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).

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.

Multilocus sequence analysis and rpoB sequencing of Mycobacterium abscessus (sensu lato) strains.

PubMed

Macheras, Edouard; Roux, Anne-Laure; Bastian, Sylvaine; Leão, Sylvia Cardoso; Palaci, Moises; Sivadon-Tardy, Valérie; Gutierrez, Cristina; Richter, Elvira; Rüsch-Gerdes, Sabine; Pfyffer, Gaby; Bodmer, Thomas; Cambau, Emmanuelle; Gaillard, Jean-Louis; Heym, Beate

2011-02-01

Mycobacterium abscessus, Mycobacterium bolletii, and Mycobacterium massiliense (Mycobacterium abscessus sensu lato) are closely related species that currently are identified by the sequencing of the rpoB gene. However, recent studies show that rpoB sequencing alone is insufficient to discriminate between these species, and some authors have questioned their current taxonomic classification. We studied here a large collection of M. abscessus (sensu lato) strains by partial rpoB sequencing (752 bp) and multilocus sequence analysis (MLSA). The final MLSA scheme developed was based on the partial sequences of eight housekeeping genes: argH, cya, glpK, gnd, murC, pgm, pta, and purH. The strains studied included the three type strains (M. abscessus CIP 104536(T), M. massiliense CIP 108297(T), and M. bolletii CIP 108541(T)) and 120 isolates recovered between 1997 and 2007 in France, Germany, Switzerland, and Brazil. The rpoB phylogenetic tree confirmed the existence of three main clusters, each comprising the type strain of one species. However, divergence values between the M. massiliense and M. bolletii clusters all were below 3% and between the M. abscessus and M. massiliense clusters were from 2.66 to 3.59%. The tree produced using the concatenated MLSA gene sequences (4,071 bp) also showed three main clusters, each comprising the type strain of one species. The M. abscessus cluster had a bootstrap value of 100% and was mostly compact. Bootstrap values for the M. massiliense and M. bolletii branches were much lower (71 and 61%, respectively), with the M. massiliense cluster having a fuzzy aspect. Mean (range) divergence values were 2.17% (1.13 to 2.58%) between the M. abscessus and M. massiliense clusters, 2.37% (1.5 to 2.85%) between the M. abscessus and M. bolletii clusters, and 2.28% (0.86 to 2.68%) between the M. massiliense and M. bolletii clusters. Adding the rpoB sequence to the MLSA-concatenated sequence (total sequence, 4,823 bp) had little effect on the clustering of strains. We found 10/120 (8.3%) isolates for which the concatenated MLSA gene sequence and rpoB sequence were discordant (e.g., M. massiliense MLSA sequence and M. abscessus rpoB sequence), suggesting the intergroup lateral transfers of rpoB. In conclusion, our study strongly supports the recent proposal that M. abscessus, M. massiliense, and M. bolletii should constitute a single species. Our findings also indicate that there has been a horizontal transfer of rpoB sequences between these subgroups, precluding the use of rpoB sequencing alone for the accurate identification of the two proposed M. abscessus subspecies.

Multilocus Sequence Analysis and rpoB Sequencing of Mycobacterium abscessus (Sensu Lato) Strains▿

PubMed Central

Macheras, Edouard; Roux, Anne-Laure; Bastian, Sylvaine; Leão, Sylvia Cardoso; Palaci, Moises; Sivadon-Tardy, Valérie; Gutierrez, Cristina; Richter, Elvira; Rüsch-Gerdes, Sabine; Pfyffer, Gaby; Bodmer, Thomas; Cambau, Emmanuelle; Gaillard, Jean-Louis; Heym, Beate

2011-01-01

Mycobacterium abscessus, Mycobacterium bolletii, and Mycobacterium massiliense (Mycobacterium abscessus sensu lato) are closely related species that currently are identified by the sequencing of the rpoB gene. However, recent studies show that rpoB sequencing alone is insufficient to discriminate between these species, and some authors have questioned their current taxonomic classification. We studied here a large collection of M. abscessus (sensu lato) strains by partial rpoB sequencing (752 bp) and multilocus sequence analysis (MLSA). The final MLSA scheme developed was based on the partial sequences of eight housekeeping genes: argH, cya, glpK, gnd, murC, pgm, pta, and purH. The strains studied included the three type strains (M. abscessus CIP 104536T, M. massiliense CIP 108297T, and M. bolletii CIP 108541T) and 120 isolates recovered between 1997 and 2007 in France, Germany, Switzerland, and Brazil. The rpoB phylogenetic tree confirmed the existence of three main clusters, each comprising the type strain of one species. However, divergence values between the M. massiliense and M. bolletii clusters all were below 3% and between the M. abscessus and M. massiliense clusters were from 2.66 to 3.59%. The tree produced using the concatenated MLSA gene sequences (4,071 bp) also showed three main clusters, each comprising the type strain of one species. The M. abscessus cluster had a bootstrap value of 100% and was mostly compact. Bootstrap values for the M. massiliense and M. bolletii branches were much lower (71 and 61%, respectively), with the M. massiliense cluster having a fuzzy aspect. Mean (range) divergence values were 2.17% (1.13 to 2.58%) between the M. abscessus and M. massiliense clusters, 2.37% (1.5 to 2.85%) between the M. abscessus and M. bolletii clusters, and 2.28% (0.86 to 2.68%) between the M. massiliense and M. bolletii clusters. Adding the rpoB sequence to the MLSA-concatenated sequence (total sequence, 4,823 bp) had little effect on the clustering of strains. We found 10/120 (8.3%) isolates for which the concatenated MLSA gene sequence and rpoB sequence were discordant (e.g., M. massiliense MLSA sequence and M. abscessus rpoB sequence), suggesting the intergroup lateral transfers of rpoB. In conclusion, our study strongly supports the recent proposal that M. abscessus, M. massiliense, and M. bolletii should constitute a single species. Our findings also indicate that there has been a horizontal transfer of rpoB sequences between these subgroups, precluding the use of rpoB sequencing alone for the accurate identification of the two proposed M. abscessus subspecies. PMID:21106786

Evolution of massive stars in very young clusters and associations

NASA Technical Reports Server (NTRS)

Stothers, R. B.

1985-01-01

Statistics concerning the stellar content of young galactic clusters and associations which show well defined main sequence turnups have been analyzed in order to derive information about stellar evolution in high-mass galaxies. The analytical approach is semiempirical and uses natural spectroscopic groups of stars on the H-R diagram together with the stars' apparent magnitudes. The new approach does not depend on absolute luminosities and requires only the most basic elements of stellar evolution theory. The following conclusions are offered on the basis of the statistical analysis: (1) O-tupe main-sequence stars evolve to a spectral type of B1 during core hydrogen burning; (2) most O-type blue stragglers are newly formed massive stars burning core hydrogen; (3) supergiants lying redward of the main-sequence turnup are burning core helium; and most Wolf-Rayet stars are burning core helium and originally had masses greater than 30-40 solar mass. The statistics of the natural spectroscopic stars in young galactic clusters and associations are given in a table.

Multiple stellar populations in Magellanic Cloud clusters - III. The first evidence of an extended main sequence turn-off in a young cluster: NGC 1856

NASA Astrophysics Data System (ADS)

Milone, A. P.; Bedin, L. R.; Piotto, G.; Marino, A. F.; Cassisi, S.; Bellini, A.; Jerjen, H.; Pietrinferni, A.; Aparicio, A.; Rich, R. M.

2015-07-01

Recent studies have shown that the extended main-sequence turn-off (eMSTO) is a common feature of intermediate-age star clusters in the Magellanic Clouds (MCs). The most simple explanation is that these stellar systems harbour multiple generations of stars with an age difference of a few hundred million years. However, while an eMSTO has been detected in a large number of clusters with ages between ˜1-2 Gyr, several studies of young clusters in both MCs and in nearby galaxies do not find any evidence for a prolonged star formation history, i. e. for multiple stellar generations. These results have suggested alternative interpretation of the eMSTOs observed in intermediate-age star clusters. The eMSTO could be due to stellar rotation mimicking an age spread or to interacting binaries. In these scenarios, intermediate-age MC clusters would be simple stellar populations, in close analogy with younger clusters. Here, we provide the first evidence for an eMSTO in a young stellar cluster. We exploit multiband Hubble Space Telescope photometry to study the ˜300-Myr old star cluster NGC 1856 in the Large Magellanic Cloud and detected a broadened MSTO that is consistent with a prolonged star formation which had a duration of about 150 Myr. Below the turn-off, the main sequence (MS) of NGC 1856 is split into a red and blue component, hosting 33 ± 5 and 67 ± 5 per cent of the total number of MS stars, respectively. We discuss these findings in the context of multiple-stellar-generation, stellar-rotation, and interacting-binary hypotheses.

The Multiple Stellar Populations in the Ancient LMC Globular Clusters Hodge 11 and NGC 2210

NASA Astrophysics Data System (ADS)

Chaboyer, Brian; Gilligan, Christina; Wagner-Kaiser, Rachel; Mackey, Dougal; Sarajedini, Ata; Cummings, Jeffrey; Grocholski, Aaron; Geisler, Doug; Cohen, Roger; Villanova, Sandro; Yang, Soung-Chul; Parisi, Celeste

2018-01-01

Hubble Space telescope images of the ancient LMC globular clusters Hodge 11 and NGC 2210 in the F336W, F606W and F814W filters were obtained between June 2016 and April 2017. These deep images has been analyzed with the Dolphot software package. High quality photometry has been obtained from three magnitudes brighter than the horizontal branch, to about four magnitudes fainter than the main sequence turn-off. Both clusters show an excess of red main sequence stars in the F336W filter, indicating that multiple stellar populations exist in both clusters. Hodge 11 shows irregularities in its horizontal branch morphology, which is indicative of the presence of an approximately 0.1 dex internal helium abundance spread.

The CCD photometry of the globular cluster Palomar 1.

NASA Astrophysics Data System (ADS)

Borissova, J.; Spassova, N.

1995-04-01

A CCD photometry of the halo cluster Palomar 1 is presented in the Thuan-Gunn photometric system. The principal sequences of the color-magnitude diagrams are delineated in different spectral bands. The color-magnitude diagrams of the cluster show a well defined red horizontal branch, a subgiant branch and a main-sequence down to about two magnitudes below the main sequence turnoff. The giant branch is absent and the brightest stars are the horizontal branch stars. The age of the cluster determined by comparison with the isochrones of Bell & Vanden Berg (1987) is consistent with an age in the interval 12-14Gyr. A distance modulus of (m-M)_g0_=15.38+/-0.15 magnitude and E(g-r)=0.16 has been derived. An estimate of the cluster structural parameters such as core radius and concentration parameter gives r_c_=1.5pc and c=1.46. A mass estimate of 1.1 10^3^Msun_ and a mass-to-light ratio of 1.79 have been obtained using King's (1966) method. The morphology of color-magnitude diagrams allows Pal 1 to be interpreted as probably a globular cluster rather than an old open one.

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

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

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

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

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

NASA Astrophysics Data System (ADS)

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

2016-12-01

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

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

Barnes, Sydney A.; Weingrill, Joerg; Fritzewski, Dario

We report rotation periods for 20 cool (FGK) main sequence member stars of the 4 Gyr-old open cluster M67 (=NGC 2682), obtained by analyzing data from Campaign 5 of the K2 mission with the Kepler Space Telescope . The rotation periods delineate a sequence in the color–period diagram (CPD) of increasing period with redder color. This sequence represents a cross-section at the cluster age of the surface P = P ( t , M ), suggested in prior work to extend to at least solar age. The current Sun is located marginally (approximately 1 σ ) above M67 in themore » CPD, as its relative age leads us to expect, and lies on the P = P ( t , M ) surface to within measurement precision. We therefore conclude that the solar rotation rate is normal as compared with cluster stars, a fact that strengthens the solar–stellar connection. The agreement between the M67 rotation period measurements and prior predictions further implies that rotation periods, especially when coupled with appropriate supporting work such as spectroscopy, can provide reliable ages via gyrochronology for other similar FGK dwarfs from the early main sequence to solar age and likely until the main sequence turnoff. The M67 rotators have a rotational age of 4.2 Gyr with a standard deviation of 0.7 Gyr, implying that similar field stars can be age-dated to precisions of ∼17%. The rotational age of the M67 cluster as a whole is therefore 4.2 Gyr, but with a lower (averaged) uncertainty of 0.2 Gyr.« less

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

NASA Technical Reports Server (NTRS)

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

1989-01-01

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

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

NASA Astrophysics Data System (ADS)

Li, Chengyuan; de Grijs, Richard; Deng, Licai; Milone, Antonino P.

2017-08-01

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 Small 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.

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.

IDENTIFICATION OF THE LITHIUM DEPLETION BOUNDARY AND AGE OF THE SOUTHERN OPEN CLUSTER BLANCO 1

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

Cargile, P. A.; James, D. J.; Jeffries, R. D., E-mail: p.cargile@vanderbilt.ed

2010-12-20

We present results from a spectroscopic study of the very low mass members of the Southern open cluster Blanco 1 using the Gemini-N telescope. We obtained intermediate resolution (R {approx} 4400) GMOS spectra for 15 cluster candidate members with I {approx} 14-20 mag, and employed a series of membership criteria-proximity to the cluster's sequence in an I/I - K{sub s} color-magnitude diagram (CMD), kinematics agreeing with the cluster systemic motion, magnetic activity as a youth indicator-to classify 10 of these objects as probable cluster members. For these objects, we searched for the presence of the Li I 6708 A featuremore » to identify the lithium depletion boundary (LDB) in Blanco 1. The I/I - K{sub s} CMD shows a clear mass segregation in the Li distribution along the cluster sequence; namely, all higher mass stars are found to be Li poor, while lower mass stars are found to be Li rich. The division between Li-poor and Li-rich (i.e., the LDB) in Blanco 1 is found at I = 18.78 {+-} 0.24 and I - K{sub s} = 3.05 {+-} 0.10. Using current pre-main-sequence evolutionary models, we determine an LDB age of 132 {+-} 24 Myr. Comparing our derived LDB age to upper-main-sequence isochrone ages for Blanco 1, as well as for other open clusters with identified LDBs, we find good chronometric consistency when using stellar evolution models that incorporate a moderate degree of convective core overshoot.« less

Implementation of hybrid clustering based on partitioning around medoids algorithm and divisive analysis on human Papillomavirus DNA

NASA Astrophysics Data System (ADS)

Arimbi, Mentari Dian; Bustamam, Alhadi; Lestari, Dian

2017-03-01

Data clustering can be executed through partition or hierarchical method for many types of data including DNA sequences. Both clustering methods can be combined by processing partition algorithm in the first level and hierarchical in the second level, called hybrid clustering. In the partition phase some popular methods such as PAM, K-means, or Fuzzy c-means methods could be applied. In this study we selected partitioning around medoids (PAM) in our partition stage. Furthermore, following the partition algorithm, in hierarchical stage we applied divisive analysis algorithm (DIANA) in order to have more specific clusters and sub clusters structures. The number of main clusters is determined using Davies Bouldin Index (DBI) value. We choose the optimal number of clusters if the results minimize the DBI value. In this work, we conduct the clustering on 1252 HPV DNA sequences data from GenBank. The characteristic extraction is initially performed, followed by normalizing and genetic distance calculation using Euclidean distance. In our implementation, we used the hybrid PAM and DIANA using the R open source programming tool. In our results, we obtained 3 main clusters with average DBI value is 0.979, using PAM in the first stage. After executing DIANA in the second stage, we obtained 4 sub clusters for Cluster-1, 9 sub clusters for Cluster-2 and 2 sub clusters in Cluster-3, with the BDI value 0.972, 0.771, and 0.768 for each main cluster respectively. Since the second stage produce lower DBI value compare to the DBI value in the first stage, we conclude that this hybrid approach can improve the accuracy of our clustering results.

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.

Photometry of Standard Stars and Open Star Clusters

NASA Astrophysics Data System (ADS)

Jefferies, Amanda; Frinchaboy, Peter

2010-10-01

Photometric CCD observations of open star clusters and standard stars were carried out at the McDonald Observatory in Fort Davis, Texas. This data was analyzed using aperture photometry algorithms (DAOPHOT II and ALLSTAR) and the IRAF software package. Color-magnitude diagrams of these clusters were produced, showing the evolution of each cluster along the main sequence.

Complex spatiotemporal evolution of the 2008 Mw 4.9 Mogul earthquake swarm (Reno, Nevada): Interplay of fluid and faulting

NASA Astrophysics Data System (ADS)

Ruhl, C. J.; Abercrombie, R. E.; Smith, K. D.; Zaliapin, I.

2016-11-01

After approximately 2 months of swarm-like earthquakes in the Mogul neighborhood of west Reno, NV, seismicity rates and event magnitudes increased over several days culminating in an Mw 4.9 dextral strike-slip earthquake on 26 April 2008. Although very shallow, the Mw 4.9 main shock had a different sense of slip than locally mapped dip-slip surface faults. We relocate 7549 earthquakes, calculate 1082 focal mechanisms, and statistically cluster the relocated earthquake catalog to understand the character and interaction of active structures throughout the Mogul, NV earthquake sequence. Rapid temporary instrument deployment provides high-resolution coverage of microseismicity, enabling a detailed analysis of swarm behavior and faulting geometry. Relocations reveal an internally clustered sequence in which foreshocks evolved on multiple structures surrounding the eventual main shock rupture. The relocated seismicity defines a fault-fracture mesh and detailed fault structure from approximately 2-6 km depth on the previously unknown Mogul fault that may be an evolving incipient strike-slip fault zone. The seismicity volume expands before the main shock, consistent with pore pressure diffusion, and the aftershock volume is much larger than is typical for an Mw 4.9 earthquake. We group events into clusters using space-time-magnitude nearest-neighbor distances between events and develop a cluster criterion through randomization of the relocated catalog. Identified clusters are largely main shock-aftershock sequences, without evidence for migration, occurring within the diffuse background seismicity. The migration rate of the largest foreshock cluster and simultaneous background events is consistent with it having triggered, or having been triggered by, an aseismic slip event.

Characterization of HIV Transmission in South-East Austria

PubMed Central

Kessler, Harald H.; Haas, Bernhard; Stelzl, Evelyn; Weninger, Karin; Little, Susan J.; Mehta, Sanjay R.

2016-01-01

To gain deeper insight into the epidemiology of HIV-1 transmission in South-East Austria we performed a retrospective analysis of 259 HIV-1 partial pol sequences obtained from unique individuals newly diagnosed with HIV infection in South-East Austria from 2008 through 2014. After quality filtering, putative transmission linkages were inferred when two sequences were ≤1.5% genetically different. Multiple linkages were resolved into putative transmission clusters. Further phylogenetic analyses were performed using BEAST v1.8.1. Finally, we investigated putative links between the 259 sequences from South-East Austria and all publicly available HIV polymerase sequences in the Los Alamos National Laboratory HIV sequence database. We found that 45.6% (118/259) of the sampled sequences were genetically linked with at least one other sequence from South-East Austria forming putative transmission clusters. Clustering individuals were more likely to be men who have sex with men (MSM; p<0.001), infected with subtype B (p<0.001) or subtype F (p = 0.02). Among clustered males who reported only heterosexual (HSX) sex as an HIV risk, 47% clustered closely with MSM (either as pairs or within larger MSM clusters). One hundred and seven of the 259 sequences (41.3%) from South-East Austria had at least one putative inferred linkage with sequences from a total of 69 other countries. In conclusion, analysis of HIV-1 sequences from newly diagnosed individuals residing in South-East Austria revealed a high degree of national and international clustering mainly within MSM. Interestingly, we found that a high number of heterosexual males clustered within MSM networks, suggesting either linkage between risk groups or misrepresentation of sexual risk behaviors by subjects. PMID:26967154

Characterization of HIV Transmission in South-East Austria.

PubMed

Hoenigl, Martin; Chaillon, Antoine; Kessler, Harald H; Haas, Bernhard; Stelzl, Evelyn; Weninger, Karin; Little, Susan J; Mehta, Sanjay R

2016-01-01

To gain deeper insight into the epidemiology of HIV-1 transmission in South-East Austria we performed a retrospective analysis of 259 HIV-1 partial pol sequences obtained from unique individuals newly diagnosed with HIV infection in South-East Austria from 2008 through 2014. After quality filtering, putative transmission linkages were inferred when two sequences were ≤1.5% genetically different. Multiple linkages were resolved into putative transmission clusters. Further phylogenetic analyses were performed using BEAST v1.8.1. Finally, we investigated putative links between the 259 sequences from South-East Austria and all publicly available HIV polymerase sequences in the Los Alamos National Laboratory HIV sequence database. We found that 45.6% (118/259) of the sampled sequences were genetically linked with at least one other sequence from South-East Austria forming putative transmission clusters. Clustering individuals were more likely to be men who have sex with men (MSM; p<0.001), infected with subtype B (p<0.001) or subtype F (p = 0.02). Among clustered males who reported only heterosexual (HSX) sex as an HIV risk, 47% clustered closely with MSM (either as pairs or within larger MSM clusters). One hundred and seven of the 259 sequences (41.3%) from South-East Austria had at least one putative inferred linkage with sequences from a total of 69 other countries. In conclusion, analysis of HIV-1 sequences from newly diagnosed individuals residing in South-East Austria revealed a high degree of national and international clustering mainly within MSM. Interestingly, we found that a high number of heterosexual males clustered within MSM networks, suggesting either linkage between risk groups or misrepresentation of sexual risk behaviors by subjects.

Compact X-ray Binary Re-creation in Core Collapse: NGC 6397

NASA Astrophysics Data System (ADS)

Grindlay, J. E.; Bogdanov, S.; van den Berg, M.; Heinke, C.

2005-12-01

We report new Chandra observations of the core collapsed globular cluster NGC 6397. In comparison with our original Chandra observations (Grindlay et al 2001, ApJ, 563, L53), we now detect some 30 sources (vs. 20) in the cluster. A new CV is confirmed, though new HST/ACS optical observations (see Cohn et al this meeting) show that one of the original CV candidates is a background AGN). The 9 CVs (optically identified) yet only one MSP and one qLMXB suggest either a factor of 7 reduction in NSs/WDs vs. what we find in 47Tuc (see Grindlay 2005, Proc. Cefalu Conf. on Interacting Binaries) or that CVs are produced in the core collapse. The possible second MSP with main sequence companion, source U18 (see Grindlay et al 2001) is similar in its X-ray and optical properties to MSP-W in 47Tuc, which must have swapped its binary companion. Together with the one confirmed (radio) MSP in NGC 6397, with an evolved main sequence secondary, the process of enhanced partner swapping in the high stellar density of core collapse is implicated. At the same time, main sequence - main sequence binaries (active binaries) are depleted in the cluster core, presumably by "binary burning" in core collapse. These binary re-creation and destruction mechanisms in core collapse have profound implications for binary evolution and mergers in globulars that have undergone core collapse.

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

Exploring the nature and synchronicity of early cluster formation in the Large Magellanic Cloud - II. Relative ages and distances for six ancient globular clusters

NASA Astrophysics Data System (ADS)

Wagner-Kaiser, R.; Mackey, Dougal; Sarajedini, Ata; Chaboyer, Brian; Cohen, Roger E.; Yang, Soung-Chul; Cummings, Jeffrey D.; Geisler, Doug; Grocholski, Aaron J.

2017-11-01

We analyse Hubble Space Telescope observations of six globular clusters in the Large Magellanic Cloud (LMC) from programme GO-14164 in Cycle 23. These are the deepest available observations of the LMC globular cluster population; their uniformity facilitates a precise comparison with globular clusters in the Milky Way. Measuring the magnitude of the main-sequence turn-off point relative to template Galactic globular clusters allows the relative ages of the clusters to be determined with a mean precision of 8.4 per cent, and down to 6 per cent for individual objects. We find that the mean age of our LMC cluster ensemble is identical to the mean age of the oldest metal-poor clusters in the Milky Way halo to 0.2 ± 0.4 Gyr. This provides the most sensitive test to date of the synchronicity of the earliest epoch of globular cluster formation in two independent galaxies. Horizontal branch magnitudes and subdwarf fitting to the main sequence allow us to determine distance estimates for each cluster and examine their geometric distribution in the LMC. Using two different methods, we find an average distance to the LMC of 18.52 ± 0.05.

Pre-main sequence variables in young cluster Stock 18

NASA Astrophysics Data System (ADS)

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

2018-04-01

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

The Age Related Properties of Solar Type Stars

NASA Technical Reports Server (NTRS)

Soderblom, David

1999-01-01

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

A clustering package for nucleotide sequences using Laplacian Eigenmaps and Gaussian Mixture Model.

PubMed

Bruneau, Marine; Mottet, Thierry; Moulin, Serge; Kerbiriou, Maël; Chouly, Franz; Chretien, Stéphane; Guyeux, Christophe

2018-02-01

In this article, a new Python package for nucleotide sequences clustering is proposed. This package, freely available on-line, implements a Laplacian eigenmap embedding and a Gaussian Mixture Model for DNA clustering. It takes nucleotide sequences as input, and produces the optimal number of clusters along with a relevant visualization. Despite the fact that we did not optimise the computational speed, our method still performs reasonably well in practice. Our focus was mainly on data analytics and accuracy and as a result, our approach outperforms the state of the art, even in the case of divergent sequences. Furthermore, an a priori knowledge on the number of clusters is not required here. For the sake of illustration, this method is applied on a set of 100 DNA sequences taken from the mitochondrially encoded NADH dehydrogenase 3 (ND3) gene, extracted from a collection of Platyhelminthes and Nematoda species. The resulting clusters are tightly consistent with the phylogenetic tree computed using a maximum likelihood approach on gene alignment. They are coherent too with the NCBI taxonomy. Further test results based on synthesized data are then provided, showing that the proposed approach is better able to recover the clusters than the most widely used software, namely Cd-hit-est and BLASTClust. Copyright © 2017 Elsevier Ltd. All rights reserved.

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

NASA Astrophysics Data System (ADS)

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

2017-09-01

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

The Open Cluster NGC 2437 (Messier 46)

NASA Astrophysics Data System (ADS)

Davidge, T. J.

2013-02-01

The stellar content of the open cluster NGC 2437 (Messier 46) is investigated using moderately deep u∗, g‧, and r‧ MegaCam images. When compared with solar metallicity isochrones, the (g‧,u‧ - g‧) and (r‧,g‧ - r‧) CMDs are consistent with an age log(tyr) = 8.35 ± 0.15, a distance modulus μ0 = 11.05 ± 0.05, and a color excess E(B - V) = 0.115 ± 0.035. The r‧ luminosity function (LF) of main sequence stars in the magnitude range r‧ < 17 (i.e., masses ≳0.8 M⊙) has a shape that follows solar neighborhood star counts. However, at fainter magnitudes, the cluster LF is flat, in contrast with what would be expected from solar neighborhood counts. The clustering properties of stars in NGC 2437 are investigated by examining the two-point angular correlation functions of main sequence stars in different brightness ranges. Main sequence stars fainter than r‧ = 17 are less centrally concentrated than brighter stars and are found over a larger area of the sky, suggesting that there is a corona of faint main sequence stars around NGC 2437. Based on the flat LF and extended spatial distribution of faint stars, it is concluded that NGC 2437 is actively shedding stars with masses ≲0.8 M⊙. Based on observations obtained with MegaPrime/MegaCam, a joint project of CFHT and Commissariat à l'énergie atomique et aux énergies alternative (CEA)/Dapnia, at the Canada-France-Hawaii Telescope (CFHT), which is operated by the National Research Council (NRC) of Canada, the Institut National des Sciences de l’Univers of the Centre National de la Recherche Scientifique (CNRS) of France, and the University of Hawaii.

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.

Investigating the long-term course of schizophrenia by sequence analysis.

PubMed

An der Heiden, Wolfram; Häfner, Heinz

2015-08-30

In the present study we set out to explore the long-term clinical course of schizophrenia in a holistic manner by adopting sequence analysis. Our aim was to identify course types of illness by means of cluster analysis. The study was based on course and outcome data for 107 patients followed up over 134 months after first admission in the ABC Schizophrenia Study. Focusing on the main syndromes (positive, negative, depressive and unspecific symptoms) and their combinations we looked for similarities in individual illness courses using the 'optimal matching' method. A cluster analysis performed on the resulting similarity matrix yielded two main groups (a 'improving' and a 'chronic' group), which comprised a total of six different types of illness course. The course types differed in both quantitative (frequency of syndromes and syndrome combinations) and qualitative terms (clinical presentation, sequence of syndromes). Cluster membership was only rarely, but clearly associated with sociodemographic characteristics, treatment data and other illness variables. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Identification and characterization of earthquake clusters: a comparative analysis for selected sequences in Italy

NASA Astrophysics Data System (ADS)

Peresan, Antonella; Gentili, Stefania

2017-04-01

Identification and statistical characterization of seismic clusters may provide useful insights about the features of seismic energy release and their relation to physical properties of the crust within a given region. Moreover, a number of studies based on spatio-temporal analysis of main-shocks occurrence require preliminary declustering of the earthquake catalogs. Since various methods, relying on different physical/statistical assumptions, may lead to diverse classifications of earthquakes into main events and related events, we aim to investigate the classification differences among different declustering techniques. Accordingly, a formal selection and comparative analysis of earthquake clusters is carried out for the most relevant earthquakes in North-Eastern Italy, as reported in the local OGS-CRS bulletins, compiled at the National Institute of Oceanography and Experimental Geophysics since 1977. The comparison is then extended to selected earthquake sequences associated with a different seismotectonic setting, namely to events that occurred in the region struck by the recent Central Italy destructive earthquakes, making use of INGV data. Various techniques, ranging from classical space-time windows methods to ad hoc manual identification of aftershocks, are applied for detection of earthquake clusters. In particular, a statistical method based on nearest-neighbor distances of events in space-time-energy domain, is considered. Results from clusters identification by the nearest-neighbor method turn out quite robust with respect to the time span of the input catalogue, as well as to minimum magnitude cutoff. The identified clusters for the largest events reported in North-Eastern Italy since 1977 are well consistent with those reported in earlier studies, which were aimed at detailed manual aftershocks identification. The study shows that the data-driven approach, based on the nearest-neighbor distances, can be satisfactorily applied to decompose the seismic catalog into background seismicity and individual sequences of earthquake clusters, also in areas characterized by moderate seismic activity, where the standard declustering techniques may turn out rather gross approximations. With these results acquired, the main statistical features of seismic clusters are explored, including complex interdependence of related events, with the aim to characterize the space-time patterns of earthquakes occurrence in North-Eastern Italy and capture their basic differences with Central Italy sequences.

Photometric and Structural Properties of NGC 6544: A Combined VVV-Hubble Space Telescope Study

NASA Astrophysics Data System (ADS)

Cohen, Roger E.; Mauro, Francesco; Geisler, Doug; Moni Bidin, Christian; Dotter, Aaron; Bonatto, Charles

2014-07-01

We combine archival Hubble Space Telescope imaging with wide-field near-infrared photometry to study the neglected metal-poor Galactic globular cluster NGC 6544. A high spatial resolution map of differential reddening over the inner portion of the cluster is constructed, revealing variations of up to half of the total reddening, and the resulting corrected color-magnitude diagrams reveal a sparse blue horizontal branch and centrally concentrated blue straggler population, verified via relative proper motions. Using the corrected photometry to investigate the cluster distance, reddening, and age via direct comparison to well-calibrated photometry of clusters with similar metallicities, we estimate (m - M)0 = 11.96, E(B - V) = 0.79, and an age coeval with M13 to within the relevant uncertainties. Although our data are insufficient to place tight constraints on the reddening law toward NGC 6544, we find no strong evidence that it is non-standard at optical or near-infrared wavelengths. We also provide near-infrared fiducial sequences extending nearly 2 mag below the cluster main sequence turnoff, generated from a statistically decontaminated sample of cluster stars. Lastly, we redetermine the cluster center and construct a radial number density profile which is well fit by an atypically flat power law with a slope of about 1.7. We discuss this result, together with a flattened main sequence luminosity function and inverted mass function, in the context of mass segregation and tidal stripping via interactions with Milky Way potential.

The Origin Of Cosmic Rays And The Stars Of Berkeley 87

NASA Astrophysics Data System (ADS)

Turner, David G.; Majaess, D. J.; Lane, D. J.; Balam, D. D.

2010-01-01

Spectroscopic observations and the results of photometric monitoring are presented for members of the heavily-reddened, young, 1.2 kpc-distant, open cluster Berkeley 87, which is spatially coincident with the strongest source of cosmic rays in the northern sky. Many cluster members exhibit evidence for extreme loss of mass over their lifetimes: the M3 Ia supergiant BC Cyg has an evolutionary mass half that of stars at the main-sequence turnoff, the B2 Iabe emission-line supergiant HDE 229059 also has an evolutionary mass smaller than that of the main-sequence turnoff, the WO2 star WR 142, the only example of an oxygen sequence Wolf-Rayet star in an open cluster, displays evidence for variable, high velocity winds in its spectrum, the curious object V439 Cyg (B0: Vnne) appears to be an example of a recent binary merger, and Vatican Emission Star VES 203 (B0.5 Ve) displays a strong P Cygni signature in its Balmer line emission. It appears that heavy mass loss is a common factor associated with cluster stars. Could that be associated with the location of a cosmic ray production factory from the vicinity of Berkeley 87?

Differentiated evolutionary relationships among chordates from comparative alignments of multiple sequences of MyoD and MyoG myogenic regulatory factors.

PubMed

Oliani, L C; Lidani, K C F; Gabriel, J E

2015-10-16

MyoD and MyoG are transcription factors that have essential roles in myogenic lineage determination and muscle differentiation. The purpose of this study was to compare multiple amino acid sequences of myogenic regulatory proteins to infer evolutionary relationships among chordates. Protein sequences from Mus musculus (P10085 and P12979), human Homo sapiens (P15172 and P15173), bovine Bos taurus (Q7YS82 and Q7YS81), wild pig Sus scrofa (P49811 and P49812), quail Coturnix coturnix (P21572 and P34060), chicken Gallus gallus (P16075 and P17920), rat Rattus norvegicus (Q02346 and P20428), domestic water buffalo Bubalus bubalis (D2SP11 and A7L034), and sheep Ovis aries (Q90477 and D3YKV7) were searched from a non-redundant protein sequence database UniProtKB/Swiss-Prot, and subsequently analyzed using the Mega6.0 software. MyoD evolutionary analyses revealed the presence of three main clusters with all mammals branched in one cluster, members of the order Rodentia (mouse and rat) in a second branch linked to the first, and birds of the order Galliformes (chicken and quail) remaining isolated in a third. MyoG evolutionary analyses aligned sequences in two main clusters, all mammalian specimens grouped in different sub-branches, and birds clustered in a second branch. These analyses suggest that the evolution of MyoD and MyoG was driven by different pathways.

Estudio de la población estelar de varios cúmulos en Carina

NASA Astrophysics Data System (ADS)

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

2015-08-01

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

RSAT 2015: Regulatory Sequence Analysis Tools

PubMed Central

Medina-Rivera, Alejandra; Defrance, Matthieu; Sand, Olivier; Herrmann, Carl; Castro-Mondragon, Jaime A.; Delerce, Jeremy; Jaeger, Sébastien; Blanchet, Christophe; Vincens, Pierre; Caron, Christophe; Staines, Daniel M.; Contreras-Moreira, Bruno; Artufel, Marie; Charbonnier-Khamvongsa, Lucie; Hernandez, Céline; Thieffry, Denis; Thomas-Chollier, Morgane; van Helden, Jacques

2015-01-01

RSAT (Regulatory Sequence Analysis Tools) is a modular software suite for the analysis of cis-regulatory elements in genome sequences. Its main applications are (i) motif discovery, appropriate to genome-wide data sets like ChIP-seq, (ii) transcription factor binding motif analysis (quality assessment, comparisons and clustering), (iii) comparative genomics and (iv) analysis of regulatory variations. Nine new programs have been added to the 43 described in the 2011 NAR Web Software Issue, including a tool to extract sequences from a list of coordinates (fetch-sequences from UCSC), novel programs dedicated to the analysis of regulatory variants from GWAS or population genomics (retrieve-variation-seq and variation-scan), a program to cluster motifs and visualize the similarities as trees (matrix-clustering). To deal with the drastic increase of sequenced genomes, RSAT public sites have been reorganized into taxon-specific servers. The suite is well-documented with tutorials and published protocols. The software suite is available through Web sites, SOAP/WSDL Web services, virtual machines and stand-alone programs at http://www.rsat.eu/. PMID:25904632

The gap in the color-magnitude diagram of NGC 2420: A test of convective overshoot and cluster age

NASA Technical Reports Server (NTRS)

Demarque, Pierre; Sarajedini, Ata; Guo, X.-J.

1994-01-01

Theoretical isochrones have been constructed using the OPAL opacities specifically to study the color-magnitude diagram of the open star cluster NGC 2420. This cluster provides a rare test of core convection in intermediate-mass stars. At the same time, its age is of interest because of its low metallicity and relatively high Galactic latitude for an open cluster. The excellent color-magnitude diagram constructed by Anthony-Twarog et al. (1990) allows a detailed fit of the isochrones to the photometric data. We discuss the importance of convective overshoot at the convective core edge in determining the morphology of the gap located near the main-sequence turnoff. We find that given the assumptions made in the models, a modest amount of overshoot (0.23 H(sub p)) is required for the best fit. Good agreement is achieved with all features of the turnoff gap for a cluster age of 2.4 +/- 0.2 Gyr. We note that a photometrically complete luminosity function near the main-sequence turnoff and subgiant branch would also provide an important test of the overshoot models.

A Photometric Survey of the Open Clusters NGC 7789 and M67

NASA Astrophysics Data System (ADS)

Janes, Kenneth

2010-01-01

Although there is strong evidence that stellar activity declines as a star ages, beyond about the age of the Hyades (600 Myr) there is little direct confirmation of this decline in stars of known age. This report is an update of an earlier report (Hayes-Gehrke, et al., 2004, AJ, 128, 2862) of a long-term project to explore stellar activity in old open clusters. I have now accumulated 12 years of photometry of the old clusters NGC 7789 (about 1.8 Gyr) and M 67 (about 4 Gyr). An analysis of these data has revealed a substantial number of low-amplitude variable stars in both clusters, including a number of previously-discovered eclipsing binary stars, and several stars near the main sequence turnoff of both clusters that exhibit apparently erratic variations. Some of the M 67 erratics are known X-ray sources. On the main sequence, the large majority of stars show little or no evidence for variability at the 0.1% - 0.2% level, consistent with a regular systematic decline in activity level with age.

Infrasound and seismic analysis of the SpaceX Falcon9 explosion sequence of 1-September-2016

NASA Astrophysics Data System (ADS)

Thompson, G.; McNutt, S. R.; Brown, R. G.; Braunmiller, J.; Mehta, C.

2017-12-01

During a static launch test on 1-Sep-2016 at Kennedy Space Center, a SpaceX Falcon 9 rocket exploded causing loss of the rocket and the payload, and extensively damaging the launch complex. The sequence was captured by a 3-element infrasound array and a broadband 3-component seismometer at the Astronaut Beach House, just 0.87 miles (1.4 km) from the launch pad. Manual picking identified 153 impulsive airwave signals over a 26-minute interval and these were compared to video recordings of the sequence. The explosion onset consisted of a moderate signal on both seismic and infrasound (52 Pa) instruments. This corresponds to the rupture of the second-stage fuel tank. We found no signals before this, so we do not believe that there was an external cause. The primary fuel tank ruptured 4 seconds later and was the strongest event by far, producing an infrasound signal that exceeded 1400 Pa ( 2000 Pa in reduced pressure). The seismic signal consists mainly of air-coupled Rayleigh waves with frequencies of 5-23 Hz. The infrasound events occurred in four clusters. The first cluster included the onset and main events and 46 smaller events. This was followed by several minutes without infrasound signals during which a 3.5 minute continuous seismic vibration occurred. Cluster 2 consisted of 4 events ranging from 117-256 Pa. Cluster 3 comprised 96 events of 7-78 Pa. Cluster 4 consisted of 5 events with overpressures of 23-63 Pa. Gaps of several minutes without infrasound and seismic signals occurred between clusters 2 and 3, and 3 and 4. In terms of energy, the main event dominated; in terms of numbers, cluster 3 had the most infrasound events. The seismic and infrasound data are complementary to video recordings of the explosion, and provide additional characterization that may be useful to interpret the sequence of events. Because of the proximity of our array to this rocket explosion, our dataset may be unique.

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.

The Evolution of Rotation and Activity in Young Open Clusters: the Zero-Age Main Sequence.

NASA Astrophysics Data System (ADS)

Patten, Brian Michael

1995-01-01

I have undertaken a program of ground- and space -based observations to measure photometric rotation periods and X-ray luminosities for late-type stars in the young open clusters IC 2391 and IC 2602. With cluster ages of ~30 Myr, IC 2391 and IC 2602 are ideal sites in which to observe conditions at the ZAMS since the solar-type stars in these clusters have not been on the main sequence long enough to undergo significant magnetic braking. The ROSAT survey of IC 2391 revealed 80 X-ray sources, 44 of which were found to be associated with stars which are now classified as new cluster members. Among the solar-type stars in both IC 2391 and IC 2602, I find a factor of ~25 spread in the distribution of rotation periods, which range from 0.21 to 4.86 day. I also find a factor of ~10-20 spread in the range of LX about a median LX value of ~10^{30 } erg s^{-1} for both clusters. These results show conclusively that stars arrive on the ZAMS with a wide range of rotation rates and coronal activity levels. When compared to data from older clusters, such as the Pleiades and the Hyades, there is an overall decline observed in both the rotation rates and median X-ray luminosity of cluster members with increasing age, however, while the spread in the range of rotation rates decreases to a small value, the spread in the range of LX values as a fraction of the median is observed to increase with age. This behavior is best explained through a dependence of LX on P rot which is weak in the young clusters and strong in the older clusters. The Rossby diagram shows there is a tight correlation between L X/Lbol and the Rossby number, Prot divided by the convective turnover time. Young, rapidly rotating, main sequence stars lie along a plateau of magnetic saturation, where LX has a weak dependence on rotation period, while older, more slowly rotating stars lie in a region on the Rossby diagram where LX has a strong dependence on rotation period.

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

NASA Technical Reports Server (NTRS)

Gagne, Marc; Caillault, Jean-Pierre

1994-01-01

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

Rotational evolution of slow-rotator sequence stars

NASA Astrophysics Data System (ADS)

Lanzafame, A. C.; Spada, F.

2015-12-01

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

Photometric and structural properties of NGC 6544: A combined VVV-Hubble space telescope study

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

Cohen, Roger E.; Mauro, Francesco; Geisler, Doug

We combine archival Hubble Space Telescope imaging with wide-field near-infrared photometry to study the neglected metal-poor Galactic globular cluster NGC 6544. A high spatial resolution map of differential reddening over the inner portion of the cluster is constructed, revealing variations of up to half of the total reddening, and the resulting corrected color-magnitude diagrams reveal a sparse blue horizontal branch and centrally concentrated blue straggler population, verified via relative proper motions. Using the corrected photometry to investigate the cluster distance, reddening, and age via direct comparison to well-calibrated photometry of clusters with similar metallicities, we estimate (m – M){sub 0}more » = 11.96, E(B – V) = 0.79, and an age coeval with M13 to within the relevant uncertainties. Although our data are insufficient to place tight constraints on the reddening law toward NGC 6544, we find no strong evidence that it is non-standard at optical or near-infrared wavelengths. We also provide near-infrared fiducial sequences extending nearly 2 mag below the cluster main sequence turnoff, generated from a statistically decontaminated sample of cluster stars. Lastly, we redetermine the cluster center and construct a radial number density profile which is well fit by an atypically flat power law with a slope of about 1.7. We discuss this result, together with a flattened main sequence luminosity function and inverted mass function, in the context of mass segregation and tidal stripping via interactions with Milky Way potential.« less

VizieR Online Data Catalog: CCD photometry of Pal 1 (Borissova+ 1995)

NASA Astrophysics Data System (ADS)

Borissova, J.; Spassova, N.

1997-06-01

A CCD photometry of the halo cluster Palomar 1 is presented in the Thuan-Gunn photometric system. The principal sequences of the color-magnitude diagrams are delineated in different spectral bands. The color- magnitude diagrams of the cluster show a well defined red horizontal branch, a subgiant branch and a main-sequence down to about two magnitudes below the main sequence turnoff. The giant branch is absent and the brightest stars are the horizontal branch stars. The age of the cluster determined by comparison with the isochrones of Bell & VandenBerg (1987ApJS...63..335B) is consistent with an age in the interval 12-14Gyr. A distance modulus of (m-M)g0=15.38+/-0.15 magnitude and E(g-r)=0.16 has been derived. An estimate of the cluster structural parameters such as core radius and concentration parameter gives rc=1.5pc and c=1.46. A mass estimate of 1.1x103M⊙ and a mass-to-light ratio of 1.79 have been obtained using King's (1966AJ.....71...64K) method. The morphology of color-magnitude diagrams allows Pal 1 to be interpreted as probably a globular cluster rather than an old open one. For a description of the uvgr photometric system, see e.g. (1 data file).

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.

The Problem of Hipparcos Distances to Open Clusters. II. Constraints from Nearby Field Theory. Report 2; ClustersConstraints from nearly Field Stars

NASA Technical Reports Server (NTRS)

Soderblom, David R.; King, Jeremy R.; Hanson, Robert B.; Jones, Burton F.; Fischer, Debra; Stauffer, John R.; Pinsonneault, Marc H.

1998-01-01

This paper examines the discrepancy between distances to nearby open clusters as determined by parallaxes from Hipparcos compared to traditional main-sequence fitting. The biggest difference is seen for the Pleiades, and our hypothesis is that if the Hipparcos distance to the Pleiades is correct, then similar subluminous zero-age main-sequence (ZAMS) stars should exist elsewhere, including in the immediate solar neighborhood. We examine a color-magnitude diagram of very young and nearby solar-type stars and show that none of them lie below the traditional ZAMS, despite the fact that the Hipparcos Pleiades parallax would place its members 0.3 mag below that ZAMS. We also present analyses and observations of solar-type stars that do lie below the ZAMS, and we show that they are subluminous because of low metallicity and that they have the kinematics of old stars.

Stellar Variability at the Main-sequence Turnoff of the Intermediate-age LMC Cluster NGC 1846

NASA Astrophysics Data System (ADS)

Salinas, R.; Pajkos, M. A.; Vivas, A. K.; Strader, J.; Contreras Ramos, R.

2018-04-01

Intermediate-age (IA) star clusters in the Large Magellanic Cloud (LMC) present extended main-sequence turn-offs (MSTO) that have been attributed to either multiple stellar populations or an effect of stellar rotation. Recently it has been proposed that these extended main sequences can also be produced by ill-characterized stellar variability. Here we present Gemini-S/Gemini Multi-Object Spectrometer (GMOS) time series observations of the IA cluster NGC 1846. Using differential image analysis, we identified 73 new variable stars, with 55 of those being of the Delta Scuti type, that is, pulsating variables close the MSTO for the cluster age. Considering completeness and background contamination effects, we estimate the number of δ Sct belonging to the cluster between 40 and 60 members, although this number is based on the detection of a single δ Sct within the cluster half-light radius. This amount of variable stars at the MSTO level will not produce significant broadening of the MSTO, albeit higher-resolution imaging will be needed to rule out variable stars as a major contributor to the extended MSTO phenomenon. Though modest, this amount of δ Sct makes NGC 1846 the star cluster with the highest number of these variables ever discovered. Lastly, our results present a cautionary tale about the adequacy of shallow variability surveys in the LMC (like OGLE) to derive properties of its δ Sct population. Based on observations obtained at the Gemini Observatory, which is operated by the Association of Universities for Research in Astronomy, Inc., under a cooperative agreement with the NSF on behalf of the Gemini partnership: the National Science Foundation (United States), the National Research Council (Canada), CONICYT (Chile), Ministerio de Ciencia, Tecnología e Innovación Productiva (Argentina), and Ministério da Ciência, Tecnologia e Inovação (Brazil).

Molecular comparison of the structural proteins encoding gene clusters of two related Lactobacillus delbrueckii bacteriophages.

PubMed Central

Vasala, A; Dupont, L; Baumann, M; Ritzenthaler, P; Alatossava, T

1993-01-01

Virulent phage LL-H and temperate phage mv4 are two related bacteriophages of Lactobacillus delbrueckii. The gene clusters encoding structural proteins of these two phages have been sequenced and further analyzed. Six open reading frames (ORF-1 to ORF-6) were detected. Protein sequencing and Western immunoblotting experiments confirmed that ORF-3 (g34) encoded the main capsid protein Gp34. The presence of a putative late promoter in front of the phage LL-H g34 gene was suggested by primer extension experiments. Comparative sequence analysis between phage LL-H and phage mv4 revealed striking similarities in the structure and organization of this gene cluster, suggesting that the genes encoding phage structural proteins belong to a highly conservative module. Images PMID:8497043

Construction of a map-based reference genome sequence for barley, Hordeum vulgare L.

PubMed Central

Beier, Sebastian; Himmelbach, Axel; Colmsee, Christian; Zhang, Xiao-Qi; Barrero, Roberto A.; Zhang, Qisen; Li, Lin; Bayer, Micha; Bolser, Daniel; Taudien, Stefan; Groth, Marco; Felder, Marius; Hastie, Alex; Šimková, Hana; Staňková, Helena; Vrána, Jan; Chan, Saki; Muñoz-Amatriaín, María; Ounit, Rachid; Wanamaker, Steve; Schmutzer, Thomas; Aliyeva-Schnorr, Lala; Grasso, Stefano; Tanskanen, Jaakko; Sampath, Dharanya; Heavens, Darren; Cao, Sujie; Chapman, Brett; Dai, Fei; Han, Yong; Li, Hua; Li, Xuan; Lin, Chongyun; McCooke, John K.; Tan, Cong; Wang, Songbo; Yin, Shuya; Zhou, Gaofeng; Poland, Jesse A.; Bellgard, Matthew I.; Houben, Andreas; Doležel, Jaroslav; Ayling, Sarah; Lonardi, Stefano; Langridge, Peter; Muehlbauer, Gary J.; Kersey, Paul; Clark, Matthew D.; Caccamo, Mario; Schulman, Alan H.; Platzer, Matthias; Close, Timothy J.; Hansson, Mats; Zhang, Guoping; Braumann, Ilka; Li, Chengdao; Waugh, Robbie; Scholz, Uwe; Stein, Nils; Mascher, Martin

2017-01-01

Barley (Hordeum vulgare L.) is a cereal grass mainly used as animal fodder and raw material for the malting industry. The map-based reference genome sequence of barley cv. ‘Morex’ was constructed by the International Barley Genome Sequencing Consortium (IBSC) using hierarchical shotgun sequencing. Here, we report the experimental and computational procedures to (i) sequence and assemble more than 80,000 bacterial artificial chromosome (BAC) clones along the minimum tiling path of a genome-wide physical map, (ii) find and validate overlaps between adjacent BACs, (iii) construct 4,265 non-redundant sequence scaffolds representing clusters of overlapping BACs, and (iv) order and orient these BAC clusters along the seven barley chromosomes using positional information provided by dense genetic maps, an optical map and chromosome conformation capture sequencing (Hi-C). Integrative access to these sequence and mapping resources is provided by the barley genome explorer (BARLEX). PMID:28448065

Biological nitrogen fixation in the oxygen-minimum region of the eastern tropical North Pacific ocean.

PubMed

Jayakumar, Amal; Chang, Bonnie X; Widner, Brittany; Bernhardt, Peter; Mulholland, Margaret R; Ward, Bess B

2017-10-01

Biological nitrogen fixation (BNF) was investigated above and within the oxygen-depleted waters of the oxygen-minimum zone of the Eastern Tropical North Pacific Ocean. BNF rates were estimated using an isotope tracer method that overcame the uncertainty of the conventional bubble method by directly measuring the tracer enrichment during the incubations. Highest rates of BNF (~4 nM day -1 ) occurred in coastal surface waters and lowest detectable rates (~0.2 nM day -1 ) were found in the anoxic region of offshore stations. BNF was not detectable in most samples from oxygen-depleted waters. The composition of the N 2 -fixing assemblage was investigated by sequencing of nifH genes. The diazotrophic assemblage in surface waters contained mainly Proteobacterial sequences (Cluster I nifH), while both Proteobacterial sequences and sequences with high identities to those of anaerobic microbes characterized as Clusters III and IV type nifH sequences were found in the anoxic waters. Our results indicate modest input of N through BNF in oxygen-depleted zones mainly due to the activity of proteobacterial diazotrophs.

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

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

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

2014-07-20

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

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

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

PubMed Central

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

2013-01-01

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

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

PubMed

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

2013-01-01

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

RSAT 2015: Regulatory Sequence Analysis Tools.

PubMed

Medina-Rivera, Alejandra; Defrance, Matthieu; Sand, Olivier; Herrmann, Carl; Castro-Mondragon, Jaime A; Delerce, Jeremy; Jaeger, Sébastien; Blanchet, Christophe; Vincens, Pierre; Caron, Christophe; Staines, Daniel M; Contreras-Moreira, Bruno; Artufel, Marie; Charbonnier-Khamvongsa, Lucie; Hernandez, Céline; Thieffry, Denis; Thomas-Chollier, Morgane; van Helden, Jacques

2015-07-01

RSAT (Regulatory Sequence Analysis Tools) is a modular software suite for the analysis of cis-regulatory elements in genome sequences. Its main applications are (i) motif discovery, appropriate to genome-wide data sets like ChIP-seq, (ii) transcription factor binding motif analysis (quality assessment, comparisons and clustering), (iii) comparative genomics and (iv) analysis of regulatory variations. Nine new programs have been added to the 43 described in the 2011 NAR Web Software Issue, including a tool to extract sequences from a list of coordinates (fetch-sequences from UCSC), novel programs dedicated to the analysis of regulatory variants from GWAS or population genomics (retrieve-variation-seq and variation-scan), a program to cluster motifs and visualize the similarities as trees (matrix-clustering). To deal with the drastic increase of sequenced genomes, RSAT public sites have been reorganized into taxon-specific servers. The suite is well-documented with tutorials and published protocols. The software suite is available through Web sites, SOAP/WSDL Web services, virtual machines and stand-alone programs at http://www.rsat.eu/. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

The Not So Simple Globular Cluster ω Cen. I. Spatial Distribution of the Multiple Stellar Populations

NASA Astrophysics Data System (ADS)

Calamida, A.; Strampelli, G.; Rest, A.; Bono, G.; Ferraro, I.; Saha, A.; Iannicola, G.; Scolnic, D.; James, D.; Smith, C.; Zenteno, A.

2017-04-01

We present a multi-band photometric catalog of ≈1.7 million cluster members for a field of view of ≈2° × 2° across ω Cen. Photometry is based on images collected with the Dark Energy Camera on the 4 m Blanco telescope and the Advanced Camera for Surveys on the Hubble Space Telescope. The unprecedented photometric accuracy and field coverage allowed us, for the first time, to investigate the spatial distribution of ω Cen multiple populations from the core to the tidal radius, confirming its very complex structure. We found that the frequency of blue main-sequence stars is increasing compared to red main-sequence stars starting from a distance of ≈25‧ from the cluster center. Blue main-sequence stars also show a clumpy spatial distribution, with an excess in the northeast quadrant of the cluster pointing toward the direction of the Galactic center. Stars belonging to the reddest and faintest red-giant branch also show a more extended spatial distribution in the outskirts of ω Cen, a region never explored before. Both these stellar sub-populations, according to spectroscopic measurements, are more metal-rich compared to the cluster main stellar population. These findings, once confirmed, make ω Cen the only stellar system currently known where metal-rich stars have a more extended spatial distribution compared to metal-poor stars. Kinematic and chemical abundance measurements are now needed for stars in the external regions of ω Cen to better characterize the properties of these sub-populations. Based on observations made with the Dark Energy Camera (DECam) on the 4 m Blanco telescope (NOAO) under programs 2014A-0327, 2015A-0151, 2016A-0189, PIs: A. Calamida, A. Rest, and on observations made with the NASA/ESA Hubble Space Telescope, obtained by the Space Telescope Science Institute. STScI is operated by the Association of Universities for Research in Astronomy, Inc., under NASA contract NAS 5-26555.

Membership and Coronal Activity in the NGC 2232 and Cr 140 Open Clusters

NASA Technical Reports Server (NTRS)

Oliversen, Ronald J. (Technical Monitor); Patten, Brian M.

2004-01-01

Making use of eight archival ROSAT HRI images in the regions of the NGC 2232 and Cr 140, this project's primary focus is to identify X-ray sources and to extract net source counts for these sources in these two open clusters. These X-ray data would be combined with ground-based photometry and spectroscopy in order to identify G, K, and early-M type cluster members. Such membership data are important because, at present, no members later than spectral type approx. F5 are currently known for either cluster. With ages estimated to be approx. 25 Myr and at distances of just approx. 350 pc, the combined late-type membership of the NGC 2232 and Cr 140 clusters would yield an almost unique sample of solar-type stars in the post-T Tauri/pre-main sequence phase of evolution. These stars could be used to assess the level and dispersion of coronal activity levels, as a part of a probe of the importance of magnetic braking and the level of magnetic dynamo activity, for solar-type stars just before they reach the zero-age main sequence.

The Hyades main sequence

NASA Astrophysics Data System (ADS)

Eggen, O. J.

1982-11-01

Intermediate band, H-beta and RI observations of 72 Hyades cluster stars to V = 11 mag are reported and discussed. A modulus of 3.2 mag is derived on the basis of a comparison with field stars of large parallax. Also presented are observations of 98 main-sequence stars of the Hyades group that were previously found to be group members from kinematical considerations. Parallaxes of the group stars, computed on the assumption that they are members of an extended Hyades cluster, yield mean values of (U, V, W) = (+40.5, -18.4, -4.9) km/s, with dispersions of (2.3, 2.3, 6.0) km/s, compared with (+41.7, -18.4, -2.0) and (2.6, 1.3, 1.9) km/s for the brightest cluster members. It is noted that all the stars discussed can be considered as members of a supercluster in which only a slight relaxation control of the W velocities is present for stars far from the nucleus. Evidence is found, including that of the Praesepe cluster at Z = +80 pc, for some interchange between the U, V, and W velocities in stars farthest from the galactic plane, with the total cluster velocity being maintained.

Extended main sequence turnoffs in intermediate-age star clusters: a correlation between turnoff width and early escape velocity

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

Goudfrooij, Paul; Kozhurina-Platais, Vera; Kalirai, Jason S.

2014-12-10

We present a color-magnitude diagram analysis of deep Hubble Space Telescope imaging of a mass-limited sample of 18 intermediate-age (1-2 Gyr old) star clusters in the Magellanic Clouds, including eight clusters for which new data were obtained. We find that all star clusters in our sample feature extended main-sequence turnoff (eMSTO) regions that are wider than can be accounted for by a simple stellar population (including unresolved binary stars). FWHM widths of the MSTOs indicate age spreads of 200-550 Myr. We evaluate the dynamical evolution of clusters with and without initial mass segregation. Our main results are (1) the fractionmore » of red clump (RC) stars in secondary RCs in eMSTO clusters scales with the fraction of MSTO stars having pseudo-ages of ≲1.35 Gyr; (2) the width of the pseudo-age distributions of eMSTO clusters is correlated with their central escape velocity v {sub esc}, both currently and at an age of 10 Myr. We find that these two results are unlikely to be reproduced by the effects of interactive binary stars or a range of stellar rotation velocities. We therefore argue that the eMSTO phenomenon is mainly caused by extended star formation within the clusters; and (3) we find that v {sub esc} ≥ 15 km s{sup –1} out to ages of at least 100 Myr for all clusters featuring eMSTOs, and v {sub esc} ≤ 12 km s{sup –1} at all ages for two lower-mass clusters in the same age range that do not show eMSTOs. We argue that eMSTOs only occur for clusters whose early escape velocities are higher than the wind velocities of stars that provide material from which second-generation stars can form. The threshold of 12-15 km s{sup –1} is consistent with wind velocities of intermediate-mass asymptotic giant branch stars and massive binary stars in the literature.« less

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.

Blue stragglers in the core of the globular cluster 47 Tucanae

NASA Technical Reports Server (NTRS)

Paresce, F.; Meylan, G.; Shara, M.; Baxter, D.; Greenfield, P.

1991-01-01

High-resolution observations of the core of the globular cluster 47 Tucanae with the Faint Object Camera on the Hubble Space Telescope reveal a high density of 'blue straggler' stars, occupying the upper end of the main sequence from which all stars in the cluster should have long since evolved. Their presence in the dense core supports the hypothesis that they formed by stellar collision and coalescence, and, as the heaviest objects in the cluster, have drifted to the core.

Analysis of human papillomavirus 16 E6, E7 genes and Long Control Region in cervical samples from Uruguayan women.

PubMed

Ramas, Viviana; Mirazo, Santiago; Bonilla, Sylvia; Ruchansky, Dora; Arbiza, Juan

2018-05-15

This study aims to investigate the HPV16 variant distribution by sequence analyses of E6, E7 oncogenes and the Long Control Region (LCR), from cervical cells collected from Uruguayan women, and to reconstruct the phylogenetic relationships among variants. Forty-seven HPV16 variants, obtained from women with HSIL, LSIL, ASCUS and NILM cytological classes were analyzed for LCR and 12 were further studied for E6 and E7. Detailed sequence comparison, genetic heterogeneity analyses and phylogenetic reconstruction were performed. A high variability was observed among LCR sequences, which were distributed in 18 different variants. E6 and E7 sequences exhibited novel non-synonymous substitutions. Uruguayan sequences mainly belonged to the European lineage, and only 5 sequences clustered in non-European branches; 3 of them in the Asian-American and North-American linage and 2 in an African branch. Additionally, 6 new variants from European and African clusters were identified. HPV16 isolates mainly belonged to the European lineage, though strains from African and Asian-American lineages were also identified. Herein is reported for the first time the distribution and molecular characterization of HPV16 variants from Uruguay, providing novel insights on the molecular epidemiology of this infectious disease in the South America. A high variability among HPV 16 isolates mainly belonged to European lineage, provides an extensive sequence dataset from a country with high burden of cervical cancer. Copyright © 2018 Elsevier B.V. All rights reserved.

Cluster and principal component analysis based on SSR markers of Amomum tsao-ko in Jinping County of Yunnan Province

NASA Astrophysics Data System (ADS)

Ma, Mengli; Lei, En; Meng, Hengling; Wang, Tiantao; Xie, Linyan; Shen, Dong; Xianwang, Zhou; Lu, Bingyue

2017-08-01

Amomum tsao-ko is a commercial plant that used for various purposes in medicinal and food industries. For the present investigation, 44 germplasm samples were collected from Jinping County of Yunnan Province. Clusters analysis and 2-dimensional principal component analysis (PCA) was used to represent the genetic relations among Amomum tsao-ko by using simple sequence repeat (SSR) markers. Clustering analysis clearly distinguished the samples groups. Two major clusters were formed; first (Cluster I) consisted of 34 individuals, the second (Cluster II) consisted of 10 individuals, Cluster I as the main group contained multiple sub-clusters. PCA also showed 2 groups: PCA Group 1 included 29 individuals, PCA Group 2 included 12 individuals, consistent with the results of cluster analysis. The purpose of the present investigation was to provide information on genetic relationship of Amomum tsao-ko germplasm resources in main producing areas, also provide a theoretical basis for the protection and utilization of Amomum tsao-ko resources.

High-Resolution Analysis by Whole-Genome Sequencing of an International Lineage (Sequence Type 111) of Pseudomonas aeruginosa Associated with Metallo-Carbapenemases in the United Kingdom.

PubMed

Turton, Jane F; Wright, Laura; Underwood, Anthony; Witney, Adam A; Chan, Yuen-Ting; Al-Shahib, Ali; Arnold, Catherine; Doumith, Michel; Patel, Bharat; Planche, Timothy D; Green, Jonathan; Holliman, Richard; Woodford, Neil

2015-08-01

Whole-genome sequencing (WGS) was carried out on 87 isolates of sequence type 111 (ST-111) of Pseudomonas aeruginosa collected between 2005 and 2014 from 65 patients and 12 environmental isolates from 24 hospital laboratories across the United Kingdom on an Illumina HiSeq instrument. Most isolates (73) carried VIM-2, but others carried IMP-1 or IMP-13 (5) or NDM-1 (1); one isolate had VIM-2 and IMP-18, and 7 carried no metallo-beta-lactamase (MBL) gene. Single nucleotide polymorphism analysis divided the isolates into distinct clusters; the NDM-1 isolate was an outlier, and the IMP isolates and 6/7 MBL-negative isolates clustered separately from the main set of 73 VIM-2 isolates. Within the VIM-2 set, there were at least 3 distinct clusters, including a tightly clustered set of isolates from 3 hospital laboratories consistent with an outbreak from a single introduction that was quickly brought under control and a much broader set dominated by isolates from a long-running outbreak in a London hospital likely seeded from an environmental source, requiring different control measures; isolates from 7 other hospital laboratories in London and southeast England were also included. Bayesian evolutionary analysis indicated that all the isolates shared a common ancestor dating back ∼50 years (1960s), with the main VIM-2 set separating approximately 20 to 30 years ago. Accessory gene profiling revealed blocks of genes associated with particular clusters, with some having high similarity (≥95%) to bacteriophage genes. WGS of widely found international lineages such as ST-111 provides the necessary resolution to inform epidemiological investigations and intervention policies. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

A Photometric Search for Planets in the Open Cluster NGC 7086

NASA Astrophysics Data System (ADS)

Rosvick, Joanne M.; Robb, Russell

2006-12-01

In an attempt to discover short-period, Jupiter-mass planets orbiting solar-type stars in open clusters, we searched for planetary transits in the populous and relatively unstudied open cluster NGC 7086. A color-magnitude diagram constructed from new B and V photometry is presented, along with revised estimates of the cluster's color excess, distance modulus, and age. Several turnoff stars were observed spectroscopically in order to determine a color excess of E(B-V)=0.83+/-0.02. Empirically fitting the main sequences of two young open clusters and the semiempirical zero-age main sequence of Vandenberg and Poll yielded a distance modulus of (V-MV)=13.4+/-0.3 mag. This corresponds to a true distance modulus of (m-M)0=10.8 mag or a distance of 1.5 kpc to NGC 7086. These values were used with isochrones from the Padova group to obtain a cluster age of 100 Myr. Eleven nights of R-band photometry were used to search for planetary transits. Differential magnitudes were constructed for each star in the cluster. Light curves for each star were produced on a night-to-night basis and inspected for variability. No planetary transits were apparent; however, some interesting variable stars were discovered: a pulsating variable that appears to be a member of the γ Dor class and four possible eclipsing binary stars, one of which actually may be a multiple system.

The Not So Simple Globular Cluster ω Cen. I. Spatial Distribution of the Multiple Stellar Populations

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

Calamida, A.; Saha, A.; Strampelli, G.

2017-04-01

We present a multi-band photometric catalog of ≈1.7 million cluster members for a field of view of ≈2° × 2° across ω Cen. Photometry is based on images collected with the Dark Energy Camera on the 4 m Blanco telescope and the Advanced Camera for Surveys on the Hubble Space Telescope . The unprecedented photometric accuracy and field coverage allowed us, for the first time, to investigate the spatial distribution of ω Cen multiple populations from the core to the tidal radius, confirming its very complex structure. We found that the frequency of blue main-sequence stars is increasing compared to red main-sequencemore » stars starting from a distance of ≈25′ from the cluster center. Blue main-sequence stars also show a clumpy spatial distribution, with an excess in the northeast quadrant of the cluster pointing toward the direction of the Galactic center. Stars belonging to the reddest and faintest red-giant branch also show a more extended spatial distribution in the outskirts of ω Cen, a region never explored before. Both these stellar sub-populations, according to spectroscopic measurements, are more metal-rich compared to the cluster main stellar population. These findings, once confirmed, make ω Cen the only stellar system currently known where metal-rich stars have a more extended spatial distribution compared to metal-poor stars. Kinematic and chemical abundance measurements are now needed for stars in the external regions of ω Cen to better characterize the properties of these sub-populations.« less

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

NASA Astrophysics Data System (ADS)

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

2017-05-01

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

Phylodynamic Analysis Revealed That Epidemic of CRF07_BC Strain in Men Who Have Sex with Men Drove Its Second Spreading Wave in China.

PubMed

Zhang, Min; Jia, Dijing; Li, Hanping; Gui, Tao; Jia, Lei; Wang, Xiaolin; Li, Tianyi; Liu, Yongjian; Bao, Zuoyi; Liu, Siyang; Zhuang, Daomin; Li, Jingyun; Li, Lin

2017-10-01

CRF07_BC was originally formed in Yunnan province of China in 1980s and spread quickly in injecting drug users (IDUs). In recent years, it has been introduced into men who have sex with men (MSM) and become the most dominant strain in China. In this study, we performed a comprehensively phylodynamic analysis of CRF07_BC sequences from China. All CRF07_BC sequences identified in China were retrieved from database. More sequences obtained in our laboratory were added to make the dataset more representative. A maximum-likelihood (ML) tree was constructed with PhyML3.0. Maximum clade credibility (MCC) tree and effective population size were predicted by using Markov Chains Monte Carlo sampling method with Beast software. A total of 610 CRF07_BC sequences coving 1,473 bp of the gag gene (from 817 to 2,289 according to HXB2 calculator) were included into the dataset. Three epidemic clusters were identified; two clusters comprised sequences from IDUs, while one cluster mainly contained sequences from MSMs. The time of the most recent common ancestor of clusters that composed of sequences from MSMs was estimated to be in 2000. Two rapid spreading waves of effective population size of CRF07_BC infections were identified in the skyline plot. The second wave coincided with the expanding of MSM cluster. The results indicated that the control of CRF07_BC infections in MSMs would help to decrease its epidemic in China.

Comparison of calculated and observed integral magnitudes for the globular cluster M13

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

Gerashchenko, A.N.; Kadla, Z.I.

On the basis of a study of the distribution of stars in the central region of the globular cluster M13 it is found that integral photoelectric observations cover stars down to about the point of turnoff from the main sequence. Here the distribution of giants and stars of the horizontal branch as a function of distance from the center of the cluster is the same within limits of 0

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

NASA Technical Reports Server (NTRS)

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

1989-01-01

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

Genotypic Diversity and Virulence Characteristics of Clinical and Environmental Vibrio vulnificus Isolates from the Baltic Sea Region

PubMed Central

Bier, Nadja; Bechlars, Silke; Diescher, Susanne; Klein, Florian; Hauk, Gerhard; Duty, Oliver; Strauch, Eckhard

2013-01-01

The genetic diversity of Vibrio vulnificus isolates from clinical and environmental sources originating from the Baltic Sea region was evaluated by multilocus sequence typing (MLST), and possible relationships between MLST clusters, potential genotypic and phenotypic traits associated with pathogenicity, and source of isolation were investigated. The studied traits included genotyping of polymorphic loci (16S rRNA, vcg, and pilF), presence/absence of potential virulence genes, including nanA, nab, and genes of pathogenicity regions, metabolic features, hemolytic activity, resistance to human serum, and cytotoxicity to human intestinal cells. MLST generated 35 (27 new) sequence types and divided the 53 isolates (including four reference strains) into two main clusters, with cluster I containing biotype 1 and 2 isolates of mainly environmental origin and cluster II containing biotype 1 isolates of mainly clinical origin. Cluster II isolates were further subdivided into two branches. Branch IIB included isolates from recent cases of wound infections that were acquired at the German Baltic Sea coastline between 2010 and 2011 and isolates from seawater samples of the same regions isolated between 1994 and 2010. Comparing the MLST data with the results of genotyping and phenotyping showed that strains of MLST cluster II possess a number of additional pathogenicity-associated traits compared to cluster I strains. Rapid microbiological methods such as matrix-assisted laser desorption ionization–time of flight (MALDI-TOF) mass spectrometry combined with typing of selected virulence-associated traits (e.g., serum resistance, mannitol fermentation, nanA, and pathogenicity region XII) could be used for risk assessment purposes regarding V. vulnificus strains isolated from the Baltic Sea region. PMID:23542621

HIV transmission patterns among The Netherlands, Suriname, and The Netherlands Antilles: a molecular epidemiological study.

PubMed

Kramer, Merlijn A; Cornelissen, Marion; Paraskevis, Dimitrios; Prins, Maria; Coutinho, Roel A; van Sighem, Ard I; Sabajo, Lesley; Duits, Ashley J; Winkel, Cai N; Prins, Jan M; van der Ende, Marchina E; Kauffmann, Robert H; Op de Coul, Eline L

2011-02-01

We aimed to study patterns of HIV transmission among Suriname, The Netherlands Antilles, and The Netherlands. Fragments of env, gag, and pol genes of 55 HIV-infected Surinamese, Antillean, and Dutch heterosexuals living in The Netherlands and 72 HIV-infected heterosexuals living in Suriname and the Antilles were amplified and sequenced. We included 145 pol sequences of HIV-infected Surinamese, Antillean, and Dutch heterosexuals living in The Netherlands from an observational cohort. All sequences were phylogenetically analyzed by neighbor-joining. Additionally, HIV-1 mobility among ethnic groups was estimated. A phylogenetic tree of all pol sequences showed two Surinamese and three Antillean clusters of related strains, but no clustering between ethnic groups. Clusters included sequences of individuals living in Suriname and the Antilles as well as those who have migrated to The Netherlands. Similar clustering patterns were observed in env and gag. Analysis of HIV mobility among ethnic groups showed significantly lower migration between groups than expected under the hypothesis of panmixis, apart from higher HIV migration between Antilleans in The Netherlands and all other groups. Our study shows that HIV transmission mainly occurs within the ethnic group. This suggests that cultural factors could have a larger impact on HIV mobility than geographic distance.

CLUSTOM-CLOUD: In-Memory Data Grid-Based Software for Clustering 16S rRNA Sequence Data in the Cloud Environment.

PubMed

Oh, Jeongsu; Choi, Chi-Hwan; Park, Min-Kyu; Kim, Byung Kwon; Hwang, Kyuin; Lee, Sang-Heon; Hong, Soon Gyu; Nasir, Arshan; Cho, Wan-Sup; Kim, Kyung Mo

2016-01-01

High-throughput sequencing can produce hundreds of thousands of 16S rRNA sequence reads corresponding to different organisms present in the environmental samples. Typically, analysis of microbial diversity in bioinformatics starts from pre-processing followed by clustering 16S rRNA reads into relatively fewer operational taxonomic units (OTUs). The OTUs are reliable indicators of microbial diversity and greatly accelerate the downstream analysis time. However, existing hierarchical clustering algorithms that are generally more accurate than greedy heuristic algorithms struggle with large sequence datasets. To keep pace with the rapid rise in sequencing data, we present CLUSTOM-CLOUD, which is the first distributed sequence clustering program based on In-Memory Data Grid (IMDG) technology-a distributed data structure to store all data in the main memory of multiple computing nodes. The IMDG technology helps CLUSTOM-CLOUD to enhance both its capability of handling larger datasets and its computational scalability better than its ancestor, CLUSTOM, while maintaining high accuracy. Clustering speed of CLUSTOM-CLOUD was evaluated on published 16S rRNA human microbiome sequence datasets using the small laboratory cluster (10 nodes) and under the Amazon EC2 cloud-computing environments. Under the laboratory environment, it required only ~3 hours to process dataset of size 200 K reads regardless of the complexity of the human microbiome data. In turn, one million reads were processed in approximately 20, 14, and 11 hours when utilizing 20, 30, and 40 nodes on the Amazon EC2 cloud-computing environment. The running time evaluation indicates that CLUSTOM-CLOUD can handle much larger sequence datasets than CLUSTOM and is also a scalable distributed processing system. The comparative accuracy test using 16S rRNA pyrosequences of a mock community shows that CLUSTOM-CLOUD achieves higher accuracy than DOTUR, mothur, ESPRIT-Tree, UCLUST and Swarm. CLUSTOM-CLOUD is written in JAVA and is freely available at http://clustomcloud.kopri.re.kr.

CLUSTOM-CLOUD: In-Memory Data Grid-Based Software for Clustering 16S rRNA Sequence Data in the Cloud Environment

PubMed Central

Park, Min-Kyu; Kim, Byung Kwon; Hwang, Kyuin; Lee, Sang-Heon; Hong, Soon Gyu; Nasir, Arshan; Cho, Wan-Sup; Kim, Kyung Mo

2016-01-01

High-throughput sequencing can produce hundreds of thousands of 16S rRNA sequence reads corresponding to different organisms present in the environmental samples. Typically, analysis of microbial diversity in bioinformatics starts from pre-processing followed by clustering 16S rRNA reads into relatively fewer operational taxonomic units (OTUs). The OTUs are reliable indicators of microbial diversity and greatly accelerate the downstream analysis time. However, existing hierarchical clustering algorithms that are generally more accurate than greedy heuristic algorithms struggle with large sequence datasets. To keep pace with the rapid rise in sequencing data, we present CLUSTOM-CLOUD, which is the first distributed sequence clustering program based on In-Memory Data Grid (IMDG) technology–a distributed data structure to store all data in the main memory of multiple computing nodes. The IMDG technology helps CLUSTOM-CLOUD to enhance both its capability of handling larger datasets and its computational scalability better than its ancestor, CLUSTOM, while maintaining high accuracy. Clustering speed of CLUSTOM-CLOUD was evaluated on published 16S rRNA human microbiome sequence datasets using the small laboratory cluster (10 nodes) and under the Amazon EC2 cloud-computing environments. Under the laboratory environment, it required only ~3 hours to process dataset of size 200 K reads regardless of the complexity of the human microbiome data. In turn, one million reads were processed in approximately 20, 14, and 11 hours when utilizing 20, 30, and 40 nodes on the Amazon EC2 cloud-computing environment. The running time evaluation indicates that CLUSTOM-CLOUD can handle much larger sequence datasets than CLUSTOM and is also a scalable distributed processing system. The comparative accuracy test using 16S rRNA pyrosequences of a mock community shows that CLUSTOM-CLOUD achieves higher accuracy than DOTUR, mothur, ESPRIT-Tree, UCLUST and Swarm. CLUSTOM-CLOUD is written in JAVA and is freely available at http://clustomcloud.kopri.re.kr. PMID:26954507

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

New Insights into the Formation of the Blue Main Sequence in NGC 1850

NASA Astrophysics Data System (ADS)

Yang, Yujiao; Li, Chengyuan; Deng, Licai; de Grijs, Richard; Milone, Antonino P.

2018-06-01

Recent discoveries of bimodal main sequences (MSs) associated with young clusters (with ages ≲1 Gyr) in the Magellanic Clouds have drawn a lot of attention. One of the prevailing formation scenarios attributes these split MSs to a bimodal distribution in stellar rotation rates, with most stars belonging to a rapidly rotating population. In this scenario, only a small fraction of stars populating a secondary blue sequence are slowly or non-rotating stars. Here, we focus on the blue MS in the young cluster NGC 1850. We compare the cumulative number fraction of the observed blue-MS stars to that of the high-mass-ratio binary systems at different radii. The cumulative distributions of both populations exhibit a clear anti-correlation, characterized by a highly significant Pearson coefficient of ‑0.97. Our observations are consistent with the possibility that blue-MS stars are low-mass-ratio binaries, and therefore their dynamical disruption is still ongoing. High-mass-ratio binaries, on the other hand, are more centrally concentrated.

The Gaia-ESO Survey: evidence of atomic diffusion in M67?

NASA Astrophysics Data System (ADS)

Bertelli Motta, C.; Pasquali, A.; Richer, J.; Michaud, G.; Salaris, M.; Bragaglia, A.; Magrini, L.; Randich, S.; Grebel, E. K.; Adibekyan, V.; Blanco-Cuaresma, S.; Drazdauskas, A.; Fu, X.; Martell, S.; Tautvaišienė, G.; Gilmore, G.; Alfaro, E. J.; Bensby, T.; Flaccomio, E.; Koposov, S. E.; Korn, A. J.; Lanzafame, A. C.; Smiljanic, R.; Bayo, A.; Carraro, G.; Casey, A. R.; Costado, M. T.; Damiani, F.; Franciosini, E.; Heiter, U.; Hourihane, A.; Jofré, P.; Lardo, C.; Lewis, J.; Monaco, L.; Morbidelli, L.; Sacco, G. G.; Sousa, S. G.; Worley, C. C.; Zaggia, S.

2018-07-01

Investigating the chemical homogeneity of stars born from the same molecular cloud at virtually the same time is very important for our understanding of the chemical enrichment of the interstellar medium and with it the chemical evolution of the Galaxy. One major cause of inhomogeneities in the abundances of open clusters is stellar evolution of the cluster members. In this work, we investigate variations in the surface chemical composition of member stars of the old open cluster M67 as a possible consequence of atomic diffusion effects taking place during the main-sequence phase. The abundances used are obtained from high-resolution UVES/FLAMES spectra within the framework of the Gaia-ESO Survey. We find that the surface abundances of stars on the main sequence decrease with increasing mass reaching a minimum at the turn-off. After deepening of the convective envelope in subgiant branch stars, the initial surface abundances are restored. We found the measured abundances to be consistent with the predictions of stellar evolutionary models for a cluster with the age and metallicity of M67. Our findings indicate that atomic diffusion poses a non-negligible constraint on the achievable precision of chemical tagging methods.

DuOCam: A Two-Channel Camera for Simultaneous Photometric Observations of Stellar Clusters

NASA Astrophysics Data System (ADS)

Maier, Erin R.; Witt, Emily; Depoy, Darren L.; Schmidt, Luke M.

2017-01-01

We have designed the Dual Observation Camera (DuOCam), which uses commercial, off-the-shelf optics to perform simultaneous photometric observations of astronomical objects at red and blue wavelengths. Collected light enters DuOCam’s optical assembly, where it is collimated by a negative doublet lens. It is then separated by a 45 degree blue dichroic filter (transmission bandpass: 530 - 800 nm, reflection bandpass: 400 - 475 nm). Finally, the separated light is focused by two identical positive doublet lenses onto two independent charge-coupled devices (CCDs), the SBIG ST-8300M and the SBIG STF-8300M. This optical assembly converts the observing telescope to an f/11 system, which balances maximum field of view with optimum focus. DuOCam was commissioned on the McDonald Observatory 0.9m, f/13.5 telescope from July 21st - 24th, 2016. Observations of three globular and three open stellar clusters were carried out. The resulting data were used to construct R vs. B-R color magnitude diagrams for a selection of the observed clusters. The diagrams display the characteristic evolutionary track for a stellar cluster, including the main sequence and main sequence turn-off.

The Gaia-ESO Survey: Evidence of atomic diffusion in M67?

NASA Astrophysics Data System (ADS)

Motta, C. Bertelli; Pasquali, A.; Richer, J.; Michaud, G.; Salaris, M.; Bragaglia, A.; Magrini, L.; Randich, S.; Grebel, E. K.; Adibekyan, V.; Blanco-Cuaresma, S.; Drazdauskas, A.; Fu, X.; Martell, S.; TautvaišienÄ--, G.; Gilmore, G.; Alfaro, E. J.; Bensby, T.; Flaccomio, E.; Koposov, S. E.; Korn, A. J.; Lanzafame, A. C.; Smiljanic, R.; Bayo, A.; Carraro, G.; Casey, A. R.; Costado, M. T.; Damiani, F.; Franciosini, E.; Heiter, U.; Hourihane, A.; Jofré, P.; Lardo, C.; Lewis, J.; Monaco, L.; Morbidelli, L.; Sacco, G. G.; Sousa, S. G.; Worley, C. C.; Zaggia, S.

2018-04-01

Investigating the chemical homogeneity of stars born from the same molecular cloud at virtually the same time is very important for our understanding of the chemical enrichment of the interstellar medium and with it the chemical evolution of the Galaxy. One major cause of inhomogeneities in the abundances of open clusters is stellar evolution of the cluster members. In this work, we investigate variations in the surface chemical composition of member stars of the old open cluster M67 as a possible consequence of atomic diffusion effects taking place during the main-sequence phase. The abundances used are obtained from high-resolution UVES/FLAMES spectra within the framework of the Gaia-ESO Survey. We find that the surface abundances of stars on the main sequence decrease with increasing mass reaching a minimum at the turn-off. After deepening of the convective envelope in sub-giant branch stars, the initial surface abundances are restored. We found the measured abundances to be consistent with the predictions of stellar evolutionary models for a cluster with the age and metallicity of M67. Our findings indicate that atomic diffusion poses a non-negligible constraint on the achievable precision of chemical tagging methods.

Ultraviolet studies of O and B stars in the LMC cluster NGC 2100, the SMC cluster NGC 330 and the Galactic cluster NGC 6530

NASA Technical Reports Server (NTRS)

Boehm-Vitense, E.; Hodge, P.

1984-01-01

High-resolution and low-resolution IUE spectra of O and B stars in the LMC cluster NGC 2100, the SMC cluster NGC 330, and the young Galactic cluster NGC 6530 are investigated. Temperatures and luminosities are determined. In the LMC and SMC clusters, the most luminous stars are evolved stars on the horizontal supergiant branch, while in NGC 6530 the stars are all still on the main sequence. Extinction laws were determined. They confirm the known differences between LMC and Galactic extinctions. No mass loss was detected for the evolved B stars in the LMC and SMC clusters, while the high-luminosity stars in NGC 6530 show P Cygni profiles.

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

NASA Astrophysics Data System (ADS)

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

2016-11-01

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

Determination of Fundamental Properties of an M31 Globular Cluster from Main-Sequence Photometry

NASA Astrophysics Data System (ADS)

Ma, Jun; Wu, Zhenyu; Wang, Song; Fan, Zhou; Zhou, Xu; Wu, Jianghua; Jiang, Zhaoji; Chen, Jiansheng

2010-10-01

M31 globular cluster B379 is the first extragalactic cluster whose age was determined by main-sequence photometry. In the main-sequence photometric method, the age of a cluster is obtained by fitting its color-magnitude diagram (CMD) with stellar evolutionary models. However, different stellar evolutionary models use different parameters of stellar evolution, such as range of stellar masses, different opacities and equations of state, and different recipes, and so on. So, it is interesting to check whether different stellar evolutionary models can give consistent results for the same cluster. Brown et al. constrained the age of B379 by comparing its CMD with isochrones of the 2006 VandenBerg models. Using SSP models of Bruzual & Charlot and its multiphotometry, ZMa et al. independently determined the age of B379, which is in good agreement with the determination of Brown et al. The models of Bruzual & Charlot are calculated based on the Padova evolutionary tracks. It is necessary to check whether the age of B379 as determined based on the Padova evolutionary tracks is in agreement with the determination of Brown et al.. In this article, we redetermine the age of B379 using isochrones of the Padova stellar evolutionary models. In addition, the metal abundance, the distance modulus, and the reddening value for B379 are reported. The results obtained are consistent with the previous determinations, which include the age obtained by Brown et al. This article thus confirms the consistency of the age scale of B379 between the Padova isochrones and the 2006 VandenBerg isochrones; i.e., the comparison between the results of Brown et al. and Ma et al. is meaningful. The results reported in this article of values found for B379 are: metallicity [M/H] = log(Z/Z ⊙) = -0.325, age τ = 11.0 ± 1.5 Gyr, reddening E(B - V) = 0.08, and distance modulus (m - M)0 = 24.44 ± 0.10.

Microstructural Indicators Of Convection In Sills And Dykes

NASA Astrophysics Data System (ADS)

Holness, M. B.; Neufeld, J. A.; Gilbert, A. J.; Macdonald, R.

2016-12-01

The question of whether or not convection occurs in crustal magma chambers is a vexed one, with some advocating vigorous convection while others argue that convection is weak and short-lived. We argue that microstructural analysis is key to determining whether crystallization took place in solidification fronts or whether crystals grew suspended in a convecting magma before settling. The 168m, composite, Shiant Isles Main Sill is dominated by a 140m unit, of which the lower 45m contains olivine phenocrysts. The phenocrysts first fine upwards, then coarsen upwards. The coarsening-upwards sequence contains clustered olivines. Both the extent of sintering and average cluster size increase upwards. The coarsening-upwards sequence is mirrored at the roof. The fining-upwards sequence formed by rapid settling of incoming cargo crystals, while the coarsening-upwards sequence represents post-emplacement growth and clustering of grains suspended in a convecting magma. Convection is also recorded by plagioclase grain shape. Well-facetted and compact plagioclase grains are platy in rapidly-cooled rocks and blocky in slowly-cooled rocks. Plagioclase grain shape varies smoothly across mafic sills, consistent with growth in solidification fronts. In contrast, grain shape is invariant across mafic dykes, consistent with growth as individual grains and clusters suspended in a convecting magma. Convection in sills occurs when the critical Rayleigh number is exceeded, but cooling at vertical walls always results in convective instabilities. That the Shiant Isles Main Sill records prolonged and vigorous convection, while other sills of comparable thickness record grain growth predominantly in solidification fronts, is most likely due to the composite nature of the Shiant. The 140m unit is underlain by 23m of picrite which intruded shortly before - the strongly asymmetric cooling and absence of a cold, stagnant basal thermal boundary layer make convection throughout the sill more likely.

A Gaia study of the Hyades open cluster

NASA Astrophysics Data System (ADS)

Reino, Stella; de Bruijne, Jos; Zari, Eleonora; d'Antona, Francesca; Ventura, Paolo

2018-03-01

We present a study of the membership of the Hyades open cluster, derive kinematically-modelled parallaxes of its members, and study the colour-absolute magnitude diagram of the cluster. We use Gaia DR1 Tycho-Gaia Astrometric Solution (TGAS) data complemented by Hipparcos-2 data for bright stars not contained in TGAS. We supplement the astrometric data with radial velocities collected from a dozen literature sources. By assuming that all cluster members move with the mean cluster velocity to within the velocity dispersion, we use the observed and the expected motions of the stars to determine individual cluster membership probabilities. We subsequently derive improved parallaxes through maximum-likelihood kinematic modelling of the cluster. This method has an iterative component to deal with 'outliers', caused for instance by double stars or escaping members. Our method extends an existing method and supports the mixed presence of stars with and without radial velocities. We find 251 candidate members, 200 of which have a literature radial velocity, and 70 of which are new candidate members with TGAS astrometry. The cluster is roughly spherical in its centre but significantly flattened at larger radii. The observed colour-absolute magnitude diagram shows a clear binary sequence. The kinematically-modelled parallaxes that we derive are a factor ˜1.7 / 2.9 more precise than the TGAS / Hipparcos-2 values and allow to derive an extremely sharp main sequence. This sequence shows evidence for fine-detailed structure which is elegantly explained by the full spectrum turbulence model of convection.

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.

Genomic V exons from whole genome shotgun data in reptiles.

PubMed

Olivieri, D N; von Haeften, B; Sánchez-Espinel, C; Faro, J; Gambón-Deza, F

2014-08-01

Reptiles and mammals diverged over 300 million years ago, creating two parallel evolutionary lineages amongst terrestrial vertebrates. In reptiles, two main evolutionary lines emerged: one gave rise to Squamata, while the other gave rise to Testudines, Crocodylia, and Aves. In this study, we determined the genomic variable (V) exons from whole genome shotgun sequencing (WGS) data in reptiles corresponding to the three main immunoglobulin (IG) loci and the four main T cell receptor (TR) loci. We show that Squamata lack the TRG and TRD genes, and snakes lack the IGKV genes. In representative species of Testudines and Crocodylia, the seven major IG and TR loci are maintained. As in mammals, genes of the IG loci can be grouped into well-defined IMGT clans through a multi-species phylogenetic analysis. We show that the reptilian IGHV and IGLV genes are distributed amongst the established mammalian clans, while their IGKV genes are found within a single clan, nearly exclusive from the mammalian sequences. The reptilian and mammalian TRAV genes cluster into six common evolutionary clades (since IMGT clans have not been defined for TR). In contrast, the reptilian TRBV genes cluster into three clades, which have few mammalian members. In this locus, the V exon sequences from mammals appear to have undergone different evolutionary diversification processes that occurred outside these shared reptilian clans. These sequences can be obtained in a freely available public repository (http://vgenerepertoire.org).

DISCOVERY OF 14 NEW SLOWLY PULSATING B STARS IN THE OPEN CLUSTER NGC 7654

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

Luo, Y. P.; Han, Z. W.; Zhang, X. B.

2012-02-10

We carried out time-series BV CCD photometric observations of the open cluster NGC 7654 (Messier 52) to search for variable stars. Eighteen slowly pulsating B (SPB) stars have been detected, among which 14 candidates are newly discovered, three known ones are confirmed, and a previously found {delta} Scuti star is also identified as an SPB candidate. Twelve SPBs are probable cluster members based on membership analysis. This makes NGC 7654 the richest galactic open cluster in terms of SPB star content. It is also a new discovery that NGC 7654 hosts three {gamma} Dor star candidates. We found that allmore » these stars (18 SPB and 3 {gamma} Dor stars) have periods longer than their corresponding fundamental radial mode. With such a big sample of g-mode pulsators in a single cluster, it is clear that multi-mode pulsation is more common in the upper part of the main sequence than in the lower part. All the stars span a narrow strip on the period-luminosity plane, which also includes the {gamma} Dor stars at the low-luminosity extension. This result implies that there may be a single period-luminosity relation applicable to all g-mode main-sequence pulsators. As a by-product, three EA-type eclipsing binaries and an EW-type eclipsing binary are also discovered.« less

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

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

NASA Astrophysics Data System (ADS)

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

2017-09-01

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

Simple Epidemiological Dynamics Explain Phylogenetic Clustering of HIV from Patients with Recent Infection

PubMed Central

Volz, Erik M.; Koopman, James S.; Ward, Melissa J.; Brown, Andrew Leigh; Frost, Simon D. W.

2012-01-01

Phylogenies of highly genetically variable viruses such as HIV-1 are potentially informative of epidemiological dynamics. Several studies have demonstrated the presence of clusters of highly related HIV-1 sequences, particularly among recently HIV-infected individuals, which have been used to argue for a high transmission rate during acute infection. Using a large set of HIV-1 subtype B pol sequences collected from men who have sex with men, we demonstrate that virus from recent infections tend to be phylogenetically clustered at a greater rate than virus from patients with chronic infection (‘excess clustering’) and also tend to cluster with other recent HIV infections rather than chronic, established infections (‘excess co-clustering’), consistent with previous reports. To determine the role that a higher infectivity during acute infection may play in excess clustering and co-clustering, we developed a simple model of HIV infection that incorporates an early period of intensified transmission, and explicitly considers the dynamics of phylogenetic clusters alongside the dynamics of acute and chronic infected cases. We explored the potential for clustering statistics to be used for inference of acute stage transmission rates and found that no single statistic explains very much variance in parameters controlling acute stage transmission rates. We demonstrate that high transmission rates during the acute stage is not the main cause of excess clustering of virus from patients with early/acute infection compared to chronic infection, which may simply reflect the shorter time since transmission in acute infection. Higher transmission during acute infection can result in excess co-clustering of sequences, while the extent of clustering observed is most sensitive to the fraction of infections sampled. PMID:22761556

Genetic characterization of Vibrio vulnificus strains isolated from oyster samples in Mexico.

PubMed

Guerrero, Abraham; Gómez Gil Rodríguez, Bruno; Wong-Chang, Irma; Lizárraga-Partida, Marcial Leonardo

2015-01-01

Vibrio vulnificus strains were isolated from oysters that were collected at the main seafood market in Mexico City. Strains were characterized with regard to vvhA, vcg genotype, PFGE, multilocus sequence typing (MLST), and rtxA1. Analyses included a comparison with rtxA1 reference sequences. Environmental (vcgE) and clinical (vcgC) genotypes were isolated at nearly equal percentages. PFGE had high heterogeneity, but the strains clustered by vcgE or vcgC genotype. Select housekeeping genes for MLST and primers that were designed for rtxA1 domains divided the strains into two clusters according to the E or C genotype. Reference rtxA1 sequences and those from this study were also clustered according to genotype. These results confirm that this genetic dimorphism is not limited to vcg genotyping, as other studies have reported. Some environmental C genotype strains had high similarity to reference strains, which have been reported to be virulent, indicating a potential risk for oyster consumers in Mexico City.

W134: A new pre-main-sequence double-lined spectroscopic binary

NASA Technical Reports Server (NTRS)

Padgett, Deborah L.; Stapelfeldt, Karl R.

1994-01-01

We report the discovery that the pre-main-sequence star Walker 134 in the young cluster NGC 2264 is a double-lined spectroscopic binary. Both components are G stars with strong Li I 6708 A absorption lines. Twenty radial velocity measurements have been used to determined the orbital elements of this system. The orbit has a period of 6.3532 +/- 0.0012 days and is circular within the limits of our velocity resolution; e less than 0.01. The total system mass is stellar mass sin(exp 3) i = 3.16 solar mass with a mass ratio of 1.04. Estimates for the orbit inclination angle and stellar radii place the system near the threshold for eclipse observability; howerver, no decrease in brightness was seen during two attempts at photometric monitoring. The circular orbit of W 134 fills an important gap in the period distribution of pre-main-sequence binaries and thereby constrains the effectiveness of tidal orbital circularization during the pre-main sequence.

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

NASA Astrophysics Data System (ADS)

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

2009-01-01

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

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

NASA Astrophysics Data System (ADS)

Guzik, Joyce Ann

1988-06-01

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

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.

The evolution of angular momentum among zero-age main-sequence solar-type stars

NASA Technical Reports Server (NTRS)

Soderblom, David R.; Stauffer, John R.; Macgregor, Keith B.; Jones, Burton F.

1993-01-01

We consider a survey of rotation among F, G, and K dwarfs of the Pleiades in the context of other young clusters (Alpha Persei and the Hyades) and pre-main-sequence (PMS) stars (in Taurus-Auriga and Orion) in order to examine how the angular momentum of a star like the sun evolves during its early life on the main sequence. The rotation of PMS stars can be evolved into distributions like those seen in the young clusters if there is only modest, rotation-independent angular momentum loss prior to the ZAMS. Even then, the ultrafast rotators (UFRs, or ZAMS G and K dwarfs with v sin i equal to or greater than 30 km/s) must owe their extra angular momentum to their conditions of formation and to different angular momentum loss rates above a threshold velocity, for it is unlikely that these stars had angular momentum added as they neared the ZAMS, nor can a spread in ages within a cluster account for the range of rotation seen. Only a fraction of solar-type stars are thus capable of becoming UFRs, and it is not a phase that all stars experience. Simple scaling relations (like the Skumanich relation) applied to the observed surface rotation rates of young solar-type stars cannot reproduce the way in which the Pleiades evolve into the Hyades. We argue that invoking internal differential rotation in these ZAMS stars can explain several aspects of the observations and thus can provide a consistent picture of ZAMS angular momentum evolution.

LITHIUM DEPLETION IS A STRONG TEST OF CORE-ENVELOPE RECOUPLING

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

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

2016-09-20

Rotational mixing is a prime candidate for explaining the gradual depletion of lithium from the photospheres of cool stars during the main sequence. However, previous mixing calculations have relied primarily on treatments of angular momentum transport in stellar interiors incompatible with solar and stellar data in the sense that they overestimate the internal differential rotation. Instead, recent studies suggest that stars are strongly differentially rotating at young ages but approach a solid body rotation during their lifetimes. We modify our rotating stellar evolution code to include an additional source of angular momentum transport, a necessary ingredient for explaining the openmore » cluster rotation pattern, and examine the consequences for mixing. We confirm that core-envelope recoupling with a ∼20 Myr timescale is required to explain the evolution of the mean rotation pattern along the main sequence, and demonstrate that it also provides a more accurate description of the Li depletion pattern seen in open clusters. Recoupling produces a characteristic pattern of efficient mixing at early ages and little mixing at late ages, thus predicting a flattening of Li depletion at a few Gyr, in agreement with the observed late-time evolution. Using Li abundances we argue that the timescale for core-envelope recoupling during the main sequence decreases sharply with increasing mass. We discuss the implications of this finding for stellar physics, including the viability of gravity waves and magnetic fields as agents of angular momentum transport. We also raise the possibility of intrinsic differences in initial conditions in star clusters using M67 as an example.« less

Dispersion of the HIV-1 Epidemic in Men Who Have Sex with Men in the Netherlands: A Combined Mathematical Model and Phylogenetic Analysis.

PubMed

Bezemer, Daniela; Cori, Anne; Ratmann, Oliver; van Sighem, Ard; Hermanides, Hillegonda S; Dutilh, Bas E; Gras, Luuk; Rodrigues Faria, Nuno; van den Hengel, Rob; Duits, Ashley J; Reiss, Peter; de Wolf, Frank; Fraser, Christophe

2015-11-01

The HIV-1 subtype B epidemic amongst men who have sex with men (MSM) is resurgent in many countries despite the widespread use of effective combination antiretroviral therapy (cART). In this combined mathematical and phylogenetic study of observational data, we aimed to find out the extent to which the resurgent epidemic is the result of newly introduced strains or of growth of already circulating strains. As of November 2011, the ATHENA observational HIV cohort of all patients in care in the Netherlands since 1996 included HIV-1 subtype B polymerase sequences from 5,852 patients. Patients who were diagnosed between 1981 and 1995 were included in the cohort if they were still alive in 1996. The ten most similar sequences to each ATHENA sequence were selected from the Los Alamos HIV Sequence Database, and a phylogenetic tree was created of a total of 8,320 sequences. Large transmission clusters that included ≥10 ATHENA sequences were selected, with a local support value ≥ 0.9 and median pairwise patristic distance below the fifth percentile of distances in the whole tree. Time-varying reproduction numbers of the large MSM-majority clusters were estimated through mathematical modeling. We identified 106 large transmission clusters, including 3,061 (52%) ATHENA and 652 Los Alamos sequences. Half of the HIV sequences from MSM registered in the cohort in the Netherlands (2,128 of 4,288) were included in 91 large MSM-majority clusters. Strikingly, at least 54 (59%) of these 91 MSM-majority clusters were already circulating before 1996, when cART was introduced, and have persisted to the present. Overall, 1,226 (35%) of the 3,460 diagnoses among MSM since 1996 were found in these 54 long-standing clusters. The reproduction numbers of all large MSM-majority clusters were around the epidemic threshold value of one over the whole study period. A tendency towards higher numbers was visible in recent years, especially in the more recently introduced clusters. The mean age of MSM at diagnosis increased by 0.45 years/year within clusters, but new clusters appeared with lower mean age. Major strengths of this study are the high proportion of HIV-positive MSM with a sequence in this study and the combined application of phylogenetic and modeling approaches. Main limitations are the assumption that the sampled population is representative of the overall HIV-positive population and the assumption that the diagnosis interval distribution is similar between clusters. The resurgent HIV epidemic amongst MSM in the Netherlands is driven by several large, persistent, self-sustaining, and, in many cases, growing sub-epidemics shifting towards new generations of MSM. Many of the sub-epidemics have been present since the early epidemic, to which new sub-epidemics are being added.

X ray studies of the Hyades cluster

NASA Technical Reports Server (NTRS)

Stern, Robert A.

1993-01-01

The Hyades cluster occupies a unique position in both the history of astronomy and at the frontiers of contemporary astronomical research. At a distance of only 45 pc, the Hyades is the nearest star cluster in the Galaxy which is localized in the sky: the UMa cluster, which is closer, but much sparser, essentially surrounds the Solar neighborhood. The Hyades is the prototype cluster for distance determination using the 'moving-cluster' method, and thus serves to define the zero-age main sequence from which the cosmic distance scale is essentially bootstrapped. The Hyades age (0.6-0.7 Gyr), nearly 8 times younger than the Sun, guarantees the Hyades critical importance to studies of stellar evolution. The results of a complete survey of the Hyades cluster using the ROSAT All Sky Survey (RASS) are reported.

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

NASA Astrophysics Data System (ADS)

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

2011-05-01

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

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.

Low-mass stars in globular clusters. III. The mass function of 47 Tucanae.

NASA Astrophysics Data System (ADS)

de Marchi, G.; Paresce, F.

1995-12-01

We have used the WFPC2 on board HST to investigate the stellar population in a field located 4'6 E of the center of the globular cluster 47 Tuc (NGC 104), close to the half-mass radius, through wide band imaging at 606 and 812nm. A total of ~3000 stars are accurately classified by two-color photometry to form a color-magnitude diagram extending down to a limiting magnitude m_814_=~m_I_=~24. A rich cluster main sequence is detected spanning the range from m_814_=~18 through m_814_=~23, where it spreads considerably due to the increasing photometric uncertainty and galaxy contamination. A secondary sequence of objects is also detected, parallel to the main sequence, as expected for a population of binary stars. The measured binary fraction in the range 195%. The main sequence luminosity function obtained from the observed CMD increases with decreasing luminosity following a power-law trend with index α=~0.15 in the range 5

Comparing the white dwarf cooling sequences in 47 Tuc and NGC 6397

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

Richer, Harvey B.; Goldsbury, Ryan; Heyl, Jeremy

2013-12-01

Using deep Hubble Space Telescope imaging, color-magnitude diagrams are constructed for the globular clusters 47 Tuc and NGC 6397. As expected, because of its lower metal abundance, the main sequence of NGC 6397 lies well to the blue of that of 47 Tuc. A comparison of the white dwarf cooling sequences of the two clusters, however, demonstrates that these sequences are indistinguishable over most of their loci—a consequence of the settling out of heavy elements in the dense white dwarf atmosphere and the near equality of their masses. Lower quality data on M4 continues this trend to a third clustermore » whose metallicity is intermediate between these two. While the path of the white dwarfs in the color-magnitude diagram is nearly identical in 47 Tuc and NGC 6397, the numbers of white dwarfs along the path are not. This results from the relatively rapid relaxation in NGC 6397 compared to 47 Tuc and provides a cautionary note that simply counting objects in star clusters in random locations as a method of testing stellar evolutionary theory is likely dangerous unless dynamical considerations are included.« less

New clues to the cause of extended main-sequence turnoffs in intermediate-age star clusters in the Magellanic Clouds

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

Correnti, Matteo; Goudfrooij, Paul; Kalirai, Jason S.

2014-10-01

We use the Wide Field Camera 3 on board the Hubble Space Telescope (HST) to obtain deep, high-resolution images of two intermediate-age star clusters in the Large Magellanic Cloud of relatively low mass (≈10{sup 4} M {sub ☉}) and significantly different core radii, namely NGC 2209 and NGC 2249. For comparison purposes, we also reanalyzed archival HST images of NGC 1795 and IC 2146, two other relatively low-mass star clusters. From the comparison of the observed color-magnitude diagrams with Monte Carlo simulations, we find that the main-sequence turnoff (MSTO) regions in NGC 2209 and NGC 2249 are significantly wider thanmore » that derived from simulations of simple stellar populations, while those in NGC 1795 and IC 2146 are not. We determine the evolution of the clusters' masses and escape velocities from an age of 10 Myr to the present age. We find that differences among these clusters can be explained by dynamical evolution arguments if the currently extended clusters (NGC 2209 and IC 2146) experienced stronger levels of initial mass segregation than the currently compact ones (NGC 2249 and NGC 1795). Under this assumption, we find that NGC 2209 and NGC 2249 have estimated escape velocities, V {sub esc} ≳ 15 km s{sup –1} at an age of 10 Myr, large enough to retain material ejected by slow winds of first-generation stars, while the two clusters that do not feature extended MSTOs have V {sub esc} ≲ 12 km s{sup –1} at that age. These results suggest that the extended MSTO phenomenon can be better explained by a range of stellar ages rather than a range of stellar rotation velocities or interacting binaries.« less

Temporal variation of aftershocks by means of multifractal characterization of their inter-event time and cluster analysis

NASA Astrophysics Data System (ADS)

Figueroa-Soto, A.; Zuñiga, R.; Marquez-Ramirez, V.; Monterrubio-Velasco, M.

2017-12-01

. The inter-event time characteristics of seismic aftershock sequences can provide important information to discern stages in the aftershock generation process. In order to investigate whether separate dynamic stages can be identified, (1) aftershock series after selected earthquake mainshocks, which took place at similar tectonic regimes were analyzed. To this end we selected two well-defined aftershock sequences from New Zealand and one aftershock sequence for Mexico, we (2) analyzed the fractal behavior of the logarithm of inter-event times (also called waiting times) of aftershocks by means of Holdeŕs exponent, and (3) their magnitude and spatial location based on a methodology proposed by Zaliapin and Ben Zion [2011] which accounts for the clustering properties of the sequence. In general, more than two coherent process stages can be identified following the main rupture, evidencing a type of "cascade" process which precludes implying a single generalized power law even though the temporal rate and average fractal character appear to be unique (as in a single Omorís p value). We found that aftershock processes indeed show multi-fractal characteristics, which may be related to different stages in the process of diffusion, as seen in the temporary-spatial distribution of aftershocks. Our method provides a way of defining the onset of the return to seismic background activity and the end of the main aftershock sequence.

Comparative analysis of prophages in Streptococcus mutans genomes

PubMed Central

Fu, Tiwei; Fan, Xiangyu; Long, Quanxin; Deng, Wanyan; Song, Jinlin

2017-01-01

Prophages have been considered genetic units that have an intimate association with novel phenotypic properties of bacterial hosts, such as pathogenicity and genomic variation. Little is known about the genetic information of prophages in the genome of Streptococcus mutans, a major pathogen of human dental caries. In this study, we identified 35 prophage-like elements in S. mutans genomes and performed a comparative genomic analysis. Comparative genomic and phylogenetic analyses of prophage sequences revealed that the prophages could be classified into three main large clusters: Cluster A, Cluster B, and Cluster C. The S. mutans prophages in each cluster were compared. The genomic sequences of phismuN66-1, phismuNLML9-1, and phismu24-1 all shared similarities with the previously reported S. mutans phages M102, M102AD, and ϕAPCM01. The genomes were organized into seven major gene clusters according to the putative functions of the predicted open reading frames: packaging and structural modules, integrase, host lysis modules, DNA replication/recombination modules, transcriptional regulatory modules, other protein modules, and hypothetical protein modules. Moreover, an integrase gene was only identified in phismuNLML9-1 prophages. PMID:29158986

Distribution of Suicin Gene Clusters in Streptococcus suis Serotype 2 Belonging to Sequence Types 25 and 28.

PubMed

Athey, Taryn B T; Vaillancourt, Katy; Frenette, Michel; Fittipaldi, Nahuel; Gottschalk, Marcelo; Grenier, Daniel

2016-01-01

Recently, we reported the purification and characterization of three distinct lantibiotics (named suicin 90-1330, suicin 3908, and suicin 65) produced by Streptococcus suis . In this study, we investigated the distribution of the three suicin lantibiotic gene clusters among serotype 2 S. suis strains belonging to sequence type (ST) 25 and ST28, the two dominant STs identified in North America. The genomes of 102 strains were interrogated for the presence of suicin gene clusters encoding suicins 90-1330, 3908, and 65. The gene cluster encoding suicin 65 was the most prevalent and mainly found among ST25 strains. In contrast, none of the genes related to suicin 90-1330 production were identified in 51 ST25 strains nor in 35/51 ST28 strains. However, the complete suicin 90-1330 gene cluster was found in ten ST28 strains, although some genes in the cluster were truncated in three of these isolates. The vast majority (101/102) of S. suis strains did not possess any of the genes encoding suicin 3908. In conclusion, this study indicates heterogeneous distribution of suicin genes in S. suis .

Stratification of co-evolving genomic groups using ranked phylogenetic profiles

PubMed Central

Freilich, Shiri; Goldovsky, Leon; Gottlieb, Assaf; Blanc, Eric; Tsoka, Sophia; Ouzounis, Christos A

2009-01-01

Background Previous methods of detecting the taxonomic origins of arbitrary sequence collections, with a significant impact to genome analysis and in particular metagenomics, have primarily focused on compositional features of genomes. The evolutionary patterns of phylogenetic distribution of genes or proteins, represented by phylogenetic profiles, provide an alternative approach for the detection of taxonomic origins, but typically suffer from low accuracy. Herein, we present rank-BLAST, a novel approach for the assignment of protein sequences into genomic groups of the same taxonomic origin, based on the ranking order of phylogenetic profiles of target genes or proteins across the reference database. Results The rank-BLAST approach is validated by computing the phylogenetic profiles of all sequences for five distinct microbial species of varying degrees of phylogenetic proximity, against a reference database of 243 fully sequenced genomes. The approach - a combination of sequence searches, statistical estimation and clustering - analyses the degree of sequence divergence between sets of protein sequences and allows the classification of protein sequences according to the species of origin with high accuracy, allowing taxonomic classification of 64% of the proteins studied. In most cases, a main cluster is detected, representing the corresponding species. Secondary, functionally distinct and species-specific clusters exhibit different patterns of phylogenetic distribution, thus flagging gene groups of interest. Detailed analyses of such cases are provided as examples. Conclusion Our results indicate that the rank-BLAST approach can capture the taxonomic origins of sequence collections in an accurate and efficient manner. The approach can be useful both for the analysis of genome evolution and the detection of species groups in metagenomics samples. PMID:19860884

Characterization of Omega-WINGS galaxy clusters. I. Stellar light and mass profiles

NASA Astrophysics Data System (ADS)

Cariddi, S.; D'Onofrio, M.; Fasano, G.; Poggianti, B. M.; Moretti, A.; Gullieuszik, M.; Bettoni, D.; Sciarratta, M.

2018-02-01

Context. Galaxy clusters are the largest virialized structures in the observable Universe. Knowledge of their properties provides many useful astrophysical and cosmological information. Aims: Our aim is to derive the luminosity and stellar mass profiles of the nearby galaxy clusters of the Omega-WINGS survey and to study the main scaling relations valid for such systems. Methods: We merged data from the WINGS and Omega-WINGS databases, sorted the sources according to the distance from the brightest cluster galaxy (BCG), and calculated the integrated luminosity profiles in the B and V bands, taking into account extinction, photometric and spatial completeness, K correction, and background contribution. Then, by exploiting the spectroscopic sample we derived the stellar mass profiles of the clusters. Results: We obtained the luminosity profiles of 46 galaxy clusters, reaching r200 in 30 cases, and the stellar mass profiles of 42 of our objects. We successfully fitted all the integrated luminosity growth profiles with one or two embedded Sérsic components, deriving the main clusters parameters. Finally, we checked the main scaling relation among the clusters parameters in comparison with those obtained for a selected sample of early-type galaxies (ETGs) of the same clusters. Conclusions: We found that the nearby galaxy clusters are non-homologous structures such as ETGs and exhibit a color-magnitude (CM) red-sequence relation very similar to that observed for galaxies in clusters. These properties are not expected in the current cluster formation scenarios. In particular the existence of a CM relation for clusters, shown here for the first time, suggests that the baryonic structures grow and evolve in a similar way at all scales.

HIV-1 subtype F1 epidemiological networks among Italian heterosexual males are associated with introduction events from South America.

PubMed

Lai, Alessia; Simonetti, Francesco R; Zehender, Gianguglielmo; De Luca, Andrea; Micheli, Valeria; Meraviglia, Paola; Corsi, Paola; Bagnarelli, Patrizia; Almi, Paolo; Zoncada, Alessia; Paolucci, Stefania; Gonnelli, Angela; Colao, Grazia; Tacconi, Danilo; Franzetti, Marco; Ciccozzi, Massimo; Zazzi, Maurizio; Balotta, Claudia

2012-01-01

About 40% of the Italian HIV-1 epidemic due to non-B variants is sustained by F1 clade, which circulates at high prevalence in South America and Eastern Europe. Aim of this study was to define clade F1 origin, population dynamics and epidemiological networks through phylogenetic approaches. We analyzed pol sequences of 343 patients carrying F1 subtype stored in the ARCA database from 1998 to 2009. Citizenship of patients was as follows: 72.6% Italians, 9.3% South Americans and 7.3% Rumanians. Heterosexuals, Homo-bisexuals, Intravenous Drug Users accounted for 58.1%, 24.0% and 8.8% of patients, respectively. Phylogenetic analysis indicated that 70% of sequences clustered in 27 transmission networks. Two distinct groups were identified; the first clade, encompassing 56 sequences, included all Rumanian patients. The second group involved the remaining clusters and included 10 South American Homo-bisexuals in 9 distinct clusters. Heterosexual modality of infection was significantly associated with the probability to be detected in transmission networks. Heterosexuals were prevalent either among Italians (67.2%) or Rumanians (50%); by contrast, Homo-bisexuals accounted for 71.4% of South Americans. Among patients with resistant strains the proportion of clustering sequences was 57.1%, involving 14 clusters (51.8%). Resistance in clusters tended to be higher in South Americans (28.6%) compared to Italian (17.7%) and Rumanian patients (14.3%). A striking proportion of epidemiological networks could be identified in heterosexuals carrying F1 subtype residing in Italy. Italian Heterosexual males predominated within epidemiological clusters while foreign patients were mainly Heterosexual Rumanians, both males and females, and South American Homo-bisexuals. Tree topology suggested that F1 variant from South America gave rise to the Italian F1 epidemic through multiple introduction events. The contact tracing also revealed an unexpected burden of resistance in epidemiological clusters underlying the need of public interventions to limit the spread of non-B subtypes and transmitted drug resistance.

Formation of black hole x-ray binaries in globular clusters

NASA Astrophysics Data System (ADS)

Kremer, Kyle; Chatterjee, Sourav; Rodriguez, Carl; Rasio, Frederic

2018-01-01

We explore the formation of mass-transferring binary systems containing black holes within globular clusters. We show that it is possible to form mass-transferring binaries with main sequence, giant, and white dwarf companions with a variety of orbital parameters in globular clusters spanning a large range in present-day properties. We show that the presence of mass-transferring black hole systems has little correlation with the total number of black holes within the cluster at any time. In addition to mass-transferring binaries retained within their host clusters at late times, we also examine the black hole and neutron star binaries that are ejected from their host clusters. These ejected systems may contribute to the low-mass x-ray binary population in the galactic field.

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

NASA Astrophysics Data System (ADS)

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

2018-01-01

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

Determination of the fundamental properties of an M31 globular cluster from main-sequence photometry

NASA Astrophysics Data System (ADS)

Ma, Jun

2013-02-01

We determined the age of the M31 globular cluster B379 using isochrones of the Padova stellar evolutionary models. At the same time, the cluster's metal abundance, its distance modulus, and reddening value were also obtained. The results obtained in this paper are consistent with previous determinations, including the age. Brown et al. constrained the age of B379 by comparing its color-magnitude diagram with isochrones of the 2006 VandenBerg models. Therefore, this paper confirms the consistency of the age scale of B379 between the Padova isochrones and the 2006 VandenBerg isochrones. The results of B379 obtained in this paper are: metallicity [M/H] = log(Z/Z⊙) = -0.325 dex, age τ = 11.0 +/- 1.5 Gyr, reddening E(B - V) = 0.08 mag, and distance modulus (m - M)0 = 24.44 +/- 0.10 mag. Using the metallicity, the reddening value and the distance modulus obtained in this paper, we constrained the age of B379 by comparing its multicolor photometry with theoretical stellar population synthesis models. The age of B379 obtained is 10.6-0.76 +0.92 Gyr, which is in very good agreement with the determination from main-sequence photometry.

Absolute Ages and Distances of 22 GCs Using Monte Carlo Main-sequence Fitting

NASA Astrophysics Data System (ADS)

O'Malley, Erin M.; Gilligan, Christina; Chaboyer, Brian

2017-04-01

The recent Gaia Data Release 1 of stellar parallaxes provides ample opportunity to find metal-poor main-sequence stars with precise parallaxes. We select 21 such stars with parallax uncertainties better than σ π /π ≤ 0.10 and accurate abundance determinations suitable for testing metal-poor stellar evolution models and determining the distance to Galactic globular clusters (GCs). A Monte Carlo analysis was used, taking into account uncertainties in the model construction parameters, to generate stellar models and isochrones to fit to the calibration stars. The isochrones that fit the calibration stars best were then used to determine the distances and ages of 22 GCs with metallicities ranging from -2.4 dex to -0.7 dex. We find distances with an average uncertainty of 0.15 mag and absolute ages ranging from 10.8 to 13.6 Gyr with an average uncertainty of 1.6 Gyr. Using literature proper motion data, we calculate orbits for the clusters, finding six that reside within the Galactic disk/bulge, while the rest are considered halo clusters. We find no strong evidence for a relationship between age and Galactocentric distance, but we do find a decreasing age-[Fe/H] relation.

First CCD UBVI photometric analysis of six open cluster candidates

NASA Astrophysics Data System (ADS)

Piatti, A. E.; Clariá, J. J.; Ahumada, A. V.

2011-04-01

We have obtained CCD UBVIKC photometry down to V ˜ 22 for the open cluster candidates Haffner 3, Haffner 5, NGC 2368, Haffner 25, Hogg 3 and Hogg 4 and their surrounding fields. None of these objects have been photometrically studied so far. Our analysis shows that these stellar groups are not genuine open clusters since no clear main sequences or other meaningful features can be seen in their colour-magnitude and colour-colour diagrams. We checked for possible differential reddening across the studied fields that could be hiding the characteristics of real open clusters. However, the dust in the directions to these objects appears to be uniformly distributed. Moreover, star counts carried out within and outside the open cluster candidate fields do not support the hypothesis that these objects are real open clusters or even open cluster remnants.

The young SMC cluster NGC 330

NASA Technical Reports Server (NTRS)

Carney, B. W.; Janes, K. A.; Flower, P. J.

1985-01-01

A color-magnitude diagram has been obtained for the young SMC cluster NGC 330. The diagram shows a well-defined main sequence, a group of blue supergiants, a group of red supergiants between B-V = 1.2 m and 1.6 m about one magnitude fainter, and an empty Hertzsprung gap. The surrounding field is a composite of a very gold population resembling galactic globular clusters and a very young population. DDO and infrared photometry strongly suggest that the cluster is metal-poor, but a definitive measure could not be made because of calibration difficulties. The cluster's age is estimated at 12 million years, with the surrounding field about 50 percent older. The cluster will prove very useful in testing stellar evolution models for young, metal-poor stars if the cluster's metallicity can be established via high-resolution spectroscopy.

Microstructural indicators of convection in sills and dykes

NASA Astrophysics Data System (ADS)

Holness, Marian; Neufeld, Jerome; Gilbert, Andrew

2016-04-01

The question of whether or not magma convects is a vexed one, with some advocating vigorous convection in crustal magma chambers while others suggest that convection is weak and short-lived. From a detailed microstructural study of a range of tabular mafic intrusions, we argue that it is possible to determine whether crystallization took place predominantly in solidification fronts (i.e. the magma was essentially crystal-free) or whether crystals grew suspended in a convecting magma. The 168m thick Shiant Isles Main Sill is a composite body, dominated by a 140m thick unit with a 45m thick base rich in olivine phenocrysts (picrodolerite). The remainder of the unit contains only interstitial olivine. The average olivine grain size in the picrodolerite decreases upwards in the lowermost 10m, but then increases upwards. The coarsening-upwards sequence is marked by the onset of clustering of olivine grains. The extent to which these clusters are sintered, and the average cluster size, increase upwards. The coarsening-upwards sequence and the clustering are mirrored in a thinner (<10m) sequence at the roof. The fining-upwards sequence of non-clustered olivine formed by the rapid settling of incoming cargo crystals, while the coarsening-upwards sequence of clustered olivine represents post-emplacement growth of grains suspended in a convecting magma. The clusters grew by synneusis, with the extensive sintering pointing to the retention of the clusters in the convecting magma for a considerable time. The presence of large clusters at the intrusion roof can be reconciled with their high Stokes settling velocity if they were brought up in rapidly moving convective currents and entangled in the downwards-propagating solidification front. A further indication of convection is provided by plagioclase grain shape. During interface-controlled growth, plagioclase grows as well-facetted compact grains: these grains are platy in rapidly-cooled rocks and blocky in slowly-cooled rocks. In mafic sills, the average apparent aspect ratio (AR), as measured in thin-section, varies smoothly with model crystallization times (calculated assuming diffusive heat loss), consistent with in situ growth in solidification fronts. However, AR is invariant across individual mafic dykes, with decreasing values (i.e. more blocky grains) as the dyke width increases. This difference can be accounted for by the plagioclase in dykes growing as individual grains and clusters suspended in a convecting magma. Cooling at a vertical wall, as is the case for dykes, will always result in a gravitational convective instability, and therefore crystal-poor magma in dykes will always convect. As solidification proceeds, the increasing volume fraction of suspended crystals will eventually damp convection: the final stages of solidification occur in static crystal-rich magma, containing a well-mixed grain population. That the Shiant Isles Main Sill exhibits evidence for prolonged convection of sufficient vigour to suspend 5 mm olivine clusters, while other sills of comparable thickness contain plagioclase with grain shapes indicative of growth predominantly in solidification fronts, is most likely due to the composite nature of the Shiant. The 140m unit is underlain by 23m of picrite which intruded shortly before - this heat source would have acted as a strong driver for convection.

Formation mechanism of atomic cluster structures in Al-Mg alloy during rapid solidification processes

NASA Astrophysics Data System (ADS)

Liu, Feng-xiang; Liu, Rang-su; Hou, Zhao-yang; Liu, Hai-Rong; Tian, Ze-an; Zhou, Li-li

2009-02-01

The rapid solidification processes of Al 50Mg 50 liquid alloy consisting of 50,000 atoms have been simulated by using molecular dynamics method based on the effective pair potential derived from the pseudopotential theory. The formation mechanisms of atomic clusters during the rapid solidification processes have been investigated adopting a new cluster description method—cluster-type index method (CTIM). The simulated partial structure factors are in good agreement with the experimental results. And Al-Mg amorphous structure characterized with Al-centered icosahedral topological short-range order (SRO) is found to form during the rapid solidification processes. The icosahedral cluster plays a key role in the microstructure transition. Besides, it is also found that the size distribution of various clusters in the system presents a magic number sequence of 13, 19, 23, 25, 29, 31, 33, 37, …. The magic clusters are more stable and mainly correspond to the incompact arrangements of linked icosahedra in the form of rings, chains or dendrites. And each magic number point stands correspondingly for one certain combining form of icosahedra. This magic number sequence is different from that generated in the solidification structure of liquid Al and those obtained by methods of gaseous deposition and ionic spray, etc.

Structure-Based Phylogenetic Analysis of the Lipocalin Superfamily.

PubMed

Lakshmi, Balasubramanian; Mishra, Madhulika; Srinivasan, Narayanaswamy; Archunan, Govindaraju

2015-01-01

Lipocalins constitute a superfamily of extracellular proteins that are found in all three kingdoms of life. Although very divergent in their sequences and functions, they show remarkable similarity in 3-D structures. Lipocalins bind and transport small hydrophobic molecules. Earlier sequence-based phylogenetic studies of lipocalins highlighted that they have a long evolutionary history. However the molecular and structural basis of their functional diversity is not completely understood. The main objective of the present study is to understand functional diversity of the lipocalins using a structure-based phylogenetic approach. The present study with 39 protein domains from the lipocalin superfamily suggests that the clusters of lipocalins obtained by structure-based phylogeny correspond well with the functional diversity. The detailed analysis on each of the clusters and sub-clusters reveals that the 39 lipocalin domains cluster based on their mode of ligand binding though the clustering was performed on the basis of gross domain structure. The outliers in the phylogenetic tree are often from single member families. Also structure-based phylogenetic approach has provided pointers to assign putative function for the domains of unknown function in lipocalin family. The approach employed in the present study can be used in the future for the functional identification of new lipocalin proteins and may be extended to other protein families where members show poor sequence similarity but high structural similarity.

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

Amplified fragment length polymorphism of Streptococcus suis strains correlates with their profile of virulence-associated genes and clinical background.

PubMed

Rehm, Thomas; Baums, Christoph G; Strommenger, Birgit; Beyerbach, Martin; Valentin-Weigand, Peter; Goethe, Ralph

2007-01-01

Amplified fragment length polymorphism (AFLP) typing was applied to 116 Streptococcus suis isolates with different clinical backgrounds (invasive/pneumonia/carrier/human) and with known profiles of virulence-associated genes (cps1, -2, -7 and -9, as well as mrp, epf and sly). A dendrogram was generated that allowed identification of two clusters (A and C) with different subclusters (A1, A2, C1 and C2) and two heterogeneous groups of strains (B and D). For comparison, three strains from each AFLP subcluster and group were subjected to multilocus sequence typing (MLST) analysis. The closest relationship and lowest diversity were found for patterns clustering within AFLP subcluster A1, which corresponded with sequence type (ST) complex 1. Strains within subcluster A1 were mainly invasive cps1 and mrp+ epf+ (or epf*) sly+ cps2+ strains of porcine or human origin. A new finding of this study was the clustering of invasive mrp* cps9 isolates within subcluster A2. MLST analysis suggested that A2 correlates with a single ST complex (ST87). In contrast to A1 and A2, subclusters C1 and C2 contained mainly pneumonia isolates of genotype cps7 or cps2 and epf- sly-. In conclusion, this study demonstrates that AFLP allows identification of clusters of S. suis strains with clinical relevance.

Molecular epidemiology is becoming complex under the dynamic HIV prevalence: The perspective from Harbin, China.

PubMed

Shao, Bing; Song, Bo; Cao, Lijun; Du, Juan; Sun, Dongying; Lin, Yuanlong; Wang, Binyou; Wang, Fuxiang; Wang, Sunran

2016-05-01

Unlike most areas of China, HIV transmission via men who have sex with men (MSM) is increasing rapidly, and has become the main route of HIV transmission in Harbin city. The purpose of the current study was to elaborate the molecular epidemiologic characteristics of the new HIV epidemic. Eighty-one HIV-1 gag gene sequences (HXB2:806-1861) from local HIV infections were isolated; CRF01_AE predominated among HIV infections (71.6%), followed by subtype B (16.5%), CRF07_BC (6.2%), and unique recombinant strains (URFs; 6.2%). URFs were most often identified in the MSM population, which consisted of a recombination of CRF01_AE with subtype B or CRF07_BC. Six clusters were formed in this analysis; clusters I and II mainly circulated in southwest China. Clusters III and IV mainly circulated in southwest, southeast, and central China. Clusters V and VI mainly circulated in north and northeast China. Clusters III and IV may facilitate the transmission of the CRF01_AE strain from the southwest to the north and northeast regions of China. HIV subtypes are becoming diverse with the persistent epidemic in this geographic region. In brief, our results indicate that the molecular epidemiology of HIV is trending to be more complex. Thus, timely molecular epidemiologic supervision of HIV is necessary, especially for the MSM population. © 2015 Wiley Periodicals, Inc.

Phylodynamic and Phylogeographic Patterns of the HIV Type 1 Subtype F1 Parenteral Epidemic in Romania

PubMed Central

Hué, Stéphane; Buckton, Andrew J.; Myers, Richard E.; Duiculescu, Dan; Ene, Luminita; Oprea, Cristiana; Tardei, Gratiela; Rugina, Sorin; Mardarescu, Mariana; Floch, Corinne; Notheis, Gundula; Zöhrer, Bettina; Cane, Patricia A.; Pillay, Deenan

2012-01-01

Abstract In the late 1980s an HIV-1 epidemic emerged in Romania that was dominated by subtype F1. The main route of infection is believed to be parenteral transmission in children. We sequenced partial pol coding regions of 70 subtype F1 samples from children and adolescents from the PENTA-EPPICC network of which 67 were from Romania. Phylogenetic reconstruction using the sequences and other publically available global subtype F sequences showed that 79% of Romanian F1 sequences formed a statistically robust monophyletic cluster. The monophyletic cluster was epidemiologically linked to parenteral transmission in children. Coalescent-based analysis dated the origins of the parenteral epidemic to 1983 [1981–1987; 95% HPD]. The analysis also shows that the epidemic's effective population size has remained fairly constant since the early 1990s suggesting limited onward spread of the virus within the population. Furthermore, phylogeographic analysis suggests that the root location of the parenteral epidemic was Bucharest. PMID:22251065

Importance of Viral Sequence Length and Number of Variable and Informative Sites in Analysis of HIV Clustering.

PubMed

Novitsky, Vlad; Moyo, Sikhulile; Lei, Quanhong; DeGruttola, Victor; Essex, M

2015-05-01

To improve the methodology of HIV cluster analysis, we addressed how analysis of HIV clustering is associated with parameters that can affect the outcome of viral clustering. The extent of HIV clustering and tree certainty was compared between 401 HIV-1C near full-length genome sequences and subgenomic regions retrieved from the LANL HIV Database. Sliding window analysis was based on 99 windows of 1,000 bp and 45 windows of 2,000 bp. Potential associations between the extent of HIV clustering and sequence length and the number of variable and informative sites were evaluated. The near full-length genome HIV sequences showed the highest extent of HIV clustering and the highest tree certainty. At the bootstrap threshold of 0.80 in maximum likelihood (ML) analysis, 58.9% of near full-length HIV-1C sequences but only 15.5% of partial pol sequences (ViroSeq) were found in clusters. Among HIV-1 structural genes, pol showed the highest extent of clustering (38.9% at a bootstrap threshold of 0.80), although it was significantly lower than in the near full-length genome sequences. The extent of HIV clustering was significantly higher for sliding windows of 2,000 bp than 1,000 bp. We found a strong association between the sequence length and proportion of HIV sequences in clusters, and a moderate association between the number of variable and informative sites and the proportion of HIV sequences in clusters. In HIV cluster analysis, the extent of detectable HIV clustering is directly associated with the length of viral sequences used, as well as the number of variable and informative sites. Near full-length genome sequences could provide the most informative HIV cluster analysis. Selected subgenomic regions with a high extent of HIV clustering and high tree certainty could also be considered as a second choice.

Importance of Viral Sequence Length and Number of Variable and Informative Sites in Analysis of HIV Clustering

PubMed Central

Novitsky, Vlad; Moyo, Sikhulile; Lei, Quanhong; DeGruttola, Victor

2015-01-01

Abstract To improve the methodology of HIV cluster analysis, we addressed how analysis of HIV clustering is associated with parameters that can affect the outcome of viral clustering. The extent of HIV clustering and tree certainty was compared between 401 HIV-1C near full-length genome sequences and subgenomic regions retrieved from the LANL HIV Database. Sliding window analysis was based on 99 windows of 1,000 bp and 45 windows of 2,000 bp. Potential associations between the extent of HIV clustering and sequence length and the number of variable and informative sites were evaluated. The near full-length genome HIV sequences showed the highest extent of HIV clustering and the highest tree certainty. At the bootstrap threshold of 0.80 in maximum likelihood (ML) analysis, 58.9% of near full-length HIV-1C sequences but only 15.5% of partial pol sequences (ViroSeq) were found in clusters. Among HIV-1 structural genes, pol showed the highest extent of clustering (38.9% at a bootstrap threshold of 0.80), although it was significantly lower than in the near full-length genome sequences. The extent of HIV clustering was significantly higher for sliding windows of 2,000 bp than 1,000 bp. We found a strong association between the sequence length and proportion of HIV sequences in clusters, and a moderate association between the number of variable and informative sites and the proportion of HIV sequences in clusters. In HIV cluster analysis, the extent of detectable HIV clustering is directly associated with the length of viral sequences used, as well as the number of variable and informative sites. Near full-length genome sequences could provide the most informative HIV cluster analysis. Selected subgenomic regions with a high extent of HIV clustering and high tree certainty could also be considered as a second choice. PMID:25560745

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

Noble, A. G.; McDonald, M.; Muzzin, A.

We present ALMA CO (2–1) detections in 11 gas-rich cluster galaxies at z ∼ 1.6, constituting the largest sample of molecular gas measurements in z > 1.5 clusters to date. The observations span three galaxy clusters, derived from the Spitzer Adaptation of the Red-sequence Cluster Survey. We augment the >5 σ detections of the CO (2–1) fluxes with multi-band photometry, yielding stellar masses and infrared-derived star formation rates, to place some of the first constraints on molecular gas properties in z ∼ 1.6 cluster environments. We measure sizable gas reservoirs of 0.5–2 × 10{sup 11} M {sub ☉} in thesemore » objects, with high gas fractions ( f {sub gas}) and long depletion timescales ( τ ), averaging 62% and 1.4 Gyr, respectively. We compare our cluster galaxies to the scaling relations of the coeval field, in the context of how gas fractions and depletion timescales vary with respect to the star-forming main sequence. We find that our cluster galaxies lie systematically off the field scaling relations at z = 1.6 toward enhanced gas fractions, at a level of ∼4 σ , but have consistent depletion timescales. Exploiting CO detections in lower-redshift clusters from the literature, we investigate the evolution of the gas fraction in cluster galaxies, finding it to mimic the strong rise with redshift in the field. We emphasize the utility of detecting abundant gas-rich galaxies in high-redshift clusters, deeming them as crucial laboratories for future statistical studies.« less

Molecular Epidemiological Survey and Genetic Characterization of Anaplasma Species in Mongolian Livestock.

PubMed

Ochirkhuu, Nyamsuren; Konnai, Satoru; Odbileg, Raadan; Murata, Shiro; Ohashi, Kazuhiko

2017-08-01

Anaplasma species are obligate intracellular rickettsial pathogens that cause great economic loss to the animal industry. Few studies on Anaplasma infections in Mongolian livestock have been conducted. This study examined the prevalence of Anaplasma marginale, Anaplasma ovis, Anaplasma phagocytophilum, and Anaplasma bovis by polymerase chain reaction assay in 928 blood samples collected from native cattle and dairy cattle (Bos taurus), yaks (Bos grunniens), sheep (Ovis aries), and goats (Capra aegagrus hircus) in four provinces of Ulaanbaatar city in Mongolia. We genetically characterized positive samples through sequencing analysis based on the heat-shock protein groEL, major surface protein 4 (msp4), and 16S rRNA genes. Only A. ovis was detected in Mongolian livestock (cattle, yaks, sheep, and goats), with 413 animals (44.5%) positive for groEL and 308 animals (33.2%) positive for msp4 genes. In the phylogenetic tree, we separated A. ovis sequences into two distinct clusters based on the groEL gene. One cluster comprised sequences derived mainly from sheep and goats, which was similar to that in A. ovis isolates from other countries. The other divergent cluster comprised sequences derived from cattle and yaks and appeared to be newly branched from that in previously published single isolates in Mongolian cattle. In addition, the msp4 gene of A. ovis using same and different samples with groEL gene of the pathogen demonstrated that all sequences derived from all animal species, except for three sequences derived from cattle and yak, were clustered together, and were identical or similar to those in isolates from other countries. We used 16S rRNA gene sequences to investigate the genetically divergent A. ovis and identified high homology of 99.3-100%. However, the sequences derived from cattle did not match those derived from sheep and goats. The results of this study on the prevalence and molecular characterization of A. ovis in Mongolian livestock can facilitate the control of infectious diseases in livestock.

Seismic clusters analysis in Northeastern Italy by the nearest-neighbor approach

NASA Astrophysics Data System (ADS)

Peresan, Antonella; Gentili, Stefania

2018-01-01

The main features of earthquake clusters in Northeastern Italy are explored, with the aim to get new insights on local scale patterns of seismicity in the area. The study is based on a systematic analysis of robustly and uniformly detected seismic clusters, which are identified by a statistical method, based on nearest-neighbor distances of events in the space-time-energy domain. The method permits us to highlight and investigate the internal structure of earthquake sequences, and to differentiate the spatial properties of seismicity according to the different topological features of the clusters structure. To analyze seismicity of Northeastern Italy, we use information from local OGS bulletins, compiled at the National Institute of Oceanography and Experimental Geophysics since 1977. A preliminary reappraisal of the earthquake bulletins is carried out and the area of sufficient completeness is outlined. Various techniques are considered to estimate the scaling parameters that characterize earthquakes occurrence in the region, namely the b-value and the fractal dimension of epicenters distribution, required for the application of the nearest-neighbor technique. Specifically, average robust estimates of the parameters of the Unified Scaling Law for Earthquakes, USLE, are assessed for the whole outlined region and are used to compute the nearest-neighbor distances. Clusters identification by the nearest-neighbor method turn out quite reliable and robust with respect to the minimum magnitude cutoff of the input catalog; the identified clusters are well consistent with those obtained from manual aftershocks identification of selected sequences. We demonstrate that the earthquake clusters have distinct preferred geographic locations, and we identify two areas that differ substantially in the examined clustering properties. Specifically, burst-like sequences are associated with the north-western part and swarm-like sequences with the south-eastern part of the study region. The territorial heterogeneity of earthquakes clustering is in good agreement with spatial variability of scaling parameters identified by the USLE. In particular, the fractal dimension is higher to the west (about 1.2-1.4), suggesting a spatially more distributed seismicity, compared to the eastern parte of the investigated territory, where fractal dimension is very low (about 0.8-1.0).

Phylogenetic and Temporal Dynamics of Human Immunodeficiency Virus Type 1 CRF01_AE in China

PubMed Central

Su, Xueli; Lu, Hongyan; Pang, Xinghuo; Yan, Hong; Feng, Xia; He, Xiong; Zeng, Yi

2013-01-01

To explore the epidemic history of HIV-1 CRF01_AE in China, 408 fragments of gag gene sequences of CRF01_AE sampled in 2002–2010 were determined from different geographical regions and risk populations in China. Phylogenetic analysis indicates that the CRF01_AE sequences can be grouped into four clusters, suggesting that at least four genetically independent CRF01_AE descendants are circulating in China, of which two were closely related to the isolates from Thailand and Vietnam. Cluster 1 has the most extensive distribution in China. In North China, cluster 1 and cluster 4 were mainly transmitted through homosexuality.The real substance of the recent HIV-1 epidemic in men who have sex with men(MSM) of North China is a rapid spread of CRF01_AE, or rather two distinctive natives CRF01_AE.The time of the most recent common ancestor (tMRCA) of four CRF01_AE clusters ranged from the years 1990.9 to 2003.8 in different regions of China. This is the first phylogenetic and temporal dynamics study of HIV-1 CRF01_AE in China. PMID:23365653

Camps 2.0: exploring the sequence and structure space of prokaryotic, eukaryotic, and viral membrane proteins.

PubMed

Neumann, Sindy; Hartmann, Holger; Martin-Galiano, Antonio J; Fuchs, Angelika; Frishman, Dmitrij

2012-03-01

Structural bioinformatics of membrane proteins is still in its infancy, and the picture of their fold space is only beginning to emerge. Because only a handful of three-dimensional structures are available, sequence comparison and structure prediction remain the main tools for investigating sequence-structure relationships in membrane protein families. Here we present a comprehensive analysis of the structural families corresponding to α-helical membrane proteins with at least three transmembrane helices. The new version of our CAMPS database (CAMPS 2.0) covers nearly 1300 eukaryotic, prokaryotic, and viral genomes. Using an advanced classification procedure, which is based on high-order hidden Markov models and considers both sequence similarity as well as the number of transmembrane helices and loop lengths, we identified 1353 structurally homogeneous clusters roughly corresponding to membrane protein folds. Only 53 clusters are associated with experimentally determined three-dimensional structures, and for these clusters CAMPS is in reasonable agreement with structure-based classification approaches such as SCOP and CATH. We therefore estimate that ∼1300 structures would need to be determined to provide a sufficient structural coverage of polytopic membrane proteins. CAMPS 2.0 is available at http://webclu.bio.wzw.tum.de/CAMPS2.0/. Copyright © 2011 Wiley Periodicals, Inc.

SOMKE: kernel density estimation over data streams by sequences of self-organizing maps.

PubMed

Cao, Yuan; He, Haibo; Man, Hong

2012-08-01

In this paper, we propose a novel method SOMKE, for kernel density estimation (KDE) over data streams based on sequences of self-organizing map (SOM). In many stream data mining applications, the traditional KDE methods are infeasible because of the high computational cost, processing time, and memory requirement. To reduce the time and space complexity, we propose a SOM structure in this paper to obtain well-defined data clusters to estimate the underlying probability distributions of incoming data streams. The main idea of this paper is to build a series of SOMs over the data streams via two operations, that is, creating and merging the SOM sequences. The creation phase produces the SOM sequence entries for windows of the data, which obtains clustering information of the incoming data streams. The size of the SOM sequences can be further reduced by combining the consecutive entries in the sequence based on the measure of Kullback-Leibler divergence. Finally, the probability density functions over arbitrary time periods along the data streams can be estimated using such SOM sequences. We compare SOMKE with two other KDE methods for data streams, the M-kernel approach and the cluster kernel approach, in terms of accuracy and processing time for various stationary data streams. Furthermore, we also investigate the use of SOMKE over nonstationary (evolving) data streams, including a synthetic nonstationary data stream, a real-world financial data stream and a group of network traffic data streams. The simulation results illustrate the effectiveness and efficiency of the proposed approach.

FIDUCIAL STELLAR POPULATION SEQUENCES FOR THE VJK{sub S} PHOTOMETRIC SYSTEM

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

Brasseur, Crystal M.; VandenBerg, Don A.; Stetson, Peter B.

2010-12-15

We have obtained broadband near-infrared photometry for seven Galactic star clusters (M 92, M 15, M 13, M 5, NGC 1851, M 71, and NGC 6791) using the WIRCam wide-field imager on the Canada-France-Hawaii Telescope, supplemented by images of NGC 1851 taken with HAWK-I on the Very Large Telescope. In addition, Two Micron All Sky Survey (2MASS) observations of the [Fe/H] {approx}0.0 open cluster M 67 were added to the cluster database. From the resultant (V - J) - V and (V - K{sub S} ) - V color-magnitude diagrams (CMDs), fiducial sequences spanning the range in metallicity, -2.4 {approx}

Mainshock-Aftershocks Clustering Detection in Volcanic Regions

NASA Astrophysics Data System (ADS)

Garza Giron, R.; Brodsky, E. E.; Prejean, S. G.

2017-12-01

Crustal earthquakes tend to break their general Poissonean process behavior by gathering into two main kinds of seismic bursts: swarms and mainshock-aftershocks sequences. The former is commonly related to volcanic or geothermal processes whereas the latter is a characteristic feature of tectonically driven seismicity. We explore the mainshock-aftershock clustering behavior of different active volcanic regions in Japan and its comparison to non-volcanic regions. We find that aftershock production in volcanoes shows mainshock-aftershocks clustering similar to what is observed in non-volcanic areas. The ratio of volanic areas that cluster in mainshock-aftershocks sequences vs the areas that do not is comparable to the ratio of non-volcanic regions that show clustering vs the ones that do not. Furthermore, the level of production of aftershocks for most volcanic areas where clustering is present seems to be of the same order of magnitude, or slightly higher, as the median of the non-volcanic regions. An interesting example of highly aftershock-productive volcanoes emerges from the 2000 Miyakejima dike intrusion. A big seismic cluster started to build up rapidly in the south-west flank of Miyakejima to later propagate to the north-west towards the Kozushima and Niijima volcanoes. In Miyakejima the seismicity showed a swarm-like signature with a constant earthquake rate, whereas Kozushima and Niijima both had expressions of highly productive mainshock-aftershocks sequences. These findings are surprising given the alternative mechanisms available in volcanic systems for releasing deviatoric strain. We speculate that aftershock behavior might hold a relationship with the rheological properties of the rocks of each system and with the capacity of a system to accumulate or release the internal pressures caused by magmatic or hydrothermal systems.

ALMA Observations of Gas-rich Galaxies in z ˜ 1.6 Galaxy Clusters: Evidence for Higher Gas Fractions in High-density Environments

NASA Astrophysics Data System (ADS)

Noble, A. G.; McDonald, M.; Muzzin, A.; Nantais, J.; Rudnick, G.; van Kampen, E.; Webb, T. M. A.; Wilson, G.; Yee, H. K. C.; Boone, K.; Cooper, M. C.; DeGroot, A.; Delahaye, A.; Demarco, R.; Foltz, R.; Hayden, B.; Lidman, C.; Manilla-Robles, A.; Perlmutter, S.

2017-06-01

We present ALMA CO (2-1) detections in 11 gas-rich cluster galaxies at z ˜ 1.6, constituting the largest sample of molecular gas measurements in z > 1.5 clusters to date. The observations span three galaxy clusters, derived from the Spitzer Adaptation of the Red-sequence Cluster Survey. We augment the >5σ detections of the CO (2-1) fluxes with multi-band photometry, yielding stellar masses and infrared-derived star formation rates, to place some of the first constraints on molecular gas properties in z ˜ 1.6 cluster environments. We measure sizable gas reservoirs of 0.5-2 × 1011 M ⊙ in these objects, with high gas fractions (f gas) and long depletion timescales (τ), averaging 62% and 1.4 Gyr, respectively. We compare our cluster galaxies to the scaling relations of the coeval field, in the context of how gas fractions and depletion timescales vary with respect to the star-forming main sequence. We find that our cluster galaxies lie systematically off the field scaling relations at z = 1.6 toward enhanced gas fractions, at a level of ˜4σ, but have consistent depletion timescales. Exploiting CO detections in lower-redshift clusters from the literature, we investigate the evolution of the gas fraction in cluster galaxies, finding it to mimic the strong rise with redshift in the field. We emphasize the utility of detecting abundant gas-rich galaxies in high-redshift clusters, deeming them as crucial laboratories for future statistical studies.

Using Grey Wolf Algorithm to Solve the Capacitated Vehicle Routing Problem

NASA Astrophysics Data System (ADS)

Korayem, L.; Khorsid, M.; Kassem, S. S.

2015-05-01

The capacitated vehicle routing problem (CVRP) is a class of the vehicle routing problems (VRPs). In CVRP a set of identical vehicles having fixed capacities are required to fulfill customers' demands for a single commodity. The main objective is to minimize the total cost or distance traveled by the vehicles while satisfying a number of constraints, such as: the capacity constraint of each vehicle, logical flow constraints, etc. One of the methods employed in solving the CVRP is the cluster-first route-second method. It is a technique based on grouping of customers into a number of clusters, where each cluster is served by one vehicle. Once clusters are formed, a route determining the best sequence to visit customers is established within each cluster. The recently bio-inspired grey wolf optimizer (GWO), introduced in 2014, has proven to be efficient in solving unconstrained, as well as, constrained optimization problems. In the current research, our main contributions are: combining GWO with the traditional K-means clustering algorithm to generate the ‘K-GWO’ algorithm, deriving a capacitated version of the K-GWO algorithm by incorporating a capacity constraint into the aforementioned algorithm, and finally, developing 2 new clustering heuristics. The resulting algorithm is used in the clustering phase of the cluster-first route-second method to solve the CVR problem. The algorithm is tested on a number of benchmark problems with encouraging results.

Mass-losing red giants in open clusters

NASA Technical Reports Server (NTRS)

Jura, M.

1987-01-01

Mass-losing stars in open clusters with main-sequence turn-offs at intermediate mass have been searched for by using the IRAS data base. The absence of many strong 60 micron sources in open clusters implies that intermediate-mass stars lose much of their mass during an intense wind phase of rather short duration. For stars of about seven solar masses, this phase, if it exists at all, lasts for not much more than 100,000 yr. For stars of about four solar masses, the intense wind phase appears to last considerably less than 10 million yr; it may well last for less than a million yr.

Hepatitis a virus genotypes and strains from an endemic area of Europe, Bulgaria 2012-2014.

PubMed

Bruni, Roberto; Taffon, Stefania; Equestre, Michele; Cella, Eleonora; Lo Presti, Alessandra; Costantino, Angela; Chionne, Paola; Madonna, Elisabetta; Golkocheva-Markova, Elitsa; Bankova, Diljana; Ciccozzi, Massimo; Teoharov, Pavel; Ciccaglione, Anna Rita

2017-07-14

Hepatitis A virus (HAV) infection is endemic in Eastern European and Balkan region countries. In 2012, Bulgaria showed the highest rate (67.13 cases per 100,000) in Europe. Nevertheless, HAV genotypes and strains circulating in this country have never been described. The present study reports the molecular characterization of HAV from 105 patients from Bulgaria. Anti-HAV IgM positive serum samples collected in 2012-2014 from different towns and villages in Bulgaria were analysed by nested RT-PCR, sequencing of the VP1/2A region and phylogenetic analysis; the results were analysed together with patient and geographical data. Phylogenetic analysis revealed two main sequence groups corresponding to the IA (78/105, 74%) and IB (27/105, 26%) sub-genotypes. In the IA group, a major and a minor cluster were observed (62 and 16 sequences, respectively). Most sequences from the major cluster (44/62, 71%) belonged to either of two strains, termed "strain 1" and "strain 2", differing only for a single specific nucleotide; the remaining sequences (18/62, 29%) showed few (1 to 4) nucleotide variations respect to strain 1 and 2. Strain 2 is identical to the strain previously responsible for an outbreak in the Czech Republic in 2008 and a large multi-country European outbreak caused by contaminated mixed frozen berries in 2013. Most sequences of the IA minor cluster and the IB group were detected in large/medium centers (LMCs). Overall, sequences from the IA major cluster were more frequent in small centers (SCs), but strain 1 and strain 2 showed an opposite relative frequency in SCs and LMCs (strain 1 more frequent in SCs, strain 2 in LMCs). Genotype IA predominated in Bulgaria in 2012-2014 and phylogenetic analysis identified a major cluster of highly related or identical IA sequences, representing 59% of the analysed cases; these isolates were mostly detected in SCs, in which HAV shows higher endemicity than in LMCs. The distribution of viral sequences suggests the existence of some differences between the transmission routes in SCs and LMCs. Molecular characterization of an increased number of isolates from Bulgaria, regularly collected over time, will be useful to explore specific transmission routes and plan appropriate preventing measures.

Reefing Line Tension in CPAS Main Parachute Clusters

NASA Technical Reports Server (NTRS)

Ray, Eric S.

2013-01-01

Reefing lines are an essential feature to manage inflation loads. During each Engineering Development Unit (EDU) test of the Capsule Parachute Assembly System (CPAS), a chase aircraft is staged to be level with the cluster of Main ringsail parachutes during the initial inflation and reefed stages. This allows for capturing high-quality still photographs of the reefed skirt, suspension line, and canopy geometry. The over-inflation angles are synchronized with measured loads data in order to compute the tension force in the reefing line. The traditional reefing tension equation assumes radial symmetry, but cluster effects cause the reefed skirt of each parachute to elongate to a more elliptical shape. This effect was considered in evaluating multiple parachutes to estimate the semi-major and semi-minor axes. Three flight tests are assessed, including one with a skipped first stage, which had peak reefing line tension over three times higher than the nominal parachute disreef sequence.

Deep HST Photometry of NGC 6388: Age and Horizontal Branch Luminosity

NASA Technical Reports Server (NTRS)

Stetson, Peter B.; Catelan, M.; Pritzl, Barton J.; Smith, Horace A.; Kinemuchi, Karen; Layden, Andrew C.; Sweigart, Allen V.; Rich, R. M.

2006-01-01

We present the first deep color-magnitude diagram (CMD) of the Galactic globular cluster NGC 6388, obtained with the Hubble Space Telescope, that is able to reach the main-sequence turnoff point of the cluster. From a detailed comparison between the cluster CMD and that of 47 Tucanae (NGC 104), we find that the bulk of the stars in these two clusters have nearly the same age and chemical composition. On the other hand, our results indicate that the blue horizontal branch and RR Lyrae components in NGC 6388 are intrinsically over-luminous, which must be due to one or more, still undetermined, non-canonical second parameter(s) affecting a relatively minor fraction of the stars in NGC 6388.

Signature of non-isotropic distribution of stellar rotation inclination angles in the Praesepe cluster

NASA Astrophysics Data System (ADS)

Kovacs, Geza

2018-04-01

The distribution of the stellar rotation axes of 113 main sequence stars in the open cluster Praesepe are examined by using current photometric rotation periods, spectroscopic rotation velocities, and estimated stellar radii. Three different samples of stellar rotation data on spotted stars from the Galactic field and two independent samples of planetary hosts are used as control samples to support the consistency of the analysis. Considering the high completeness of the Praesepe sample and the behavior of the control samples, we find that the main sequence F - K stars in this cluster are susceptible to rotational axis alignment. Using a cone model, the most likely inclination angle is 76° ± 14° with a half opening angle of 47° ± 24°. Non-isotropic distribution of the inclination angles is preferred over the isotropic distribution, except if the rotation velocities used in this work are systematically overestimated. We found no indication of this being the case on the basis of the currently available data. Data are only available at the CDS, together with the other two compiled datasets used in this paper, via anonymous ftp to http://cdsarc.u-strasbg.fr (http://130.79.128.5) or via http://cdsarc.u-strasbg.fr/viz-bin/qcat?J/A+A/612/L2

Application of hybrid clustering using parallel k-means algorithm and DIANA algorithm

NASA Astrophysics Data System (ADS)

Umam, Khoirul; Bustamam, Alhadi; Lestari, Dian

2017-03-01

DNA is one of the carrier of genetic information of living organisms. Encoding, sequencing, and clustering DNA sequences has become the key jobs and routine in the world of molecular biology, in particular on bioinformatics application. There are two type of clustering, hierarchical clustering and partitioning clustering. In this paper, we combined two type clustering i.e. K-Means (partitioning clustering) and DIANA (hierarchical clustering), therefore it called Hybrid clustering. Application of hybrid clustering using Parallel K-Means algorithm and DIANA algorithm used to clustering DNA sequences of Human Papillomavirus (HPV). The clustering process is started with Collecting DNA sequences of HPV are obtained from NCBI (National Centre for Biotechnology Information), then performing characteristics extraction of DNA sequences. The characteristics extraction result is store in a matrix form, then normalize this matrix using Min-Max normalization and calculate genetic distance using Euclidian Distance. Furthermore, the hybrid clustering is applied by using implementation of Parallel K-Means algorithm and DIANA algorithm. The aim of using Hybrid Clustering is to obtain better clusters result. For validating the resulted clusters, to get optimum number of clusters, we use Davies-Bouldin Index (DBI). In this study, the result of implementation of Parallel K-Means clustering is data clustered become 5 clusters with minimal IDB value is 0.8741, and Hybrid Clustering clustered data become 13 sub-clusters with minimal IDB values = 0.8216, 0.6845, 0.3331, 0.1994 and 0.3952. The IDB value of hybrid clustering less than IBD value of Parallel K-Means clustering only that perform at 1ts stage. Its means clustering using Hybrid Clustering have the better result to clustered DNA sequence of HPV than perform parallel K-Means Clustering only.

Phylogenetic structure of Leishmania tropica in the new endemic focus Birjand in East Iran in comparison to other Iranian endemic regions.

PubMed

Karamian, Mehdi; Kuhls, Katrin; Hemmati, Mina; Ghatee, Mohammad Amin

2016-06-01

Iran has been identified being among the countries with the highest number of cutaneous leishmaniasis (CL) cases. South Khorasan province in East Iran is an emerging focus of CL. Species identification of sixty clinical samples by ITS1 PCR-RFLP presented evidence for the dominance of Leishmania tropica (90%) in this region. Analysis of the ITS1 sequence of 19 L. tropica isolates revealed seven closely related sequence types. In addition, ITS1 sequences available in GenBank from other Iranian regions were compiled for comparison with the studied isolates. Iranian L. tropica was distributed in two main clusters. All East Iranian sequence types were grouped with strains from foci from Southeast and Central regions in cluster A, showing highly similar sequences. The highest similarity was observed between most L. tropica from East and all isolates from Southeast regions and from Savojbolagh county in Central Iran. Southwest L. tropica was shown to be paraphyletic as the isolates were distributed in both clusters A and B. All Northeastern L. tropica were part of cluster B, however they showed significant heterogeneity and were distributed in different subclusters. Distribution of L. tropica populations was to some extent congruent with genetic lineages of Phlebotomus sergenti in Iran and may be an evidence for parasite-vector co-evolution. Southeast-East L. tropica was also similar to strains from Herat province in Afghanistan at the East border of Iran. This is the first comprehensive study on population structure of L. tropica in Iran that provides a guideline for appropriate sampling for further molecular based epidemiological studies. Copyright © 2016 Elsevier B.V. All rights reserved.

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

NASA Astrophysics Data System (ADS)

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

2005-02-01

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

The K2 M67 Study: A Curiously Young Star in an Eclipsing Binary in an Old Open Cluster

NASA Astrophysics Data System (ADS)

Sandquist, Eric L.; Mathieu, Robert D.; Quinn, Samuel N.; Pollack, Maxwell L.; Latham, David W.; Brown, Timothy M.; Esselstein, Rebecca; Aigrain, Suzanne; Parviainen, Hannu; Vanderburg, Andrew; Stello, Dennis; Somers, Garrett; Pinsonneault, Marc H.; Tayar, Jamie; Orosz, Jerome A.; Bedin, Luigi R.; Libralato, Mattia; Malavolta, Luca; Nardiello, Domenico

2018-04-01

We present an analysis of a slightly eccentric (e = 0.05), partially eclipsing, long-period (P = 69.73 days) main-sequence binary system (WOCS 12009, Sanders 1247) in the benchmark old open cluster M67. Using Kepler K2 and ground-based photometry, along with a large set of new and reanalyzed spectra, we derived highly precise masses (1.111 ± 0.015 and 0.748 ± 0.005 M ⊙) and radii (1.071 ± 0.008 ± 0.003 and 0.713 ± 0.019 ± 0.026 R ⊙, with statistical and systematic error estimates) for the stars. The radius of the secondary star is in agreement with theory. The primary, however, is approximately 15% smaller than reasonable isochrones for the cluster predict. Our best explanation is that the primary star was produced from the merger of two stars, as this can also account for the nondetection of photospheric lithium and its higher temperature relative to other cluster main-sequence stars at the same V magnitude. To understand the dynamical characteristics (low measured rotational line broadening of the primary star and low eccentricity of the current binary orbit), we believe that the most probable (but not the only) explanation is the tidal evolution of a close binary within a primordial triple system (possibly after a period of Kozai–Lidov oscillations), leading to merger approximately 1 Gyr ago. This star appears to be a future blue straggler that is being revealed as the cluster ages and the most massive main-sequence stars die out. Based on observations made at Kitt Peak National Observatory, National Optical Astronomy Observatory, which is operated by the Association of Universities for Research in Astronomy (AURA) under a cooperative agreement with the National Science Foundation; with the Tillinghast Reflector Echelle Spectrograph (TRES) on the 1.5 m Tillinghast telescope, located at the Smithsonian Astrophysical Observatory’s Fred L. Whipple Observatory on Mt. Hopkins in Arizona; the HARPS-N spectrograph on the Italian Telescopio Nazionale Galileo (TNG), operated on the island of La Palma by the INAF Fundacion Galileo Galilei (Spanish Observatory of Roque de los Muchachos of the IAC); and the Las Cumbres Observatory Global Telescope network.

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

Tai, Lin-Ru; Chou, Chang-Wei; Lee, I-Fang

In this study, we used a multiple copy (EGFP){sub 3} reporter system to establish a numeric nuclear index system to assess the degree of nuclear import. The system was first validated by a FRAP assay, and then was applied to evaluate the essential and multifaceted nature of basic amino acid clusters during the nuclear import of ribosomal protein L7. The results indicate that the sequence context of the basic cluster determines the degree of nuclear import, and that the number of basic residues in the cluster is irrelevant; rather the position of the pertinent basic residues is crucial. Moreover, itmore » also found that the type of carrier protein used by basic cluster has a great impact on the degree of nuclear import. In case of L7, importin β2 or importin β3 are preferentially used by clusters with a high import efficiency, notwithstanding that other importins are also used by clusters with a weaker level of nuclear import. Such a preferential usage of multiple basic clusters and importins to gain nuclear entry would seem to be a common practice among ribosomal proteins in order to ensure their full participation in high rate ribosome synthesis. - Highlights: ► We introduce a numeric index system that represents the degree of nuclear import. ► The rate of nuclear import is dictated by the sequence context of the basic cluster. ► Importin β2 and β3 were mainly responsible for the N4 mediated nuclear import.« less

Evaluating gyrochronology on the zero-age-main-sequence: rotation periods in the southern open cluster Blanco 1 from the Kelt-South survey

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

Cargile, P. A.; Pepper, J.; Siverd, R.

2014-02-10

We report periods for 33 members of Blanco 1 as measured from Kilodegree Extremely Little Telescope-South light curves, the first reported rotation periods for this benchmark zero-age-main-sequence open cluster. The distribution of these stars spans from late-A or early-F dwarfs to mid-K with periods ranging from less than a day to ∼8 days. The rotation period distribution has a morphology similar to the coeval Pleiades cluster, suggesting the universal nature of stellar rotation distributions. Employing two different gyrochronology methods, we find an age of 146{sub −14}{sup +13} Myr for the cluster. Using the same techniques, we infer an age ofmore » 134{sub −10}{sup +9} Myr for the Pleiades measured from existing literature rotation periods. These rotation-derived ages agree with independently determined cluster ages based on the lithium depletion boundary technique. Additionally, we evaluate different gyrochronology models and quantify levels of agreement between the models and the Blanco 1/Pleiades rotation period distributions, including incorporating the rotation distributions of clusters at ages up to 1.1 Gyr. We find the Skumanich-like spin-down rate sufficiently describes the rotation evolution of stars hotter than the Sun; however, we find cooler stars rotating faster than predicted by a Skumanich law, suggesting a mass dependence in the efficiency of stellar angular momentum loss rate. Finally, we compare the Blanco 1 and Pleiades rotation period distributions to available nonlinear angular momentum evolution models. We find they require a significant mass dependence on the initial rotation rate of solar-type stars to reproduce the observed range of rotation periods at a given stellar mass and are furthermore unable to predict the observed over-density of stars along the upper envelope of the clusters' rotation distributions.« less

A theoretical and observational study of the Red Giant Branch phase transition in Magellanic Cloud clusters - A progress report

NASA Technical Reports Server (NTRS)

Buonanno, R.; Corsi, C. E.; Fusi Pecci, F.; Greggio, L.; Renzini, A.; Sweigart, A. V.

1986-01-01

Preliminary results are reported for an investigation comparing theoretical models of the sudden appearance of an extended RGB (and its effects on the spectral energy distributions of stellar populations) with data from ESO CCD observations of clusters in the LMC and SMC. Isochrones for the entire RGB are being constructed on the basis of 100 new evolutionary sequences (calculated using the evolution code of Sweigart and Gross, 1976 and 1978) to permit determination of synthetic colors and spectral energy distributions. The observations so far indicate a main sequence about 0.1 mag redder than that predicted by the present models or by the isochrones of VandenBerg and Bell (1985), and fail to show a B-V color difference at the RGB phase transition.

Multicolor CCD photometry of the open cluster NGC 752

NASA Astrophysics Data System (ADS)

Bartašiūtė, Stanislava; Janusz, Robert; Boyle, Richard P.; Philip, A. G. Davis; Deveikis, Viktoras

2010-01-01

We obtained CCD observations of the open cluster NGC 752 with the 1.8m Vatican Advanced Technology Telescope (Mt. Graham, Arizona) with a 4K CCD camera and eight intermediate-band filters of the Stromvil (Strömgren + Vilnius) system. Four 12‧ × 12‧ fields were observed, covering the central part of the cluster. The good-quality multicolor data made it possible to obtain precise estimates of distance moduli, metallicity and foreground reddening for individual stars down to the limiting magnitude, V = 17.5, enabling photometric identification of faint cluster members. The new observations provide an extension of the lower main sequence to three magnitudes beyond the previous (photographic) limit. A relatively small number of photometric members identified at fainter magnitudes seems to be indicative of actual dissolution of the cluster from the low-mass end.

Identification of a current hot spot of HIV type 1 transmission in Mongolia by molecular epidemiological analysis.

PubMed

Davaalkham, Jagdagsuren; Unenchimeg, Puntsag; Baigalmaa, Chultem; Erdenetuya, Gombo; Nyamkhuu, Dulmaa; Shiino, Teiichiro; Tsuchiya, Kiyoto; Hayashida, Tsunefusa; Gatanaga, Hiroyuki; Oka, Shinichi

2011-10-01

We investigated the current molecular epidemiological status of HIV-1 in Mongolia, a country with very low incidence of HIV-1 though with rapid expansion in recent years. HIV-1 pol (1065 nt) and env (447 nt) genes were sequenced to construct phylogenetic trees. The evolutionary rates, molecular clock phylogenies, and other evolutionary parameters were estimated from heterochronous genomic sequences of HIV-1 subtype B by the Bayesian Markov chain Monte Carlo method. We obtained 41 sera from 56 reported HIV-1-positive cases as of May 2009. The main route of infection was men who have sex with men (MSM). Dominant subtypes were subtype B in 32 cases (78%) followed by subtype CRF02_AG (9.8%). The phylogenetic analysis of the pol gene identified two clusters in subtype B sequences. Cluster 1 consisted of 21 cases including MSM and other routes of infection, and cluster 2 consisted of eight MSM cases. The tree analyses demonstrated very short branch lengths in cluster 1, suggesting a surprisingly active expansion of HIV-1 transmission during a short period with the same ancestor virus. Evolutionary analysis indicated that the outbreak started around the early 2000s. This study identified a current hot spot of HIV-1 transmission and potential seed of the epidemic in Mongolia. Comprehensive preventive measures targeting this group are urgently needed.

Communities of ammonia-oxidizing bacteria in activated sludge of various sewage treatment plants in Tokyo.

PubMed

Limpiyakorn, Tawan; Shinohara, Yuko; Kurisu, Futoshi; Yagi, Osami

2005-10-01

We investigated ammonia-oxidizing bacteria in activated sludge collected from 12 sewage treatment systems, whose ammonia removal and treatment processes differed, during three different seasons. We used real-time PCR quantification to reveal total bacterial numbers and total ammonia oxidizer numbers, and used specific PCR followed by denaturing gel gradient electrophoresis, cloning, and sequencing of 16S rRNA genes to analyze ammonia-oxidizing bacterial communities. Total bacterial numbers and total ammonia oxidizer numbers were in the range of 1.6 x 10(12) - 2.4 x 10(13) and 1.0 x 10(9) - 9.2 x 10(10)cellsl(-1), respectively. Seasonal variation was observed in the total ammonia oxidizer numbers, but not in the ammonia-oxidizing bacterial communities. Members of the Nitrosomonas oligotropha cluster were found in all samples, and most sequences within this cluster grouped within two of the four sequence types identified. Members of the clusters of Nitrosomonas europaea-Nitrosococcus mobilis, Nitrosomonas cryotolerans, and unknown Nitrosomonas, occurred solely in one anaerobic/anoxic/aerobic (A2O) system. Members of the Nitrosomonas communis cluster occurred almost exclusively in association with A2O and anaerobic/aerobic systems. Solid residence time mainly influenced the total numbers of ammonia-oxidizing bacteria, whereas dissolved oxygen concentration primarily affected the ammonia-oxidizing activity per ammonia oxidizer cell.

The Low Mass IMF in Young Open Clusters

NASA Astrophysics Data System (ADS)

Williams, Douglas M.

1995-01-01

We present the results of the investigation of the Initial Mass Function at the end of the Main Sequence in young open clusters. We find that over a large range in age and environment the IMFs are similar to each other, and to recent determinations of the field star IMF. We have obtained V, I, and K band photometry of fields in the three relatively unembedded open clusters. The photometry reaches down to various masses in each cluster: 0.08{cal M}_⊙ for Praesepe, 0.04{cal M}odot for the Pleiades, and 0.15{cal M}_⊙ for NGC 7160. We compare the methods for estimating the masses of young, embedded stars developed by Comeron et al. (1993 - CRBR) and by Strom, Kepner, & Strom (1995) and show them to be in good agreement. Spectra in the 2 mu m region of six low mass objects from CRBR are also in agreement with the mass estimates using these methods. The spectrum of a brown dwarf candidate is used to place an upper limit on its mass of 60% of the minimum required for hydrogen burning. The IMFs from these four clusters plus NGC 2024 are shown to be in agreement with each other. The composite MF can be fitted with a power law between 0.04 and 0.5 {cal M}_⊙ with a slope of -0.75 +/- 0.3. There is no evidence for a cutoff at the bottom of the main sequence (0.08{cal M}odot); brown dwarfs appear to be abundant in open clusters. However, the slope of the MF is well above the value of _sp {~}<-2 required for very low mass stars and brown dwarfs to contribute a significant portion of the mass of open clusters. The composite cluster MF also is in agreement with recent determinations of the field star IMF for stellar masses. The field star data do not extend into the brown dwarf range; however, if we extrapolate in accordance with the cluster MF, we conclude that brown dwarfs probably do not contribute significantly to the dark matter.

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.

Longitudinal Metagenomic Analysis of Hospital Air Identifies Clinically Relevant Microbes.

PubMed

King, Paula; Pham, Long K; Waltz, Shannon; Sphar, Dan; Yamamoto, Robert T; Conrad, Douglas; Taplitz, Randy; Torriani, Francesca; Forsyth, R Allyn

2016-01-01

We describe the sampling of sixty-three uncultured hospital air samples collected over a six-month period and analysis using shotgun metagenomic sequencing. Our primary goals were to determine the longitudinal metagenomic variability of this environment, identify and characterize genomes of potential pathogens and determine whether they are atypical to the hospital airborne metagenome. Air samples were collected from eight locations which included patient wards, the main lobby and outside. The resulting DNA libraries produced 972 million sequences representing 51 gigabases. Hierarchical clustering of samples by the most abundant 50 microbial orders generated three major nodes which primarily clustered by type of location. Because the indoor locations were longitudinally consistent, episodic relative increases in microbial genomic signatures related to the opportunistic pathogens Aspergillus, Penicillium and Stenotrophomonas were identified as outliers at specific locations. Further analysis of microbial reads specific for Stenotrophomonas maltophilia indicated homology to a sequenced multi-drug resistant clinical strain and we observed broad sequence coverage of resistance genes. We demonstrate that a shotgun metagenomic sequencing approach can be used to characterize the resistance determinants of pathogen genomes that are uncharacteristic for an otherwise consistent hospital air microbial metagenomic profile.

Chromosomal arrangement of leghemoglobin genes in soybean.

PubMed Central

Lee, J S; Brown, G G; Verma, D P

1983-01-01

A cluster of four different leghemoglobin (Lb) genes was isolated from AluI-HaeIII and EcoRI genomic libraries of soybean in a set of overlapping clones which together include 45 kilobases (kb) of contiguous DNA. These four genes, including a pseudogene, are present in the same orientation and are arranged in the order: 5'-Lba-Lbc1-Lb psi-Lbc3-3'. The intergenic regions average 2.5 kb. In addition to this main Lb locus, there are other Lb genes which do not appear to be contiguous to this locus. A sequence probably common to the 3' region of Lb loci was found flanking the Lbc3 gene. The 3' flanking region of the main Lb locus also contains a sequence that appears to be expressed more abundantly in root tissue. Another sequence which is primarily expressed in root and leaf is found 5' to two Lb loci. Overall, the main leghemoglobin locus is similar in structure to the mammalian globin gene loci. Images PMID:6310504

Molecular epidemiological study of HIV-1 CRF01_AE transmission in Hong Kong.

PubMed

Chen, J H K; Wong, K H; Li, P; Chan, K C; Lee, M P; Lam, H Y; Cheng, V C C; Yuen, K Y; Yam, W C

2009-08-15

The objective of this study was to investigate the transmission history of the HIV-1 CRF01_AE epidemics in Hong Kong between 1994 and 2007. A total of 465 HIV-1 CRF01_AE pol sequences were derived from an in-house or a commercial HIV-1 genotyping system. Phylogenies of CRF01_AE sequences were analyzed by the Bayesian coalescent method. CRF01_AE patient population included 363 males (78.1%) and 102 females (21.9%), whereas 65% (314 of 465) were local Chinese. Major transmission routes were heterosexual contact (63%), followed by intravenous drug use (IDU) (19%) and men having sex with men (MSM) (17%). From phylogenetic analysis, local CRF01_AE strains were from multiple origins with 3 separate transmission clusters identified. Cluster 1 consisted mainly of Chinese male IDUs and heterosexuals. Clusters 2 and 3 included mainly local Chinese MSM and non-Chinese Asian IDUs, respectively. Chinese reference isolates available from China (Fujian, Guangxi, or Liaoning) were clonally related to our transmission clusters, demonstrating the epidemiological linkage of CRF01_AE infections between Hong Kong and China. The 3 individual local transmission clusters were estimated to have initiated since late 1980s and late 1990s, causing subsequent epidemics in the early 2000s. This is the first comprehensive molecular epidemiological study of HIV-1 CRF01_AE in Hong Kong. It revealed that MSM contact is becoming a major route of local CRF01_AE transmission in Hong Kong. Epidemiological linkage of CRF01_AE between Hong Kong and China observed in this study indicates the importance of regular molecular epidemiological surveillance for the HIV-1 epidemic in our region.

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.

Molecular epidemiology of hepatitis B virus in Misiones, Argentina.

PubMed

Mojsiejczuk, Laura Noelia; Torres, Carolina; Sevic, Ina; Badano, Inés; Malan, Richard; Flichman, Diego Martin; Liotta, Domingo Javier; Campos, Rodolfo Hector

2016-10-01

Hepatitis B virus (HBV) infection is a major public health problem worldwide. The aims of this study were to describe the molecular epidemiology of HBV in the Province of Misiones, Argentina and estimate the phylodynamic of the main groups in a Bayesian coalescent framework. To this end, partial or complete genome sequences were obtained from 52 blood donor candidates. The phylogenetic analysis based on partial sequences of S/P region showed a predominance of genotype D (65.4%), followed by genotype F (30.8%) and genotype A as a minority (3.8%). At subgenotype level, the circulation of subgenotypes D3 (42.3%), D2 (13.5%), F1b (11.5%) and F4 (9.6%) was mainly identified. The Bayesian coalescent analysis of 29 complete genome sequences for the main groups revealed that the subgenotypes D2 and D3 had several introductions to the region, with ancestors dating back from 1921 to 1969 and diversification events until the late '70s. The genotype F in Misiones has a more recent history; subgenotype F4 isolates were intermixed with sequences from Argentina and neighboring countries and only one significant cluster dated back in 1994 was observed. Subgenotype F1b isolates exhibited low genetic distance and formed a closely related monophyletic cluster, suggesting a very recent introduction. In conclusion, the phylogenetic and coalescent analyses showed that the European genotype D has a higher circulation, a longer history of diversification and may be responsible for the largest proportion of chronic HBV infections in the Province of Misiones. Genotype F, especially subgenotype F1b, had a more recent introduction and its diversification in the last 20years might be related to its involvement in new transmission events. Copyright © 2016 Elsevier B.V. All rights reserved.

The optimal design of stepped wedge trials with equal allocation to sequences and a comparison to other trial designs.

PubMed

Thompson, Jennifer A; Fielding, Katherine; Hargreaves, James; Copas, Andrew

2017-12-01

Background/Aims We sought to optimise the design of stepped wedge trials with an equal allocation of clusters to sequences and explored sample size comparisons with alternative trial designs. Methods We developed a new expression for the design effect for a stepped wedge trial, assuming that observations are equally correlated within clusters and an equal number of observations in each period between sequences switching to the intervention. We minimised the design effect with respect to (1) the fraction of observations before the first and after the final sequence switches (the periods with all clusters in the control or intervention condition, respectively) and (2) the number of sequences. We compared the design effect of this optimised stepped wedge trial to the design effects of a parallel cluster-randomised trial, a cluster-randomised trial with baseline observations, and a hybrid trial design (a mixture of cluster-randomised trial and stepped wedge trial) with the same total cluster size for all designs. Results We found that a stepped wedge trial with an equal allocation to sequences is optimised by obtaining all observations after the first sequence switches and before the final sequence switches to the intervention; this means that the first sequence remains in the control condition and the last sequence remains in the intervention condition for the duration of the trial. With this design, the optimal number of sequences is [Formula: see text], where [Formula: see text] is the cluster-mean correlation, [Formula: see text] is the intracluster correlation coefficient, and m is the total cluster size. The optimal number of sequences is small when the intracluster correlation coefficient and cluster size are small and large when the intracluster correlation coefficient or cluster size is large. A cluster-randomised trial remains more efficient than the optimised stepped wedge trial when the intracluster correlation coefficient or cluster size is small. A cluster-randomised trial with baseline observations always requires a larger sample size than the optimised stepped wedge trial. The hybrid design can always give an equally or more efficient design, but will be at most 5% more efficient. We provide a strategy for selecting a design if the optimal number of sequences is unfeasible. For a non-optimal number of sequences, the sample size may be reduced by allowing a proportion of observations before the first or after the final sequence has switched. Conclusion The standard stepped wedge trial is inefficient. To reduce sample sizes when a hybrid design is unfeasible, stepped wedge trial designs should have no observations before the first sequence switches or after the final sequence switches.

Phytoplasma phylogenetics based on analysis of secA and 23S rRNA gene sequences for improved resolution of candidate species of 'Candidatus Phytoplasma'.

PubMed

Hodgetts, Jennifer; Boonham, Neil; Mumford, Rick; Harrison, Nigel; Dickinson, Matthew

2008-08-01

Phytoplasma phylogenetics has focused primarily on sequences of the non-coding 16S rRNA gene and the 16S-23S rRNA intergenic spacer region (16-23S ISR), and primers that enable amplification of these regions from all phytoplasmas by PCR are well established. In this study, primers based on the secA gene have been developed into a semi-nested PCR assay that results in a sequence of the expected size (about 480 bp) from all 34 phytoplasmas examined, including strains representative of 12 16Sr groups. Phylogenetic analysis of secA gene sequences showed similar clustering of phytoplasmas when compared with clusters resolved by similar sequence analyses of a 16-23S ISR-23S rRNA gene contig or of the 16S rRNA gene alone. The main differences between trees were in the branch lengths, which were elongated in the 16-23S ISR-23S rRNA gene tree when compared with the 16S rRNA gene tree and elongated still further in the secA gene tree, despite this being a shorter sequence. The improved resolution in the secA gene-derived phylogenetic tree resulted in the 16SrII group splitting into two distinct clusters, while phytoplasmas associated with coconut lethal yellowing-type diseases split into three distinct groups, thereby supporting past proposals that they represent different candidate species within 'Candidatus Phytoplasma'. The ability to differentiate 16Sr groups and subgroups by virtual RFLP analysis of secA gene sequences suggests that this gene may provide an informative alternative molecular marker for pathogen identification and diagnosis of phytoplasma diseases.

The Gemini/HST Galaxy Cluster Project: Redshift 0.2–1.0 Cluster Sample, X-Ray Data, and Optical Photometry Catalog

NASA Astrophysics Data System (ADS)

Jørgensen, Inger; Chiboucas, Kristin; Hibon, Pascale; Nielsen, Louise D.; Takamiya, Marianne

2018-04-01

The Gemini/HST Galaxy Cluster Project (GCP) covers 14 z = 0.2–1.0 clusters with X-ray luminosity of {L}500≥slant {10}44 {erg} {{{s}}}-1 in the 0.1–2.4 keV band. In this paper, we provide homogeneously calibrated X-ray luminosities, masses, and radii, and we present the complete catalog of the ground-based photometry for the GCP clusters. The clusters were observed with either Gemini North or South in three or four of the optical passbands g‧, r‧, i‧, and z‧. The photometric catalog includes consistently calibrated total magnitudes, colors, and geometrical parameters. The photometry reaches ≈25 mag in the passband closest to the rest-frame B band. We summarize comparisons of our photometry with data from the Sloan Digital Sky Survey. We describe the sample selection for our spectroscopic observations, and establish the calibrations to obtain rest-frame magnitudes and colors. Finally, we derive the color–magnitude relations for the clusters, and briefly discuss these in the context of evolution with redshift. Consistent with our results based on spectroscopic data, the color–magnitude relations support passive evolution of the red sequence galaxies. The absence of change in the slope with redshift constrains the allowable age variation along the red sequence to <0.05 dex between the brightest cluster galaxies and those four magnitudes fainter. This paper serves as the main reference for the GCP cluster and galaxy selection, X-ray data, and ground-based photometry.

Comparative Genomic Hybridization Analysis of Two Predominant Nordic Group I (Proteolytic) Clostridium botulinum Type B Clusters▿ †

PubMed Central

Lindström, Miia; Hinderink, Katja; Somervuo, Panu; Kiviniemi, Katri; Nevas, Mari; Chen, Ying; Auvinen, Petri; Carter, Andrew T.; Mason, David R.; Peck, Michael W.; Korkeala, Hannu

2009-01-01

Comparative genomic hybridization analysis of 32 Nordic group I Clostridium botulinum type B strains isolated from various sources revealed two homogeneous clusters, clusters BI and BII. The type B strains differed from reference strain ATCC 3502 by 413 coding sequence (CDS) probes, sharing 88% of all the ATCC 3502 genes represented on the microarray. The two Nordic type B clusters differed from each other by their response to 145 CDS probes related mainly to transport and binding, adaptive mechanisms, fatty acid biosynthesis, the cell membranes, bacteriophages, and transposon-related elements. The most prominent differences between the two clusters were related to resistance to toxic compounds frequently found in the environment, such as arsenic and cadmium, reflecting different adaptive responses in the evolution of the two clusters. Other relatively variable CDS groups were related to surface structures and the gram-positive cell wall, suggesting that the two clusters possess different antigenic properties. All the type B strains carried CDSs putatively related to capsule formation, which may play a role in adaptation to different environmental and clinical niches. Sequencing showed that representative strains of the two type B clusters both carried subtype B2 neurotoxin genes. As many of the type B strains studied have been isolated from foods or associated with botulism, it is expected that the two group I C. botulinum type B clusters present a public health hazard in Nordic countries. Knowing the genetic and physiological markers of these clusters will assist in targeting control measures against these pathogens. PMID:19270141

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

NASA Astrophysics Data System (ADS)

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

2017-12-01

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

[Effective management of an outbreak with multiresistent Klebsiella pneumoniae in a neurorehabilitation unit].

PubMed

Dohle, Christian; Korr, Gerit; Friedrichs, Michael; Kullmann, Volker; Tung, Mei-Lin; Kaase, Martin; Rüssmann, Holger; Sissolak, Dagmar; Werber, Dirk; Becker, Laura; Fuchs, Stephan; Pfeifer, Yvonne; Semmler, Torsten; Widders, Gudrun; Eckmanns, Tim; Werner, Guido; Zill, Edith; Haller, Sebastian

2018-05-01

In addition to acute care hospitals, rehabilitation centres are increasingly confronted with multi-resistant pathogens. Long durations of stay and intensive treatments impose special hygienic challenges. We investigated an extended spectrum beta-lactamase-Klebsiella pneumoniae (ESBL-K. pneumoniae) outbreak in a neurorehabilitation centre. We defined confirmed cases as patients who stayed in the centre during the outbreak period and from whom ESBL-K. pneumoniae was isolated with the outbreak sequence type. Probable cases had an epidemiological link to at least one confirmed case but no isolate for typing. Next generation sequencing (NGS) was performed on 53 isolates from patients. Environmental sampling was performed. Systematic microbiological screening was implemented and ESBL-K. pneumoniae-positive patients were cohorted in a designated ward. We identified 30 confirmed and 6 probable cases. NGS revealed three genetic clusters: Cluster 1 - the outbreak cluster - with isolates of 30 cases (sequence type ST15), Cluster 2 with 7 patients (ST405) and Cluster 3 with 8 patients (ST414). In two patients, the outbreak strain developed further antibiotic resistance, one with colistin resistance and the other carbapenem resistance. The outbreak ceased after strict isolation measures. Epidemiology and NGS results paired with the effectiveness of cohorting suggest that transmission occurred mainly from person to person in this outbreak. There was an apparent association of the probability to acquire ESBL-K. pneumoniae and treatment intensity, whereas infection rate was related to morbidity. The identification of the outbreak clone and additional clusters plus the development of additional antibiotic resistance shows the relevance of NGS and highlights the need for timely and efficient outbreak management.

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

NASA Astrophysics Data System (ADS)

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

2008-02-01

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

Phenotypic and genetic characterizations of Streptococcus dysgalactiae strains isolated from fish collected in Japan and other Asian countries.

PubMed

Abdelsalam, Mohamed; Chen, Shih-Chu; Yoshida, Terutoyo

2010-01-01

Lancefield group C Streptococcus dysgalactiae is an emerging fish pathogen, which was first isolated in 2002 in Japan. Streptococcus dysgalactiae isolates collected from diseased fish in Japan (n=12), Taiwan (n=12), China (n=2), Malaysia (n=3), and Indonesia (n=1) were characterized using biased sinusoidal field gel electrophoresis (BSFGE), sodA gene sequence analysis, and antimicrobial susceptibility. These isolates exhibited high phenotypic homogeneity irrespective of the countries from where the strains were collected. Seventeen isolates were found to be resistant to oxytetracycline and carried the tet(M) gene, except for the strains collected in Taiwan and the PP1564 strain collected in China. The sodA gene sequence analysis revealed that 23 isolates were identical, except for one Japanese isolate (KNH07902), in which a single nucleotide differed from that of the other isolates. Based on BSFGE typing by ApaI macrorestriction, the isolates - including the Japanese, Taiwanese, and Chinese isolates - could be grouped into one main cluster at a 70% similarity level. However, the macrorestriction genotypes of some isolates were apparently distinct from those of the main cluster.

Evidence for a Significant Intermediate-Age Population in the M31 Halo from Main Sequence Photometry

NASA Technical Reports Server (NTRS)

Brown, Thomas M.; Ferguson, Henry C.; Smith, Ed; Kimble, Randy A.; Sweigart, Allen V.; Renzini, Alvio; Rich, R. Michael; Vandenberg, Don A.

2003-01-01

We present a color-magnitude diagram (CMD) for a minor-axis field in the halo of the Andromeda galaxy (M3l), 51 arcmin (11 kpc) from the nucleus. These observations, taken with the Advanced Camera for Surveys (ACS) on the Hubble Space Telescope, are the deepest optical images yet obtained, attaining 50% completeness at m(sub v) = 30.7 mag. The CMD, constructed from approx. 3 x 10(exp 5) stars, reaches more than 1.5 mag fainter than the old main-sequence turnoff. Our analysis is based on direct comparisons to ACS observations of four globular clusters through the same filters, as well as chi square fitting to a finely-spaced grid of calibrated stellar-population models. We find that the M31 halo contains a major (approx. 30% by mass) intermediate-age (6-8 Gyr) metal-rich ([Fe/H] greater than -0.5) population, as well as a significant globular-cluster age (11-13.5 Gyr) metal-poor population. These findings support the idea that galaxy mergers played an important role in the formation of the M31 halo.

Galactic helium-to-metals enrichment ratio (Delta Y/ Delta Z) from the analysis of local main sequence stars observed by HIPPARCOS

NASA Astrophysics Data System (ADS)

Gennaro, M.; Prada Moroni, P. G.; Degl'Innocenti, S.

We discuss the reliability of one of the most used method to determine the Helium-to-metals enrichment ratio, Delta Y / Delta Z, i.e. the photometric comparison of a selected data set of local disk low Main Sequence (MS) stars observed by HIPPARCOS and a new grid of stellar models with up-to-date input physics. Most of the attention has been devoted to evaluate the effects on the final results of different sources of uncertainty (observational errors, evolutionary effects, selection criteria, systematic uncertainties of the models, numerical errors). As a check of the result the procedure has been repeated using another, independent, data set: the low-MS of the Hyades cluster. The obtained of Delta Y/ Delta Z for the Hyades, together with spectroscopic determinations of [Fe/H] ratio, have been used to obtain the Y and Z values for the cluster. Isochrones have been calculated with the estimated chemical composition, obtaining a very good agreement between the predicted position of the Hyades MS and the observational data in the Color - Magnitude Diagram (CMD).

Galactic ΔY/ΔZ from the analysis of solar neighborhood main sequence stars

NASA Astrophysics Data System (ADS)

Gennaro, M.; Moroni, P. G. Prada; Degl'Innocenti, S.

2009-05-01

We discuss the reliability of one of the most used method to determine the helium-to-metals enrichment ratio (ΔY/ΔZ), i.e. the photometric comparison of a selected data set of local disk low main sequence (MS) stars observed by Hipparcos with a new grid of stellar models with up-to-date input physics. Most of the attention has been devoted to evaluate the effects on the final results of different sources of uncertainty (observational errors, evolutionary effects, selection criteria, systematic uncertainties of the models, numerical errors). As a check of the result the procedure has been repeated using another, independent, data set: the low-MS of the Hyades cluster. The obtained ΔY/ΔZ for the Hyades, together with spectroscopic determinations of [Fe/H] ratio, have been used to obtain the Y and Z values for the cluster. Isochrones have been calculated with the estimated chemical composition, obtaining a very good agreement between the predicted position of the Hyades MS and the observational data in the color-magnitude diagram.

STELLAR BORON ABUNDANCES NEAR THE MAIN-SEQUENCE TURNOFF OF THE OPEN CLUSTER NGC 3293 AND IMPLICATIONS FOR THE EFFICIENCY OF ROTATIONALLY DRIVEN MIXING IN STELLAR ENVELOPES

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

Proffitt, Charles R.; Lennon, Daniel J.; Langer, Norbert

2016-06-10

Spectra from the Hubble Space Telescope Cosmic Origins Spectrograph and the Space Telescope Imaging Spectrograph covering the B iii resonance line have been obtained for 10 early-B stars near the turnoff of the young Galactic open cluster NGC 3293. This is the first sample of boron abundance determinations in a single, clearly defined population of early-B stars that also covers a substantial range of projected rotational velocities. In most of these stars we detect partial depletion of boron at a level consistent with that expected for rotational mixing in single stars, but inconsistent with expectations for depletion from close binarymore » evolution. However, our results do suggest that the efficiency of rotational mixing is at or slightly below the low end of the range predicted by the available theoretical calculations. The two most luminous targets observed have a very large boron depletion and may be the products of either binary interactions or post-main-sequence evolution.« less

Rotational velocities of newly discovered, low-mass members of the Alpha Persei cluster

NASA Technical Reports Server (NTRS)

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

1989-01-01

About 30 new, low-mass members of the young open cluster Alpha Persei are identified via a proper-motion study and subsequent photometric and spectroscopic observations. Membership in the cluster is confirmed for a number of the fainter proper-motion candidates from Heckman, Dieckvoss, and Kox (1956). Coordinates, finding charts, BVRI photometry, and rotational velocities are provided for most of the stars. At least two of the stars show peculiar H-alpha emission profiles, with weak but very broad emission wings, and relatively narrow absorption reversals. The rotational velocity distribution for low-mass stars in the Alpha Per cluster are compared with recently derived rotational velocity distributions for T Tauri stars, placing strong constraints on the mechanisms for angular momentum loss during pre-main-sequence evolution.

GibbsCluster: unsupervised clustering and alignment of peptide sequences.

PubMed

Andreatta, Massimo; Alvarez, Bruno; Nielsen, Morten

2017-07-03

Receptor interactions with short linear peptide fragments (ligands) are at the base of many biological signaling processes. Conserved and information-rich amino acid patterns, commonly called sequence motifs, shape and regulate these interactions. Because of the properties of a receptor-ligand system or of the assay used to interrogate it, experimental data often contain multiple sequence motifs. GibbsCluster is a powerful tool for unsupervised motif discovery because it can simultaneously cluster and align peptide data. The GibbsCluster 2.0 presented here is an improved version incorporating insertion and deletions accounting for variations in motif length in the peptide input. In basic terms, the program takes as input a set of peptide sequences and clusters them into meaningful groups. It returns the optimal number of clusters it identified, together with the sequence alignment and sequence motif characterizing each cluster. Several parameters are available to customize cluster analysis, including adjustable penalties for small clusters and overlapping groups and a trash cluster to remove outliers. As an example application, we used the server to deconvolute multiple specificities in large-scale peptidome data generated by mass spectrometry. The server is available at http://www.cbs.dtu.dk/services/GibbsCluster-2.0. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Genetic diversity studies and identification of SSR markers associated with Fusarium wilt (Fusarium udum) resistance in cultivated pigeonpea (Cajanus cajan).

PubMed

Singh, A K; Rai, V P; Chand, R; Singh, R P; Singh, M N

2013-01-01

Genetic diversity and identification of simple sequence repeat markers correlated with Fusarium wilt resistance was performed in a set of 36 elite cultivated pigeonpea genotypes differing in levels of resistance to Fusarium wilt. Twenty-four polymorphic sequence repeat markers were screened across these genotypes, and amplified a total of 59 alleles with an average high polymorphic information content value of 0.52. Cluster analysis, done by UPGMA and PCA, grouped the 36 pigeonpea genotypes into two main clusters according to their Fusarium wilt reaction. Based on the Kruskal-Wallis ANOVA and simple regression analysis, six simple sequence repeat markers were found to be significantly associated with Fusarium wilt resistance. The phenotypic variation explained by these markers ranged from 23.7 to 56.4%. The present study helps in finding out feasibility of prescreened SSR markers to be used in genetic diversity analysis and their potential association with disease resistance.

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.

ExtLaw_H18: Extinction law code

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

ExtLaw_H18 generates the extinction law between 0.8 - 2.2 microns. The law is derived using the Westerlund 1 (Wd1) main sequence (A_Ks 0.6 mag) and Arches cluster field Red Clump at the Galactic Center (A_Ks 2.7 mag). To derive the law a Wd1 cluster age of 5 Myr is assumed, though changing the cluster age between 4 Myr - 7 Myr has no effect on the law. This extinction law can be applied to highly reddened stellar populations that have similar foreground material as Wd1 and the Arches RC, namely dust from the spiral arms of the Milky Way in the Galactic Plane.

UVBY beta photometry of the young southern cluster NGC3293 and comparison with other young clusters

NASA Astrophysics Data System (ADS)

Shobbrook, R. R.

1980-09-01

Stromgren uvby photometry has been obtained for 42 members and beta photometry for 37 members of the young southern galactic cluster NGC 3293. The distance modulus obtained from using Crawford's beta/M(V) calibration is 12.75 mag, corresponding to a distance of 3.55 kpc. Comparison of the colour/colour and the HR diagrams of NGC 3293 with those of the five other young northern and southern clusters reveals large differences between the clusters which may possibly be due to metal abundance variations across the Galaxy. Apparently correlated with this effect is a variation of the luminosities of the lower main sequences over about 1 mag. The fainter stars in the southern clusters appear to be an average of 0.7 mag brighter than those in the northern clusters, but it is not certain at present how much of this difference is due to possible systematic errors in the beta index zero point between the northern and southern hemispheres.

Clustering and visualizing similarity networks of membrane proteins.

PubMed

Hu, Geng-Ming; Mai, Te-Lun; Chen, Chi-Ming

2015-08-01

We proposed a fast and unsupervised clustering method, minimum span clustering (MSC), for analyzing the sequence-structure-function relationship of biological networks, and demonstrated its validity in clustering the sequence/structure similarity networks (SSN) of 682 membrane protein (MP) chains. The MSC clustering of MPs based on their sequence information was found to be consistent with their tertiary structures and functions. For the largest seven clusters predicted by MSC, the consistency in chain function within the same cluster is found to be 100%. From analyzing the edge distribution of SSN for MPs, we found a characteristic threshold distance for the boundary between clusters, over which SSN of MPs could be properly clustered by an unsupervised sparsification of the network distance matrix. The clustering results of MPs from both MSC and the unsupervised sparsification methods are consistent with each other, and have high intracluster similarity and low intercluster similarity in sequence, structure, and function. Our study showed a strong sequence-structure-function relationship of MPs. We discussed evidence of convergent evolution of MPs and suggested applications in finding structural similarities and predicting biological functions of MP chains based on their sequence information. © 2015 Wiley Periodicals, Inc.

Rock avalanches clusters along the northern Chile coastal scarp

NASA Astrophysics Data System (ADS)

Crosta, G. B.; Hermanns, R. L.; Dehls, J.; Lari, S.; Sepulveda, S.

2017-07-01

Rock avalanche clusters can be relevant indicators of the evolution of specific regions. They can be used to define: the type and intensity of triggering events, their recurrence and potential probability of occurrence, the progressive damage of the rock mass, the mechanisms of transport and deposition, as well as the environmental conditions at the time of occurrence. This paper tackles these subjects by analyzing two main clusters of rock avalanches (each event between 0.6 and 30 Mm3), separated by few kilometers and located along the coastal scarp of Northern Chile, south of Iquique. It lies, hence, within a seismic area characterized by a long seismic gap that ended on April 1st, 2014 with a Mw 8.2 earthquake. The scar position, high along the coastal cliff, supports seismic triggering for these clusters. The deposits' relative positions are used to obtain the sequence of rock avalanching events for each cluster. The progressive decrease of volume in the sequence of rock avalanches forming each cluster fits well the theoretical models for successive slope failures. These sequences seem to agree with those derived by dating the deposits with ages spanning between 4 kyr and 60 kyr. An average uplift rate of 0.2 mm/yr in the last 40 kyr is estimated for the coastal plain giving a further constraint to the rock avalanche deposition considering the absence of reworking of the deposits. Volume estimates and datings allow the estimation of an erosion rate contribution of about 0.098-0.112 mm km- 2 yr- 1 which is well comparable to values presented in the literature for earthquake induced landslides. We have carried out numerical modeling in order to analyze the mobility of the rock avalanches and examine the environmental conditions that controlled the runout. In doing so, we have considered the sequence of individual rock avalanches within the specific clusters, thus including in the models the confining effect caused by the presence of previous deposits. Bingham rheology was the most successful at explaining both the distance and the geometry of the observed events.

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.

Visualizing and Clustering Protein Similarity Networks: Sequences, Structures, and Functions.

PubMed

Mai, Te-Lun; Hu, Geng-Ming; Chen, Chi-Ming

2016-07-01

Research in the recent decade has demonstrated the usefulness of protein network knowledge in furthering the study of molecular evolution of proteins, understanding the robustness of cells to perturbation, and annotating new protein functions. In this study, we aimed to provide a general clustering approach to visualize the sequence-structure-function relationship of protein networks, and investigate possible causes for inconsistency in the protein classifications based on sequences, structures, and functions. Such visualization of protein networks could facilitate our understanding of the overall relationship among proteins and help researchers comprehend various protein databases. As a demonstration, we clustered 1437 enzymes by their sequences and structures using the minimum span clustering (MSC) method. The general structure of this protein network was delineated at two clustering resolutions, and the second level MSC clustering was found to be highly similar to existing enzyme classifications. The clustering of these enzymes based on sequence, structure, and function information is consistent with each other. For proteases, the Jaccard's similarity coefficient is 0.86 between sequence and function classifications, 0.82 between sequence and structure classifications, and 0.78 between structure and function classifications. From our clustering results, we discussed possible examples of divergent evolution and convergent evolution of enzymes. Our clustering approach provides a panoramic view of the sequence-structure-function network of proteins, helps visualize the relation between related proteins intuitively, and is useful in predicting the structure and function of newly determined protein sequences.

Prokaryotic ancestry of eukaryotic protein networks mediating innate immunity and apoptosis.

PubMed

Dunin-Horkawicz, Stanislaw; Kopec, Klaus O; Lupas, Andrei N

2014-04-03

Protein domains characteristic of eukaryotic innate immunity and apoptosis have many prokaryotic counterparts of unknown function. By reconstructing interactomes computationally, we found that bacterial proteins containing these domains are part of a network that also includes other domains not hitherto associated with immunity. This network is connected to the network of prokaryotic signal transduction proteins, such as histidine kinases and chemoreceptors. The network varies considerably in domain composition and degree of paralogy, even between strains of the same species, and its repetitive domains are often amplified recently, with individual repeats sharing up to 100% sequence identity. Both phenomena are evidence of considerable evolutionary pressure and thus compatible with a role in the "arms race" between host and pathogen. In order to investigate the relationship of this network to its eukaryotic counterparts, we performed a cluster analysis of organisms based on a census of its constituent domains across all fully sequenced genomes. We obtained a large central cluster of mainly unicellular organisms, from which multicellular organisms radiate out in two main directions. One is taken by multicellular bacteria, primarily cyanobacteria and actinomycetes, and plants form an extension of this direction, connected via the basal, unicellular cyanobacteria. The second main direction is taken by animals and fungi, which form separate branches with a common root in the α-proteobacteria of the central cluster. This analysis supports the notion that the innate immunity networks of eukaryotes originated from their endosymbionts and that increases in the complexity of these networks accompanied the emergence of multicellularity. Copyright © 2014 The Authors. Published by Elsevier Ltd.. All rights reserved.

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.

Sejong Open Cluster Survey (SOS). 0. Target Selection and Data Analysis

NASA Astrophysics Data System (ADS)

Sung, Hwankyung; Lim, Beomdu; Bessell, Michael S.; Kim, Jinyoung S.; Hur, Hyeonoh; Chun, Moo-Young; Park, Byeong-Gon

2013-06-01

Star clusters are superb astrophysical laboratories containing cospatial and coeval samples of stars with similar chemical composition. We initiate the Sejong Open cluster Survey (SOS) - a project dedicated to providing homogeneous photometry of a large number of open clusters in the SAAO Johnson-Cousins' UBVI system. To achieve our main goal, we pay much attention to the observation of standard stars in order to reproduce the SAAO standard system. Many of our targets are relatively small sparse clusters that escaped previous observations. As clusters are considered building blocks of the Galactic disk, their physical properties such as the initial mass function, the pattern of mass segregation, etc. give valuable information on the formation and evolution of the Galactic disk. The spatial distribution of young open clusters will be used to revise the local spiral arm structure of the Galaxy. In addition, the homogeneous data can also be used to test stellar evolutionary theory, especially concerning rare massive stars. In this paper we present the target selection criteria, the observational strategy for accurate photometry, and the adopted calibrations for data analysis such as color-color relations, zero-age main sequence relations, Sp - M_V relations, Sp - T_{eff} relations, Sp - color relations, and T_{eff} - BC relations. Finally we provide some data analysis such as the determination of the reddening law, the membership selection criteria, and distance determination.

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

NASA Astrophysics Data System (ADS)

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

2013-09-01

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

Applications of graph theory in protein structure identification

PubMed Central

2011-01-01

There is a growing interest in the identification of proteins on the proteome wide scale. Among different kinds of protein structure identification methods, graph-theoretic methods are very sharp ones. Due to their lower costs, higher effectiveness and many other advantages, they have drawn more and more researchers’ attention nowadays. Specifically, graph-theoretic methods have been widely used in homology identification, side-chain cluster identification, peptide sequencing and so on. This paper reviews several methods in solving protein structure identification problems using graph theory. We mainly introduce classical methods and mathematical models including homology modeling based on clique finding, identification of side-chain clusters in protein structures upon graph spectrum, and de novo peptide sequencing via tandem mass spectrometry using the spectrum graph model. In addition, concluding remarks and future priorities of each method are given. PMID:22165974

Whole Genome Sequencing Demonstrates Limited Transmission within Identified Mycobacterium tuberculosis Clusters in New South Wales, Australia

PubMed Central

Gurjav, Ulziijargal; Outhred, Alexander C.; Jelfs, Peter; McCallum, Nadine; Wang, Qinning; Hill-Cawthorne, Grant A.; Marais, Ben J.; Sintchenko, Vitali

2016-01-01

Australia has a low tuberculosis incidence rate with most cases occurring among recent immigrants. Given suboptimal cluster resolution achieved with 24-locus mycobacterium interspersed repetitive unit (MIRU-24) genotyping, the added value of whole genome sequencing was explored. MIRU-24 profiles of all Mycobacterium tuberculosis culture-confirmed tuberculosis cases diagnosed between 2009 and 2013 in New South Wales (NSW), Australia, were examined and clusters identified. The relatedness of cases within the largest MIRU-24 clusters was assessed using whole genome sequencing and phylogenetic analyses. Of 1841 culture-confirmed TB cases, 91.9% (1692/1841) had complete demographic and genotyping data. East-African Indian (474; 28.0%) and Beijing (470; 27.8%) lineage strains predominated. The overall rate of MIRU-24 clustering was 20.1% (340/1692) and was highest among Beijing lineage strains (35.7%; 168/470). One Beijing and three East-African Indian (EAI) clonal complexes were responsible for the majority of observed clusters. Whole genome sequencing of the 4 largest clusters (30 isolates) demonstrated diverse single nucleotide polymorphisms (SNPs) within identified clusters. All sequenced EAI strains and 70% of Beijing lineage strains clustered by MIRU-24 typing demonstrated distinct SNP profiles. The superior resolution provided by whole genome sequencing demonstrated limited M. tuberculosis transmission within NSW, even within identified MIRU-24 clusters. Routine whole genome sequencing could provide valuable public health guidance in low burden settings. PMID:27737005

The Problem of Hipparcos Distances to Open Clusters. Report 1; Constraints from Multicolor a Main-Sequence Fitting

NASA Technical Reports Server (NTRS)

Pinsonneault, Marc H.; Stauffer, John; Soderblom, David R.; King, Jeremy R.; Hanson, Robert B.

1998-01-01

Parallax data from the Hipparcos mission allow the direct distance to open clusters to be compared with the distance inferred from main-sequence (MS) fitting. There are surprising differences between the two distance measurements. indicating either the need for changes in the cluster compositions or reddening, underlying problems with the technique of MS fitting, or systematic errors in the Hipparcos parallaxes at the 1 mas level. We examine the different possibilities, focusing on MS fitting in both metallicity-sensitive B-V and metallicity-insensitive V-I for five well-studied systems (the Hyades, Pleiades, alpha Per, Praesepe, and Coma Ber). The Hipparcos distances to the Hyades and alpha Per are within 1 sigma of the MS-fitting distance in B-V and V-I, while the Hipparcos distances to Coma Ber and the Pleiades are in disagreement with the MS-fitting distance at more than the 3 sigma level. There are two Hipparcos measurements of the distance to Praesepe; one is in good agreement with the MS-fitting distance and the other disagrees at the 2 sigma level. The distance estimates from the different colors are in conflict with one another for Coma but in agreement for the Pleiades. Changes in the relative cluster metal abundances, age related effects, helium, and reddening are shown to be unlikely to explain the puzzling behavior of the Pleiades. We present evidence for spatially dependent systematic errors at the 1 mas level in the parallaxes of Pleiades stars. The implications of this result are discussed.

DEBRIS DISKS OF MEMBERS OF THE BLANCO 1 OPEN CLUSTER

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

Stauffer, John R.; Noriega-Crespo, Alberto; Rebull, Luisa M.

2010-08-20

We have used the Spitzer Space Telescope to obtain Multiband Imaging Photometer for Spitzer (MIPS) 24 {mu}m photometry for 37 members of the {approx}100 Myr old open cluster Blanco 1. For the brightest 25 of these stars (where we have 3{sigma} uncertainties less than 15%), we find significant mid-IR excesses for eight stars, corresponding to a debris disk detection frequency of about 32%. The stars with excesses include two A stars, four F dwarfs, and two G dwarfs. The most significant linkage between 24 {mu}m excess and any other stellar property for our Blanco 1 sample of stars is withmore » binarity. Blanco 1 members that are photometric binaries show few or no detected 24 {mu}m excesses whereas a quarter of the apparently single Blanco 1 members do have excesses. We have examined the MIPS data for two other clusters of similar age to Blanco 1-NGC 2547 and the Pleiades. The AFGK photometric binary star members of both of these clusters also show a much lower frequency of 24 {mu}m excesses compared to stars that lie near the single-star main sequence. We provide a new determination of the relation between the V - K {sub s} color and K {sub s} - [24] color for main sequence photospheres based on Hyades members observed with MIPS. As a result of our analysis of the Hyades data, we identify three low mass Hyades members as candidates for having debris disks near the MIPS detection limit.« less

THE HUBBLE SPACE TELESCOPE UV LEGACY SURVEY OF GALACTIC GLOBULAR CLUSTERS: THE INTERNAL KINEMATICS OF THE MULTIPLE STELLAR POPULATIONS IN NGC 2808

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

Bellini, A.; Anderson, J.; Marel, R. P. van der

2015-09-01

Numerous observational studies have revealed the ubiquitous presence of multiple stellar populations in globular clusters and cast many difficult challenges for the study of the formation and dynamical history of these stellar systems. In this Letter we present the results of a study of the kinematic properties of multiple populations in NGC 2808 based on high-precision Hubble Space Telescope proper-motion measurements. In a recent study, Milone et al. identified five distinct populations (A–E) in NGC 2808. Populations D and E coincide with the helium-enhanced populations in the middle and the blue main sequences (mMS and bMS) previously discovered by Piottomore » et al.; populations A–C correspond to the redder main sequence that, in Piotto et al., was associated with the primordial stellar population. Our analysis shows that, in the outermost regions probed (between about 1.5 and 2 times the cluster half-light radius), the velocity distribution of populations D and E is radially anisotropic (the deviation from an isotropic distribution is significant at the ∼3.5σ level). Stars of populations D and E have a smaller tangential velocity dispersion than those of populations A–C, while no significant differences are found in the radial velocity dispersion. We present the results of a numerical simulation showing that the observed differences between the kinematics of these stellar populations are consistent with the expected kinematic fingerprint of the diffusion toward the cluster outer regions of stellar populations initially more centrally concentrated.« less

Two haplotype clusters of Echinococcus granulosus sensu stricto in northern Iraq (Kurdistan region) support the hypothesis of a parasite cradle in the Middle East.

PubMed

Hassan, Zuber Ismael; Meerkhan, Azad Abdullah; Boufana, Belgees; Hama, Abdullah A; Ahmed, Bayram Dawod; Mero, Wijdan Mohammed Salih; Orsten, Serra; Interisano, Maria; Pozio, Edoardo; Casulli, Adriano

2017-08-01

Human cystic echinococcosis (CE) caused by Echinococcus granulosus s.s. is a major public health problem in Iraqi Kurdistan with a reported surgical incidence of 6.3 per 100,000 Arbil inhabitants. A total of 125 Echinococcus isolates retrieved from sheep, goats and cattle were used in this study. Our aim was to determine species/genotypes infecting livestock in Iraqi Kurdistan and examine intraspecific variation and population structure of Echinococcus granulosus s.s. in this region and relate it to that of other regions worldwide. Using nucleotide sequences of the mitochondrial cytochrome c oxidase subunit 1 (cox 1) we identified E. granulosus s.s. as the cause of hydatidosis in all examined animals. The haplotype network displayed a double-clustered topology with two main E. granulosus s.s. haplotypes, (KU05) and (KU33). The 'founder' haplotype (KU05) confirmed the presence of a common lineage of non-genetically differentiated populations as inferred by the low non-significant fixation index values. Overall diversity and neutrality indices indicated demographic expansion. We used E. granulosus s.s. nucleotide sequences from GenBank to draw haplotype networks for the Middle East (Iran, Jordan and Turkey), Europe (Albania, Greece, Italy, Romania and Spain), China, Mongolia, Russia, South America (Argentina, Brazil, Chile and Mexico) and Tunisia. Networks with two haplotype clusters like that reported here for Iraqi Kurdistan were seen for the Middle East, Europe, Mongolia, Russia and Tunisia using both 827bp and 1609bp cox1 nucleotide sequences, whereas a star-like network was observed for China and South America. We hypothesize that the double clustering seen at what is generally assumed to be the cradle of domestication may have emerged independently and dispersed from the Middle East to other regions and that haplotype (KU33) may be the main haplotype within a second cluster in the Middle East from where it has spread into Europe, Mongolia, Russia and North Africa. Further studies using metacestodes of human origin are required to investigate the biological importance of E. granulosus s.s. haplotypes/clusters and their association, if any with clinical manifestations of CE infection. Copyright © 2017 Elsevier B.V. All rights reserved.

Mutiple Stellar Populations in Blanco DECam Bulge Survey Globular Clusters

NASA Astrophysics Data System (ADS)

Miller, Doryan; Pilachowski, C. A.; Johnson, C. I.; Rich, R. Michael; Clarkson, William I.; Young, M.; Michael, S.

2018-01-01

Preliminary SDSS ugrizY photometric observations of globular cluster stars included in the Blanco DECam Bulge Survey (BDBS) were examined to determine the suitability of these data to characterize stellar populations within clusters. The BDBS fields include around two dozen globular clusters, including the iron-complex cluster M22 and the pulsar-rich cluster Terzan 5. Many globular clusters show evidence for multiple stellar populations as a spread in the u-g color of stars in a given phase of stellar evolution, and in some clusters, the populations have different radial distributions. BDBS clusters with low and/or non-variable reddening and long dynamical mixing time scales were selected for study, and photometry for RGB and main sequence stars within two half-light radii from the center of each cluster was extracted from the BDBS preliminary catalog. Field contamination was reduced in each candidate cluster by removing all stars more than a tenth of a magnitude from the best-fit fiducial curves following the g-r vs r color-magnitude diagram. The remaining stars were split into separate populations based on u-g color, and effective cumulative distribution functions vs. half-light radius were compared to identify differences in the populations’ radial distributions.

Primordial black holes in globular clusters

NASA Technical Reports Server (NTRS)

Sigurdsson, Steinn; Hernquist, Lars

1993-01-01

It has recently been recognized that significant numbers of medium-mass back holes (of order 10 solar masses) should form in globular clusters during the early stages of their evolution. Here we explore the dynamical and observational consequences of the presence of such a primordial black-hole population in a globular cluster. The holes initially segregate to the cluster cores, where they form binary and multiple black-hole systems. The subsequent dynamical evolution of the black-hole population ejects most of the holes on a relatively short timescale: a typical cluster will retain between zero and four black holes in its core, and possibly a few black holes in its halo. The presence of binary, triple, and quadruple black-hole systems in cluster cores will disrupt main-sequence and giant stellar binaries; this may account for the observed anomalies in the distribution of binaries in globular clusters. Furthermore, tidal interactions between a multiple black-hole system and a red giant star can remove much of the red giant's stellar envelope, which may explain the puzzling absence of larger red giants in the cores of some very dense clusters.

Accreting Black Hole Binaries in Globular Clusters

NASA Astrophysics Data System (ADS)

Kremer, Kyle; Chatterjee, Sourav; Rodriguez, Carl L.; Rasio, Frederic A.

2018-01-01

We explore the formation of mass-transferring binary systems containing black holes (BHs) within globular clusters (GC). We show that it is possible to form mass-transferring BH binaries with main sequence, giant, and white dwarf companions with a variety of orbital parameters in GCs spanning a large range in present-day properties. All mass-transferring BH binaries found in our models at late times are dynamically created. The BHs in these systems experienced a median of ∼30 dynamical encounters within the cluster before and after acquiring the donor. Furthermore, we show that the presence of mass-transferring BH systems has little correlation with the total number of BHs within the cluster at any time. This is because the net rate of formation of BH–non-BH binaries in a cluster is largely independent of the total number of retained BHs. Our results suggest that the detection of a mass-transferring BH binary in a GC does not necessarily indicate that the host cluster contains a large BH population.

Low-luminosity stellar mass functions in globular clusters

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

Richer, H.B.; Fahlman, G.G.; Buonanno, R.

New data are presented on cluster luminosity functions and mass functions for selected fields in the globular clusters M13 and M71, extending down the main sequence to at least 0.2 solar mass. In this experiment, CCD photometry data were obtained at the prime focus of the CFHT on the cluster fields that were far from the cluster center. Luminosity functions were constructed, using the ADDSTAR routine to correct for the background, and mass functions were derived using the available models. The mass functions obtained for M13 and M71 were compared to existing data for NGC 6397. Results show that (1)more » all three globular clusters display a marked change in slope at about 0.4 solar mass, with the slopes becoming considerably steeper toward lower masses; (2) there is no correlation between the slope of the mass function and metallicity; and (3) the low-mass slope of the mass function for M13 is much steeper than for NGC 6397 and M71. 22 refs.« less

Characteristics of the Variable Star P Cygni Determined from Cluster Membership

NASA Technical Reports Server (NTRS)

Turner, David G.; Welch, Gary; Graham, Marianne; Fairweather, David; Horsford, Andrew; Seymour, Michael; Feibelman, Walter; Fisher, Richard (Technical Monitor)

2001-01-01

Empirical information on the luminosity, reddening, age, and mass of the variable B2 Oe supergiant P Cygni is derived from its assumed membership in the sparse anonymous cluster on which it is projected, as well as its association with the spatially adjacent cluster IC 4996, which forms a double cluster with the P Cyg cluster. Evidence for the high luminosity of P Cyg is confirmed by its derived absolute magnitude of M(sub V)= -8.46 +/- 0.03, which translates to log (L/L(sun)) = 5.54 +/- 0.02 for an effective temperature consistent with the star's derived space reddening (E(sub B-V) = 0.53 +/- 0.02). More surprising is an age for the associated clusters of 6 (+/- 1.5) x 10(exp 6) years, corresponding to a turnoff point mass of 25.1 (+/- 5.5) M(sun). By inference, P Cygni, as a post main-sequence object, should have a mass of no more than approximately 23-35 M(sun).

Improved efficiency in amplification of Escherichia coli o-antigen gene clusters using genome-wide sequence comparison

USDA-ARS?s Scientific Manuscript database

Background: In many bacteria including E. coli, genes encoding O-antigens are clustered in the chromosome, with a 39-bp JUMPstart sequence and gnd gene located upstream and downstream of the cluster, respectively. For determining the DNA sequence of the E. coli O-antigen gene cluster, one set of P...

Low-resolution spectroscopy of main sequence stars belonging to 12 Galactic globular clusters. I. CH and CN band strength variations

NASA Astrophysics Data System (ADS)

Pancino, E.; Rejkuba, M.; Zoccali, M.; Carrera, R.

2010-12-01

Context. Globular clusters show star-to-star abundance variations for light elements that are not yet well understood. The preferred explanation involves a self-enrichment scenario, within which two subsequent generations of stars co-exist in globular clusters. Observations of chemical abundances in the main sequence and sub-giant branch stars allow us to investigate the signature of this chemically processed material without the complicating effects caused by stellar evolution and internal mixing. Aims: Our main goal is to investigate the carbon-nitrogen anti-correlation with low-resolution spectroscopy of 20-50 stars fainter than the first dredge-up in seven Galactic globular clusters (NGC 288, NGC 1851, NGC 5927, NGC 6352, NGC 6388, and Pal 12) with different properties. We complemented our observations with 47 Tuc archival data, with four additional clusters from the literature (M 15, M 22, M 55, NGC 362), and with additional literature data on NGC 288. Methods: In this first paper, we measured the strengh of the CN and CH band indices, which correlate with the N and C abundances, and we investigated the anti-correlation and bimodality of these indices. We compared rCN, the ratio of stars belonging to the CN-strong and weak groups, with 15 different cluster parameters. Results: We clearly see bimodal anti-correlation of the CH and CN band stregths in the metal-rich clusters (Pal 12, 47 Tuc, NGC 6352, NGC 5927). Only M 15 among the metal-poor clusters shows a clearly bimodal anti-correlation. We found weak correlations (sligthly above 1σ) of rCN with the cluster orbital parameters, present-day total mass, cluster concentration, and age. Conclusions: Our findings support the self-enrichment scenario, and suggest that the occurrence of more than two major generations of stars in a GGC should be rare. Small additional generations (<10-20% of the total) would be difficult to detect with our samples. The first generation, which corresponds to the CN-weak stars, usually contains more stars than the second one ( = 0.82±0.29), as opposed to results based on the Na-O anti-correlations. Based on FORS observations collected at the European Southern Observatory, Chile, within the observing programs 68.D-0510 and 69.D-0056. Also based on data obtained from the ESO Archive, within the observing program 67.D-0153.Complete Table 2 is 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/524/A44

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

NASA Astrophysics Data System (ADS)

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

2017-06-01

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

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

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

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

IMPLICATIONS OF RAPID CORE ROTATION IN RED GIANTS FOR INTERNAL ANGULAR MOMENTUM TRANSPORT IN STARS

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

Tayar, Jamie; Pinsonneault, Marc H., E-mail: tayar.1@osu.edu

2013-09-20

Core rotation rates have been measured for red giant stars using asteroseismology. These data, along with helioseismic measurements and open cluster spin-down studies, provide powerful clues about the nature and timescale for internal angular momentum transport in stars. We focus on two cases: the metal-poor red giant KIC 7341231 ({sup O}tto{sup )} and intermediate-mass core helium burning stars. For both, we examine limiting case studies for angular momentum coupling between cores and envelopes under the assumption of rigid rotation on the main sequence. We discuss the expected pattern of core rotation as a function of mass and radius. In themore » case of Otto, strong post-main-sequence coupling is ruled out and the measured core rotation rate is in the range of 23-33 times the surface value expected from standard spin-down models. The minimum coupling timescale (0.17-0.45 Gyr) is significantly longer than that inferred for young open cluster stars. This implies ineffective internal angular momentum transport in early first ascent giants. By contrast, the core rotation rates of evolved secondary clump stars are found to be consistent with strong coupling given their rapid main-sequence rotation. An extrapolation to the white dwarf regime predicts rotation periods between 330 and 0.0052 days, depending on mass and decoupling time. We identify two key ingredients that explain these features: the presence of a convective core and inefficient angular momentum transport in the presence of larger mean molecular weight gradients. Observational tests that can disentangle these effects are discussed.« less

A segmentation method for lung nodule image sequences based on superpixels and density-based spatial clustering of applications with noise

PubMed Central

Zhang, Wei; Zhang, Xiaolong; Qiang, Yan; Tian, Qi; Tang, Xiaoxian

2017-01-01

The fast and accurate segmentation of lung nodule image sequences is the basis of subsequent processing and diagnostic analyses. However, previous research investigating nodule segmentation algorithms cannot entirely segment cavitary nodules, and the segmentation of juxta-vascular nodules is inaccurate and inefficient. To solve these problems, we propose a new method for the segmentation of lung nodule image sequences based on superpixels and density-based spatial clustering of applications with noise (DBSCAN). First, our method uses three-dimensional computed tomography image features of the average intensity projection combined with multi-scale dot enhancement for preprocessing. Hexagonal clustering and morphological optimized sequential linear iterative clustering (HMSLIC) for sequence image oversegmentation is then proposed to obtain superpixel blocks. The adaptive weight coefficient is then constructed to calculate the distance required between superpixels to achieve precise lung nodules positioning and to obtain the subsequent clustering starting block. Moreover, by fitting the distance and detecting the change in slope, an accurate clustering threshold is obtained. Thereafter, a fast DBSCAN superpixel sequence clustering algorithm, which is optimized by the strategy of only clustering the lung nodules and adaptive threshold, is then used to obtain lung nodule mask sequences. Finally, the lung nodule image sequences are obtained. The experimental results show that our method rapidly, completely and accurately segments various types of lung nodule image sequences. PMID:28880916

Self-Organizing Hidden Markov Model Map (SOHMMM): Biological Sequence Clustering and Cluster Visualization.

PubMed

Ferles, Christos; Beaufort, William-Scott; Ferle, Vanessa

2017-01-01

The present study devises mapping methodologies and projection techniques that visualize and demonstrate biological sequence data clustering results. The Sequence Data Density Display (SDDD) and Sequence Likelihood Projection (SLP) visualizations represent the input symbolical sequences in a lower-dimensional space in such a way that the clusters and relations of data elements are depicted graphically. Both operate in combination/synergy with the Self-Organizing Hidden Markov Model Map (SOHMMM). The resulting unified framework is in position to analyze automatically and directly raw sequence data. This analysis is carried out with little, or even complete absence of, prior information/domain knowledge.

Defining objective clusters for rabies virus sequences using affinity propagation clustering

PubMed Central

Fischer, Susanne; Freuling, Conrad M.; Pfaff, Florian; Bodenhofer, Ulrich; Höper, Dirk; Fischer, Mareike; Marston, Denise A.; Fooks, Anthony R.; Mettenleiter, Thomas C.; Conraths, Franz J.; Homeier-Bachmann, Timo

2018-01-01

Rabies is caused by lyssaviruses, and is one of the oldest known zoonoses. In recent years, more than 21,000 nucleotide sequences of rabies viruses (RABV), from the prototype species rabies lyssavirus, have been deposited in public databases. Subsequent phylogenetic analyses in combination with metadata suggest geographic distributions of RABV. However, these analyses somewhat experience technical difficulties in defining verifiable criteria for cluster allocations in phylogenetic trees inviting for a more rational approach. Therefore, we applied a relatively new mathematical clustering algorythm named ‘affinity propagation clustering’ (AP) to propose a standardized sub-species classification utilizing full-genome RABV sequences. Because AP has the advantage that it is computationally fast and works for any meaningful measure of similarity between data samples, it has previously been applied successfully in bioinformatics, for analysis of microarray and gene expression data, however, cluster analysis of sequences is still in its infancy. Existing (516) and original (46) full genome RABV sequences were used to demonstrate the application of AP for RABV clustering. On a global scale, AP proposed four clusters, i.e. New World cluster, Arctic/Arctic-like, Cosmopolitan, and Asian as previously assigned by phylogenetic studies. By combining AP with established phylogenetic analyses, it is possible to resolve phylogenetic relationships between verifiably determined clusters and sequences. This workflow will be useful in confirming cluster distributions in a uniform transparent manner, not only for RABV, but also for other comparative sequence analyses. PMID:29357361

Late-Type Membership of the Open Cluster NGC 2232

NASA Technical Reports Server (NTRS)

Orban, Chris; Patten, Brian

2004-01-01

NGC 2232 is one of the nearest open clusters (approx.360 pc) with an age of approx.25 Myr. This places it in the unique position to study the transition from T Tauri activity to the Zero Age Main Sequence. In order for those studies to begin, late-type members must be identified for the cluster. X-ray observations combined with ground-based photometry and spectroscopy offers the best way to accomplish this goal. We present photometry in the VRI bands, 2MASS near-infrared measurements in the J, H , Ks bands and spectra for the suspected optical counterparts to the X-ray sources in the field of NGC 2232. 46 candidate members were identified through these efforts ranging from F5 to M5.

Genomic characterization and expression analysis of four apolipoprotein A-IV paralogs in Senegalese sole (Solea senegalensis Kaup).

PubMed

Roman-Padilla, J; Rodríguez-Rua, A; Claros, M G; Hachero-Cruzado, I; Manchado, M

2016-01-01

The apolipoprotein A-IV (ApoA-IV) plays a key role in lipid transport and feed intake regulation. In this work, four cDNA sequences encoding ApoA-IV paralogs were identified. Sequence analysis revealed conserved structural features including the common 33-codon block and nine repeated motifs. Gene structure analysis identified four exons and three introns except for apoA-IVAa1 (with only 3 exons). Synteny analysis showed that the four paralogs were structured into two clusters (cluster A containing apoA-IVAa1 and apoA-IVAa2 and cluster B with apoA-IVBa3 and apoA-IVBa4) linked to an apolipoprotein E. Phylogenetic analysis clearly separated the paralogs according to their cluster organization as well as revealed four subclades highly conserved in Acanthopterygii. Whole-mount analyses (WISH) in early larvae (0 and 1day post-hatch (dph)) showed that the four paralogs were mainly expressed in yolk syncytial layer surrounding the oil globules. Later, at 3 and 5dph, the four paralogs were mainly expressed in liver and intestine although with differences in their relative abundance and temporal expression patterns. Diet supply triggered the intensity of WISH signals in the intestine of the four paralogs. Quantification of mRNA abundance by qPCR using whole larvae only detected the induction by diet at 5dph. Moreover, transcript levels increased progressively with age except for apoA-IVAa2, which appeared as a low-expressed isoform. Expression analysis in juvenile tissues confirmed that the four paralogs were mainly expressed in liver and intestine and secondary in other tissues. The role of these ApoA-IV genes in lipid transport and the possible role of apoA-IVAa2 as a regulatory form are discussed. Copyright © 2015 Elsevier Inc. All rights reserved.

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

PubMed

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

2002-12-01

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

Eruptive history of the Ubehebe Crater cluster, Death Valley, California

NASA Astrophysics Data System (ADS)

Fierstein, Judy; Hildreth, Wes

2017-04-01

A sequence of late Holocene eruptions from the Ubehebe Crater cluster in Death Valley was short-lived, emplacing several phreatomagmatic and magmatic deposits. Seven craters form the main group, which erupted along a north-south alignment 1.5 km long. At least five more make a 500-m east-west alignment west of the main crater group. One more is an isolated shallow crater 400 m south of that alignment. All erupted through Miocene fanglomerate and sandstone, which are now distributed as comminuted matrix and lithic clasts in all Ubehebe deposits. Stratigraphic evidence showing that all Ubehebe strata were emplaced within a short time interval includes: (1) deposits from the many Ubehebe vents make a multi-package sequence that conformably drapes paleo-basement topography with no erosive gullying between emplacement units; (2) several crater rims that formed early in the eruptive sequence are draped smoothly by subsequent deposits; and (3) tack-welded to agglutinated spatter and bombs that erupted at various times through the sequence remained hot enough to oxidize the overlying youngest emplacement package. In addition, all deposits sufficiently consolidated to be drilled yield reliable paleomagnetic directions, with site mean directions showing no evidence of geomagnetic secular variation. Chemical analyses of juvenile components representing every eruptive package yield a narrow range in major elements [SiO2 (48.65-50.11); MgO (4.98-6.23); K2O (2.24-2.39)] and trace elements [Rb (28-33); Sr (1513-1588); Zr (373-404)]. Despite lithologic similarities, individual fall units can be traced outward from vent by recording layer thicknesses, maximum scoria and lithic sizes, and juvenile clast textural variations. This permits reconstruction of the eruptive sequence, which produced a variety of eruptive styles. The largest and northernmost of the craters, Ubehebe Crater, is the youngest of the group. Its largely phreatomagmatic deposits drape all of the others, thicken in paleogullies and thin over several newly created crater rims. Evidence in-hand virtually requires that the Ubehebe cluster of craters erupted over a brief time interval, not protracted over centuries.

On the physical nature of six galactic open cluster candidates

NASA Astrophysics Data System (ADS)

Piatti, A. E.; Clariá, J. J.; Ahumada, A. V.

We present CCD UBVI_(KC) photometry in the fields of the unstudied open cluster (OC) candidates Haffner 3, Haffner 5, NGC 2368, Haffner 25, Hogg 3 and Hogg 4. Our analysis shows that none of these objects are genuine OCs since no clear main sequences or other typical features can be seen in their colour-magnitude and colour-colour diagrams. Star counts performed within and outside the OC candidate fields not only support these results but also suggest that these objects are not OC remnants. A detailed version of this work can be seen in New Astronomy, 16, 161 (2011).

Characterization of the Praesepe Star Cluster by Photometry and Proper Motions With 2MASS, PPMXL, and Pan-STARRS

DTIC Science & Technology

2014-03-20

reserved. Printed in the U.S.A. CHARACTERIZATION OF THE PRAESEPE STAR CLUSTER BY PHOTOMETRY AND PROPER MOTIONS WITH 2MASS , PPMXL, AND Pan-STARRS P. F. Wang1... 2MASS ) and the Sloan Digital Sky Survey (SDSS) data, covering a sky area of 100 deg2, Adams et al. (2002) extended the lower main sequence to 0.1M, and...incompleteness is caused by the detection limits of USNO-B1 and 2MASS . Recently, Khalaj & Baumgardt (2013) used SDSS and PPMXL data to characterize

Evaluation of genetic diversity in Chinese kale (Brassica oleracea L. var. alboglabra Bailey) by using rapid amplified polymorphic DNA and sequence-related amplified polymorphism markers.

PubMed

Zhang, J; Zhang, L G

2014-02-14

Chinese kale is an original Chinese vegetable of the Cruciferae family. To select suitable parents for hybrid breeding, we thoroughly analyzed the genetic diversity of Chinese kale. Random amplified polymorphic DNA (RAPD) and sequence-related amplified polymorphism (SRAP) molecular markers were used to evaluate the genetic diversity across 21 Chinese kale accessions from AVRDC and Guangzhou in China. A total of 104 bands were detected by 11 RAPD primers, of which 66 (63.5%) were polymorphic, and 229 polymorphic bands (68.4%) were observed in 335 bands amplified by 17 SRAP primer combinations. The dendrogram showed the grouping of the 21 accessions into 4 main clusters based on RAPD data, and into 6 clusters based on SRAP and combined data (RAPD + SRAP). The clustering of accessions based on SRAP data was consistent with petal colors. The Mantel test indicated a poor fit for the RAPD and SRAP data (r = 0.16). These results have an important implication for Chinese kale germplasm characterization and improvement.

3D Micro-tomography on Aggregates from the 2014- 2015 Eruption of Hunga Tonga-Hunga Ha'apai Volcano

NASA Astrophysics Data System (ADS)

Colombier, M.; Scheu, B.; Cronin, S. J.; Tost, M.; Dobson, K. J.; Dingwell, D. B.

2016-12-01

In December 2014- January 2015, a surtseyan eruption at Hunga Tonga-Hunga Ha'apai volcano (Tonga) formed a new island. Three main eruptive phases were distinguished by observation and deposits: (i) mound and cone construction, involving collapse of 300-600 m-high wet tephra jets, grain flows, slope-remobilisation and energetic surges, with little or no convective plume (ii) The upper cone-building phase with lower jets (mainly <300 m) but greater ash production (weak, steam-rich plumes to 6 km) and weak surges, and (iii) final phase with weak surge, fall and ballistic deposits with more vesicular pyroclasts producing proximal capping deposits. Most sampled deposits contain ash, lapilli and bombs, and lapilli-sized aggregates are ubiquitous. We used high-resolution 3D X-ray microcomputed tomography (XCT) to quantify the grain size distribution (GSD) and porosity by sampling multiple stratigraphic units within the main eruptive sequences. We visualized and quantified the internal structure of the aggregates to understand the evolution of this surtseyan eruption. We present here an overview of the textural information: porosity, vesicle size distribution and morphology as well as the variability of the aggregation features. Aggregates from the fall deposits of the early wet phase are mostly loosely packed, poorly-structured ash clusters. Aggregates from the early surge sequence and the main cone building phase dominantly exhibit a central particle coated by ash cluster material. Vesicles in the particles from the early fall deposits tend to be smaller and more isolated than in the particles from the surge sequence and the main cone building phase. The GSD of aggregates obtained by XCT is highly valuable to correct the total GSD of volcaniclastic deposits. The strong variations in the aggregation features across the eruption suggest a range of different formation and deposition mechanisms related to varying degrees of magma-water-interaction, which changed the morphology and textural properties of the individual particles.

Approximation algorithm for the problem of partitioning a sequence into clusters

NASA Astrophysics Data System (ADS)

Kel'manov, A. V.; Mikhailova, L. V.; Khamidullin, S. A.; Khandeev, V. I.

2017-08-01

We consider the problem of partitioning a finite sequence of Euclidean points into a given number of clusters (subsequences) using the criterion of the minimal sum (over all clusters) of intercluster sums of squared distances from the elements of the clusters to their centers. It is assumed that the center of one of the desired clusters is at the origin, while the center of each of the other clusters is unknown and determined as the mean value over all elements in this cluster. Additionally, the partition obeys two structural constraints on the indices of sequence elements contained in the clusters with unknown centers: (1) the concatenation of the indices of elements in these clusters is an increasing sequence, and (2) the difference between an index and the preceding one is bounded above and below by prescribed constants. It is shown that this problem is strongly NP-hard. A 2-approximation algorithm is constructed that is polynomial-time for a fixed number of clusters.

The Bologna Annotation Resource (BAR 3.0): improving protein functional annotation

PubMed Central

Casadio, Rita

2017-01-01

Abstract BAR 3.0 updates our server BAR (Bologna Annotation Resource) for predicting protein structural and functional features from sequence. We increase data volume, query capabilities and information conveyed to the user. The core of BAR 3.0 is a graph-based clustering procedure of UniProtKB sequences, following strict pairwise similarity criteria (sequence identity ≥40% with alignment coverage ≥90%). Each cluster contains the available annotation downloaded from UniProtKB, GO, PFAM and PDB. After statistical validation, GO terms and PFAM domains are cluster-specific and annotate new sequences entering the cluster after satisfying similarity constraints. BAR 3.0 includes 28 869 663 sequences in 1 361 773 clusters, of which 22.2% (22 241 661 sequences) and 47.4% (24 555 055 sequences) have at least one validated GO term and one PFAM domain, respectively. 1.4% of the clusters (36% of all sequences) include PDB structures and the cluster is associated to a hidden Markov model that allows building template-target alignment suitable for structural modeling. Some other 3 399 026 sequences are singletons. BAR 3.0 offers an improved search interface, allowing queries by UniProtKB-accession, Fasta sequence, GO-term, PFAM-domain, organism, PDB and ligand/s. When evaluated on the CAFA2 targets, BAR 3.0 largely outperforms our previous version and scores among state-of-the-art methods. BAR 3.0 is publicly available and accessible at http://bar.biocomp.unibo.it/bar3. PMID:28453653

An improved determination of the lithium depletion boundary age of Blanco 1 and a first look on the effects of magnetic activity

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

Juarez, Aaron J.; Stassun, Keivan G.; Cargile, Phillip A.

2014-11-10

The lithium depletion boundary (LDB) is a robust method for accurately determining the ages of young clusters, but most pre-main-sequence models used to derive LDB ages do not include the effects of magnetic activity on stellar properties. In light of this, we present results from our spectroscopic study of the very-low-mass members of the southern open cluster Blanco 1 using the Gemini-North Telescope, program IDs: GN-2009B-Q-53 and GN-2010B-Q-96. We obtained Gemini Multi-Object Spectrograph spectra at intermediate resolution for cluster candidate members with I ≈ 13-20 mag. From our sample of 43 spectra, we find 14 probable cluster members by consideringmore » proximity to the cluster sequence in an I/I – K {sub s} color-magnitude diagram, agreement with the cluster's systemic radial velocity, and magnetic activity as a youth indicator. We systematically analyze the Hα and Li features and update the LDB age of Blanco 1 to be 126{sub −14}{sup +13} Myr. Our new LDB age for Blanco 1 shows remarkable coevality with the benchmark Pleiades open cluster. Using available empirical activity corrections, we investigate the effects of magnetic activity on the LDB age of Blanco 1. Accounting for activity, we infer a corrected LDB age of 114{sub −10}{sup +9} Myr. This work demonstrates the importance of accounting for magnetic activity on LDB inferred stellar ages, suggesting the need to reinvestigate previous LDB age determinations.« less

THE RED-SEQUENCE CLUSTER SURVEY-2 (RCS-2): SURVEY DETAILS AND PHOTOMETRIC CATALOG CONSTRUCTION

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

Gilbank, David G.; Gladders, M. D.; Yee, H. K. C.

2011-03-15

The second Red-sequence Cluster Survey (RCS-2) is a {approx}1000 deg{sup 2}, multi-color imaging survey using the square-degree imager, MegaCam, on the Canada-France-Hawaii Telescope. It is designed to detect clusters of galaxies over the redshift range 0.1 {approx}< z {approx}< 1. The primary aim is to build a statistically complete, large ({approx}10{sup 4}) sample of clusters, covering a sufficiently long redshift baseline to be able to place constraints on cosmological parameters via the evolution of the cluster mass function. Other main science goals include building a large sample of high surface brightness, strongly gravitationally lensed arcs associated with these clusters, andmore » an unprecedented sample of several tens of thousands of galaxy clusters and groups, spanning a large range of halo mass, with which to study the properties and evolution of their member galaxies. This paper describes the design of the survey and the methodology for acquiring, reducing, and calibrating the data for the production of high-precision photometric catalogs. We describe the method for calibrating our griz imaging data using the colors of the stellar locus and overlapping Two Micron All Sky Survey photometry. This yields an absolute accuracy of <0.03 mag on any color and {approx}0.05 mag in the r-band magnitude, verified with respect to the Sloan Digital Sky Survey (SDSS). Our astrometric calibration is accurate to <<0.''3 from comparison with SDSS positions. RCS-2 reaches average 5{sigma} point-source limiting magnitudes of griz = [24.4, 24.3, 23.7, 22.8], approximately 1-2 mag deeper than the SDSS. Due to the queue-scheduled nature of the observations, the data are highly uniform and taken in excellent seeing, mostly FWHM {approx}< 0.''7 in the r band. In addition to the main science goals just described, these data form the basis for a number of other planned and ongoing projects (including the WiggleZ survey), making RCS-2 an important next-generation imaging survey.« less

Whole-Genome Sequencing and Comparative Genome Analysis of Bacillus subtilis Strains Isolated from Non-Salted Fermented Soybean Foods.

PubMed

Kamada, Mayumi; Hase, Sumitaka; Fujii, Kazushi; Miyake, Masato; Sato, Kengo; Kimura, Keitarou; Sakakibara, Yasubumi

2015-01-01

Bacillus subtilis is the main component in the fermentation of soybeans. To investigate the genetics of the soybean-fermenting B. subtilis strains and its relationship with the productivity of extracellular poly-γ-glutamic acid (γPGA), we sequenced the whole genome of eight B. subtilis stains isolated from non-salted fermented soybean foods in Southeast Asia. Assembled nucleotide sequences were compared with those of a natto (fermented soybean food) starter strain B. subtilis BEST195 and the laboratory standard strain B. subtilis 168 that is incapable of γPGA production. Detected variants were investigated in terms of insertion sequences, biotin synthesis, production of subtilisin NAT, and regulatory genes for γPGA synthesis, which were related to fermentation process. Comparing genome sequences, we found that the strains that produce γPGA have a deletion in a protein that constitutes the flagellar basal body, and this deletion was not found in the non-producing strains. We further identified diversity in variants of the bio operon, which is responsible for the biotin auxotrophism of the natto starter strains. Phylogenetic analysis using multilocus sequencing typing revealed that the B. subtilis strains isolated from the non-salted fermented soybeans were not clustered together, while the natto-fermenting strains were tightly clustered; this analysis also suggested that the strain isolated from "Tua Nao" of Thailand traces a different evolutionary process from other strains.

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

DISSECTING THE QUASAR MAIN SEQUENCE: INSIGHT FROM HOST GALAXY PROPERTIES

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

Sun, Jiayi; Shen, Yue

2015-05-01

The diverse properties of broad-line quasars appear to follow a well-defined main sequence along which the optical Fe ii strength increases. It has been suggested that this sequence is mainly driven by the Eddington ratio (L/L{sub Edd}) of the black hole (BH) accretion. Shen and Ho demonstrated with quasar clustering analysis that the average BH mass decreases with increasing Fe ii strength when quasar luminosity is fixed, consistent with this suggestion. Here we perform an independent test by measuring the stellar velocity dispersion σ{sub *} (hence, the BH mass via the M–σ{sub *} relation) from decomposed host spectra in low-redshiftmore » Sloan Digital Sky Survey quasars. We found that at fixed quasar luminosity, σ{sub *} systematically decreases with increasing Fe ii strength, confirming that the Eddington ratio increases with Fe ii strength. We also found that at fixed luminosity and Fe ii strength, there is little dependence of σ{sub *} on the broad Hβ FWHM. These new results reinforce the framework that the Eddington ratio and orientation govern most of the diversity seen in broad-line quasar properties.« less

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.

A novel alignment-free method to classify protein folding types by combining spectral graph clustering with Chou's pseudo amino acid composition.

PubMed

Tripathi, Pooja; Pandey, Paras N

2017-07-07

The present work employs pseudo amino acid composition (PseAAC) for encoding the protein sequences in their numeric form. Later this will be arranged in the similarity matrix, which serves as input for spectral graph clustering method. Spectral methods are used previously also for clustering of protein sequences, but they uses pair wise alignment scores of protein sequences, in similarity matrix. The alignment score depends on the length of sequences, so clustering short and long sequences together may not good idea. Therefore the idea of introducing PseAAC with spectral clustering algorithm came into scene. We extensively tested our method and compared its performance with other existing machine learning methods. It is consistently observed that, the number of clusters that we obtained for a given set of proteins is close to the number of superfamilies in that set and PseAAC combined with spectral graph clustering shows the best classification results. Copyright © 2017 Elsevier Ltd. All rights reserved.

LOD-based clustering techniques for efficient large-scale terrain storage and visualization

NASA Astrophysics Data System (ADS)

Bao, Xiaohong; Pajarola, Renato

2003-05-01

Large multi-resolution terrain data sets are usually stored out-of-core. To visualize terrain data at interactive frame rates, the data needs to be organized on disk, loaded into main memory part by part, then rendered efficiently. Many main-memory algorithms have been proposed for efficient vertex selection and mesh construction. Organization of terrain data on disk is quite difficult because the error, the triangulation dependency and the spatial location of each vertex all need to be considered. Previous terrain clustering algorithms did not consider the per-vertex approximation error of individual terrain data sets. Therefore, the vertex sequences on disk are exactly the same for any terrain. In this paper, we propose a novel clustering algorithm which introduces the level-of-detail (LOD) information to terrain data organization to map multi-resolution terrain data to external memory. In our approach the LOD parameters of the terrain elevation points are reflected during clustering. The experiments show that dynamic loading and paging of terrain data at varying LOD is very efficient and minimizes page faults. Additionally, the preprocessing of this algorithm is very fast and works from out-of-core.

Molecular evolution of the HoxA cluster in the three major gnathostome lineages

PubMed Central

Chiu, Chi-hua; Amemiya, Chris; Dewar, Ken; Kim, Chang-Bae; Ruddle, Frank H.; Wagner, Günter P.

2002-01-01

The duplication of Hox clusters and their maintenance in a lineage has a prominent but little understood role in chordate evolution. Here we examined how Hox cluster duplication may influence changes in cluster architecture and patterns of noncoding sequence evolution. We sequenced the entire duplicated HoxAa and HoxAb clusters of zebrafish (Danio rerio) and extended the 5′ (posterior) part of the HoxM (HoxA-like) cluster of horn shark (Heterodontus francisci) containing the hoxa11 and hoxa13 orthologs as well as intergenic and flanking noncoding sequences. The duplicated HoxA clusters in zebrafish each house considerably fewer genes and are dramatically shorter than the single HoxA clusters of human and horn shark. We compared the intergenic sequences of the HoxA clusters of human, horn shark, zebrafish (Aa, Ab), and striped bass and found extensive conservation of noncoding sequence motifs, i.e., phylogenetic footprints, between the human and horn shark, representing two of the three gnathostome lineages. These are putative cis-regulatory elements that may play a role in the regulation of the ancestral HoxA cluster. In contrast, homologous regions of the duplicated HoxAa and HoxAb clusters of zebrafish and the HoxA cluster of striped bass revealed a striking loss of conservation of these putative cis-regulatory sequences in the 3′ (anterior) segment of the cluster, where zebrafish only retains single representatives of group 1, 3, 4, and 5 (HoxAa) and group 2 (HoxAb) genes and in the 5′ part of the clusters, where zebrafish retains two copies of the group 13, 11, and 9 genes, i.e., AbdB-like genes. In analyzing patterns of cis-sequence evolution in the 5′ part of the clusters, we explicitly looked for evidence of complementary loss of conserved noncoding sequences, as predicted by the duplication-degeneration-complementation model in which genetic redundancy after gene duplication is resolved because of the fixation of complementary degenerative mutations. Our data did not yield evidence supporting this prediction. We conclude that changes in the pattern of cis-sequence conservation after Hox cluster duplication are more consistent with being the outcome of adaptive modification rather than passive mechanisms that erode redundancy created by the duplication event. These results support the view that genome duplications may provide a mechanism whereby master control genes undergo radical modifications conducive to major alterations in body plan. Such genomic revolutions may contribute significantly to the evolutionary process. PMID:11943847

Coupling molecules and morphology to discover new clades of ciliates.

NASA Astrophysics Data System (ADS)

Grattepanche, J. D.; Maurer-Alcalá, X. X.; Tucker, S. J.; McManus, G. B.; Katz, L. A.

2016-02-01

In a previous study using high-throughput sequencing (Grattepanche et al submitted, oral presentation?), we observe the presence of two clades of spirotrich ciliates mainly present in marine deep-water along the New England coast. These clades, clusters X1 and X2, are characterized by several deletions in their SSU-rDNA and have been observed elsewhere as both identical and similar sequences have been deposited on GenBank from other environmental studies, but lack morphological description. In order to link molecules (SSU-rDNA sequence) to their morphology, we sample below the photic zone (between 60 to 400m of depth) in the New England coast (Northeast Atlantic) in a transect crossing the continental shelf. We designed an oligonucleotide probe specific for choreotrich and oligotrich ciliates and another specific to clusters X1 and X2 to describe these clades through a combination of Fluorescence In Situ Hybridization (FISH) and light microscopy. Our aim is to increase our knowledge on the morphology of these `unknown' clades of ciliates, which will allow for future ecological studies.

Molecular epidemiological characteristics of Salmonella enterica serovars Enteritidis, Typhimurium and Livingstone strains isolated in a Tunisian university hospital.

PubMed

Ktari, Sonia; Ksibi, Boutheina; Gharsallah, Houda; Mnif, Basma; Maalej, Sonda; Rhimi, Fouzia; Hammami, Adnene

2016-03-01

Enteritidis, Typhimurium and Livingstone are the main Salmonella enterica serovars recovered in Tunisia. Here, we aimed to assess the genetic diversity of fifty-seven Salmonella enterica strains from different sampling periods, origins and settings using pulsed-field gel electrophoresis (PFGE), multi-locus sequence typing (MLST) and multi-locus variable-number tandem repeat analysis (MLVA). Salmonella Enteritidis, isolated from human and food sources from two regions in Sfax in 2007, were grouped into one cluster using PFGE. However, using MLVA these strains were divided into two clusters. Salmonella Typhimurium strains, recovered in 2012 and represent sporadic cases of human clinical isolates, were included in one PFGE cluster. Nevertheless, the MLVA technique, divided Salmonella Typhimurium isolates into six clusters with diversity index reaching (DI = 0.757). For Salmonella Livingstone which was responsible of two nosocomial outbreaks during 2000-2003, the PFGE and MLVA methods showed that these strains were genetically closely related. Salmonella Enteritidis and Salmonella Livingstone populations showed a single ST lineage ST11 and ST543 respectively. For Salmonella Typhimurium, two MLST sequence types ST19 and ST328 were defined. Salmonella Enteritidis and Salmonella Typhimurium strains were clearly differentiated by MLVA which was not the case using PFGE. © 2015 APMIS. Published by John Wiley & Sons Ltd.

Deep HST Imaging in 47 Tucanae: A Global Dynamical Model

NASA Astrophysics Data System (ADS)

Heyl, J.; Caiazzo, I.; Richer, H.; Anderson, J.; Kalirai, J.; Parada, J.

2017-12-01

Multi-epoch observations with the Advanced Camera Survey and WFC3 on the Hubble Space Telescope provide a unique and comprehensive probe of stellar dynamics within 47 Tucanae. We confront analytic models of the globular cluster with the observed stellar proper motions that probe along the main sequence from just above 0.8-0.1M ⊙ as well as white dwarfs younger than 1 Gyr. One field lies just beyond the half-light radius where dynamical models (e.g., lowered Maxwellian distributions) make robust predictions for the stellar proper motions. The observed proper motions in this outer field show evidence for anisotropy in the velocity distribution as well as skewness; the latter is evidence of rotation. The measured velocity dispersions and surface brightness distributions agree in detail with a rotating anisotropic model of the stellar distribution function with mild dependence of the proper-motion dispersion on mass. However, the best-fitting models underpredict the rotation and skewness of the stellar velocities. In the second field, centered on the core of the cluster, the mass segregation in proper motion is much stronger. Nevertheless the model developed in the outer field can be extended inward by taking this mass segregation into account in a heuristic fashion. The proper motions of the main-sequence stars yield a mass estimate of the cluster of 1.31+/- 0.02× {10}6{M}⊙ at a distance of 4.7 kpc. By comparing the proper motions of a sample of giant and subgiant stars with the observed radial velocities we estimate the distance to the cluster kinematically to be 4.29 ± 0.47 kpc.

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.

Hyperfast pulsars as the remnants of massive stars ejected from young star clusters

NASA Astrophysics Data System (ADS)

Gvaramadze, Vasilii V.; Gualandris, Alessia; Portegies Zwart, Simon

2008-04-01

Recent proper motion and parallax measurements for the pulsar PSR B1508+55 indicate a transverse velocity of ~1100kms-1, which exceeds earlier measurements for any neutron star. The spin-down characteristics of PSR B1508+55 are typical for a non-recycled pulsar, which implies that the velocity of the pulsar cannot have originated from the second supernova disruption of a massive binary system. The high velocity of PSR B1508+55 can be accounted for by assuming that it received a kick at birth or that the neutron star was accelerated after its formation in the supernova explosion. We propose an explanation for the origin of hyperfast neutron stars based on the hypothesis that they could be the remnants of a symmetric supernova explosion of a high-velocity massive star which attained its peculiar velocity (similar to that of the pulsar) in the course of a strong dynamical three- or four-body encounter in the core of dense young star cluster. To check this hypothesis, we investigated three dynamical processes involving close encounters between: (i) two hard massive binaries, (ii) a hard binary and an intermediate-mass black hole (IMBH) and (iii) a single stars and a hard binary IMBH. We find that main-sequence O-type stars cannot be ejected from young massive star clusters with peculiar velocities high enough to explain the origin of hyperfast neutron stars, but lower mass main-sequence stars or the stripped helium cores of massive stars could be accelerated to hypervelocities. Our explanation for the origin of hyperfast pulsars requires a very dense stellar environment of the order of 106- 107starspc-3. Although such high densities may exist during the core collapse of young massive star clusters, we caution that they have never been observed.

An Eccentric Binary Millisecond Pulsar in the Galactic Plane

NASA Technical Reports Server (NTRS)

Champion, David J.; Ransom, Scott M.; Lazarus, Patrick; Camilo, Fernando; Bassa, Cess; Kaspi, Victoria M.; Nice, David J.; Freire, Paulo C. C.; Stairs, Ingrid H.; vanLeeuwen, Joeri;

A novel mechanism for creating double pulsars

NASA Technical Reports Server (NTRS)

Sigurdsson, Steinn; Hernquist, Lars

1992-01-01

Simulations of encounters between pairs of hard binaries, each containing a neutron star and a main-sequence star, reveal a new formation mechanism for double pulsars in dense cores of globular clusters. In many cases, the two normal stars are disrupted to form a common envelope around the pair of neutron stars, both of which will be spun up to become millisecond pulsars. We predict that a new class of pulsars, double millisecond pulsars, will be discovered in the cores of dense globular clusters. The genesis proceeds through a short-lived double-core common envelope phase, with the envelope ejected in a fast wind. It is possible that the progenitor may also undergo a double X-ray binary phase. Any circular, short-period double pulsar found in the galaxy would necessarily come from disrupted disk clusters, unlike Hulse-Taylor class pulsars or low-mass X-ray binaries which may be ejected from clusters or formed in the galaxy.

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.

The Bologna Annotation Resource (BAR 3.0): improving protein functional annotation.

PubMed

Profiti, Giuseppe; Martelli, Pier Luigi; Casadio, Rita

2017-07-03

BAR 3.0 updates our server BAR (Bologna Annotation Resource) for predicting protein structural and functional features from sequence. We increase data volume, query capabilities and information conveyed to the user. The core of BAR 3.0 is a graph-based clustering procedure of UniProtKB sequences, following strict pairwise similarity criteria (sequence identity ≥40% with alignment coverage ≥90%). Each cluster contains the available annotation downloaded from UniProtKB, GO, PFAM and PDB. After statistical validation, GO terms and PFAM domains are cluster-specific and annotate new sequences entering the cluster after satisfying similarity constraints. BAR 3.0 includes 28 869 663 sequences in 1 361 773 clusters, of which 22.2% (22 241 661 sequences) and 47.4% (24 555 055 sequences) have at least one validated GO term and one PFAM domain, respectively. 1.4% of the clusters (36% of all sequences) include PDB structures and the cluster is associated to a hidden Markov model that allows building template-target alignment suitable for structural modeling. Some other 3 399 026 sequences are singletons. BAR 3.0 offers an improved search interface, allowing queries by UniProtKB-accession, Fasta sequence, GO-term, PFAM-domain, organism, PDB and ligand/s. When evaluated on the CAFA2 targets, BAR 3.0 largely outperforms our previous version and scores among state-of-the-art methods. BAR 3.0 is publicly available and accessible at http://bar.biocomp.unibo.it/bar3. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

THREE DISCRETE GROUPS WITH HOMOGENEOUS CHEMISTRY ALONG THE RED GIANT BRANCH IN THE GLOBULAR CLUSTER NGC 2808

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

Carretta, E., E-mail: eugenio.carretta@oabo.inaf.it

2014-11-10

We present the homogeneous reanalysis of Mg and Al abundances from high resolution UVES/FLAMES spectra for 31 red giants in the globular cluster NGC 2808. We found a well defined Mg-Al anticorrelation reaching a regime of subsolar Mg abundance ratios, with a spread of about 1.4 dex in [Al/Fe]. The main result from the improved statistics of our sample is that the distribution of stars is not continuous along the anticorrelation because they are neatly clustered into three distinct clumps, each with different chemical compositions. One group (P) shows a primordial composition of field stars of similar metallicity, and the other twomore » (I and E) have increasing abundances of Al and decreasing abundances of Mg. The fraction of stars we found in the three components (P: 68%, I: 19%, E: 13%) is in excellent agreement with the ratios computed for the three distinct main sequences in NGC 2808: for the first time there is a clear correspondence between discrete photometric sequences of dwarfs and distinct groups of giants with homogeneous chemistry. The composition of the I group cannot be reproduced by mixing of matter with extreme processing in hot H-burning and gas with pristine, unprocessed composition, as also found in the recent analysis of three discrete groups in NGC 6752. This finding suggests that different classes of polluters were probably at work in NGC 2808 as well.« less

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.

Color-magnitude diagram of Palomar 4 - CCD photometry

NASA Astrophysics Data System (ADS)

Christian, C. A.; Heasley, J. N.

1986-04-01

Photometry of the globular cluster Pal 4 was obtained with the RCA CCD camera on the 3.6 m Canada-France-Hawaii Telescope on Mauna Kea. The color-magnitude diagram of the cluster shows a well-defined red horizontal branch, typical of outer halo systems, and an asymptotic giant branch well separated from the giant branch. The population of Pal 4 has been sampled to the main-sequence turnoff region (V = 25), allowing a detailed comparison of this distant object with theoretical models. The cluster parameters consistent with the CCD data are (m - M)0 = 20.1 + or - 0.1 mag, E(B - V) = 0.02 + or - 0.02, and Fe/H forbidden line = -1.7 + or - 0.1 with Y =0.2. The age of the cluster, determined by comparison with the isochrones of VandenBerg and Bell (1985) is consistent with an age of 15 + or - 1 Gyr, similar to inner halo globular clusters with ages determined in the same way.

Photometric Calibrations of Gemini Images of NGC 6253

NASA Astrophysics Data System (ADS)

Pearce, Sean; Jeffery, Elizabeth

2017-01-01

We present preliminary results of our analysis of the metal-rich open cluster NGC 6253 using imaging data from GMOS on the Gemini-South Observatory. These data are part of a larger project to observe the effects of high metallicity on white dwarf cooling processes, especially the white dwarf cooling age, which have important implications on the processes of stellar evolution. To standardize the Gemini photometry, we have also secured imaging data of both the cluster and standard star fields using the 0.6-m SARA Observatory at CTIO. By analyzing and comparing the standard star fields of both the SARA data and the published Gemini zero-points of the standard star fields, we will calibrate the data obtained for the cluster. These calibrations are an important part of the project to obtain a standardized deep color-magnitude diagram to analyze the cluster. We present the process of verifying our standardization process. With a standardized CMD, we also present an analysis of the cluster's main sequence turn off age.

Identifying and reducing error in cluster-expansion approximations of protein energies.

PubMed

Hahn, Seungsoo; Ashenberg, Orr; Grigoryan, Gevorg; Keating, Amy E

2010-12-01

Protein design involves searching a vast space for sequences that are compatible with a defined structure. This can pose significant computational challenges. Cluster expansion is a technique that can accelerate the evaluation of protein energies by generating a simple functional relationship between sequence and energy. The method consists of several steps. First, for a given protein structure, a training set of sequences with known energies is generated. Next, this training set is used to expand energy as a function of clusters consisting of single residues, residue pairs, and higher order terms, if required. The accuracy of the sequence-based expansion is monitored and improved using cross-validation testing and iterative inclusion of additional clusters. As a trade-off for evaluation speed, the cluster-expansion approximation causes prediction errors, which can be reduced by including more training sequences, including higher order terms in the expansion, and/or reducing the sequence space described by the cluster expansion. This article analyzes the sources of error and introduces a method whereby accuracy can be improved by judiciously reducing the described sequence space. The method is applied to describe the sequence-stability relationship for several protein structures: coiled-coil dimers and trimers, a PDZ domain, and T4 lysozyme as examples with computationally derived energies, and SH3 domains in amphiphysin-1 and endophilin-1 as examples where the expanded pseudo-energies are obtained from experiments. Our open-source software package Cluster Expansion Version 1.0 allows users to expand their own energy function of interest and thereby apply cluster expansion to custom problems in protein design. © 2010 Wiley Periodicals, Inc.

Determinants of HIV Phylogenetic Clustering in Chicago Among Young Black Men Who Have Sex With Men From the uConnect Cohort.

PubMed

Morgan, Ethan; Nyaku, Amesika N; DʼAquila, Richard T; Schneider, John A

2017-07-01

Phylogenetic analysis determines similarities among HIV genetic sequences from persons infected with HIV, identifying clusters of transmission. We determined characteristics associated with both membership in an HIV transmission cluster and the number of clustered sequences among a cohort of young black men who have sex with men (YBMSM) in Chicago. Pairwise genetic distances of HIV-1 pol sequences were collected during 2013-2016. Potential transmission ties were identified among HIV-infected persons whose sequences were ≤1.5% genetically distant. Putative transmission pairs were defined as ≥1 tie to another sequence. We then determined demographic and risk attributes associated with both membership in an HIV transmission cluster and the number of ties to the sequences from other persons in the cluster. Of 86 available sequences, 31 (36.0%) were tied to ≥1 other sequence. Through multivariable analyses, we determined that those who reported symptoms of depression and those who had a higher number of confidants in their network had significantly decreased odds of membership in transmission clusters. We found that those who had unstable housing and who reported heavy marijuana use had significantly more ties to other individuals within transmission clusters, whereas those identifying as bisexual, those participating in group sex, and those with higher numbers of sexual partners had significantly fewer ties. This study demonstrates the potential for combining phylogenetic and individual and network attributes to target HIV control efforts to persons with potentially higher transmission risk, as well as suggesting some unappreciated specific predictors of transmission risk among YBMSM in Chicago for future study.

No energy equipartition in globular clusters

NASA Astrophysics Data System (ADS)

Trenti, Michele; van der Marel, Roeland

2013-11-01

It is widely believed that globular clusters evolve over many two-body relaxation times towards a state of energy equipartition, so that velocity dispersion scales with stellar mass as σ ∝ m-η with η = 0.5. We show here that this is incorrect, using a suite of direct N-body simulations with a variety of realistic initial mass functions and initial conditions. No simulated system ever reaches a state close to equipartition. Near the centre, the luminous main-sequence stars reach a maximum ηmax ≈ 0.15 ± 0.03. At large times, all radial bins convergence on an asymptotic value η∞ ≈ 0.08 ± 0.02. The development of this `partial equipartition' is strikingly similar across our simulations, despite the range of different initial conditions employed. Compact remnants tend to have higher η than main-sequence stars (but still η < 0.5), due to their steeper (evolved) mass function. The presence of an intermediate-mass black hole (IMBH) decreases η, consistent with our previous findings of a quenching of mass segregation under these conditions. All these results can be understood as a consequence of the Spitzer instability for two-component systems, extended by Vishniac to a continuous mass spectrum. Mass segregation (the tendency of heavier stars to sink towards the core) has often been studied observationally, but energy equipartition has not. Due to the advent of high-quality proper motion data sets from the Hubble Space Telescope, it is now possible to measure η for real clusters. Detailed data-model comparisons open up a new observational window on globular cluster dynamics and evolution. A first comparison of our simulations to observations of Omega Cen yields good agreement, supporting the view that globular clusters are not generally in energy equipartition. Modelling techniques that assume equipartition by construction (e.g. multi-mass Michie-King models) are approximate at best.

Computational identification of developmental enhancers:conservation and function of transcription factor binding-site clustersin drosophila melanogaster and drosophila psedoobscura

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

Berman, Benjamin P.; Pfeiffer, Barret D.; Laverty, Todd R.

2004-08-06

The identification of sequences that control transcription in metazoans is a major goal of genome analysis. In a previous study, we demonstrated that searching for clusters of predicted transcription factor binding sites could discover active regulatory sequences, and identified 37 regions of the Drosophila melanogaster genome with high densities of predicted binding sites for five transcription factors involved in anterior-posterior embryonic patterning. Nine of these clusters overlapped known enhancers. Here, we report the results of in vivo functional analysis of 27 remaining clusters. We generated transgenic flies carrying each cluster attached to a basal promoter and reporter gene, and assayedmore » embryos for reporter gene expression. Six clusters are enhancers of adjacent genes: giant, fushi tarazu, odd-skipped, nubbin, squeeze and pdm2; three drive expression in patterns unrelated to those of neighboring genes; the remaining 18 do not appear to have enhancer activity. We used the Drosophila pseudoobscura genome to compare patterns of evolution in and around the 15 positive and 18 false-positive predictions. Although conservation of primary sequence cannot distinguish true from false positives, conservation of binding-site clustering accurately discriminates functional binding-site clusters from those with no function. We incorporated conservation of binding-site clustering into a new genome-wide enhancer screen, and predict several hundred new regulatory sequences, including 85 adjacent to genes with embryonic patterns. Measuring conservation of sequence features closely linked to function--such as binding-site clustering--makes better use of comparative sequence data than commonly used methods that examine only sequence identity.« less

The origin and evolution of short-period Miras in the solar neighborhood: Constraints on the life cycle of old stars

NASA Technical Reports Server (NTRS)

Jura, M.

1994-01-01

The spatial distribution of the short-period (P less than 300 days) oxygen-rich Miras in the solar neighborhood can be fitted with an exponential scale height above the Galactic plane of about 600 pc. Using the Gliese catalog of local main-sequence stars, we estimate that the density of suitable G-type progenitor dwarfs within 20 pc of the Sun for these short-period Miras is 6 x 10(exp -4)/cu pc. The portion of the H-R diagram near the main-sequence turnoff of these velocity-selected Gliese stars is intermediate between that of the old open cluster NGC 188 and that of the metal-rich globular cluster, 47 Tuc. We infer that the main-sequence progenitors of the short-period Miras have masses near 1.0 solar mass, and we estimate that these Miras have ages approximately 9 x 10(exp 9). We also identify a few old disk red giants in the neighborhood of the Sun. On the basis of very limited information, we estimate that the total amount of mass lost from these stars during their first ascent up the red giant branch is less than or equal to 0.1 solar mass. We derive a duration of the short-period Mira phase of close to 5 x 10(exp 5) yr. This estimate for the duration of the short period Mira phase is longer than our estimate of 2 x 10(exp 5) yr for the duration of the Mira phase for stars with periods longer than 300 days. From their infrared colors, we estimate a typical mass-loss rate from the short-period Miras of approximately 1 x 10(exp -7) solar mass/yr.

The origin and evolution of short-period Miras in the solar neighborhood: Constraints on the life cycle of old stars

NASA Astrophysics Data System (ADS)

Jura, M.

1994-02-01

The spatial distribution of the short-period (P less than 300 days) oxygen-rich Miras in the solar neighborhood can be fitted with an exponential scale height above the Galactic plane of about 600 pc. Using the Gliese catalog of local main-sequence stars, we estimate that the density of suitable G-type progenitor dwarfs within 20 pc of the Sun for these short-period Miras is 6 x 10-4/cu pc. The portion of the H-R diagram near the main-sequence turnoff of these velocity-selected Gliese stars is intermediate between that of the old open cluster NGC 188 and that of the metal-rich globular cluster, 47 Tuc. We infer that the main-sequence progenitors of the short-period Miras have masses near 1.0 solar mass, and we estimate that these Miras have ages approximately 9 x 109. We also identify a few old disk red giants in the neighborhood of the Sun. On the basis of very limited information, we estimate that the total amount of mass lost from these stars during their first ascent up the red giant branch is less than or equal to 0.1 solar mass. We derive a duration of the short-period Mira phase of close to 5 x 105 yr. This estimate for the duration of the short period Mira phase is longer than our estimate of 2 x 105 yr for the duration of the Mira phase for stars with periods longer than 300 days. From their infrared colors, we estimate a typical mass-loss rate from the short-period Miras of approximately 1 x 10-7 solar mass/yr.

The Clusters AgeS Experiment (CASE). Variable Stars in the Field of the Globular Cluster NGC 6362

NASA Astrophysics Data System (ADS)

Kaluzny, J.; Thompson, I. B.; Rozyczka, M.; Pych, W.; Narloch, W.

2014-12-01

The field of the globular cluster NGC 6362 was monitored between 1995 and 2009 in a search for variable stars. BV light curves were obtained for 69 periodic variable stars including 34 known RR Lyr stars, 10 known objects of other types and 25 newly detected variable stars. Among the latter we identified 18 proper-motion members of the cluster: seven detached eclipsing binaries (DEBs), six SX Phe stars, two W UMa binaries, two spotted red giants, and a very interesting eclipsing binary composed of two red giants - the first example of such a system found in a globular cluster. Five of the DEBs are located at the turnoff region, and the remaining two are redward of the lower main sequence. Eighty-four objects from the central 9×9 arcmin2 of the cluster were found in the region of cluster blue stragglers. Of these 70 are proper motion (PM) members of NGC 6362 (including all SX Phe and two W UMa stars), and five are field stars. The remaining nine objects lacking PM information are located at the very core of the cluster, and as such they are likely genuine blue stragglers.

A TALE OF DWARFS AND GIANTS: USING A z = 1.62 CLUSTER TO UNDERSTAND HOW THE RED SEQUENCE GREW OVER THE LAST 9.5 BILLION YEARS

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

Rudnick, Gregory H.; Tran, Kim-Vy; Papovich, Casey

2012-08-10

We study the red sequence in a cluster of galaxies at z = 1.62 and follow its evolution over the intervening 9.5 Gyr to the present day. Using deep YJK{sub s} imaging with the HAWK-I instrument on the Very Large Telescope, we identify a tight red sequence and construct its rest-frame i-band luminosity function (LF). There is a marked deficit of faint red galaxies in the cluster that causes a turnover in the LF. We compare the red-sequence LF to that for clusters at z < 0.8, correcting the luminosities for passive evolution. The shape of the cluster red-sequence LFmore » does not evolve between z = 1.62 and z = 0.6 but at z < 0.6 the faint population builds up significantly. Meanwhile, between z = 1.62 and 0.6 the inferred total light on the red sequence grows by a factor of {approx}2 and the bright end of the LF becomes more populated. We construct a simple model for red-sequence evolution that grows the red sequence in total luminosity and matches the constant LF shape at z > 0.6. In this model the cluster accretes blue galaxies from the field whose star formation is quenched and who are subsequently allowed to merge. We find that three to four mergers among cluster galaxies during the 4 Gyr between z = 1.62 and z = 0.6 match the observed LF evolution between the two redshifts. The inferred merger rate is consistent with other studies of this cluster. Our result supports the picture that galaxy merging during the major growth phase of massive clusters is an important process in shaping the red-sequence population at all luminosities.« less

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

PubMed

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

2015-01-01

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

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

PubMed

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

2010-05-13

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

ClusterMine360: a database of microbial PKS/NRPS biosynthesis

PubMed Central

Conway, Kyle R.; Boddy, Christopher N.

2013-01-01

ClusterMine360 (http://www.clustermine360.ca/) is a database of microbial polyketide and non-ribosomal peptide gene clusters. It takes advantage of crowd-sourcing by allowing members of the community to make contributions while automation is used to help achieve high data consistency and quality. The database currently has >200 gene clusters from >185 compound families. It also features a unique sequence repository containing >10 000 polyketide synthase/non-ribosomal peptide synthetase domains. The sequences are filterable and downloadable as individual or multiple sequence FASTA files. We are confident that this database will be a useful resource for members of the polyketide synthases/non-ribosomal peptide synthetases research community, enabling them to keep up with the growing number of sequenced gene clusters and rapidly mine these clusters for functional information. PMID:23104377

Genetic diversity and variation of Chinese fir from Fujian province and Taiwan, China, based on ISSR markers

PubMed Central

Chen, Yu; Peng, Zhuqing; Wu, Chao; Ma, Zhihui; Ding, Guochang; Cao, Guangqiu; Ruan, Shaoning; Lin, Sizu

2017-01-01

Genetic diversity and variation among 11 populations of Chinese fir from Fujian province and Taiwan were assessed using inter-simple sequence repeat (ISSR) markers to reveal the evolutionary relationship in their distribution range in this report. Analysis of genetic parameters of the different populations showed that populations in Fujian province exhibited a greater level of genetic diversity than did the populations in Taiwan. Compared to Taiwan populations, significant limited gene flow were observed among Fujian populations. An UPGMA cluster analysis showed that the most individuals of Taiwan populations formed a single cluster, whereas 6 discrete clusters were formed by each population from Fujian. All populations were divided into 3 main groups and that all 5 populations from Taiwan were gathered into a subgroup combined with 2 populations, Dehua and Liancheng, formed one of the 3 main groups, which indicated relative stronger relatedness. It is supported by a genetic structure analysis. All those results are suggesting different levels of genetic diversity and variation of Chinese fir between Fujian and Taiwan, and indicating different patterns of evolutionary process and local environmental adaption. PMID:28406956

Genetic diversity and variation of Chinese fir from Fujian province and Taiwan, China, based on ISSR markers.

PubMed

Chen, Yu; Peng, Zhuqing; Wu, Chao; Ma, Zhihui; Ding, Guochang; Cao, Guangqiu; Ruan, Shaoning; Lin, Sizu

2017-01-01

Genetic diversity and variation among 11 populations of Chinese fir from Fujian province and Taiwan were assessed using inter-simple sequence repeat (ISSR) markers to reveal the evolutionary relationship in their distribution range in this report. Analysis of genetic parameters of the different populations showed that populations in Fujian province exhibited a greater level of genetic diversity than did the populations in Taiwan. Compared to Taiwan populations, significant limited gene flow were observed among Fujian populations. An UPGMA cluster analysis showed that the most individuals of Taiwan populations formed a single cluster, whereas 6 discrete clusters were formed by each population from Fujian. All populations were divided into 3 main groups and that all 5 populations from Taiwan were gathered into a subgroup combined with 2 populations, Dehua and Liancheng, formed one of the 3 main groups, which indicated relative stronger relatedness. It is supported by a genetic structure analysis. All those results are suggesting different levels of genetic diversity and variation of Chinese fir between Fujian and Taiwan, and indicating different patterns of evolutionary process and local environmental adaption.

Sequence analysis of a few species of termites (Order: Isoptera) on the basis of partial characterization of COII gene.

PubMed

Sobti, Ranbir Chander; Kumari, Mamtesh; Sharma, Vijay Lakshmi; Sodhi, Monika; Mukesh, Manishi; Shouche, Yogesh

2009-11-01

The present study was aimed to get the nucleotide sequences of a part of COII mitochondrial gene amplified from individuals of five species of Termites (Isoptera: Termitidae: Macrotermitinae). Four of them belonged to the genus Odontotermes (O. obesus, O. horni, O. bhagwatii and Odontotermes sp.) and one to Microtermes (M. obesi). Partial COII gene fragments were amplified by using specific primers. The sequences so obtained were characterized to calculate the frequencies of each nucleotide bases and a high A + T content was observed. The interspecific pairwise sequence divergence in Odontotermes species ranged from 6.5% to 17.1% across COII fragment. M. obesi sequence diversity ranged from 2.5 with Odontotermes sp. to 19.0% with O. bhagwatii. Phylogenetic trees drawn on the basis of distance neighbour-joining method revealed three main clades clustering all the individuals according to their genera and families.

Phylogenetic investigation of a statewide HIV-1 epidemic reveals ongoing and active transmission networks among men who have sex with men

PubMed Central

Chan, Philip A.; Hogan, Joseph W.; Huang, Austin; DeLong, Allison; Salemi, Marco; Mayer, Kenneth H.; Kantor, Rami

2015-01-01

Background Molecular epidemiologic evaluation of HIV-1 transmission networks can elucidate behavioral components of transmission that can be targets for intervention. Methods We combined phylogenetic and statistical approaches using pol sequences from patients diagnosed 2004-2011 at a large HIV center in Rhode Island, following 75% of the state’s HIV population. Phylogenetic trees were constructed using maximum likelihood and putative transmission clusters were evaluated using latent class analyses (LCA) to determine association of cluster size with underlying demographic/behavioral characteristics. A logistic growth model was used to assess intra-cluster dynamics over time and predict “active” clusters that were more likely to harbor undiagnosed infections. Results Of 1,166 HIV-1 subtype B sequences, 31% were distributed among 114 statistically-supported, monophyletic clusters (range: 2-15 sequences/cluster). Sequences from men who have sex with men (MSM) formed 52% of clusters. LCA demonstrated that sequences from recently diagnosed (2008-2011) MSM with primary HIV infection (PHI) and other sexually transmitted infections (STIs) were more likely to form larger clusters (Odds Ratio 1.62-11.25, p<0.01). MSM in clusters were more likely to have anonymous partners and meet partners at sex clubs and pornographic stores. Four large clusters with 38 sequences (100% male, 89% MSM) had a high-probability of harboring undiagnosed infections and included younger MSM with PHI and STIs. Conclusions In this first large-scale molecular epidemiologic investigation of HIV-1 transmission in New England, sexual networks among recently diagnosed MSM with PHI and concomitant STIs contributed to ongoing transmission. Characterization of transmission dynamics revealed actively growing clusters which may be targets for intervention. PMID:26258569

Spectroscopic characterization of galaxy clusters in RCS-1: spectroscopic confirmation, redshift accuracy, and dynamical mass-richness relation

NASA Astrophysics Data System (ADS)

Gilbank, David G.; Barrientos, L. Felipe; Ellingson, Erica; Blindert, Kris; Yee, H. K. C.; Anguita, T.; Gladders, M. D.; Hall, P. B.; Hertling, G.; Infante, L.; Yan, R.; Carrasco, M.; Garcia-Vergara, Cristina; Dawson, K. S.; Lidman, C.; Morokuma, T.

2018-05-01

We present follow-up spectroscopic observations of galaxy clusters from the first Red-sequence Cluster Survey (RCS-1). This work focuses on two samples, a lower redshift sample of ˜30 clusters ranging in redshift from z ˜ 0.2-0.6 observed with multiobject spectroscopy (MOS) on 4-6.5-m class telescopes and a z ˜ 1 sample of ˜10 clusters 8-m class telescope observations. We examine the detection efficiency and redshift accuracy of the now widely used red-sequence technique for selecting clusters via overdensities of red-sequence galaxies. Using both these data and extended samples including previously published RCS-1 spectroscopy and spectroscopic redshifts from SDSS, we find that the red-sequence redshift using simple two-filter cluster photometric redshifts is accurate to σz ≈ 0.035(1 + z) in RCS-1. This accuracy can potentially be improved with better survey photometric calibration. For the lower redshift sample, ˜5 per cent of clusters show some (minor) contamination from secondary systems with the same red-sequence intruding into the measurement aperture of the original cluster. At z ˜ 1, the rate rises to ˜20 per cent. Approximately ten per cent of projections are expected to be serious, where the two components contribute significant numbers of their red-sequence galaxies to another cluster. Finally, we present a preliminary study of the mass-richness calibration using velocity dispersions to probe the dynamical masses of the clusters. We find a relation broadly consistent with that seen in the local universe from the WINGS sample at z ˜ 0.05.

Multilocus Sequence Typing Analysis of Staphylococcus lugdunensis Implies a Clonal Population Structure

PubMed Central

Chassain, Benoît; Lemée, Ludovic; Didi, Jennifer; Thiberge, Jean-Michel; Brisse, Sylvain; Pons, Jean-Louis

2012-01-01

Staphylococcus lugdunensis is recognized as one of the major pathogenic species within the genus Staphylococcus, even though it belongs to the coagulase-negative group. A multilocus sequence typing (MLST) scheme was developed to study the genetic relationships and population structure of 87 S. lugdunensis isolates from various clinical and geographic sources by DNA sequence analysis of seven housekeeping genes (aroE, dat, ddl, gmk, ldh, recA, and yqiL). The number of alleles ranged from four (gmk and ldh) to nine (yqiL). Allelic profiles allowed the definition of 20 different sequence types (STs) and five clonal complexes. The 20 STs lacked correlation with geographic source. Isolates recovered from hematogenic infections (blood or osteoarticular isolates) or from skin and soft tissue infections did not cluster in separate lineages. Penicillin-resistant isolates clustered mainly in one clonal complex, unlike glycopeptide-tolerant isolates, which did not constitute a distinct subpopulation within S. lugdunensis. Phylogenies from the sequences of the seven individual housekeeping genes were congruent, indicating a predominantly mutational evolution of these genes. Quantitative analysis of the linkages between alleles from the seven loci revealed a significant linkage disequilibrium, thus confirming a clonal population structure for S. lugdunensis. This first MLST scheme for S. lugdunensis provides a new tool for investigating the macroepidemiology and phylogeny of this unusually virulent coagulase-negative Staphylococcus. PMID:22785196

Revising Star and Planet Formation Timescales

NASA Astrophysics Data System (ADS)

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

2013-07-01

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

Genetic characteristics of Streptococcus dysgalactiae isolated from cage cultured cobia, Rachycentron canadum (L.).

PubMed

Tsai, M-A; Wang, P-C; Yoshida, T; Chen, S-C

2015-12-01

Disease outbreaks occurred during 2007-2013 in Taiwan with 2.5-10% mortality among the cage cultured cobia, Rachycentron canadum (L.), characterized by the presence of polyserositis, pericarditis and peritonitis. The micro-organisms isolated from internal organs were Gram-positive cocci. The isolates were confirmed as Streptococcus dysgalactiae by a polymerase chain reaction assay that yielded the expected specific 259 bp amplicon. Additionally, partial sequence of the 16S-23S rDNA intergenic spacer region of the GCS strain isolates from fish was also compared and produced 100% sequence identity with S. dysgalactiae (GenBank accession number AB252398). The genetic characterization was then determined by pulsed-field gel electrophoresis (PFGE) analysis. Based on PFGE, the Apa I or Sma I digestion patterns of chromosomal DNA of these isolates were grouped into three main clusters. Taiwanese strains were divided into two clusters, and the tet(M) gene was detected in cluster 1 (pulsotypes: A1-A2 and S1-S3), but not in cluster 2 strains (pulsotypes: A3-A4 and S4-S5). Three Japanese strains from amberjack, Seriola dumerili (Risso), were grouped into cluster 3 (pulsotypes: A5-A7 and S6-S8) and displayed no mortality to cobia in the challenge experiment. Conversely, Taiwanese strains from cobia and snubnose pompano, Trachinotus blochii (L.), displayed a mortality rate of 50-87.5% in cobia. © 2014 John Wiley & Sons Ltd.

A Multiwavelength Study of the Segue 3 Cluster

NASA Astrophysics Data System (ADS)

Hughes, Joanne; Lacy, Brianna; Sakari, Charli; Wallerstein, George; Davis, Christoper Evan; Schiefelbein, Spencer; Corrin, Olivia; Joudi, Hanah; Le, Donna; Haynes, Rose Marie

2017-08-01

We present new SDSS and Washington photometry of the young outer-halo stellar system Segue 3. Combined with archival VI-observations, our most consistent results yield Z=0.006+/- 0.001, {log}({Age})=9.42+/- 0.08, {(m-M)}0=17.35+/- 0.08, and E(B-V)=0.09+/- 0.01, with a high binary fraction of 0.39 ± 0.05 derived using the Padova models. We confirm that mass-segregation has occurred, supporting the hypothesis that this cluster is being tidally disrupted. A three-parameter King model yields a cluster radius of {r}{cl}=0\\mathop{.}\\limits^\\circ 017+/- 0\\mathop{.}\\limits^\\circ 007, a core radius of {r}{{c}}=0\\mathop{.}\\limits^\\circ 003+/- 0\\mathop{.}\\limits^\\circ 001, and a tidal radius of {r}{{t}}=0\\mathop{.}\\limits^\\circ 04+/- 0\\mathop{.}\\limits^\\circ 02. A comparison of Padova and Dartmouth model-grids indicates that the cluster is not significantly α-enhanced, with a mean [{Fe}/{{H}}]=-{0.55}-0.12+0.15 dex, and a population age of only 2.6 ± 0.4 Gyr. We rule out a statistically significant age spread at the main-sequence turnoff because of a narrow subgiant branch, and discuss the role of stellar rotation and cluster age, using Dartmouth and Geneva models: approximately 70% of the Seg 3 stars at or below the main-sequence turnoff have enhanced rotation. Our results for Segue 3 indicate that it is younger and more metal-rich than all previous studies have reported to date. From colors involving Washington C and SDSS-u filters, we identify several giants and a possible blue straggler for future follow-up spectroscopic studies, and we produce spectral energy distributions of previously known members and potential Segue 3 sources with Washington (CT 1), Sloan (ugri), and VI-filters. Segue 3 shares the characteristics of unusual stellar systems that have likely been stripped from external dwarf galaxies as they are being accreted by the Milky Way, or that have been formed during such an event. Its youth, metallicity, and location are all inconsistent with Segue 3 being a cluster native to the Milky Way.

Computational identification of developmental enhancers:conservation and function of transcription factor binding-site clustersin drosophila melanogaster and drosophila psedoobscura

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

Berman, Benjamin P.; Pfeiffer, Barret D.; Laverty, Todd R.

2004-08-06

Background The identification of sequences that control transcription in metazoans is a major goal of genome analysis. In a previous study, we demonstrated that searching for clusters of predicted transcription factor binding sites could discover active regulatory sequences, and identified 37 regions of the Drosophila melanogaster genome with high densities of predicted binding sites for five transcription factors involved in anterior-posterior embryonic patterning. Nine of these clusters overlapped known enhancers. Here, we report the results of in vivo functional analysis of 27 remaining clusters. Results We generated transgenic flies carrying each cluster attached to a basal promoter and reporter gene,more » and assayed embryos for reporter gene expression. Six clusters are enhancers of adjacent genes: giant, fushi tarazu, odd-skipped, nubbin, squeeze and pdm2; three drive expression in patterns unrelated to those of neighboring genes; the remaining 18 do not appear to have enhancer activity. We used the Drosophila pseudoobscura genome to compare patterns of evolution in and around the 15 positive and 18 false-positive predictions. Although conservation of primary sequence cannot distinguish true from false positives, conservation of binding-site clustering accurately discriminates functional binding-site clusters from those with no function. We incorporated conservation of binding-site clustering into a new genome-wide enhancer screen, and predict several hundred new regulatory sequences, including 85 adjacent to genes with embryonic patterns. Conclusions Measuring conservation of sequence features closely linked to function - such as binding-site clustering - makes better use of comparative sequence data than commonly used methods that examine only sequence identity.« less

The Nature of Red-Sequence Cluster Spiral Galaxies

NASA Astrophysics Data System (ADS)

Kashur, Lane; Barkhouse, Wayne; Sultanova, Madina; Kalawila Vithanage, Sandanuwa; Archer, Haylee; Foote, Gregory; Mathew, Elijah; Rude, Cody; Lopez-Cruz, Omar

2017-01-01

Preliminary analysis of the red-sequence galaxy population from a sample of 57 low-redshift galaxy clusters observed using the KPNO 0.9m telescope and 74 clusters from the WINGS dataset, indicates that a small fraction of red-sequence galaxies have a morphology consistent with spiral systems. For spiral galaxies to acquire the color of elliptical/S0s at a similar luminosity, they must either have been stripped of their star-forming gas at an earlier epoch, or contain a larger than normal fraction of dust. To test these ideas we have compiled a sample of red-sequence spiral galaxies and examined their infrared properties as measured by 2MASS, WISE, Spitzer, and Herschel. These IR data allows us to estimate the amount of dust in each of our red-sequence spiral galaxies. We compare the estimated dust mass in each of these red-sequence late-type galaxies with spiral galaxies located in the same cluster field but having colors inconsistent with the red-sequence. We thus provide a statistical measure to discriminate between purely passive spiral galaxy evolution and dusty spirals to explain the presence of these late-type systems in cluster red-sequences.

Whole-Genome Sequencing and Comparative Genome Analysis of Bacillus subtilis Strains Isolated from Non-Salted Fermented Soybean Foods

PubMed Central

Kamada, Mayumi; Hase, Sumitaka; Fujii, Kazushi; Miyake, Masato; Sato, Kengo; Kimura, Keitarou; Sakakibara, Yasubumi

2015-01-01

Bacillus subtilis is the main component in the fermentation of soybeans. To investigate the genetics of the soybean-fermenting B. subtilis strains and its relationship with the productivity of extracellular poly-γ-glutamic acid (γPGA), we sequenced the whole genome of eight B. subtilis stains isolated from non-salted fermented soybean foods in Southeast Asia. Assembled nucleotide sequences were compared with those of a natto (fermented soybean food) starter strain B. subtilis BEST195 and the laboratory standard strain B. subtilis 168 that is incapable of γPGA production. Detected variants were investigated in terms of insertion sequences, biotin synthesis, production of subtilisin NAT, and regulatory genes for γPGA synthesis, which were related to fermentation process. Comparing genome sequences, we found that the strains that produce γPGA have a deletion in a protein that constitutes the flagellar basal body, and this deletion was not found in the non-producing strains. We further identified diversity in variants of the bio operon, which is responsible for the biotin auxotrophism of the natto starter strains. Phylogenetic analysis using multilocus sequencing typing revealed that the B. subtilis strains isolated from the non-salted fermented soybeans were not clustered together, while the natto-fermenting strains were tightly clustered; this analysis also suggested that the strain isolated from “Tua Nao” of Thailand traces a different evolutionary process from other strains. PMID:26505996

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

Bragaglia, A.; Carretta, E.; Gratton, R. G.

We present the first chemical composition study of two unevolved stars in the globular cluster NGC 2808, obtained with the X-shooter spectrograph at VLT. NGC 2808 shows three discrete, well-separated main sequences. The most accepted explanation for this phenomenon is that their stars have different helium contents. We observed one star on the bluest main sequence (bMS, claimed to have a high helium content, Y {approx}0.4) and the other on the reddest main sequence (rMS, consistent with a canonical helium content, Y = 0.245). We analyzed features of NH, CH, Na, Mg, Al, and Fe. While Fe, Ca, and othermore » elements have the same abundances in the two stars, the bMS star shows a huge enhancement of N, a depletion of C, an enhancement of Na and Al, and a small depletion of Mg with respect to the rMS star. This is exactly what is expected if stars on the bMS formed from the ejecta produced by an earlier stellar generation in the complete CNO and MgAl cycles whose main product is helium. The elemental abundance pattern differences in these two stars are consistent with the differences in the helium content suggested by the color-magnitude diagram positions of the stars.« less

EVIDENCE FOR THE UNIVERSALITY OF PROPERTIES OF RED-SEQUENCE GALAXIES IN X-RAY- AND RED-SEQUENCE-SELECTED CLUSTERS AT z ∼ 1

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

Foltz, R.; Wilson, G.; DeGroot, A.

We study the slope, intercept, and scatter of the color–magnitude and color–mass relations for a sample of 10 infrared red-sequence-selected clusters at z ∼ 1. The quiescent galaxies in these clusters formed the bulk of their stars above z ≳ 3 with an age spread Δt ≳ 1 Gyr. We compare UVJ color–color and spectroscopic-based galaxy selection techniques, and find a 15% difference in the galaxy populations classified as quiescent by these methods. We compare the color–magnitude relations from our red-sequence selected sample with X-ray- and photometric-redshift-selected cluster samples of similar mass and redshift. Within uncertainties, we are unable tomore » detect any difference in the ages and star formation histories of quiescent cluster members in clusters selected by different methods, suggesting that the dominant quenching mechanism is insensitive to cluster baryon partitioning at z ∼ 1.« less

A binary origin for 'blue stragglers' in globular clusters.

PubMed

Knigge, Christian; Leigh, Nathan; Sills, Alison

2009-01-15

Blue stragglers in globular clusters are abnormally massive stars that should have evolved off the stellar main sequence long ago. There are two known processes that can create these objects: direct stellar collisions and binary evolution. However, the relative importance of these processes has remained unclear. In particular, the total number of blue stragglers found in a given cluster does not seem to correlate with the predicted collision rate, providing indirect support for the binary-evolution model. Yet the radial distributions of blue stragglers in many clusters are bimodal, with a dominant central peak: this has been interpreted as an indication that collisions do dominate blue straggler production, at least in the high-density cluster cores. Here we report that there is a clear, but sublinear, correlation between the number of blue stragglers found in a cluster core and the total stellar mass contained within it. From this we conclude that most blue stragglers, even those found in cluster cores, come from binary systems. The parent binaries, however, may themselves have been affected by dynamical encounters. This may be the key to reconciling all of the seemingly conflicting results found to date.

Chloroplast DNA sequence of the green alga Oedogonium cardiacum (Chlorophyceae): Unique genome architecture, derived characters shared with the Chaetophorales and novel genes acquired through horizontal transfer

PubMed Central

Brouard, Jean-Simon; Otis, Christian; Lemieux, Claude; Turmel, Monique

2008-01-01

Background To gain insight into the branching order of the five main lineages currently recognized in the green algal class Chlorophyceae and to expand our understanding of chloroplast genome evolution, we have undertaken the sequencing of chloroplast DNA (cpDNA) from representative taxa. The complete cpDNA sequences previously reported for Chlamydomonas (Chlamydomonadales), Scenedesmus (Sphaeropleales), and Stigeoclonium (Chaetophorales) revealed tremendous variability in their architecture, the retention of only few ancestral gene clusters, and derived clusters shared by Chlamydomonas and Scenedesmus. Unexpectedly, our recent phylogenies inferred from these cpDNAs and the partial sequences of three other chlorophycean cpDNAs disclosed two major clades, one uniting the Chlamydomonadales and Sphaeropleales (CS clade) and the other uniting the Oedogoniales, Chaetophorales and Chaetopeltidales (OCC clade). Although molecular signatures provided strong support for this dichotomy and for the branching of the Oedogoniales as the earliest-diverging lineage of the OCC clade, more data are required to validate these phylogenies. We describe here the complete cpDNA sequence of Oedogonium cardiacum (Oedogoniales). Results Like its three chlorophycean homologues, the 196,547-bp Oedogonium chloroplast genome displays a distinctive architecture. This genome is one of the most compact among photosynthetic chlorophytes. It has an atypical quadripartite structure, is intron-rich (17 group I and 4 group II introns), and displays 99 different conserved genes and four long open reading frames (ORFs), three of which are clustered in the spacious inverted repeat of 35,493 bp. Intriguingly, two of these ORFs (int and dpoB) revealed high similarities to genes not usually found in cpDNA. At the gene content and gene order levels, the Oedogonium genome most closely resembles its Stigeoclonium counterpart. Characters shared by these chlorophyceans but missing in members of the CS clade include the retention of psaM, rpl32 and trnL(caa), the loss of petA, the disruption of three ancestral clusters and the presence of five derived gene clusters. Conclusion The Oedogonium chloroplast genome disclosed additional characters that bolster the evidence for a close alliance between the Oedogoniales and Chaetophorales. Our unprecedented finding of int and dpoB in this cpDNA provides a clear example that novel genes were acquired by the chloroplast genome through horizontal transfers, possibly from a mitochondrial genome donor. PMID:18558012

Protein sequences clustering of herpes virus by using Tribe Markov clustering (Tribe-MCL)

NASA Astrophysics Data System (ADS)

Bustamam, A.; Siswantining, T.; Febriyani, N. L.; Novitasari, I. D.; Cahyaningrum, R. D.

2017-07-01

The herpes virus can be found anywhere and one of the important characteristics is its ability to cause acute and chronic infection at certain times so as a result of the infection allows severe complications occurred. The herpes virus is composed of DNA containing protein and wrapped by glycoproteins. In this work, the Herpes viruses family is classified and analyzed by clustering their protein-sequence using Tribe Markov Clustering (Tribe-MCL) algorithm. Tribe-MCL is an efficient clustering method based on the theory of Markov chains, to classify protein families from protein sequences using pre-computed sequence similarity information. We implement the Tribe-MCL algorithm using an open source program of R. We select 24 protein sequences of Herpes virus obtained from NCBI database. The dataset consists of three types of glycoprotein B, F, and H. Each type has eight herpes virus that infected humans. Based on our simulation using different inflation factor r=1.5, 2, 3 we find a various number of the clusters results. The greater the inflation factor the greater the number of their clusters. Each protein will grouped together in the same type of protein.

Portuguese Lexical Clusters and CVC Sequences in Speech Perception and Production.

PubMed

Cunha, Conceição

2015-01-01

This paper investigates similarities between lexical consonant clusters and CVC sequences differing in the presence or absence of a lexical vowel in speech perception and production in two Portuguese varieties. The frequent high vowel deletion in the European variety (EP) and the realization of intervening vocalic elements between lexical clusters in Brazilian Portuguese (BP) may minimize the contrast between lexical clusters and CVC sequences in the two Portuguese varieties. In order to test this hypothesis we present a perception experiment with 72 participants and a physiological analysis of 3-dimensional movement data from 5 EP and 4 BP speakers. The perceptual results confirmed a gradual confusion of lexical clusters and CVC sequences in EP, which corresponded roughly to the gradient consonantal overlap found in production. © 2015 S. Karger AG, Basel.

On the age and mass function of the globular cluster M 4: A different interpretation of recent deep HST observations

NASA Astrophysics Data System (ADS)

De Marchi, G.; Paresce, F.; Straniero, O.; Prada Moroni, P. G.

2004-03-01

Very deep images of the Galactic globular cluster M 4 (NGC 6121) through the F606W and F814W filters were taken in 2001 with the WFPC2 on board the HST. A first published analysis of this data set (Richer et al. \\cite{Richer2002}) produced the result that the age of M 4 is 12.7± 0.7 Gyr (Hansen et al. \\cite{Hansen2002}), thus setting a robust lower limit to the age of the universe. In view of the great astronomical importance of getting this number right, we have subjected the same data set to the simplest possible photometric analysis that completely avoids uncertain assumptions about the origin of the detected sources. This analysis clearly reveals both a thin main sequence, from which can be deduced the deepest statistically complete mass function yet determined for a globular cluster, and a white dwarf (WD) sequence extending all the way down to the 5 \\sigma detection limit at I ≃ 27. The WD sequence is abruptly terminated at exactly this limit as expected by detection statistics. Using our most recent theoretical WD models (Prada Moroni & Straniero \\cite{Prada2002}) to obtain the expected WD sequence for different ages in the observed bandpasses, we find that the data so far obtained do not reach the peak of the WD luminosity function, thus only allowing one to set a lower limit to the age of M 4 of ˜9 Gyr. Thus, the problem of determining the absolute age of a globular cluster and, therefore, the onset of GC formation with cosmologically significant accuracy remains completely open. Only observations several magnitudes deeper than the limit obtained so far would allow one to approach this objective. Based on observations with the NASA/ESA Hubble Space Telescope, obtained at the Space Telescope Science Institute, which is operated by AURA for NASA under contract NAS5-26555.

Necessary Sequencing Depth and Clustering Method to Obtain Relatively Stable Diversity Patterns in Studying Fish Gut Microbiota.

PubMed

Xiao, Fanshu; Yu, Yuhe; Li, Jinjin; Juneau, Philippe; Yan, Qingyun

2018-05-25

The 16S rRNA gene is one of the most commonly used molecular markers for estimating bacterial diversity during the past decades. However, there is no consistency about the sequencing depth (from thousand to millions of sequences per sample), and the clustering methods used to generate OTUs may also be different among studies. These inconsistent premises make effective comparisons among studies difficult or unreliable. This study aims to examine the necessary sequencing depth and clustering method that would be needed to ensure a stable diversity patterns for studying fish gut microbiota. A total number of 42 samples dataset of Siniperca chuatsi (carnivorous fish) gut microbiota were used to test how the sequencing depth and clustering may affect the alpha and beta diversity patterns of fish intestinal microbiota. Interestingly, we found that the sequencing depth (resampling 1000-11,000 per sample) and the clustering methods (UPARSE and UCLUST) did not bias the estimates of the diversity patterns during the fish development from larva to adult. Although we should acknowledge that a suitable sequencing depth may differ case by case, our finding indicates that a shallow sequencing such as 1000 sequences per sample may be also enough to reflect the general diversity patterns of fish gut microbiota. However, we have shown in the present study that strict pre-processing of the original sequences is required to ensure reliable results. This study provides evidences to help making a strong scientific choice of the sequencing depth and clustering method for future studies on fish gut microbiota patterns, but at the same time reducing as much as possible the costs related to the analysis.

[Analysis on HIV-1 subtypes and transmission clusters in newly reported HIV/AIDS cases in Yiwu, Zhejiang Province, 2016].

PubMed

Zhang, J F; Yao, J M; Fan, Q; Chen, W J; Pan, X H; Ding, X B; Yang, J Z; Fu, T

2017-12-10

Objective: To understand the characteristics of distribution on HIV-1 subtypes and the transmission clusters in Yiwu in Zhejiang province. Methods: A cross-sectional study of molecular epidemiology was carried out on newly reported HIV/AIDS cases in Yiwu. RNA was extracted from 168 plasma samples, followed by RT-PCR and nest-PCR for pol gene amplification, sequencing, phylogenetic tree construction used for analyzing the subtypes and transmission clusters. Mutations on drug resistance was analyzed by CPR 6.0 online tool. Results: Subjects were mainly males (86.3%, 145/168), with average age as (39.1±13.4) years old and most of them were migrants (66.7%, 112/168). The major routes of transmission included homosexual (51.2%, 86/168) and heterosexual (48.8%, 82/168) contacts. The rate of success for sequence acquisition was 89.9% (151/168). The dominant subtypes showed as CRF01_AE (74, 49.0%) and CRF07_BC (64, 42.4%), followed by CRF08_BC (5, 3.3%), CRF55_01B (3, 2.0%), each case of subtype B, CRF45_cpx, CRF59_01B, CRF85_BC and URF (B/C). CRF45_cpx and CRF85_BC were discovered the first time in Zhejiang province. Twenty-six transmission clusters involving 65 cases were found, with the total clustered rate as 43.0% (65/151), in which the CRF01_AE clustered rate appeared as 54.1% (40/74), higher than that of CRF07_BC (21/64, 32.8%). The average size of cluster was 2.5 cases/cluster, with average size of cluster in CRF01_AE patients infected through heterosexual transmission as the largest (3.5 cases/cluster). The prevalence of transmitted drug resistance was 4.6% (7/151). Seven cases with surveillance drug resistant mutations (SDRM) were found, including 5 cases of M46L (3.3%), and one case of F77L or Y181C. Conclusion: HIV genetic diversity and a variety of transmission clusters had been noticed in this study area (Yiwu). Programs on monitoring the subtypes and transmission clusters should be continued and strengthened.

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).

The STREGA survey - II. Globular cluster Palomar 12

NASA Astrophysics Data System (ADS)

Musella, I.; Di Criscienzo, M.; Marconi, M.; Raimondo, G.; Ripepi, V.; Cignoni, M.; Bono, G.; Brocato, E.; Dall'Ora, M.; Ferraro, I.; Grado, A.; Iannicola, G.; Limatola, L.; Molinaro, R.; Moretti, M. I.; Stetson, P. B.; Capaccioli, M.; Cioni, M.-R. L.; Getman, F.; Schipani, P.

2018-01-01

In the framework of the STREGA (STRucture and Evolution of the GAlaxy) survey, two fields around the globular cluster Pal 12 were observed with the aim of detecting the possible presence of streams and/or an extended halo. The adopted stellar tracers are the main sequence, turn-off and red giant branch stars. We discuss the luminosity function and the star counts in the observed region covering about 2 tidal radii, confirming that Pal 12 appears to be embedded in the Sagittarius Stream. Adopting an original approach to separate cluster and field stars, we do not find any evidence of significant extra-tidal Pal 12 stellar populations. The presence of the Sagittarius stream seems to have mimicked a larger tidal radius in previous studies. Indeed, adopting a King model, a redetermination of this value gives rT = 0.22 ± 0.1 deg.

Classification of Cowpox Viruses into Several Distinct Clades and Identification of a Novel Lineage

PubMed Central

Franke, Annika; Pfaff, Florian; Jenckel, Maria; Hoffmann, Bernd; Höper, Dirk; Antwerpen, Markus; Meyer, Hermann; Beer, Martin; Hoffmann, Donata

2017-01-01

Cowpox virus (CPXV) was considered as uniform species within the genus Orthopoxvirus (OPV). Previous phylogenetic analysis indicated that CPXV is polyphyletic and isolates may cluster into different clades with two of these clades showing genetic similarities to either variola (VARV) or vaccinia viruses (VACV). Further analyses were initiated to assess both the genetic diversity and the evolutionary background of circulating CPXVs. Here we report the full-length sequences of 20 CPXV strains isolated from different animal species and humans in Germany. A phylogenetic analysis of altogether 83 full-length OPV genomes confirmed the polyphyletic character of the species CPXV and suggested at least four different clades. The German isolates from this study mainly clustered into two CPXV-like clades, and VARV- and VACV-like strains were not observed. A single strain, isolated from a cotton-top tamarin, clustered distantly from all other CPXVs and might represent a novel and unique evolutionary lineage. The classification of CPXV strains into clades roughly followed their geographic origin, with the highest clade diversity so far observed for Germany. Furthermore, we found evidence for recombination between OPV clades without significant disruption of the observed clustering. In conclusion, this analysis markedly expands the number of available CPXV full-length sequences and confirms the co-circulation of several CPXV clades in Germany, and provides the first data about a new evolutionary CPXV lineage. PMID:28604604

Molecular characterization of three common olive (Olea europaea L.) cultivars in Palestine, using simple sequence repeat (SSR) markers.

PubMed

Obaid, Ramiz; Abu-Qaoud, Hassan; Arafeh, Rami

2014-09-03

Eight accessions of olive trees from three common varieties in Palestine, Nabali Baladi, Nabali Mohassan and Surri, were genetically evaluated using five simple sequence repeat (SSR) markers. A total of 17 alleles from 5 loci were observed in which 15 (88.2%) were polymorphic and 2 (11.8%) were monomorphic. An average of 3.4 alleles per locus was found ranging from 2.0 alleles with the primers GAPU-103 and DCA-9 to 5.0 alleles with U9932 and DCA-16. The smallest amplicon size observed was 50 bp with the primer DCA-16, whereas the largest one (450 bp) with the primer U9932. Cluster analysis with the unweighted pair group method with arithmetic average (UPGMA) showed three clusters: a cluster with four accessions from the 'Nabali Baladi' cultivar, another cluster with three accessions that represents the 'Nabali Mohassen' cultivar and finally the 'Surri' cultivar. The similarity coefficient for the eight olive tree samples ranged from a maximum of 100% between two accessions from Nabali Baladi and also in two other samples from Nabali Mohassan, to a minimum similarity coefficient (0.315) between the Surri and two Nabali Baladi accessions. The results in this investigation clearly highlight the genetic dissimilarity between the three main olive cultivars that have been misidentified and mixed up in the past, based on conventional morphological characters.

Clusters of isoleucine, leucine, and valine side chains define cores of stability in high-energy states of globular proteins: Sequence determinants of structure and stability.

PubMed

Kathuria, Sagar V; Chan, Yvonne H; Nobrega, R Paul; Özen, Ayşegül; Matthews, C Robert

2016-03-01

Measurements of protection against exchange of main chain amide hydrogens (NH) with solvent hydrogens in globular proteins have provided remarkable insights into the structures of rare high-energy states that populate their folding free-energy surfaces. Lacking, however, has been a unifying theory that rationalizes these high-energy states in terms of the structures and sequences of their resident proteins. The Branched Aliphatic Side Chain (BASiC) hypothesis has been developed to explain the observed patterns of protection in a pair of TIM barrel proteins. This hypothesis supposes that the side chains of isoleucine, leucine, and valine (ILV) residues often form large hydrophobic clusters that very effectively impede the penetration of water to their underlying hydrogen bond networks and, thereby, enhance the protection against solvent exchange. The linkage between the secondary and tertiary structures enables these ILV clusters to serve as cores of stability in high-energy partially folded states. Statistically significant correlations between the locations of large ILV clusters in native conformations and strong protection against exchange for a variety of motifs reported in the literature support the generality of the BASiC hypothesis. The results also illustrate the necessity to elaborate this simple hypothesis to account for the roles of adjacent hydrocarbon moieties in defining stability cores of partially folded states along folding reaction coordinates. © 2015 The Protein Society.

Development of a Suite of Luciferase Gene Probes for the Screening and Detection of Marine Bioluminescent Systems and Organisms

DTIC Science & Technology

2006-01-01

catenella (Balech), Alexandrium fundyense (Balech) and also from a strain of Gonyaulax spinifera (Diesing), which produces bioluminescence...main clusters of the dinoflagellate luciferase sequences, a L. polyedrum clade, Pyrocystis clade, Alexandrium clade, Gonyaulax spinifera and a... Alexandrium cf catenella CCMP 1911 Alexandrium fundyense CCMP 1978 Alexandrium sp CCMP 1909 Alexandrium sp CCMP 1910 100/100 100/100 75/97 100

Main-Sequence O Stars in NGC 6231: Enhanced Winds

NASA Astrophysics Data System (ADS)

Morrison, Nancy D.

Three late O-type main-sequence stars in the open cluster NGC 6231 will be observed with IUE at high dispersion, and their C IV and N V resonance-line profiles will be studied. From low-dispersion IUE observations, 10 members of the cluster have been found to have anomalously strong C IV resonance lines for their spectral types. Massa, Savage, and Cassinelli (1984) observed two of these "UV peculiar" stars (spectral types B0.5 V and B1 V) at high dispersion. They found that the C IV lines have a strong, broad, shortward-shifted absorption component, which suggests a greatly enhanced wind relative to the average for the spectral type. They proposed that the enhancement is due to an overabundance of C. Recently, however, Grigsby, Gordon, Morrison, and Zimba (1992) showed from optical spectra that these stars have normal C abundances. Thus, there is not yet a convincing explanation for these strikingly anomalous stellar winds. By extending the temperature range over which the phenomenon has been studied at high dispersion, however, we expect to gain new physical information. From wind modeling of the line profiles, we will derive mass-loss rates and terminal velocities, and we will test whether these winds are described by radiation-driven wind theory.

The ultraviolet morphology of evolved populations

NASA Astrophysics Data System (ADS)

Chávez, Miguel

2009-04-01

In this paper I present a summary of the recent investigations we have developed at the Stellar Atmospheres and Populations Research Group (GrAPEs-for its designation in Spanish) at INAOE and collaborators in Italy. These investigations have aimed at providing updated stellar tools for the analysis of the UV spectra of a variety of stellar aggregates, mainly evolved ones. The sequence of material here presented roughly corresponds to the steps we have identified as mandatory to properly establish the applicability of synthetic populations in the analyses of observational data of globular clusters and more complex aged aggregates. The sequence is composed of four main stages, namely, (a) the creation of a theoretical stellar data base that we have called UVBLUE, (b) the comparison of such data base with observational stellar data, (c) the calculation of a set of synthetic spectral energy distributions (SEDs) of simple stellar populations (SSPs) and their validation through a comparison with observations of a sample of galactic globular clusters (GGCs), (d) construction of models for dating local ellipticals and distant red-envelope galaxies. Most of the work relies on the analysis of absorption line spectroscopic indices. The global results are more than satisfactory in the sense that theoretical indices closely follow the overall trends with chemical composition depicted by their empirical counterparts (stars and GGCs).

Using White Dwarf Companions of Blue Stragglers to Constrain Mass Transfer Physics

NASA Astrophysics Data System (ADS)

Gosnell, Natalie M.; Leiner, Emily; Geller, Aaron M.; Knigge, Christian; Mathieu, Robert D.; Sills, Alison; Leigh, Nathan

2018-06-01

Complete membership studies of old open clusters reveal that 25% of the evolved stars follow pathways in stellar evolution that are impacted by binary evolution. Recent studies show that the majority of blue straggler stars, traditionally defined to be stars brighter and bluer than the corresponding main sequence turnoff, are formed through mass transfer from a giant star onto a main sequence companion, resulting in a white dwarf in a binary system with a blue straggler. We will present constraints on the histories and mass transfer efficiencies for two blue straggler-white dwarf binaries in open cluster NGC 188. The constraints are a result of measuring white dwarf cooling temperatures and surface gravities with HST COS far-ultraviolet spectroscopy. This information sets both the timeline for mass transfer and the stellar masses in the pre-mass transfer binary, allowing us to constrain aspects of the mass transfer physics. One system is formed through Case C mass transfer, leaving a CO-core white dwarf, and provides an interesting test case for mass transfer from an asymptotic giant branch star in an eccentric system. The other system formed through Case B mass transfer, leaving a He-core white dwarf, and challenges our current understanding of the expected regimes for stable mass transfer from red giant branch stars.

Transmission clustering among newly diagnosed HIV patients in Chicago, 2008 to 2011: using phylogenetics to expand knowledge of regional HIV transmission patterns

PubMed Central

Lubelchek, Ronald J.; Hoehnen, Sarah C.; Hotton, Anna L.; Kincaid, Stacey L.; Barker, David E.; French, Audrey L.

2014-01-01

Introduction HIV transmission cluster analyses can inform HIV prevention efforts. We describe the first such assessment for transmission clustering among HIV patients in Chicago. Methods We performed transmission cluster analyses using HIV pol sequences from newly diagnosed patients presenting to Chicago’s largest HIV clinic between 2008 and 2011. We compared sequences via progressive pairwise alignment, using neighbor joining to construct an un-rooted phylogenetic tree. We defined clusters as >2 sequences among which each sequence had at least one partner within a genetic distance of ≤ 1.5%. We used multivariable regression to examine factors associated with clustering and used geospatial analysis to assess geographic proximity of phylogenetically clustered patients. Results We compared sequences from 920 patients; median age 35 years; 75% male; 67% Black, 23% Hispanic; 8% had a Rapid Plasma Reagin (RPR) titer ≥ 1:16 concurrent with their HIV diagnosis. We had HIV transmission risk data for 54%; 43% identified as men who have sex with men (MSM). Phylogenetic analysis demonstrated 123 patients (13%) grouped into 26 clusters, the largest having 20 members. In multivariable regression, age < 25, Black race, MSM status, male gender, higher HIV viral load, and RPR ≥ 1:16 associated with clustering. We did not observe geographic grouping of genetically clustered patients. Discussion Our results demonstrate high rates of HIV transmission clustering, without local geographic foci, among young Black MSM in Chicago. Applied prospectively, phylogenetic analyses could guide prevention efforts and help break the cycle of transmission. PMID:25321182

The second molecular epidemiological study of HIV infection in Mongolia between 2010 and 2016.

PubMed

Jagdagsuren, Davaalkham; Hayashida, Tsunefusa; Takano, Misao; Gombo, Erdenetuya; Zayasaikhan, Setsen; Kanayama, Naomi; Tsuchiya, Kiyoto; Oka, Shinichi

2017-01-01

Our previous 2005-2009 molecular epidemiological study in Mongolia identified a hot spot of HIV-1 transmission in men who have sex with men (MSM). To control the infection, we collaborated with NGOs to promote safer sex and HIV testing since mid-2010. In this study, we carried out the second molecular epidemiological survey between 2010 and 2016 to determine the status of HIV-1 infection in Mongolia. The study included 143 new cases of HIV-1 infection. Viral RNA was extracted from stocked plasma samples and sequenced for the pol and the env regions using the Sanger method. Near-full length sequencing using MiSeq was performed in 3 patients who were suspected to be infected with recombinant HIV-1. Phylogenetic analysis was performed using the neighbor-joining method and Bayesian Markov chain Monte Carlo method. MSM was the main transmission route in the previous and current studies. However, heterosexual route showed a significant increase in recent years. Phylogenetic analysis documented three taxa; Mongolian B, Korean B, and CRF51_01B, though the former two were also observed in the previous study. CRF51_01B, which originated from Singapore and Malaysia, was confirmed by near-full length sequencing. Although these strains were mainly detected in MSM, they were also found in increasing numbers of heterosexual males and females. Bayesian phylogenetic analysis estimated transmission of CRF51_01B into Mongolia around early 2000s. An extended Bayesian skyline plot showed a rapid increase in the effective population size of Mongolian B cluster around 2004 and that of CRF51_01B cluster around 2011. HIV-1 infection might expand to the general population in Mongolia. Our study documented a new cluster of HIV-1 transmission, enhancing our understanding of the epidemiological status of HIV-1 in Mongolia.

Identification of the Microbiota in Carious Dentin Lesions Using 16S rRNA Gene Sequencing

PubMed Central

Obata, Junko; Takeshita, Toru; Shibata, Yukie; Yamanaka, Wataru; Unemori, Masako; Akamine, Akifumi; Yamashita, Yoshihisa

2014-01-01

While mutans streptococci have long been assumed to be the specific pathogen responsible for human dental caries, the concept of a complex dental caries-associated microbiota has received significant attention in recent years. Molecular analyses revealed the complexity of the microbiota with the predominance of Lactobacillus and Prevotella in carious dentine lesions. However, characterization of the dentin caries-associated microbiota has not been extensively explored in different ethnicities and races. In the present study, the bacterial communities in the carious dentin of Japanese subjects were analyzed comprehensively with molecular approaches using the16S rRNA gene. Carious dentin lesion samples were collected from 32 subjects aged 4–76 years, and the 16S rRNA genes, amplified from the extracted DNA with universal primers, were sequenced with a pyrosequencer. The bacterial composition was classified into clusters I, II, and III according to the relative abundance (high, middle, low) of Lactobacillus. The bacterial composition in cluster II was composed of relatively high proportions of Olsenella and Propionibacterium or subdominated by heterogeneous genera. The bacterial communities in cluster III were characterized by the predominance of Atopobium, Prevotella, or Propionibacterium with Streptococcus or Actinomyces. Some samples in clusters II and III, mainly related to Atopobium and Propionibacterium, were novel combinations of microbiota in carious dentin lesions and may be characteristic of the Japanese population. Clone library analysis revealed that Atopobium sp. HOT-416 and P. acidifaciens were specific species associated with dentinal caries among these genera in a Japanese population. We summarized the bacterial composition of dentinal carious lesions in a Japanese population using next-generation sequencing and found typical Japanese types with Atopobium or Propionibacterium predominating. PMID:25083880

Identification of the microbiota in carious dentin lesions using 16S rRNA gene sequencing.

PubMed

Obata, Junko; Takeshita, Toru; Shibata, Yukie; Yamanaka, Wataru; Unemori, Masako; Akamine, Akifumi; Yamashita, Yoshihisa

2014-01-01

While mutans streptococci have long been assumed to be the specific pathogen responsible for human dental caries, the concept of a complex dental caries-associated microbiota has received significant attention in recent years. Molecular analyses revealed the complexity of the microbiota with the predominance of Lactobacillus and Prevotella in carious dentine lesions. However, characterization of the dentin caries-associated microbiota has not been extensively explored in different ethnicities and races. In the present study, the bacterial communities in the carious dentin of Japanese subjects were analyzed comprehensively with molecular approaches using the16S rRNA gene. Carious dentin lesion samples were collected from 32 subjects aged 4-76 years, and the 16S rRNA genes, amplified from the extracted DNA with universal primers, were sequenced with a pyrosequencer. The bacterial composition was classified into clusters I, II, and III according to the relative abundance (high, middle, low) of Lactobacillus. The bacterial composition in cluster II was composed of relatively high proportions of Olsenella and Propionibacterium or subdominated by heterogeneous genera. The bacterial communities in cluster III were characterized by the predominance of Atopobium, Prevotella, or Propionibacterium with Streptococcus or Actinomyces. Some samples in clusters II and III, mainly related to Atopobium and Propionibacterium, were novel combinations of microbiota in carious dentin lesions and may be characteristic of the Japanese population. Clone library analysis revealed that Atopobium sp. HOT-416 and P. acidifaciens were specific species associated with dentinal caries among these genera in a Japanese population. We summarized the bacterial composition of dentinal carious lesions in a Japanese population using next-generation sequencing and found typical Japanese types with Atopobium or Propionibacterium predominating.

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.

Abundance differences among globular-cluster giants: Primordial versus evolutionary scenarios

NASA Astrophysics Data System (ADS)

Kraft, Robert P.

1994-06-01

Contrary to historical expectation, stars within a given globular cluster often exhibit wide variations in the abundance of C, N, and O as well as certain light metals, particularly Na and Al. Owing to flux limitations, studies have been confined to evolved stars, especially giants, but in few instances variations have been detected among main-sequence stars. Among giants, the variations are of two kinds. The abundances of C and N are often anticorrelated, and in the limited number of cases in which both have been measured, O and N abundances have also often proved to be anticorrelated (Pilachowski 1988; Sneden et al. 1991; Brown et al. 1991; Kraft et al. 1992). Following pioneering work by Cohen (1978) and Peterson (1980), strong evidence has recently emerged for the existence of a significant global anticorrelation between O and Na abundances (Drake et al. 1992, Kraft et al. 1993). The observations are discussed in terms of contrasting hypotheses: evolutionary versus primordial. In the former, the variations are attributed to the dredgeup of material that has been processed through the CNO cycle in the globular-cluster stars themselves. In the latter, the variations are attributed to primordial chemical inhomogeneities in the material out of which the cluster stars were formed, the composition of these 'clumps' having been determined by nuclear processing in a prior generation of more massive stars. Observational evidence supporting each of these scenarios is cited. Recent studies of stellar rotation among horizontal branch stars in certain clusters (Peterson et al. 1994) as well as new calculations of Na-23 and Al-27 production in the CNO processing regions of evolving low-mass giants (Langer et al. 1993) lend fresh support to the evolutionary hypothesis. However, such calculations do not explain the variation of C and N abundances found among cluster main-sequence stars (Suntzeff 1989; Briley et al. 1991) which therefore seem explicable only on the basis of a primordial scenario. Among mildly metal-poor giants, i.e., those in the range from solar metallicity to (Fe/H) approximately -1, recent observational evidence suggesting the existence of a substructure in the (el/Fe) ratios of the heavier alpha elements, e.g., Si, Mg, Ca, and Ti, is discussed. The possible influence of this effect on the interpretation of the integrated spectra of extragalactic globular clusters and E galaxies is noted.

Characterization of the flgG operon of Rhodobacter sphaeroides WS8 and its role in flagellum biosynthesis.

PubMed

González-Pedrajo, Bertha; de la Mora, Javier; Ballado, Teresa; Camarena, Laura; Dreyfus, Georges

2002-11-13

In this work, we show evidence regarding the functionality of a large cluster of flagellar genes in Rhodobacter sphaeroides. The genes of this cluster, flgGHIJKL and orf-1, are mainly involved in the formation of the basal body, and flgK and flgL encode the hook-associated proteins HAP1 and HAP3. In general, these genes showed a good similarity as compared with those reported for Salmonella enterica. However, flgJ and flgK showed particular features that make them unique among the flagellar sequences already reported. flgJ is only a third of the size reported for flgJ from Salmonella; whereas flgK is about three times larger than any other flgK sequence previously known. Our results indicate that both genes are functional, and their products are essential for flagellar assembly. In contrast, the interruption of orf-1, did not affect motility suggesting that this sequence, if functional, is not indispensable for flagellar assembly. Finally, we present genetic evidence suggesting that the flgGHIJKL genes are expressed as a single transcriptional unit depending on the sigma-54 factor.

Clustering evolving proteins into homologous families.

PubMed

Chan, Cheong Xin; Mahbob, Maisarah; Ragan, Mark A

2013-04-08

Clustering sequences into groups of putative homologs (families) is a critical first step in many areas of comparative biology and bioinformatics. The performance of clustering approaches in delineating biologically meaningful families depends strongly on characteristics of the data, including content bias and degree of divergence. New, highly scalable methods have recently been introduced to cluster the very large datasets being generated by next-generation sequencing technologies. However, there has been little systematic investigation of how characteristics of the data impact the performance of these approaches. Using clusters from a manually curated dataset as reference, we examined the performance of a widely used graph-based Markov clustering algorithm (MCL) and a greedy heuristic approach (UCLUST) in delineating protein families coded by three sets of bacterial genomes of different G+C content. Both MCL and UCLUST generated clusters that are comparable to the reference sets at specific parameter settings, although UCLUST tends to under-cluster compositionally biased sequences (G+C content 33% and 66%). Using simulated data, we sought to assess the individual effects of sequence divergence, rate heterogeneity, and underlying G+C content. Performance decreased with increasing sequence divergence, decreasing among-site rate variation, and increasing G+C bias. Two MCL-based methods recovered the simulated families more accurately than did UCLUST. MCL using local alignment distances is more robust across the investigated range of sequence features than are greedy heuristics using distances based on global alignment. Our results demonstrate that sequence divergence, rate heterogeneity and content bias can individually and in combination affect the accuracy with which MCL and UCLUST can recover homologous protein families. For application to data that are more divergent, and exhibit higher among-site rate variation and/or content bias, MCL may often be the better choice, especially if computational resources are not limiting.

Early history of European domestic cattle as revealed by ancient DNA.

PubMed

Bollongino, R; Edwards, C J; Alt, K W; Burger, J; Bradley, D G

2006-03-22

We present an extensive ancient DNA analysis of mainly Neolithic cattle bones sampled from archaeological sites along the route of Neolithic expansion, from Turkey to North-Central Europe and Britain. We place this first reasonable population sample of Neolithic cattle mitochondrial DNA sequence diversity in context to illustrate the continuity of haplotype variation patterns from the first European domestic cattle to the present. Interestingly, the dominant Central European pattern, a starburst phylogeny around the modal sequence, T3, has a Neolithic origin, and the reduced diversity within this cluster in the ancient samples accords with their shorter history of post-domestic accumulation of mutation.

DoOP: Databases of Orthologous Promoters, collections of clusters of orthologous upstream sequences from chordates and plants

PubMed Central

Barta, Endre; Sebestyén, Endre; Pálfy, Tamás B.; Tóth, Gábor; Ortutay, Csaba P.; Patthy, László

2005-01-01

DoOP (http://doop.abc.hu/) is a database of eukaryotic promoter sequences (upstream regions) aiming to facilitate the recognition of regulatory sites conserved between species. The annotated first exons of human and Arabidopsis thaliana genes were used as queries in BLAST searches to collect the most closely related orthologous first exon sequences from Chordata and Viridiplantae species. Up to 3000 bp DNA segments upstream from these first exons constitute the clusters in the chordate and plant sections of the Database of Orthologous Promoters. Release 1.0 of DoOP contains 21 061 chordate clusters from 284 different species and 7548 plant clusters from 269 different species. The database can be used to find and retrieve promoter sequences of a given gene from various species and it is also suitable to see the most trivial conserved sequence blocks in the orthologous upstream regions. Users can search DoOP with either sequence or text (annotation) to find promoter clusters of various genes. In addition to the sequence data, the positions of the conserved sequence blocks derived from multiple alignments, the positions of repetitive elements and the positions of transcription start sites known from the Eukaryotic Promoter Database (EPD) can be viewed graphically. PMID:15608291

DoOP: Databases of Orthologous Promoters, collections of clusters of orthologous upstream sequences from chordates and plants.

PubMed

Barta, Endre; Sebestyén, Endre; Pálfy, Tamás B; Tóth, Gábor; Ortutay, Csaba P; Patthy, László

2005-01-01

DoOP (http://doop.abc.hu/) is a database of eukaryotic promoter sequences (upstream regions) aiming to facilitate the recognition of regulatory sites conserved between species. The annotated first exons of human and Arabidopsis thaliana genes were used as queries in BLAST searches to collect the most closely related orthologous first exon sequences from Chordata and Viridiplantae species. Up to 3000 bp DNA segments upstream from these first exons constitute the clusters in the chordate and plant sections of the Database of Orthologous Promoters. Release 1.0 of DoOP contains 21,061 chordate clusters from 284 different species and 7548 plant clusters from 269 different species. The database can be used to find and retrieve promoter sequences of a given gene from various species and it is also suitable to see the most trivial conserved sequence blocks in the orthologous upstream regions. Users can search DoOP with either sequence or text (annotation) to find promoter clusters of various genes. In addition to the sequence data, the positions of the conserved sequence blocks derived from multiple alignments, the positions of repetitive elements and the positions of transcription start sites known from the Eukaryotic Promoter Database (EPD) can be viewed graphically.

Acquisition of initial /s/-stop and stop-/s/sequences in Greek.

PubMed

Syrika, Asimina; Nicolaidis, Katerina; Edwards, Jan; Beckman, Mary E

2011-09-01

Previous work on children's acquisition of complex sequences points to a tendency for affricates to be acquired before clusters, but there is no clear evidence of a difference in order of acquisition between clusters with /s/ that violate the Sonority Sequencing Principle (SSP), such as /s/ followed by stop in onset position, and other clusters that obey the SSP. One problem with studies that have compared the acquisition of SSP-obeying and SSP-violating clusters is that the component sounds in the two types of sequences were different.This paper examines the acquisition of initial /s/-stop and stop-/s/ sequences by sixty Greek children aged 2 through 5 years. Results showed greater accuracy for the /s/-stop relative to the stop-/s/ sequences, but no difference in accuracy between /ts/, which is usually analyzed as an affricate in Greek, and the other stop-/s/ sequences. Moreover, errors for the /s/-stop sequences and /ts/ primarily involved stop substitutions, whereas errors for /ps/ and /ks/ were more variable and often involved fricative substitutions, a pattern which may have a perceptual explanation. Finally, /ts/ showed a distinct temporal pattern relative to the stop-/s/ clusters /ps/ and /ks/, similar to what has been reported for productions of Greek adults.

Acquisition of initial /s/-stop and stop-/s/ sequences in Greek

PubMed Central

Syrika, Asimina; Nicolaidis, Katerina; Edwards, Jan; Beckman, Mary E.

2010-01-01

Previous work on children’s acquisition of complex sequences points to a tendency for affricates to be acquired before clusters, but there is no clear evidence of a difference in order of acquisition between clusters with /s/ that violate the Sonority Sequencing Principle (SSP), such as /s/ followed by stop in onset position, and other clusters that obey the SSP. One problem with studies that have compared the acquisition of SSP-obeying and SSP-violating clusters is that the component sounds in the two types of sequences were different. This paper examines the acquisition of initial /s/-stop and stop-/s/ sequences by sixty Greek children aged 2 through 5 years. Results showed greater accuracy for the /s/-stop relative to the stop-/s/ sequences, but no difference in accuracy between /ts/, which is usually analyzed as an affricate in Greek, and the other stop-/s/ sequences. Moreover, errors for the /s/-stop sequences and /ts/ primarily involved stop substitutions, whereas errors for /ps/ and /ks/ were more variable and often involved fricative substitutions, a pattern which may have a perceptual explanation. Finally, /ts/ showed a distinct temporal pattern relative to the stop-/s/ clusters /ps/ and /ks/, similarly to what has been reported for productions of Greek adults. PMID:22070044

Patterns of genetic diversity in Hepatozoon spp. infecting snakes from North Africa and the Mediterranean Basin.

PubMed

Tomé, Beatriz; Maia, João P; Salvi, Daniele; Brito, José C; Carretero, Miguel A; Perera, Ana; Meimberg, Harald; Harris, David James

2014-03-01

Species of Hepatozoon Miller, 1908 are blood parasites most commonly found in snakes but some have been described from all tetrapod groups and a wide variety of hematophagous invertebrates. Previous studies have suggested possible associations between Hepatozoon spp. found in predators and prey. Particularly, some saurophagous snakes from North Africa and the Mediterranean region have been found to be infected with Hepatozoon spp. similar to those of various sympatric lizard hosts. In this study, we have screened tissue samples of 111 North African and Mediterranean snakes, using specific primers for the 18S rRNA gene. In the phylogenetic analysis, the newly-generated Hepatozoon spp. sequences grouped separately into five main clusters. Three of these clusters were composed by Hepatozoon spp. also found in snakes and other reptiles from the Mediterranean Basin and North Africa. In the other two clusters, the new sequences were not closely related to geographically proximate known sequences. The phylogeny of Hepatozoon spp. inferred here was not associated with intermediate host taxonomy or geographical distribution. From the other factors that could explain these evolutionary patterns, the most likely seems series of intermediate hosts providing similar ribotypes of Hepatozoon and a high prevalence of host shifts for Hepatozoon spp. This is indicated by ribotypes of high similarity found in different reptile families, as well as by divergent ribotypes found in the same host species. This potentially low host specificity has profound implications for the systematics of Hepatozoon spp.

Evolutionary Trends of Perkinsozoa (Alveolata) Characters Based on Observations of Two New Genera of Parasitoids of dinoflagellates, Dinovorax gen. nov. and Snorkelia gen. nov.

PubMed Central

Reñé, Albert; Alacid, Elisabet; Ferrera, Isabel; Garcés, Esther

2017-01-01

Parasites are one of the ecologically most relevant groups of marine food webs, but their taxonomic and biological complexity hampers the assessment of their diversity and evolutionary trends. Moreover, the within-host processes that govern parasitoid infection, development and reproduction are often unknown. In this study, we describe a new species of a perkinsozoan endoparasitoid that infects the toxic dinoflagellate Dinophysis sacculus, by including observations of its morphology, ultrastructure, life-cycle development and phylogeny. The SSU rDNA sequence and main morphological features were also obtained for a second parasitoid species infecting the bloom-forming dinoflagellate Levanderina fissa. Phylogenetic analyses including the sequences obtained show that all known Perkinsozoa species infecting dinoflagellates cluster together. However, sequences of Parvilucifera prorocentri and those obtained in this study cluster at the base of the clade, while the rest of Parvilucifera representatives form a separated highly-supported cluster. These results, together with differing morphological characters like the formation of a germ-tube, the presence of trichocysts, or the heterochromatin presence in zoospores nucleus justify the erection of Dinovorax pyriformis gen. nov. et sp. nov., and Snorkelia prorocentri gen. nov. et comb. nov. (=Parvilucifera prorocentri). The morphological features and phylogenetic position of these parasitoids represent ancestral characters for the Perkinsozoa phylum, and also for Dinozoa clade, allowing the inference of the evolutionary framework of these Alveolata members. PMID:28970818

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.

Detection of a late B star companion of the bright cluster giant C PUP equals HD 63032

NASA Astrophysics Data System (ADS)

Groote, D.; Reimers, D.

1983-03-01

IUE observations show that c Pup, the central bright K giant in the open cluster NGC 2451, has a blue companion. A fit of theoretical line blanketed model atmosphere fluxes to the observed energy distribution yields reddening E(B-V) = 0.15 (from λ2200 Å feature), an effective temperature Te = 10,200K, and an angular diameter θ = 0.060. If the companion is a main-sequence star, c Pup and its companion are located at a distance of 310 ± 50 pc which lends additional support to membership of c Pup in NGC 2451. The evolutionary status of c Pup is briefly discussed.

Discrete Cosine Transform Image Coding With Sliding Block Codes

NASA Astrophysics Data System (ADS)

Divakaran, Ajay; Pearlman, William A.

1989-11-01

A transform trellis coding scheme for images is presented. A two dimensional discrete cosine transform is applied to the image followed by a search on a trellis structured code. This code is a sliding block code that utilizes a constrained size reproduction alphabet. The image is divided into blocks by the transform coding. The non-stationarity of the image is counteracted by grouping these blocks in clusters through a clustering algorithm, and then encoding the clusters separately. Mandela ordered sequences are formed from each cluster i.e identically indexed coefficients from each block are grouped together to form one dimensional sequences. A separate search ensues on each of these Mandela ordered sequences. Padding sequences are used to improve the trellis search fidelity. The padding sequences absorb the error caused by the building up of the trellis to full size. The simulations were carried out on a 256x256 image ('LENA'). The results are comparable to any existing scheme. The visual quality of the image is enhanced considerably by the padding and clustering.

MetaCAA: A clustering-aided methodology for efficient assembly of metagenomic datasets.

PubMed

Reddy, Rachamalla Maheedhar; Mohammed, Monzoorul Haque; Mande, Sharmila S

2014-01-01

A key challenge in analyzing metagenomics data pertains to assembly of sequenced DNA fragments (i.e. reads) originating from various microbes in a given environmental sample. Several existing methodologies can assemble reads originating from a single genome. However, these methodologies cannot be applied for efficient assembly of metagenomic sequence datasets. In this study, we present MetaCAA - a clustering-aided methodology which helps in improving the quality of metagenomic sequence assembly. MetaCAA initially groups sequences constituting a given metagenome into smaller clusters. Subsequently, sequences in each cluster are independently assembled using CAP3, an existing single genome assembly program. Contigs formed in each of the clusters along with the unassembled reads are then subjected to another round of assembly for generating the final set of contigs. Validation using simulated and real-world metagenomic datasets indicates that MetaCAA aids in improving the overall quality of assembly. A software implementation of MetaCAA is available at https://metagenomics.atc.tcs.com/MetaCAA. Copyright © 2014 Elsevier Inc. All rights reserved.

The Mass Function in h+(chi) Persei

NASA Astrophysics Data System (ADS)

Bragg, Ann; Kenyon, Scott

2000-08-01

Knowledge of the stellar initial mass function (IMF) is critical to understanding star formation and galaxy evolution. Past studies of the IMF in open clusters have primarily used luminosity functions to determine mass functions, frequently in relatively sparse clusters. Our goal with this project is to derive a reliable, well- sampled IMF for a pair of very dense young clusters (h+(chi) Persei) with ages, 1-2 × 10^7 yr (e.g., Vogt A& A 11:359), where stellar evolution theory is robust. We will construct the HR diagram using both photometry and spectral types to derive more accurate stellar masses and ages than are possible using photometry alone. Results from the two clusters will be compared to examine the universality of the IMF. We currently have a spectroscopic sample covering an area within 9 arc-minutes of the center of each cluster taken with the FAST Spectrograph. The sample is complete to V=15.4 and contains ~ 1000 stars. We request 2 nights at WIYN/HYDRA to extend this sample to deeper magnitudes, allowing us to determine the IMF of the clusters to a lower limiting mass and to search for a pre-main sequence, theoretically predicted to be present for clusters of this age. Note that both clusters are contained within a single HYDRA field.

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

A generalized analysis of hydrophobic and loop clusters within globular protein sequences

PubMed Central

Eudes, Richard; Le Tuan, Khanh; Delettré, Jean; Mornon, Jean-Paul; Callebaut, Isabelle

2007-01-01

Background Hydrophobic Cluster Analysis (HCA) is an efficient way to compare highly divergent sequences through the implicit secondary structure information directly derived from hydrophobic clusters. However, its efficiency and application are currently limited by the need of user expertise. In order to help the analysis of HCA plots, we report here the structural preferences of hydrophobic cluster species, which are frequently encountered in globular domains of proteins. These species are characterized only by their hydrophobic/non-hydrophobic dichotomy. This analysis has been extended to loop-forming clusters, using an appropriate loop alphabet. Results The structural behavior of hydrophobic cluster species, which are typical of protein globular domains, was investigated within banks of experimental structures, considered at different levels of sequence redundancy. The 294 more frequent hydrophobic cluster species were analyzed with regard to their association with the different secondary structures (frequencies of association with secondary structures and secondary structure propensities). Hydrophobic cluster species are predominantly associated with regular secondary structures, and a large part (60 %) reveals preferences for α-helices or β-strands. Moreover, the analysis of the hydrophobic cluster amino acid composition generally allows for finer prediction of the regular secondary structure associated with the considered cluster within a cluster species. We also investigated the behavior of loop forming clusters, using a "PGDNS" alphabet. These loop clusters do not overlap with hydrophobic clusters and are highly associated with coils. Finally, the structural information contained in the hydrophobic structural words, as deduced from experimental structures, was compared to the PSI-PRED predictions, revealing that β-strands and especially α-helices are generally over-predicted within the limits of typical β and α hydrophobic clusters. Conclusion The dictionary of hydrophobic clusters described here can help the HCA user to interpret and compare the HCA plots of globular protein sequences, as well as provides an original fundamental insight into the structural bricks of protein folds. Moreover, the novel loop cluster analysis brings additional information for secondary structure prediction on the whole sequence through a generalized cluster analysis (GCA), and not only on regular secondary structures. Such information lays the foundations for developing a new and original tool for secondary structure prediction. PMID:17210072

A Predominant Variable-Number Tandem-Repeat Cluster of Mycobacterium tuberculosis Isolates among Asylum Seekers in the Netherlands and Denmark, Deciphered by Whole-Genome Sequencing

PubMed Central

de Neeling, Albert; Rasmussen, Erik Michael; Norman, Anders; Mulder, Arnout; van Hunen, Rianne; de Vries, Gerard; Haddad, Walid; Anthony, Richard; Lillebaek, Troels; van der Hoek, Wim; van Soolingen, Dick

2017-01-01

ABSTRACT In many countries, Mycobacterium tuberculosis isolates are routinely subjected to variable-number tandem-repeat (VNTR) typing to investigate M. tuberculosis transmission. Unexpectedly, cross-border clusters were identified among African refugees in the Netherlands and Denmark, although transmission in those countries was unlikely. Whole-genome sequencing (WGS) was applied to analyze transmission in depth and to assess the precision of VNTR typing. WGS was applied to 40 M. tuberculosis isolates from refugees in the Netherlands and Denmark (most of whom were from the Horn of Africa) that shared the exact same VNTR profile. Cluster investigations were undertaken to identify in-country epidemiological links. Combining WGS results for the isolates (all members of the central Asian strain [CAS]/Delhi genotype), from both European countries, an average genetic distance of 80 single-nucleotide polymorphisms (SNPs) (maximum, 153 SNPs) was observed. The few pairs of isolates with confirmed epidemiological links, except for one pair, had a maximum distance of 12 SNPs. WGS divided this refugee cluster into several subclusters of patients from the same country of origin. Although the M. tuberculosis cases, mainly originating from African countries, shared the exact same VNTR profile, most were clearly distinguished by WGS. The average genetic distance in this specific VNTR cluster was 2 times greater than that in other VNTR clusters. Thus, identical VNTR profiles did not represent recent direct M. tuberculosis transmission for this group of patients. It appears that either these strains from Africa are extremely conserved genetically or there is ongoing transmission of this genotype among refugees on their long migration routes from Africa to Europe. PMID:29167288

A Predominant Variable-Number Tandem-Repeat Cluster of Mycobacterium tuberculosis Isolates among Asylum Seekers in the Netherlands and Denmark, Deciphered by Whole-Genome Sequencing.

PubMed

Jajou, Rana; de Neeling, Albert; Rasmussen, Erik Michael; Norman, Anders; Mulder, Arnout; van Hunen, Rianne; de Vries, Gerard; Haddad, Walid; Anthony, Richard; Lillebaek, Troels; van der Hoek, Wim; van Soolingen, Dick

2018-02-01

In many countries, Mycobacterium tuberculosis isolates are routinely subjected to variable-number tandem-repeat (VNTR) typing to investigate M. tuberculosis transmission. Unexpectedly, cross-border clusters were identified among African refugees in the Netherlands and Denmark, although transmission in those countries was unlikely. Whole-genome sequencing (WGS) was applied to analyze transmission in depth and to assess the precision of VNTR typing. WGS was applied to 40 M. tuberculosis isolates from refugees in the Netherlands and Denmark (most of whom were from the Horn of Africa) that shared the exact same VNTR profile. Cluster investigations were undertaken to identify in-country epidemiological links. Combining WGS results for the isolates (all members of the central Asian strain [CAS]/Delhi genotype), from both European countries, an average genetic distance of 80 single-nucleotide polymorphisms (SNPs) (maximum, 153 SNPs) was observed. The few pairs of isolates with confirmed epidemiological links, except for one pair, had a maximum distance of 12 SNPs. WGS divided this refugee cluster into several subclusters of patients from the same country of origin. Although the M. tuberculosis cases, mainly originating from African countries, shared the exact same VNTR profile, most were clearly distinguished by WGS. The average genetic distance in this specific VNTR cluster was 2 times greater than that in other VNTR clusters. Thus, identical VNTR profiles did not represent recent direct M. tuberculosis transmission for this group of patients. It appears that either these strains from Africa are extremely conserved genetically or there is ongoing transmission of this genotype among refugees on their long migration routes from Africa to Europe. Copyright © 2018 Jajou et al.

Linking Dynamical and Stellar Evolution in the Metal-Poor Globular Cluster M92

NASA Astrophysics Data System (ADS)

Kalirai, Jason

2017-08-01

We propose a 5 orbit HST program to acquire UV imaging at the center of the ancient, metal-poor globular cluster NGC 6341 (M92). Our program is designed to achieve two science goals with a single data set, 1.) to directly measure the diffusion of stars through the massive cluster's core, 2.) to pinpoint the phase of post main-sequence evolution at which [Fe/H] = -2.3 stars lose their mass. Our novel technique will achieve these goals by using the full power of WFC3's exquisite UV sensitivity at <0.3 microns combined with its high spatial resolution. We will uncover 1000 newly-formed white dwarfs in the center of M92 and track how their spatial distribution changes as they get older on the cooling sequence. Having just experienced significant mass loss, the youngest remnants with ages <10s of Myr will still be moving slowly like their 0.8 Msun progenitors, whereas the older remnants with t_cool > 100s Myr will be fully relaxed. Using the methodology we developed and successfully applied to 47 Tuc (Heyl et al. 2015a; 2015b), we will watch this dynamical evolution to measure the diffusion coefficient due to gravitational relaxation in the cluster's core and the past timing of stellar mass loss that was responsible for the current cluster mass segregation profile. M92 is the ideal target for this study as it complements our existing study of the relatively metal-rich cluster 47 Tuc; it has an extremely low metallicity of [Fe/H] = -2.3, very low foreground reddening (E(B-V) = 0.02), moderate concentration index, and a theoretically-expected relaxation timescale in its core of 90 Myr, which nicely splits the young and old white dwarfs that can be observed with Hubble.

Insights into magmatic processes and hydrothermal alteration of in situ superfast spreading ocean crust at ODP/IODP site 1256 from a cluster analysis of rock magnetic properties

NASA Astrophysics Data System (ADS)

Dekkers, Mark J.; Heslop, David; Herrero-Bervera, Emilio; Acton, Gary; Krasa, David

2014-08-01

We analyze magnetic properties from Ocean Drilling Program (ODP)/Integrated ODP (IODP) Hole 1256D (6°44.1' N, 91°56.1' W) on the Cocos Plate in ˜15.2 Ma oceanic crust generated by superfast seafloor spreading, the only drill hole that has sampled all three oceanic crust layers in a tectonically undisturbed setting. Fuzzy c-means cluster analysis and nonlinear mapping are utilized to study down-hole trends in the ratio of the saturation remanent magnetization and the saturation magnetization, the coercive force, the ratio of the remanent coercive force and coercive force, the low-field magnetic susceptibility, and the Curie temperature, to evaluate the effects of magmatic and hydrothermal processes on magnetic properties. A statistically robust five cluster solution separates the data predominantly into three clusters that express increasing hydrothermal alteration of the lavas, which differ from two distinct clusters mainly representing the dikes and gabbros. Extensive alteration can obliterate magnetic property differences between lavas, dikes, and gabbros. The imprint of thermochemical alteration on the iron-titanium oxides is only partially related to the porosity of the rocks. Thus, the analysis complements interpretation based on electrofacies analysis. All clusters display rock magnetic characteristics compatible with an ability to retain a stable natural remanent magnetization suggesting that the entire sampled sequence of ocean crust can contribute to marine magnetic anomalies. Paleointensity determination is difficult because of the propensity of oxyexsolution during laboratory heating and/or the presence of intergrowths. The upper part of the extrusive sequence, the granoblastic dikes, and moderately altered gabbros may contain a comparatively uncontaminated thermoremanent magnetization.

Red giants and yellow stragglers in the young open cluster NGC 2447

NASA Astrophysics Data System (ADS)

da Silveira, M. D.; Pereira, C. B.; Drake, N. A.

2018-06-01

In this work we analysed, using high-resolution spectroscopy, a sample of 12 single and 4 spectroscopic binary stars of the open cluster NGC 2447. For the single stars, we obtained atmospheric parameters and chemical abundances of Li, C, N, O, Na, Mg, Al, Ca, Si, Ti, Ni, Cr, Y, Zr, La, Ce, Nd, Eu. Rotational velocities were obtained for all the stars. The abundances of the light elements and Eu and the rotational velocities were derived using spectral synthesis technique. We obtained a mean metallicity of [Fe/H] = -0.17 ± 0.05. We found that the abundances of all elements are similar to field giants and/or giants of open clusters, even for the s-process elements, which are enhanced as in other young open clusters. We show that the spectroscopic binaries NGC 2447-26, 38, and 42 are yellow-straggler stars, of which the primary is a giant star and the secondary a main-sequence A-type star.

Lithium Abundances in the Young Open Cluster IC 2602

NASA Technical Reports Server (NTRS)

Randich, S.; Aharpour, N.; Pallavicini, R.; Prosser, C. F.; Stauffer, J. R.

1997-01-01

We have obtained high-resolution spectra for 28 candidate late-type stars in the 30 Myr old cluster IC 2602. NLTE Li abundances have been derived from measured equivalent widths. The log n(Li) - T(sub eff) and log n(Li) - mass distributions for our sample stars have been compared with those of the Pleiades and alpha Persei. Our data show that F stars in the three clusters have the same lithium content, which corresponds to the initial content for Pop. I stars. G and early-K IC 2602 stars are, on average, somewhat more Li-rich than their counterparts in the two slightly older clusters. Finally, the latest-type IC 2602 stars are heavily Li depleted, with their Li content being as low as the lowest measured among the Pleiades. As in the Pleiades and alpha Per, a star-to-star scatter in lithium is observed among 30 Myr old late-K/early-K dwarfs in IC 2602, indicating that this spread develops in the pre-main sequence phases.

Strain-Level Diversity of Secondary Metabolism in Streptomyces albus

PubMed Central

Seipke, Ryan F.

2015-01-01

Streptomyces spp. are robust producers of medicinally-, industrially- and agriculturally-important small molecules. Increased resistance to antibacterial agents and the lack of new antibiotics in the pipeline have led to a renaissance in natural product discovery. This endeavor has benefited from inexpensive high quality DNA sequencing technology, which has generated more than 140 genome sequences for taxonomic type strains and environmental Streptomyces spp. isolates. Many of the sequenced streptomycetes belong to the same species. For instance, Streptomyces albus has been isolated from diverse environmental niches and seven strains have been sequenced, consequently this species has been sequenced more than any other streptomycete, allowing valuable analyses of strain-level diversity in secondary metabolism. Bioinformatics analyses identified a total of 48 unique biosynthetic gene clusters harboured by Streptomyces albus strains. Eighteen of these gene clusters specify the core secondary metabolome of the species. Fourteen of the gene clusters are contained by one or more strain and are considered auxiliary, while 16 of the gene clusters encode the production of putative strain-specific secondary metabolites. Analysis of Streptomyces albus strains suggests that each strain of a Streptomyces species likely harbours at least one strain-specific biosynthetic gene cluster. Importantly, this implies that deep sequencing of a species will not exhaust gene cluster diversity and will continue to yield novelty. PMID:25635820

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).

SEAN: SNP prediction and display program utilizing EST sequence clusters.

PubMed

Huntley, Derek; Baldo, Angela; Johri, Saurabh; Sergot, Marek

2006-02-15

SEAN is an application that predicts single nucleotide polymorphisms (SNPs) using multiple sequence alignments produced from expressed sequence tag (EST) clusters. The algorithm uses rules of sequence identity and SNP abundance to determine the quality of the prediction. A Java viewer is provided to display the EST alignments and predicted SNPs.

Genetic characterization and phylogenetic analysis of porcine circovirus type 2 (PCV2) in Serbia.

PubMed

Savic, Bozidar; Milicevic, Vesna; Jakic-Dimic, Dobrila; Bojkovski, Jovan; Prodanovic, Radisa; Kureljusic, Branislav; Potkonjak, Aleksandar; Savic, Borivoje

2012-01-01

Porcine circovirus type 2 (PCV2) is the main causative agent of postweaning multisystemic wasting syndrome (PMWS). To characterize and determine the genetic diversity of PCV2 in the porcine population of Serbia, nucleotide and deduced amino acid sequences of the open reading frame 2 (ORF2) of PCV2 collected from the tissues of pigs that either had died as a result of PMWS or did not exhibit disease symptoms were analyzed. Sequencing and phylogenetic analysis showed considerable diversity among PCV2 ORF2 sequences and the existence of two main PCV2 genotypes, PCV2b and PCV2a, with at least three clusters, 1A/B, 1C and 2D. In order to provide further proof that the 1C strain is circulating in the porcine population, the whole viral genome of one PCV2 isolate was sequenced. Genotyping and phylogenetic analysis using the entire viral genome sequences confirmed that there was a PMWS-associated 1C strain emerging in Serbia. Our analysis also showed that PCV2b is dominant in the porcine population, and that it is exclusively associated with PMWS occurrences in the country. These data constitute a useful basis for further epidemiological studies regarding the heterogeneity of PCV2 strains on the European continent.

A Public Health Model for the Molecular Surveillance of HIV Transmission in San Diego, California

PubMed Central

May, Susanne; Tweeten, Samantha; Drumright, Lydia; Pacold, Mary E.; Kosakovsky Pond, Sergei L.; Pesano, Rick L.; Lie, Yolanda S.; Richman, Douglas D.; Frost, Simon D.W.; Woelk, Christopher H.; Little, Susan J.

2009-01-01

Background Current public health efforts often use molecular technologies to identify and contain communicable disease networks, but not for HIV. Here, we investigate how molecular epidemiology can be used to identify highly-related HIV networks within a population and how voluntary contact tracing of sexual partners can be used to selectively target these networks. Methods We evaluated the use of HIV-1 pol sequences obtained from participants of a community-recruited cohort (n=268) and a primary infection research cohort (n=369) to define highly related transmission clusters and the use of contact tracing to link other individuals (n=36) within these clusters. The presence of transmitted drug resistance was interpreted from the pol sequences (Calibrated Population Resistance v3.0). Results Phylogenetic clustering was conservatively defined when the genetic distance between any two pol sequences was <1%, which identified 34 distinct transmission clusters within the combined community-recruited and primary infection research cohorts containing 160 individuals. Although sequences from the epidemiologically-linked partners represented approximately 5% of the total sequences, they clustered with 60% of the sequences that clustered from the combined cohorts (O.R. 21.7; p=<0.01). Major resistance to at least one class of antiretroviral medication was found in 19% of clustering sequences. Conclusions Phylogenetic methods can be used to identify individuals who are within highly related transmission groups, and contact tracing of epidemiologically-linked partners of recently infected individuals can be used to link into previously-defined transmission groups. These methods could be used to implement selectively targeted prevention interventions. PMID:19098493

Comparison of single-use and reusable metal laryngoscope blades for orotracheal intubation during rapid sequence induction of anesthesia: a multicenter cluster randomized study.

PubMed

Amour, Julien; Le Manach, Yannick Le; Borel, Marie; Lenfant, François; Nicolas-Robin, Armelle; Carillion, Aude; Ripart, Jacques; Riou, Bruno; Langeron, Olivier

2010-02-01

Single-use metal laryngoscope blades are cheaper and carry a lower risk of infection than reusable metal blades. The authors compared single-use and reusable metal blades during rapid sequence induction of anesthesia in a multicenter cluster randomized trial. One thousand seventy-two adult patients undergoing general anesthesia under emergency conditions and requiring rapid sequence induction were randomly assigned on a weekly basis to either single-use or reusable metal blades (cluster randomization). After induction, a 60-s period was allowed to complete intubation. In the case of failed intubation, a second attempt was performed using the opposite type of blade. The primary endpoint was the rate of failed intubation, and the secondary endpoints were the incidence of complications (oxygen desaturation, lung aspiration, and/or oropharynx trauma) and the Cormack and Lehane score. Both groups were similar in their main characteristics, including the risk factors for difficult intubation. The rate of failed intubation was significantly decreased with single-use metal blades at the first attempt compared with reusable blades (2.8 vs. 5.4%, P < 0.05). In addition, the proportion of grades III and IV in Cormack and Lehane score were also significantly decreased with single-use metal blades (6 vs. 10%, P < 0.05). The global complication rate did not reach statistical significance, although the same trend was noted (6.8% vs. 11.5%, P = not significant). An investigator survey and a measure of illumination pointed that illumination might have been responsible for this result. The single-use metal blade was more efficient than a reusable metal blade in rapid sequence induction of anesthesia.

The Gap Procedure: for the identification of phylogenetic clusters in HIV-1 sequence data.

PubMed

Vrbik, Irene; Stephens, David A; Roger, Michel; Brenner, Bluma G

2015-11-04

In the context of infectious disease, sequence clustering can be used to provide important insights into the dynamics of transmission. Cluster analysis is usually performed using a phylogenetic approach whereby clusters are assigned on the basis of sufficiently small genetic distances and high bootstrap support (or posterior probabilities). The computational burden involved in this phylogenetic threshold approach is a major drawback, especially when a large number of sequences are being considered. In addition, this method requires a skilled user to specify the appropriate threshold values which may vary widely depending on the application. This paper presents the Gap Procedure, a distance-based clustering algorithm for the classification of DNA sequences sampled from individuals infected with the human immunodeficiency virus type 1 (HIV-1). Our heuristic algorithm bypasses the need for phylogenetic reconstruction, thereby supporting the quick analysis of large genetic data sets. Moreover, this fully automated procedure relies on data-driven gaps in sorted pairwise distances to infer clusters, thus no user-specified threshold values are required. The clustering results obtained by the Gap Procedure on both real and simulated data, closely agree with those found using the threshold approach, while only requiring a fraction of the time to complete the analysis. Apart from the dramatic gains in computational time, the Gap Procedure is highly effective in finding distinct groups of genetically similar sequences and obviates the need for subjective user-specified values. The clusters of genetically similar sequences returned by this procedure can be used to detect patterns in HIV-1 transmission and thereby aid in the prevention, treatment and containment of the disease.

Sequence spaces [Formula: see text] and [Formula: see text] with application in clustering.

PubMed

Khan, Mohd Shoaib; Alamri, Badriah As; Mursaleen, M; Lohani, Qm Danish

2017-01-01

Distance measures play a central role in evolving the clustering technique. Due to the rich mathematical background and natural implementation of [Formula: see text] distance measures, researchers were motivated to use them in almost every clustering process. Beside [Formula: see text] distance measures, there exist several distance measures. Sargent introduced a special type of distance measures [Formula: see text] and [Formula: see text] which is closely related to [Formula: see text]. In this paper, we generalized the Sargent sequence spaces through introduction of [Formula: see text] and [Formula: see text] sequence spaces. Moreover, it is shown that both spaces are BK -spaces, and one is a dual of another. Further, we have clustered the two-moon dataset by using an induced [Formula: see text]-distance measure (induced by the Sargent sequence space [Formula: see text]) in the k-means clustering algorithm. The clustering result established the efficacy of replacing the Euclidean distance measure by the [Formula: see text]-distance measure in the k-means algorithm.

Impact of Sampling Density on the Extent of HIV Clustering

PubMed Central

Novitsky, Vlad; Moyo, Sikhulile; Lei, Quanhong; DeGruttola, Victor

2014-01-01

Abstract Identifying and monitoring HIV clusters could be useful in tracking the leading edge of HIV transmission in epidemics. Currently, greater specificity in the definition of HIV clusters is needed to reduce confusion in the interpretation of HIV clustering results. We address sampling density as one of the key aspects of HIV cluster analysis. The proportion of viral sequences in clusters was estimated at sampling densities from 1.0% to 70%. A set of 1,248 HIV-1C env gp120 V1C5 sequences from a single community in Botswana was utilized in simulation studies. Matching numbers of HIV-1C V1C5 sequences from the LANL HIV Database were used as comparators. HIV clusters were identified by phylogenetic inference under bootstrapped maximum likelihood and pairwise distance cut-offs. Sampling density below 10% was associated with stochastic HIV clustering with broad confidence intervals. HIV clustering increased linearly at sampling density >10%, and was accompanied by narrowing confidence intervals. Patterns of HIV clustering were similar at bootstrap thresholds 0.7 to 1.0, but the extent of HIV clustering decreased with higher bootstrap thresholds. The origin of sampling (local concentrated vs. scattered global) had a substantial impact on HIV clustering at sampling densities ≥10%. Pairwise distances at 10% were estimated as a threshold for cluster analysis of HIV-1 V1C5 sequences. The node bootstrap support distribution provided additional evidence for 10% sampling density as the threshold for HIV cluster analysis. The detectability of HIV clusters is substantially affected by sampling density. A minimal genotyping density of 10% and sampling density of 50–70% are suggested for HIV-1 V1C5 cluster analysis. PMID:25275430

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

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

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

2015-11-20

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

Molecular and morphological discrimination of stipitate hydnoids in the genera Hydnellum and Phellodon.

PubMed

Parfitt, David; Martyn Ainsworth, A; Simpson, Deborah; Rogers, Hilary J; Boddy, Lynne

2007-07-01

Hydnellum and Phellodon species, generally considered ectomycorrhizal partners of a range of woody angiosperms and gymnosperms particularly within Fagaceae and Pinaceae, appear to be declining in continental Europe. They are listed as priority species in the UK Biodiversity Action Plan, but their UK conservation status remains uncertain. Interpretation of species distribution data is hampered by a lack of consensus regarding some key discriminatory morphological characters and difficulties with their interpretation. DNA sequencing of the ITS1 region of the ribosomal gene cluster discriminated between the known British species of Phellodon but revealed more terminal clusters than currently recognised taxa. Although the main focus within Hydnellum was on the very similar species pair H. concrescens and H. scrobiculatum, a few samples of H. caeruleum, H. ferrugineum, H. peckii, and H. spongiosipes were included in the study for reference. DNA sequencing of material identified on spore-based criteria as H. concrescens yielded two main groups, but samples received as H. scrobiculatum were generally more variable. Of these, two were reassigned and the remaining group, with very similar spores (although shorter than in published descriptions of H. scrobiculatum), had highly variable sequence data. The results and conservation importance of these fungi highlight the need for a taxonomic reassessment of P. melaleucus, P. niger, H. concrescens, and H. scrobiculatum collections from Britain and continental Europe using a combined molecular and morphological approach. Specific PCR primers were constructed to discriminate fruit bodies, mycelium, and mycorrhizal roots of P. niger and P. confluens from each other and from other stipitate hydnoids.

Draft genome of the living fossil Ginkgo biloba.

PubMed

Guan, Rui; Zhao, Yunpeng; Zhang, He; Fan, Guangyi; Liu, Xin; Zhou, Wenbin; Shi, Chengcheng; Wang, Jiahao; Liu, Weiqing; Liang, Xinming; Fu, Yuanyuan; Ma, Kailong; Zhao, Lijun; Zhang, Fumin; Lu, Zuhong; Lee, Simon Ming-Yuen; Xu, Xun; Wang, Jian; Yang, Huanming; Fu, Chengxin; Ge, Song; Chen, Wenbin

2016-11-21

Ginkgo biloba L. (Ginkgoaceae) is one of the most distinctive plants. It possesses a suite of fascinating characteristics including a large genome, outstanding resistance/tolerance to abiotic and biotic stresses, and dioecious reproduction, making it an ideal model species for biological studies. However, the lack of a high-quality genome sequence has been an impediment to our understanding of its biology and evolution. The 10.61 Gb genome sequence containing 41,840 annotated genes was assembled in the present study. Repetitive sequences account for 76.58% of the assembled sequence, and long terminal repeat retrotransposons (LTR-RTs) are particularly prevalent. The diversity and abundance of LTR-RTs is due to their gradual accumulation and a remarkable amplification between 16 and 24 million years ago, and they contribute to the long introns and large genome. Whole genome duplication (WGD) may have occurred twice, with an ancient WGD consistent with that shown to occur in other seed plants, and a more recent event specific to ginkgo. Abundant gene clusters from tandem duplication were also evident, and enrichment of expanded gene families indicates a remarkable array of chemical and antibacterial defense pathways. The ginkgo genome consists mainly of LTR-RTs resulting from ancient gradual accumulation and two WGD events. The multiple defense mechanisms underlying the characteristic resilience of ginkgo are fostered by a remarkable enrichment in ancient duplicated and ginkgo-specific gene clusters. The present study sheds light on sequencing large genomes, and opens an avenue for further genetic and evolutionary research.

B, V Photometry for ~19,000 Stars in and around the Magellanic Cloud Globular Clusters NGC 1466, NGC 1841, NGC 2210, NGC 2257, and Reticulum

NASA Astrophysics Data System (ADS)

Jeon, Young-Beom; Nemec, James M.; Walker, Alistair R.; Kunder, Andrea M.

2014-06-01

Homogeneous B, V photometry is presented for 19,324 stars in and around 5 Magellanic Cloud globular clusters: NGC 1466, NGC 1841, NGC 2210, NGC 2257, and Reticulum. The photometry is derived from eight nights of CCD imaging with the Cerro Tololo Inter-American Observatory 0.9 m SMARTS telescope. Instrumental magnitudes were transformed to the Johnson B, V system using accurate calibration relations based on a large sample of Landolt-Stetson equatorial standard stars, which were observed on the same nights as the cluster stars. Residual analysis of the equatorial standards used for the calibration, and validation of the new photometry using Stetson's sample of secondary standards in the vicinities of the five Large Magellanic Cloud clusters, shows excellent agreement with our values in both magnitudes and colors. Color-magnitude diagrams reaching to the main-sequence turnoffs at V ~ 22 mag, sigma-magnitude diagrams, and various other summaries are presented for each cluster to illustrate the range and quality of the new photometry. The photometry should prove useful for future studies of the Magellanic Cloud globular clusters, particularly studies of their variable stars.

The Clusters AgeS Experiment (CASE). Variable Stars in the Field of the Globular Cluster M12

NASA Astrophysics Data System (ADS)

Kaluzny, J.; Thompson, I. B.; Narloch, W.; Pych, W.; Rozyczka, M.

2015-09-01

The field of the globular cluster M12 (NGC 6218) was monitored between 1995 and 2009 in a search for variable stars. BV light curves were obtained for thirty-six periodic or likely periodic variable stars. Thirty-four of these are new detections. Among the latter we identified twenty proper-motion members of the cluster: six detached or semi-detached eclipsing binaries, five contact binaries, five SX Phe pulsators, and three yellow stragglers. Two of the eclipsing binaries are located in the turnoff region, one on the lower main sequence and the remaining three among the blue stragglers. Two contact systems are blue stragglers, and the remaining three reside in the turnoff region. In the blue straggler region a total of 103 objects were found, of which 42 are proper motion members of M12, and another four are field stars. 55 of the remaining objects are located within two core radii from the center of the cluster, and as such they are likely genuine blue stragglers. We also report the discoveries of a radial color gradient of M12, and the shortest period among contact systems in globular clusters in general.

A national study of the molecular epidemiology of HIV-1 in Australia 2005-2012.

PubMed

Castley, Alison; Sawleshwarkar, Shailendra; Varma, Rick; Herring, Belinda; Thapa, Kiran; Dwyer, Dominic; Chibo, Doris; Nguyen, Nam; Hawke, Karen; Ratcliff, Rodney; Garsia, Roger; Kelleher, Anthony; Nolan, David

2017-01-01

Rates of new HIV-1 diagnoses are increasing in Australia, with evidence of an increasing proportion of non-B HIV-1 subtypes reflecting a growing impact of migration and travel. The present study aims to define HIV-1 subtype diversity patterns and investigate possible HIV-1 transmission networks within Australia. The Australian Molecular Epidemiology Network (AMEN) HIV collaborating sites in Western Australia, South Australia, Victoria, Queensland and western Sydney (New South Wales), provided baseline HIV-1 partial pol sequence, age and gender information for 4,873 patients who had genotypes performed during 2005-2012. HIV-1 phylogenetic analyses utilised MEGA V6, with a stringent classification of transmission pairs or clusters (bootstrap ≥98%, genetic distance ≤1.5% from at least one other sequence in the cluster). HIV-1 subtype B represented 74.5% of the 4,873 sequences (WA 59%, SA 68.4%, w-Syd 73.8%, Vic 75.6%, Qld 82.1%), with similar proportion of transmission pairs and clusters found in the B and non-B cohorts (23% vs 24.5% of sequences, p = 0.3). Significantly more subtype B clusters were comprised of ≥3 sequences compared with non-B clusters (45.0% vs 24.0%, p = 0.021) and significantly more subtype B pairs and clusters were male-only (88% compared to 53% CRF01_AE and 17% subtype C clusters). Factors associated with being in a cluster of any size included; being sequenced in a more recent time period (p<0.001), being younger (p<0.001), being male (p = 0.023) and having a B subtype (p = 0.02). Being in a larger cluster (>3) was associated with being sequenced in a more recent time period (p = 0.05) and being male (p = 0.008). This nationwide HIV-1 study of 4,873 patient sequences highlights the increased diversity of HIV-1 subtypes within the Australian epidemic, as well as differences in transmission networks associated with these HIV-1 subtypes. These findings provide epidemiological insights not readily available using standard surveillance methods and can inform the development of effective public health strategies in the current paradigm of HIV prevention in Australia.

Segue: A Spectroscopic Survey of 240,000 Stars With g = 14-20

DTIC Science & Technology

2009-05-01

24 Research School of Astronomy and Astrophysics, Australian National University, Weston, ACT 2611, Australia 25 Lawrence Berkeley National...main-sequence and evolved objects, with the goal of studying the kinematics and populations of our Galaxy and its halo. The spectra are clustered in 212...SEGUE Survey is the subject of this paper . The pro- cessed, searchable data archive from SEGUE was made publicly available in the Fall of 2008 as part

Development of a Suite of Luciferase Gene Probes for the Screening and Detection of Marine Bioluminescent Systems and Organisms

DTIC Science & Technology

2007-09-30

strains of Alexandrium cf catenella (Balech), Alexandrium fundyense (Balech) and also from a strain of Gonyaulax spinifera (Diesing), which produces...amino acids, revealed 5 main clusters of the dinoflagellate luciferase sequences, a L. polyedrum clade, Pyrocystis clade, Alexandrium clade, Gonyaulax ...tamarense CCMP 1598 Alexandrium cf catenella CCMP 1911 Alexandrium fundyense CCMP 1978 Alexandrium sp CCMP 1909 Alexandrium sp CCMP 1910 100/100

Genome-Based Comparison of Clostridioides difficile: Average Amino Acid Identity Analysis of Core Genomes.

PubMed

Cabal, Adriana; Jun, Se-Ran; Jenjaroenpun, Piroon; Wanchai, Visanu; Nookaew, Intawat; Wongsurawat, Thidathip; Burgess, Mary J; Kothari, Atul; Wassenaar, Trudy M; Ussery, David W

2018-02-14

Infections due to Clostridioides difficile (previously known as Clostridium difficile) are a major problem in hospitals, where cases can be caused by community-acquired strains as well as by nosocomial spread. Whole genome sequences from clinical samples contain a lot of information but that needs to be analyzed and compared in such a way that the outcome is useful for clinicians or epidemiologists. Here, we compare 663 public available complete genome sequences of C. difficile using average amino acid identity (AAI) scores. This analysis revealed that most of these genomes (640, 96.5%) clearly belong to the same species, while the remaining 23 genomes produce four distinct clusters within the Clostridioides genus. The main C. difficile cluster can be further divided into sub-clusters, depending on the chosen cutoff. We demonstrate that MLST, either based on partial or full gene-length, results in biased estimates of genetic differences and does not capture the true degree of similarity or differences of complete genomes. Presence of genes coding for C. difficile toxins A and B (ToxA/B), as well as the binary C. difficile toxin (CDT), was deduced from their unique PfamA domain architectures. Out of the 663 C. difficile genomes, 535 (80.7%) contained at least one copy of ToxA or ToxB, while these genes were missing from 128 genomes. Although some clusters were enriched for toxin presence, these genes are variably present in a given genetic background. The CDT genes were found in 191 genomes, which were restricted to a few clusters only, and only one cluster lacked the toxin A/B genes consistently. A total of 310 genomes contained ToxA/B without CDT (47%). Further, published metagenomic data from stools were used to assess the presence of C. difficile sequences in blinded cases of C. difficile infection (CDI) and controls, to test if metagenomic analysis is sensitive enough to detect the pathogen, and to establish strain relationships between cases from the same hospital. We conclude that metagenomics can contribute to the identification of CDI and can assist in characterization of the most probable causative strain in CDI patients.

Phylogenetic diversity in the genus Bacillus as seen by 16S rRNA sequencing studies

NASA Technical Reports Server (NTRS)

Rossler, D.; Ludwig, W.; Schleifer, K. H.; Lin, C.; McGill, T. J.; Wisotzkey, J. D.; Jurtshuk, P. Jr; Fox, G. E.

1991-01-01

Comparative sequence analysis of 16S ribosomal (r)RNAs or DNAs of Bacillus alvei, B. laterosporus, B. macerans, B. macquariensis, B. polymyxa and B. stearothermophilus revealed the phylogenetic diversity of the genus Bacillus. Based on the presently available data set of 16S rRNA sequences from bacilli and relatives at least four major "Bacillus clusters" can be defined: a "Bacillus subtilis cluster" including B. stearothermophilus, a "B. brevis cluster" including B. laterosporus, a "B. alvei cluster" including B. macerans, B. maquariensis and B. polymyxa and a "B. cycloheptanicus branch".

A YOUNG ECLIPSING BINARY AND ITS LUMINOUS NEIGHBORS IN THE EMBEDDED STAR CLUSTER Sh 2-252E

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

Lester, Kathryn V.; Gies, Douglas R.; Guo, Zhao, E-mail: lester@chara.gsu.edu, E-mail: gies@chara.gsu.edu, E-mail: guo@chara.gsu.edu

We present a photometric and light curve analysis of an eccentric eclipsing binary in the K2 Campaign 0 field, which resides in Sh 2-252E, a young star cluster embedded in an H ii region. We describe a spectroscopic investigation of the three brightest stars in the crowded aperture to identify which is the binary system. We find that none of these stars are components of the eclipsing binary system, which must be one of the fainter nearby stars. These bright cluster members all have remarkable spectra: Sh 2-252a (EPIC 202062176) is a B0.5 V star with razor sharp absorption lines, Sh 2-252b is amore » Herbig A0 star with disk-like emission lines, and Sh 2-252c is a pre-main-sequence star with very red color.« less

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.

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.

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.

VizieR Online Data Catalog: HST photometry of stars in HD 97950 (Pang+, 2016)

NASA Astrophysics Data System (ADS)

Pang, X.; Pasquali, A.; Grebel, E. K.

2016-07-01

The HD97950 cluster and its immediate surroundings in the giant HII region NGC3603 were observed with the Hubble Space Telescope (HST). The ultraviolet (UV) data were taken with the High Resolution Channel (HRC) of the Advanced Camera for Surveys (ACS) in 2005 (GO 10602, PI: Jesus Maiz Apellaniz) through the F220W, F250W, F330W, and F435W filters. The HRC is characterized by a spatial resolution of 0.03"/pixel and a field of view of 29''*25''. The optical observations were carried out with the Wide Field and Planetary Camera 2 (WFPC2) in two epochs: 1997 (GO 6763, PI: Laurent Drissen) and 2007 (GO 11193, PI: Wolfgang Brandner) through the F555W, F675W, and F814W filters. The Planetary Camera (PC) chip was centered on the cluster (0.045"/pixel, 40''*40'') for both programs. Pang et al. 2013 (cat. J/ApJ/764/73) reduced the two-epoch WFPC2 data and identified more than 400 member stars on the PC chip via relative proper motions. Of these member stars, 142 are in common between the HRC and PC images and thus have UV and optical photometry available (see Table1). Among the HD97950 cluster member stars determined from relative proper motions (Pang et al. 2013, cat. J/ApJ/764/73, Table2), there are five main-sequence (MS) stars located in the cluster with projected distances of r<0.7pc from the center, for which there are also spectral types available from Table3 of Melena et al. (2008AJ....135..878M). The photometry of these five MS stars is presented in Table2. The individual color excesses and extinctions of the member main sequence stars are listed in Table3. (3 data files).

Genetic diversity of Guangxi chicken breeds assessed with microsatellites and the mitochondrial DNA D-loop region.

PubMed

Liao, Yuying; Mo, Guodong; Sun, Junli; Wei, Fengying; Liao, Dezhong Joshua

2016-05-01

The domestic chicken (Gallus gallus domesticus) is an excellent model for genetic studies of phenotypic diversity. The Guangxi Region of China possesses several native chicken breeds displaying a broad range of phenotypes well adapted to the extreme hot-and-wet environments in the region. We thus evaluated the genetic diversity and relationships among six native chicken populations of the Guangxi region and also evaluated two commercial breeds (Arbor Acres and Roman chickens). We analyzed the sequences of the D-loop region of the mitochondrial DNA (mtDNA) and 18 microsatellite loci of 280 blood samples from six Guangxi native chicken breeds and from Arbor Acres and Roman chickens, and used the neighbor-joining method to construct the phylogenetic tree of these eight breeds. Our results showed that the genetic diversity of Guangxi native breeds was relatively rich. The phylogenetic tree using the unweighed pair-group method with arithmetic means (UPGAM) on microsatellite marks revealed two main clusters. Arbor Acres chicken and Roman chicken were in one cluster, while the Guangxi breeds were in the other cluster. Moreover, the UPGAM tree of Guangxi native breeds based on microsatellite loci was more consistent with the genesis, breeding history, differentiation and location than the mtDNA D-loop region. STRUCTURE analysis further confirmed the genetic structure of Guangxi native breeds in the Neighbor-Net dendrogram. The nomenclature of mtDNA sequence polymorphisms suggests that the Guangxi native chickens are distributed across four clades, but most of them are clustered in two main clades (B and E), with the other haplotypes within the clades A and C. The Guangxi native breeds revealed abundant genetic diversity not only on microsatellite loci but also on mtDNA D-loop region, and contained multiple maternal lineages, including one from China and another from Europe or the Middle East.

[EST-SSR identification, markers development of Ligusticum chuanxiong based on Ligusticum chuanxiong transcriptome sequences].

PubMed

Yuan, Can; Peng, Fang; Yang, Ze-Mao; Zhong, Wen-Juan; Mou, Fang-Sheng; Gong, Yi-Yun; Ji, Pei-Cheng; Pu, De-Qiang; Huang, Hai-Yan; Yang, Xiao; Zhang, Chao

2017-09-01

Ligusticum chuanxiong is a well-known traditional Chinese medicine plant. The study on its molecular markers development and germplasm resources is very important. In this study, we obtained 24 422 unigenes by assembling transcriptome sequencing reads of L. chuanxiong root. EST-SSR was detected and 4 073 SSR loci were identified. EST-SSR distribution and characteristic analysis results showed that the mono-nucleotide repeats were the main repeat types, accounting for 41.0%. In addition, the sequences containing SSR were functionally annotated in Gene Ontology (GO) and KEGG pathway and were assigned to 49 GO categories, 242 KEGG pathways, among them 2 201 sequences were annotated against Nr database. By validating 235 EST-SSRs,74 primer pairs were ultimately proved to have high quality amplification. Subsequently, genetic diversity analysis, UPGMA cluster analysis, PCoA analysis and population structure analysis of 34 L. chuanxiong germplasm resources were carried out with 74 primer pairs. In both UPGMA tree and PCoA results, L. chuanxiong resources were clustered into two groups, which are believed to be partial related to their geographical distribution. In this study, EST-SSRs in L. chuanxiong was firstly identified, and newly developed molecular markers would contribute significantly to further genetic diversity study, the purity detection, gene mapping, and molecular breeding. Copyright© by the Chinese Pharmaceutical Association.

The B chromosomes in Brachycome.

PubMed

Leach, C R; Houben, A; Timmis, J N

2004-01-01

This review presents a historical account of studies of B chromosomes in the genus Brachycome Cass. (synonym: Brachyscome) from the earliest cytological investigations carried out in the late 1960s though to the most recent molecular analyses. Molecular analyses provide insights into the origin and evolution of the B chromosomes (Bs) of Brachycome dichromosomatica, a species which has Bs of two different sizes. The larger Bs are somatically stable whereas the smaller, or micro, Bs are somatically unstable. Both B types contain clusters of ribosomal RNA genes that have been shown unequivocally to be inactive in the case of the larger Bs. The large Bs carry a family of tandem repeat sequences (Bd49) that are located mainly at the centromere. Multiple copies of sequences related to this repeat are present on the A chromosomes (As) of related species, whereas only a few copies exist in the A chromosomes of B. dichromosomatica. The micro Bs share DNA sequences with the As and the larger Bs, and they also have B-specific repeats (Bdm29 and Bdm54). In some cases repeat sequences on the micro Bs have been shown to occur as clusters on the A chromosomes in a proportion of individuals within a population. It is clear that none of these B types originated by simple excision of segments from the A chromosomes. Copyright 2004 S. Karger AG, Basel

Genetic Diversity among Clostridium botulinum Strains Harboring bont/A2 and bont/A3 Genes

PubMed Central

Raphael, Brian H.; Joseph, Lavin A.; Meno, Sarah R.; Fernández, Rafael A.; Maslanka, Susan E.

2012-01-01

Clostridium botulinum type A strains are known to be genetically diverse and widespread throughout the world. Genetic diversity studies have focused mainly on strains harboring one type A botulinum toxin gene, bont/A1, although all reported bont/A gene variants have been associated with botulism cases. Our study provides insight into the genetic diversity of C. botulinum type A strains, which contain bont/A2 (n = 42) and bont/A3 (n = 4) genes, isolated from diverse samples and geographic origins. Genetic diversity was assessed by using bont nucleotide sequencing, content analysis of the bont gene clusters, multilocus sequence typing (MLST), and pulsed-field gel electrophoresis (PFGE). Sequences of bont genes obtained in this study showed 99.9 to 100% identity with other bont/A2 or bont/A3 gene sequences available in public databases. The neurotoxin gene clusters of the subtype A2 and A3 strains analyzed in this study were similar in gene content. C. botulinum strains harboring bont/A2 and bont/A3 genes were divided into six and two MLST profiles, respectively. Four groups of strains shared a similarity of at least 95% by PFGE; the largest group included 21 out of 46 strains. The strains analyzed in this study showed relatively limited genetic diversity using either MLST or PFGE. PMID:23042179

The ACS Survey of Galactic Globular Clusters. VIII. Effects of Environment on Globular Cluster Global Mass Functions

NASA Astrophysics Data System (ADS)

Paust, Nathaniel E. Q.; Reid, I. Neill; Piotto, Giampaolo; Aparicio, Antonio; Anderson, Jay; Sarajedini, Ata; Bedin, Luigi R.; Chaboyer, Brian; Dotter, Aaron; Hempel, Maren; Majewski, Steven; Marín-Franch, A.; Milone, Antonino; Rosenberg, Alfred; Siegel, Michael

2010-02-01

We have used observations obtained as part of the Hubble Space Telescope/ACS Survey of Galactic Globular Clusters to construct global present-day mass functions for 17 globular clusters utilizing multi-mass King models to extrapolate from our observations to the global cluster behavior. The global present-day mass functions for these clusters are well matched by power laws from the turnoff, ≈0.8 M sun, to 0.2-0.3 M sun on the lower main sequence. The slopes of those power-law fits, α, have been correlated with an extensive set of intrinsic and extrinsic cluster properties to investigate which parameters may influence the form of the present-day mass function. We do not confirm previous suggestions of correlations between α and either metallicity or Galactic location. However, we do find a strong statistical correlation with the related parameters central surface brightness, μ V , and inferred central density, ρ0. The correlation is such that clusters with denser cores (stronger binding energy) tend to have steeper mass functions (a higher proportion of low-mass stars), suggesting that dynamical evolution due to external interactions may have played a key role in determining α. Thus, the present-day mass function may owe more to nurture than to nature. Detailed modeling of external dynamical effects is therefore a requisite for determining the initial mass function for Galactic globular clusters.

HIV-1 diversity, transmission dynamics and primary drug resistance in Angola.

PubMed

Bártolo, Inês; Zakovic, Suzana; Martin, Francisco; Palladino, Claudia; Carvalho, Patrícia; Camacho, Ricardo; Thamm, Sven; Clemente, Sofia; Taveira, Nuno

2014-01-01

To assess HIV-1 diversity, transmission dynamics and prevalence of transmitted drug resistance (TDR) in Angola, five years after ART scale-up. Population sequencing of the pol gene was performed on 139 plasma samples collected in 2009 from drug-naive HIV-1 infected individuals living in Luanda. HIV-1 subtypes were determined using phylogenetic analysis. Drug resistance mutations were identified using the Calibrated Population Resistance Tool (CPR). Transmission networks were determined using phylogenetic analysis of all Angolan sequences present in the databases. Evolutionary trends were determined by comparison with a similar survey performed in 2001. 47.1% of the viruses were pure subtypes (all except B), 47.1% were recombinants and 5.8% were untypable. The prevalence of subtype A decreased significantly from 2001 to 2009 (40.0% to 10.8%, P = 0.0019) while the prevalence of unique recombinant forms (URFs) increased > 2-fold (40.0% to 83.1%, P < 0.0001). The most frequent URFs comprised untypable sequences with subtypes H (U/H, n = 7, 10.8%), A (U/A, n = 6, 9.2%) and G (G/U, n = 4, 6.2%). Newly identified U/H recombinants formed a highly supported monophyletic cluster suggesting a local and common origin. TDR mutation K103N was found in one (0.7%) patient (1.6% in 2001). Out of the 364 sequences sampled for transmission network analysis, 130 (35.7%) were part of a transmission network. Forty eight transmission clusters were identified; the majority (56.3%) comprised sequences sampled in 2008-2010 in Luanda which is consistent with a locally fuelled epidemic. Very low genetic distance was found in 27 transmission pairs sampled in the same year, suggesting recent transmission events. Transmission of drug resistant strains was still negligible in Luanda in 2009, five years after the scale-up of ART. The dominance of small and recent transmission clusters and the emergence of new URFs are consistent with a rising HIV-1 epidemics mainly driven by heterosexual transmission.

Spectroscopic Confirmation of a Massive Red-sequence Selected Galaxy Cluster at Z=1.34 in the SpARCS-South Cluster Survey

NASA Technical Reports Server (NTRS)

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

Using RSAT oligo-analysis and dyad-analysis tools to discover regulatory signals in nucleic sequences.

PubMed

Defrance, Matthieu; Janky, Rekin's; Sand, Olivier; van Helden, Jacques

2008-01-01

This protocol explains how to discover functional signals in genomic sequences by detecting over- or under-represented oligonucleotides (words) or spaced pairs thereof (dyads) with the Regulatory Sequence Analysis Tools (http://rsat.ulb.ac.be/rsat/). Two typical applications are presented: (i) predicting transcription factor-binding motifs in promoters of coregulated genes and (ii) discovering phylogenetic footprints in promoters of orthologous genes. The steps of this protocol include purging genomic sequences to discard redundant fragments, discovering over-represented patterns and assembling them to obtain degenerate motifs, scanning sequences and drawing feature maps. The main strength of the method is its statistical ground: the binomial significance provides an efficient control on the rate of false positives. In contrast with optimization-based pattern discovery algorithms, the method supports the detection of under- as well as over-represented motifs. Computation times vary from seconds (gene clusters) to minutes (whole genomes). The execution of the whole protocol should take approximately 1 h.

Analysis of group B streptococcal isolates from infants and pregnant women in Portugal revealing two lineages with enhanced invasiveness.

PubMed

Martins, E R; Pessanha, M A; Ramirez, M; Melo-Cristino, J

2007-10-01

The populations of group B streptococcus (GBS) associated with vaginal carriage in pregnant women and invasive neonatal infections in Portugal were compared. GBS isolates were characterized by serotyping, pulsed-field gel electrophoresis (PFGE) profiling, and multilocus sequence typing (MLST). Serotypes III and V accounted for 44% of all colonization isolates (n = 269), whereas serotypes III and Ia amounted to 69% of all invasive isolates (n = 64). Whereas serotype Ia was associated with early-onset disease (EOD), serotype III was associated with late-onset disease (LOD). Characterization by PFGE and MLST identified very diverse populations in carriage and invasive disease. Serotype Ia was represented mainly by a single PFGE cluster defined by sequence type 23 (ST23) and the infrequent ST24. In contrast, serotype III was found in a large number of PFGE clusters and STs, but a single PFGE cluster defined by ST17 was found to be associated with invasive disease. Although serotype III was associated only with LOD, ST17 showed an enhanced capacity to cause both EOD and LOD. Our data reinforce the evidence for enhanced invasiveness of ST17 and identify a lineage expressing serotype Ia capsule and represented by ST23 and ST24 as having enhanced potential to cause EOD.

PCR detection of uncultured rumen bacteria.

PubMed

Rosero, Jaime A; Strosová, Lenka; Mrázek, Jakub; Fliegerová, Kateřina; Kopečný, Jan

2012-07-01

16S rRNA sequences of ruminal uncultured bacterial clones from public databases were phylogenetically examined. The sequences were found to form two unique clusters not affiliated with any known bacterial species: cluster of unidentified sequences of free floating rumen fluid uncultured bacteria (FUB) and cluster of unidentified sequences of bacteria associated with rumen epithelium (AUB). A set of PCR primers targeting 16S rRNA of ruminal free uncultured bacteria and rumen epithelium adhering uncultured bacteria was designed based on these sequences. FUB primers were used for relative quantification of uncultured bacteria in ovine rumen samples. The effort to increase the population size of FUB group has been successful in sulfate reducing broth and culture media supplied with cellulose.

Quantiprot - a Python package for quantitative analysis of protein sequences.

PubMed

Konopka, Bogumił M; Marciniak, Marta; Dyrka, Witold

2017-07-17

The field of protein sequence analysis is dominated by tools rooted in substitution matrices and alignments. A complementary approach is provided by methods of quantitative characterization. A major advantage of the approach is that quantitative properties defines a multidimensional solution space, where sequences can be related to each other and differences can be meaningfully interpreted. Quantiprot is a software package in Python, which provides a simple and consistent interface to multiple methods for quantitative characterization of protein sequences. The package can be used to calculate dozens of characteristics directly from sequences or using physico-chemical properties of amino acids. Besides basic measures, Quantiprot performs quantitative analysis of recurrence and determinism in the sequence, calculates distribution of n-grams and computes the Zipf's law coefficient. We propose three main fields of application of the Quantiprot package. First, quantitative characteristics can be used in alignment-free similarity searches, and in clustering of large and/or divergent sequence sets. Second, a feature space defined by quantitative properties can be used in comparative studies of protein families and organisms. Third, the feature space can be used for evaluating generative models, where large number of sequences generated by the model can be compared to actually observed sequences.

VizieR Online Data Catalog: VFTS. O-type stellar content of 30 Dor (Walborn+, 2014)

NASA Astrophysics Data System (ADS)

Walborn, N. R.; Sana, H.; Simon-Diaz, S.; Maiz Apellaniz, J.; Taylor, W. D.; Evans, C. J.; Markova, N.; Lennon, D. J.; de Koter, A.

2014-06-01

Detailed spectral classifications are presented for 352 O-B0 stars in the VLT-FLAMES Tarantula Survey ESO Large Programme, of which 213 O-type are judged of sufficiently high quality for further morphological analysis. Among them, six subcategories of special interest are distinguished. (1) Several new examples of the earliest spectral types O2-O3 have been found, while a previously known example has been determined to belong to the nitrogen-rich ON2 class. (2) A group of extremely rapidly rotating main-sequence objects has been isolated, including the largest vsini values known, the spatial and radial-velocity distributions of which suggest ejection from the two principal ionizing clusters NGC 2070 and NGC 2060. (3) Several new examples of the evolved, rapidly rotating Onfp class show similar evidence, although at least some of them are spectroscopic binaries. (4) No fewer than 48 members of the Vz category, hypothesized to be on or near the zero-age main sequence, are found in this sample; in contrast to the rapid rotators, they are strongly concentrated to the ionizing clusters and a newly recognized region of current and recent star formation to the north, supporting their interpretation as very young objects, as do their relatively faint absolute magnitudes. (5) A surprisingly large fraction of the main-sequence spectra belong to the recently recognized V((fc)) class, with CIII emission lines of similar strength to the usual NIII in V((f)) spectra, although a comparable number of the latter are also present, as well as six objects with very high-quality data but no trace of either emission feature, presenting new challenges to physical interpretations. (6) Two mid-O Vz and three late-O giant/supergiant spectra with morphologically enhanced nitrogen lines have been detected. Absolute visual magnitudes have been derived for each star with individual extinction laws, and composite Hertzsprung-Russell diagrams provide evidence of the multiple generations present in this field. Spectroscopic binaries, resolved visual multiples, and possible associations with X-ray sources are noted. Astrophysical and dynamical analyses of this unique dataset underway will provide new insights into the evolution of massive stars and starburst clusters. (2 data files).

Molecular epidemiology demonstrated three emerging clusters of human immunodeficiency virus type 1 subtype B infection in Hong Kong.

PubMed

Leung, Tommy W C; Mak, Darwin; Wong, K H; Wang, Y; Song, Y H; Tsang, D N C; Wong, C; Shao, Y M; Lim, W L

2008-07-01

We conducted a molecular epidemiological study on newly diagnosed human immunodeficiency virus type 1 (HIV-1)-infected patients in Hong Kong to identify the epidemiological linkage of HIV-1 infection in the locality. Reverse transcription polymerase chain reaction (RT-PCR) for HIV-1 was performed on newly diagnosed HIV-1-positive sera collected from January 2002 to December 2006. PCR products correspond to the env C2V3V4 region and gag p17/p24 junction of the HIV-1 genome were nucleotide sequenced. Phylogenetic analyses performed on the acquired nucleotide sequences revealed that CRF01_AE and subtype B were the two dominant HIV-1 subtypes. Analyses also demonstrated the presence of three emerging HIV-1 clusters among the subtype B sequences in Hong Kong. Individual cluster possesses a unique cluster-specific amino acid signature for identification. Data show that one of the clusters (Cluster I) is rapidly expanding. In addition to the unique cluster-specific amino acid signature, the majority of sequences in Cluster I harbor a 6-amino acid insertion at the gag p17/p24 junction in a region that is thought to be closely associated with HIV-1 infectivity.

Ecological Consistency of SSU rRNA-Based Operational Taxonomic Units at a Global Scale

PubMed Central

Schmidt, Thomas S. B.; Matias Rodrigues, João F.; von Mering, Christian

2014-01-01

Operational Taxonomic Units (OTUs), usually defined as clusters of similar 16S/18S rRNA sequences, are the most widely used basic diversity units in large-scale characterizations of microbial communities. However, it remains unclear how well the various proposed OTU clustering algorithms approximate ‘true’ microbial taxa. Here, we explore the ecological consistency of OTUs – based on the assumption that, like true microbial taxa, they should show measurable habitat preferences (niche conservatism). In a global and comprehensive survey of available microbial sequence data, we systematically parse sequence annotations to obtain broad ecological descriptions of sampling sites. Based on these, we observe that sequence-based microbial OTUs generally show high levels of ecological consistency. However, different OTU clustering methods result in marked differences in the strength of this signal. Assuming that ecological consistency can serve as an objective external benchmark for cluster quality, we conclude that hierarchical complete linkage clustering, which provided the most ecologically consistent partitions, should be the default choice for OTU clustering. To our knowledge, this is the first approach to assess cluster quality using an external, biologically meaningful parameter as a benchmark, on a global scale. PMID:24763141

Molecular characterization of three common olive (Olea europaea L.) cultivars in Palestine, using simple sequence repeat (SSR) markers

PubMed Central

Obaid, Ramiz; Abu-Qaoud, Hassan; Arafeh, Rami

2014-01-01

Eight accessions of olive trees from three common varieties in Palestine, Nabali Baladi, Nabali Mohassan and Surri, were genetically evaluated using five simple sequence repeat (SSR) markers. A total of 17 alleles from 5 loci were observed in which 15 (88.2%) were polymorphic and 2 (11.8%) were monomorphic. An average of 3.4 alleles per locus was found ranging from 2.0 alleles with the primers GAPU-103 and DCA-9 to 5.0 alleles with U9932 and DCA-16. The smallest amplicon size observed was 50 bp with the primer DCA-16, whereas the largest one (450 bp) with the primer U9932. Cluster analysis with the unweighted pair group method with arithmetic average (UPGMA) showed three clusters: a cluster with four accessions from the ‘Nabali Baladi’ cultivar, another cluster with three accessions that represents the ‘Nabali Mohassen’ cultivar and finally the ‘Surri’ cultivar. The similarity coefficient for the eight olive tree samples ranged from a maximum of 100% between two accessions from Nabali Baladi and also in two other samples from Nabali Mohassan, to a minimum similarity coefficient (0.315) between the Surri and two Nabali Baladi accessions. The results in this investigation clearly highlight the genetic dissimilarity between the three main olive cultivars that have been misidentified and mixed up in the past, based on conventional morphological characters. PMID:26019564

Abundance and composition dynamics of soil ammonia-oxidizing archaea in an alpine fir forest on the eastern Tibetan Plateau of China.

PubMed

Wang, Ao; Wu, Fu-Zhong; Yang, Wan-Qin; Wu, Zhi-Chao; Wang, Xu-Xi; Tan, Bo

2012-05-01

Real-time qPCR and clone library sequencing targeting amoA genes were used to investigate the seasonal dynamics of an ammonia-oxidizing archaea (AOA) community in an alpine fir forest in western China. AOA were detected at all sampling dates, and there were significant variations in archaeal amoA gene copy numbers (7.63 × 10(5) to 8.35 × 10(8) per gram of dry soil) throughout the nongrowing season. Compared with ammonia-oxidizing bacteria (AOB), the AOA displayed a higher abundance on the majority of sampling dates during the freeze-thaw period. All of the AOA sequences fell within soil and sediment lineages and were affiliated with 7 clusters. Compared with the other clusters, cluster 1 was more sensitive to low temperature and was the dominant group in August. In contrast, cluster 3 dominated the AOA community in winter and probably represents a group of cold-adapted archaea. Redundancy analysis (RDA) revealed that the seasonality of the AOA community was mainly attributed to changes in soil temperature and nutrient availability (e.g., dissolved organic nitrogen and carbon). Our results indicate that AOA exist in frozen soils in the alpine coniferous forest ecosystem of the eastern Tibetan Plateau. Moreover, soil temperature may directly and (or) indirectly affect AOA abundance and composition and may further influence the soil N cycle during the winter.

Interspecific and intraspecific gene variability in a 1-Mb region containing the highest density of NBS-LRR genes found in the melon genome.

PubMed

González, Víctor M; Aventín, Núria; Centeno, Emilio; Puigdomènech, Pere

2014-12-17

Plant NBS-LRR -resistance genes tend to be found in clusters, which have been shown to be hot spots of genome variability. In melon, half of the 81 predicted NBS-LRR genes group in nine clusters, and a 1 Mb region on linkage group V contains the highest density of R-genes and presence/absence gene polymorphisms found in the melon genome. This region is known to contain the locus of Vat, an agronomically important gene that confers resistance to aphids. However, the presence of duplications makes the sequencing and annotation of R-gene clusters difficult, usually resulting in multi-gapped sequences with higher than average errors. A 1-Mb sequence that contains the largest NBS-LRR gene cluster found in melon was improved using a strategy that combines Illumina paired-end mapping and PCR-based gap closing. Unknown sequence was decreased by 70% while about 3,000 SNPs and small indels were corrected. As a result, the annotations of 18 of a total of 23 NBS-LRR genes found in this region were modified, including additional coding sequences, amino acid changes, correction of splicing boundaries, or fussion of ORFs in common transcription units. A phylogeny analysis of the R-genes and their comparison with syntenic sequences in other cucurbits point to a pattern of local gene amplifications since the diversification of cucurbits from other families, and through speciation within the family. A candidate Vat gene is proposed based on the sequence similarity between a reported Vat gene from a Korean melon cultivar and a sequence fragment previously absent in the unrefined sequence. A sequence refinement strategy allowed substantial improvement of a 1 Mb fragment of the melon genome and the re-annotation of the largest cluster of NBS-LRR gene homologues found in melon. Analysis of the cluster revealed that resistance genes have been produced by sequence duplication in adjacent genome locations since the divergence of cucurbits from other close families, and through the process of speciation within the family a candidate Vat gene was also identified using sequence previously unavailable, which demonstrates the advantages of genome assembly refinements when analyzing complex regions such as those containing clusters of highly similar genes.

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

NASA Astrophysics Data System (ADS)

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

2015-09-01

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

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 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.

An XMM-Newton Observation of the Lagoon Nebula and the Very Young Open Cluster NGC 6530

NASA Technical Reports Server (NTRS)

Rauw, G.; Naze, Y.; Gosset, E.; Stevens, I. R.; Blomme, R.; Corcoran, M. F.; Pittard, J. M.; Runacres, M. C.

2002-01-01

We report the results of an XMM-Newton observation of the Lagoon Nebula (M 8). Our EPIC images of this region reveal a cluster of point sources, most of which have optical counterparts inside the very young open cluster NGC 6530. The bulk of these X-ray sources are probably associated with low and intermediate mass pre-main sequence stars. One of the sources experiences a flare-like increase of its X-ray flux making it the second brightest source in M 8 after the O4 star 9 Sgr. The X-ray spectra of most of the brightest sources can be fitted with thermal plasma models with temperatures of kT approximately a few keV. Only a few of the X-ray selected PMS candidates are known to display H(alpha) emission and were previously classified as classical T Tauri stars. This suggests that most of the X-ray emitting PMS stars in NGC 6530 are weak line T Tauri stars. In addition to 9 Sgr, our EPIC field of view contains also a few early-type stars. The X-ray emission from HD 164816 is found to be typical for an O9.5III-IV star. At least one of the known Herbig Be stars in NGC 6530 (LkH(alpha) 115) exhibits a relatively strong X-ray emission, while most of the main sequence stars of spectral type B1 and later are not detected. We also detect (probably) diffuse X-ray emission from the Hourglass Region that might reveal a hot bubble blown by the stellar wind of Herschel 36, the ionizing star of the Hourglass Region.

SCPS: a fast implementation of a spectral method for detecting protein families on a genome-wide scale.

PubMed

Nepusz, Tamás; Sasidharan, Rajkumar; Paccanaro, Alberto

2010-03-09

An important problem in genomics is the automatic inference of groups of homologous proteins from pairwise sequence similarities. Several approaches have been proposed for this task which are "local" in the sense that they assign a protein to a cluster based only on the distances between that protein and the other proteins in the set. It was shown recently that global methods such as spectral clustering have better performance on a wide variety of datasets. However, currently available implementations of spectral clustering methods mostly consist of a few loosely coupled Matlab scripts that assume a fair amount of familiarity with Matlab programming and hence they are inaccessible for large parts of the research community. SCPS (Spectral Clustering of Protein Sequences) is an efficient and user-friendly implementation of a spectral method for inferring protein families. The method uses only pairwise sequence similarities, and is therefore practical when only sequence information is available. SCPS was tested on difficult sets of proteins whose relationships were extracted from the SCOP database, and its results were extensively compared with those obtained using other popular protein clustering algorithms such as TribeMCL, hierarchical clustering and connected component analysis. We show that SCPS is able to identify many of the family/superfamily relationships correctly and that the quality of the obtained clusters as indicated by their F-scores is consistently better than all the other methods we compared it with. We also demonstrate the scalability of SCPS by clustering the entire SCOP database (14,183 sequences) and the complete genome of the yeast Saccharomyces cerevisiae (6,690 sequences). Besides the spectral method, SCPS also implements connected component analysis and hierarchical clustering, it integrates TribeMCL, it provides different cluster quality tools, it can extract human-readable protein descriptions using GI numbers from NCBI, it interfaces with external tools such as BLAST and Cytoscape, and it can produce publication-quality graphical representations of the clusters obtained, thus constituting a comprehensive and effective tool for practical research in computational biology. Source code and precompiled executables for Windows, Linux and Mac OS X are freely available at http://www.paccanarolab.org/software/scps.

A Case-Control Study of Molecular Epidemiology in Relation to Azithromycin Resistance in Neisseria gonorrhoeae Isolates Collected in Amsterdam, the Netherlands, between 2008 and 2015

PubMed Central

Wind, Carolien M.; Bruisten, Sylvia M.; Schim van der Loeff, Maarten F.; Dierdorp, Mirjam; de Vries, Henry J. C.

2017-01-01

ABSTRACT Neisseria gonorrhoeae resistance to ceftriaxone and azithromycin is increasing, which threatens the recommended dual therapy. We used molecular epidemiology to identify N. gonorrhoeae clusters and associations with azithromycin resistance in Amsterdam, the Netherlands. N. gonorrhoeae isolates (n = 143) were selected from patients visiting the Amsterdam STI Outpatient Clinic from January 2008 through September 2015. We included all 69 azithromycin-resistant isolates (MIC ≥ 2.0 mg/liter) and 74 frequency-matched susceptible controls (MIC ≤ 0.25 mg/liter). The methods used were 23S rRNA and mtrR sequencing, N. gonorrhoeae multiantigen sequence typing (NG-MAST), N. gonorrhoeae multilocus variable-number tandem-repeat analysis (NG-MLVA), and a specific PCR to detect mosaic penA genes. A hierarchical cluster analysis of NG-MLVA related to resistance and epidemiological characteristics was performed. Azithromycin-resistant isolates had C2611T mutations in 23S rRNA (n = 62, 89.9%, P < 0.001) and were NG-MAST genogroup G2992 (P < 0.001), G5108 (P < 0.001), or G359 (P = 0.02) significantly more often than susceptible isolates and were more often part of NG-MLVA clusters (P < 0.001). Two resistant isolates (2.9%) had A2059G mutations, and five (7.3%) had wild-type 23S rRNA. No association between mtrR mutations and azithromycin resistance was found. Twenty-four isolates, including 10 azithromycin-resistant isolates, showed reduced susceptibility to extended-spectrum cephalosporins. Of these, five contained a penA mosaic gene. Four of the five NG-MLVA clusters contained resistant and susceptible isolates. Two clusters consisting mainly of resistant isolates included strains from men who have sex with men and from heterosexual males and females. The co-occurrence of resistant and susceptible strains in NG-MLVA clusters and the frequent occurrence of resistant strains outside of clusters suggest that azithromycin resistance develops independently from the background genome. PMID:28373191

Winds in hot main-sequence stars near the static limit

NASA Technical Reports Server (NTRS)

Morrison, Nancy D.

1995-01-01

This project began with the acquisition of short-wavelength, high-dispersion IUE spectra of selected late O- and early B-type stars that are near the main sequence in open clusters and associations. The profiles of the resonance lines of N(V), Si(IV), and C(IV) were studied, and we found that the C(IV) lines are the most sensitive indicators of mass loss (stellar winds) in stars of this type. The mass loss manifests itself as an extension of the short-wavelength absorption wing of the doublet, while there is no P Cygni-type emission on the long-wavelength side of the line profile. We investigated whether the short-wavelength extension could be caused by blended lines of other ionic species formed in the photosphere. Although blending is present and introduces uncertainty into the estimation of the precise location on the main sequence of the onset of the mass-loss signature, it is a crucial issue only in a few marginal cases. Mass loss certainly overwhelms blending in its influence on the spectrum between spectral types B0 and B1 (effective temperatures in the range 25,000-27,000 K). We defined a parameter called P(sub w), to describe the degree of asymmetry of the C(IV) resonance-line profile, and we studied the dependence of this parameter on the fundamental stellar parameters. For this purpose, we derived new estimates of the stellar T(eff) and log g from a non-LTE, line-blanketed model-atmosphere analysis of these stars (Grigsby, Morrison, and Anderson 1992). In order to estimate the stellar luminosities, we performed an exhaustive search of the literature for the most reliable available estimates of the distances of the clusters and associations to which the program stars belong. The dependence of P(sub w) on stellar temperature and luminosity is also studied.

Non-LTE Stellar Population Synthesis of Globular Clusters Using Synthetic Integrated Light Spectra. I. Constructing the IL Spectra

NASA Astrophysics Data System (ADS)

Young, Mitchell. E.; Short, C. Ian

2017-02-01

We present an investigation of the globular cluster population synthesis method of McWilliam & Bernstein, focusing on the impact of non-LTE (NLTE) modeling effects and color-magnitude diagram (CMD) discretization. Johnson-Cousins-Bessel U - B, B-V, V-I, and J-K colors are produced for 96 synthetic integrated light (IL) spectra with two different discretization prescriptions and three degrees of NLTE treatment. These color values are used to compare NLTE- and LTE-derived population ages. Relative contributions of different spectral types to the IL spectra for different wavebands are measured. IL NLTE spectra are shown to be more luminous in the UV and optical than LTE spectra, but show stronger absorption features in the IR. The main features showing discrepancies between NLTE and LTE IL spectra may be attributed to light metals, primarily Fe I, Ca I, and Ti I, as well as TiO molecular bands. Main-sequence stars are shown to have negligible NLTE effects at IR wavelengths compared to more evolved stars. Photometric color values are shown to vary at the millimagnitude level as a function of CMD discretization. Finer CMD sampling for the upper main sequence and turnoff, base of the red giant branch, and the horizontal branch minimizes this variation. Differences in ages derived from LTE and NLTE IL spectra are found to range from 0.55 to 2.54 Gyr, comparable to the uncertainty in GC ages derived from color indices with observational uncertainties of 0.01 mag, the limiting precision of the Harris catalog.

On the Nature of Ultra-faint Dwarf Galaxy Candidates. II. The Case of Cetus II

NASA Astrophysics Data System (ADS)

Conn, Blair C.; Jerjen, Helmut; Kim, Dongwon; Schirmer, Mischa

2018-04-01

We obtained deep Gemini GMOS-S g, r photometry of the ultra-faint dwarf galaxy candidate Cetus II with the aim of providing stronger constraints on its size, luminosity, and stellar population. Cetus II is an important object in the size–luminosity plane, as it occupies the transition zone between dwarf galaxies and star clusters. All known objects smaller than Cetus II (r h ∼ 20 pc) are reported to be star clusters, while most larger objects are likely dwarf galaxies. We found a prominent excess of main-sequence stars in the color–magnitude diagram of Cetus II, best described by a single stellar population with an age of 11.2 Gyr, metallicity of [Fe/H] = ‑1.28 dex, an [α/Fe] = 0.0 dex at a heliocentric distance of 26.3 ± 1.2 kpc. As well as being spatially located within the Sagittarius dwarf tidal stream, these properties are well matched to the Sagittarius galaxy’s Population B stars. Interestingly, like our recent findings on the ultra-faint dwarf galaxy candidate Tucana V, the stellar field in the direction of Cetus II shows no evidence of a concentrated overdensity despite tracing the main sequence for over six magnitudes. These results strongly support the picture that Cetus II is not an ultra-faint stellar system in the Milky Way halo, but made up of stars from the Sagittarius tidal stream.

Clustering execution in a processing system to increase power savings

DOEpatents

Bose, Pradip; Buyuktosunoglu, Alper; Jacobson, Hans M.; Vega, Augusto J.

2018-03-20

Embodiments relate to clustering execution in a processing system. An aspect includes accessing a control flow graph that defines a data dependency and an execution sequence of a plurality of tasks of an application that executes on a plurality of system components. The execution sequence of the tasks in the control flow graph is modified as a clustered control flow graph that clusters active and idle phases of a system component while maintaining the data dependency. The clustered control flow graph is sent to an operating system, where the operating system utilizes the clustered control flow graph for scheduling the tasks.

Visualization of genome signatures of eukaryote genomes by batch-learning self-organizing map with a special emphasis on Drosophila genomes.

PubMed

Abe, Takashi; Hamano, Yuta; Ikemura, Toshimichi

2014-01-01

A strategy of evolutionary studies that can compare vast numbers of genome sequences is becoming increasingly important with the remarkable progress of high-throughput DNA sequencing methods. We previously established a sequence alignment-free clustering method "BLSOM" for di-, tri-, and tetranucleotide compositions in genome sequences, which can characterize sequence characteristics (genome signatures) of a wide range of species. In the present study, we generated BLSOMs for tetra- and pentanucleotide compositions in approximately one million sequence fragments derived from 101 eukaryotes, for which almost complete genome sequences were available. BLSOM recognized phylotype-specific characteristics (e.g., key combinations of oligonucleotide frequencies) in the genome sequences, permitting phylotype-specific clustering of the sequences without any information regarding the species. In our detailed examination of 12 Drosophila species, the correlation between their phylogenetic classification and the classification on the BLSOMs was observed to visualize oligonucleotides diagnostic for species-specific clustering.

On the relative ages of galactic globular clusters. A new observable, a semi-empirical calibration and problems with the theoretical isochrones

NASA Astrophysics Data System (ADS)

Buonanno, R.; Corsi, C. E.; Pulone, L.; Fusi Pecci, F.; Bellazzini, M.

1998-05-01

A new procedure is described to derive homogeneous relative ages from the Color-Magnitude Diagrams (CMDs) of Galactic globular clusters (GGCs). It is based on the use of a new observable, Delta V(0.05) , namely the difference in magnitude between an arbitrary point on the upper main sequence (V_{+0.05} -the V magnitude of the MS-ridge, 0.05 mag redder than the Main Sequence (MS) Turn-off, (TO)) and the horizontal branch (HB). The observational error associated to Delta V(0.05) is substantially smaller than that of previous age-indicators, keeping the property of being strictly independent of distance and reddening and of being based on theoretical luminosities rather than on still uncertain theoretical temperatures. As an additional bonus, the theoretical models show that Delta V(0.05) has a low dependence on metallicity. Moreover, the estimates of the relative age so obtained are also sufficiently invariant (to within ~ +/- 1 Gyr) with varying adopted models and transformations. Since the difference in the color difference Delta (B-V)_{TO,RGB} (VandenBerg, Bolte and Stetson 1990 -VBS, Sarajedini and Demarque 1990 -SD) remains the most reliable technique to estimate relative cluster ages for clusters where the horizontal part of the HB is not adequately populated, we have used the differential ages obtained via the "vertical" Delta V(0.05) parameter for a selected sample of clusters (with high quality CMDs, well populated HBs, trustworthy calibrations) to perform an empirical calibration of the "horizontal" observable in terms of [Fe/H] and age. A direct comparison with the corresponding calibration derived from the theoretical models reveals the existence of clear-cut discrepancies, which call into question the model scaling with metallicity in the observational planes. Starting from the global sample of considered clusters, we have thus evaluated, within a homogeneous procedure, relative ages for 33 GGCs having different metallicity, HB-morphologies, and galactocentric distances. These new estimates have also been compared with previous latest determinations (Chaboyer, Demarque and Sarajedini 1996, and Richer {et al. } 1996). The distribution of the cluster ages with varying metallicity and galactocentric distance are briefly discussed: (a) there is no direct indication for any evident age-metallicity relationship; (b) there is some spread in age (still partially compatible with the errors), and the largest dispersion is found for intermediate metal-poor clusters; (c) older clusters populate both the inner and the outer regions of the Milky Way, while the younger globulars are present only in the outer regions, but the sample is far too poor to yield conclusive evidences.

Intracluster age gradients in numerous young stellar clusters

NASA Astrophysics Data System (ADS)

Getman, K. V.; Feigelson, E. D.; Kuhn, M. A.; Bate, M. R.; Broos, P. S.; Garmire, G. P.

2018-05-01

The pace and pattern of star formation leading to rich young stellar clusters is quite uncertain. In this context, we analyse the spatial distribution of ages within 19 young (median t ≲ 3 Myr on the Siess et al. time-scale), morphologically simple, isolated, and relatively rich stellar clusters. Our analysis is based on young stellar object (YSO) samples from the Massive Young Star-Forming Complex Study in Infrared and X-ray and Star Formation in Nearby Clouds surveys, and a new estimator of pre-main sequence (PMS) stellar ages, AgeJX, derived from X-ray and near-infrared photometric data. Median cluster ages are computed within four annular subregions of the clusters. We confirm and extend the earlier result of Getman et al. (2014): 80 per cent of the clusters show age trends where stars in cluster cores are younger than in outer regions. Our cluster stacking analyses establish the existence of an age gradient to high statistical significance in several ways. Time-scales vary with the choice of PMS evolutionary model; the inferred median age gradient across the studied clusters ranges from 0.75 to 1.5 Myr pc-1. The empirical finding reported in the present study - late or continuing formation of stars in the cores of star clusters with older stars dispersed in the outer regions - has a strong foundation with other observational studies and with the astrophysical models like the global hierarchical collapse model of Vázquez-Semadeni et al.

Genomic signature of successful colonization of Eurasia by the allopolyploid shepherd's purse (Capsella bursa-pastoris).

PubMed

Cornille, A; Salcedo, A; Kryvokhyzha, D; Glémin, S; Holm, K; Wright, S I; Lascoux, M

2016-01-01

Polyploidization is a dominant feature of flowering plant evolution. However, detailed genomic analyses of the interpopulation diversification of polyploids following genome duplication are still in their infancy, mainly because of methodological limits, both in terms of sequencing and computational analyses. The shepherd's purse (Capsella bursa-pastoris) is one of the most common weed species in the world. It is highly self-fertilizing, and recent genomic data indicate that it is an allopolyploid, resulting from hybridization between the ancestors of the diploid species Capsella grandiflora and Capsella orientalis. Here, we investigated the genomic diversity of C. bursa-pastoris, its population structure and demographic history, following allopolyploidization in Eurasia. To that end, we genotyped 261 C. bursa-pastoris accessions spread across Europe, the Middle East and Asia, using genotyping-by-sequencing, leading to a total of 4274 SNPs after quality control. Bayesian clustering analyses revealed three distinct genetic clusters in Eurasia: one cluster grouping samples from Western Europe and Southeastern Siberia, the second one centred on Eastern Asia and the third one in the Middle East. Approximate Bayesian computation (ABC) supported the hypothesis that C. bursa-pastoris underwent a typical colonization history involving low gene flow among colonizing populations, likely starting from the Middle East towards Europe and followed by successive human-mediated expansions into Eastern Asia. Altogether, these findings bring new insights into the recent multistage colonization history of the allotetraploid C. bursa-pastoris and highlight ABC and genotyping-by-sequencing data as promising but still challenging tools to infer demographic histories of selfing allopolyploids. © 2015 John Wiley & Sons Ltd.

Application of k-means clustering algorithm in grouping the DNA sequences of hepatitis B virus (HBV)

NASA Astrophysics Data System (ADS)

Bustamam, A.; Tasman, H.; Yuniarti, N.; Frisca, Mursidah, I.

2017-07-01

Based on WHO data, an estimated of 15 millions people worldwide who are infected with hepatitis B (HBsAg+), which is caused by HBV virus, are also infected by hepatitis D, which is caused by HDV virus. Hepatitis D infection can occur simultaneously with hepatitis B (co infection) or after a person is exposed to chronic hepatitis B (super infection). Since HDV cannot live without HBV, HDV infection is closely related to HBV infection, hence it is very realistic that every effort of prevention against hepatitis B can indirectly prevent hepatitis D. This paper presents clustering of HBV DNA sequences by using k-means clustering algorithm and R programming. Clustering processes are started with collecting HBV DNA sequences from GenBank, then performing extraction HBV DNA sequences using n-mers frequency and furthermore the extraction results are collected as a matrix and normalized using the min-max normalization with interval [0, 1] which will later be used as an input data. The number of clusters is two and the initial centroid selected of the cluster is chosen randomly. In each iteration, the distance of every object to each centroid are calculated using the Euclidean distance and the minimum distance is selected to determine the membership in a cluster until two convergent clusters are created. As the result, the HBV viruses in the first cluster is more virulent than the HBV viruses in the second cluster, so the HBV viruses in the first cluster can potentially evolve with HDV viruses that cause hepatitis D.

Spatial stress variations in the aftershock sequence following the 2008 M6 earthquake doublet in the South Iceland Seismic Zone

NASA Astrophysics Data System (ADS)

Hensch, M.; Árnadóttir, Th.; Lund, B.; Brandsdóttir, B.

2012-04-01

The South Iceland Seismic Zone (SISZ) is an approximately 80 km wide E-W transform zone, bridging the offset between the Eastern Volcanic Zone and the Hengill triple junction to the west. The plate motion is accommodated in the brittle crust by faulting on many N-S trending right-lateral strike-slip faults of 2-5 km separation. Major sequences of large earthquakes (M>6) has occurred repeatedly in the SISZ since the settlement in Iceland more than thousand years ago. On 29th May 2008, two M6 earthquakes hit the western part of the SISZ on two adjacent N-S faults within a few seconds. The intense aftershock sequence was recorded by the permanent Icelandic SIL network and a promptly installed temporary network of 11 portable seismometers in the source region. The network located thousands of aftershocks during the following days, illuminating a 12-17 km long region along both major fault ruptures as well as several smaller parallel faults along a diffuse E-W trending region west of the mainshock area without any preceding main rupture. This episode is suggested to be the continuation of an earthquake sequence which started with two M6.5 and several M5-6 events in June 2000. The time delay between the 2000 and 2008 events could be due to an inflation episode in Hengill during 1993-1998, that potentially locked N-S strike slip faults in the western part of the SISZ. Around 300 focal solutions for aftershocks have been derived by analyzing P-wave polarities, showing predominantly strike-slip movements with occasional normal faulting components (unstable P-axis direction), which suggests an extensional stress regime as their driving force. A subsequent stress inversion of four different aftershock clusters reveals slight variations of the directions of the average σ3 axes. While for both southern clusters, including the E-W cluster, the σ3 axes are rather elongated perpendicular to the overall plate spreading axis, they are more northerly trending for shallower clusters located further north. In this study we will try to shed light into whether the azimuth variations of σ3 is caused by stress changes due to the inflation-deflation episode in Hengill (NW of the activated fault zone) or solely depending to the depth of the aftershock clusters.

Metagenome assembly through clustering of next-generation sequencing data using protein sequences.

PubMed

Sim, Mikang; Kim, Jaebum

2015-02-01

The study of environmental microbial communities, called metagenomics, has gained a lot of attention because of the recent advances in next-generation sequencing (NGS) technologies. Microbes play a critical role in changing their environments, and the mode of their effect can be solved by investigating metagenomes. However, the difficulty of metagenomes, such as the combination of multiple microbes and different species abundance, makes metagenome assembly tasks more challenging. In this paper, we developed a new metagenome assembly method by utilizing protein sequences, in addition to the NGS read sequences. Our method (i) builds read clusters by using mapping information against available protein sequences, and (ii) creates contig sequences by finding consensus sequences through probabilistic choices from the read clusters. By using simulated NGS read sequences from real microbial genome sequences, we evaluated our method in comparison with four existing assembly programs. We found that our method could generate relatively long and accurate metagenome assemblies, indicating that the idea of using protein sequences, as a guide for the assembly, is promising. Copyright © 2015 Elsevier B.V. All rights reserved.

Acquisition and evolution of plant pathogenesis-associated gene clusters and candidate determinants of tissue-specificity in xanthomonas.

PubMed

Lu, Hong; Patil, Prabhu; Van Sluys, Marie-Anne; White, Frank F; Ryan, Robert P; Dow, J Maxwell; Rabinowicz, Pablo; Salzberg, Steven L; Leach, Jan E; Sonti, Ramesh; Brendel, Volker; Bogdanove, Adam J

2008-01-01

Xanthomonas is a large genus of plant-associated and plant-pathogenic bacteria. Collectively, members cause diseases on over 392 plant species. Individually, they exhibit marked host- and tissue-specificity. The determinants of this specificity are unknown. To assess potential contributions to host- and tissue-specificity, pathogenesis-associated gene clusters were compared across genomes of eight Xanthomonas strains representing vascular or non-vascular pathogens of rice, brassicas, pepper and tomato, and citrus. The gum cluster for extracellular polysaccharide is conserved except for gumN and sequences downstream. The xcs and xps clusters for type II secretion are conserved, except in the rice pathogens, in which xcs is missing. In the otherwise conserved hrp cluster, sequences flanking the core genes for type III secretion vary with respect to insertion sequence element and putative effector gene content. Variation at the rpf (regulation of pathogenicity factors) cluster is more pronounced, though genes with established functional relevance are conserved. A cluster for synthesis of lipopolysaccharide varies highly, suggesting multiple horizontal gene transfers and reassortments, but this variation does not correlate with host- or tissue-specificity. Phylogenetic trees based on amino acid alignments of gum, xps, xcs, hrp, and rpf cluster products generally reflect strain phylogeny. However, amino acid residues at four positions correlate with tissue specificity, revealing hpaA and xpsD as candidate determinants. Examination of genome sequences of xanthomonads Xylella fastidiosa and Stenotrophomonas maltophilia revealed that the hrp, gum, and xcs clusters are recent acquisitions in the Xanthomonas lineage. Our results provide insight into the ancestral Xanthomonas genome and indicate that differentiation with respect to host- and tissue-specificity involved not major modifications or wholesale exchange of clusters, but subtle changes in a small number of genes or in non-coding sequences, and/or differences outside the clusters, potentially among regulatory targets or secretory substrates.

AntiClustal: Multiple Sequence Alignment by antipole clustering and linear approximate 1-median computation.

PubMed

Di Pietro, C; Di Pietro, V; Emmanuele, G; Ferro, A; Maugeri, T; Modica, E; Pigola, G; Pulvirenti, A; Purrello, M; Ragusa, M; Scalia, M; Shasha, D; Travali, S; Zimmitti, V

2003-01-01

In this paper we present a new Multiple Sequence Alignment (MSA) algorithm called AntiClusAl. The method makes use of the commonly use idea of aligning homologous sequences belonging to classes generated by some clustering algorithm, and then continue the alignment process ina bottom-up way along a suitable tree structure. The final result is then read at the root of the tree. Multiple sequence alignment in each cluster makes use of the progressive alignment with the 1-median (center) of the cluster. The 1-median of set S of sequences is the element of S which minimizes the average distance from any other sequence in S. Its exact computation requires quadratic time. The basic idea of our proposed algorithm is to make use of a simple and natural algorithmic technique based on randomized tournaments which has been successfully applied to large size search problems in general metric spaces. In particular a clustering algorithm called Antipole tree and an approximate linear 1-median computation are used. Our algorithm compared with Clustal W, a widely used tool to MSA, shows a better running time results with fully comparable alignment quality. A successful biological application showing high aminoacid conservation during evolution of Xenopus laevis SOD2 is also cited.

A national study of the molecular epidemiology of HIV-1 in Australia 2005–2012

PubMed Central

Castley, Alison; Sawleshwarkar, Shailendra; Varma, Rick; Herring, Belinda; Thapa, Kiran; Dwyer, Dominic; Chibo, Doris; Nguyen, Nam; Hawke, Karen; Ratcliff, Rodney; Garsia, Roger; Kelleher, Anthony; Nolan, David

2017-01-01

Introduction Rates of new HIV-1 diagnoses are increasing in Australia, with evidence of an increasing proportion of non-B HIV-1 subtypes reflecting a growing impact of migration and travel. The present study aims to define HIV-1 subtype diversity patterns and investigate possible HIV-1 transmission networks within Australia. Methods The Australian Molecular Epidemiology Network (AMEN) HIV collaborating sites in Western Australia, South Australia, Victoria, Queensland and western Sydney (New South Wales), provided baseline HIV-1 partial pol sequence, age and gender information for 4,873 patients who had genotypes performed during 2005–2012. HIV-1 phylogenetic analyses utilised MEGA V6, with a stringent classification of transmission pairs or clusters (bootstrap ≥98%, genetic distance ≤1.5% from at least one other sequence in the cluster). Results HIV-1 subtype B represented 74.5% of the 4,873 sequences (WA 59%, SA 68.4%, w-Syd 73.8%, Vic 75.6%, Qld 82.1%), with similar proportion of transmission pairs and clusters found in the B and non-B cohorts (23% vs 24.5% of sequences, p = 0.3). Significantly more subtype B clusters were comprised of ≥3 sequences compared with non-B clusters (45.0% vs 24.0%, p = 0.021) and significantly more subtype B pairs and clusters were male-only (88% compared to 53% CRF01_AE and 17% subtype C clusters). Factors associated with being in a cluster of any size included; being sequenced in a more recent time period (p<0.001), being younger (p<0.001), being male (p = 0.023) and having a B subtype (p = 0.02). Being in a larger cluster (>3) was associated with being sequenced in a more recent time period (p = 0.05) and being male (p = 0.008). Conclusion This nationwide HIV-1 study of 4,873 patient sequences highlights the increased diversity of HIV-1 subtypes within the Australian epidemic, as well as differences in transmission networks associated with these HIV-1 subtypes. These findings provide epidemiological insights not readily available using standard surveillance methods and can inform the development of effective public health strategies in the current paradigm of HIV prevention in Australia. PMID:28489920

The ergot alkaloid gene cluster in Claviceps purpurea: extension of the cluster sequence and intra species evolution.

PubMed

Haarmann, Thomas; Machado, Caroline; Lübbe, Yvonne; Correia, Telmo; Schardl, Christopher L; Panaccione, Daniel G; Tudzynski, Paul

2005-06-01

The genomic region of Claviceps purpurea strain P1 containing the ergot alkaloid gene cluster [Tudzynski, P., Hölter, K., Correia, T., Arntz, C., Grammel, N., Keller, U., 1999. Evidence for an ergot alkaloid gene cluster in Claviceps purpurea. Mol. Gen. Genet. 261, 133-141] was explored by chromosome walking, and additional genes probably involved in the ergot alkaloid biosynthesis have been identified. The putative cluster sequence (extending over 68.5kb) contains 4 different nonribosomal peptide synthetase (NRPS) genes and several putative oxidases. Northern analysis showed that most of the genes were co-regulated (repressed by high phosphate), and identified probable flanking genes by lack of co-regulation. Comparison of the cluster sequences of strain P1, an ergotamine producer, with that of strain ECC93, an ergocristine producer, showed high conservation of most of the cluster genes, but significant variation in the NRPS modules, strongly suggesting that evolution of these chemical races of C. purpurea is determined by evolution of NRPS module specificity.

Cloning and Characterization of the Pyrrolomycin Biosynthetic Gene Clusters from Actinosporangium vitaminophilum ATCC 31673 and Streptomyces sp. Strain UC 11065▿

PubMed Central

Zhang, Xiujun; Parry, Ronald J.

2007-01-01

The pyrrolomycins are a family of polyketide antibiotics, some of which contain a nitro group. To gain insight into the nitration mechanism associated with the formation of these antibiotics, the pyrrolomycin biosynthetic gene cluster from Actinosporangium vitaminophilum was cloned. Sequencing of ca. 56 kb of A. vitaminophilum DNA revealed 35 open reading frames (ORFs). Sequence analysis revealed a clear relationship between some of these ORFs and the biosynthetic gene cluster for pyoluteorin, a structurally related antibiotic. Since a gene transfer system could not be devised for A. vitaminophilum, additional proof for the identity of the cloned gene cluster was sought by cloning the pyrrolomycin gene cluster from Streptomyces sp. strain UC 11065, a transformable pyrrolomycin producer. Sequencing of ca. 26 kb of UC 11065 DNA revealed the presence of 17 ORFs, 15 of which exhibit strong similarity to ORFs in the A. vitaminophilum cluster as well as a nearly identical organization. Single-crossover disruption of two genes in the UC 11065 cluster abolished pyrrolomycin production in both cases. These results confirm that the genetic locus cloned from UC 11065 is essential for pyrrolomycin production, and they also confirm that the highly similar locus in A. vitaminophilum encodes pyrrolomycin biosynthetic genes. Sequence analysis revealed that both clusters contain genes encoding the two components of an assimilatory nitrate reductase. This finding suggests that nitrite is required for the formation of the nitrated pyrrolomycins. However, sequence analysis did not provide additional insights into the nitration process, suggesting the operation of a novel nitration mechanism. PMID:17158935

Analysis of the genomic sequences and metabolites of Serratia surfactantfaciens sp. nov. YD25T that simultaneously produces prodigiosin and serrawettin W2.

PubMed

Su, Chun; Xiang, Zhaoju; Liu, Yibo; Zhao, Xinqing; Sun, Yan; Li, Zhi; Li, Lijun; Chang, Fan; Chen, Tianjun; Wen, Xinrong; Zhou, Yidan; Zhao, Furong

2016-11-03

Gram-negative bacteria of the genus Serratia are potential producers of many useful secondary metabolites, such as prodigiosin and serrawettins, which have potential applications in environmental bioremediation or in the pharmaceutical industry. Several Serratia strains produce prodigiosin and serrawettin W1 as the main bioactive compounds, and the biosynthetic pathways are co-regulated by quorum sensing (QS). In contrast, the Serratia strain, which can simultaneously produce prodigiosin and serrawettin W2, has not been reported. This study focused on analyzing the genomic sequence of Serratia sp. strain YD25 T isolated from rhizosphere soil under continuously planted burley tobacco collected from Yongding, Fujian province, China, which is unique in producing both prodigiosin and serrawettin W2. A hybrid polyketide synthases (PKS)-non-ribosomal peptide synthetases (NRPS) gene cluster putatively involved in biosynthesis of antimicrobial serrawettin W2 was identified in the genome of YD25 T , and its biosynthesis pathway was proposed. We found potent antimicrobial activity of serrawettin W2 purified from YD25 T against various pathogenic bacteria and fungi as well as antitumor activity against Hela cells. Subsequently, comparative genomic analyses were performed among a total of 133 Serratia species. The prodigiosin biosynthesis gene cluster in YD25 T belongs to the type I pig cluster, which is the main form of pig-encoding genes existing in most of the pigmented Serratia species. In addition, a complete autoinducer-2 (AI-2) system (including luxS, lsrBACDEF, lsrGK, and lsrR) as a conserved bacterial operator is found in the genome of Serratia sp. strain YD25 T . Phylogenetic analysis based on concatenated Lsr and LuxS proteins revealed that YD25 T formed an independent branch and was clearly distant from the strains that solely produce either prodigiosin or serrawettin W2. The Fe (III) ion reduction assay confirmed that strain YD25 T could produce an AI-2 signal molecule. Phylogenetic analysis using the genomic sequence of YD25 T combined with phylogenetic and phenotypic analyses support this strain as a member of a novel and previously uncharacterized Serratia species. Genomic sequence and metabolite analysis of Serratia surfactantfaciens YD25 T indicate that this strain can be further explored for the production of useful metabolites. Unveiling the genomic sequence of S. surfactantfaciens YD25 T benefits the usage of this unique strain as a model system for studying the biosynthesis regulation of both prodigiosin and serrawettin W2 by the QS system.

Core-halo age gradients and star formation in the Orion Nebula and NGS 2024 young stellar clusters

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

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

2014-06-01

We analyze age distributions of two nearby rich stellar clusters, the NGC 2024 (Flame Nebula) and Orion Nebula cluster (ONC) in the Orion molecular cloud complex. Our analysis is based on samples from the MYStIX survey and a new estimator of pre-main sequence (PMS) stellar ages, Age{sub JX} , derived from X-ray and near-infrared photometric data. To overcome the problem of uncertain individual ages and large spreads of age distributions for entire clusters, we compute median ages and their confidence intervals of stellar samples within annular subregions of the clusters. We find core-halo age gradients in both the NGC 2024more » cluster and ONC: PMS stars in cluster cores appear younger and thus were formed later than PMS stars in cluster peripheries. These findings are further supported by the spatial gradients in the disk fraction and K-band excess frequency. Our age analysis is based on Age{sub JX} estimates for PMS stars and is independent of any consideration of OB stars. The result has important implications for the formation of young stellar clusters. One basic implication is that clusters form slowly and the apparent age spreads in young stellar clusters, which are often controversial, are (at least in part) real. The result further implies that simple models where clusters form inside-out are incorrect and more complex models are needed. We provide several star formation scenarios that alone or in combination may lead to the observed core-halo age gradients.« less

2-Way k-Means as a Model for Microbiome Samples.

PubMed

Jackson, Weston J; Agarwal, Ipsita; Pe'er, Itsik

2017-01-01

Motivation . Microbiome sequencing allows defining clusters of samples with shared composition. However, this paradigm poorly accounts for samples whose composition is a mixture of cluster-characterizing ones and which therefore lie in between them in the cluster space. This paper addresses unsupervised learning of 2-way clusters. It defines a mixture model that allows 2-way cluster assignment and describes a variant of generalized k -means for learning such a model. We demonstrate applicability to microbial 16S rDNA sequencing data from the Human Vaginal Microbiome Project.

2-Way k-Means as a Model for Microbiome Samples

PubMed Central

2017-01-01

Motivation. Microbiome sequencing allows defining clusters of samples with shared composition. However, this paradigm poorly accounts for samples whose composition is a mixture of cluster-characterizing ones and which therefore lie in between them in the cluster space. This paper addresses unsupervised learning of 2-way clusters. It defines a mixture model that allows 2-way cluster assignment and describes a variant of generalized k-means for learning such a model. We demonstrate applicability to microbial 16S rDNA sequencing data from the Human Vaginal Microbiome Project. PMID:29177026

[Detection of CRISPR and its relationship to drug resistance in Shigella].

PubMed

Wang, Linlin; Wang, Yingfang; Duan, Guangcai; Xue, Zerun; Guo, Xiangjiao; Wang, Pengfei; Xi, Yuanlin; Yang, Haiyan

2015-04-04

To detect clustered regularly interspaced short palindromic repeats (CRISPR) in Shigella, and to analyze its relationship to drug resistance. Four pairs of primers were used for the detection of convincing CRISPR structures CRISPR-S2 and CRISPR-S4, questionable CRISPR structures CRISPR-S1 and CRISPR-S3 in 60 Shigella strains. All primers were designed using sequences in CRISPR database. CRISPR Finder was used to analyze CRISPR and susceptibilities of Shigella strains were tested by agar diffusion method. Furthermore, we analyzed the relationship between drug resistance and CRISPR-S4. The positive rate of convincing CRISPR structures was 95%. The four CRISPR loci formed 12 spectral patterns (A-L), all of which contained convincing CRISPR structures except type K. We found one new repeat and 12 new spacers. The multi-drug resistance rate was 53. 33% . We found no significant difference between CRISPR-S4 and drug resistant. However, the repeat sequence of CRISPR-S4 in multi- or TE-resistance strains was mainly R4.1 with AC deletions in the 3' end, and the spacer sequences of CRISPR-S4 in multi-drug resistance strains were mainly Sp5.1, Sp6.1 and Sp7. CRISPR was common in Shigella. Variations df repeat sequences and diversities of spacer sequences might be related to drug resistance in Shigella.

Divergence, differential methylation and interspersion of melon satellite DNA sequences.

PubMed Central

Shmookler Reis, R; Timmis, J N; Ingle, J

1981-01-01

Melon (Cucumis melo) satellite DNA consists of two components, Q and S, each with a buoyant density in CsCl of 1.707 g/ml, but differing by 9 degrees C in "melting" temperature. These physical properties appear to be in contradiction, since both depend on G + C content. In order to resolve this anomaly, base compositions were directly determined for isolated fractions. the low-"melting" component S contains 41.8% G + C, with 6% of C present as 5-methylcytosine, whereas Q DNA contains 54% G + C, with 41% of C methylated. Analyses of restriction site loss agreed well with the direct determinations of methylation and divergence, and indicated some clustering of methylated sites in Q DNA. Analysis of restricted main-band DNA by hydridization with RNA complementary to Q satellite DNA ("Southern transfer") showed satellite Q tandem arrays interspersed in DNA of main-band density. Sequence divergence and extent of methylation did not appear to depend on whether a repeat array was present as satellite or interspersed in main-band DNA. Hydridization in situ indicated considerable heterogeneity in the genomic proportion of the Q-DNA sequences in melon fruit nuclei, implying over- and under-representation consistent with extensive unequal recombination in satellite Q tandem arrays. The cucumber, Cucumis sativus, contains less than 8% as much Q-homologous DNA per genome as the melon, suggesting rapid evolutionary gain or loss of these tandem repeat sequences. Images Fig. 2. PLATE 1 Fig. 4. Fig. 10. PMID:6172117

Spatio-Temporal Structure, Path Characteristics, and Perceptual Grouping in Immediate Serial Spatial Recall

PubMed Central

De Lillo, Carlo; Kirby, Melissa; Poole, Daniel

2016-01-01

Immediate serial spatial recall measures the ability to retain sequences of locations in short-term memory and is considered the spatial equivalent of digit span. It is tested by requiring participants to reproduce sequences of movements performed by an experimenter or displayed on a monitor. Different organizational factors dramatically affect serial spatial recall but they are often confounded or underspecified. Untangling them is crucial for the characterization of working-memory models and for establishing the contribution of structure and memory capacity to spatial span. We report five experiments assessing the relative role and independence of factors that have been reported in the literature. Experiment 1 disentangled the effects of spatial clustering and path-length by manipulating the distance of items displayed on a touchscreen monitor. Long-path sequences segregated by spatial clusters were compared with short-path sequences not segregated by clusters. Recall was more accurate for sequences segregated by clusters independently from path-length. Experiment 2 featured conditions where temporal pauses were introduced between or within cluster boundaries during the presentation of sequences with the same paths. Thus, the temporal structure of the sequences was either consistent or inconsistent with a hierarchical representation based on segmentation by spatial clusters but the effect of structure could not be confounded with effects of path-characteristics. Pauses at cluster boundaries yielded more accurate recall, as predicted by a hierarchical model. In Experiment 3, the systematic manipulation of sequence structure, path-length, and presence of path-crossings of sequences showed that structure explained most of the variance, followed by the presence/absence of path-crossings, and path-length. Experiments 4 and 5 replicated the results of the previous experiments in immersive virtual reality navigation tasks where the viewpoint of the observer changed dynamically during encoding and recall. This suggested that the effects of structure in spatial span are not dependent on perceptual grouping processes induced by the aerial view of the stimulus array typically afforded by spatial recall tasks. These results demonstrate the independence of coding strategies based on structure from effects of path characteristics and perceptual grouping in immediate serial spatial recall. PMID:27891101

Length-independent structural similarities enrich the antibody CDR canonical class model.

PubMed

Nowak, Jaroslaw; Baker, Terry; Georges, Guy; Kelm, Sebastian; Klostermann, Stefan; Shi, Jiye; Sridharan, Sudharsan; Deane, Charlotte M

2016-01-01

Complementarity-determining regions (CDRs) are antibody loops that make up the antigen binding site. Here, we show that all CDR types have structurally similar loops of different lengths. Based on these findings, we created length-independent canonical classes for the non-H3 CDRs. Our length variable structural clusters show strong sequence patterns suggesting either that they evolved from the same original structure or result from some form of convergence. We find that our length-independent method not only clusters a larger number of CDRs, but also predicts canonical class from sequence better than the standard length-dependent approach. To demonstrate the usefulness of our findings, we predicted cluster membership of CDR-L3 sequences from 3 next-generation sequencing datasets of the antibody repertoire (over 1,000,000 sequences). Using the length-independent clusters, we can structurally classify an additional 135,000 sequences, which represents a ∼20% improvement over the standard approach. This suggests that our length-independent canonical classes might be a highly prevalent feature of antibody space, and could substantially improve our ability to accurately predict the structure of novel CDRs identified by next-generation sequencing.

Gate sequence for continuous variable one-way quantum computation

PubMed Central

Su, Xiaolong; Hao, Shuhong; Deng, Xiaowei; Ma, Lingyu; Wang, Meihong; Jia, Xiaojun; Xie, Changde; Peng, Kunchi

2013-01-01

Measurement-based one-way quantum computation using cluster states as resources provides an efficient model to perform computation and information processing of quantum codes. Arbitrary Gaussian quantum computation can be implemented sufficiently by long single-mode and two-mode gate sequences. However, continuous variable gate sequences have not been realized so far due to an absence of cluster states larger than four submodes. Here we present the first continuous variable gate sequence consisting of a single-mode squeezing gate and a two-mode controlled-phase gate based on a six-mode cluster state. The quantum property of this gate sequence is confirmed by the fidelities and the quantum entanglement of two output modes, which depend on both the squeezing and controlled-phase gates. The experiment demonstrates the feasibility of implementing Gaussian quantum computation by means of accessible gate sequences.

Assessing historical rate changes in global tsunami occurrence

USGS Publications Warehouse

Geist, E.L.; Parsons, T.

2011-01-01

The global catalogue of tsunami events is examined to determine if transient variations in tsunami rates are consistent with a Poisson process commonly assumed for tsunami hazard assessments. The primary data analyzed are tsunamis with maximum sizes >1m. The record of these tsunamis appears to be complete since approximately 1890. A secondary data set of tsunamis >0.1m is also analyzed that appears to be complete since approximately 1960. Various kernel density estimates used to determine the rate distribution with time indicate a prominent rate change in global tsunamis during the mid-1990s. Less prominent rate changes occur in the early- and mid-20th century. To determine whether these rate fluctuations are anomalous, the distribution of annual event numbers for the tsunami catalogue is compared to Poisson and negative binomial distributions, the latter of which includes the effects of temporal clustering. Compared to a Poisson distribution, the negative binomial distribution model provides a consistent fit to tsunami event numbers for the >1m data set, but the Poisson null hypothesis cannot be falsified for the shorter duration >0.1m data set. Temporal clustering of tsunami sources is also indicated by the distribution of interevent times for both data sets. Tsunami event clusters consist only of two to four events, in contrast to protracted sequences of earthquakes that make up foreshock-main shock-aftershock sequences. From past studies of seismicity, it is likely that there is a physical triggering mechanism responsible for events within the tsunami source 'mini-clusters'. In conclusion, prominent transient rate increases in the occurrence of global tsunamis appear to be caused by temporal grouping of geographically distinct mini-clusters, in addition to the random preferential location of global M >7 earthquakes along offshore fault zones.

Star Formation in Nearby Clusters (SFiNCs)

NASA Astrophysics Data System (ADS)

Getman, Konstantin

Most stars form in clusters that rapidly disperse, yet we have a poor understanding of the processes of cluster formation and early evolution. Do clusters form `top-down', rapidly in a dense molecular cloud core? Or, since clouds are turbulent, do clusters form `bottomup' by merging subclusters produced in small kinematically-distinct molecular structures? Do clusters principally form in elongated molecular structures such as Infrared Dark Clouds and Herschel filaments? One of the central reasons for slow progress in resolving these questions is the lack of homogeneous and reliable census of stellar members (both disk-bearing and disk-free) for a wide range of star forming environments. To address these issues we are now completing our major effort, called MYStIX (Massive Young Star-Forming Complex Study in Infrared and X-ray). It combines the Chandra archive with UKIRT+2MASS near-infrared and Spitzer mid-infrared surveys to identify young stellar objects in a wide range of evolutionary stages, from protostars to disk-free pre-main sequence stars, in 20 star forming regions at distances from 0.4 to 3.6 kpc. Each MYStIX region was chosen to have a rich OB-dominated cluster. Started in 2009 with NASA/ADAP and NSF funding, MYStIX has emerged with 8 technical/catalog and the first 4 of a series of science papers (http://astro.psu.edu/mystix). Early MYStIX results include: demonstration of diverse morphologies of young clusters from simple ellipsoids to elongated, clumpy substructures; demonstration of spatio-age gradients across star formation regions; the discovery of core-halo age gradients within two rich nearby MYStIX clusters; and the discovery of important astrophysically empirical correlations among different subcluster properties such as age, absorption, core radius, central stellar density, and total intrinsic population. The early MYStIX result provide new observational evidence for subcluster merging and cluster expansion following gas dissipation. We propose here to extend the MYStIX effort to an archive study of 19 nearer and smaller star forming regions where the stellar clusters are dominated by a single late-OB star rather than numerous O stars as in the MYStIX fields. We call this project `Star Formation in Nearby Clusters' or SFiNCs (homophonic with `sphinx'). With a homogeneous analysis of the Chandra, 2MASS, Spitzer and Herschel archives, we expect to identify and characterize over 50 SFiNCs subclusters. The inferred empirical correlations among different cluster properties for nearly 200 SFiNCs+MYStIX subclusters with 30-3000 detected stars on scales of 0.1-20 pc will allow, for the first time, direct comparison with the results of theoretical simulations of cluster formation to seek deeper answers to the fundamental questions posed above. It is possible, for example, that smaller molecular clouds have less turbulence and thus produce small clusters in a single event rather than through subcluster mergers. Models based on meteoritic isotopes suggest that our Solar System formed in a complex of SFiNCs/MYStIX-like clusters (Gounelle & Meynet 2012, A&A, 545, 4). This project addresses NASA SMD Strategic Subgoals 3C (Advance scientific knowledge of the origin and history of the solar system) and 3D.3 (Understand how individual stars form and how those processes ultimately affect the formation of planetary systems). It lies in the `Star formation and pre-main sequence stars' Research Area of the Astrophysics Data Analysis program.

Faster sequence homology searches by clustering subsequences.

PubMed

Suzuki, Shuji; Kakuta, Masanori; Ishida, Takashi; Akiyama, Yutaka

2015-04-15

Sequence homology searches are used in various fields. New sequencing technologies produce huge amounts of sequence data, which continuously increase the size of sequence databases. As a result, homology searches require large amounts of computational time, especially for metagenomic analysis. We developed a fast homology search method based on database subsequence clustering, and implemented it as GHOSTZ. This method clusters similar subsequences from a database to perform an efficient seed search and ungapped extension by reducing alignment candidates based on triangle inequality. The database subsequence clustering technique achieved an ∼2-fold increase in speed without a large decrease in search sensitivity. When we measured with metagenomic data, GHOSTZ is ∼2.2-2.8 times faster than RAPSearch and is ∼185-261 times faster than BLASTX. The source code is freely available for download at http://www.bi.cs.titech.ac.jp/ghostz/ akiyama@cs.titech.ac.jp Supplementary data are available at Bioinformatics online. © The Author 2014. Published by Oxford University Press.

Diversity and Characterization of Sulfate-Reducing Bacteria in Groundwater at a Uranium Mill Tailings Site

PubMed Central

Chang, Yun-Juan; Peacock, Aaron D.; Long, Philip E.; Stephen, John R.; McKinley, James P.; Macnaughton, Sarah J.; Hussain, A. K. M. Anwar; Saxton, Arnold M.; White, David C.

2001-01-01

Microbially mediated reduction and immobilization of U(VI) to U(IV) plays a role in both natural attenuation and accelerated bioremediation of uranium-contaminated sites. To realize bioremediation potential and accurately predict natural attenuation, it is important to first understand the microbial diversity of such sites. In this paper, the distribution of sulfate-reducing bacteria (SRB) in contaminated groundwater associated with a uranium mill tailings disposal site at Shiprock, N.Mex., was investigated. Two culture-independent analyses were employed: sequencing of clone libraries of PCR-amplified dissimilatory sulfite reductase (DSR) gene fragments and phospholipid fatty acid (PLFA) biomarker analysis. A remarkable diversity among the DSR sequences was revealed, including sequences from δ-Proteobacteria, gram-positive organisms, and the Nitrospira division. PLFA analysis detected at least 52 different mid-chain-branched saturate PLFA and included a high proportion of 10me16:0. Desulfotomaculum and Desulfotomaculum-like sequences were the most dominant DSR genes detected. Those belonging to SRB within δ-Proteobacteria were mainly recovered from low-uranium (≤302 ppb) samples. One Desulfotomaculum-like sequence cluster overwhelmingly dominated high-U (>1,500 ppb) sites. Logistic regression showed a significant influence of uranium concentration over the dominance of this cluster of sequences (P = 0.0001). This strong association indicates that Desulfotomaculum has remarkable tolerance and adaptation to high levels of uranium and suggests the organism's possible involvement in natural attenuation of uranium. The in situ activity level of Desulfotomaculum in uranium-contaminated environments and its comparison to the activities of other SRB and other functional groups should be an important area for future research. PMID:11425735

Molecular Identification of Sibling Species of Sclerodermus (Hymenoptera: Bethylidae) That Parasitize Buprestid and Cerambycid Beetles by Using Partial Sequences of Mitochondrial DNA Cytochrome Oxidase Subunit 1 and 28S Ribosomal RNA Gene

PubMed Central

Jiang, Yuan; Yang, Zhongqi; Wang, Xiaoyi; Hou, Yuxia

2015-01-01

The species belonging to Sclerodermus (Hymenoptera: Bethylidae) are currently the most important insect natural enemies of wood borer pests, mainly buprestid and cerambycid beetles, in China. However, some sibling species of this genus are very difficult to distinguish because of their similar morphological features. To address this issue, we conducted phylogenetic and genetic analyses of cytochrome oxidase subunit I (COI) and 28S RNA gene sequences from eight species of Sclerodermus reared from different wood borer pests. The eight sibling species were as follows: S. guani Xiao et Wu, S. sichuanensis Xiao, S. pupariae Yang et Yao, and Sclerodermus spp. (Nos. 1–5). A 594-bp fragment of COI and 750-bp fragment of 28S were subsequently sequenced. For COI, the G-C content was found to be low in all the species, averaging to about 30.0%. Sequence divergences (Kimura-2-parameter distances) between congeneric species averaged to 4.5%, and intraspecific divergences averaged to about 0.09%. Further, the maximum sequence divergences between congeneric species and Sclerodermus sp. (No. 5) averaged to about 16.5%. All 136 samples analyzed were included in six reciprocally monophyletic clades in the COI neighbor-joining (NJ) tree. The NJ tree inferred from the 28S rRNA sequence yielded almost identical results, but the samples from S. guani, S. sichuanensis, S. pupariae, and Sclerodermus spp. (Nos. 1–4) clustered together and only Sclerodermus sp. (No. 5) clustered separately. Our findings indicate that the standard barcode region of COI can be efficiently used to distinguish morphologically similar Sclerodermus species. Further, we speculate that Sclerodermus sp. (No. 5) might be a new species of Sclerodermus. PMID:25782000

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

NASA Astrophysics Data System (ADS)

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

2018-04-01

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

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

Salinas, R.; Pajkos, M. A.; Strader, J.

Intermediate-age star clusters in the Large Magellanic Cloud show extended main sequence turnoffs (MSTOs) that are not consistent with a canonical single stellar population. These broad turnoffs have been interpreted as evidence for extended star formation and/or stellar rotation. Since most of these studies use single frames per filter to do the photometry, the presence of variable stars near the MSTO in these clusters has remained unnoticed and their impact has been totally ignored. We model the influence of Delta Scuti using synthetic CMDs, adding variable stars following different levels of incidence and amplitude distributions. We show that Delta Scutimore » observed at a single phase will produce a broadening of the MSTO without affecting other areas of a CMD such as the upper MS or the red clump; furthermore, the amount of spread introduced correlates with cluster age, as observed. This broadening is constrained to ages ∼1–3 Gyr when the MSTO area crosses the instability strip, which is also consistent with observations. Variable stars cannot explain bifurcarted MSTOs or the extended MSTOs seen in some young clusters, but they can make an important contribution to the extended MSTOs in intermediate-age clusters.« less

COS Spectroscopy of White Dwarf Companions to Blue Stragglers

NASA Astrophysics Data System (ADS)

Gosnell, Natalie M.; Geller, Aaron M.; Knigge, Christian; Mathieu, Robert D.; Sills, Alison; Leiner, Emily; Leigh, Nathan

2017-01-01

Complete membership studies of open stellar clusters reveal that 25% of the evolved stars follow alternative pathways in stellar evolution, meaning something in the history of these stars changed their composition or mass (or both). In order to draw a complete picture of stellar evolution we must include these canonically "strange" stars in our definition of standard stellar populations. The formation mechanism of blue straggler stars, traditionally defined to be brighter and bluer than the main sequence turnoff in a star cluster, has been an outstanding question for almost six decades. Recent Hubble Space Telescope (HST) far-ultraviolet (far-UV) observations directly reveal that the blue straggler stars in the old (7 Gyr) open cluster NGC 188 are predominantly formed through mass transfer. We will present HST far-UV COS spectroscopy of white dwarf companions to blue stragglers. These white dwarfs are the remnants of the mass transfer formation process. The effective temperatures and surface gravities of the white dwarfs delineate the timeline of blue straggler formation in this cluster. The existence of these binaries in a well-studied cluster environment provides an unprecedented opportunity to observationally constrain mass transfer models and inform our understanding of many other alternative pathway stellar products.

Updates on the genetics and the clinical impacts on phaeochromocytoma and paraganglioma in the new era.

PubMed

Pillai, Suja; Gopalan, Vinod; Smith, Robert A; Lam, Alfred K-Y

2016-04-01

Genetic mutations of phaeochromocytoma (PCC) and paraganglioma (PGL) are mainly classified into two major clusters. Cluster 1 mutations are involved with the pseudo hypoxic pathway and comprised of PHD2, VHL, SDHx, IDH, HIF2A, MDH2 and FH mutated PCC/PGL. Cluster 2 mutations are associated with abnormal activation of kinase signalling pathways and included mutations of RET, NF1, KIF1Bβ, MAX and TMEM127. In addition, VHL, SDHx (cluster 1 genes) and RET, NF1 (cluster 2 genes) germline mutations are involved in the neuronal precursor cell pathway in the pathogeneses of PCC/PGL. Also, GDNF, H-ras, K-ras, GNAS, CDKN2A (p16), p53, BAP1, BRCA1&2, ATRX and KMT2D mutations have roles in the development of PCC/PGLs. Overall, known genetic mutations account for the pathogenesis of approximately 60% of PCC/PGLs. Genetic mutations, pathological parameters and biochemical markers are used for better prediction of the outcome of patients with this group of tumours. Immunohistochemistry and gene sequencing can ensure a more effective detection, prediction of malignant potential and treatment of PCC/PCLs. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

AGORA : Organellar genome annotation from the amino acid and nucleotide references.

PubMed

Jung, Jaehee; Kim, Jong Im; Jeong, Young-Sik; Yi, Gangman

2018-03-29

Next-generation sequencing (NGS) technologies have led to the accumulation of highthroughput sequence data from various organisms in biology. To apply gene annotation of organellar genomes for various organisms, more optimized tools for functional gene annotation are required. Almost all gene annotation tools are mainly focused on the chloroplast genome of land plants or the mitochondrial genome of animals.We have developed a web application AGORA for the fast, user-friendly, and improved annotations of organellar genomes. AGORA annotates genes based on a BLAST-based homology search and clustering with selected reference sequences from the NCBI database or user-defined uploaded data. AGORA can annotate the functional genes in almost all mitochondrion and plastid genomes of eukaryotes. The gene annotation of a genome with an exon-intron structure within a gene or inverted repeat region is also available. It provides information of start and end positions of each gene, BLAST results compared with the reference sequence, and visualization of gene map by OGDRAW. Users can freely use the software, and the accessible URL is https://bigdata.dongguk.edu/gene_project/AGORA/.The main module of the tool is implemented by the python and php, and the web page is built by the HTML and CSS to support all browsers. gangman@dongguk.edu.

Analysis of expressed sequence tags from the four main developmental stages of Trypanosoma congolense

PubMed Central

Helm, Jared R.; Hertz-Fowler, Christiane; Aslett, Martin; Berriman, Matthew; Sanders, Mandy; Quail, Michael A.; Soares, Marcelo B.; Bonaldo, Maria F.; Sakurai, Tatsuya; Inoue, Noboru; Donelson, John E.

2009-01-01

Trypanosoma congolense is one of the most economically important pathogens of livestock in Africa. Culture-derived parasites of each of the three main insect stages of the T. congolense life cycle, i.e., the procyclic, epimastigote and metacyclic stages, and bloodstream stage parasites isolated from infected mice, were used to construct stage-specific cDNA libraries and expressed sequence tags (ESTs or cDNA clones) in each library were sequenced. Thirteen EST clusters encoding different variant surface glycoproteins (VSGs) were detected in the metacyclic library and twenty-six VSG EST clusters were found in the bloodstream library, six of which are shared by the metacyclic library. Rare VSG ESTs are present in the epimastigote library, and none were detected in the procyclic library. ESTs encoding enzymes that catalyze oxidative phosphorylation and amino acid metabolism are about twice as abundant in the procyclic and epimastigote stages as in the metacyclic and bloodstream stages. In contrast, ESTs encoding enzymes involved in glycolysis, the citric acid cycle and nucleotide metabolism are about the same in all four developmental stages. Cysteine proteases, kinases and phosphatases are the most abundant enzyme groups represented by the ESTs. All four libraries contain T. congolense-specific expressed sequences not present in the T. brucei and T. cruzi genomes. Normalized cDNA libraries were constructed from the metacyclic and bloodstream stages, and found to be further enriched for T. congolense-specific ESTs. Given that cultured T. congolense offers an experimental advantage over other African trypanosome species, these ESTs provide a basis for further investigation of the molecular properties of these four developmental stages, especially the epimastigote and metacyclic stages for which it is difficult to obtain large quantities of organisms. The T. congolense EST databases are available at: http://www.sanger.ac.uk/Projects/T_congolense/EST_index.shtml. PMID:19559733

Antigenic and genotypic characterization of rabies virus isolated from bats (Mammalia: Chiroptera) from municipalities in São Paulo State, Southeastern Brazil.

PubMed

Menozzi, Benedito Donizete; de Novaes Oliveira, Rafael; Paiz, Laís Moraes; Richini-Pereira, Virgínia Bodelão; Langoni, Helio

2017-05-01

Bats have aroused growing attention in the public health sphere because they are considered the main reservoir of rabies virus (RABV) in the Americas, in places where canine rabies is under control. Antigenic and genetic studies of RABV isolates have been used to describe the epidemiological profile of rabies and to identify possible hosts/reservoirs for different epidemiological cycles. This study describes the antigenic and genotypic characterization of 19 RABV isolates from central nervous system samples of non-hematophagous bats (Mammalia: Chiroptera). These bats were diagnosed as RABV positive by direct fluorescent antibody and mouse inoculation tests. Antigenic characterization using a panel of eight monoclonal antibodies revealed that 7 of 19 RABV isolates from these bats belonged to variant 3, for which the hematophagous bat species Desmodus rotundus is the main reservoir, and 1 of 19 RABV isolates from an insectivorous bat belonged to variant 4, which is characteristic of these bats. The remaining 11 RABV samples were divided into six non-compatible profiles. The isolates were subjected to reverse transcription polymerase chain reaction for the N gene and partially sequenced. Genetic characterization of these isolates was performed by grouping the sequences obtained with known RABV lineages. The sequences were grouped in clusters by the phylogenetic inference neighbor-joining method, together with another 89 homologous sequences obtained from GenBank. This analysis grouped the isolates into four known lineages: Nyctinomops Brazil, Myotis Brazil, Eptesicus Brazil and D. rotundus Brazil, as well as another cluster that may define a RABV lineage not yet characterized, here named Myotis Brazil II, for which bats of the genus Myotis apparently act as reservoirs. This assumption of a new lineage is also based on the observation of amino acid substitutions, with an average intraspecific identity of 99.8%, varying from 99.6 to 100.0% for nucleotides and 100.0% for amino acids.

Identification of Habitat-Specific Biomes of Aquatic Fungal Communities Using a Comprehensive Nearly Full-Length 18S rRNA Dataset Enriched with Contextual Data

PubMed Central

Panzer, Katrin; Yilmaz, Pelin; Weiß, Michael; Reich, Lothar; Richter, Michael; Wiese, Jutta; Schmaljohann, Rolf; Labes, Antje; Imhoff, Johannes F.; Glöckner, Frank Oliver; Reich, Marlis

2015-01-01

Molecular diversity surveys have demonstrated that aquatic fungi are highly diverse, and that they play fundamental ecological roles in aquatic systems. Unfortunately, comparative studies of aquatic fungal communities are few and far between, due to the scarcity of adequate datasets. We combined all publicly available fungal 18S ribosomal RNA (rRNA) gene sequences with new sequence data from a marine fungi culture collection. We further enriched this dataset by adding validated contextual data. Specifically, we included data on the habitat type of the samples assigning fungal taxa to ten different habitat categories. This dataset has been created with the intention to serve as a valuable reference dataset for aquatic fungi including a phylogenetic reference tree. The combined data enabled us to infer fungal community patterns in aquatic systems. Pairwise habitat comparisons showed significant phylogenetic differences, indicating that habitat strongly affects fungal community structure. Fungal taxonomic composition differed considerably even on phylum and class level. Freshwater fungal assemblage was most different from all other habitat types and was dominated by basal fungal lineages. For most communities, phylogenetic signals indicated clustering of sequences suggesting that environmental factors were the main drivers of fungal community structure, rather than species competition. Thus, the diversification process of aquatic fungi must be highly clade specific in some cases.The combined data enabled us to infer fungal community patterns in aquatic systems. Pairwise habitat comparisons showed significant phylogenetic differences, indicating that habitat strongly affects fungal community structure. Fungal taxonomic composition differed considerably even on phylum and class level. Freshwater fungal assemblage was most different from all other habitat types and was dominated by basal fungal lineages. For most communities, phylogenetic signals indicated clustering of sequences suggesting that environmental factors were the main drivers of fungal community structure, rather than species competition. Thus, the diversification process of aquatic fungi must be highly clade specific in some cases. PMID:26226014

Poly(A)-tag deep sequencing data processing to extract poly(A) sites.

PubMed

Wu, Xiaohui; Ji, Guoli; Li, Qingshun Quinn

2015-01-01

Polyadenylation [poly(A)] is an essential posttranscriptional processing step in the maturation of eukaryotic mRNA. The advent of next-generation sequencing (NGS) technology has offered feasible means to generate large-scale data and new opportunities for intensive study of polyadenylation, particularly deep sequencing of the transcriptome targeting the junction of 3'-UTR and the poly(A) tail of the transcript. To take advantage of this unprecedented amount of data, we present an automated workflow to identify polyadenylation sites by integrating NGS data cleaning, processing, mapping, normalizing, and clustering. In this pipeline, a series of Perl scripts are seamlessly integrated to iteratively map the single- or paired-end sequences to the reference genome. After mapping, the poly(A) tags (PATs) at the same genome coordinate are grouped into one cleavage site, and the internal priming artifacts removed. Then the ambiguous region is introduced to parse the genome annotation for cleavage site clustering. Finally, cleavage sites within a close range of 24 nucleotides and from different samples can be clustered into poly(A) clusters. This procedure could be used to identify thousands of reliable poly(A) clusters from millions of NGS sequences in different tissues or treatments.

A Comparison of Anammox Bacterial Abundance and Community Structures in Three Different Emerged Plants-Related Sediments.

PubMed

Chu, Jinyu; Zhang, Jinping; Zhou, Xiaohong; Liu, Biao; Li, Yimin

2015-09-01

Quantitative polymerase chain reaction (qPCR) assays and 16S rRNA gene clone libraries were used to document the abundance, diversity and community structure of anaerobic ammonia-oxidising (anammox) bacteria in the rhizosphere and non-rhizosphere sediments of three emergent macrophyte species (Iris pseudacorus, Thalia dealbata and Typha orientalis). The qPCR results confirmed the existence of anammox bacteria (AMX) with observed log number of gene copies per dry gram sediment ranging from 5.00 to 6.78. AMX was more abundant in T. orientalis-associated sediments than in the other two plant species. The I. pseudacorus- and T. orientalis-associated sediments had higher Shannon diversity values, indicating higher AMX diversity in these sediments. Based on the 16S rRNA gene, Candidatus 'Brocadia', Candidatus 'Kuenenia', Candidatus 'Jettenia' and new clusters were observed with the predominant Candidatus 'Kuenenia' cluster. The I. pseudacorus-associated sediments contained all the sequences of the C. 'Jettenia' cluster. Sequences obtained from T. orientalis-associated sediments contributed more than 90 % sequences in the new cluster, whereas none was found from I. pseudacorus. The new cluster was distantly related to known sequences; thus, this cluster was grouped outside the known clusters, indicating that the new cluster may be a new Planctomycetales genus. Further studies should be undertaken to confirm this finding.

Detecting Genomic Clustering of Risk Variants from Sequence Data: Cases vs. Controls

PubMed Central

Schaid, Daniel J.; Sinnwell, Jason P.; McDonnell, Shannon K.; Thibodeau, Stephen N.

2013-01-01

As the ability to measure dense genetic markers approaches the limit of the DNA sequence itself, taking advantage of possible clustering of genetic variants in, and around, a gene would benefit genetic association analyses, and likely provide biological insights. The greatest benefit might be realized when multiple rare variants cluster in a functional region. Several statistical tests have been developed, one of which is based on the popular Kulldorff scan statistic for spatial clustering of disease. We extended another popular spatial clustering method – Tango’s statistic – to genomic sequence data. An advantage of Tango’s method is that it is rapid to compute, and when single test statistic is computed, its distribution is well approximated by a scaled chi-square distribution, making computation of p-values very rapid. We compared the Type-I error rates and power of several clustering statistics, as well as the omnibus sequence kernel association test (SKAT). Although our version of Tango’s statistic, which we call “Kernel Distance” statistic, took approximately half the time to compute than the Kulldorff scan statistic, it had slightly less power than the scan statistic. Our results showed that the Ionita-Laza version of Kulldorff’s scan statistic had the greatest power over a range of clustering scenarios. PMID:23842950

A proper motion study of the globular cluster M55

NASA Astrophysics Data System (ADS)

Zloczewski, K.; Kaluzny, J.; Thompson, I. B.

2011-07-01

We have derived the absolute proper motion (PM) of the globular cluster M55 using a large set of CCD images collected with the du Pont telescope between 1997 and 2008. We find (μα cos δ, μδ) = (-3.31 ± 0.10, -9.14 ± 0.15) mas yr-1 relative to background galaxies. Membership status was determined for 16 945 stars with 14 < V < 21 from the central part of the cluster. The PM catalogue includes 52 variables, of which 43 are probable members of M55. This sample not only is dominated by pulsating blue straggler stars, but also includes five eclipsing binaries, three of which are main-sequence objects. The survey also identified several candidate blue, yellow and red straggler stars belonging to the cluster. We detected 15 likely members of the Sgr dSph galaxy located behind M55. The average PM for these stars was measured to be (μα cos δ, μδ) = (-2.23 ± 0.14, -1.83 ± 0.24) mas yr-1.

Inference of Markovian properties of molecular sequences from NGS data and applications to comparative genomics.

PubMed

Ren, Jie; Song, Kai; Deng, Minghua; Reinert, Gesine; Cannon, Charles H; Sun, Fengzhu

2016-04-01

Next-generation sequencing (NGS) technologies generate large amounts of short read data for many different organisms. The fact that NGS reads are generally short makes it challenging to assemble the reads and reconstruct the original genome sequence. For clustering genomes using such NGS data, word-count based alignment-free sequence comparison is a promising approach, but for this approach, the underlying expected word counts are essential.A plausible model for this underlying distribution of word counts is given through modeling the DNA sequence as a Markov chain (MC). For single long sequences, efficient statistics are available to estimate the order of MCs and the transition probability matrix for the sequences. As NGS data do not provide a single long sequence, inference methods on Markovian properties of sequences based on single long sequences cannot be directly used for NGS short read data. Here we derive a normal approximation for such word counts. We also show that the traditional Chi-square statistic has an approximate gamma distribution ,: using the Lander-Waterman model for physical mapping. We propose several methods to estimate the order of the MC based on NGS reads and evaluate those using simulations. We illustrate the applications of our results by clustering genomic sequences of several vertebrate and tree species based on NGS reads using alignment-free sequence dissimilarity measures. We find that the estimated order of the MC has a considerable effect on the clustering results ,: and that the clustering results that use a N: MC of the estimated order give a plausible clustering of the species. Our implementation of the statistics developed here is available as R package 'NGS.MC' at http://www-rcf.usc.edu/∼fsun/Programs/NGS-MC/NGS-MC.html fsun@usc.edu Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Nuclear counterparts of the cytoplasmic mitochondrial 12S rRNA gene: a problem of ancient DNA and molecular phylogenies.

PubMed

van der Kuyl, A C; Kuiken, C L; Dekker, J T; Perizonius, W R; Goudsmit, J

1995-06-01

Monkey mummy bones and teeth originating from the North Saqqara Baboon Galleries (Egypt), soft tissue from a mummified baboon in a museum collection, and nineteenth/twentieth-century skin fragments from mangabeys were used for DNA extraction and PCR amplification of part of the mitochondrial 12S rRNA gene. Sequences aligning with the 12S rRNA gene were recovered but were only distantly related to contemporary monkey mitochondrial 12S rRNA sequences. However, many of these sequences were identical or closely related to human nuclear DNA sequences resembling mitochondrial 12S rRNA (isolated from a cell line depleted in mitochondria) and therefore have to be considered contamination. Subsequently in a separate study we were able to recover genuine mitochondrial 12S rRNA sequences from many extant species of nonhuman Old World primates and sequences closely resembling the human nuclear integrations. Analysis of all sequences by the neighbor-joining (NJ) method indicated that mitochondrial DNA sequences and their nuclear counterparts can be divided into two distinct clusters. One cluster contained all temporary cytoplasmic mitochondrial DNA sequences and approximately half of the monkey nuclear mitochondriallike sequences. A second cluster contained most human nuclear sequences and the other half of monkey nuclear sequences with a separate branch leading to human and gorilla mitochondrial and nuclear sequences. Sequences recovered from ancient materials were equally divided between the two clusters. These results constitute a warning for when working with ancient DNA or performing phylogenetic analysis using mitochondrial DNA as a target sequence: Nuclear counterparts of mitochondrial genes may lead to faulty interpretation of results.

A Direct Comparison of Two Densely Sampled HIV Epidemics: The UK and Switzerland

NASA Astrophysics Data System (ADS)

Ragonnet-Cronin, Manon L.; Shilaih, Mohaned; Günthard, Huldrych F.; Hodcroft, Emma B.; Böni, Jürg; Fearnhill, Esther; Dunn, David; Yerly, Sabine; Klimkait, Thomas; Aubert, Vincent; Yang, Wan-Lin; Brown, Alison E.; Lycett, Samantha J.; Kouyos, Roger; Brown, Andrew J. Leigh

2016-09-01

Phylogenetic clustering approaches can elucidate HIV transmission dynamics. Comparisons across countries are essential for evaluating public health policies. Here, we used a standardised approach to compare the UK HIV Drug Resistance Database and the Swiss HIV Cohort Study while maintaining data-protection requirements. Clusters were identified in subtype A1, B and C pol phylogenies. We generated degree distributions for each risk group and compared distributions between countries using Kolmogorov-Smirnov (KS) tests, Degree Distribution Quantification and Comparison (DDQC) and bootstrapping. We used logistic regression to predict cluster membership based on country, sampling date, risk group, ethnicity and sex. We analysed >8,000 Swiss and >30,000 UK subtype B sequences. At 4.5% genetic distance, the UK was more clustered and MSM and heterosexual degree distributions differed significantly by the KS test. The KS test is sensitive to variation in network scale, and jackknifing the UK MSM dataset to the size of the Swiss dataset removed the difference. Only heterosexuals varied based on the DDQC, due to UK male heterosexuals who clustered exclusively with MSM. Their removal eliminated this difference. In conclusion, the UK and Swiss HIV epidemics have similar underlying dynamics and observed differences in clustering are mainly due to different population sizes.

Use of Conserved Randomly Amplified Polymorphic DNA (RAPD) Fragments and RAPD Pattern for Characterization of Lactobacillus fermentum in Ghanaian Fermented Maize Dough

PubMed Central

Hayford, Alice E.; Petersen, Anne; Vogensen, Finn K.; Jakobsen, Mogens

1999-01-01

The present work describes the use of randomly amplified polymorphic DNA (RAPD) for the characterization of 172 dominant Lactobacillus isolates from present and previous studies of Ghanaian maize fermentation. Heterofermentative lactobacilli dominate the fermentation flora, since approximately 85% of the isolates belong to this group. Cluster analysis of the RAPD profiles obtained showed the presence of two main clusters. Cluster 1 included Lactobacillus fermentum, whereas cluster 2 comprised the remaining Lactobacillus spp. The two distinct clusters emerged at the similarity level of <50%. All isolates in cluster 1 showed similarity in their RAPD profile to the reference strains of L. fermentum included in the study. These isolates, yielding two distinct bands of approximately 695 and 773 bp with the primers used, were divided into four subclusters, indicating that several strains are involved in the fermentation and remain dominant throughout the process. The two distinct RAPD fragments were cloned, sequenced, and used as probes in Southern hybridization experiments. With one exception, Lactobacillus reuteri LMG 13045, the probes hybridized only to fragments of different sizes in EcoRI-digested chromosomal DNA of L. fermentum strains, thus indicating the specificity of the probes and variation within the L. fermentum isolates. PMID:10388723

Clustering execution in a processing system to increase power savings

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

Bose, Pradip; Buyuktosunoglu, Alper; Jacobson, Hans M.

Embodiments relate to clustering execution in a processing system. An aspect includes accessing a control flow graph that defines a data dependency and an execution sequence of a plurality of tasks of an application that executes on a plurality of system components. The execution sequence of the tasks in the control flow graph is modified as a clustered control flow graph that clusters active and idle phases of a system component while maintaining the data dependency. The clustered control flow graph is sent to an operating system, where the operating system utilizes the clustered control flow graph for scheduling themore » tasks.« less

Detailed spatiotemporal evolution of microseismicity and repeating earthquakes following the 2012 Mw 7.6 Nicoya earthquake

NASA Astrophysics Data System (ADS)

Yao, Dongdong; Walter, Jacob I.; Meng, Xiaofeng; Hobbs, Tiegan E.; Peng, Zhigang; Newman, Andrew V.; Schwartz, Susan Y.; Protti, Marino

2017-01-01

We apply a waveform matching technique to obtain a detailed earthquake catalog around the rupture zone of the 5 September 2012 moment magnitude 7.6 Nicoya earthquake, with emphasis on its aftershock sequence. Starting from a preliminary catalog, we relocate 7900 events using TomoDD to better quantify their spatiotemporal behavior. Relocated aftershocks are mostly clustered in two groups. The first is immediately above the major coseismic slip patch, partially overlapping with shallow afterslip. The second one is 50 km SE to the main shock nucleation point and near the terminus of coseismic rupture, in a zone that exhibited little resolvable afterslip. Using the relocated events as templates, we scan through the continuous recording from 29 June 2012 to 30 December 2012, detecting approximately 17 times more than template events. We find 190 aftershocks in the first half hour following the main shock, mostly along the plate interface. Later events become more scattered in location, showing moderate expansion in both along-trench and downdip directions. From the detected catalog we identify 53 repeating aftershock clusters with mean cross-correlation values larger than 0.9, and indistinguishably intracluster event locations, suggesting slip on the same fault patch. Most repeating clusters occurred within the first major aftershock group. Very few repeating clusters were found in the aftershock grouping along the southern edge of the Peninsula, which is not associated with substantial afterslip. Our observations suggest that loading from nearby afterslip along the plate interface drives spatiotemporal evolution of aftershocks just above the main shock rupture patch, while aftershocks in the SE group are to the SE of the observed updip afterslip and poorly constrained.

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.

Mainshock-aftershock clustering in volcanic regions

USGS Publications Warehouse

Giron, Ricardo Garza; Brodsky, Emily E.; Prejean, Stephanie

2018-01-01

swarms and mainshock-aftershock sequences. The former is commonly thought to dominate in volcanic and geothermal regions, but aftershock production, including within swarms, is not well studied in volcanic regions. Here we compare mainshock-aftershock clustering in active volcanic regions in Japan to nearby nonvolcanic regions. We find that aftershock production is similar in both areas by two separate metrics: (1) Both volcanic and nonvolcanic regions have similar proportions of areas that cluster into mainshock-aftershock sequences. (2) Volcanic areas with mainshock-aftershock sequences have aftershock productivity at least as high as nonvolcanic regions. We also find that volcano-tectonic events that are precursors to an eruption are more common at volcanoes without mainshock-aftershock clusters than at volcanoes with well-defined mainshock-aftershock clusters. This last finding hints at a strategy to identify volcanic systems where cataloged earthquakes are good predictors of behavior.

Acquisition of Initial /s/-Stop and Stop-/s/ Sequences in Greek

ERIC Educational Resources Information Center

Syrika, Asimina; Nicolaidis, Katerina; Edwards, Jan; Beckman, Mary E.

2011-01-01

Previous work on children's acquisition of complex sequences points to a tendency for affricates to be acquired before clusters, but there is no clear evidence of a difference in order of acquisition between clusters with /s/ that violate the Sonority Sequencing Principle (SSP), such as /s/ followed by stop in onset position, and other clusters…

Diversity and evolution analysis of glycoprotein GP85 from avian leukosis virus subgroup J isolates from chickens of different genetic backgrounds during 1989-2016: Coexistence of five extremely different clusters.

PubMed

Wang, Peikun; Lin, Lulu; Li, Haijuan; Yang, Yongli; Huang, Teng; Wei, Ping

2018-02-01

ALV-J has caused the most serious losses to the poultry industry in China. The gp85-coding sequence of ALV-J is known to be prone to mutation, but any association between the gp85 gene and breed of chicken remains unclear. A comprehensive and systematic study of the evolutionary process of ALV-J in China is needed. In this study, we compared and analyzed gp85 gene sequences from 198 ALV-J isolates, originating from China, USA, UK and France during 1989-2016. These were sorted into five clusters. Cluster 1, 2, 3, 4 and 5 included isolates from chicken types of different genetic backgrounds, e.g. white-feather broiler, Guangxi indigenous chicken breeds, Yellow chickens and layer chickens respectively. A correlation comparison of amino acid sequence similarities in the gp85 protein among the five clusters showed significant differences (P < 0.01) with the exception being when the third and fifth cluster were compared (P > 0.05). Results of entropy analysis of the gp85 sequences revealed that cluster 3 had the largest variation and cluster 1 had the least variation. The N-glycosylation sites in the majority of isolates numbered 14, 16, 17, 16 and 16, respectively, with regards to clusters 1-5. In addition, 5 isolates from cluster 3 had one more glycosylation site than the other isolates from cluster 3. Our study provides evidence that there were five extremely different ALV-J clusters during 1989-2016 and that the gp85 genes isolated from indigenous chicken breed isolates had the largest variation.

GraphTeams: a method for discovering spatial gene clusters in Hi-C sequencing data.

PubMed

Schulz, Tizian; Stoye, Jens; Doerr, Daniel

2018-05-08

Hi-C sequencing offers novel, cost-effective means to study the spatial conformation of chromosomes. We use data obtained from Hi-C experiments to provide new evidence for the existence of spatial gene clusters. These are sets of genes with associated functionality that exhibit close proximity to each other in the spatial conformation of chromosomes across several related species. We present the first gene cluster model capable of handling spatial data. Our model generalizes a popular computational model for gene cluster prediction, called δ-teams, from sequences to graphs. Following previous lines of research, we subsequently extend our model to allow for several vertices being associated with the same label. The model, called δ-teams with families, is particular suitable for our application as it enables handling of gene duplicates. We develop algorithmic solutions for both models. We implemented the algorithm for discovering δ-teams with families and integrated it into a fully automated workflow for discovering gene clusters in Hi-C data, called GraphTeams. We applied it to human and mouse data to find intra- and interchromosomal gene cluster candidates. The results include intrachromosomal clusters that seem to exhibit a closer proximity in space than on their chromosomal DNA sequence. We further discovered interchromosomal gene clusters that contain genes from different chromosomes within the human genome, but are located on a single chromosome in mouse. By identifying δ-teams with families, we provide a flexible model to discover gene cluster candidates in Hi-C data. Our analysis of Hi-C data from human and mouse reveals several known gene clusters (thus validating our approach), but also few sparsely studied or possibly unknown gene cluster candidates that could be the source of further experimental investigations.

Exploring the sequence-structure protein landscape in the glycosyltransferase family

PubMed Central

Zhang, Ziding; Kochhar, Sunil; Grigorov, Martin

2003-01-01

To understand the molecular basis of glycosyltransferases’ (GTFs) catalytic mechanism, extensive structural information is required. Here, fold recognition methods were employed to assign 3D protein shapes (folds) to the currently known GTF sequences, available in public databases such as GenBank and Swissprot. First, GTF sequences were retrieved and classified into clusters, based on sequence similarity only. Intracluster sequence similarity was chosen sufficiently high to ensure that the same fold is found within a given cluster. Then, a representative sequence from each cluster was selected to compose a subset of GTF sequences. The members of this reduced set were processed by three different fold recognition methods: 3D-PSSM, FUGUE, and GeneFold. Finally, the results from different fold recognition methods were analyzed and compared to sequence-similarity search methods (i.e., BLAST and PSI-BLAST). It was established that the folds of about 70% of all currently known GTF sequences can be confidently assigned by fold recognition methods, a value which is higher than the fold identification rate based on sequence comparison alone (48% for BLAST and 64% for PSI-BLAST). The identified folds were submitted to 3D clustering, and we found that most of the GTF sequences adopt the typical GTF A or GTF B folds. Our results indicate a lack of evidence that new GTF folds (i.e., folds other than GTF A and B) exist. Based on cases where fold identification was not possible, we suggest several sequences as the most promising targets for a structural genomics initiative focused on the GTF protein family. PMID:14500887

[Chlorobaculum macestae sp. nov., a new green sulfur bacterium].

PubMed

Koppen, O I; Berg, I A; Lebedeva, N V; Taisova, A S; Kolganova, T V; Slobodova, N V; Bulygina, E S; Turova, T P; Ivanovskiĭ, R N

2008-01-01

The investigated green sulfur bacterium, strain M, was isolated from a sulfidic spring on the Black Sea Coast of the Caucasus. The cells of strain M are straight or curved rods 0.6-0.9 x 1.8-4.2 microm in size. According to the cell wall structure, the bacteria are gram-negative. Chlorosomes are located along the cell periphery. Strain M is an obligate anaerobe capable of photoautotrophic growth on sulfide, thiosulfate, and H2. It utilizes ammonium, urea, casein hydrolysate, and N2 as nitrogen sources and sulfide, thiosulfate, and elemental sulfur as sulfur sources. Bacteriochlorophyll c and the carotenoid chlorobactene are the main pigments. The optimal growth temperature is 25-28 degrees C; the optimal pH is 6.8. The strain does not require NaCl. Vitamin B12 stimulates growth. The content of the G+C base pairs in the DNA of strain M is 58.3 mol %. In the phylogenetic tree constructed on the basis of analysis of nucleotide sequences of 16S rRNA genes, strain M forms a separate branch, which occupies an intermediate position between the phylogenetic cluster containing representatives of the genus Chlorobaculum (94.9-96.8%) and the cluster containing species of the genus Chlorobium (94.1-96.5%). According to the results of analysis of the amino acid sequence corresponding to the fmo gene, strain M represents a branch which, unlike that in the "ribosomal" tree, falls into the cluster of the genus Chlorobaculum (95.8-97.2%). Phylogenetic analysis of the amino acid sequence corresponding to the nifH gene placed species of the genera Chlorobaculum and Chlorobium into a single cluster, whereas strain M formed a separate branch. The results obtained allow us to describe strain M as a new species of the genus Chlorobaculum. Chlorobaculum macestae sp. nov.

HIV Transmission Networks in the San Diego–Tijuana Border Region

PubMed Central

Mehta, Sanjay R.; Wertheim, Joel O.; Brouwer, Kimberly C.; Wagner, Karla D.; Chaillon, Antoine; Strathdee, Steffanie; Patterson, Thomas L.; Rangel, Maria G.; Vargas, Mlenka; Murrell, Ben; Garfein, Richard; Little, Susan J.; Smith, Davey M.

2015-01-01

Background HIV sequence data can be used to reconstruct local transmission networks. Along international borders, like the San Diego–Tijuana region, understanding the dynamics of HIV transmission across reported risks, racial/ethnic groups, and geography can help direct effective prevention efforts on both sides of the border. Methods We gathered sociodemographic, geographic, clinical, and viral sequence data from HIV infected individuals participating in ten studies in the San Diego–Tijuana border region. Phylogenetic and network analysis was performed to infer putative relationships between HIV sequences. Correlates of identified clusters were evaluated and spatiotemporal relationships were explored using Bayesian phylogeographic analysis. Findings After quality filtering, 843 HIV sequences with associated demographic data and 263 background sequences from the region were analyzed, and 138 clusters were inferred (2–23 individuals). Overall, the rate of clustering did not differ by ethnicity, residence, or sex, but bisexuals were less likely to cluster than heterosexuals or men who have sex with men (p = 0.043), and individuals identifying as white (p ≤ 0.01) were more likely to cluster than other races. Clustering individuals were also 3.5 years younger than non-clustering individuals (p < 0.001). Although the sampled San Diego and Tijuana epidemics were phylogenetically compartmentalized, five clusters contained individuals residing on both sides of the border. Interpretation This study sampled ~ 7% of HIV infected individuals in the border region, and although the sampled networks on each side of the border were largely separate, there was evidence of persistent bidirectional cross-border transmissions that linked risk groups, thus highlighting the importance of the border region as a “melting pot” of risk groups. Funding NIH, VA, and Pendleton Foundation. PMID:26629540

HIV Transmission Networks in the San Diego-Tijuana Border Region.

PubMed

Mehta, Sanjay R; Wertheim, Joel O; Brouwer, Kimberly C; Wagner, Karla D; Chaillon, Antoine; Strathdee, Steffanie; Patterson, Thomas L; Rangel, Maria G; Vargas, Mlenka; Murrell, Ben; Garfein, Richard; Little, Susan J; Smith, Davey M

2015-10-01

HIV sequence data can be used to reconstruct local transmission networks. Along international borders, like the San Diego-Tijuana region, understanding the dynamics of HIV transmission across reported risks, racial/ethnic groups, and geography can help direct effective prevention efforts on both sides of the border. We gathered sociodemographic, geographic, clinical, and viral sequence data from HIV infected individuals participating in ten studies in the San Diego-Tijuana border region. Phylogenetic and network analysis was performed to infer putative relationships between HIV sequences. Correlates of identified clusters were evaluated and spatiotemporal relationships were explored using Bayesian phylogeographic analysis. After quality filtering, 843 HIV sequences with associated demographic data and 263 background sequences from the region were analyzed, and 138 clusters were inferred (2-23 individuals). Overall, the rate of clustering did not differ by ethnicity, residence, or sex, but bisexuals were less likely to cluster than heterosexuals or men who have sex with men (p = 0.043), and individuals identifying as white (p ≤ 0.01) were more likely to cluster than other races. Clustering individuals were also 3.5 years younger than non-clustering individuals (p < 0.001). Although the sampled San Diego and Tijuana epidemics were phylogenetically compartmentalized, five clusters contained individuals residing on both sides of the border. This study sampled ~ 7% of HIV infected individuals in the border region, and although the sampled networks on each side of the border were largely separate, there was evidence of persistent bidirectional cross-border transmissions that linked risk groups, thus highlighting the importance of the border region as a "melting pot" of risk groups. NIH, VA, and Pendleton Foundation.

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

NASA Astrophysics Data System (ADS)

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

2014-07-01

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

T cell receptor repertoires of mice and humans are clustered in similarity networks around conserved public CDR3 sequences

PubMed Central

Madi, Asaf; Poran, Asaf; Shifrut, Eric; Reich-Zeliger, Shlomit; Greenstein, Erez; Zaretsky, Irena; Arnon, Tomer; Laethem, Francois Van; Singer, Alfred; Lu, Jinghua; Sun, Peter D; Cohen, Irun R; Friedman, Nir

2017-01-01

Diversity of T cell receptor (TCR) repertoires, generated by somatic DNA rearrangements, is central to immune system function. However, the level of sequence similarity of TCR repertoires within and between species has not been characterized. Using network analysis of high-throughput TCR sequencing data, we found that abundant CDR3-TCRβ sequences were clustered within networks generated by sequence similarity. We discovered a substantial number of public CDR3-TCRβ segments that were identical in mice and humans. These conserved public sequences were central within TCR sequence-similarity networks. Annotated TCR sequences, previously associated with self-specificities such as autoimmunity and cancer, were linked to network clusters. Mechanistically, CDR3 networks were promoted by MHC-mediated selection, and were reduced following immunization, immune checkpoint blockade or aging. Our findings provide a new view of T cell repertoire organization and physiology, and suggest that the immune system distributes its TCR sequences unevenly, attending to specific foci of reactivity. DOI: http://dx.doi.org/10.7554/eLife.22057.001 PMID:28731407

SSR analysis of genetic diversity and structure of the germplasm of faba bean (Vicia faba L.).

PubMed

El-Esawi, Mohamed A

Assessing the diversity and genetic structure of faba bean (Vicia faba L.) germplasm is essential to improve the quality and yield of this economically important crop. In this study, simple sequence repeats (SSRs) were utilized to evaluate the diversity and structure of 35 faba bean genotypes originating from three different geographical regions (Northern Africa, Eastern Africa, and Near East). All 15 SSR loci generated a total of 100 alleles. The allele number per locus varied from 4 to 11, with a mean of 6.67. The expected heterozygosity (H e ) of SSR loci ranged between 0.51 and 0.81, with a mean of 0.63. The PIC value also varied from 0.44 to 0.78, with an average of 0.58. The expected heterozygosity of 22 faba bean genotypes was higher than the observed one. Interestingly, AMOVA analysis showed that much of variability resided within accessions (79.2%). A highly significant difference among regions was also evidenced, and represented 5.3% of the total variation. Moreover, cluster analysis divided the 35 faba bean genotypes into two main clusters. The first main cluster comprised all faba bean genotypes originating from the Near East region, whereas the second main cluster comprised all the genotypes originating from the Northern and Eastern Africa regions, indicating that the Northern and Eastern African faba bean genotypes were more closely related to each other than to the Near East genotypes. Structure analysis also revealed that the 35 faba bean genotypes might be assigned to two populations, in complete accordance with cluster analysis data. In conclusion, this study showed high levels of diversity in the analysed genotypes of faba bean, and could be utilized in future breeding programmes to develop new cultivars of high yield. Copyright © 2017 Académie des sciences. Published by Elsevier Masson SAS. All rights reserved.

The Hubble Space Telescope UV Legacy Survey of Galactic Globular Clusters. XV. The Dynamical Clock: Reading Cluster Dynamical Evolution from the Segregation Level of Blue Straggler Stars

NASA Astrophysics Data System (ADS)

Ferraro, F. R.; Lanzoni, B.; Raso, S.; Nardiello, D.; Dalessandro, E.; Vesperini, E.; Piotto, G.; Pallanca, C.; Beccari, G.; Bellini, A.; Libralato, M.; Anderson, J.; Aparicio, A.; Bedin, L. R.; Cassisi, S.; Milone, A. P.; Ortolani, S.; Renzini, A.; Salaris, M.; van der Marel, R. P.

2018-06-01

The parameter A +, defined as the area enclosed between the cumulative radial distribution of blue straggler stars (BSSs) and that of a reference population, is a powerful indicator of the level of BSS central segregation. As part of the Hubble Space Telescope UV Legacy Survey of Galactic globular clusters (GCs), here we present the BSS population and the determination of A + in 27 GCs observed out to about one half-mass radius. In combination with 21 additional clusters discussed in a previous paper, this provides us with a global sample of 48 systems (corresponding to ∼32% of the Milky Way GC population), for which we find a strong correlation between A + and the ratio of cluster age to the current central relaxation time. Tight relations have also been found with the core radius and the central luminosity density, which are expected to change with the long-term cluster dynamical evolution. An interesting relation is emerging between A + and the ratio of the BSS velocity dispersion relative to that of main sequence turn-off stars, which measures the degree of energy equipartition experienced by BSSs in the cluster. These results provide further confirmation that BSSs are invaluable probes of GC internal dynamics and that A + is a powerful dynamical clock.

Patterns of Community Change among Ammonia Oxidizers in Meadow Soils upon Long-Term Incubation at Different Temperatures

PubMed Central

Avrahami, Sharon; Conrad, Ralf

2003-01-01

The effect of temperature on the community structure of ammonia-oxidizing bacteria was investigated in three different meadow soils. Two of the soils (OMS and GMS) were acidic (pH 5.0 to 5.8) and from sites in Germany with low annual mean temperature (about 10°C), while KMS soil was slightly alkaline (pH 7.9) and from a site in Israel with a high annual mean temperature (about 22°C). The soils were fertilized and incubated for up to 20 weeks in a moist state and as a buffered (pH 7) slurry amended with urea at different incubation temperatures (4 to 37°C). OMS soil was also incubated with less fertilizer than the other soils. The community structure of ammonia oxidizers was analyzed before and after incubation by denaturing gradient gel electrophoresis (DGGE) of the amoA gene, which codes for the α subunit of ammonia monooxygenase. All amoA gene sequences found belonged to the genus Nitrosospira. The analysis showed community change due to temperature both in moist soil and in the soil slurry. Two patterns of community change were observed. One pattern was a change between the different Nitrosospira clusters, which was observed in moist soil and slurry incubations of GMS and OMS. Nitrosospira AmoA cluster 1 was mainly detected below 30°C, while Nitrosospira cluster 4 was predominant at 25°C. Nitrosospira clusters 3a, 3b, and 9 dominated at 30°C. The second pattern, observed in KMS, showed a community shift predominantly within a single Nitrosospira cluster. The sequences of the individual DGGE bands that exhibited different trends with temperature belonged almost exclusively to Nitrosospira cluster 3a. We conclude that ammonia oxidizer populations are influenced by temperature. In addition, we confirmed previous observations that N fertilizer also influences the community structure of ammonia oxidizers. Thus, Nitrosospira cluster 1 was absent in OMS soil treated with less fertilizer, while Nitrosospira cluster 9 was only found in the sample given less fertilizer. PMID:14532075

Screening and expression of selected taxonomically conserved and unique hypothetical proteins in Burkholderia pseudomallei K96243

NASA Astrophysics Data System (ADS)

Akhir, Nor Azurah Mat; Nadzirin, Nurul; Mohamed, Rahmah; Firdaus-Raih, Mohd

2015-09-01

Hypothetical proteins of bacterial pathogens represent a large numbers of novel biological mechanisms which could belong to essential pathways in the bacteria. They lack functional characterizations mainly due to the inability of sequence homology based methods to detect functional relationships in the absence of detectable sequence similarity. The dataset derived from this study showed 550 candidates conserved in genomes that has pathogenicity information and only present in the Burkholderiales order. The dataset has been narrowed down to taxonomic clusters. Ten proteins were selected for ORF amplification, seven of them were successfully amplified, and only four proteins were successfully expressed. These proteins will be great candidates in determining the true function via structural biology.

Morphological and Molecular Characterization of a New Trichuris Species (Nematoda- Trichuridae), and Phylogenetic Relationships of Trichuris Species of Cricetid Rodents from Argentina

PubMed Central

Robles, María del Rosario; Cutillas, Cristina; Panei, Carlos Javier; Callejón, Rocío

2014-01-01

Populations of Trichuris spp. isolated from six species of sigmodontine rodents from Argentina were analyzed based on morphological characteristics and ITS2 (rDNA) region sequences. Molecular data provided an opportunity to discuss the phylogenetic relationships among the Trichuris spp. from Noth and South America (mainly from Argentina). Trichuris specimens were identified morphologically as Trichuris pardinasi, T. navonae, Trichuris sp. and Trichuris new species, described in this paper. Sequences analyzed by Maximum Parsimony, Maximum Likelihood and Bayesian inference methods showed four main clades corresponding with the four different species regardless of geographical origin and host species. These four species from sigmodontine rodents clustered together and separated from Trichuris species isolated from murine and arvicoline rodents (outgroup). Different genetic lineages observed among Trichuris species from sigmodontine rodents which supported the proposal of a new species. Moreover, host distribution showed correspondence with the different tribes within the subfamily Sigmodontinae. PMID:25393618

Dynamics of adaptive immunity against phage in bacterial populations

NASA Astrophysics Data System (ADS)

Bradde, Serena; Vucelja, Marija; Tesileanu, Tiberiu; Balasubramanian, Vijay

The CRISPR (clustered regularly interspaced short palindromic repeats) mechanism allows bacteria to adaptively defend against phages by acquiring short genomic sequences (spacers) that target specific sequences in the viral genome. We propose a population dynamical model where immunity can be both acquired and lost. The model predicts regimes where bacterial and phage populations can co-exist, others where the populations oscillate, and still others where one population is driven to extinction. Our model considers two key parameters: (1) ease of acquisition and (2) spacer effectiveness in conferring immunity. Analytical calculations and numerical simulations show that if spacers differ mainly in ease of acquisition, or if the probability of acquiring them is sufficiently high, bacteria develop a diverse population of spacers. On the other hand, if spacers differ mainly in their effectiveness, their final distribution will be highly peaked, akin to a ``winner-take-all'' scenario, leading to a specialized spacer distribution. Bacteria can interpolate between these limiting behaviors by actively tuning their overall acquisition rate.

Genome sequence analysis of a flocculant-producing bacterium, Paenibacillus shenyangensis.

PubMed

Fu, Lili; Jiang, Binhui; Liu, Jinliang; Zhao, Xin; Liu, Qian; Hu, Xiaomin

2016-03-01

To explore the metabolic process of Paenibacillus shenyangensis that is an efficient bioflocculant-producing bacterium. The biosynthesis mechanism of bioflocculation was used to enrich the genome of Paenibacillus shenyangensis and provide a basis for molecular genetics and functional genomics analyses. According to the analysis of de novo assembly, a total of 5,501,467 bp clean reads were generated, and were assembled into 92 contigs. 4800 unigenes were predicted of which 4393 were annotated showing a specific gene function in the NCBI-Nr database. 3423 genes were found in the database of cluster of orthologous groups. Among the 168 Kyoto Encyclopedia of Genes and Genomes database, cell growth and metabolism were the main biological processes, and a potential metabolic pathway was predicted from glucose to exopolysaccharide within the starch and sucrose metabolism pathway. By using the high-throughput sequencing technology, we provide a genome analysis of Paenibacillus shenyangensis that predicts the main metabolic processes and a potential pathway of exopolysaccharide biosynthesis.

RNA-Seq Analysis Using De Novo Transcriptome Assembly as a Reference for the Salmon Louse Caligus rogercresseyi

PubMed Central

Gallardo-Escárate, Cristian; Valenzuela-Muñoz, Valentina; Nuñez-Acuña, Gustavo

2014-01-01

Despite the economic and environmental impacts that sea lice infestations have on salmon farming worldwide, genomic data generated by high-throughput transcriptome sequencing for different developmental stages, sexes, and strains of sea lice is still limited or unknown. In this study, RNA-seq analysis was performed using de novo transcriptome assembly as a reference for evidenced transcriptional changes from six developmental stages of the salmon louse Caligus rogercresseyi. EST-datasets were generated from the nauplius I, nauplius II, copepodid and chalimus stages and from female and male adults using MiSeq Illumina sequencing. A total of 151,788,682 transcripts were yielded, which were assembled into 83,444 high quality contigs and subsequently annotated into roughly 24,000 genes based on known proteins. To identify differential transcription patterns among salmon louse stages, cluster analyses were performed using normalized gene expression values. Herein, four clusters were differentially expressed between nauplius I–II and copepodid stages (604 transcripts), five clusters between copepodid and chalimus stages (2,426 transcripts), and six clusters between female and male adults (2,478 transcripts). Gene ontology analysis revealed that the nauplius I–II, copepodid and chalimus stages are mainly annotated to aminoacid transfer/repair/breakdown, metabolism, molting cycle, and nervous system development. Additionally, genes showing differential transcription in female and male adults were highly related to cytoskeletal and contractile elements, reproduction, cell development, morphogenesis, and transcription-translation processes. The data presented in this study provides the most comprehensive transcriptome resource available for C. rogercresseyi, which should be used for future genomic studies linked to host-parasite interactions. PMID:24691066

RNA-Seq analysis using de novo transcriptome assembly as a reference for the salmon louse Caligus rogercresseyi.

PubMed

Gallardo-Escárate, Cristian; Valenzuela-Muñoz, Valentina; Nuñez-Acuña, Gustavo

2014-01-01

Despite the economic and environmental impacts that sea lice infestations have on salmon farming worldwide, genomic data generated by high-throughput transcriptome sequencing for different developmental stages, sexes, and strains of sea lice is still limited or unknown. In this study, RNA-seq analysis was performed using de novo transcriptome assembly as a reference for evidenced transcriptional changes from six developmental stages of the salmon louse Caligus rogercresseyi. EST-datasets were generated from the nauplius I, nauplius II, copepodid and chalimus stages and from female and male adults using MiSeq Illumina sequencing. A total of 151,788,682 transcripts were yielded, which were assembled into 83,444 high quality contigs and subsequently annotated into roughly 24,000 genes based on known proteins. To identify differential transcription patterns among salmon louse stages, cluster analyses were performed using normalized gene expression values. Herein, four clusters were differentially expressed between nauplius I-II and copepodid stages (604 transcripts), five clusters between copepodid and chalimus stages (2,426 transcripts), and six clusters between female and male adults (2,478 transcripts). Gene ontology analysis revealed that the nauplius I-II, copepodid and chalimus stages are mainly annotated to aminoacid transfer/repair/breakdown, metabolism, molting cycle, and nervous system development. Additionally, genes showing differential transcription in female and male adults were highly related to cytoskeletal and contractile elements, reproduction, cell development, morphogenesis, and transcription-translation processes. The data presented in this study provides the most comprehensive transcriptome resource available for C. rogercresseyi, which should be used for future genomic studies linked to host-parasite interactions.

Lithium in giant stars in NGC 752 and M67

NASA Astrophysics Data System (ADS)

Pilachowski, Catherine; Saha, A.; Hobbs, L. M.

1988-04-01

Spectra of giant stars in the intermediate-age galactic cluster NGC 752 and in the old cluster M67 have been examined for the presence of Li I λ6707. The lithium feature is not present in any of the M67 giants observed, leading to upper-limit abundances of log ɛ(Li) ≤ -1.0 to 0.3. While lithium is not present in most NGC 752 giants, the feature is strong in two giants, Heinemann 77 and 208, log ɛ(Li) = +1.1 and +1.4, respectively. In the remaining giants in NGC 752, log ɛ(Li) < 0.5. The absence of lithium in M67 giants may be because these giants evolve from progenitors in the region of the main-sequence lithium dip.

Analisis fotometrico del cumulo abierto NGC 6611

NASA Astrophysics Data System (ADS)

Suarez Nunez, Johanna

2007-08-01

Matlab programs were designed to apply differential aperture photometry. Two images were taken with a charge-couple device ( CCD ) in the visible V and blue filters, to calculate physical parameters (the flux( f ), the apparent magnitude ( m V ) and its reddening corrected value ( V 0 ), color index ( B- V ) and ( B-V ) 0 , the log of effective temperature (log T eff ), the absolute magnitude ( M V ), the bolometric magnitude ( M B ) & log(L [low *] /[Special characters omitted.] )) of each studied star pertaining to the open cluster NGC 6611. Upon obtaining the parameters, the color-magnitude diagram was graphed and by fitting to the main sequence, the distance modulus and thus the distance to the cluster was found. The stars were assumed to be at the same distance and born at approximately the same moment.

Diversity and genetic stability in banana genotypes in a breeding program using inter simple sequence repeats (ISSR) markers.

PubMed

Silva, A V C; Nascimento, A L S; Vitória, M F; Rabbani, A R C; Soares, A N R; Lédo, A S

2017-02-23

Banana (Musa spp) is a fruit species frequently cultivated and consumed worldwide. Molecular markers are important for estimating genetic diversity in germplasm and between genotypes in breeding programs. The objective of this study was to analyze the genetic diversity of 21 banana genotypes (FHIA 23, PA42-44, Maçã, Pacovan Ken, Bucaneiro, YB42-47, Grand Naine, Tropical, FHIA 18, PA94-01, YB42-17, Enxerto, Japira, Pacovã, Prata-Anã, Maravilha, PV79-34, Caipira, Princesa, Garantida, and Thap Maeo), by using inter-simple sequence repeat (ISSR) markers. Material was generated from the banana breeding program of Embrapa Cassava & Fruits and evaluated at Embrapa Coastal Tablelands. The 12 primers used in this study generated 97.5% polymorphism. Four clusters were identified among the different genotypes studied, and the sum of the first two principal components was 48.91%. From the Unweighted Pair Group Method using Arithmetic averages (UPGMA) dendrogram, it was possible to identify two main clusters and subclusters. Two genotypes (Garantida and Thap Maeo) remained isolated from the others, both in the UPGMA clustering and in the principal cordinate analysis (PCoA). Using ISSR markers, we could analyze the genetic diversity of the studied material and state that these markers were efficient at detecting sufficient polymorphism to estimate the genetic variability in banana genotypes.

Marine protist diversity in European coastal waters and sediments as revealed by high-throughput sequencing.

PubMed

Massana, Ramon; Gobet, Angélique; Audic, Stéphane; Bass, David; Bittner, Lucie; Boutte, Christophe; Chambouvet, Aurélie; Christen, Richard; Claverie, Jean-Michel; Decelle, Johan; Dolan, John R; Dunthorn, Micah; Edvardsen, Bente; Forn, Irene; Forster, Dominik; Guillou, Laure; Jaillon, Olivier; Kooistra, Wiebe H C F; Logares, Ramiro; Mahé, Frédéric; Not, Fabrice; Ogata, Hiroyuki; Pawlowski, Jan; Pernice, Massimo C; Probert, Ian; Romac, Sarah; Richards, Thomas; Santini, Sébastien; Shalchian-Tabrizi, Kamran; Siano, Raffaele; Simon, Nathalie; Stoeck, Thorsten; Vaulot, Daniel; Zingone, Adriana; de Vargas, Colomban

2015-10-01

Although protists are critical components of marine ecosystems, they are still poorly characterized. Here we analysed the taxonomic diversity of planktonic and benthic protist communities collected in six distant European coastal sites. Environmental deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) from three size fractions (pico-, nano- and micro/mesoplankton), as well as from dissolved DNA and surface sediments were used as templates for tag pyrosequencing of the V4 region of the 18S ribosomal DNA. Beta-diversity analyses split the protist community structure into three main clusters: picoplankton-nanoplankton-dissolved DNA, micro/mesoplankton and sediments. Within each cluster, protist communities from the same site and time clustered together, while communities from the same site but different seasons were unrelated. Both DNA and RNA-based surveys provided similar relative abundances for most class-level taxonomic groups. Yet, particular groups were overrepresented in one of the two templates, such as marine alveolates (MALV)-I and MALV-II that were much more abundant in DNA surveys. Overall, the groups displaying the highest relative contribution were Dinophyceae, Diatomea, Ciliophora and Acantharia. Also, well represented were Mamiellophyceae, Cryptomonadales, marine alveolates and marine stramenopiles in the picoplankton, and Monadofilosa and basal Fungi in sediments. Our extensive and systematic sequencing of geographically separated sites provides the most comprehensive molecular description of coastal marine protist diversity to date. © 2015 Society for Applied Microbiology and John Wiley & Sons Ltd.

Genetic diversity among Puccinia melanocephala isolates from Brazil assessed using simple sequence repeat markers.

PubMed

Peixoto-Junior, R F; Creste, S; Landell, M G A; Nunes, D S; Sanguino, A; Campos, M F; Vencovsky, R; Tambarussi, E V; Figueira, A

2014-09-26

Brown rust (causal agent Puccinia melanocephala) is an important sugarcane disease that is responsible for large losses in yield worldwide. Despite its importance, little is known regarding the genetic diversity of this pathogen in the main Brazilian sugarcane cultivation areas. In this study, we characterized the genetic diversity of 34 P. melanocephala isolates from 4 Brazilian states using loci identified from an enriched simple sequence repeat (SSR) library. The aggressiveness of 3 isolates from major sugarcane cultivation areas was evaluated by inoculating an intermediately resistant and a susceptible cultivar. From the enriched library, 16 SSR-specific primers were developed, which produced scorable alleles. Of these, 4 loci were polymorphic and 12 were monomorphic for all isolates evaluated. The molecular characterization of the 34 isolates of P. melanocephala conducted using 16 SSR loci revealed the existence of low genetic variability among the isolates. The average estimated genetic distance was 0.12. Phenetic analysis based on Nei's genetic distance clustered the isolates into 2 major groups. Groups I and II included 18 and 14 isolates, respectively, and both groups contained isolates from all 4 geographic regions studied. Two isolates did not cluster with these groups. It was not possible to obtain clusters according to location or state of origin. Analysis of disease severity data revealed that the isolates did not show significant differences in aggressiveness between regions.

Genome-wide SNP discovery and population structure analysis in pepper (Capsicum annuum) using genotyping by sequencing.

PubMed

Taranto, F; D'Agostino, N; Greco, B; Cardi, T; Tripodi, P

2016-11-21

Knowledge on population structure and genetic diversity in vegetable crops is essential for association mapping studies and genomic selection. Genotyping by sequencing (GBS) represents an innovative method for large scale SNP detection and genotyping of genetic resources. Herein we used the GBS approach for the genome-wide identification of SNPs in a collection of Capsicum spp. accessions and for the assessment of the level of genetic diversity in a subset of 222 cultivated pepper (Capsicum annum) genotypes. GBS analysis generated a total of 7,568,894 master tags, of which 43.4% uniquely aligned to the reference genome CM334. A total of 108,591 SNP markers were identified, of which 105,184 were in C. annuum accessions. In order to explore the genetic diversity of C. annuum and to select a minimal core set representing most of the total genetic variation with minimum redundancy, a subset of 222 C. annuum accessions were analysed using 32,950 high quality SNPs. Based on Bayesian and Hierarchical clustering it was possible to divide the collection into three clusters. Cluster I had the majority of varieties and landraces mainly from Southern and Northern Italy, and from Eastern Europe, whereas clusters II and III comprised accessions of different geographical origins. Considering the genome-wide genetic variation among the accessions included in cluster I, a second round of Bayesian (K = 3) and Hierarchical (K = 2) clustering was performed. These analysis showed that genotypes were grouped not only based on geographical origin, but also on fruit-related features. GBS data has proven useful to assess the genetic diversity in a collection of C. annuum accessions. The high number of SNP markers, uniformly distributed on the 12 chromosomes, allowed the accessions to be distinguished according to geographical origin and fruit-related features. SNP markers and information on population structure developed in this study will undoubtedly support genome-wide association mapping studies and marker-assisted selection programs.

IMG-ABC: A Knowledge Base To Fuel Discovery of Biosynthetic Gene Clusters and Novel Secondary Metabolites.

PubMed

Hadjithomas, Michalis; Chen, I-Min Amy; Chu, Ken; Ratner, Anna; Palaniappan, Krishna; Szeto, Ernest; Huang, Jinghua; Reddy, T B K; Cimermančič, Peter; Fischbach, Michael A; Ivanova, Natalia N; Markowitz, Victor M; Kyrpides, Nikos C; Pati, Amrita

2015-07-14

In the discovery of secondary metabolites, analysis of sequence data is a promising exploration path that remains largely underutilized due to the lack of computational platforms that enable such a systematic approach on a large scale. In this work, we present IMG-ABC (https://img.jgi.doe.gov/abc), an atlas of biosynthetic gene clusters within the Integrated Microbial Genomes (IMG) system, which is aimed at harnessing the power of "big" genomic data for discovering small molecules. IMG-ABC relies on IMG's comprehensive integrated structural and functional genomic data for the analysis of biosynthetic gene clusters (BCs) and associated secondary metabolites (SMs). SMs and BCs serve as the two main classes of objects in IMG-ABC, each with a rich collection of attributes. A unique feature of IMG-ABC is the incorporation of both experimentally validated and computationally predicted BCs in genomes as well as metagenomes, thus identifying BCs in uncultured populations and rare taxa. We demonstrate the strength of IMG-ABC's focused integrated analysis tools in enabling the exploration of microbial secondary metabolism on a global scale, through the discovery of phenazine-producing clusters for the first time in Alphaproteobacteria. IMG-ABC strives to fill the long-existent void of resources for computational exploration of the secondary metabolism universe; its underlying scalable framework enables traversal of uncovered phylogenetic and chemical structure space, serving as a doorway to a new era in the discovery of novel molecules. IMG-ABC is the largest publicly available database of predicted and experimental biosynthetic gene clusters and the secondary metabolites they produce. The system also includes powerful search and analysis tools that are integrated with IMG's extensive genomic/metagenomic data and analysis tool kits. As new research on biosynthetic gene clusters and secondary metabolites is published and more genomes are sequenced, IMG-ABC will continue to expand, with the goal of becoming an essential component of any bioinformatic exploration of the secondary metabolism world. Copyright © 2015 Hadjithomas et al.

Efficient algorithms for accurate hierarchical clustering of huge datasets: tackling the entire protein space.

PubMed

Loewenstein, Yaniv; Portugaly, Elon; Fromer, Menachem; Linial, Michal

2008-07-01

UPGMA (average linking) is probably the most popular algorithm for hierarchical data clustering, especially in computational biology. However, UPGMA requires the entire dissimilarity matrix in memory. Due to this prohibitive requirement, UPGMA is not scalable to very large datasets. We present a novel class of memory-constrained UPGMA (MC-UPGMA) algorithms. Given any practical memory size constraint, this framework guarantees the correct clustering solution without explicitly requiring all dissimilarities in memory. The algorithms are general and are applicable to any dataset. We present a data-dependent characterization of hardness and clustering efficiency. The presented concepts are applicable to any agglomerative clustering formulation. We apply our algorithm to the entire collection of protein sequences, to automatically build a comprehensive evolutionary-driven hierarchy of proteins from sequence alone. The newly created tree captures protein families better than state-of-the-art large-scale methods such as CluSTr, ProtoNet4 or single-linkage clustering. We demonstrate that leveraging the entire mass embodied in all sequence similarities allows to significantly improve on current protein family clusterings which are unable to directly tackle the sheer mass of this data. Furthermore, we argue that non-metric constraints are an inherent complexity of the sequence space and should not be overlooked. The robustness of UPGMA allows significant improvement, especially for multidomain proteins, and for large or divergent families. A comprehensive tree built from all UniProt sequence similarities, together with navigation and classification tools will be made available as part of the ProtoNet service. A C++ implementation of the algorithm is available on request.

Molecular analysis of the microbial diversity present in the colonic wall, colonic lumen, and cecal lumen of a pig.

PubMed

Pryde, S E; Richardson, A J; Stewart, C S; Flint, H J

1999-12-01

Random clones of 16S ribosomal DNA gene sequences were isolated after PCR amplification with eubacterial primers from total genomic DNA recovered from samples of the colonic lumen, colonic wall, and cecal lumen from a pig. Sequences were also obtained for cultures isolated anaerobically from the same colonic-wall sample. Phylogenetic analysis showed that many sequences were related to those of Lactobacillus or Streptococcus spp. or fell into clusters IX, XIVa, and XI of gram-positive bacteria. In addition, 59% of randomly cloned sequences showed less than 95% similarity to database entries or sequences from cultivated organisms. Cultivation bias is also suggested by the fact that the majority of isolates (54%) recovered from the colon wall by culturing were related to Lactobacillus and Streptococcus, whereas this group accounted for only one-third of the sequence variation for the same sample from random cloning. The remaining cultured isolates were mainly Selenomonas related. A higher proportion of Lactobacillus reuteri-related sequences than of Lactobacillus acidophilus- and Lactobacillus amylovorus-related sequences were present in the colonic-wall sample. Since the majority of bacterial ribosomal sequences recovered from the colon wall are less than 95% related to known organisms, the roles of many of the predominant wall-associated bacteria remain to be defined.

Molecular Analysis of the Microbial Diversity Present in the Colonic Wall, Colonic Lumen, and Cecal Lumen of a Pig

PubMed Central

Pryde, Susan E.; Richardson, Anthony J.; Stewart, Colin S.; Flint, Harry J.

1999-01-01

Random clones of 16S ribosomal DNA gene sequences were isolated after PCR amplification with eubacterial primers from total genomic DNA recovered from samples of the colonic lumen, colonic wall, and cecal lumen from a pig. Sequences were also obtained for cultures isolated anaerobically from the same colonic-wall sample. Phylogenetic analysis showed that many sequences were related to those of Lactobacillus or Streptococcus spp. or fell into clusters IX, XIVa, and XI of gram-positive bacteria. In addition, 59% of randomly cloned sequences showed less than 95% similarity to database entries or sequences from cultivated organisms. Cultivation bias is also suggested by the fact that the majority of isolates (54%) recovered from the colon wall by culturing were related to Lactobacillus and Streptococcus, whereas this group accounted for only one-third of the sequence variation for the same sample from random cloning. The remaining cultured isolates were mainly Selenomonas related. A higher proportion of Lactobacillus reuteri-related sequences than of Lactobacillus acidophilus- and Lactobacillus amylovorus-related sequences were present in the colonic-wall sample. Since the majority of bacterial ribosomal sequences recovered from the colon wall are less than 95% related to known organisms, the roles of many of the predominant wall-associated bacteria remain to be defined. PMID:10583991

MOCASSIN-prot: a multi-objective clustering approach for protein similarity networks.

PubMed

Keel, Brittney N; Deng, Bo; Moriyama, Etsuko N

2018-04-15

Proteins often include multiple conserved domains. Various evolutionary events including duplication and loss of domains, domain shuffling, as well as sequence divergence contribute to generating complexities in protein structures, and consequently, in their functions. The evolutionary history of proteins is hence best modeled through networks that incorporate information both from the sequence divergence and the domain content. Here, a game-theoretic approach proposed for protein network construction is adapted into the framework of multi-objective optimization, and extended to incorporate clustering refinement procedure. The new method, MOCASSIN-prot, was applied to cluster multi-domain proteins from ten genomes. The performance of MOCASSIN-prot was compared against two protein clustering methods, Markov clustering (TRIBE-MCL) and spectral clustering (SCPS). We showed that compared to these two methods, MOCASSIN-prot, which uses both domain composition and quantitative sequence similarity information, generates fewer false positives. It achieves more functionally coherent protein clusters and better differentiates protein families. MOCASSIN-prot, implemented in Perl and Matlab, is freely available at http://bioinfolab.unl.edu/emlab/MOCASSINprot. emoriyama2@unl.edu. Supplementary data are available at Bioinformatics online.

New cataclysmic variables and other exotic binaries in the globular cluster 47 Tucanae*

NASA Astrophysics Data System (ADS)

Rivera Sandoval, L. E.; van den Berg, M.; Heinke, C. O.; Cohn, H. N.; Lugger, P. M.; Anderson, J.; Cool, A. M.; Edmonds, P. D.; Wijnands, R.; Ivanova, N.; Grindlay, J. E.

2018-04-01

We present 22 new (+3 confirmed) cataclysmic variables (CVs) in the non-core-collapsed globular cluster 47 Tucanae (47 Tuc). The total number of CVs in the cluster is now 43, the largest sample in any globular cluster so far. For the identifications we used near-ultraviolet (NUV) and optical images from the Hubble Space Telescope, in combination with X-ray results from the Chandra X-ray Observatory. This allowed us to build the deepest NUV CV luminosity function of the cluster to date. We found that the CVs in 47 Tuc are more concentrated towards the cluster centre than the main-sequence turn-off stars. We compared our results to the CV populations of the core-collapsed globular clusters NGC 6397 and NGC 6752. We found that 47 Tuc has fewer bright CVs per unit mass than those two other clusters. That suggests that dynamical interactions in core-collapsed clusters play a major role creating new CVs. In 47 Tuc, the CV population is probably dominated by primordial and old dynamically formed systems. We estimated that the CVs in 47 Tuc have total masses of ˜1.4 M⊙. We also found that the X-ray luminosity function of the CVs in the three clusters is bimodal. Additionally, we discuss a possible double degenerate system and an intriguing/unclassified object. Finally, we present four systems that could be millisecond pulsar companions given their X-ray and NUV/optical colours. For one of them we present very strong evidence for being an ablated companion. The other three could be CO or He white dwarfs.

Star Formation in NGC 6531-Evidence From the age Spread and Initial Mass Function

NASA Astrophysics Data System (ADS)

Forbes, Douglas

1996-09-01

The results of a photometric UBV study of the young open cluster NGC 6531 are presented. The cluster is found to have a mean reddening E(B-V)=0.28±0.04 (s.d.) and distance modulus (V0-Mv)=10.70±0.13 (s.e.), and 105±11 likely cluster members have been identified within the cluster coronal radius of 9 arcmin. A comparison of the high-luminosity end of the cluster color-magnitude diagram to the evolutionary models by Maeder & Meynet [A&AS, 76, 411(1988)] suggests a nuclear age of (8±2) Myr. The very clear gap in the distribution of stars with 0≤(B-V)0≤0.20, corresponding to the "burn-off" of 3He in stars contracting to the main sequence [Ulrich, ApJ, 168, 57 (1971)], implies a contraction age of (8±3) Myr. There would seem to be no evidence of a spread in the ages of cluster stars, as has been observed in several other young open clusters [Herbst & Miller, AJ, 87, 1478 (1982)]. The initial mass function (IMF) constructed from the cluster luminosity function and the mass-luminosity relation given by Scab (1986) shows good agreement with the field star IMF, and with the IMFS of a number of clusters of similar age and richness. The relative deficiency of low-mass stars seen by Herbst and Miller in NGC 3293 (a cluster of quite similar age and reddening) is not evident in NGC 6531.

Organization of the Escherichia coli K-12 gene cluster responsible for production of the extracellular polysaccharide colanic acid.

PubMed Central

Stevenson, G; Andrianopoulos, K; Hobbs, M; Reeves, P R

1996-01-01

Colanic acid (CA) is an extracellular polysaccharide produced by most Escherichia coli strains as well as by other species of the family Enterobacteriaceae. We have determined the sequence of a 23-kb segment of the E. coli K-12 chromosome which includes the cluster of genes necessary for production of CA. The CA cluster comprises 19 genes. Two other sequenced genes (orf1.3 and galF), which are situated between the CA cluster and the O-antigen cluster, were shown to be unnecessary for CA production. The CA cluster includes genes for synthesis of GDP-L-fucose, one of the precursors of CA, and the gene for one of the enzymes in this pathway (GDP-D-mannose 4,6-dehydratase) was identified by biochemical assay. Six of the inferred proteins show sequence similarity to glycosyl transferases, and two others have sequence similarity to acetyl transferases. Another gene (wzx) is predicted to encode a protein with multiple transmembrane segments and may function in export of the CA repeat unit from the cytoplasm into the periplasm in a process analogous to O-unit export. The first three genes of the cluster are predicted to encode an outer membrane lipoprotein, a phosphatase, and an inner membrane protein with an ATP-binding domain. Since homologs of these genes are found in other extracellular polysaccharide gene clusters, they may have a common function, such as export of polysaccharide from the cell. PMID:8759852

Mainshock-Aftershock Clustering in Volcanic Regions

NASA Astrophysics Data System (ADS)

Garza-Giron, Ricardo; Brodsky, Emily E.; Prejean, Stephanie G.

2018-02-01

Earthquakes break their general Poissonean behavior through two types of seismic bursts: swarms and mainshock-aftershock sequences. The former is commonly thought to dominate in volcanic and geothermal regions, but aftershock production, including within swarms, is not well studied in volcanic regions. Here we compare mainshock-aftershock clustering in active volcanic regions in Japan to nearby nonvolcanic regions. We find that aftershock production is similar in both areas by two separate metrics: (1) Both volcanic and nonvolcanic regions have similar proportions of areas that cluster into mainshock-aftershock sequences. (2) Volcanic areas with mainshock-aftershock sequences have aftershock productivity at least as high as nonvolcanic regions. We also find that volcano-tectonic events that are precursors to an eruption are more common at volcanoes without mainshock-aftershock clusters than at volcanoes with well-defined mainshock-aftershock clusters. This last finding hints at a strategy to identify volcanic systems where cataloged earthquakes are good predictors of behavior.

Photometric light curves for seven rapidly-rotating K dwarfs in the Pleiades and Alpha Persei clusters

NASA Technical Reports Server (NTRS)

Stauffer, John R.; Schild, Rudolph A.; Baliunas, Sallie L.; Africano, John L.

1987-01-01

Light curves and period estimates were obtained for several Pleiades and Alpha Persei cluster K dwarfs which were identified as rapid rotators in earlier spectroscopic studies. A few of the stars have previously-published light curves, making it possible to study the long-term variability of the light-curve shapes. The general cause of the photometric variability observed for these stars is an asymmetric distribution of photospheric inhomogeneities (starspots). The presence of these inhomogeneities combined with the rotation of the star lead to the light curves observed. The photometric periods derived are thus identified with the rotation period of the star, making it possible to estimate equatorial rotational velocities for these K dwarfs. These data are of particular importance because the clusters are sufficiently young that stars of this mass should have just arrived on the main sequence. These data could be used to estimate the temperatures and sizes of the spot groups necessary to produce the observed light curves for these stars.

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.

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.

Vilnius Multicolor CCD Photometry of the Open Cluster NGC 752

NASA Astrophysics Data System (ADS)

Bartašiūtė, S.; Janusz, R.; Boyle, R. P.; Philip, A. G. Davis

We have performed multicolor CCD observations of the central area of NGC 752 to search for faint, low-mass members of this open cluster. Four 12'x12' fields were taken on the 1.8 m Vatican Advanced Technology Telescope (Mt. Graham, Arizona) using a 4K CCD camera and eight intermediate-band filters of the Strömvil system. In this paper we present a catalog of photometry for 405 stars down to the limiting magnitude V=18.5, which contains V magnitudes and color indices of the Vilnius system, together with photometric determinations of spectral types, absolute magnitudes MV, interstellar reddening values EY-V and metallicity parameters [Fe/H]. The good quality multicolor data made it possible to identify the locus of the lower main sequence to four magnitudes beyond the previous (photographic) limit. A relatively small number of photometric members identified at faint magnitudes seems to be indicative of actual dissolution of the cluster from the low-mass end.

Evaluation of null-point detection methods on simulation data

NASA Astrophysics Data System (ADS)

Olshevsky, Vyacheslav; Fu, Huishan; Vaivads, Andris; Khotyaintsev, Yuri; Lapenta, Giovanni; Markidis, Stefano

2014-05-01

We model the measurements of artificial spacecraft that resemble the configuration of CLUSTER propagating in the particle-in-cell simulation of turbulent magnetic reconnection. The simulation domain contains multiple isolated X-type null-points, but the majority are O-type null-points. Simulations show that current pinches surrounded by twisted fields, analogous to laboratory pinches, are formed along the sequences of O-type nulls. In the simulation, the magnetic reconnection is mainly driven by the kinking of the pinches, at spatial scales of several ion inertial lentghs. We compute the locations of magnetic null-points and detect their type. When the satellites are separated by the fractions of ion inertial length, as it is for CLUSTER, they are able to locate both the isolated null-points, and the pinches. We apply the method to the real CLUSTER data and speculate how common are pinches in the magnetosphere, and whether they play a dominant role in the dissipation of magnetic energy.

The real population of star clusters in the bar of the Large Magellanic Cloud

NASA Astrophysics Data System (ADS)

Piatti, Andrés E.

2017-09-01

We report results on star clusters located in the south-eastern half of the Large Magellanic (LMC) bar from Washington CT1 photometry. Using appropriate kernel density estimators, we detected 73 star cluster candidates, three of which do not show any detectable trace of star cluster sequences in their colour-magnitude diagrams (CMDs). We did not detect the other 38 previously catalogued clusters, which could not be recognized when visually inspecting the C and T1 images either; the distribution of stars in their respective fields do not resemble that of a stellar aggregate. They represent 33 per cent of all catalogued objects located within the analysed LMC bar field. From matching theoretical isochrones to the cluster CMDs cleaned from field star contamination, we derived ages in the range 7.2 < log(t yr-1) < 10.1. As far as we are aware, this is the first time that homogeneous age estimates based on resolved stellar photometry are obtained for most of the studied clusters. We built the cluster frequency (CF) for the surveyed area, and found that the main star cluster formation activity has taken place during the period log(t yr-1) 8.0-9.0. Since 100 Myr ago, clusters have been formed during a few bursting formation episodes. When comparing the observed CF to that recovered from the star formation rate, we found noticeable differences, which suggests that field star and star cluster formation histories could have been significantly different. Photometric catalogues of the studied star clusters are only available at the CDS via anonymous ftp to http://cdsarc.u-strasbg.fr (http://130.79.128.5) or via http://cdsarc.u-strasbg.fr/viz-bin/qcat?J/A+A/606/A21

Bayesian clustering of DNA sequences using Markov chains and a stochastic partition model.

PubMed

Jääskinen, Väinö; Parkkinen, Ville; Cheng, Lu; Corander, Jukka

2014-02-01

In many biological applications it is necessary to cluster DNA sequences into groups that represent underlying organismal units, such as named species or genera. In metagenomics this grouping needs typically to be achieved on the basis of relatively short sequences which contain different types of errors, making the use of a statistical modeling approach desirable. Here we introduce a novel method for this purpose by developing a stochastic partition model that clusters Markov chains of a given order. The model is based on a Dirichlet process prior and we use conjugate priors for the Markov chain parameters which enables an analytical expression for comparing the marginal likelihoods of any two partitions. To find a good candidate for the posterior mode in the partition space, we use a hybrid computational approach which combines the EM-algorithm with a greedy search. This is demonstrated to be faster and yield highly accurate results compared to earlier suggested clustering methods for the metagenomics application. Our model is fairly generic and could also be used for clustering of other types of sequence data for which Markov chains provide a reasonable way to compress information, as illustrated by experiments on shotgun sequence type data from an Escherichia coli strain.

Complete Genome Sequence and Comparative Analysis of the Fish Pathogen Lactococcus garvieae

PubMed Central

Oshima, Kenshiro; Yoshizaki, Mariko; Kawanishi, Michiko; Nakaya, Kohei; Suzuki, Takehito; Miyauchi, Eiji; Ishii, Yasuo; Tanabe, Soichi; Murakami, Masaru; Hattori, Masahira

2011-01-01

Lactococcus garvieae causes fatal haemorrhagic septicaemia in fish such as yellowtail. The comparative analysis of genomes of a virulent strain Lg2 and a non-virulent strain ATCC 49156 of L. garvieae revealed that the two strains shared a high degree of sequence identity, but Lg2 had a 16.5-kb capsule gene cluster that is absent in ATCC 49156. The capsule gene cluster was composed of 15 genes, of which eight genes are highly conserved with those in exopolysaccharide biosynthesis gene cluster often found in Lactococcus lactis strains. Sequence analysis of the capsule gene cluster in the less virulent strain L. garvieae Lg2-S, Lg2-derived strain, showed that two conserved genes were disrupted by a single base pair deletion, respectively. These results strongly suggest that the capsule is crucial for virulence of Lg2. The capsule gene cluster of Lg2 may be a genomic island from several features such as the presence of insertion sequences flanked on both ends, different GC content from the chromosomal average, integration into the locus syntenic to other lactococcal genome sequences, and distribution in human gut microbiomes. The analysis also predicted other potential virulence factors such as haemolysin. The present study provides new insights into understanding of the virulence mechanisms of L. garvieae in fish. PMID:21829716

Tardigrade workbench: comparing stress-related proteins, sequence-similar and functional protein clusters as well as RNA elements in tardigrades

PubMed Central

2009-01-01

Background Tardigrades represent an animal phylum with extraordinary resistance to environmental stress. Results To gain insights into their stress-specific adaptation potential, major clusters of related and similar proteins are identified, as well as specific functional clusters delineated comparing all tardigrades and individual species (Milnesium tardigradum, Hypsibius dujardini, Echiniscus testudo, Tulinus stephaniae, Richtersius coronifer) and functional elements in tardigrade mRNAs are analysed. We find that 39.3% of the total sequences clustered in 58 clusters of more than 20 proteins. Among these are ten tardigrade specific as well as a number of stress-specific protein clusters. Tardigrade-specific functional adaptations include strong protein, DNA- and redox protection, maintenance and protein recycling. Specific regulatory elements regulate tardigrade mRNA stability such as lox P DICE elements whereas 14 other RNA elements of higher eukaryotes are not found. Further features of tardigrade specific adaption are rapidly identified by sequence and/or pattern search on the web-tool tardigrade analyzer http://waterbear.bioapps.biozentrum.uni-wuerzburg.de. The work-bench offers nucleotide pattern analysis for promotor and regulatory element detection (tardigrade specific; nrdb) as well as rapid COG search for function assignments including species-specific repositories of all analysed data. Conclusion Different protein clusters and regulatory elements implicated in tardigrade stress adaptations are analysed including unpublished tardigrade sequences. PMID:19821996

Tardigrade workbench: comparing stress-related proteins, sequence-similar and functional protein clusters as well as RNA elements in tardigrades.

PubMed

Förster, Frank; Liang, Chunguang; Shkumatov, Alexander; Beisser, Daniela; Engelmann, Julia C; Schnölzer, Martina; Frohme, Marcus; Müller, Tobias; Schill, Ralph O; Dandekar, Thomas

2009-10-12

Tardigrades represent an animal phylum with extraordinary resistance to environmental stress. To gain insights into their stress-specific adaptation potential, major clusters of related and similar proteins are identified, as well as specific functional clusters delineated comparing all tardigrades and individual species (Milnesium tardigradum, Hypsibius dujardini, Echiniscus testudo, Tulinus stephaniae, Richtersius coronifer) and functional elements in tardigrade mRNAs are analysed. We find that 39.3% of the total sequences clustered in 58 clusters of more than 20 proteins. Among these are ten tardigrade specific as well as a number of stress-specific protein clusters. Tardigrade-specific functional adaptations include strong protein, DNA- and redox protection, maintenance and protein recycling. Specific regulatory elements regulate tardigrade mRNA stability such as lox P DICE elements whereas 14 other RNA elements of higher eukaryotes are not found. Further features of tardigrade specific adaption are rapidly identified by sequence and/or pattern search on the web-tool tardigrade analyzer http://waterbear.bioapps.biozentrum.uni-wuerzburg.de. The work-bench offers nucleotide pattern analysis for promotor and regulatory element detection (tardigrade specific; nrdb) as well as rapid COG search for function assignments including species-specific repositories of all analysed data. Different protein clusters and regulatory elements implicated in tardigrade stress adaptations are analysed including unpublished tardigrade sequences.

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 red-sequence of 72 WINGS local galaxy clusters

NASA Astrophysics Data System (ADS)

Valentinuzzi, T.; Poggianti, B. M.; Fasano, G.; D'Onofrio, M.; Moretti, A.; Ramella, M.; Biviano, A.; Fritz, J.; Varela, J.; Bettoni, D.; Vulcani, B.; Moles, M.; Couch, W. J.; Dressler, A.; Kjærgaard, P.; Omizzolo, A.; Cava, A.

2011-12-01

We study the color - magnitude red sequence and blue fraction of 72 X-ray selected galaxy clusters at z = 0.04-0.07 from the WINGS survey, searching for correlations between the characteristics of the red sequence (RS) and the environment. We consider the slope and scatter of the red sequence, the number ratio of red luminous-to-faint galaxies, the blue fraction, and the fractions of ellipticals, S0s, and spirals that compose the RS. None of these quantities correlate with the cluster velocity dispersion, X-ray luminosity, number of cluster substructures, BCG prevalence over next brightest galaxies, and the spatial concentration of ellipticals. The properties of the RS, instead, depend strongly on local galaxy density. Higher density regions have a smaller RS scatter, a higher luminous-to-faint ratio, a lower blue fraction, and a lower spiral fraction on the RS. Our results clearly illustrate the prominent effect of the local density in setting the epoch when galaxies become passive and join the red sequence, as opposed to the mass of the galaxy host structure.

Wheat EST resources for functional genomics of abiotic stress

PubMed Central

Houde, Mario; Belcaid, Mahdi; Ouellet, François; Danyluk, Jean; Monroy, Antonio F; Dryanova, Ani; Gulick, Patrick; Bergeron, Anne; Laroche, André; Links, Matthew G; MacCarthy, Luke; Crosby, William L; Sarhan, Fathey

2006-01-01

Background Wheat is an excellent species to study freezing tolerance and other abiotic stresses. However, the sequence of the wheat genome has not been completely characterized due to its complexity and large size. To circumvent this obstacle and identify genes involved in cold acclimation and associated stresses, a large scale EST sequencing approach was undertaken by the Functional Genomics of Abiotic Stress (FGAS) project. Results We generated 73,521 quality-filtered ESTs from eleven cDNA libraries constructed from wheat plants exposed to various abiotic stresses and at different developmental stages. In addition, 196,041 ESTs for which tracefiles were available from the National Science Foundation wheat EST sequencing program and DuPont were also quality-filtered and used in the analysis. Clustering of the combined ESTs with d2_cluster and TGICL yielded a few large clusters containing several thousand ESTs that were refractory to routine clustering techniques. To resolve this problem, the sequence proximity and "bridges" were identified by an e-value distance graph to manually break clusters into smaller groups. Assembly of the resolved ESTs generated a 75,488 unique sequence set (31,580 contigs and 43,908 singletons/singlets). Digital expression analyses indicated that the FGAS dataset is enriched in stress-regulated genes compared to the other public datasets. Over 43% of the unique sequence set was annotated and classified into functional categories according to Gene Ontology. Conclusion We have annotated 29,556 different sequences, an almost 5-fold increase in annotated sequences compared to the available wheat public databases. Digital expression analysis combined with gene annotation helped in the identification of several pathways associated with abiotic stress. The genomic resources and knowledge developed by this project will contribute to a better understanding of the different mechanisms that govern stress tolerance in wheat and other cereals. PMID:16772040

Resistance gene candidates identified by PCR with degenerate oligonucleotide primers map to clusters of resistance genes in lettuce.

PubMed

Shen, K A; Meyers, B C; Islam-Faridi, M N; Chin, D B; Stelly, D M; Michelmore, R W

1998-08-01

The recent cloning of genes for resistance against diverse pathogens from a variety of plants has revealed that many share conserved sequence motifs. This provides the possibility of isolating numerous additional resistance genes by polymerase chain reaction (PCR) with degenerate oligonucleotide primers. We amplified resistance gene candidates (RGCs) from lettuce with multiple combinations of primers with low degeneracy designed from motifs in the nucleotide binding sites (NBSs) of RPS2 of Arabidopsis thaliana and N of tobacco. Genomic DNA, cDNA, and bacterial artificial chromosome (BAC) clones were successfully used as templates. Four families of sequences were identified that had the same similarity to each other as to resistance genes from other species. The relationship of the amplified products to resistance genes was evaluated by several sequence and genetic criteria. The amplified products contained open reading frames with additional sequences characteristic of NBSs. Hybridization of RGCs to genomic DNA and to BAC clones revealed large numbers of related sequences. Genetic analysis demonstrated the existence of clustered multigene families for each of the four RGC sequences. This parallels classical genetic data on clustering of disease resistance genes. Two of the four families mapped to known clusters of resistance genes; these two families were therefore studied in greater detail. Additional evidence that these RGCs could be resistance genes was gained by the identification of leucine-rich repeat (LRR) regions in sequences adjoining the NBS similar to those in RPM1 and RPS2 of A. thaliana. Fluorescent in situ hybridization confirmed the clustered genomic distribution of these sequences. The use of PCR with degenerate oligonucleotide primers is therefore an efficient method to identify numerous RGCs in plants.

Vertical Segregation and Phylogenetic Characterization of Ammonia-Oxidizing Bacteria and Archaea in the Sediment of a Freshwater Aquaculture Pond

PubMed Central

Lu, Shimin; Liu, Xingguo; Ma, Zhuojun; Liu, Qigen; Wu, Zongfan; Zeng, Xianlei; Shi, Xu; Gu, Zhaojun

2016-01-01

Pond aquaculture is the major freshwater aquaculture method in China. Ammonia-oxidizing communities inhabiting pond sediments play an important role in controlling culture water quality. However, the distribution and activities of ammonia-oxidizing microbial communities along sediment profiles are poorly understood in this specific environment. Vertical variations in the abundance, transcription, potential ammonia oxidizing rate, and community composition of ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) in sediment samples (0–50 cm depth) collected from a freshwater aquaculture pond were investigated. The concentrations of the AOA amoA gene were higher than those of the AOB by an order of magnitude, which suggested that AOA, as opposed to AOB, were the numerically predominant ammonia-oxidizing organisms in the surface sediment. This could be attributed to the fact that AOA are more resistant to low levels of dissolved oxygen. However, the concentrations of the AOB amoA mRNA were higher than those of the AOA by 2.5- to 39.9-fold in surface sediments (0–10 cm depth), which suggests that the oxidation of ammonia was mainly performed by AOB in the surface sediments, and by AOA in the deeper sediments, where only AOA could be detected. Clone libraries of AOA and AOB amoA sequences indicated that the diversity of AOA and AOB decreased with increasing depth. The AOB community consisted of two groups: the Nitrosospira and Nitrosomonas clusters, and Nitrosomonas were predominant in the freshwater pond sediment. All AOA amoA gene sequences in the 0–2 cm deep sediment were grouped into the Nitrososphaera cluster, while other AOA sequences in deeper sediments (10–15 and 20–25 cm depths) were grouped into the Nitrosopumilus cluster. PMID:26834709

Significance of flow clustering and sequencing on sediment transport: 1D sediment transport modelling

NASA Astrophysics Data System (ADS)

Hassan, Kazi; Allen, Deonie; Haynes, Heather

2016-04-01

This paper considers 1D hydraulic model data on the effect of high flow clusters and sequencing on sediment transport. Using observed flow gauge data from the River Caldew, England, a novel stochastic modelling approach was developed in order to create alternative 50 year flow sequences. Whilst the observed probability density of gauge data was preserved in all sequences, the order in which those flows occurred was varied using the output from a Hidden Markov Model (HMM) with generalised Pareto distribution (GP). In total, one hundred 50 year synthetic flow series were generated and used as the inflow boundary conditions for individual flow series model runs using the 1D sediment transport model HEC-RAS. The model routed graded sediment through the case study river reach to define the long-term morphological changes. Comparison of individual simulations provided a detailed understanding of the sensitivity of channel capacity to flow sequence. Specifically, each 50 year synthetic flow sequence was analysed using a 3-month, 6-month or 12-month rolling window approach and classified for clusters in peak discharge. As a cluster is described as a temporal grouping of flow events above a specified threshold, the threshold condition used herein is considered as a morphologically active channel forming discharge event. Thus, clusters were identified for peak discharges in excess of 10%, 20%, 50%, 100% and 150% of the 1 year Return Period (RP) event. The window of above-peak flows also required cluster definition and was tested for timeframes 1, 2, 10 and 30 days. Subsequently, clusters could be described in terms of the number of events, maximum peak flow discharge, cumulative flow discharge and skewness (i.e. a description of the flow sequence). The model output for each cluster was analysed for the cumulative flow volume and cumulative sediment transport (mass). This was then compared to the total sediment transport of a single flow event of equivalent flow volume. Results illustrate that clustered flood events generated sediment loads up to an order of magnitude greater than that of individual events of the same flood volume. Correlations were significant for sediment volume compared to both maximum flow discharge (R2<0.8) and number of events (R2 -0.5 to -0.7) within the cluster. The strongest correlations occurred for clusters with a greater number of flow events only slightly above-threshold. This illustrates that the numerical model can capture a degree of the non-linear morphological response to flow magnitude. Analysis of the relationship between morphological change and the skewness of flow events within each cluster was also determined, illustrating only minor sensitivity to cluster peak distribution skewness. This is surprising and discussion is presented on model limitations, including the capability of sediment transport formulae to effectively account for temporal processes of antecedent flow, hysteresis, local supply etc.

Contribution of Primordial Binary Evolution to the Two Blue-straggler Sequences in Globular Cluster M30

NASA Astrophysics Data System (ADS)

Jiang, Dengkai; Chen, Xuefei; Li, Lifang; Han, Zhanwen

2017-11-01

Two blue-straggler sequences discovered in globular cluster M30 provide a strong constraint on the formation mechanisms of blue stragglers. We study the formation of blue-straggler binaries through binary evolution, and find that binary evolution can contribute to the blue stragglers in both of the sequences. Whether a blue-straggler is located in the blue sequence or red sequence depends on the contribution of the mass donor to the total luminosity of the binary, which is generally observed as a single star in globular clusters. The blue stragglers in the blue sequence have a cool white dwarf companion, while the majority (˜60%) of the objects in the red sequence are binaries that are still experiencing mass transfer. However, there are also some objects for which the donors have just finished the mass transfer (the stripped-core stars, ˜10%) or the blue stragglers (the accretors) have evolved away from the blue sequence (˜30%). Meanwhile, W UMa contact binaries found in both sequences may be explained by various mass ratios, that is, W UMa contact binaries in the red sequence have two components with comparable masses (e.g., mass ratio q ˜ 0.3-1.0), while those in the blue sequence have low mass ratios (e.g., q< 0.3). However, the fraction of the blue sequence in M30 cannot be reproduced by binary population synthesis if we assumed the initial parameters of a binary sample to be the same as those of the field. This possibly indicates that dynamical effects on binary systems are very important in globular clusters.

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

NASA Astrophysics Data System (ADS)

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

2016-06-01

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

A guide to enterotypes across the human body: meta-analysis of microbial community structures in human microbiome datasets.

PubMed

Koren, Omry; Knights, Dan; Gonzalez, Antonio; Waldron, Levi; Segata, Nicola; Knight, Rob; Huttenhower, Curtis; Ley, Ruth E

2013-01-01

Recent analyses of human-associated bacterial diversity have categorized individuals into 'enterotypes' or clusters based on the abundances of key bacterial genera in the gut microbiota. There is a lack of consensus, however, on the analytical basis for enterotypes and on the interpretation of these results. We tested how the following factors influenced the detection of enterotypes: clustering methodology, distance metrics, OTU-picking approaches, sequencing depth, data type (whole genome shotgun (WGS) vs.16S rRNA gene sequence data), and 16S rRNA region. We included 16S rRNA gene sequences from the Human Microbiome Project (HMP) and from 16 additional studies and WGS sequences from the HMP and MetaHIT. In most body sites, we observed smooth abundance gradients of key genera without discrete clustering of samples. Some body habitats displayed bimodal (e.g., gut) or multimodal (e.g., vagina) distributions of sample abundances, but not all clustering methods and workflows accurately highlight such clusters. Because identifying enterotypes in datasets depends not only on the structure of the data but is also sensitive to the methods applied to identifying clustering strength, we recommend that multiple approaches be used and compared when testing for enterotypes.

A Guide to Enterotypes across the Human Body: Meta-Analysis of Microbial Community Structures in Human Microbiome Datasets

PubMed Central

Waldron, Levi; Segata, Nicola; Knight, Rob; Huttenhower, Curtis; Ley, Ruth E.

2013-01-01

Recent analyses of human-associated bacterial diversity have categorized individuals into ‘enterotypes’ or clusters based on the abundances of key bacterial genera in the gut microbiota. There is a lack of consensus, however, on the analytical basis for enterotypes and on the interpretation of these results. We tested how the following factors influenced the detection of enterotypes: clustering methodology, distance metrics, OTU-picking approaches, sequencing depth, data type (whole genome shotgun (WGS) vs.16S rRNA gene sequence data), and 16S rRNA region. We included 16S rRNA gene sequences from the Human Microbiome Project (HMP) and from 16 additional studies and WGS sequences from the HMP and MetaHIT. In most body sites, we observed smooth abundance gradients of key genera without discrete clustering of samples. Some body habitats displayed bimodal (e.g., gut) or multimodal (e.g., vagina) distributions of sample abundances, but not all clustering methods and workflows accurately highlight such clusters. Because identifying enterotypes in datasets depends not only on the structure of the data but is also sensitive to the methods applied to identifying clustering strength, we recommend that multiple approaches be used and compared when testing for enterotypes. PMID:23326225

Assembly and features of secondary metabolite biosynthetic gene clusters in Streptomyces ansochromogenes.

PubMed

Zhong, Xingyu; Tian, Yuqing; Niu, Guoqing; Tan, Huarong

2013-07-01

A draft genome sequence of Streptomyces ansochromogenes 7100 was generated using 454 sequencing technology. In combination with local BLAST searches and gap filling techniques, a comprehensive antiSMASH-based method was adopted to assemble the secondary metabolite biosynthetic gene clusters in the draft genome of S. ansochromogenes. A total of at least 35 putative gene clusters were identified and assembled. Transcriptional analysis showed that 20 of the 35 gene clusters were expressed in either or all of the three different media tested, whereas the other 15 gene clusters were silent in all three different media. This study provides a comprehensive method to identify and assemble secondary metabolite biosynthetic gene clusters in draft genomes of Streptomyces, and will significantly promote functional studies of these secondary metabolite biosynthetic gene clusters.

Statistical Features of the 2010 Beni-Ilmane, Algeria, Aftershock Sequence

NASA Astrophysics Data System (ADS)

Hamdache, M.; Peláez, J. A.; Gospodinov, D.; Henares, J.

2018-03-01

The aftershock sequence of the 2010 Beni-Ilmane ( M W 5.5) earthquake is studied in depth to analyze the spatial and temporal variability of seismicity parameters of the relationships modeling the sequence. The b value of the frequency-magnitude distribution is examined rigorously. A threshold magnitude of completeness equal to 2.1, using the maximum curvature procedure or the changing point algorithm, and a b value equal to 0.96 ± 0.03 have been obtained for the entire sequence. Two clusters have been identified and characterized by their faulting type, exhibiting b values equal to 0.99 ± 0.05 and 1.04 ± 0.05. Additionally, the temporal decay of the aftershock sequence was examined using a stochastic point process. The analysis was done through the restricted epidemic-type aftershock sequence (RETAS) stochastic model, which allows the possibility to recognize the prevailing clustering pattern of the relaxation process in the examined area. The analysis selected the epidemic-type aftershock sequence (ETAS) model to offer the most appropriate description of the temporal distribution, which presumes that all events in the sequence can cause secondary aftershocks. Finally, the fractal dimensions are estimated using the integral correlation. The obtained D 2 values are 2.15 ± 0.01, 2.23 ± 0.01 and 2.17 ± 0.02 for the entire sequence, and for the first and second cluster, respectively. An analysis of the temporal evolution of the fractal dimensions D -2, D 0, D 2 and the spectral slope has been also performed to derive and characterize the different clusters included in the sequence.

Mechanisms of haplotype divergence at the RGA08 nucleotide-binding leucine-rich repeat gene locus in wild banana (Musa balbisiana).

PubMed

Baurens, Franc-Christophe; Bocs, Stéphanie; Rouard, Mathieu; Matsumoto, Takashi; Miller, Robert N G; Rodier-Goud, Marguerite; MBéguié-A-MBéguié, Didier; Yahiaoui, Nabila

2010-07-16

Comparative sequence analysis of complex loci such as resistance gene analog clusters allows estimating the degree of sequence conservation and mechanisms of divergence at the intraspecies level. In banana (Musa sp.), two diploid wild species Musa acuminata (A genome) and Musa balbisiana (B genome) contribute to the polyploid genome of many cultivars. The M. balbisiana species is associated with vigour and tolerance to pests and disease and little is known on the genome structure and haplotype diversity within this species. Here, we compare two genomic sequences of 253 and 223 kb corresponding to two haplotypes of the RGA08 resistance gene analog locus in M. balbisiana "Pisang Klutuk Wulung" (PKW). Sequence comparison revealed two regions of contrasting features. The first is a highly colinear gene-rich region where the two haplotypes diverge only by single nucleotide polymorphisms and two repetitive element insertions. The second corresponds to a large cluster of RGA08 genes, with 13 and 18 predicted RGA genes and pseudogenes spread over 131 and 152 kb respectively on each haplotype. The RGA08 cluster is enriched in repetitive element insertions, in duplicated non-coding intergenic sequences including low complexity regions and shows structural variations between haplotypes. Although some allelic relationships are retained, a large diversity of RGA08 genes occurs in this single M. balbisiana genotype, with several RGA08 paralogs specific to each haplotype. The RGA08 gene family has evolved by mechanisms of unequal recombination, intragenic sequence exchange and diversifying selection. An unequal recombination event taking place between duplicated non-coding intergenic sequences resulted in a different RGA08 gene content between haplotypes pointing out the role of such duplicated regions in the evolution of RGA clusters. Based on the synonymous substitution rate in coding sequences, we estimated a 1 million year divergence time for these M. balbisiana haplotypes. A large RGA08 gene cluster identified in wild banana corresponds to a highly variable genomic region between haplotypes surrounded by conserved flanking regions. High level of sequence identity (70 to 99%) of the genic and intergenic regions suggests a recent and rapid evolution of this cluster in M. balbisiana.

Motif-independent prediction of a secondary metabolism gene cluster using comparative genomics: application to sequenced genomes of Aspergillus and ten other filamentous fungal species.

PubMed

Takeda, Itaru; Umemura, Myco; Koike, Hideaki; Asai, Kiyoshi; Machida, Masayuki

2014-08-01

Despite their biological importance, a significant number of genes for secondary metabolite biosynthesis (SMB) remain undetected due largely to the fact that they are highly diverse and are not expressed under a variety of cultivation conditions. Several software tools including SMURF and antiSMASH have been developed to predict fungal SMB gene clusters by finding core genes encoding polyketide synthase, nonribosomal peptide synthetase and dimethylallyltryptophan synthase as well as several others typically present in the cluster. In this work, we have devised a novel comparative genomics method to identify SMB gene clusters that is independent of motif information of the known SMB genes. The method detects SMB gene clusters by searching for a similar order of genes and their presence in nonsyntenic blocks. With this method, we were able to identify many known SMB gene clusters with the core genes in the genomic sequences of 10 filamentous fungi. Furthermore, we have also detected SMB gene clusters without core genes, including the kojic acid biosynthesis gene cluster of Aspergillus oryzae. By varying the detection parameters of the method, a significant difference in the sequence characteristics was detected between the genes residing inside the clusters and those outside the clusters. © The Author 2014. Published by Oxford University Press on behalf of Kazusa DNA Research Institute.

Brain changes following four weeks of unimanual motor training: Evidence from behavior, neural stimulation, cortical thickness, and functional MRI.

PubMed

Sale, Martin V; Reid, Lee B; Cocchi, Luca; Pagnozzi, Alex M; Rose, Stephen E; Mattingley, Jason B

2017-09-01

Although different aspects of neuroplasticity can be quantified with behavioral probes, brain stimulation, and brain imaging assessments, no study to date has combined all these approaches into one comprehensive assessment of brain plasticity. Here, 24 healthy right-handed participants practiced a sequence of finger-thumb opposition movements for 10 min each day with their left hand. After 4 weeks, performance for the practiced sequence improved significantly (P < 0.05 FWE) relative to a matched control sequence, with both the left (mean increase: 53.0% practiced, 6.5% control) and right (21.0%; 15.8%) hands. Training also induced significant (cluster p-FWE < 0.001) reductions in functional MRI activation for execution of the trained sequence, relative to the control sequence. These changes were observed as clusters in the premotor and supplementary motor cortices (right hemisphere, 301 voxel cluster; left hemisphere 700 voxel cluster), and sensorimotor cortices and superior parietal lobules (right hemisphere 864 voxel cluster; left hemisphere, 1947 voxel cluster). Transcranial magnetic stimulation over the right ("trained") primary motor cortex yielded a 58.6% mean increase in a measure of motor evoked potential amplitude, as recorded at the left abductor pollicis brevis muscle. Cortical thickness analyses based on structural MRI suggested changes in the right precentral gyrus, right post central gyrus, right dorsolateral prefrontal cortex, and potentially the right supplementary motor area. Such findings are consistent with LTP-like neuroplastic changes in areas that were already responsible for finger sequence execution, rather than improved recruitment of previously nonutilized tissue. Hum Brain Mapp 38:4773-4787, 2017. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Analysis of the cytochrome c oxidase subunit II (COX2) gene in giant panda, Ailuropoda melanoleuca.

PubMed

Ling, S S; Zhu, Y; Lan, D; Li, D S; Pang, H Z; Wang, Y; Li, D Y; Wei, R P; Zhang, H M; Wang, C D; Hu, Y D

2017-01-23

The giant panda, Ailuropoda melanoleuca (Ursidae), has a unique bamboo-based diet; however, this low-energy intake has been sufficient to maintain the metabolic processes of this species since the fourth ice age. As mitochondria are the main sites for energy metabolism in animals, the protein-coding genes involved in mitochondrial respiratory chains, particularly cytochrome c oxidase subunit II (COX2), which is the rate-limiting enzyme in electron transfer, could play an important role in giant panda metabolism. Therefore, the present study aimed to isolate, sequence, and analyze the COX2 DNA from individuals kept at the Giant Panda Protection and Research Center, China, and compare these sequences with those of the other Ursidae family members. Multiple sequence alignment showed that the COX2 gene had three point mutations that defined three haplotypes, with 60% of the sequences corresponding to haplotype I. The neutrality tests revealed that the COX2 gene was conserved throughout evolution, and the maximum likelihood phylogenetic analysis, using homologous sequences from other Ursidae species, showed clustering of the COX2 sequences of giant pandas, suggesting that this gene evolved differently in them.

Optimization process planning using hybrid genetic algorithm and intelligent search for job shop machining.

PubMed

Salehi, Mojtaba; Bahreininejad, Ardeshir

2011-08-01

Optimization of process planning is considered as the key technology for computer-aided process planning which is a rather complex and difficult procedure. A good process plan of a part is built up based on two elements: (1) the optimized sequence of the operations of the part; and (2) the optimized selection of the machine, cutting tool and Tool Access Direction (TAD) for each operation. In the present work, the process planning is divided into preliminary planning, and secondary/detailed planning. In the preliminary stage, based on the analysis of order and clustering constraints as a compulsive constraint aggregation in operation sequencing and using an intelligent searching strategy, the feasible sequences are generated. Then, in the detailed planning stage, using the genetic algorithm which prunes the initial feasible sequences, the optimized operation sequence and the optimized selection of the machine, cutting tool and TAD for each operation based on optimization constraints as an additive constraint aggregation are obtained. The main contribution of this work is the optimization of sequence of the operations of the part, and optimization of machine selection, cutting tool and TAD for each operation using the intelligent search and genetic algorithm simultaneously.

Optimization process planning using hybrid genetic algorithm and intelligent search for job shop machining

PubMed Central

Salehi, Mojtaba

2010-01-01

Optimization of process planning is considered as the key technology for computer-aided process planning which is a rather complex and difficult procedure. A good process plan of a part is built up based on two elements: (1) the optimized sequence of the operations of the part; and (2) the optimized selection of the machine, cutting tool and Tool Access Direction (TAD) for each operation. In the present work, the process planning is divided into preliminary planning, and secondary/detailed planning. In the preliminary stage, based on the analysis of order and clustering constraints as a compulsive constraint aggregation in operation sequencing and using an intelligent searching strategy, the feasible sequences are generated. Then, in the detailed planning stage, using the genetic algorithm which prunes the initial feasible sequences, the optimized operation sequence and the optimized selection of the machine, cutting tool and TAD for each operation based on optimization constraints as an additive constraint aggregation are obtained. The main contribution of this work is the optimization of sequence of the operations of the part, and optimization of machine selection, cutting tool and TAD for each operation using the intelligent search and genetic algorithm simultaneously. PMID:21845020

Prediction of CpG-island function: CpG clustering vs. sliding-window methods

PubMed Central

2010-01-01

Background Unmethylated stretches of CpG dinucleotides (CpG islands) are an outstanding property of mammal genomes. Conventionally, these regions are detected by sliding window approaches using %G + C, CpG observed/expected ratio and length thresholds as main parameters. Recently, clustering methods directly detect clusters of CpG dinucleotides as a statistical property of the genome sequence. Results We compare sliding-window to clustering (i.e. CpGcluster) predictions by applying new ways to detect putative functionality of CpG islands. Analyzing the co-localization with several genomic regions as a function of window size vs. statistical significance (p-value), CpGcluster shows a higher overlap with promoter regions and highly conserved elements, at the same time showing less overlap with Alu retrotransposons. The major difference in the prediction was found for short islands (CpG islets), often exclusively predicted by CpGcluster. Many of these islets seem to be functional, as they are unmethylated, highly conserved and/or located within the promoter region. Finally, we show that window-based islands can spuriously overlap several, differentially regulated promoters as well as different methylation domains, which might indicate a wrong merge of several CpG islands into a single, very long island. The shorter CpGcluster islands seem to be much more specific when concerning the overlap with alternative transcription start sites or the detection of homogenous methylation domains. Conclusions The main difference between sliding-window approaches and clustering methods is the length of the predicted islands. Short islands, often differentially methylated, are almost exclusively predicted by CpGcluster. This suggests that CpGcluster may be the algorithm of choice to explore the function of these short, but putatively functional CpG islands. PMID:20500903

The HST Large Programme on ω Centauri. II. Internal Kinematics

NASA Astrophysics Data System (ADS)

Bellini, Andrea; Libralato, Mattia; Bedin, Luigi R.; Milone, Antonino P.; van der Marel, Roeland P.; Anderson, Jay; Apai, Dániel; Burgasser, Adam J.; Marino, Anna F.; Rees, Jon M.

2018-01-01

In this second installment of the series, we look at the internal kinematics of the multiple stellar populations of the globular cluster ω Centauri in one of the parallel Hubble Space Telescope (HST) fields, located at about 3.5 half-light radii from the center of the cluster. Thanks to the over 15 yr long baseline and the exquisite astrometric precision of the HST cameras, well-measured stars in our proper-motion catalog have errors as low as ∼10 μas yr‑1, and the catalog itself extends to near the hydrogen-burning limit of the cluster. We show that second-generation (2G) stars are significantly more radially anisotropic than first-generation (1G) stars. The latter are instead consistent with an isotropic velocity distribution. In addition, 1G stars have excess systemic rotation in the plane of the sky with respect to 2G stars. We show that the six populations below the main-sequence (MS) knee identified in our first paper are associated with the five main population groups recently isolated on the upper MS in the core of cluster. Furthermore, we find both 1G and 2G stars in the field to be far from being in energy equipartition, with {η }1{{G}}=-0.007+/- 0.026 for the former and {η }2{{G}}=0.074+/- 0.029 for the latter, where η is defined so that the velocity dispersion {σ }μ scales with stellar mass as {σ }μ \\propto {m}-η . The kinematical differences reported here can help constrain the formation mechanisms for the multiple stellar populations in ω Centauri and other globular clusters. We make our astro-photometric catalog publicly available.

Towards a physical map of the fertility genes on the heterochromatic Y chromosome of Drosophila hydei: families of repetitive sequences transcribed on the lampbrush loops Nooses and Threads are organized in extended clusters of several hundred kilobases.

PubMed

Trapitz, P; Glätzer, K H; Bünemann, H

1992-11-01

The understanding of structure and function of the so-called fertility genes of Drosophila is very limited due to their unusual size--several megabases--and their location on the heterochromatic Y chromosome. Since mapping of these genes has mainly been done by classical cytogenetic analyses using a small number of cytologically visible lampbrush loops as the sole markers for particular fertility genes, the resolution of the genetic map of the Y chromosome is restricted to 3-5 Mb. Here we demonstrate that a substantially finer subdivision of the megabase-sized fertility genes in the subtelomeric regions of the Y chromosome of Drosophila hydei can be achieved by a combination of digestion with restriction enzymes having 6 bp recognition sequences, and pulsed field gel electrophoresis. The physical subdivision is based upon large conserved fragments of repetitive DNA in the size range from 50 up to 1600 kb and refers to the long-range organization of several families of repetitive DNA involved in Y chromosomal transcription processes in primary spermatocytes. We conclude from our results that at least five different families of repetitive DNA specifically transcribed on the lampbrush loops nooses and threads are organized as extended clusters of several hundred kb, essentially free of interspersed non-repetitive sequences.

Wide distribution of O157-antigen biosynthesis gene clusters in Escherichia coli.

PubMed

Iguchi, Atsushi; Shirai, Hiroki; Seto, Kazuko; Ooka, Tadasuke; Ogura, Yoshitoshi; Hayashi, Tetsuya; Osawa, Kayo; Osawa, Ro

2011-01-01

Most Escherichia coli O157-serogroup strains are classified as enterohemorrhagic E. coli (EHEC), which is known as an important food-borne pathogen for humans. They usually produce Shiga toxin (Stx) 1 and/or Stx2, and express H7-flagella antigen (or nonmotile). However, O157 strains that do not produce Stxs and express H antigens different from H7 are sometimes isolated from clinical and other sources. Multilocus sequence analysis revealed that these 21 O157:non-H7 strains tested in this study belong to multiple evolutionary lineages different from that of EHEC O157:H7 strains, suggesting a wide distribution of the gene set encoding the O157-antigen biosynthesis in multiple lineages. To gain insight into the gene organization and the sequence similarity of the O157-antigen biosynthesis gene clusters, we conducted genomic comparisons of the chromosomal regions (about 59 kb in each strain) covering the O-antigen gene cluster and its flanking regions between six O157:H7/non-H7 strains. Gene organization of the O157-antigen gene cluster was identical among O157:H7/non-H7 strains, but was divided into two distinct types at the nucleotide sequence level. Interestingly, distribution of the two types did not clearly follow the evolutionary lineages of the strains, suggesting that horizontal gene transfer of both types of O157-antigen gene clusters has occurred independently among E. coli strains. Additionally, detailed sequence comparison revealed that some positions of the repetitive extragenic palindromic (REP) sequences in the regions flanking the O-antigen gene clusters were coincident with possible recombination points. From these results, we conclude that the horizontal transfer of the O157-antigen gene clusters induced the emergence of multiple O157 lineages within E. coli and speculate that REP sequences may involve one of the driving forces for exchange and evolution of O-antigen loci.

Theoretical investigation about secondary deposition of thin-film formation by molecular dynamics simulation

NASA Astrophysics Data System (ADS)

Chen, Huawei; Hagiwara, Ichiro; Kiet Tieu, A.; Kishimoto, Kikuo; Liu, Qiang

2007-05-01

The thin-film growth has been confirmed to be assembled by an enormous number of clusters in experiments of CVD. Sequence of clusters' depositions proceeds to form the thin-film in short time as gas fluids through surface of substrate. Such growth mechanism has been mainly investigated on the basis of experiment. Due to immense cost of the experimental equipment and low level of current measurement technology, the comprehension about authentic effect of formation condition on properties of nanomaterial is limited in qualitative manner. Three quantitative items: flatness of primary deposition, adhesion between cluster and substrate, and degree of epitaxial growth were proposed to evaluate the property of thin-film. In this simulation, three different cluster sizes of 203, 653, and 1563 atoms with different velocities (0, 10, 100, 1000, and 3000 m/s) were deposited on a Cu(0 0 1) substrate whose temperatures were set between 300 and 1000 K. Four clusters and one cluster were used in primary deposition and secondary deposition, respectively. To increase initial velocity not only enhanced the speed of epitaxial growth, adhesion between clusters and substrate, but also increased the degree of epitaxy for primary deposition and secondary deposition. Exfoliation pattern of thin-film was profoundly dependent on initial velocity through comparison between adhesion of primary and secondary deposition. Moreover, the epitaxial growth became well as the temperature of substrate was raised, and the degree of epitaxy of small cluster was larger than that of larger cluster, no matter of primary and secondary deposition.

Task shifting of frontline community health workers for cardiovascular risk reduction: design and rationale of a cluster randomised controlled trial (DISHA study) in India.

PubMed

Jeemon, Panniyammakal; Narayanan, Gitanjali; Kondal, Dimple; Kahol, Kashvi; Bharadwaj, Ashok; Purty, Anil; Negi, Prakash; Ladhani, Sulaiman; Sanghvi, Jyoti; Singh, Kuldeep; Kapoor, Deksha; Sobti, Nidhi; Lall, Dorothy; Manimunda, Sathyaprakash; Dwivedi, Supriya; Toteja, Gurudyal; Prabhakaran, Dorairaj

2016-03-15

Effective task-shifting interventions targeted at reducing the global cardiovascular disease (CVD) epidemic in low and middle-income countries (LMICs) are urgently needed. DISHA is a cluster randomised controlled trial conducted across 10 sites (5 in phase 1 and 5 in phase 2) in India in 120 clusters. At each site, 12 clusters were randomly selected from a district. A cluster is defined as a small village with 250-300 households and well defined geographical boundaries. They were then randomly allocated to intervention and control clusters in a 1:1 allocation sequence. If any of the intervention and control clusters were <10 km apart, one was dropped and replaced with another randomly selected cluster from the same district. The study included a representative baseline cross-sectional survey, development of a structured intervention model, delivery of intervention for a minimum period of 18 months by trained frontline health workers (mainly Anganwadi workers and ASHA workers) and a post intervention survey in a representative sample. The study staff had no information on intervention allocation until the completion of the baseline survey. In order to ensure comparability of data across sites, the DISHA study follows a common protocol and manual of operation with standardized measurement techniques. Our study is the largest community based cluster randomised trial in low and middle-income country settings designed to test the effectiveness of 'task shifting' interventions involving frontline health workers for cardiovascular risk reduction. CTRI/2013/10/004049 . Registered 7 October 2013.

A Nomadic Subtelomeric Disease Resistance Gene Cluster in Common Bean1[W

PubMed Central

David, Perrine; Chen, Nicolas W.G.; Pedrosa-Harand, Andrea; Thareau, Vincent; Sévignac, Mireille; Cannon, Steven B.; Debouck, Daniel; Langin, Thierry; Geffroy, Valérie

2009-01-01

The B4 resistance (R) gene cluster is one of the largest clusters known in common bean (Phaseolus vulgaris [Pv]). It is located in a peculiar genomic environment in the subtelomeric region of the short arm of chromosome 4, adjacent to two heterochromatic blocks (knobs). We sequenced 650 kb spanning this locus and annotated 97 genes, 26 of which correspond to Coiled-Coil-Nucleotide-Binding-Site-Leucine-Rich-Repeat (CNL). Conserved microsynteny was observed between the Pv B4 locus and corresponding regions of Medicago truncatula and Lotus japonicus in chromosomes Mt6 and Lj2, respectively. The notable exception was the CNL sequences, which were completely absent in these regions. The origin of the Pv B4-CNL sequences was investigated through phylogenetic analysis, which reveals that, in the Pv genome, paralogous CNL genes are shared among nonhomologous chromosomes (4 and 11). Together, our results suggest that Pv B4-CNL was derived from CNL sequences from another cluster, the Co-2 cluster, through an ectopic recombination event. Integration of the soybean (Glycine max) genome data enables us to date more precisely this event and also to infer that a single CNL moved from the Co-2 to the B4 cluster. Moreover, we identified a new 528-bp satellite repeat, referred to as khipu, specific to the Phaseolus genus, present both between B4-CNL sequences and in the two knobs identified at the B4 R gene cluster. The khipu repeat is present on most chromosomal termini, indicating the existence of frequent ectopic recombination events in Pv subtelomeric regions. Our results highlight the importance of ectopic recombination in R gene evolution. PMID:19776165

Efficient algorithms for accurate hierarchical clustering of huge datasets: tackling the entire protein space

PubMed Central

Loewenstein, Yaniv; Portugaly, Elon; Fromer, Menachem; Linial, Michal

2008-01-01

Motivation: UPGMA (average linking) is probably the most popular algorithm for hierarchical data clustering, especially in computational biology. However, UPGMA requires the entire dissimilarity matrix in memory. Due to this prohibitive requirement, UPGMA is not scalable to very large datasets. Application: We present a novel class of memory-constrained UPGMA (MC-UPGMA) algorithms. Given any practical memory size constraint, this framework guarantees the correct clustering solution without explicitly requiring all dissimilarities in memory. The algorithms are general and are applicable to any dataset. We present a data-dependent characterization of hardness and clustering efficiency. The presented concepts are applicable to any agglomerative clustering formulation. Results: We apply our algorithm to the entire collection of protein sequences, to automatically build a comprehensive evolutionary-driven hierarchy of proteins from sequence alone. The newly created tree captures protein families better than state-of-the-art large-scale methods such as CluSTr, ProtoNet4 or single-linkage clustering. We demonstrate that leveraging the entire mass embodied in all sequence similarities allows to significantly improve on current protein family clusterings which are unable to directly tackle the sheer mass of this data. Furthermore, we argue that non-metric constraints are an inherent complexity of the sequence space and should not be overlooked. The robustness of UPGMA allows significant improvement, especially for multidomain proteins, and for large or divergent families. Availability: A comprehensive tree built from all UniProt sequence similarities, together with navigation and classification tools will be made available as part of the ProtoNet service. A C++ implementation of the algorithm is available on request. Contact: lonshy@cs.huji.ac.il PMID:18586742

Detection of extrasolar planets by the large deployable reflector

NASA Technical Reports Server (NTRS)

Hollenbach, D. J.; Takahashi, T.

1984-01-01

The best wavelength for observing Jupiter-size planetary companions to stars other than the Sun is one at which a planet's thermal emission is strongest; typically this would occur in the far-infrared region. It is assumed that the orbiting infrared telescope used is diffraction-limited so that the resolution of the planet from the central star is accomplished in the wings of the star's Airy pattern. Proxima Centauri, Barnard's Star, Wolf 359, and Epsilon Eridani are just a few of the many nearest main-sequence stars that could be studied with the large deployable relfector (LDR). The detectability of a planet improves for warmer planets and less luminous stars; therefore, planets around white dwarfs and those young planets which have sufficient internal gravitational energy release so as to cause a significant increase in their temperatures are considered. If white dwarfs are as old as they are usually assumed to be (5-10 billion yr), then only the nearest white dwarf (Sirius B) is within the range of LDR. The Ursa Major cluster and Perseu cluster are within LDR's detection range mainly because of their proximity and young age, respectively.

Genome Sequences of 12 Cluster AN Arthrobacter Phages

PubMed Central

Lee-Soety, Julia Y.; Bhatt, Shantanu; Adair, Tamarah L.; Bonilla, J. Alfred; Klyczek, Karen K.; Harrison, Melinda; Garlena, Rebecca A.; Bowman, Charles A.; Russell, Daniel A.; Jacobs-Sera, Deborah

2017-01-01

ABSTRACT Twelve siphoviral phages isolated using Arthrobacter sp. strain ATCC 21022 were sequenced. The phages all have relatively small genomes, ranging from 15,319 to 15,556 bp. All 12 phages are closely related to previously described cluster AN Arthrobacter phages. PMID:29122859

The threshold bootstrap clustering: a new approach to find families or transmission clusters within molecular quasispecies.

PubMed

Prosperi, Mattia C F; De Luca, Andrea; Di Giambenedetto, Simona; Bracciale, Laura; Fabbiani, Massimiliano; Cauda, Roberto; Salemi, Marco

2010-10-25

Phylogenetic methods produce hierarchies of molecular species, inferring knowledge about taxonomy and evolution. However, there is not yet a consensus methodology that provides a crisp partition of taxa, desirable when considering the problem of intra/inter-patient quasispecies classification or infection transmission event identification. We introduce the threshold bootstrap clustering (TBC), a new methodology for partitioning molecular sequences, that does not require a phylogenetic tree estimation. The TBC is an incremental partition algorithm, inspired by the stochastic Chinese restaurant process, and takes advantage of resampling techniques and models of sequence evolution. TBC uses as input a multiple alignment of molecular sequences and its output is a crisp partition of the taxa into an automatically determined number of clusters. By varying initial conditions, the algorithm can produce different partitions. We describe a procedure that selects a prime partition among a set of candidate ones and calculates a measure of cluster reliability. TBC was successfully tested for the identification of type-1 human immunodeficiency and hepatitis C virus subtypes, and compared with previously established methodologies. It was also evaluated in the problem of HIV-1 intra-patient quasispecies clustering, and for transmission cluster identification, using a set of sequences from patients with known transmission event histories. TBC has been shown to be effective for the subtyping of HIV and HCV, and for identifying intra-patient quasispecies. To some extent, the algorithm was able also to infer clusters corresponding to events of infection transmission. The computational complexity of TBC is quadratic in the number of taxa, lower than other established methods; in addition, TBC has been enhanced with a measure of cluster reliability. The TBC can be useful to characterise molecular quasipecies in a broad context.

Biased phylodynamic inferences from analysing clusters of viral sequences

PubMed Central

Xiang, Fei; Frost, Simon D. W.

2017-01-01

Abstract Phylogenetic methods are being increasingly used to help understand the transmission dynamics of measurably evolving viruses, including HIV. Clusters of highly similar sequences are often observed, which appear to follow a ‘power law’ behaviour, with a small number of very large clusters. These clusters may help to identify subpopulations in an epidemic, and inform where intervention strategies should be implemented. However, clustering of samples does not necessarily imply the presence of a subpopulation with high transmission rates, as groups of closely related viruses can also occur due to non-epidemiological effects such as over-sampling. It is important to ensure that observed phylogenetic clustering reflects true heterogeneity in the transmitting population, and is not being driven by non-epidemiological effects. We qualify the effect of using a falsely identified ‘transmission cluster’ of sequences to estimate phylodynamic parameters including the effective population size and exponential growth rate under several demographic scenarios. Our simulation studies show that taking the maximum size cluster to re-estimate parameters from trees simulated under a randomly mixing, constant population size coalescent process systematically underestimates the overall effective population size. In addition, the transmission cluster wrongly resembles an exponential or logistic growth model 99% of the time. We also illustrate the consequences of false clusters in exponentially growing coalescent and birth-death trees, where again, the growth rate is skewed upwards. This has clear implications for identifying clusters in large viral databases, where a false cluster could result in wasted intervention resources. PMID:28852573

A young solar twin in the Rosette cluster NGC 2244 line of sight

NASA Astrophysics Data System (ADS)

Huber, Jeremy M.; Kielkopf, John F.; Mengel, Matthew; Carter, Bradley D.; Ferland, Gary J.; Clark, Frank O.

2018-05-01

Based on prior precision photometry and cluster age analysis, the bright star GSC 00154-01819 is a possible young pre-main sequence member of the Rosette cluster, NGC 2244. As part of a comprehensive study of the large-scale structure of the Rosette and its excitation by the cluster stars, we noted this star as a potential backlight for a probe of the interstellar medium and extinction along the sight line towards a distinctive nebular feature projected on to the cluster centre. New high-resolution spectra of the star were taken with the University College London Echelle Spectrograph of the AAT. They reveal that rather than being a reddened spectral type B or A star within the Mon OB2 association, it is a nearby, largely unreddened, solar twin of spectral type G2V less than 180 Myr old. It is about 219 pc from the Sun with a barycentric radial velocity of +14.35 ± 1.99 km s-1. The spectrum of the Rosette behind it and along this line of sight shows a barycentric radial velocity of +26.0 ± 2.4 km s-1 in H α, and a full width at half-maximum velocity dispersion of 61.94 ± 1.38 km s-1.

A High-precision Trigonometric Parallax to an Ancient Metal-poor Globular Cluster

NASA Astrophysics Data System (ADS)

Brown, T. M.; Casertano, S.; Strader, J.; Riess, A.; VandenBerg, D. A.; Soderblom, D. R.; Kalirai, J.; Salinas, R.

2018-03-01

Using the Wide Field Camera 3 (WFC3) on the Hubble Space Telescope (HST), we have obtained a direct trigonometric parallax for the nearest metal-poor globular cluster, NGC 6397. Although trigonometric parallaxes have been previously measured for many nearby open clusters, this is the first parallax for an ancient metal-poor population—one that is used as a fundamental template in many stellar population studies. This high-precision measurement was enabled by the HST/WFC3 spatial-scanning mode, providing hundreds of astrometric measurements for dozens of stars in the cluster and also for Galactic field stars along the same sightline. We find a parallax of 0.418 ± 0.013 ± 0.018 mas (statistical, systematic), corresponding to a true distance modulus of 11.89 ± 0.07 ± 0.09 mag (2.39 ± 0.07 ± 0.10 kpc). The V luminosity at the stellar main-sequence turnoff implies an absolute cluster age of 13.4 ± 0.7 ± 1.2 Gyr. Based on 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 NAS 5-26555. These observations are associated with programs GO-13817, GO-14336, and GO-14773.

The Clusters AgeS Experiment (CASE). Variable Stars in the Field of the Globular Cluster NGC 3201

NASA Astrophysics Data System (ADS)

Kaluzny, J.; Rozyczka, M.; Thompson, I. B.; Narloch, W.; Mazur, B.; Pych, W.; Schwarzenberg-Czerny, A.

2016-01-01

The field of the globular cluster NGC 3201 was monitored between 1998 and 2009 in a search for variable stars. BV light curves were obtained for 152 periodic or likely periodic variables, fifty-seven of which are new detections. Thirty-seven newly detected variables are proper motion members of the cluster. Among them we found seven detached or semi-detached eclipsing binaries, four contact binaries, and eight SX Phe pulsators. Four of the eclipsing binaries are located in the turnoff region, one on the lower main sequence and the remaining two slightly above the subgiant branch. Two contact systems are blue stragglers, and another two reside in the turnoff region. In the blue straggler region a total of 266 objects were found, of which 140 are proper motion (PM) members of NGC 3201, and another nineteen are field stars. Seventy-eight of the remaining objects for which we do not have PM data are located within the half-light radius from the center of the cluster, and most of them are likely genuine blue stragglers. Four variable objects in our field of view were found to coincide with X-ray sources: three chromospherically active stars and a quasar at a redshift z≍0.5.

Low-dimensional clustering reveals new influenza strains before they become dominant

NASA Astrophysics Data System (ADS)

He, Jiankui; Deem, Michael

2010-03-01

Influenza A virus has been circulating in the human population and has caused three pandemics in the last century (1918 H1N1, 1957 H2N2, 1968 H3N2). The newly appeared 2009 A(H1N1) has been classified by the World Health Organization (WHO) as the fourth pandemic virus strain. We here consider an approach for early detection of new dominant strains. We first construct a network model and apply it to the evolution of the 2009 A(H1N1) virus. By clustering the sequence data, we found two main clusters. We then define a metric to detect the emergence of dominant strains. We show on historical H3N2 data that this method is able to find a cluster around an incipient dominant strain before it becomes dominant. For example, for H3N2 as of 30 March 2009, we see the cluster for the new A/BritishColumbia/RV1222/2009 strain. Turning to H1N1 and the 2009 A(H1N1), we do not see evidence for antigenically novel 2009 A(H1N1) strains as of August 2009. This strain detection tool combines a projection operator with a density estimation.

The Genome Sequence of the Cyanobacterium Oscillatoria sp. PCC 6506 Reveals Several Gene Clusters Responsible for the Biosynthesis of Toxins and Secondary Metabolites▿

PubMed Central

Méjean, Annick; Mazmouz, Rabia; Mann, Stéphane; Calteau, Alexandra; Médigue, Claudine; Ploux, Olivier

2010-01-01

We report a draft sequence of the genome of Oscillatoria sp. PCC 6506, a cyanobacterium that produces anatoxin-a and homoanatoxin-a, two neurotoxins, and cylindrospermopsin, a cytotoxin. Beside the clusters of genes responsible for the biosynthesis of these toxins, we have found other clusters of genes likely involved in the biosynthesis of not-yet-identified secondary metabolites. PMID:20675499