

2012-01-01

Here we present a standard developed by the Genomic Standards Consortium (GSC) for reporting marker gene sequences—the minimum information about a marker gene sequence (MIMARKS). We also introduce a system for describing the environment from which a biological sample originates. The ‘environmental packages’ apply to any genome sequence of known origin and can be used in combination with MIMARKS and other GSC checklists. Finally, to establish a unified standard for describing sequence data and to provide a single point of entry for the scientific community to access and learn about GSC checklists, we present the minimum information about any (x) sequence (MIxS). Adoption of MIxS will enhance our ability to analyze natural genetic diversity documented by massive DNA sequencing efforts from myriad ecosystems in our ever-changing biosphere. PMID:21552244

Open-Source Sequence Clustering Methods Improve the State Of the Art.

PubMed

Kopylova, Evguenia; Navas-Molina, Jose A; Mercier, Céline; Xu, Zhenjiang Zech; Mahé, Frédéric; He, Yan; Zhou, Hong-Wei; Rognes, Torbjørn; Caporaso, J Gregory; Knight, Rob

2016-01-01

Sequence clustering is a common early step in amplicon-based microbial community analysis, when raw sequencing reads are clustered into operational taxonomic units (OTUs) to reduce the run time of subsequent analysis steps. Here, we evaluated the performance of recently released state-of-the-art open-source clustering software products, namely, OTUCLUST, Swarm, SUMACLUST, and SortMeRNA, against current principal options (UCLUST and USEARCH) in QIIME, hierarchical clustering methods in mothur, and USEARCH's most recent clustering algorithm, UPARSE. All the latest open-source tools showed promising results, reporting up to 60% fewer spurious OTUs than UCLUST, indicating that the underlying clustering algorithm can vastly reduce the number of these derived OTUs. Furthermore, we observed that stringent quality filtering, such as is done in UPARSE, can cause a significant underestimation of species abundance and diversity, leading to incorrect biological results. Swarm, SUMACLUST, and SortMeRNA have been included in the QIIME 1.9.0 release. IMPORTANCE Massive collections of next-generation sequencing data call for fast, accurate, and easily accessible bioinformatics algorithms to perform sequence clustering. A comprehensive benchmark is presented, including open-source tools and the popular USEARCH suite. Simulated, mock, and environmental communities were used to analyze sensitivity, selectivity, species diversity (alpha and beta), and taxonomic composition. The results demonstrate that recent clustering algorithms can significantly improve accuracy and preserve estimated diversity without the application of aggressive filtering. Moreover, these tools are all open source, apply multiple levels of multithreading, and scale to the demands of modern next-generation sequencing data, which is essential for the analysis of massive multidisciplinary studies such as the Earth Microbiome Project (EMP) (J. A. Gilbert, J. K. Jansson, and R. Knight, BMC Biol 12:69, 2014, http://dx.doi.org/10.1186/s12915-014-0069-1).

Unmanned aerial vehicles for high-throughput phenotyping and agronomic research

USDA-ARS?s Scientific Manuscript database

Advances in automation and data science have led agriculturists to seek real-time, high-quality, high-volume crop data to accelerate crop improvement through breeding and to optimize agronomic practices. Breeders have recently gained massive data-collection capability in genome sequencing of plants....

Estimating population diversity with CatchAll

USDA-ARS?s Scientific Manuscript database

The massive quantity of data produced by next-generation sequencing has created a pressing need for advanced statistical tools, in particular for analysis of bacterial and phage communities. Here we address estimating the total diversity in a population – the species richness. This is an important s...

Sewage Reflects the Distriubtion of Human Faecal Lachnospiraceae

EPA Science Inventory

Faecal pollution contains a rich and diverse community of bacteria derived from animals and humans,many of which might serve as alternatives to the traditional enterococci and Escherichia coli faecal indicators. We used massively parallel sequencing (MPS)of the 16S rRNA gene to ...

Genetics Home Reference: medullary cystic kidney disease type 1

MedlinePlus

... They lead to the production of an altered protein. It is unclear how this change causes kidney disease. ... cystic kidney disease type 1 lie in a large VNTR in MUC1 missed by massively parallel sequencing. Nat Genet. 2013 Mar;45(3):299-303. ...

Massively parallel sequencing and the emergence of forensic genomics: Defining the policy and legal issues for law enforcement.

PubMed

Scudder, Nathan; McNevin, Dennis; Kelty, Sally F; Walsh, Simon J; Robertson, James

2018-03-01

Use of DNA in forensic science will be significantly influenced by new technology in coming years. Massively parallel sequencing and forensic genomics will hasten the broadening of forensic DNA analysis beyond short tandem repeats for identity towards a wider array of genetic markers, in applications as diverse as predictive phenotyping, ancestry assignment, and full mitochondrial genome analysis. With these new applications come a range of legal and policy implications, as forensic science touches on areas as diverse as 'big data', privacy and protected health information. Although these applications have the potential to make a more immediate and decisive forensic intelligence contribution to criminal investigations, they raise policy issues that will require detailed consideration if this potential is to be realised. The purpose of this paper is to identify the scope of the issues that will confront forensic and user communities. Copyright © 2017 The Chartered Society of Forensic Sciences. All rights reserved.

Massively parallel de novo protein design for targeted therapeutics.

PubMed

Chevalier, Aaron; Silva, Daniel-Adriano; Rocklin, Gabriel J; Hicks, Derrick R; Vergara, Renan; Murapa, Patience; Bernard, Steffen M; Zhang, Lu; Lam, Kwok-Ho; Yao, Guorui; Bahl, Christopher D; Miyashita, Shin-Ichiro; Goreshnik, Inna; Fuller, James T; Koday, Merika T; Jenkins, Cody M; Colvin, Tom; Carter, Lauren; Bohn, Alan; Bryan, Cassie M; Fernández-Velasco, D Alejandro; Stewart, Lance; Dong, Min; Huang, Xuhui; Jin, Rongsheng; Wilson, Ian A; Fuller, Deborah H; Baker, David

2017-10-05

De novo protein design holds promise for creating small stable proteins with shapes customized to bind therapeutic targets. We describe a massively parallel approach for designing, manufacturing and screening mini-protein binders, integrating large-scale computational design, oligonucleotide synthesis, yeast display screening and next-generation sequencing. We designed and tested 22,660 mini-proteins of 37-43 residues that target influenza haemagglutinin and botulinum neurotoxin B, along with 6,286 control sequences to probe contributions to folding and binding, and identified 2,618 high-affinity binders. Comparison of the binding and non-binding design sets, which are two orders of magnitude larger than any previously investigated, enabled the evaluation and improvement of the computational model. Biophysical characterization of a subset of the binder designs showed that they are extremely stable and, unlike antibodies, do not lose activity after exposure to high temperatures. The designs elicit little or no immune response and provide potent prophylactic and therapeutic protection against influenza, even after extensive repeated dosing.

Massively parallel de novo protein design for targeted therapeutics

NASA Astrophysics Data System (ADS)

Chevalier, Aaron; Silva, Daniel-Adriano; Rocklin, Gabriel J.; Hicks, Derrick R.; Vergara, Renan; Murapa, Patience; Bernard, Steffen M.; Zhang, Lu; Lam, Kwok-Ho; Yao, Guorui; Bahl, Christopher D.; Miyashita, Shin-Ichiro; Goreshnik, Inna; Fuller, James T.; Koday, Merika T.; Jenkins, Cody M.; Colvin, Tom; Carter, Lauren; Bohn, Alan; Bryan, Cassie M.; Fernández-Velasco, D. Alejandro; Stewart, Lance; Dong, Min; Huang, Xuhui; Jin, Rongsheng; Wilson, Ian A.; Fuller, Deborah H.; Baker, David

2017-10-01

De novo protein design holds promise for creating small stable proteins with shapes customized to bind therapeutic targets. We describe a massively parallel approach for designing, manufacturing and screening mini-protein binders, integrating large-scale computational design, oligonucleotide synthesis, yeast display screening and next-generation sequencing. We designed and tested 22,660 mini-proteins of 37-43 residues that target influenza haemagglutinin and botulinum neurotoxin B, along with 6,286 control sequences to probe contributions to folding and binding, and identified 2,618 high-affinity binders. Comparison of the binding and non-binding design sets, which are two orders of magnitude larger than any previously investigated, enabled the evaluation and improvement of the computational model. Biophysical characterization of a subset of the binder designs showed that they are extremely stable and, unlike antibodies, do not lose activity after exposure to high temperatures. The designs elicit little or no immune response and provide potent prophylactic and therapeutic protection against influenza, even after extensive repeated dosing.

Massive thymic hemorrhage and hemothorax occurring in utero.

PubMed

Gargano, Giancarlo; Paltrinieri, Anna Lucia; Gallo, Claudio; Di Pancrazio, Luciana; Roversi, Maria Federica; Ferrari, Fabrizio

2015-11-14

Thymic enlargement is a common and physiological finding in children and neonates' X-rays, but it is usually asymptomatic. Occasionally it can cause respiratory distress. In most cases the aetiology of this expansion remains unclear and it is diagnosed as a thymic hyperplasia. True thymic hyperplasia is defined as a gland expansion, both in size and weight, while maintaining normal microscopic architecture. Often it is a diagnosis of exclusion and prognosis is good. Thymic haemorrhage is an unusual condition related to high foetal and neonatal mortality. We report a case of spontaneous massive thymic haemorrhage in a newborn developing at birth acute respiratory distress associated with severe bilateral haemothorax. Thymic enlargement was evident after pleural evacuation and confirmed by radiographic, Computed Tomography (CT) images and Magnetic Resonance Imaging (MRI) sequences. The spontaneous resolution of this enlargement seen with CT scan and MRI sequences suggested a thymic haemorrhage; surgery was not necessary. Thymic haemorrhage should be considered in newborn infants with pleural effusion, mediastinal space enlargement and Respiratory Distress.

Massively parallel de novo protein design for targeted therapeutics

PubMed Central

Chevalier, Aaron; Silva, Daniel-Adriano; Rocklin, Gabriel J.; Hicks, Derrick R.; Vergara, Renan; Murapa, Patience; Bernard, Steffen M.; Zhang, Lu; Lam, Kwok-Ho; Yao, Guorui; Bahl, Christopher D.; Miyashita, Shin-Ichiro; Goreshnik, Inna; Fuller, James T.; Koday, Merika T.; Jenkins, Cody M.; Colvin, Tom; Carter, Lauren; Bohn, Alan; Bryan, Cassie M.; Fernández-Velasco, D. Alejandro; Stewart, Lance; Dong, Min; Huang, Xuhui; Jin, Rongsheng; Wilson, Ian A.; Fuller, Deborah H.; Baker, David

2018-01-01

De novo protein design holds promise for creating small stable proteins with shapes customized to bind therapeutic targets. We describe a massively parallel approach for designing, manufacturing and screening mini-protein binders, integrating large-scale computational design, oligonucleotide synthesis, yeast display screening and next-generation sequencing. We designed and tested 22,660 mini-proteins of 37–43 residues that target influenza haemagglutinin and botulinum neurotoxin B, along with 6,286 control sequences to probe contributions to folding and binding, and identified 2,618 high-affinity binders. Comparison of the binding and non-binding design sets, which are two orders of magnitude larger than any previously investigated, enabled the evaluation and improvement of the computational model. Biophysical characterization of a subset of the binder designs showed that they are extremely stable and, unlike antibodies, do not lose activity after exposure to high temperatures. The designs elicit little or no immune response and provide potent prophylactic and therapeutic protection against influenza, even after extensive repeated dosing. PMID:28953867

An extraterrestrial trigger for the Early Cretaceous massive volcanism? Evidence from the paleo-Tethys Ocean.

PubMed

Tejada, M L G; Ravizza, G; Suzuki, K; Paquay, F S

2012-01-01

The Early Cretaceous Greater Ontong Java Event in the Pacific Ocean may have covered ca. 1% of the Earth's surface with volcanism. It has puzzled scientists trying to explain its origin by several mechanisms possible on Earth, leading others to propose an extraterrestrial trigger to explain this event. A large oceanic extraterrestrial impact causing such voluminous volcanism may have traces of its distal ejecta in sedimentary rocks around the basin, including the paleo-Tethys Ocean which was then contiguous with the Pacific Ocean. The contemporaneous marine sequence at central Italy, containing the sedimentary expression of a global oceanic anoxic event (OAE1a), may have recorded such ocurrence as indicated by two stratigraphic intervals with (187)Os/(188)Os indicative of meteoritic influence. Here we show, for the first time, that platinum group element abundances and inter-element ratios in this paleo-Tethyan marine sequence provide no evidence for an extraterrestrial trigger for the Early Cretaceous massive volcanism.

An extraterrestrial trigger for the Early Cretaceous massive volcanism? Evidence from the paleo-Tethys Ocean

PubMed Central

Tejada, M. L. G.; Ravizza, G.; Suzuki, K.; Paquay, F. S.

2012-01-01

The Early Cretaceous Greater Ontong Java Event in the Pacific Ocean may have covered ca. 1% of the Earth's surface with volcanism. It has puzzled scientists trying to explain its origin by several mechanisms possible on Earth, leading others to propose an extraterrestrial trigger to explain this event. A large oceanic extraterrestrial impact causing such voluminous volcanism may have traces of its distal ejecta in sedimentary rocks around the basin, including the paleo-Tethys Ocean which was then contiguous with the Pacific Ocean. The contemporaneous marine sequence at central Italy, containing the sedimentary expression of a global oceanic anoxic event (OAE1a), may have recorded such ocurrence as indicated by two stratigraphic intervals with 187Os/188Os indicative of meteoritic influence. Here we show, for the first time, that platinum group element abundances and inter-element ratios in this paleo-Tethyan marine sequence provide no evidence for an extraterrestrial trigger for the Early Cretaceous massive volcanism. PMID:22355780

FDSTools: A software package for analysis of massively parallel sequencing data with the ability to recognise and correct STR stutter and other PCR or sequencing noise.

PubMed

Hoogenboom, Jerry; van der Gaag, Kristiaan J; de Leeuw, Rick H; Sijen, Titia; de Knijff, Peter; Laros, Jeroen F J

2017-03-01

Massively parallel sequencing (MPS) is on the advent of a broad scale application in forensic research and casework. The improved capabilities to analyse evidentiary traces representing unbalanced mixtures is often mentioned as one of the major advantages of this technique. However, most of the available software packages that analyse forensic short tandem repeat (STR) sequencing data are not well suited for high throughput analysis of such mixed traces. The largest challenge is the presence of stutter artefacts in STR amplifications, which are not readily discerned from minor contributions. FDSTools is an open-source software solution developed for this purpose. The level of stutter formation is influenced by various aspects of the sequence, such as the length of the longest uninterrupted stretch occurring in an STR. When MPS is used, STRs are evaluated as sequence variants that each have particular stutter characteristics which can be precisely determined. FDSTools uses a database of reference samples to determine stutter and other systemic PCR or sequencing artefacts for each individual allele. In addition, stutter models are created for each repeating element in order to predict stutter artefacts for alleles that are not included in the reference set. This information is subsequently used to recognise and compensate for the noise in a sequence profile. The result is a better representation of the true composition of a sample. Using Promega Powerseq™ Auto System data from 450 reference samples and 31 two-person mixtures, we show that the FDSTools correction module decreases stutter ratios above 20% to below 3%. Consequently, much lower levels of contributions in the mixed traces are detected. FDSTools contains modules to visualise the data in an interactive format allowing users to filter data with their own preferred thresholds. Copyright © 2016 The Authors. Published by Elsevier B.V. All rights reserved.

Detection of [O III] at z ∼ 3: A Galaxy Above the Main Sequence, Rapidly Assembling Its Stellar Mass

NASA Astrophysics Data System (ADS)

Vishwas, Amit; Ferkinhoff, Carl; Nikola, Thomas; Parshley, Stephen C.; Schoenwald, Justin P.; Stacey, Gordon J.; Higdon, Sarah J. U.; Higdon, James L.; Weiss, Axel; Güsten, Rolf; Menten, Karl M.

2018-04-01

We detect bright emission in the far-infrared (far-IR) fine structure [O III] 88 μm line from a strong lensing candidate galaxy, H-ATLAS J113526.3-014605, hereafter G12v2.43, at z = 3.127, using the second-generation Redshift (z) and Early Universe Spectrometer (ZEUS-2) at the Atacama Pathfinder Experiment Telescope (APEX). This is only the fifth detection of this far-IR line from a submillimeter galaxy at the epoch of galaxy assembly. The observed [O III] luminosity of 7.1 × 109 ≤ft(\\tfrac{10}{μ }\\right) L ⊙ likely arises from H II regions around massive stars, and the amount of Lyman continuum photons required to support the ionization indicate the presence of (1.2–5.2) × 106 ≤ft(\\tfrac{10}{μ }\\right) equivalent O5.5 or higher stars, where μ would be the lensing magnification factor. The observed line luminosity also requires a minimum mass of ∼2 × 108 ≤ft(\\tfrac{10}{μ }\\right) M ⊙ in ionized gas, that is 0.33% of the estimated total molecular gas mass of 6 × 1010 ≤ft(\\tfrac{10}{μ }\\right) M ⊙. We compile multi-band photometry tracing rest-frame ultraviolet to millimeter continuum emission to further constrain the properties of this dusty high-redshift, star-forming galaxy. Via SED modeling we find G12v2.43 is forming stars at a rate of 916 ≤ft(\\tfrac{10}{μ }\\right) M ⊙ yr‑1 and already has a stellar mass of 8 × 1010 ≤ft(\\tfrac{10}{μ }\\right) M ⊙. We also constrain the age of the current starburst to be ≤slant 5 Myr, making G12v2.43 a gas-rich galaxy lying above the star-forming main sequence at z ∼ 3, undergoing a growth spurt, and it could be on the main sequence within the derived gas depletion timescale of ∼66 Myr.

REDItools: high-throughput RNA editing detection made easy.

PubMed

Picardi, Ernesto; Pesole, Graziano

2013-07-15

The reliable detection of RNA editing sites from massive sequencing data remains challenging and, although several methodologies have been proposed, no computational tools have been released to date. Here, we introduce REDItools a suite of python scripts to perform high-throughput investigation of RNA editing using next-generation sequencing data. REDItools are in python programming language and freely available at http://code.google.com/p/reditools/. ernesto.picardi@uniba.it or graziano.pesole@uniba.it Supplementary data are available at Bioinformatics online.

Noninvasive Prenatal Screening for Genetic Diseases Using Massively Parallel Sequencing of Maternal Plasma DNA

PubMed Central

Chitty, Lyn S.; Lo, Y. M. Dennis

2015-01-01

The identification of cell-free fetal DNA (cffDNA) in maternal plasma in 1997 heralded the most significant change in obstetric care for decades, with the advent of safer screening and diagnosis based on analysis of maternal blood. Here, we describe how the technological advances offered by next-generation sequencing have allowed for the development of a highly sensitive screening test for aneuploidies as well as definitive prenatal molecular diagnosis for some monogenic disorders. PMID:26187875

Radiation transfer of models of massive star formation. III. The evolutionary sequence

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

Zhang, Yichen; Tan, Jonathan C.; Hosokawa, Takashi, E-mail: yichen.zhang@yale.edu, E-mail: jt@astro.ufl.edu, E-mail: takashi.hosokawa@phys.s.u-tokyo.ac.jp

2014-06-20

We present radiation transfer simulations of evolutionary sequences of massive protostars forming from massive dense cores in environments of high mass surface densities, based on the Turbulent Core Model. The protostellar evolution is calculated with a multi-zone numerical model, with the accretion rate regulated by feedback from an evolving disk wind outflow cavity. The disk evolution is calculated assuming a fixed ratio of disk to protostellar mass, while the core envelope evolution assumes an inside-out collapse of the core with a fixed outer radius. In this framework, an evolutionary track is determined by three environmental initial conditions: the core massmore » M{sub c} , the mass surface density of the ambient clump Σ{sub cl}, and the ratio of the core's initial rotational to gravitational energy β {sub c}. Evolutionary sequences with various M{sub c} , Σ{sub cl}, and β {sub c} are constructed. We find that in a fiducial model with M{sub c} = 60 M {sub ☉}, Σ{sub cl} = 1 g cm{sup –2}, and β {sub c} = 0.02, the final mass of the protostar reaches at least ∼26 M {sub ☉}, making the final star formation efficiency ≳ 0.43. For each of the evolutionary tracks, radiation transfer simulations are performed at selected stages, with temperature profiles, spectral energy distributions (SEDs), and multiwavelength images produced. At a given stage, the envelope temperature depends strongly on Σ{sub cl}, with higher temperatures in a higher Σ{sub cl} core, but only weakly on M{sub c} . The SED and MIR images depend sensitively on the evolving outflow cavity, which gradually widens as the protostar grows. The fluxes at ≲ 100 μm increase dramatically, and the far-IR peaks move to shorter wavelengths. The influence of Σ{sub cl} and β {sub c} (which determines disk size) are discussed. We find that, despite scatter caused by different M{sub c} , Σ{sub cl}, β {sub c}, and inclinations, sources at a given evolutionary stage appear in similar regions of color-color diagrams, especially when using colors with fluxes at ≳ 70 μm, where scatter due to inclination is minimized, implying that such diagrams can be useful diagnostic tools for identifying the evolutionary stages of massive protostars. We discuss how intensity profiles along or perpendicular to the outflow axis are affected by environmental conditions and source evolution and can thus act as additional diagnostics of the massive star formation process.« less

Genome Evolution and Meiotic Maps by Massively Parallel DNA Sequencing: Spotted Gar, an Outgroup for the Teleost Genome Duplication

PubMed Central

Amores, Angel; Catchen, Julian; Ferrara, Allyse; Fontenot, Quenton; Postlethwait, John H.

2011-01-01

Genomic resources for hundreds of species of evolutionary, agricultural, economic, and medical importance are unavailable due to the expense of well-assembled genome sequences and difficulties with multigenerational studies. Teleost fish provide many models for human disease but possess anciently duplicated genomes that sometimes obfuscate connectivity. Genomic information representing a fish lineage that diverged before the teleost genome duplication (TGD) would provide an outgroup for exploring the mechanisms of evolution after whole-genome duplication. We exploited massively parallel DNA sequencing to develop meiotic maps with thrift and speed by genotyping F1 offspring of a single female and a single male spotted gar (Lepisosteus oculatus) collected directly from nature utilizing only polymorphisms existing in these two wild individuals. Using Stacks, software that automates the calling of genotypes from polymorphisms assayed by Illumina sequencing, we constructed a map containing 8406 markers. RNA-seq on two map-cross larvae provided a reference transcriptome that identified nearly 1000 mapped protein-coding markers and allowed genome-wide analysis of conserved synteny. Results showed that the gar lineage diverged from teleosts before the TGD and its genome is organized more similarly to that of humans than teleosts. Thus, spotted gar provides a critical link between medical models in teleost fish, to which gar is biologically similar, and humans, to which gar is genomically similar. Application of our F1 dense mapping strategy to species with no prior genome information promises to facilitate comparative genomics and provide a scaffold for ordering the numerous contigs arising from next generation genome sequencing. PMID:21828280

Touch imprint cytology with massively parallel sequencing (TIC-seq): a simple and rapid method to snapshot genetic alterations in tumors.

PubMed

Amemiya, Kenji; Hirotsu, Yosuke; Goto, Taichiro; Nakagomi, Hiroshi; Mochizuki, Hitoshi; Oyama, Toshio; Omata, Masao

2016-12-01

Identifying genetic alterations in tumors is critical for molecular targeting of therapy. In the clinical setting, formalin-fixed paraffin-embedded (FFPE) tissue is usually employed for genetic analysis. However, DNA extracted from FFPE tissue is often not suitable for analysis because of its low levels and poor quality. Additionally, FFPE sample preparation is time-consuming. To provide early treatment for cancer patients, a more rapid and robust method is required for precision medicine. We present a simple method for genetic analysis, called touch imprint cytology combined with massively paralleled sequencing (touch imprint cytology [TIC]-seq), to detect somatic mutations in tumors. We prepared FFPE tissues and TIC specimens from tumors in nine lung cancer patients and one patient with breast cancer. We found that the quality and quantity of TIC DNA was higher than that of FFPE DNA, which requires microdissection to enrich DNA from target tissues. Targeted sequencing using a next-generation sequencer obtained sufficient sequence data using TIC DNA. Most (92%) somatic mutations in lung primary tumors were found to be consistent between TIC and FFPE DNA. We also applied TIC DNA to primary and metastatic tumor tissues to analyze tumor heterogeneity in a breast cancer patient, and showed that common and distinct mutations among primary and metastatic sites could be classified into two distinct histological subtypes. TIC-seq is an alternative and feasible method to analyze genomic alterations in tumors by simply touching the cut surface of specimens to slides. © 2016 The Authors. Cancer Medicine published by John Wiley & Sons Ltd.

Detection of inherited mutations for breast and ovarian cancer using genomic capture and massively parallel sequencing

PubMed Central

Walsh, Tom; Lee, Ming K.; Casadei, Silvia; Thornton, Anne M.; Stray, Sunday M.; Pennil, Christopher; Nord, Alex S.; Mandell, Jessica B.; Swisher, Elizabeth M.; King, Mary-Claire

2010-01-01

Inherited loss-of-function mutations in the tumor suppressor genes BRCA1, BRCA2, and multiple other genes predispose to high risks of breast and/or ovarian cancer. Cancer-associated inherited mutations in these genes are collectively quite common, but individually rare or even private. Genetic testing for BRCA1 and BRCA2 mutations has become an integral part of clinical practice, but testing is generally limited to these two genes and to women with severe family histories of breast or ovarian cancer. To determine whether massively parallel, “next-generation” sequencing would enable accurate, thorough, and cost-effective identification of inherited mutations for breast and ovarian cancer, we developed a genomic assay to capture, sequence, and detect all mutations in 21 genes, including BRCA1 and BRCA2, with inherited mutations that predispose to breast or ovarian cancer. Constitutional genomic DNA from subjects with known inherited mutations, ranging in size from 1 to >100,000 bp, was hybridized to custom oligonucleotides and then sequenced using a genome analyzer. Analysis was carried out blind to the mutation in each sample. Average coverage was >1200 reads per base pair. After filtering sequences for quality and number of reads, all single-nucleotide substitutions, small insertion and deletion mutations, and large genomic duplications and deletions were detected. There were zero false-positive calls of nonsense mutations, frameshift mutations, or genomic rearrangements for any gene in any of the test samples. This approach enables widespread genetic testing and personalized risk assessment for breast and ovarian cancer. PMID:20616022

The diploid genome sequence of an Asian individual

PubMed Central

Wang, Jun; Wang, Wei; Li, Ruiqiang; Li, Yingrui; Tian, Geng; Goodman, Laurie; Fan, Wei; Zhang, Junqing; Li, Jun; Zhang, Juanbin; Guo, Yiran; Feng, Binxiao; Li, Heng; Lu, Yao; Fang, Xiaodong; Liang, Huiqing; Du, Zhenglin; Li, Dong; Zhao, Yiqing; Hu, Yujie; Yang, Zhenzhen; Zheng, Hancheng; Hellmann, Ines; Inouye, Michael; Pool, John; Yi, Xin; Zhao, Jing; Duan, Jinjie; Zhou, Yan; Qin, Junjie; Ma, Lijia; Li, Guoqing; Yang, Zhentao; Zhang, Guojie; Yang, Bin; Yu, Chang; Liang, Fang; Li, Wenjie; Li, Shaochuan; Li, Dawei; Ni, Peixiang; Ruan, Jue; Li, Qibin; Zhu, Hongmei; Liu, Dongyuan; Lu, Zhike; Li, Ning; Guo, Guangwu; Zhang, Jianguo; Ye, Jia; Fang, Lin; Hao, Qin; Chen, Quan; Liang, Yu; Su, Yeyang; san, A.; Ping, Cuo; Yang, Shuang; Chen, Fang; Li, Li; Zhou, Ke; Zheng, Hongkun; Ren, Yuanyuan; Yang, Ling; Gao, Yang; Yang, Guohua; Li, Zhuo; Feng, Xiaoli; Kristiansen, Karsten; Wong, Gane Ka-Shu; Nielsen, Rasmus; Durbin, Richard; Bolund, Lars; Zhang, Xiuqing; Li, Songgang; Yang, Huanming; Wang, Jian

2009-01-01

Here we present the first diploid genome sequence of an Asian individual. The genome was sequenced to 36-fold average coverage using massively parallel sequencing technology. We aligned the short reads onto the NCBI human reference genome to 99.97% coverage, and guided by the reference genome, we used uniquely mapped reads to assemble a high-quality consensus sequence for 92% of the Asian individual's genome. We identified approximately 3 million single-nucleotide polymorphisms (SNPs) inside this region, of which 13.6% were not in the dbSNP database. Genotyping analysis showed that SNP identification had high accuracy and consistency, indicating the high sequence quality of this assembly. We also carried out heterozygote phasing and haplotype prediction against HapMap CHB and JPT haplotypes (Chinese and Japanese, respectively), sequence comparison with the two available individual genomes (J. D. Watson and J. C. Venter), and structural variation identification. These variations were considered for their potential biological impact. Our sequence data and analyses demonstrate the potential usefulness of next-generation sequencing technologies for personal genomics. PMID:18987735

An Unusual Massive Be Star HD 53367: Circumstellar Activity and Evidence for Binarity

NASA Astrophysics Data System (ADS)

Pogodin, M. A.; Malanushenko, V. P.; Kozlova, O. V.; Tarasova, T. N.; Franco, G. A. P.

2006-12-01

We present the results of high-resolution spectroscopy of the young B0e star HD 53367 obtained within the framework of a cooperative observing program in 1994--2005. We confirm that a long-term photometric variability of the object is indeed connected with the alternation of two states of the object when the gaseous circumstellar envelope disappears and arises again. Both these processes start near the star and then spread to remote parts of the envelope. We find that the radial velocities of He I and O II photospheric lines demonstrate a cyclic variability with the period P=183.7 days and the semi-amplitude K=19 km s-1. The radial velocity variation is interpreted in the framework of a model, in which the star is a companion of an eccentric binary system. An orbital solution is derived and the system's parameters are estimated. We find that the orbital eccentricity is e=0.28, the mean companion separation is 1.7 AU, and the secondary companion is most likely to be a 5 solar mass pre-main sequence object. The main part of circumstellar gas in the system is collected near the secondary companion.

GUM 48d: AN EVOLVED H II REGION WITH ONGOING STAR FORMATION

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

Karr, J. L.; Ohashi, N.; Manoj, P.

2009-05-20

High-mass star formation and the evolution of H II regions have a substantial impact on the morphology and star formation history of molecular clouds. The H II region Gum 48d, located in the Centaurus Arm at a distance of 3.5 kpc, is an old, well evolved H II region whose ionizing stars have moved off the main sequence. As such, it represents a phase in the evolution of H II regions that is less well studied than the earlier, more energetic, main-sequence phase. In this paper, we use multiwavelength archive data from a variety of sources to perform a detailedmore » study of this interesting region. Morphologically, Gum 48d displays a ring-like faint H II region associated with diffuse emission from the associated photodissociation region, and is formed from part of a large, massive molecular cloud complex. There is extensive ongoing star formation in the region, at scales ranging from low to high mass, which is consistent with triggered star formation scenarios. We investigate the dynamical history and evolution of this region, and conclude that the original H II region was once larger and more energetic than the faint region currently seen. The proposed history of this molecular cloud complex is one of multiple, linked generations of star formation, over a period of 10 Myr. Gum 48d differs significantly in morphology and star formation from the other H II regions in the molecular cloud; these differences are likely the result of the advanced age of the region, and its different evolutionary status.« less

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

Optical spectroscopy of the blue supergiant Sk-69° 279 and its circumstellar shell with SALT

NASA Astrophysics Data System (ADS)

Gvaramadze, V. V.; Kniazev, A. Y.; Maryeva, O. V.; Berdnikov, L. N.

2018-02-01

We report the results of optical spectroscopy of the blue supergiant Sk-69° 279 and its circular shell in the Large Magellanic Cloud (LMC) with the Southern African Large Telescope (SALT). We classify Sk-69° 279 as an O9.2 Iaf star and analyse its spectrum by using the stellar atmosphere code CMFGEN, obtaining a stellar temperature of ≈30 kK, a luminosity of log (L*/ L⊙) = 5.54, a mass-loss rate of log (\\dot{M}/ M_{⊙} yr^{-1}) = -5.26, and a wind velocity of 800km s-1. We found also that Sk-69° 279 possesses an extended atmosphere with an effective temperature of ≈24 kK and that its surface helium and nitrogen abundances are enhanced, respectively, by factors of ≈2 and 20-30. This suggests that either Sk-69° 279 was initially a (single) fast-rotating ( ≳ 400 km s- 1) star, which only recently evolved off the main sequence, or that it is a product of close binary evolution. The long-slit spectroscopy of the shell around Sk-69° 279 revealed that its nitrogen abundance is enhanced by the same factor as the stellar atmosphere, which implies that the shell is composed mostly of the CNO processed material lost by the star. Our findings support previous propositions that some massive stars can produce compact circumstellar shells and, presumably, appear as luminous blue variables while they are still on the main sequence or have only recently left it.

The phylogeny of quasars and the ontogeny of their central black holes

NASA Astrophysics Data System (ADS)

Fraix-Burnet, Didier; Marziani, Paola; D'Onofrio, Mauro; Dultzin, Deborah

2017-02-01

The connection between multifrequency quasar observational and physical parameters related to accretion processes is still open to debate. In the last 20 year, Eigenvector 1-based approaches developed since the early papers by Boroson and Green (1992) and Sulentic et al. (2000b) have been proved to be a remarkably powerful tool to investigate this issue, and have led to the definition of a quasar "main sequence". In this paper we perform a cladistic analysis on two samples of 215 and 85 low-z quasars (z ~ 0.7) which were studied in several previous works and which offer a satisfactory coverage of the Eigenvector 1-derived main sequence. The data encompass accurate measurements of observational parameters which represents key aspects associated with the structural diversity of quasars. Cladistics is able to group sources radiating at higher Eddington ratios, as well as to separate radio-quiet (RQ) and radio-loud (RL) quasars. The analysis suggests a black hole mass threshold for powerful radio emission and also properly distinguishes core-dominated and lobe-dominated quasars, in accordance with the basic tenet of RL unification schemes. Considering that black hole mass provides a sort of "arrow of time" of nuclear activity, a phylogenetic interpretation becomes possible if cladistic trees are rooted on black hole mass: the ontogeny of black holes is represented by their monotonic increase in mass. More massive radio-quiet Population B sources at low-z become a more evolved counterpart of Population A i.e., wind dominated sources to which the "local" Narrow-Line Seyfert 1s belong.

Massive vulvar edema in a woman with preeclampsia: a case report.

PubMed

Daponte, Alexandros; Skentou, Hara; Dimopoulos, Konstantinos D; Kallitsaris, Athanasios; Messinis, Ioannis E

2007-11-01

Massive vulvar edema in a woman with preeclampsia preceded the development of massive ascites and impending eclampsia. A 17-year-old preeclamptic, primiparous woman was admitted with preeclampsia and massive vulvar edema. Other causes were excluded. The vulvar edema increased as the blood pressure and ascites increased, and a severe headache developed. Cesarean section for increasing preclampsia was performed. In the puerperium, the blood pressure improved and vulvar edema resolved. The clinical picture of the vulvar edema correlated with the severity of the preeclampsia. The presence of vulvar edema in women with preeclampsia should indicate immediate admission to the hospital. These patients must be considered as at high risk, and close monitoring must be instituted. In our case, vulvar edema preceded massive ascites development. We assume a common development mechanism for these signs in preeclampsia, due mainly to increased capillary permeability and hypoalbuminemia. The attending physician must be prepared for immediate delivery and possible preeclampsia complications in these patients.

Oceanic Pb-isotopic sources of proterozoic and paleozoic volcanogenic massive sulfide deposits on Prince of Wales Island and vicinity, southeastern Alaska

USGS Publications Warehouse

Ayuso, Robert A.; Karl, Susan M.; Slack, John F.; Haeussler, Peter J.; Bittenbender, Peter E.; Wandless, Gregory A.; Colvin, Anna

2005-01-01

Volcanogenic massive sulfide (VMS) deposits on Prince of Wales Island and vicinity in southeastern Alaska are associated with Late Proterozoic through Cambrian volcanosedimentary rocks of the Wales Group and with Ordovician through Early Silurian felsic volcanic rocks of the Moira Sound unit (new informal name). The massive sulfide deposits in the Wales Group include the Big Harbor, Copper City, Corbin, Keete Inlet, Khayyam, Ruby Tuesday, and Stumble-On deposits, and those in the Moira Sound unit include the Barrier Islands, Moira Copper, Niblack, and Nichols Bay deposits. Pb-isotopic signatures were determined on sulfide minerals (galena, pyrite, chalcopyrite, pyrrhotite, and sphalerite) to constrain metal sources of the massive sulfides and for comparison with data for other deposits in the region. Except for the Ruby Tuesday deposit, galena is relatively rare in most of these deposits. Pb-isotopic signatures distinguish the mainly Cu+Zn±Ag±Au massive sulfide deposits in the Wales Group from the Zn+Cu±Ag±Au massive sulfide deposits in the Moira Sound unit. Among the older group of deposits, the Khayyam deposit has the widest variation in Pb-isotopic ratios (206Pb/204Pb=17.169–18.021, 207Pb/204Pb=15.341–15.499, 208Pb/204Pb=36.546–37.817); data for the other massive sulfide deposits in the Wales Group overlap the isotopic variations in the Khayyam deposit. Pb-isotopic ratios for both groups of deposits are lower than those on the average crustal Pbevolution curve (µ=9.74), attesting to a large mantle influence in the Pb source. All the deposits show no evidence for Pb evolution primarily in the upper or lower continental crust. Samples from the younger group of deposits have scattered Pb-isotopic compositions and plot as a broad band on uranogenic and thorogenic Pb diagrams. Data for these deposits overlap the trend for massive sulfide deposits in the Wales Group but extend to significantly more radiogenic Pb-isotopic values. Pb-isotopic ratios of samples from the massive sulfide deposits in the Moira Sound unit plot on a different trend (206Pb/204Pb=17.375–19.418, 207Pb/204Pb=15.361–15.519, 208Pb/204Pb=36.856–37.241) from the steep slope defined by the massive sulfide deposits in the Wales Group. In comparison, the Pb-isotopic ratios of Devonian polymetallic (Pb-Zn-Au-Ag) quartz-sulfide veins vary widely ( 206Pb/204Pb=18.339–18.946, 207Pb/204Pb=15.447–15.561, 208Pb/204Pb=37.358–38.354), straddling the slope defined by the massive sulfide deposits in the Moira Sound unit. The general decrease in 207Pb/204Pb ratio in these deposits, relative to the average crustal Pb-evolution curve, suggests that the most likely lead sources were those associated with oceanic volcanic rocks. The massive sulfide deposits in the Wales Group may have resided within an intraoceanic tectonic setting where the mantle was the predominant contributor of metals. Some contribution from reworked arc material or recycled older, hydrothermally altered oceanic crust (including pelagic sediment) is also possible. Lead sources of the massive sulfide deposits in the Moira Sound unit also included an older source region, possibly a Late Proterozoic or Cambrian volcanosedimentary sequence and the massive sulfide deposits in the Wales Group. Preliminary regional comparison of the Pb-isotopic data indicates that the Greens Creek (Admiralty Island, Alaska) and Windy Craggy (northern British Columbia) deposits probably did not share a common lead source with the VMS deposits on Prince of Wales Island. Other sulfide occurrences on Admiralty Island are also more radiogenic than those on Prince of Wales Island. Large differences in 207Pb/204Pb ratio suggest that the lead in the VMS deposits in different parts of the Alexander terrane evolved from sources with heterogeneous U/Pb ratios, resulting from mixing of mantle and crustal components. 

Multi-source and ontology-based retrieval engine for maize mutant phenotypes

USDA-ARS?s Scientific Manuscript database

In the midst of this genomics era, major plant genome databases are collecting massive amounts of heterogeneous information, including sequence data, gene product information, images of mutant phenotypes, etc., as well as textual descriptions of many of these entities. While basic browsing and sear...

DNA methylation profiling using HpaII tiny fragment enrichment by ligation-mediated PCR (HELP)

PubMed Central

Suzuki, Masako; Greally, John M.

2010-01-01

The HELP assay is a technique that allows genome-wide analysis of cytosine methylation. Here we describe the assay, its relative strengths and weaknesses, and the transition of the assay from a microarray to massively-parallel sequencing-based foundation. PMID:20434563

Genetics Home Reference: Ochoa syndrome

MedlinePlus

... Other researchers believe that a defective heparanase 2 protein may lead to problems with the development of the urinary tract or with muscle ... Peng W, Xu J, Li J, Owens KM, Bloom D, Innis JW. Exome capture and massively parallel sequencing identifies a novel HPSE2 mutation in a Saudi ...

Sedimentology of the fluvial and fluvio-marine facies of the Bahariya Formation (Early Cenomanian), Bahariya Oasis, Western Desert, Egypt

NASA Astrophysics Data System (ADS)

Khalifa, M. A.; Catuneanu, O.

2008-05-01

The Lower Cenomanian Bahariya Formation in the Bahariya Oasis, Western Desert, Egypt, was deposited under two coeval environmental conditions. A fully fluvial system occurs in the southern portion of the Bahariya Oasis, including depositional products of meandering and braided streams, and a coeval fluvio-marine setting is dominant to the north. These deposits are organized into four unconformity-bounded depositional sequences, whose architecture is shaped by a complex system of incised valleys. The fluvial portion of the lower two depositional sequences is dominated by low-energy, meandering systems with a tabular geometry, dominated by overbank facies. The fluvial deposits of the upper two sequences represent the product of sedimentation within braided streams, and consist mainly of amalgamated channel-fills. The braided fluvial systems form the fill of incised valleys whose orientation follows a southeast-northwest trending direction, and which truncate the underlying sequences. Four sedimentary facies have been identified within the braided-channel systems, namely thin-laminated sandstones (Sh), cross-bedded sandstones (Sp, St), massive ferruginous sandstones (Sm) and variegated mudstones (Fm). The exposed off-channel overbank facies of the meandering systems include floodplain (Fm) and crevasse splay (Sl) facies. The fluvio-marine depositional systems consist of interbedded floodplain, coastal and shallow-marine deposits. The floodplain facies include fine-grained sandstones (Sf), laminated siltstones (Stf) and mudstones (Mf) that show fining-upward cycles. The coastal to shallow-marine facies consist primarily of mudstones (Mc) and glauconitic sandstones (Gc) organized vertically in coarsening-upward prograding cyclothems topped by thin crusts of ferricrete (Fc). The four depositional sequences are present across the Bahariya Oasis, albeit with varying degrees of preservation related to post-depositional erosion associated with the formation of sequence boundaries. These unconformities may be overlain by braided-stream channel sandstones at the base of incised valleys, or marked by ferricrete paleosols (lithofacies Fc) in the interfluve areas.

Wind accretion in the massive X-ray binary 4U 2206+54: abnormally slow wind and a moderately eccentric orbit

NASA Astrophysics Data System (ADS)

Ribó, M.; Negueruela, I.; Blay, P.; Torrejón, J. M.; Reig, P.

2006-04-01

Massive X-ray binaries are usually classified by the properties of the donor star in classical, supergiant and Be X-ray binaries, the main difference being the mass transfer mechanism between the two components. The massive X-ray binary 4U 2206+54 does not fit in any of these groups, and deserves a detailed study to understand how the transfer of matter and the accretion on to the compact object take place. To this end we study an IUE spectrum of the donor and obtain a wind terminal velocity (v_∞) of ~350 km s-1, which is abnormally slow for its spectral type. We also analyse here more than 9 years of available RXTE/ASM data. We study the long-term X-ray variability of the source and find it to be similar to that observed in the wind-fed supergiant system Vela X-1, reinforcing the idea that 4U 2206+54 is also a wind-fed system. We find a quasi-period decreasing from ~270 to ~130 d, noticed in previous works but never studied in detail. We discuss possible scenarios for its origin and conclude that long-term quasi-periodic variations in the mass-loss rate of the primary are probably driving such variability in the measured X-ray flux. We obtain an improved orbital period of P_orb=9.5591±0.0007 d with maximum X-ray flux at MJD 51856.6±0.1. Our study of the orbital X-ray variability in the context of wind accretion suggests a moderate eccentricity around 0.15 for this binary system. Moreover, the low value of v_∞ solves the long-standing problem of the relatively high X-ray luminosity for the unevolved nature of the donor, BD +53°2790, which is probably an O9.5 V star. We note that changes in v_∞ and/or the mass-loss rate of the primary alone cannot explain the different patterns displayed by the orbital X-ray variability. We finally emphasize that 4U 2206+54, together with LS 5039, could be part of a new population of wind-fed HMXBs with main sequence donors, the natural progenitors of supergiant X-ray binaries.

Constructing DNA Barcode Sets Based on Particle Swarm Optimization.

PubMed

Wang, Bin; Zheng, Xuedong; Zhou, Shihua; Zhou, Changjun; Wei, Xiaopeng; Zhang, Qiang; Wei, Ziqi

2018-01-01

Following the completion of the human genome project, a large amount of high-throughput bio-data was generated. To analyze these data, massively parallel sequencing, namely next-generation sequencing, was rapidly developed. DNA barcodes are used to identify the ownership between sequences and samples when they are attached at the beginning or end of sequencing reads. Constructing DNA barcode sets provides the candidate DNA barcodes for this application. To increase the accuracy of DNA barcode sets, a particle swarm optimization (PSO) algorithm has been modified and used to construct the DNA barcode sets in this paper. Compared with the extant results, some lower bounds of DNA barcode sets are improved. The results show that the proposed algorithm is effective in constructing DNA barcode sets.

Highly multiplexed subcellular RNA sequencing in situ

PubMed Central

Lee, Je Hyuk; Daugharthy, Evan R.; Scheiman, Jonathan; Kalhor, Reza; Ferrante, Thomas C.; Yang, Joyce L.; Terry, Richard; Jeanty, Sauveur S. F.; Li, Chao; Amamoto, Ryoji; Peters, Derek T.; Turczyk, Brian M.; Marblestone, Adam H.; Inverso, Samuel A.; Bernard, Amy; Mali, Prashant; Rios, Xavier; Aach, John; Church, George M.

2014-01-01

Understanding the spatial organization of gene expression with single nucleotide resolution requires localizing the sequences of expressed RNA transcripts within a cell in situ. Here we describe fluorescent in situ RNA sequencing (FISSEQ), in which stably cross-linked cDNA amplicons are sequenced within a biological sample. Using 30-base reads from 8,742 genes in situ, we examined RNA expression and localization in human primary fibroblasts using a simulated wound healing assay. FISSEQ is compatible with tissue sections and whole mount embryos, and reduces the limitations of optical resolution and noisy signals on single molecule detection. Our platform enables massively parallel detection of genetic elements, including gene transcripts and molecular barcodes, and can be used to investigate cellular phenotype, gene regulation, and environment in situ. PMID:24578530

Experience of targeted Usher exome sequencing as a clinical test

PubMed Central

Besnard, Thomas; García-García, Gema; Baux, David; Vaché, Christel; Faugère, Valérie; Larrieu, Lise; Léonard, Susana; Millan, Jose M; Malcolm, Sue; Claustres, Mireille; Roux, Anne-Françoise

2014-01-01

We show that massively parallel targeted sequencing of 19 genes provides a new and reliable strategy for molecular diagnosis of Usher syndrome (USH) and nonsyndromic deafness, particularly appropriate for these disorders characterized by a high clinical and genetic heterogeneity and a complex structure of several of the genes involved. A series of 71 patients including Usher patients previously screened by Sanger sequencing plus newly referred patients was studied. Ninety-eight percent of the variants previously identified by Sanger sequencing were found by next-generation sequencing (NGS). NGS proved to be efficient as it offers analysis of all relevant genes which is laborious to reach with Sanger sequencing. Among the 13 newly referred Usher patients, both mutations in the same gene were identified in 77% of cases (10 patients) and one candidate pathogenic variant in two additional patients. This work can be considered as pilot for implementing NGS for genetically heterogeneous diseases in clinical service. PMID:24498627

Application of whole genome shotgun sequencing for detection and characterization of genetically modified organisms and derived products.

PubMed

Holst-Jensen, Arne; Spilsberg, Bjørn; Arulandhu, Alfred J; Kok, Esther; Shi, Jianxin; Zel, Jana

2016-07-01

The emergence of high-throughput, massive or next-generation sequencing technologies has created a completely new foundation for molecular analyses. Various selective enrichment processes are commonly applied to facilitate detection of predefined (known) targets. Such approaches, however, inevitably introduce a bias and are prone to miss unknown targets. Here we review the application of high-throughput sequencing technologies and the preparation of fit-for-purpose whole genome shotgun sequencing libraries for the detection and characterization of genetically modified and derived products. The potential impact of these new sequencing technologies for the characterization, breeding selection, risk assessment, and traceability of genetically modified organisms and genetically modified products is yet to be fully acknowledged. The published literature is reviewed, and the prospects for future developments and use of the new sequencing technologies for these purposes are discussed.

Noninvasive prenatal screening for fetal common sex chromosome aneuploidies from maternal blood.

PubMed

Zhang, Bin; Lu, Bei-Yi; Yu, Bin; Zheng, Fang-Xiu; Zhou, Qin; Chen, Ying-Ping; Zhang, Xiao-Qing

2017-04-01

Objective To explore the feasibility of high-throughput massively parallel genomic DNA sequencing technology for the noninvasive prenatal detection of fetal sex chromosome aneuploidies (SCAs). Methods The study enrolled pregnant women who were prepared to undergo noninvasive prenatal testing (NIPT) in the second trimester. Cell-free fetal DNA (cffDNA) was extracted from the mother's peripheral venous blood and a high-throughput sequencing procedure was undertaken. Patients identified as having pregnancies associated with SCAs were offered prenatal fetal chromosomal karyotyping. Results The study enrolled 10 275 pregnant women who were prepared to undergo NIPT. Of these, 57 pregnant women (0.55%) showed fetal SCA, including 27 with Turner syndrome (45,X), eight with Triple X syndrome (47,XXX), 12 with Klinefelter syndrome (47,XXY) and three with 47,XYY. Thirty-three pregnant women agreed to undergo fetal karyotyping and 18 had results consistent with NIPT, while 15 patients received a normal karyotype result. The overall positive predictive value of NIPT for detecting SCAs was 54.54% (18/33) and for detecting Turner syndrome (45,X) was 29.41% (5/17). Conclusion NIPT can be used to identify fetal SCAs by analysing cffDNA using massively parallel genomic sequencing, although the accuracy needs to be improved particularly for Turner syndrome (45,X).

Surface display of a massively variable lipoprotein by a Legionella diversity-generating retroelement.

PubMed

Arambula, Diego; Wong, Wenge; Medhekar, Bob A; Guo, Huatao; Gingery, Mari; Czornyj, Elizabeth; Liu, Minghsun; Dey, Sanghamitra; Ghosh, Partho; Miller, Jeff F

2013-05-14

Diversity-generating retroelements (DGRs) are a unique family of retroelements that confer selective advantages to their hosts by facilitating localized DNA sequence evolution through a specialized error-prone reverse transcription process. We characterized a DGR in Legionella pneumophila, an opportunistic human pathogen that causes Legionnaires disease. The L. pneumophila DGR is found within a horizontally acquired genomic island, and it can theoretically generate 10(26) unique nucleotide sequences in its target gene, legionella determinent target A (ldtA), creating a repertoire of 10(19) distinct proteins. Expression of the L. pneumophila DGR resulted in transfer of DNA sequence information from a template repeat to a variable repeat (VR) accompanied by adenine-specific mutagenesis of progeny VRs at the 3'end of ldtA. ldtA encodes a twin-arginine translocated lipoprotein that is anchored in the outer leaflet of the outer membrane, with its C-terminal variable region surface exposed. Related DGRs were identified in L. pneumophila clinical isolates that encode unique target proteins with homologous VRs, demonstrating the adaptability of DGR components. This work characterizes a DGR that diversifies a bacterial protein and confirms the hypothesis that DGR-mediated mutagenic homing occurs through a conserved mechanism. Comparative bioinformatics predicts that surface display of massively variable proteins is a defining feature of a subset of bacterial DGRs.

Argo_CUDA: Exhaustive GPU based approach for motif discovery in large DNA datasets.

PubMed

Vishnevsky, Oleg V; Bocharnikov, Andrey V; Kolchanov, Nikolay A

2018-02-01

The development of chromatin immunoprecipitation sequencing (ChIP-seq) technology has revolutionized the genetic analysis of the basic mechanisms underlying transcription regulation and led to accumulation of information about a huge amount of DNA sequences. There are a lot of web services which are currently available for de novo motif discovery in datasets containing information about DNA/protein binding. An enormous motif diversity makes their finding challenging. In order to avoid the difficulties, researchers use different stochastic approaches. Unfortunately, the efficiency of the motif discovery programs dramatically declines with the query set size increase. This leads to the fact that only a fraction of top "peak" ChIP-Seq segments can be analyzed or the area of analysis should be narrowed. Thus, the motif discovery in massive datasets remains a challenging issue. Argo_Compute Unified Device Architecture (CUDA) web service is designed to process the massive DNA data. It is a program for the detection of degenerate oligonucleotide motifs of fixed length written in 15-letter IUPAC code. Argo_CUDA is a full-exhaustive approach based on the high-performance GPU technologies. Compared with the existing motif discovery web services, Argo_CUDA shows good prediction quality on simulated sets. The analysis of ChIP-Seq sequences revealed the motifs which correspond to known transcription factor binding sites.

Novel myosin mutations for hereditary hearing loss revealed by targeted genomic capture and massively parallel sequencing

PubMed Central

Brownstein, Zippora; Abu-Rayyan, Amal; Karfunkel-Doron, Daphne; Sirigu, Serena; Davidov, Bella; Shohat, Mordechai; Frydman, Moshe; Houdusse, Anne; Kanaan, Moien; Avraham, Karen B

2014-01-01

Hereditary hearing loss is genetically heterogeneous, with a large number of genes and mutations contributing to this sensory, often monogenic, disease. This number, as well as large size, precludes comprehensive genetic diagnosis of all known deafness genes. A combination of targeted genomic capture and massively parallel sequencing (MPS), also referred to as next-generation sequencing, was applied to determine the deafness-causing genes in hearing-impaired individuals from Israeli Jewish and Palestinian Arab families. Among the mutations detected, we identified nine novel mutations in the genes encoding myosin VI, myosin VIIA and myosin XVA, doubling the number of myosin mutations in the Middle East. Myosin VI mutations were identified in this population for the first time. Modeling of the mutations provided predicted mechanisms for the damage they inflict in the molecular motors, leading to impaired function and thus deafness. The myosin mutations span all regions of these molecular motors, leading to a wide range of hearing phenotypes, reinforcing the key role of this family of proteins in auditory function. This study demonstrates that multiple mutations responsible for hearing loss can be identified in a relatively straightforward manner by targeted-gene MPS technology and concludes that this is the optimal genetic diagnostic approach for identification of mutations responsible for hearing loss. PMID:24105371

DEPDC5 mutations are not a frequent cause of familial temporal lobe epilepsy.

PubMed

Striano, Pasquale; Serioli, Elena; Santulli, Lia; Manna, Ida; Labate, Angelo; Dazzo, Emanuela; Pasini, Elena; Gambardella, Antonio; Michelucci, Roberto; Striano, Salvatore; Nobile, Carlo

2015-10-01

Mutations in the DEPDC5 (DEP domain-containing protein 5) gene are a major cause of familial focal epilepsy with variable foci (FFEVF) and are predicted to account for 12-37% of families with inherited focal epilepsies. To assess the clinical impact of DEPDC5 mutations in familial temporal lobe epilepsy, we screened a collection of Italian families with either autosomal dominant lateral temporal epilepsy (ADLTE) or familial mesial temporal lobe epilepsy (FMTLE). The probands of 28 families classified as ADLTE and 17 families as FMTLE were screened for DEPDC5 mutations by whole exome or targeted massive parallel sequencing. Putative mutations were validated by Sanger sequencing. We identified a DEPDC5 nonsense mutation (c.918C>G; p.Tyr306*) in a family with two affected members, clinically classified as FMTLE. The proband had temporal lobe seizures with prominent psychic symptoms (déjà vu, derealization, and forced thoughts); her mother had temporal lobe seizures, mainly featuring visceral epigastric auras and anxiety. In total, we found a single DEPDC5 mutation in one of (2.2%) 45 families with genetic temporal lobe epilepsy, a proportion much lower than that reported in other inherited focal epilepsies. © 2015 The Authors. Epilepsia published by Wiley Periodicals Inc. on behalf of International League Against Epilepsy.

GPU-BSM: A GPU-Based Tool to Map Bisulfite-Treated Reads

PubMed Central

Manconi, Andrea; Orro, Alessandro; Manca, Emanuele; Armano, Giuliano; Milanesi, Luciano

2014-01-01

Cytosine DNA methylation is an epigenetic mark implicated in several biological processes. Bisulfite treatment of DNA is acknowledged as the gold standard technique to study methylation. This technique introduces changes in the genomic DNA by converting cytosines to uracils while 5-methylcytosines remain nonreactive. During PCR amplification 5-methylcytosines are amplified as cytosine, whereas uracils and thymines as thymine. To detect the methylation levels, reads treated with the bisulfite must be aligned against a reference genome. Mapping these reads to a reference genome represents a significant computational challenge mainly due to the increased search space and the loss of information introduced by the treatment. To deal with this computational challenge we devised GPU-BSM, a tool based on modern Graphics Processing Units. Graphics Processing Units are hardware accelerators that are increasingly being used successfully to accelerate general-purpose scientific applications. GPU-BSM is a tool able to map bisulfite-treated reads from whole genome bisulfite sequencing and reduced representation bisulfite sequencing, and to estimate methylation levels, with the goal of detecting methylation. Due to the massive parallelization obtained by exploiting graphics cards, GPU-BSM aligns bisulfite-treated reads faster than other cutting-edge solutions, while outperforming most of them in terms of unique mapped reads. PMID:24842718

National Borders Effectively Halt the Spread of Rabies: The Current Rabies Epidemic in China Is Dislocated from Cases in Neighboring Countries

PubMed Central

Guo, Zhenyang; Tao, Xiaoyan; Yin, Cuiping; Han, Na; Yu, Jinning; Li, Hao; Liu, Haizhou; Fang, Wei; Adams, James; Wang, Jun; Liang, Guodong; Tang, Qing; Rayner, Simon

2013-01-01

China has seen a massive resurgence of rabies cases in the last 15 years with more than 25,000 human fatalities. Initial cases were reported in the southwest but are now reported in almost every province. There have been several phylogenetic investigations into the origin and spread of the virus within China but few reports investigating the impact of the epidemic on neighboring countries. We therefore collected nucleoprotein sequences from China and South East Asia and investigated their phylogenetic and phylogeographic relationship. Our results indicate that within South East Asia, isolates mainly cluster according to their geographic origin. We found evidence of sporadic exchange of strains between neighboring countries, but it appears that the major strain responsible for the current Chinese epidemic has not been exported. This suggests that national geographical boundaries and border controls are effective at halting the spread of rabies from China into adjacent regions. We further investigated the geographic structure of Chinese sequences and found that the current epidemic is dominated by variant strains that were likely present at low levels in previous domestic epidemics. We also identified epidemiological linkages between high incidence provinces consistent with observations based on surveillance data from human rabies cases. PMID:23383359

National borders effectively halt the spread of rabies: the current rabies epidemic in China is dislocated from cases in neighboring countries.

PubMed

Guo, Zhenyang; Tao, Xiaoyan; Yin, Cuiping; Han, Na; Yu, Jinning; Li, Hao; Liu, Haizhou; Fang, Wei; Adams, James; Wang, Jun; Liang, Guodong; Tang, Qing; Rayner, Simon

2013-01-01

China has seen a massive resurgence of rabies cases in the last 15 years with more than 25,000 human fatalities. Initial cases were reported in the southwest but are now reported in almost every province. There have been several phylogenetic investigations into the origin and spread of the virus within China but few reports investigating the impact of the epidemic on neighboring countries. We therefore collected nucleoprotein sequences from China and South East Asia and investigated their phylogenetic and phylogeographic relationship. Our results indicate that within South East Asia, isolates mainly cluster according to their geographic origin. We found evidence of sporadic exchange of strains between neighboring countries, but it appears that the major strain responsible for the current Chinese epidemic has not been exported. This suggests that national geographical boundaries and border controls are effective at halting the spread of rabies from China into adjacent regions. We further investigated the geographic structure of Chinese sequences and found that the current epidemic is dominated by variant strains that were likely present at low levels in previous domestic epidemics. We also identified epidemiological linkages between high incidence provinces consistent with observations based on surveillance data from human rabies cases.

Tumor Genomic Profiling in Breast Cancer Patients Using Targeted Massively Parallel Sequencing

DTIC Science & Technology

2015-04-30

recently, we identified several novel alterations in in ER+ breast tumors, including translocations in ESR1 , the gene that encodes the estrogen receptor...modified our bait design to include genomic coordinates across select introns in ESR1 . In addition, two recent papers from the Broad Institute published

[Strongyloidosis. Part IX. Treatment].

PubMed

Soroczan, Wiesław

2002-01-01

The treatment of chronic and massive (uncomplicated) and severe (complicated) disseminated strongyloidosis, was presented from the historical point of view. The sequence of achievements in regard of treatment of the gentian violet, dithiazine iodide, benzimidazoles (thiabendazole, mebendazole, albendazole, cambendazole), ivermectin and cyclosporin A, was described. The recommendations for treatment of strongyloidosis are also given.

Agroecological niches and thrips (Thysanoptera: Thripidae) dynamics

Treesearch

Michael E. Irwin

1991-01-01

In 1975, Illinois experienced an exceptionally mild winter, followed by a warm spring. This sequence of climatic events resulted in a massive outbreak of the soybean thrips, Sericothrips variabilis (Beach), along with large numbers of the flower thrips, Frankliniella tritici (Fitch). The outbreak covered an area of over 600...

Origin of the high velocity gas in NGC 6231

NASA Astrophysics Data System (ADS)

Massa, Derck

2017-08-01

It is well known that clusters of massive stars are influenced by the presence of strong winds, that they are sources of diffuse X-rays from shocked gas, and that this gas can be vented into the surrounding region or the halo, forming a critical element in the process of galactic feedback. However, the details of how these different environments interact and evolve are far from complete. Recently, Massa (2017) showed that the peculiar C IV 1550 Ang absorption seen in several otherwise normal main sequence B stars in NGC 6231 is not intrinsic to the stars. Instead, this absorption, which extends to more than -2000 km/s, is due to intervening carbon rich, high speed gas in the cluster environment. In this proposal, we seek to identify the origin of the high speed gas. The proposed observations will enable us to determine whether it is due to the outer wind of the WC star WR79, or to a collective cluster wind, enriched by carbon from the wind of WR79. If it is due to the wind of WR79, then the new data will furnish a novel, less model dependent estimate of the mass loss rate of a WC star. If it is due to a collective wind from the cluster, then we could be witnessing an important stage of galactic feedback. In either case, the proposed observations will provide a unique and significant insight on how massive, open clusters evolve - insight that can only be obtained through UV spectroscopy.

KMOS3D Reveals Low-level Star Formation Activity in Massive Quiescent Galaxies at 0.7 < z < 2.7

NASA Astrophysics Data System (ADS)

Belli, Sirio; Genzel, Reinhard; Förster Schreiber, Natascha M.; Wisnioski, Emily; Wilman, David J.; Wuyts, Stijn; Mendel, J. Trevor; Beifiori, Alessandra; Bender, Ralf; Brammer, Gabriel B.; Burkert, Andreas; Chan, Jeffrey; Davies, Rebecca L.; Davies, Ric; Fabricius, Maximilian; Fossati, Matteo; Galametz, Audrey; Lang, Philipp; Lutz, Dieter; Momcheva, Ivelina G.; Nelson, Erica J.; Saglia, Roberto P.; Tacconi, Linda J.; Tadaki, Ken-ichi; Übler, Hannah; van Dokkum, Pieter

2017-05-01

We explore the Hα emission in the massive quiescent galaxies observed by the KMOS3D survey at 0.7 < z < 2.7. The Hα line is robustly detected in 20 out of 120 UVJ-selected quiescent galaxies, and we classify the emission mechanism using the Hα line width and the [N II]/Hα line ratio. We find that AGNs are likely to be responsible for the line emission in more than half of the cases. We also find robust evidence for star formation activity in nine quiescent galaxies, which we explore in detail. The Hα kinematics reveal rotating disks in five of the nine galaxies. The dust-corrected Hα star formation rates are low (0.2-7 M ⊙ yr-1), and place these systems significantly below the main sequence. The 24 μm-based, infrared luminosities, instead, overestimate the star formation rates. These galaxies present a lower gas-phase metallicity compared to star-forming objects with similar stellar mass, and many of them have close companions. We therefore conclude that the low-level star formation activity in these nine quiescent galaxies is likely to be fueled by inflowing gas or minor mergers, and could be a sign of rejuvenation events. Based on observations collected at the European Southern Observatory under programs 092.A-0091, 093.A-0079, 094.A-0217, 095.A-0047, 096.A-0025, and 097.A-0028.

The highly ionized, high-velocity gas in NGC 6231

NASA Astrophysics Data System (ADS)

Massa, Derck

2017-02-01

It is well known that clusters of massive stars are influenced by the presence of strong winds, that they are sources of diffuse X-rays from shocked gas, and that this gas can be vented into the surrounding region or the halo through the champagne effect. However, the details of how these different environments interact and evolve are far from complete. This paper attributes the broad C IVλλ1500 absorption features (extending to -1900 km s-1) that are seen in the spectra of main sequence B stars in NGC 6231 to gas in the cluster environment and not the B stars themselves. It is shown that the presence of a WC star, WR 79, in the cluster makes this gas detectable because its wind enriches the cluster gas with carbon. Given the available data, it is not clear whether the absorbing gas is simply the far wind of WR 79 or a collective cluster wind enriched by carbon from the wind of WR 79. If it is simply due to the wind, then this wind must flow, unimpeded for more than 2 pc, suggesting that the inner region of the cluster is nearly devoid of obstructing material. If it is actually a collective wind from the cluster, then we could be witnessing an important stage of galactic feedback. In either case, the observations provide a unique and significant piece to the puzzle of how massive, open clusters evolve.

The primordial and evolutionary abundance variations in globular-cluster stars: a problem with two unknowns

NASA Astrophysics Data System (ADS)

Denissenkov, P. A.; VandenBerg, D. A.; Hartwick, F. D. A.; Herwig, F.; Weiss, A.; Paxton, B.

2015-04-01

We demonstrate that among the potential sources of the primordial abundance variations of the proton-capture elements in globular-cluster stars proposed so far, such as the hot-bottom burning in massive asymptotic giant branch stars and H burning in the convective cores of supermassive and fast-rotating massive main-sequence (MS) stars, only the supermassive MS stars with M > 104 M⊙ can explain all the observed abundance correlations without any fine-tuning of model parameters. We use our assumed chemical composition for the pristine gas in M13 (NGC 6205) and its mixtures with 50 and 90 per cent of the material partially processed in H burning in the 6 × 104 M⊙ MS model star as the initial compositions for the normal, intermediate, and extreme populations of low-mass stars in this globular cluster, as suggested by its O-Na anticorrelation. We evolve these stars from the zero-age MS to the red giant branch (RGB) tip with the thermohaline and parametric prescriptions for the RGB extra mixing. We find that the 3He-driven thermohaline convection cannot explain the evolutionary decline of [C/Fe] in M13 RGB stars, which, on the other hand, is well reproduced with the universal values for the mixing depth and rate calibrated using the observed decrease of [C/Fe] with MV in the globular cluster NGC5466 that does not have the primordial abundance variations.

Rotational and radial velocities of 1.3-2.2 M {sub ☉} red giants in open clusters

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

Carlberg, Joleen K., E-mail: jcarlberg@dtm.ciw.edu

2014-06-01

This study presents the rotational distribution of red giant (RG) stars in 11 old to intermediate age open clusters. The masses of these stars are all above the Kraft break, so they lose negligible amounts of their birth angular momentum (AM) during the main-sequence (MS) evolution. However, they do span a mass range with quite different AM distributions imparted during formation, with the stars less massive than ∼1.6M {sub ☉} arriving on the MS with lower rotation rates than the more massive stars. The majority of RGs in this study are slow rotators across the entire red giant branch regardlessmore » of mass, supporting the picture that intermediate-mass stars rapidly spin down when they evolve off the MS and develop convection zones capable of driving a magnetic dynamo. Nevertheless, a small fraction of RGs in open clusters show some level of enhanced rotation, and faster rotators are as common in these clusters as in the field RG population. Most of these enhanced rotators appear to be red clump stars, which is also true of the underlying stellar sample, while others are clearly RGs that are above or below the clump. In addition to rotational velocities, the radial velocities (RVs) and membership probabilities of individual stars are also presented. Cluster heliocentric RVs for NGC 6005 and Pismis 18 are reported for the first time.« less

Formation of Giant Planets and Brown Dwarves

NASA Technical Reports Server (NTRS)

Lissauer, Jack J.

2003-01-01

According to the prevailing core instability model, giant planets begin their growth by the accumulation of small solid bodies, as do terrestrial planets. However, unlike terrestrial planets, the growing giant planet cores become massive enough that they are able to accumulate substantial amounts of gas before the protoplanetary disk dissipates. Models predict that rocky planets should form in orbit about most stars. It is uncertain whether or not gas giant planet formation is common, because most protoplanetary disks may dissipate before solid planetary cores can grow large enough to gravitationally trap substantial quantities of gas. Ongoing theoretical modeling of accretion of giant planet atmospheres, as well as observations of protoplanetary disks, will help decide this issue. Observations of extrasolar planets around main sequence stars can only provide a lower limit on giant planet formation frequency . This is because after giant planets form, gravitational interactions with material within the protoplanetary disk may cause them to migrat inwards and be lost to the central star. The core instability model can only produce planets greater than a few jovian masses within protoplanetary disks that are more viscous than most such disks are believed to be. Thus, few brown dwarves (objects massive enough to undergo substantial deuterium fusion, estimated to occur above approximately 13 jovian masses) are likely to be formed in this manner. Most brown dwarves, as well as an unknown number of free-floating objects of planetary mass, are probably formed as are stars, by the collapse of extended gas/dust clouds into more compact objects.

GENETICS IN ENDOCRINOLOGY: Genetic counseling for congenital hypogonadotropic hypogonadism and Kallmann syndrome: new challenges in the era of oligogenism and next-generation sequencing.

PubMed

Maione, Luigi; Dwyer, Andrew A; Francou, Bruno; Guiochon-Mantel, Anne; Binart, Nadine; Bouligand, Jérôme; Young, Jacques

2018-03-01

Congenital hypogonadotropic hypogonadism (CHH) and Kallmann syndrome (KS) are rare, related diseases that prevent normal pubertal development and cause infertility in affected men and women. However, the infertility carries a good prognosis as increasing numbers of patients with CHH/KS are now able to have children through medically assisted procreation. These are genetic diseases that can be transmitted to patients' offspring. Importantly, patients and their families should be informed of this risk and given genetic counseling. CHH and KS are phenotypically and genetically heterogeneous diseases in which the risk of transmission largely depends on the gene(s) responsible(s). Inheritance may be classically Mendelian yet more complex; oligogenic modes of transmission have also been described. The prevalence of oligogenicity has risen dramatically since the advent of massively parallel next-generation sequencing (NGS) in which tens, hundreds or thousands of genes are sequenced at the same time. NGS is medically and economically more efficient and more rapid than traditional Sanger sequencing and is increasingly being used in medical practice. Thus, it seems plausible that oligogenic forms of CHH/KS will be increasingly identified making genetic counseling even more complex. In this context, the main challenge will be to differentiate true oligogenism from situations when several rare variants that do not have a clear phenotypic effect are identified by chance. This review aims to summarize the genetics of CHH/KS and to discuss the challenges of oligogenic transmission and also its role in incomplete penetrance and variable expressivity in a perspective of genetic counseling. © 2018 European Society of Endocrinology.

Photometric Metallicities of the Small and Large Magellanic Clouds

NASA Astrophysics Data System (ADS)

Miller, Amy Elizabeth

2018-06-01

In the field of astronomy, the study of galaxies is vitally important to understanding the structure and evolution of the universe. Within the study of galaxies, of particular interest are the Small and Large Magellanic Clouds (SMC and LMC, respectively), two of the Milky Way’s closest and most massive satellite galaxies. Their close proximity make them ideal candidates for understanding astrophysical processes such as galaxy interactions. In order to fully understand the Magellanic Clouds, it is imperative that the metallicity of the clouds be mapped in detail. In order to accomplish this task, I will use data from the Survey of Magellanic Stellar History (SMASH) which is a deep, multi-band (ugriz) photometric survey of the Magellanic Clouds that contains approximately 400 million objects in 197 fully-calibrated fields. SMASH is an extensive and deep photometric data set that enables the full-scale study of the galactic structure in the Clouds. The SMASH u-band is sensitive to metallicity for main-sequence turn-off stars which we calibrate using SDSS spectroscopy in overlapping regions (mainly standard star fields). The final steps will be to make metallicity maps of the main bodies and peripheries of the LMC and SMC. Ultimately, these metallicity maps will help us trace out population gradients in the Clouds and uncover the origin of their very extended stellar peripheries.

Characterization of enterotoxigenic Escherichia coli strains isolated from the massive multi-pathogen gastroenteritis outbreak in the Antofagasta region following the Chilean earthquake, 2010.

PubMed

Montero, David; Vidal, Maricel; Pardo, Mirka; Torres, Alexia; Kruger, Eduardo; Farfán, Mauricio; O'Ryan, Miguel; Luo, Qingwei; Fleckenstein, James; Del Canto, Felipe; Vidal, Roberto

2017-08-01

In March 2010, a massive outbreak of gastroenteritis started in the region of Antofagasta (northern Chile). The outbreak was mainly attributed to Norovirus genogroup II although ETEC strains were also isolated with high frequency from clinical samples. We review this outbreak and determined that ETEC was an underestimated etiologic agent. Copyright © 2017 Elsevier B.V. All rights reserved.

Peering into the Dark Side: Magnesium Lines Establish a Massive Neutron Star in PSR J2215+5135

NASA Astrophysics Data System (ADS)

Linares, M.; Shahbaz, T.; Casares, J.

2018-05-01

New millisecond pulsars (MSPs) in compact binaries provide a good opportunity to search for the most massive neutron stars. Their main-sequence companion stars are often strongly irradiated by the pulsar, displacing the effective center of light from their barycenter and making mass measurements uncertain. We present a series of optical spectroscopic and photometric observations of PSR J2215+5135, a “redback” binary MSP in a 4.14 hr orbit, and measure a drastic temperature contrast between the dark/cold (T N = 5660{}-380+260 K) and bright/hot (T D = 8080{}-280+470 K) sides of the companion star. We find that the radial velocities depend systematically on the atmospheric absorption lines used to measure them. Namely, the semi-amplitude of the radial velocity curve (RVC) of J2215 measured with magnesium triplet lines is systematically higher than that measured with hydrogen Balmer lines, by 10%. We interpret this as a consequence of strong irradiation, whereby metallic lines dominate the dark side of the companion (which moves faster) and Balmer lines trace its bright (slower) side. Further, using a physical model of an irradiated star to fit simultaneously the two-species RVCs and the three-band light curves, we find a center-of-mass velocity of K 2 = 412.3 ± 5.0 km s‑1 and an orbital inclination i = 63.°9{}-2.7+2.4. Our model is able to reproduce the observed fluxes and velocities without invoking irradiation by an extended source. We measure masses of M 1 = 2.27{}-0.15+0.17 M ⊙ and M 2 = 0.33{}-0.02+0.03 M ⊙ for the neutron star and the companion star, respectively. If confirmed, such a massive pulsar would rule out some of the proposed equations of state for the neutron star interior.

The Magellanic Bridge Cluster NGC 796: Deep Optical AO Imaging Reveals the Stellar Content and Initial Mass Function of a Massive Open Cluster

NASA Astrophysics Data System (ADS)

Kalari, Venu M.; Carraro, Giovanni; Evans, Christopher J.; Rubio, Monica

2018-04-01

NGC 796 is a massive young cluster located 59 kpc from us in the diffuse intergalactic medium of the 1/5–1/10 Z⊙ Magellanic Bridge, allowing us to probe variations in star formation and stellar evolution processes as a function of metallicity in a resolved fashion, and providing a link between resolved studies of nearby solar-metallicity and unresolved distant metal-poor clusters located in high-redshift galaxies. In this paper, we present adaptive optics griHα imaging of NGC 796 (at 0.″5, which is ∼0.14 pc at the cluster distance) along with optical spectroscopy of two bright members to quantify the cluster properties. Our aim is to explore whether star formation and stellar evolution vary as a function of metallicity by comparing the properties of NGC 796 to higher-metallicity clusters. We find an age of {20}-5+12 Myr from isochronal fitting of the cluster main sequence in the color–magnitude diagram. Based on the cluster luminosity function, we derive a top-heavy stellar initial mass function (IMF) with a slope α = 1.99 ± 0.2, hinting at a metallicity and/or environmental dependence of the IMF, which may lead to a top-heavy IMF in the early universe. Study of the Hα emission-line stars reveals that classical Be stars constitute a higher fraction of the total B-type stars when compared with similar clusters at greater metallicity, providing some support to the chemically homogeneous theory of stellar evolution. Overall, NGC 796 has a total estimated mass of 990 ± 200 M⊙, and a core radius of 1.4 ± 0.3 pc, which classifies it as a massive young open cluster, unique in the diffuse interstellar medium of the Magellanic Bridge.

Massively parallel sequencing of forensic STRs: Considerations of the DNA commission of the International Society for Forensic Genetics (ISFG) on minimal nomenclature requirements.

PubMed

Parson, Walther; Ballard, David; Budowle, Bruce; Butler, John M; Gettings, Katherine B; Gill, Peter; Gusmão, Leonor; Hares, Douglas R; Irwin, Jodi A; King, Jonathan L; Knijff, Peter de; Morling, Niels; Prinz, Mechthild; Schneider, Peter M; Neste, Christophe Van; Willuweit, Sascha; Phillips, Christopher

2016-05-01

The DNA Commission of the International Society for Forensic Genetics (ISFG) is reviewing factors that need to be considered ahead of the adoption by the forensic community of short tandem repeat (STR) genotyping by massively parallel sequencing (MPS) technologies. MPS produces sequence data that provide a precise description of the repeat allele structure of a STR marker and variants that may reside in the flanking areas of the repeat region. When a STR contains a complex arrangement of repeat motifs, the level of genetic polymorphism revealed by the sequence data can increase substantially. As repeat structures can be complex and include substitutions, insertions, deletions, variable tandem repeat arrangements of multiple nucleotide motifs, and flanking region SNPs, established capillary electrophoresis (CE) allele descriptions must be supplemented by a new system of STR allele nomenclature, which retains backward compatibility with the CE data that currently populate national DNA databases and that will continue to be produced for the coming years. Thus, there is a pressing need to produce a standardized framework for describing complex sequences that enable comparison with currently used repeat allele nomenclature derived from conventional CE systems. It is important to discern three levels of information in hierarchical order (i) the sequence, (ii) the alignment, and (iii) the nomenclature of STR sequence data. We propose a sequence (text) string format the minimal requirement of data storage that laboratories should follow when adopting MPS of STRs. We further discuss the variant annotation and sequence comparison framework necessary to maintain compatibility among established and future data. This system must be easy to use and interpret by the DNA specialist, based on a universally accessible genome assembly, and in place before the uptake of MPS by the general forensic community starts to generate sequence data on a large scale. While the established nomenclature for CE-based STR analysis will remain unchanged in the future, the nomenclature of sequence-based STR genotypes will need to follow updated rules and be generated by expert systems that translate MPS sequences to match CE conventions in order to guarantee compatibility between the different generations of STR data. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Investigation into the sequence structure of 23 Y chromosomal STR loci using massively parallel sequencing.

PubMed

Kwon, So Yeun; Lee, Hwan Young; Kim, Eun Hye; Lee, Eun Young; Shin, Kyoung-Jin

2016-11-01

Next-generation sequencing (NGS) can produce massively parallel sequencing (MPS) data for many targeted regions with a high depth of coverage, suggesting its successful application to the amplicons of forensic genetic markers. In the present study, we evaluated the practical utility of MPS in Y-chromosome short tandem repeat (Y-STR) analysis using a multiplex polymerase chain reaction (PCR) system. The multiplex PCR system simultaneously amplified 24 Y-chromosomal markers, including the PowerPlex ® Y23 loci (DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS481, DYS533, DYS549, DYS570, DYS576, DYS635, DYS643, and YGATAH4) and the M175 marker with the small-sized amplicons ranging from 85 to 253bp. The barcoded libraries for the amplicons of the 24 Y-chromosomal markers were produced using a simplified PCR-based library preparation method and successfully sequenced using MPS on a MiSeq ® System with samples from 250 unrelated Korean males. The genotyping concordance between MPS and the capillary electrophoresis (CE) method, as well as the sequence structure of the 23 Y-STRs, were investigated. Three samples exhibited discordance between the MPS and CE results at DYS385, DYS439, and DYS576. There were 12 Y-STR loci that showed sequence variations in the alleles by a fragment size determination, and the most varied alleles occurred in DYS389II with a different sequence structure in the repeat region. The largest increase in gene diversity between the CE and MPS results was in DYS437 at +34.41%. Single nucleotide polymorphisms (SNPs), insertions, and deletions (indels) were observed in the flanking regions of DYS481, DYS576, and DYS385, respectively. Stutter and noise ratios of the 23 Y-STRs using the developed MPS system were also investigated. Based on these results, the MPS analysis system used in this study could facilitate the investigation into the sequences of the 23 Y-STRs in forensic genetics laboratories. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Noninvasive prenatal screening for fetal trisomies 21, 18, 13 and the common sex chromosome aneuploidies from maternal blood using massively parallel genomic sequencing of DNA.

PubMed

Porreco, Richard P; Garite, Thomas J; Maurel, Kimberly; Marusiak, Barbara; Ehrich, Mathias; van den Boom, Dirk; Deciu, Cosmin; Bombard, Allan

2014-10-01

The objective of this study was to validate the clinical performance of massively parallel genomic sequencing of cell-free deoxyribonucleic acid contained in specimens from pregnant women at high risk for fetal aneuploidy to test fetuses for trisomies 21, 18, and 13; fetal sex; and the common sex chromosome aneuploidies (45, X; 47, XXX; 47, XXY; 47, XYY). This was a prospective multicenter observational study of pregnant women at high risk for fetal aneuploidy who had made the decision to pursue invasive testing for prenatal diagnosis. Massively parallel single-read multiplexed sequencing of cell-free deoxyribonucleic acid was performed in maternal blood for aneuploidy detection. Data analysis was completed using sequence reads unique to the chromosomes of interest. A total of 3430 patients were analyzed for demographic characteristics and medical history. There were 137 fetuses with trisomy 21, 39 with trisomy 18, and 16 with trisomy 13 for a prevalence rate of the common autosomal trisomies of 5.8%. There were no false-negative results for trisomy 21, 3 for trisomy 18, and 2 for trisomy 13; all 3 false-positive results were for trisomy 21. The positive predictive values for trisomies 18 and 13 were 100% and 97.9% for trisomy 21. A total of 8.6% of the pregnancies were 21 weeks or beyond; there were no aneuploid fetuses in this group. All 15 of the common sex chromosome aneuploidies in this population were identified, although there were 11 false-positive results for 45,X. Taken together, the positive predictive value for the sex chromosome aneuploidies was 48.4% and the negative predictive value was 100%. Our prospective study demonstrates that noninvasive prenatal analysis of cell-free deoxyribonucleic acid from maternal plasma is an accurate advanced screening test with extremely high sensitivity and specificity for trisomy 21 (>99%) but with less sensitivity for trisomies 18 and 13. Despite high sensitivity, there was modest positive predictive value for the small number of common sex chromosome aneuploidies because of their very low prevalence rate. Copyright © 2014 Elsevier Inc. All rights reserved.

Accurate and exact CNV identification from targeted high-throughput sequence data.

PubMed

Nord, Alex S; Lee, Ming; King, Mary-Claire; Walsh, Tom

2011-04-12

Massively parallel sequencing of barcoded DNA samples significantly increases screening efficiency for clinically important genes. Short read aligners are well suited to single nucleotide and indel detection. However, methods for CNV detection from targeted enrichment are lacking. We present a method combining coverage with map information for the identification of deletions and duplications in targeted sequence data. Sequencing data is first scanned for gains and losses using a comparison of normalized coverage data between samples. CNV calls are confirmed by testing for a signature of sequences that span the CNV breakpoint. With our method, CNVs can be identified regardless of whether breakpoints are within regions targeted for sequencing. For CNVs where at least one breakpoint is within targeted sequence, exact CNV breakpoints can be identified. In a test data set of 96 subjects sequenced across ~1 Mb genomic sequence using multiplexing technology, our method detected mutations as small as 31 bp, predicted quantitative copy count, and had a low false-positive rate. Application of this method allows for identification of gains and losses in targeted sequence data, providing comprehensive mutation screening when combined with a short read aligner.

Secular resonances with massive asteroids and their impact on the dynamics of small bodies

NASA Astrophysics Data System (ADS)

Tsirvoulis, Georgios; Novaković, Bojan; Djošović, Valdimir

2015-08-01

The quest for understanding the dynamical structure of the main belt has been a long-lasting endeavor. From the discovery of the Kirkwood gaps and the Hirayama families, to the more recent advances in secular perturbation theory, the refinement of the proper elements and the discovery of the three-body mean-motion resonances, only to name a few, the progress has been immense. Dynamical models coupled with the outbursts in computational power and observations have greatly improved our knowledge of the dynamical evolution of the small bodies in the Solar System.While our set of tools for studying the dynamical porperties of the main belt is believed to be sufficiently complete, our assumptions on how to use them seem to have hindered this effort.The concensus has been that, judging by their mass, only the planets, especially the giant ones, can act as efficient perturbers of the orbits of asteroids. Thus a lot of studies have been made on the locations and effects of secular resonances with the giant planets in different parts of the main belt, explaining among other things the presence of gaps in the distribution of asteroids, strange shapes of some asteroid families and transport mechanisms of asteroids to the near-Earth region.Our work is motivated by the first discovery that a secular resonance with the most massive asteroid, Ceres, is the dominant dynamical mechanism responsible for the post-impact evolution of the Hoffmeister family members. Thus the concensus is wrong. Knowing now, that secular resonances with massive asteroids can be effective on asteroid dynamics, we set out to construct a dynamical map of these resonances across the main belt.Our study is focused on the linear and degree four non-linear secular resonances with the two most massive asteroids (1) Ceres and (4) Vesta. First we determine the locations of these secular resonances in the proper elements space, acquiring an understanding of the potentially affected regions, and then we perform numerical simulations to investigate the importance of each secular resonance on the dynamical evolution of asteroid orbits in the different parts of the main belt.

An excess of massive stars in the local 30 Doradus starburst

NASA Astrophysics Data System (ADS)

Schneider, F. R. N.; Sana, H.; Evans, C. J.; Bestenlehner, J. M.; Castro, N.; Fossati, L.; Gräfener, G.; Langer, N.; Ramírez-Agudelo, O. H.; Sabín-Sanjulián, C.; Simón-Díaz, S.; Tramper, F.; Crowther, P. A.; de Koter, A.; de Mink, S. E.; Dufton, P. L.; Garcia, M.; Gieles, M.; Hénault-Brunet, V.; Herrero, A.; Izzard, R. G.; Kalari, V.; Lennon, D. J.; Maíz Apellániz, J.; Markova, N.; Najarro, F.; Podsiadlowski, Ph.; Puls, J.; Taylor, W. D.; van Loon, J. Th.; Vink, J. S.; Norman, C.

2018-01-01

The 30 Doradus star-forming region in the Large Magellanic Cloud is a nearby analog of large star-formation events in the distant universe. We determined the recent formation history and the initial mass function (IMF) of massive stars in 30 Doradus on the basis of spectroscopic observations of 247 stars more massive than 15 solar masses (M☉). The main episode of massive star formation began about 8 million years (My) ago, and the star-formation rate seems to have declined in the last 1 My. The IMF is densely sampled up to 200 M☉ and contains 32 ± 12% more stars above 30 M☉ than predicted by a standard Salpeter IMF. In the mass range of 15 to 200 M☉, the IMF power-law exponent is 1.90‑0.26+0.37, shallower than the Salpeter value of 2.35.

An excess of massive stars in the local 30 Doradus starburst.

PubMed

Schneider, F R N; Sana, H; Evans, C J; Bestenlehner, J M; Castro, N; Fossati, L; Gräfener, G; Langer, N; Ramírez-Agudelo, O H; Sabín-Sanjulián, C; Simón-Díaz, S; Tramper, F; Crowther, P A; de Koter, A; de Mink, S E; Dufton, P L; Garcia, M; Gieles, M; Hénault-Brunet, V; Herrero, A; Izzard, R G; Kalari, V; Lennon, D J; Maíz Apellániz, J; Markova, N; Najarro, F; Podsiadlowski, Ph; Puls, J; Taylor, W D; van Loon, J Th; Vink, J S; Norman, C

2018-01-05

The 30 Doradus star-forming region in the Large Magellanic Cloud is a nearby analog of large star-formation events in the distant universe. We determined the recent formation history and the initial mass function (IMF) of massive stars in 30 Doradus on the basis of spectroscopic observations of 247 stars more massive than 15 solar masses ([Formula: see text]). The main episode of massive star formation began about 8 million years (My) ago, and the star-formation rate seems to have declined in the last 1 My. The IMF is densely sampled up to 200 [Formula: see text] and contains 32 ± 12% more stars above 30 [Formula: see text] than predicted by a standard Salpeter IMF. In the mass range of 15 to 200 [Formula: see text], the IMF power-law exponent is [Formula: see text], shallower than the Salpeter value of 2.35. Copyright © 2018, American Association for the Advancement of Science.

GenoMycDB: a database for comparative analysis of mycobacterial genes and genomes.

PubMed

Catanho, Marcos; Mascarenhas, Daniel; Degrave, Wim; Miranda, Antonio Basílio de

2006-03-31

Several databases and computational tools have been created with the aim of organizing, integrating and analyzing the wealth of information generated by large-scale sequencing projects of mycobacterial genomes and those of other organisms. However, with very few exceptions, these databases and tools do not allow for massive and/or dynamic comparison of these data. GenoMycDB (http://www.dbbm.fiocruz.br/GenoMycDB) is a relational database built for large-scale comparative analyses of completely sequenced mycobacterial genomes, based on their predicted protein content. Its central structure is composed of the results obtained after pair-wise sequence alignments among all the predicted proteins coded by the genomes of six mycobacteria: Mycobacterium tuberculosis (strains H37Rv and CDC1551), M. bovis AF2122/97, M. avium subsp. paratuberculosis K10, M. leprae TN, and M. smegmatis MC2 155. The database stores the computed similarity parameters of every aligned pair, providing for each protein sequence the predicted subcellular localization, the assigned cluster of orthologous groups, the features of the corresponding gene, and links to several important databases. Tables containing pairs or groups of potential homologs between selected species/strains can be produced dynamically by user-defined criteria, based on one or multiple sequence similarity parameters. In addition, searches can be restricted according to the predicted subcellular localization of the protein, the DNA strand of the corresponding gene and/or the description of the protein. Massive data search and/or retrieval are available, and different ways of exporting the result are offered. GenoMycDB provides an on-line resource for the functional classification of mycobacterial proteins as well as for the analysis of genome structure, organization, and evolution.

Early rifting deposition: examples from carbonate sequences of Sardinia (Cambrian) and Tuscany (Triassic-Jurassic), Italy: an analogous tectono-sedimentary and climatic context

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

Cocozza, T.; Gandin, A.

Lower Cambrian Ceroide Limestone (Sardinia) and Lower Jurassic Massiccio Limestone (Tuscany) belong to sequences deposited in analogous tectono-sedimentary context: the former linked to the Caledonian Sardic Phase, the latter to the Alpine Orogeny. Both units consist of massive pure limestone characterized by marginal and lagoonal sequences repeatedly interfingering in the same geological structure. This distribution indicates a morphology of the platforms composed of banks (marginal facies) and shallow basins (lagoonal facies) comparable with a Bahamian complex. Dolomitization affects patchily the massive limestone bodies, and karstic features, breccias, and sedimentary dikes occur at their upper boundary. Both units overlie early dolomitemore » and evaporites (sabkha facies) containing siliciclastic intercalations in their lower and/or upper part and are unconformably covered by open-shelf red (hematitic), nodular limestone Ammonitico Rosso facies). The sedimentary evolution of the two sequences appears to have been controlled by synsedimentary tectonics whose major effects are the end of the terrigenous input, the bank-and-basin morphology of the platform, the irregular distribution of the dolomitization, and the nodular fabric of the overlying facies. The end of the Bahamian-type system is marked by the karstification of the emerged blocks and is followed by their differential sinking and burial under red-nodular facies. From a geodynamic viewpoint, sequences composed of Bahamian-like platform carbonates followed by Ammonitico Rosso facies imply deposition along continental margins subjected to block-faulting during an extensional regime connected with the beginning of continental rifting. Moreover, the variation from sabkha to Bahamian conditions suggests the drifting of the continent from arid to humid, tropical areas.« less

Enhanced sequencing coverage with digital droplet multiple displacement amplification

PubMed Central

Sidore, Angus M.; Lan, Freeman; Lim, Shaun W.; Abate, Adam R.

2016-01-01

Sequencing small quantities of DNA is important for applications ranging from the assembly of uncultivable microbial genomes to the identification of cancer-associated mutations. To obtain sufficient quantities of DNA for sequencing, the small amount of starting material must be amplified significantly. However, existing methods often yield errors or non-uniform coverage, reducing sequencing data quality. Here, we describe digital droplet multiple displacement amplification, a method that enables massive amplification of low-input material while maintaining sequence accuracy and uniformity. The low-input material is compartmentalized as single molecules in millions of picoliter droplets. Because the molecules are isolated in compartments, they amplify to saturation without competing for resources; this yields uniform representation of all sequences in the final product and, in turn, enhances the quality of the sequence data. We demonstrate the ability to uniformly amplify the genomes of single Escherichia coli cells, comprising just 4.7 fg of starting DNA, and obtain sequencing coverage distributions that rival that of unamplified material. Digital droplet multiple displacement amplification provides a simple and effective method for amplifying minute amounts of DNA for accurate and uniform sequencing. PMID:26704978

Molecular line study of massive star-forming regions from the Red MSX Source survey

NASA Astrophysics Data System (ADS)

Yu, Naiping; Wang, Jun-Jie

2014-05-01

In this paper, we have selected a sample of massive star-forming regions from the Red MSX Source survey, in order to study star formation activities (mainly outflow and inflow signatures). We have focused on three molecular lines from the Millimeter Astronomy Legacy Team Survey at 90 GHz: HCO+(1-0), H13CO+(1-0) and SiO(2-1). According to previous observations, our sources can be divided into two groups: nine massive young stellar object candidates (radio-quiet) and 10 H II regions (which have spherical or unresolved radio emissions). Outflow activities have been found in 11 sources, while only three show inflow signatures in all. The high outflow detection rate means that outflows are common in massive star-forming regions. The inflow detection rate was relatively low. We suggest that this was because of the beam dilution of the telescope. All three inflow candidates have outflow(s). The outward radiation and thermal pressure from the central massive star(s) do not seem to be strong enough to halt accretion in G345.0034-00.2240. Our simple model of G318.9480-00.1969 shows that it has an infall velocity of about 1.8 km s-1. The spectral energy distribution analysis agrees our sources are massive and intermediate-massive star formation regions.

Cosmic Explosions, Life in the Universe, and the Cosmological Constant.

PubMed

Piran, Tsvi; Jimenez, Raul; Cuesta, Antonio J; Simpson, Fergus; Verde, Licia

2016-02-26

Gamma-ray bursts (GRBs) are copious sources of gamma rays whose interaction with a planetary atmosphere can pose a threat to complex life. Using recent determinations of their rate and probability of causing massive extinction, we explore what types of universes are most likely to harbor advanced forms of life. We use cosmological N-body simulations to determine at what time and for what value of the cosmological constant (Λ) the chances of life being unaffected by cosmic explosions are maximized. Life survival to GRBs favors Lambda-dominated universes. Within a cold dark matter model with a cosmological constant, the likelihood of life survival to GRBs is governed by the value of Λ and the age of the Universe. We find that we seem to live in a favorable point in this parameter space that minimizes the exposure to cosmic explosions, yet maximizes the number of main sequence (hydrogen-burning) stars around which advanced life forms can exist.

A Model Connecting Galaxy Masses, Star Formation Rates, and Dust Temperatures across Cosmic Time

NASA Astrophysics Data System (ADS)

Imara, Nia; Loeb, Abraham; Johnson, Benjamin D.; Conroy, Charlie; Behroozi, Peter

2018-02-01

We investigate the evolution of dust content in galaxies from redshifts z = 0 to z = 9.5. Using empirically motivated prescriptions, we model galactic-scale properties—including halo mass, stellar mass, star formation rate, gas mass, and metallicity—to make predictions for the galactic evolution of dust mass and dust temperature in main-sequence galaxies. Our simple analytic model, which predicts that galaxies in the early universe had greater quantities of dust than their low-redshift counterparts, does a good job of reproducing observed trends between galaxy dust and stellar mass out to z ≈ 6. We find that for fixed galaxy stellar mass, the dust temperature increases from z = 0 to z = 6. Our model forecasts a population of low-mass, high-redshift galaxies with interstellar dust as hot as, or hotter than, their more massive counterparts; but this prediction needs to be constrained by observations. Finally, we make predictions for observing 1.1 mm flux density arising from interstellar dust emission with the Atacama Large Millimeter Array.

Stellar encounters involving neutron stars in globular cluster cores

NASA Technical Reports Server (NTRS)

Davies, M. B.; Benz, W.; Hills, J. G.

1992-01-01

Encounters between a 1.4 solar mass neutron star and a 0.8 solar mass red giant (RG) and between a 1.4 solar mass neutron star (NS) and an 0.8 solar mass main-sequence (MS) star have been successfully simulated. In the case of encounters involving an RG, bound systems are produced when the separation at periastron passage R(MIN) is less than about 2.5 R(RG). At least 70 percent of these bound systems are composed of the RG core and NS forming a binary engulfed in a common envelope of what remains of the former RG envelope. Once the envelope is ejected, a tight white dwarf-NS binary remains. For MS stars, encounters with NSs will produce bound systems when R(MIN) is less than about 3.5 R(MS). Some 50 percent of these systems will be single objects with the NS engulfed in a thick disk of gas almost as massive as the original MS star. The ultimate fate of such systems is unclear.

A stellar audit: the computation of encounter rates for 47 Tucanae and omega Centauri

NASA Astrophysics Data System (ADS)

Davies, Melvyn B.; Benz, Willy

1995-10-01

Using King-Mitchie models, we compute encounter rates between the various stellar species in the globular clusters omega Cen and 47 Tuc. We also compute event rates for encounters between single stars and a population of primordial binaries. Using these rates, and what we have learnt from hydrodynamical simulations of encounters performed earlier, we compute the production rates of objects such as low-mass X-ray binaries (LMXBs), smothered neutron stars and blue stragglers (massive main-sequence stars). If 10 per cent of the stars are contained in primordial binaries, the production rate of interesting objects from encounters involving these binaries is as large as that from encounters between single stars. For example, encounters involving binaries produce a significant number of blue stragglers in both globular cluster models. The number of smothered neutron stars may exceed the number of LMXBs by a factor of 5-20, which may help to explain why millisecond pulsars are observed to outnumber LMXBs in globular clusters.

The black tide model of QSOs

NASA Technical Reports Server (NTRS)

Young, P. J.; Shields, G. A.; Wheeler, J. C.

1977-01-01

The paper develops certain aspects of a model wherein a QSO is a massive black hole located in a dense galactic nucleus, with its growth and luminosity fueled by tidal disruption of passing stars. Cross sections for tidal disruptions are calculated, taking into account the thermal energy of stars, relativistic effects, and partial disruption removing only the outer layers of a star. Accretion rates are computed for a realistic distribution of stellar masses and evolutionary phases, the effect of the black hole on the cluster distribution is examined, and the red-giant disruption rate is evaluated for hole mass of at least 300 million solar masses, the cutoff of disruption of main-sequence stars. The results show that this black-tide model can explain QSO luminosities of at least 1 trillion suns if the black hole remains almost maximally Kerr as it grows above 100 million solar masses and if 'loss-cone' depletion of the number of stars in disruptive orbits is unimportant.

Fluid-faulting interactions: Fracture-mesh and fault-valve behavior in the February 2014 Mammoth Mountain, California, earthquake swarm

USGS Publications Warehouse

Shelly, David R.; Taira, Taka’aki; Prejean, Stephanie; Hill, David P.; Dreger, Douglas S.

2015-01-01

Faulting and fluid transport in the subsurface are highly coupled processes, which may manifest seismically as earthquake swarms. A swarm in February 2014 beneath densely monitored Mammoth Mountain, California, provides an opportunity to witness these interactions in high resolution. Toward this goal, we employ massive waveform-correlation-based event detection and relative relocation, which quadruples the swarm catalog to more than 6000 earthquakes and produces high-precision locations even for very small events. The swarm's main seismic zone forms a distributed fracture mesh, with individual faults activated in short earthquake bursts. The largest event of the sequence, M 3.1, apparently acted as a fault valve and was followed by a distinct wave of earthquakes propagating ~1 km westward from the updip edge of rupture, 1–2 h later. Late in the swarm, multiple small, shallower subsidiary faults activated with pronounced hypocenter migration, suggesting that a broader fluid pressure pulse propagated through the subsurface.

New Binaries in the ɛ Cha Association

NASA Astrophysics Data System (ADS)

Briceño, César; Tokovinin, Andrei

2017-11-01

We present Adaptive Optics-aided speckle observations of 47 young stars in the ɛ Cha association made at the 4 m Southern Astrophysical Research Telescope in the I-band. We resolved 10 new binary pairs, 5 previously known binaries, and 2 triple systems, also previously known. In the separation range between 4 and 300 au, the 30 association members of spectral types G0 and later host 6 binary companions, leading to the raw companion frequency of 0.010 ± 0.04 per decade of separation, comparable to the main sequence dwarfs in the field. On the other hand, all five massive association members of spectral types A and B have companions in this range. We discuss the newly resolved and known binaries in our sample. Observed motions in the triple system ɛ Cha, composed of three similar B9V stars, can be described by tentative orbits with periods 13 and ˜900 years and a large mutual inclination. Based on observations obtained at the Southern Astrophysical Research (SOAR) telescope.

Feedback and Feeding in the Context of Galaxy Evolution with SPICA: Direct Characterisation of Molecular Outflows and Inflows

NASA Astrophysics Data System (ADS)

González-Alfonso, E.; Armus, L.; Carrera, F. J.; Charmandaris, V.; Efstathiou, A.; Egami, E.; Fernández-Ontiveros, J. A.; Fischer, J.; Granato, G. L.; Gruppioni, C.; Hatziminaoglou, E.; Imanishi, M.; Isobe, N.; Kaneda, H.; Koziel-Wierzbowska, D.; Malkan, M. A.; Martín-Pintado, J.; Mateos, S.; Matsuhara, H.; Miniutti, G.; Nakagawa, T.; Pozzi, F.; Rico-Villas, F.; Rodighiero, G.; Roelfsema, P.; Spinoglio, L.; Spoon, H. W. W.; Sturm, E.; van der Tak, F.; Vignali, C.; Wang, L.

2017-11-01

A far-infrared observatory such as the SPace Infrared telescope for Cosmology and Astrophysics, with its unprecedented spectroscopic sensitivity, would unveil the role of feedback in galaxy evolution during the last 10 Gyr of the Universe (z = 1.5-2), through the use of far- and mid-infrared molecular and ionic fine structure lines that trace outflowing and infalling gas. Outflowing gas is identified in the far-infrared through P-Cygni line shapes and absorption blueshifted wings in molecular lines with high dipolar moments, and through emission line wings of fine-structure lines of ionised gas. We quantify the detectability of galaxy-scale massive molecular and ionised outflows as a function of redshift in AGN-dominated, starburst-dominated, and main-sequence galaxies, explore the detectability of metal-rich inflows in the local Universe, and describe the most significant synergies with other current and future observatories that will measure feedback in galaxies via complementary tracers at other wavelengths.

TYC 3159-6-1: a runaway blue supergiant

NASA Astrophysics Data System (ADS)

Gvaramadze, V. V.; Miroshnichenko, A. S.; Castro, N.; Langer, N.; Zharikov, S. V.

2014-01-01

We report the results of optical spectroscopy of a candidate evolved massive star in the Cygnus-X region, TYC 3159-6-1, revealed via detection of its curious circumstellar nebula in archival data of the Spitzer Space Telescope. We classify TYC 3159-6-1 as an O9.5-O9.7 Ib star and derive its fundamental parameters by using the stellar atmosphere code FASTWIND. The He and CNO abundances in the photosphere of TYC 3159-6-1 are consistent with the solar abundances, suggesting that the star only recently evolved off the main sequence. Proper motion and radial velocity measurements for TYC 3159-6-1 show that it is a runaway star. We propose that Dolidze 7 is its parent cluster. We discuss the origin of the nebula around TYC 3159-6-1 and suggest that it might be produced in several successive episodes of enhanced mass-loss rate (outbursts) caused by rotation of the star near the critical Ω limit.

Cosmic Explosions, Life in the Universe, and the Cosmological Constant

NASA Astrophysics Data System (ADS)

Piran, Tsvi; Jimenez, Raul; Cuesta, Antonio J.; Simpson, Fergus; Verde, Licia

2016-02-01

Gamma-ray bursts (GRBs) are copious sources of gamma rays whose interaction with a planetary atmosphere can pose a threat to complex life. Using recent determinations of their rate and probability of causing massive extinction, we explore what types of universes are most likely to harbor advanced forms of life. We use cosmological N -body simulations to determine at what time and for what value of the cosmological constant (Λ ) the chances of life being unaffected by cosmic explosions are maximized. Life survival to GRBs favors Lambda-dominated universes. Within a cold dark matter model with a cosmological constant, the likelihood of life survival to GRBs is governed by the value of Λ and the age of the Universe. We find that we seem to live in a favorable point in this parameter space that minimizes the exposure to cosmic explosions, yet maximizes the number of main sequence (hydrogen-burning) stars around which advanced life forms can exist.

Forensic Analysis of the May 2014 West Salt Creek Rock Avalanche in Western Colorado

NASA Astrophysics Data System (ADS)

Coe, J. A.; Baum, R. L.; Allstadt, K.; Kochevar, B. F.; Schmitt, R. G.; Morgan, M. L.; White, J. L.; Stratton, B. T.; Hayashi, T. A.; Kean, J. W.

2015-12-01

The rain-on-snow induced West Salt Creek rock avalanche occurred on May 25, 2014 on the northern flank of Grand Mesa. The avalanche was rare for the contiguous U.S. because of its large size (59 M m3) and high mobility (Length/Height=7.2). To understand the avalanche failure sequence, mechanisms, and mobility, we conducted a forensic analysis using large-scale (1:1000) structural mapping and seismic data. We used high-resolution, Unmanned Aircraft System (UAS) imagery as a base for our field mapping and analyzed seismic data from 22 broadband stations (distances <656 km) and one short-period network. We inverted broadband data to derive a time series of forces that the avalanche exerted on the earth and tracked these forces using curves in the avalanche path. Our results revealed that the rock avalanche was a cascade of landslide events, rather than a single massive failure. The sequence began with a landslide/debris flow that started about 10 hours before the main avalanche. The main avalanche lasted just over 3 minutes and traveled at average velocities ranging from 15 to 36 m/s. For at least two hours after the avalanche ceased movement, a central, hummock-rich, strike-slip bound core continued to move slowly. Following movement of the core, numerous shallow landslides, rock slides, and rock falls created new structures and modified topography. Mobility of the main avalanche and central core were likely enhanced by valley floor material that liquefied from undrained loading by the overriding avalanche. Although the base was likely at least partially liquefied, our mapping indicates that the overriding avalanche internally deformed predominantly by sliding along discrete shear surfaces in material that was nearly dry and had substantial frictional strength. These results indicate that the West Salt Creek avalanche, and probably other long-traveled avalanches, could be modeled as two layers: a liquefied basal layer; and a thicker and stronger overriding layer.

GOODS-HERSCHEL: STAR FORMATION, DUST ATTENUATION, AND THE FIR–RADIO CORRELATION ON THE MAIN SEQUENCE OF STAR-FORMING GALAXIES UP TO z ≃ 4

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

Pannella, M.; Elbaz, D.; Daddi, E.

We use deep panchromatic data sets in the GOODS-N field, from GALEX to the deepest Herschel far-infrared (FIR) and VLA radio continuum imaging, to explore the evolution of star-formation activity and dust attenuation properties of star-forming galaxies to z ≃ 4, using mass-complete samples. Our main results can be summarized as follows: (i) the slope of the star-formation rate–M{sub *} correlation is consistent with being constant ≃0.8 up to z ≃ 1.5, while its normalization keeps increasing with redshift; (ii) for the first time we are able to explore the FIR–radio correlation for a mass-selected sample of star-forming galaxies: themore » correlation does not evolve up to z ≃ 4; (iii) we confirm that galaxy stellar mass is a robust proxy for UV dust attenuation in star-forming galaxies, with more massive galaxies being more dust attenuated. Strikingly, we find that this attenuation relation evolves very weakly with redshift, with the amount of dust attenuation increasing by less than 0.3 mag over the redshift range [0.5–4] for a fixed stellar mass; (iv) the correlation between dust attenuation and the UV spectral slope evolves with redshift, with the median UV slope becoming bluer with redshift. By z ≃ 3, typical UV slopes are inconsistent, given the measured dust attenuations, with the predictions of commonly used empirical laws. (v) Finally, building on existing results, we show that gas reddening is marginally larger (by a factor of around 1.3) than the stellar reddening at all redshifts probed. Our results support a scenario where the ISM conditions of typical star-forming galaxies evolve with redshift, such that at z ≥ 1.5 Main Sequence galaxies have ISM conditions moving closer to those of local starbursts.« less

A massive expansion of effector genes underlies gall-formation in the wheat pest Mayetiola destructor

USDA-ARS?s Scientific Manuscript database

The mechanisms arthropods use to induce plant gall formation are poorly understood. However, there is growing evidence that effector proteins are involved. To examine this hypothesis, we sequenced the genome of the Hessian fly (Mayetiola destructor, M. des), an obligate plant parasitic gall midge an...

Phylogeny and active ingredients of artificial Ophiocordyceps lanpingensis ascomata

NASA Astrophysics Data System (ADS)

Chen, Zihong; Xu, Ling; Yu, Hong; Zeng, Wenbo; Dai, Yongdong; Wang, Yuanbing

2018-04-01

To evaluate the morphological character, phylogenesis and functional components of artificial Ophiocordyceps lanpingensis, a related species of O. sinensis. The ascomata of O. lanpingensis was induced with its asexual strain, HLANY0707 and its microscopic feature was described. Phylogenesis was analyzed with ITS-5.8S sequences of HLANY0707, its cultured stroma, and 39 relative sequences of Hirsutella and Ophiocordyceps based on the maximum likelihood tree. Six nucleosides of artificial O. lanpingensis, natural O. lanpingensis and natural O. sinensis were compared with HPLC analysis. Artificial ascomata of O. lanpingensis could be massively produced with HLANY0707 and had similar microscopic features as the nature specimens. Phylogenetic analysis showed that both the artificial and natural O. lanpingensis had closer relationship with O. sinensis, O. xuefengensis, H. uncinata and O. robertsii, the species whose massively cultured ascomata being not reported. Nucleosides of artificial O. lanpingensis were very similar to natural O. sinensis, implying a promising application prospect of artificial O. lanpingensis as an alternative to O. sinensis. It showed a promising way to develop artificial O. lanpingensis and conserve the rare and endangered species, O. sinensis.

Massive contribution of transposable elements to mammalian regulatory sequences.

PubMed

Rayan, Nirmala Arul; Del Rosario, Ricardo C H; Prabhakar, Shyam

2016-09-01

Barbara McClintock discovered the existence of transposable elements (TEs) in the late 1940s and initially proposed that they contributed to the gene regulatory program of higher organisms. This controversial idea gained acceptance only much later in the 1990s, when the first examples of TE-derived promoter sequences were uncovered. It is now known that half of the human genome is recognizably derived from TEs. It is thus important to understand the scope and nature of their contribution to gene regulation. Here, we provide a timeline of major discoveries in this area and discuss how transposons have revolutionized our understanding of mammalian genomes, with a special emphasis on the massive contribution of TEs to primate evolution. Our analysis of primate-specific functional elements supports a simple model for the rate at which new functional elements arise in unique and TE-derived DNA. Finally, we discuss some of the challenges and unresolved questions in the field, which need to be addressed in order to fully characterize the impact of TEs on gene regulation, evolution and disease processes. Copyright © 2016 Elsevier Ltd. All rights reserved.

HuH-7 reference genome profile: complex karyotype composed of massive loss of heterozygosity.

PubMed

Kasai, Fumio; Hirayama, Noriko; Ozawa, Midori; Satoh, Motonobu; Kohara, Arihiro

2018-05-17

Human cell lines represent a valuable resource as in vitro experimental models. A hepatoma cell line, HuH-7 (JCRB0403), has been used extensively in various research fields and a number of studies using this line have been published continuously since it was established in 1982. However, an accurate genome profile, which can be served as a reliable reference, has not been available. In this study, we performed M-FISH, SNP microarray and amplicon sequencing to characterize the cell line. Single cell analysis of metaphases revealed a high level of heterogeneity with a mode of 60 chromosomes. Cytogenetic results demonstrated chromosome abnormalities involving every chromosome in addition to a massive loss of heterozygosity, which accounts for 55.3% of the genome, consistent with the homozygous variants seen in the sequence analysis. We provide empirical data that the HuH-7 cell line is composed of highly heterogeneous cell populations, suggesting that besides cell line authentication, the quality of cell lines needs to be taken into consideration in the future use of tumor cell lines.

Toward a new paradigm of DNA writing using a massively parallel sequencing platform and degenerate oligonucleotide

PubMed Central

Hwang, Byungjin; Bang, Duhee

2016-01-01

All synthetic DNA materials require prior programming of the building blocks of the oligonucleotide sequences. The development of a programmable microarray platform provides cost-effective and time-efficient solutions in the field of data storage using DNA. However, the scalability of the synthesis is not on par with the accelerating sequencing capacity. Here, we report on a new paradigm of generating genetic material (writing) using a degenerate oligonucleotide and optomechanical retrieval method that leverages sequencing (reading) throughput to generate the desired number of oligonucleotides. As a proof of concept, we demonstrate the feasibility of our concept in digital information storage in DNA. In simulation, the ability to store data is expected to exponentially increase with increase in degenerate space. The present study highlights the major framework change in conventional DNA writing paradigm as a sequencer itself can become a potential source of making genetic materials. PMID:27876825

Toward a new paradigm of DNA writing using a massively parallel sequencing platform and degenerate oligonucleotide.

PubMed

Hwang, Byungjin; Bang, Duhee

2016-11-23

All synthetic DNA materials require prior programming of the building blocks of the oligonucleotide sequences. The development of a programmable microarray platform provides cost-effective and time-efficient solutions in the field of data storage using DNA. However, the scalability of the synthesis is not on par with the accelerating sequencing capacity. Here, we report on a new paradigm of generating genetic material (writing) using a degenerate oligonucleotide and optomechanical retrieval method that leverages sequencing (reading) throughput to generate the desired number of oligonucleotides. As a proof of concept, we demonstrate the feasibility of our concept in digital information storage in DNA. In simulation, the ability to store data is expected to exponentially increase with increase in degenerate space. The present study highlights the major framework change in conventional DNA writing paradigm as a sequencer itself can become a potential source of making genetic materials.

Protein Science by DNA Sequencing: How Advances in Molecular Biology Are Accelerating Biochemistry.

PubMed

Higgins, Sean A; Savage, David F

2018-01-09

A fundamental goal of protein biochemistry is to determine the sequence-function relationship, but the vastness of sequence space makes comprehensive evaluation of this landscape difficult. However, advances in DNA synthesis and sequencing now allow researchers to assess the functional impact of every single mutation in many proteins, but challenges remain in library construction and the development of general assays applicable to a diverse range of protein functions. This Perspective briefly outlines the technical innovations in DNA manipulation that allow massively parallel protein biochemistry and then summarizes the methods currently available for library construction and the functional assays of protein variants. Areas in need of future innovation are highlighted with a particular focus on assay development and the use of computational analysis with machine learning to effectively traverse the sequence-function landscape. Finally, applications in the fundamentals of protein biochemistry, disease prediction, and protein engineering are presented.

The loess-paleosol profile Datthausen, on the penultimate-glacial terrace of the upper Danube River: Sedimentological and paleopedological characteristics

NASA Astrophysics Data System (ADS)

Sauer, Daniela; Kadereit, Annette; Kühn, Peter; Herrmann, Ludger; Kösel, Michael; Miller, Christopher; Shinonaga, Taeko; Kreutzer, Sebastian; Starkovich, Britt

2015-04-01

Here we present a new loess profile, exposed in the gravel quarry Datthausen on the penultimate-glacial terrace of the upper Danube River, 40 km SW of Ulm, Germany. The loess in this region is by far not as thick and differentiated as in the Upper and Middle Rhine regions or in the Basin of Mainz; nevertheless, we found several similarities between those and the profile Datthausen. The profile is located in the East wall of the quarry, in a flat channel filled by reworked loess. It was sampled for grain size analysis, chemical standard analyses, analysis of the clay mineral assemblage (XRD of oriented clay specimen) and soil thin section analysis. Five luminescence dates provide a time frame (see Kadereit et al. in this session for further details). The profile starts above the Eemian paleosol, which is developed in penultimate-glacial gravel of the Danube River. No early Würmian soils are preserved; the basal section of the profile comprises a succession of several middle Würmian (MIS3) brown soil horizons (9BCr to 6Bg5; Table 1). Two additional brown horizons (5Bg4 and 5Bg3) follow on top. They both have a slight olive tint, and the upper one shows clear features of redox processes and reworking. A thin gravel band on top of the olive-brown soil horizons can be traced over ca. 170 m along the wall (4Bg2). Above the gravel band two brown, only slightly de-carbonated soil horizons (3Bw1 and 2Bg1) and two hydromorphic horizons (Cg2 and Cg1) follow. The top of the profile is made up of a Luvisol comprising the horizon sequence Ap-Bt-BCtg1-BCtg2. Table 1: Main soil-morphological characteristics of the loess-paleosol profile Datthausen Depth; horizon (FAO); color (dry, moist); structure; major characteristics -30 cm: Ap -70 cm: Bt; 10YR5/6, 10YR4/6; angular blocky and prismatic; earthworm feces, channels, clay coatings -100 cm: BCtg1; 10YR7/4, 10YR5/4; massive, pinholes; mottled, fine Mn nodules, clay coatings in channels -125 cm: BCtg2; 10YR6/4, 10YR4/4; massive, pinholes; mottled, fine Mn nodules, clay coatings in channels -150 cm: Cg1; 2.5Y7/4, 2.5Y5/; massive (fine sandy layers); fine rusty spots and Mn nodules -190 cm: Cg2; 2.5Y7/3, 2.5Y5/4; massive (fine sandy layers); mottled, fine rusty spots (2 mm) -220 cm: 2Bg1; 10YR6/4, 10YR4/4; massive to fine platy, pinholes; intense brown, slightly mottled -260 cm: 3Bw1; 10YR6/4, 10YR5/4; massive to fine platy, pinholes; snail shell fragments -275 cm: 4Bg2; 10YR6/4, 10YR5/4; massive to fine platy, pinholes; slightly mottled -300 cm: 5Bg3; 10YR6/4, 10YR5/4; massive to fine platy, pinholes; very fine Fe+Mn mottles, slight olive tint -312 cm: 5Bg4; 10YR6/4, 10YR4/4; massive to fine platy; slight olive tint, fine Fe mottles and Mn nodules -355 cm: 6Bg5; 10YR6/4, 10YR4/6; massive to fine platy; more reddish than 5Bg4, fine Mn nodules -400 cm: 7Bg6; 10YR6/4, 10YR4/4; weakly fine platy and sub. blocky, pinholes; Mn mottles and coatings -435 cm: 8Bw2; 10YR6/4, 10YR4/4; weakly subangular blocky, pinholes -465 cm: 9BCr; 2.5Y7/4, 2.5Y5/4; weakly subangular blocky; grayish, bleached and rusty mottles

Duality for massive spin two theories in arbitrary dimensions

NASA Astrophysics Data System (ADS)

González, B.; Khoudeir, A.; Montemayor, R.; Urrutia, L. F.

2008-09-01

Using the parent Lagrangian approach we construct a dual formulation, in the sense originally proposed by Curtright and Freund, of a massive spin two Fierz-Pauli theory in arbitrary dimensions D. This is achieved in terms of a mixed symmetry tensor TA[B1B2...BD-2], without the need of auxiliary fields. The relation of this method with an alternative formulation based on a gauge symmetry principle proposed by Zinoviev is elucidated. We show that the latter formulation in four dimensions, with a given gauge fixing together with a definite sequence of auxiliary fields elimination via their equations of motion, leads to the parent Lagrangian already considered by West completed by a Fierz-Pauli mass term, which in turns yields the Curtright-Freund action. This motivates our generalization to arbitrary dimensions leading to the corresponding extension of the four dimensional result. We identify the transverse true degrees of freedom of the dual theory and verify that their number is in accordance with those of the massive Fierz-Pauli field.

Flow Fields of the 3.5 Ga Komati Formation, South Africa: Geochemical, Stratigraphic, and Temporal relationships between Massive, Vesicular, and Spinifex flows

NASA Astrophysics Data System (ADS)

Dann, J. C.

2007-12-01

A challenge of Archean volcanology is to reconstruct submarine flow fields by mapping and analyzing vertically dipping sequences of lavas. Some flow fields are bound by sediments and/or seafloor alteration that mark clear gaps in volcanism. Flow fields in the Lower Komati Fm are defined by alternating layers of komatiite (26% MgO) and komatiitic basalt (15% MgO). Five komatiite flow fields (100-200m thick) repeat the same stratigraphic zoning of spinifex overlying massive komatiite, and each flow field has a distinct Al2O3/CaO, a ratio unaffected by olivine fractionation, consistent with the contention that each komatiite flow field represents a distinct batch of mantle melting. Although massive and spinifex komatiite form distinct stratigraphic units on a map scale, detailed outcrop mapping reveals that the change in flow type represents a transition within a single flow field. In one type of transition, thin massive flows alternate with spinifex flow lobes of a compound flow unit. In another, a vesicular flow along the boundary links the underlying massive komatiite and overlying spinifex flows in time. The vesicular flow has alternating spinifex and vesicular layers that form a distinctive crust above a thick massive interior. Locally, this crust is tilted, intruded by massive komatiite from the interior, and overlain by a thick breccia including a spinifex flow broken into blocks and rotated like dominoes by the tilting. These outcrop relations indicate that spinifex flow lobes were starting to flow over the vesicular flow before it had undergone differential inflation, a temporal link between the lower massive and upper spinifex komatiites consistent with their belonging to the same flow field. The transition in flow type may reflect 1) an overlap of proximal and distal facies of komatiite flows as eruption rates waned and/or 2) thermal maturation prior to eruption. Early, cooler, crystal-rich, massive lava, flowing out as thick sheet flows, was replaced by hotter, crystal-poor, less degassed lava, flowing out as spinifex flows.

Comparative expression profiling in grape (Vitis vinifera) berries derived from frequency analysis of ESTs and MPSS signatures.

PubMed

Iandolino, Alberto; Nobuta, Kan; da Silva, Francisco Goes; Cook, Douglas R; Meyers, Blake C

2008-05-12

Vitis vinifera (V. vinifera) is the primary grape species cultivated for wine production, with an industry valued annually in the billions of dollars worldwide. In order to sustain and increase grape production, it is necessary to understand the genetic makeup of grape species. Here we performed mRNA profiling using Massively Parallel Signature Sequencing (MPSS) and combined it with available Expressed Sequence Tag (EST) data. These tag-based technologies, which do not require a priori knowledge of genomic sequence, are well-suited for transcriptional profiling. The sequence depth of MPSS allowed us to capture and quantify almost all the transcripts at a specific stage in the development of the grape berry. The number and relative abundance of transcripts from stage II grape berries was defined using Massively Parallel Signature Sequencing (MPSS). A total of 2,635,293 17-base and 2,259,286 20-base signatures were obtained, representing at least 30,737 and 26,878 distinct sequences. The average normalized abundance per signature was approximately 49 TPM (Transcripts Per Million). Comparisons of the MPSS signatures with available Vitis species' ESTs and a unigene set demonstrated that 6,430 distinct contigs and 2,190 singletons have a perfect match to at least one MPSS signature. Among the matched sequences, ESTs were identified from tissues other than berries or from berries at different developmental stages. Additional MPSS signatures not matching to known grape ESTs can extend our knowledge of the V. vinifera transcriptome, particularly when these data are used to assist in annotation of whole genome sequences from Vitis vinifera. The MPSS data presented here not only achieved a higher level of saturation than previous EST based analyses, but in doing so, expand the known set of transcripts of grape berries during the unique stage in development that immediately precedes the onset of ripening. The MPSS dataset also revealed evidence of antisense expression not previously reported in grapes but comparable to that reported in other plant species. Finally, we developed a novel web-based, public resource for utilization of the grape MPSS data [1].

The mitochondrial genome of Frankliniella intonsa: insights into the evolution of mitochondrial genomes at lower taxonomic levels in Thysanoptera.

PubMed

Yan, Dankan; Tang, Yunxia; Hu, Min; Liu, Fengquan; Zhang, Dongfang; Fan, Jiaqin

2014-10-01

Thrips is an ideal group for studying the evolution of mitochondrial (mt) genomes in the genus and family due to independent rearrangements within this order. The complete sequence of the mitochondrial DNA (mtDNA) of the flower thrips Frankliniella intonsa has been completed and annotated in this study. The circular genome is 15,215bp in length with an A+T content of 75.9% and contains the typical 37 genes and it has triplicate putative control regions. Nucleotide composition is A+T biased, and the majority of the protein-coding genes present opposite CG skew which is reflected by the nucleotide composition, codon and amino acid usage. Although the known thrips have massive gene rearrangements, it showed no reversal of strand asymmetry. Gene rearrangements have been found in the lower taxonomic levels of thrips. Three tRNA genes were translocated in the genus Frankliniella and eight tRNA genes in the family Thripidae. Although the gene arrangements of mt genomes of all three thrips species differ massively from the ancestral insect, they are all very similar to each other, indicating that there was a large rearrangement somewhere before the most recent common ancestor of these three species and very little genomic evolution or rearrangements after then. The extremely similar sequences among the CRs suggest that they are ongoing concerted evolution. Analyses of the up and downstream sequence of CRs reveal that the CR2 is actually the ancestral CR. The three CRs are in the same spot in each of the three thrips mt genomes which have the identical inverted genes. These characteristics might be obtained from the most recent common ancestor of this three thrips. Above observations suggest that the mt genomes of the three thrips keep a single massive rearrangement from the common ancestor and have low evolutionary rates among them. Copyright © 2014 Elsevier Inc. All rights reserved.

Technical Failure of MR Elastography Examinations of the Liver: Experience from a Large Single-Center Study.

PubMed

Wagner, Mathilde; Corcuera-Solano, Idoia; Lo, Grace; Esses, Steven; Liao, Joseph; Besa, Cecilia; Chen, Nelson; Abraham, Ginu; Fung, Maggie; Babb, James S; Ehman, Richard L; Taouli, Bachir

2017-08-01

Purpose To assess the determinants of technical failure of magnetic resonance (MR) elastography of the liver in a large single-center study. Materials and Methods This retrospective study was approved by the institutional review board. Seven hundred eighty-one MR elastography examinations performed in 691 consecutive patients (mean age, 58 years; male patients, 434 [62.8%]) in a single center between June 2013 and August 2014 were retrospectively evaluated. MR elastography was performed at 3.0 T (n = 443) or 1.5 T (n = 338) by using a gradient-recalled-echo pulse sequence. MR elastography and anatomic image analysis were performed by two observers. Additional observers measured liver T2* and fat fraction. Technical failure was defined as no pixel value with a confidence index higher than 95% and/or no apparent shear waves imaged. Logistic regression analysis was performed to assess potential predictive factors of technical failure of MR elastography. Results The technical failure rate of MR elastography at 1.5 T was 3.5% (12 of 338), while it was higher, 15.3% (68 of 443), at 3.0 T. On the basis of univariate analysis, body mass index, liver iron deposition, massive ascites, use of 3.0 T, presence of cirrhosis, and alcoholic liver disease were all significantly associated with failure of MR elastography (P < .004); but on the basis of multivariable analysis, only body mass index, liver iron deposition, massive ascites, and use of 3.0 T were significantly associated with failure of MR elastography (P < .004). Conclusion The technical failure rate of MR elastography with a gradient-recalled-echo pulse sequence was low at 1.5 T but substantially higher at 3.0 T. Massive ascites, iron deposition, and high body mass index were additional independent factors associated with failure of MR elastography of the liver with a two-dimensional gradient-recalled-echo pulse sequence. © RSNA, 2017.

Successful treatment of massive ascites due to lupus peritonitis with hydroxychloroquine in old- onset lupus erythematosus.

PubMed

Hammami, Sonia; Bdioui, Fethia; Ouaz, Afef; Loghmari, Hichem; Mahjoub, Sylvia; Saffar, Hamouda

2014-01-01

Systemic lupus erythematous (SLE) is an auto-immune disease with multiple organ involvements that occurs mainly in young women. Literature data suggest that serositis is more frequent in late-onset SLE. However, peritoneal serositis with massive ascites is an extremely rare manifestation. We report a case of old-onset lupus peritonitis treated successfully by Hydroxychloroquine. A 77-year-old Tunisian woman was hospitalized because of massive painful ascites. Her family history did not include any autoimmune disease. She was explored 4 years prior to admission for exudative pleuritis of the right lung without any established diagnosis. Physical examination showed only massive ascites. Laboratory investigations showed leucopenia: 3100/mm3, lymphopenia: 840/mm3 and trace protein (0.03 g/24 h). Ascitic fluid contained 170 cells mm(3) (67% lymphocytes), 46 g/L protein, but no malignant cells. The main etiologies of exudative ascites were excluded. She had markedly elevated anti-nuclear antibody (ANA) titer of 1/1600 and a significantly elevated titer of antibody to double-stranded DNA (83 IU/mL) with hypo-complementemia (C3 levl was at 67 mg/dL). Antibody against the Smith antigen was also positive. Relying on these findings, the patient was diagnosed with SLE and treated with Hydroxychloroquine 200 mg daily in combination with diuretics. One month later, there was no detectable ascitic fluid and no pleural effusions. Five months later she remained free from symptoms while continuing to take chloroquine. This case was characterized by old age of onset of SLE, the extremely rare initial presentation with lupus peritonitis and massive painful ascites with dramatic response to only hydroxychloroquine treatment.

Ground-based detectability of terrestrial and Jovian extrasolar planets: observations of CM Draconis at Lick Observatory.

PubMed

Doyle, L R; Dunham, E T; Deeg, H J; Blue, J E; Jenkins, J M

1996-06-25

The detection of terrestrial-sized extrasolar planets from the ground has been thought to be virtually impossible due to atmospheric scintillation limits. However, we show that this is not the case especially selected (but nevertheless main sequence) stars, namely small eclipsing binaries. For the smallest of these systems, CM Draconis, several months to a few years of photometric observations with 1-m-class telescopes will be sufficient to detect the transits of any short-period planets of sizes > or = 1.5 Earth radii (RE), using cross-correlation analysis with moderately good photometry. Somewhat larger telescopes will be needed to extend this detectability to terrestrial planets in larger eclipsing binary systems. (We arbitrarily define "terrestrial planets" herein as those whose disc areas are closer to that of Earth's than Neptune's i.e., less than about 2.78 RE.) As a "spin-off" of such observations, we will also be able to detect the presence of Jovian-mass planets without transits using the timing of the eclipse minima. Eclipse minima will drift in time as the binary system is offset by a sufficiently massive planet (i.e., one Jupiter mass) about the binary/giant-planet barycenter, causing a periodic variation in the light travel time to the observer. We present here an outline of present observations taking place at the University of California Lick Observatory using the Crossley 0.9-m telescope in collaboration with other observatories (in South Korea, Crete, France, Canary Islands, and New York) to detect or constrain the existence of terrestrial planets around main sequence eclipsing binary star systems, starting with CM Draconis. We demonstrate the applicability of photometric data to the general detection of gas giant planets via eclipse minima timings in many other small-mass eclipsing binary systems as well.

Kepler-4b: A Hot Neptune-like Planet of a G0 Star Near Main-sequence Turnoff

NASA Astrophysics Data System (ADS)

Borucki, William J.; Koch, David G.; Brown, Timothy M.; Basri, Gibor; Batalha, Natalie M.; Caldwell, Douglas A.; Cochran, William D.; Dunham, Edward W.; Gautier, Thomas N., III; Geary, John C.; Gilliland, Ronald L.; Howell, Steve B.; Jenkins, Jon M.; Latham, David W.; Lissauer, Jack J.; Marcy, Geoffrey W.; Monet, David; Rowe, Jason F.; Sasselov, Dimitar

2010-04-01

Early time-series photometry from NASA's Kepler spacecraft has revealed a planet transiting the star we term Kepler-4, at R.A. = 19h02m27.s68, δ = +50°08'08farcs7. The planet has an orbital period of 3.213 days and shows transits with a relative depth of 0.87 × 10-3 and a duration of about 3.95 hr. Radial velocity (RV) measurements from the Keck High Resolution Echelle Spectrometer show a reflex Doppler signal of 9.3+1.1 -1.9 m s-1, consistent with a low-eccentricity orbit with the phase expected from the transits. Various tests show no evidence for any companion star near enough to affect the light curve or the RVs for this system. From a transit-based estimate of the host star's mean density, combined with analysis of high-resolution spectra, we infer that the host star is near turnoff from the main sequence, with estimated mass and radius of 1.223+0.053 -0.091 M sun and 1.487+0.071 -0.084 R sun. We estimate the planet mass and radius to be {M P, R P} = {24.5 ± 3.8 M ⊕, 3.99 ± 0.21 R ⊕}. The planet's density is near 1.9 g cm-3 it is thus slightly denser and more massive than Neptune, but about the same size. Some of the 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 CNO Bi-cycle in the Open Cluster NGC 752

NASA Astrophysics Data System (ADS)

Hawkins, Keith; Schuler, S.; King, J.; The, L.

2011-01-01

The CNO bi-cycle is the primary energy source for main sequence stars more massive than the sun. To test our understanding of stellar evolution models using the CNO bi-cycle, we have undertaken light-element (CNO) abundance analysis of three main sequence dwarf stars and three red giant stars in the open cluster NGC 752 utilizing high resolution (R 50,000) spectroscopy from the Keck Observatory. Preliminary results indicate, as expected, there is a depletion of carbon in the giants relative to the dwarfs. Additional analysis is needed to determine if the amount of depletion is in line with model predictions, as seen in the Hyades open cluster. Oxygen abundances are derived from the high-excitation O I triplet, and there is a 0.19 dex offset in the [O/H] abundances between the giants and dwarfs which may be explained by non-local thermodynamic equilibrium (NLTE), although further analysis is needed to verify this. The standard procedure for spectroscopically determining stellar parameters used here allows for a measurement of the cluster metallicity, [Fe/H] = 0.04 ± 0.02. In addition to the Fe abundances we have determined Na, Mg, and Al abundances to determine the status of other nucleosynthesis processes. The Na, Mg and Al abundances of the giants are enhanced relative to the dwarfs, which is consistent with similar findings in giants of other open clusters. Support for K. Hawkins was provided by the NOAO/KPNO Research Experiences for Undergraduates (REU) Program which is funded by the National Science Foundation Research Experiences for Undergraduates Program and the Department of Defense ASSURE program through Scientific Program Order No. 13 (AST-0754223) of the Cooperative Agreement No. AST-0132798 between the Association of Universities for Research in Astronomy (AURA) and the NSF.

Ground-based detectability of terrestrial and Jovian extrasolar planets: observations of CM Draconis at Lick Observatory

NASA Technical Reports Server (NTRS)

Doyle, L. R.; Dunham, E. T.; Deeg, H. J.; Blue, J. E.; Jenkins, J. M.

1996-01-01

The detection of terrestrial-sized extrasolar planets from the ground has been thought to be virtually impossible due to atmospheric scintillation limits. However, we show that this is not the case especially selected (but nevertheless main sequence) stars, namely small eclipsing binaries. For the smallest of these systems, CM Draconis, several months to a few years of photometric observations with 1-m-class telescopes will be sufficient to detect the transits of any short-period planets of sizes > or = 1.5 Earth radii (RE), using cross-correlation analysis with moderately good photometry. Somewhat larger telescopes will be needed to extend this detectability to terrestrial planets in larger eclipsing binary systems. (We arbitrarily define "terrestrial planets" herein as those whose disc areas are closer to that of Earth's than Neptune's i.e., less than about 2.78 RE.) As a "spin-off" of such observations, we will also be able to detect the presence of Jovian-mass planets without transits using the timing of the eclipse minima. Eclipse minima will drift in time as the binary system is offset by a sufficiently massive planet (i.e., one Jupiter mass) about the binary/giant-planet barycenter, causing a periodic variation in the light travel time to the observer. We present here an outline of present observations taking place at the University of California Lick Observatory using the Crossley 0.9-m telescope in collaboration with other observatories (in South Korea, Crete, France, Canary Islands, and New York) to detect or constrain the existence of terrestrial planets around main sequence eclipsing binary star systems, starting with CM Draconis. We demonstrate the applicability of photometric data to the general detection of gas giant planets via eclipse minima timings in many other small-mass eclipsing binary systems as well.

Stellar Mass Function of Active and Quiescent Galaxies via the Continuity Equation

NASA Astrophysics Data System (ADS)

Lapi, A.; Mancuso, C.; Bressan, A.; Danese, L.

2017-09-01

The continuity equation is developed for the stellar mass content of galaxies and exploited to derive the stellar mass function of active and quiescent galaxies over the redshift range z˜ 0{--}8. The continuity equation requires two specific inputs gauged from observations: (I) the star formation rate functions determined on the basis of the latest UV+far-IR/submillimeter/radio measurements and (II) average star formation histories for individual galaxies, with different prescriptions for disks and spheroids. The continuity equation also includes a source term taking into account (dry) mergers, based on recent numerical simulations and consistent with observations. The stellar mass function derived from the continuity equation is coupled with the halo mass function and with the SFR functions to derive the star formation efficiency and the main sequence of star-forming galaxies via the abundance-matching technique. A remarkable agreement of the resulting stellar mass functions for active and quiescent galaxies of the galaxy main sequence, and of the star formation efficiency with current observations is found; the comparison with data also allows the characteristic timescales for star formation and quiescence of massive galaxies, the star formation history of their progenitors, and the amount of stellar mass added by in situ star formation versus that contributed by external merger events to be robustly constrained. The continuity equation is shown to yield quantitative outcomes that detailed physical models must comply with, that can provide a basis for improving the (subgrid) physical recipes implemented in theoretical approaches and numerical simulations, and that can offer a benchmark for forecasts on future observations with multiband coverage, as will become routinely achievable in the era of JWST.

Low energy proton capture study of the 14N(p, gamma)15O reaction

NASA Astrophysics Data System (ADS)

Daigle, Stephen Michael

The 14N(p,gamma)15O reaction regulates the rate of energy production for stars slightly more massive than the sun throughout stable hydrogen burning on the main sequence. The 14N(p,gamma)15O reaction rate also determines the luminosity for all stars after leaving the main sequence when their cores have exhausted hydrogen fuel, and later when they become red giant stars. The significant role that this reaction plays in stellar evolution has far-reaching consequences, from neutrino production in our Sun, to age estimates of globular clusters in our Galaxy. The weak cross section and inherent coincidence summing in the 15O gamma-ray decay scheme make a precision measurement of the astrophysical S-factor especially challenging, particularly for the ground-state transition. The present study, performed in the Laboratory for Experimental Nuclear Astrophysics (LENA), was aimed at measuring the ground-state transition at low energy by utilizing a new 24-element, position-sensitive, NaI(Tl) detector array. Because the array is highly segmented, the 14N( p,gamma)15O S-factor was evaluated for transitions to the ground, 5.18, 6.18, and 6.79 MeV states without the need for coincidence summing corrections. Additionally, the position-sensitivity of the detector was exploited to measure the angular correlation of the two-photon cascades. Software cuts were made to the data in order to identify single and coincident gamma-ray events and a fraction fit analysis technique was used to extract the characteristic 15O peaks from the composite gamma-ray spectrum. The results from the current work demonstrated a new approach to measuring weak nuclear cross sections near astrophysically relevant energies that, with refinements, has broader applications in gamma-ray spectroscopy.

The Optical/Near-infrared Extinction Law in Highly Reddened Regions

NASA Astrophysics Data System (ADS)

Hosek, Matthew W., Jr.; Lu, Jessica R.; Anderson, Jay; Do, Tuan; Schlafly, Edward F.; Ghez, Andrea M.; Clarkson, William I.; Morris, Mark R.; Albers, Saundra M.

2018-03-01

A precise extinction law is a critical input when interpreting observations of highly reddened sources such as young star clusters and the Galactic Center (GC). We use Hubble Space Telescope observations of a region of moderate extinction and a region of high extinction to measure the optical and near-infrared extinction law (0.8–2.2 μm). The moderate-extinction region is the young massive cluster Westerlund 1 (Wd1; A Ks ∼ 0.6 mag), where 453 proper-motion selected main-sequence stars are used to measure the shape of the extinction law. To quantify the shape, we define the parameter {{ \\mathcal S }}1/λ , which behaves similarly to a color-excess ratio, but is continuous as a function of wavelength. The high-extinction region is the GC (A Ks ∼ 2.5 mag), where 819 red clump stars are used to determine the normalization of the law. The best-fit extinction law is able to reproduce the Wd1 main-sequence colors, which previous laws misestimate by 10%–30%. The law is inconsistent with a single power law, even when only the near-infrared filters are considered, and has A F125W/A Ks and A F814W/A Ks values that are 18% and 24% higher than the commonly used Nishiyama et al. law, respectively. Using this law, we recalculate the Wd1 distance to be 3905 ± 422 pc from published observations of the eclipsing binary W13. This new extinction law should be used for highly reddened populations in the Milky Way, such as the Quintuplet cluster and Young Nuclear Cluster. A python code is provided to generate the law for future use.

Very Low Mass Stars with Extremely Low Metallicity in the Milky Way's Halo

NASA Astrophysics Data System (ADS)

Aoki, Wako; Beers, Timothy C.; Takuma, Suda; Honda, Satoshi; Lee, Young Sun

2015-08-01

Large surveys and follow-up spectroscopic studies in the past few decades have been providing chemical abundance data for a growing number of very metal-poor ([Fe/H] <-2) stars. Most of them are red giants or main-sequence turn-off stars having masses near 0.8 solar masses. Lower mass stars with extremely low metallicity ([Fe/H] <-3) have yet to be well explored. Our high-resolution spectroscopic study for very metal-poor stars found with SDSS has identified four cool main-sequence stars with [Fe/H] <-2.5 among 137 objects (Aoki et al. 2013, AJ, 145, 13). The effective temperatures of these stars are 4500--5000 K, corresponding to a mass of around 0.5 solar masses. Our standard analysis of the high-resolution spectra based on 1D-LTE model atmospheres have obtained self-consistent chemical abundances for these objects, assuming small values of micro-turbulent velocities compared with giants and turn-off stars. The low temperature of the atmospheres of these objects enables us to measure their detailed chemical abundances. Interestingly, two of the four stars have extreme chemical abundance patterns: one has the largest excesses of heavy neutron-capture elements associated with the r-process abundance pattern known to date (Aoki et al. 2010, ApJL 723, L201), and the other exhibits low abundances of the alpha-elements and odd-Z elements, suggested to be the signatures of the yields of very massive stars ( >100 solar masses; Aoki et al. 2014, Science 345, 912). Although the sample size is still small, these results indicate the potential of very low-mass stars as probes to study the early stages of the Milky Way's halo formation.

Very Low-Mass Stars with Extremely Low Metallicity in the Milky Way's Halo

NASA Astrophysics Data System (ADS)

Aoki, Wako; Beers, Timothy C.; Suda, Takuma; Honda, Satoshi; Lee, Young Sun

2016-08-01

Large surveys and follow-up spectroscopic studies in the past few decades have been providing chemical abundance data for a growing number of very metal-poor ([Fe/H] <-2) stars. Most of them are red giants or main-sequence turn-off stars having masses near 0.8 solar masses. Lower mass stars with extremely low metallicity ([Fe/H] <-3) are yet to be explored. Our high-resolution spectroscopic study for very metal-poor stars found with SDSS has identified four cool main-sequence stars with [Fe/H] <-2.5 among 137 objects (Aoki et al. 2013). The effective temperatures of these stars are 4500-5000 K, corresponding to a mass of around 0.5 solar masses. Our standard analysis of the high-resolution spectra based on 1D-LTE model atmospheres has obtained self-consistent chemical abundances for these objects, assuming small values of micro-turbulent velocities compared with giants and turn-off stars. The low temperature of the atmospheres of these objects enables us to measure their detailed chemical abundances. Interestingly, two of the four stars have extreme chemical-abundance patterns: one has the largest excesses of heavy neutron-capture elements associated with the r-process abundance pattern known to date (Aoki et al. 2010), and the other exhibits low abundances of the α-elements and odd-Z elements, suggested to be signatures of the yields of very massive stars (> 100 solar masses; Aoki et al. 2014). Although the sample size is still small, these results indicate the potential of very low-mass stars as probes to study the early stages of the Milky Way's halo formation.

A phylogenetic framework facilitates Y-STR variant discovery and classification via massively parallel sequencing.

PubMed

Huszar, Tunde I; Jobling, Mark A; Wetton, Jon H

2018-04-12

Short tandem repeats on the male-specific region of the Y chromosome (Y-STRs) are permanently linked as haplotypes, and therefore Y-STR sequence diversity can be considered within the robust framework of a phylogeny of haplogroups defined by single nucleotide polymorphisms (SNPs). Here we use massively parallel sequencing (MPS) to analyse the 23 Y-STRs in Promega's prototype PowerSeq™ Auto/Mito/Y System kit (containing the markers of the PowerPlex® Y23 [PPY23] System) in a set of 100 diverse Y chromosomes whose phylogenetic relationships are known from previous megabase-scale resequencing. Including allele duplications and alleles resulting from likely somatic mutation, we characterised 2311 alleles, demonstrating 99.83% concordance with capillary electrophoresis (CE) data on the same sample set. The set contains 267 distinct sequence-based alleles (an increase of 58% compared to the 169 detectable by CE), including 60 novel Y-STR variants phased with their flanking sequences which have not been reported previously to our knowledge. Variation includes 46 distinct alleles containing non-reference variants of SNPs/indels in both repeat and flanking regions, and 145 distinct alleles containing repeat pattern variants (RPV). For DYS385a,b, DYS481 and DYS390 we observed repeat count variation in short flanking segments previously considered invariable, and suggest new MPS-based structural designations based on these. We considered the observed variation in the context of the Y phylogeny: several specific haplogroup associations were observed for SNPs and indels, reflecting the low mutation rates of such variant types; however, RPVs showed less phylogenetic coherence and more recurrence, reflecting their relatively high mutation rates. In conclusion, our study reveals considerable additional diversity at the Y-STRs of the PPY23 set via MPS analysis, demonstrates high concordance with CE data, facilitates nomenclature standardisation, and places Y-STR sequence variants in their phylogenetic context. Copyright © 2018 The Authors. Published by Elsevier B.V. All rights reserved.

Genomic Characterization of Non–Small-Cell Lung Cancer in African Americans by Targeted Massively Parallel Sequencing

PubMed Central

Araujo, Luiz H.; Timmers, Cynthia; Bell, Erica Hlavin; Shilo, Konstantin; Lammers, Philip E.; Zhao, Weiqiang; Natarajan, Thanemozhi G.; Miller, Clinton J.; Zhang, Jianying; Yilmaz, Ayse S.; Liu, Tom; Coombes, Kevin; Amann, Joseph; Carbone, David P.

2015-01-01

Purpose Technologic advances have enabled the comprehensive analysis of genetic perturbations in non–small-cell lung cancer (NSCLC); however, African Americans have often been underrepresented in these studies. This ethnic group has higher lung cancer incidence and mortality rates, and some studies have suggested a lower incidence of epidermal growth factor receptor mutations. Herein, we report the most in-depth molecular profile of NSCLC in African Americans to date. Methods A custom panel was designed to cover the coding regions of 81 NSCLC-related genes and 40 ancestry-informative markers. Clinical samples were sequenced on a massively parallel sequencing instrument, and anaplastic lymphoma kinase translocation was evaluated by fluorescent in situ hybridization. Results The study cohort included 99 patients (61% males, 94% smokers) comprising 31 squamous and 68 nonsquamous cell carcinomas. We detected 227 nonsilent variants in the coding sequence, including 24 samples with nonoverlapping, classic driver alterations. The frequency of driver mutations was not significantly different from that of whites, and no association was found between genetic ancestry and the presence of somatic mutations. Copy number alteration analysis disclosed distinguishable amplifications in the 3q chromosome arm in squamous cell carcinomas and pointed toward a handful of targetable alterations. We also found frequent SMARCA4 mutations and protein loss, mostly in driver-negative tumors. Conclusion Our data suggest that African American ancestry may not be significantly different from European/white background for the presence of somatic driver mutations in NSCLC. Furthermore, we demonstrated that using a comprehensive genotyping approach could identify numerous targetable alterations, with potential impact on therapeutic decisions. PMID:25918285

De novo characterization of Larimichthys crocea transcriptome for growth-/immune-related gene identification and massive microsatellite (SSR) marker development

NASA Astrophysics Data System (ADS)

Han, Zhaofang; Xiao, Shijun; Liu, Xiande; Liu, Yang; Li, Jiakai; Xie, Yangjie; Wang, Zhiyong

2017-03-01

The large yellow croaker, Larimichthys crocea is an important marine fish in China with a high economic value. In the last decade, the stock conservation and aquaculture industry of this species have been facing severe challenges because of wild population collapse and degeneration of important economic traits. However, genes contributing to growth and immunity in L. crocea have not been thoroughly analyzed, and available molecular markers are still not sufficient for genetic resource management and molecular selection. In this work, we sequenced the transcriptome in L. crocea liver tissue with a Roche 454 sequencing platform and assembled the transcriptome into 93 801 transcripts. Of them, 38 856 transcripts were successfully annotated in nt, nr, Swiss-Prot, InterPro, COG, GO and KEGG databases. Based on the annotation information, 3 165 unigenes related to growth and immunity were identified. Additionally, a total of 6 391 simple sequence repeats (SSRs) were identified from the transcriptome, among which 4 498 SSRs had enough flanking regions to design primers for polymerase chain reactions (PCR). To access the polymorphism of these markers, 30 primer pairs were randomly selected for PCR amplification and validation in 30 individuals, and 12 primer pairs (40.0%) exhibited obvious length polymorphisms. This work applied RNA-Seq to assemble and analyze a live transcriptome in L. crocea. With gene annotation and sequence information, genes related to growth and immunity were identified and massive SSR markers were developed, providing valuable genetic resources for future gene functional analysis and selective breeding of L. crocea.