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

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

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

2014-07-01

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

A method for determining the radius of an open cluster from stellar proper motions

NASA Astrophysics Data System (ADS)

Sánchez, Néstor; Alfaro, Emilio J.; López-Martínez, Fátima

2018-04-01

We propose a method for calculating the radius of an open cluster in an objective way from an astrometric catalogue containing, at least, positions and proper motions. It uses the minimum spanning tree in the proper motion space to discriminate cluster stars from field stars and it quantifies the strength of the cluster-field separation by means of a statistical parameter defined for the first time in this paper. This is done for a range of different sampling radii from where the cluster radius is obtained as the size at which the best cluster-field separation is achieved. The novelty of this strategy is that the cluster radius is obtained independently of how its stars are spatially distributed. We test the reliability and robustness of the method with both simulated and real data from a well-studied open cluster (NGC 188), and apply it to UCAC4 data for five other open clusters with different catalogued radius values. NGC 188, NGC 1647, NGC 6603, and Ruprecht 155 yielded unambiguous radius values of 15.2 ± 1.8, 29.4 ± 3.4, 4.2 ± 1.7, and 7.0 ± 0.3 arcmin, respectively. ASCC 19 and Collinder 471 showed more than one possible solution, but it is not possible to know whether this is due to the involved uncertainties or due to the presence of complex patterns in their proper motion distributions, something that could be inherent to the physical object or due to the way in which the catalogue was sampled.

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.

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.

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

Searching for the birthplaces of open clusters with ages of several billion years

NASA Astrophysics Data System (ADS)

Acharova, I. A.; Shevtsova, E. S.

2016-01-01

We discuss the possibility of finding the birthplaces of open clusters (OC) with ages of several billion years. The proposed method is based on the comparison of the results of the chemical evolution modeling of the Galactic disk with the parameters of the cluster. Five OCs older than 7 Gyr are known: NGC6791, BH176, Collinder 261, Berkeley 17, and Berkeley 39. The oxygen and iron abundances in NGC6791 and the oxygen abundance in BH176 are twice the solar level, the heavy-element abundances in other clusters are close to the corresponding solar values. According to chemical evolution models, at the time of the formation of the objects considered the regions where the oxygen and iron abundances reached the corresponding levels extended out to 5 kpc from the Galactic center.At present time theOCs considered are located several kpc from the Galactic center. Some of these clusters are located extremely high, about 1 kpc above the disk midplane, i.e., they have been subject to some mechanism that has carried them into orbits uncharacteristic of this type of objects. It follows from a comparison with the results of chemical evolution that younger clusters with ages of 4-5 Gyr, e.g., NGC1193,M67, and others, may have formed in a broad range of Galactocentric distances. Their large heights above the disk midplane is sufficient to suggest that these clusters have moved away from their likely birthplaces. Clusters are carried far away from the Galactic disk until the present time: about 40 clusters with ages from 0 to 2 Gyr are observed at heights ranging from 300 to 750 pc.

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.

Phylogenetically Structured Differences in rRNA Gene Sequence Variation among Species of Arbuscular Mycorrhizal Fungi and Their Implications for Sequence Clustering

PubMed Central

Ekanayake, Saliya; Ruan, Yang; Schütte, Ursel M. E.; Kaonongbua, Wittaya; Fox, Geoffrey; Ye, Yuzhen; Bever, James D.

2016-01-01

ABSTRACT Arbuscular mycorrhizal (AM) fungi form mutualisms with plant roots that increase plant growth and shape plant communities. Each AM fungal cell contains a large amount of genetic diversity, but it is unclear if this diversity varies across evolutionary lineages. We found that sequence variation in the nuclear large-subunit (LSU) rRNA gene from 29 isolates representing 21 AM fungal species generally assorted into genus- and species-level clades, with the exception of species of the genera Claroideoglomus and Entrophospora. However, there were significant differences in the levels of sequence variation across the phylogeny and between genera, indicating that it is an evolutionarily constrained trait in AM fungi. These consistent patterns of sequence variation across both phylogenetic and taxonomic groups pose challenges to interpreting operational taxonomic units (OTUs) as approximations of species-level groups of AM fungi. We demonstrate that the OTUs produced by five sequence clustering methods using 97% or equivalent sequence similarity thresholds failed to match the expected species of AM fungi, although OTUs from AbundantOTU, CD-HIT-OTU, and CROP corresponded better to species than did OTUs from mothur or UPARSE. This lack of OTU-to-species correspondence resulted both from sequences of one species being split into multiple OTUs and from sequences of multiple species being lumped into the same OTU. The OTU richness therefore will not reliably correspond to the AM fungal species richness in environmental samples. Conservatively, this error can overestimate species richness by 4-fold or underestimate richness by one-half, and the direction of this error will depend on the genera represented in the sample. IMPORTANCE Arbuscular mycorrhizal (AM) fungi form important mutualisms with the roots of most plant species. Individual AM fungi are genetically diverse, but it is unclear whether the level of this diversity differs among evolutionary lineages. We found that the amount of sequence variation in an rRNA gene that is commonly used to identify AM fungal species varied significantly between evolutionary groups that correspond to different genera, with the exception of two genera that are genetically indistinguishable from each other. When we clustered groups of similar sequences into operational taxonomic units (OTUs) using five different clustering methods, these patterns of sequence variation caused the number of OTUs to either over- or underestimate the actual number of AM fungal species, depending on the genus. Our results indicate that OTU-based inferences about AM fungal species composition from environmental sequences can be improved if they take these taxonomically structured patterns of sequence variation into account. PMID:27260357

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

NASA Astrophysics Data System (ADS)

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

1986-08-01

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

Microbial diversity of an anoxic zone of a hydroelectric power station reservoir in Brazilian Amazonia.

PubMed

Graças, Diego A; Miranda, Paulo R; Baraúna, Rafael A; McCulloch, John A; Ghilardi, Rubens; Schneider, Maria Paula C; Silva, Artur

2011-11-01

Microbial diversity was evaluated in an anoxic zone of Tucuruí Hydroelectric Power Station reservoir in Brazilian Amazonia using a culture-independent approach by amplifying and sequencing fragments of the 16S rRNA gene using metagenomic DNA as a template. Samples obtained from the photic, aphotic (40 m) and sediment (60 m) layers were used to construct six 16S rDNA libraries containing a total of 1,152 clones. The sediment, aphotic and photic layers presented 64, 33 and 35 unique archaeal operational taxonomic units (OTUs). The estimated richness of these layers was evaluated to be 153, 106 and 79 archaeal OTUs, respectively, using the abundance-based coverage estimator (ACE) and 114, 83 and 77 OTUs using the Chao1 estimator. For bacterial sequences, 114, 69 and 57 OTUs were found in the sediment, aphotic and photic layers, which presented estimated richnesses of 1,414, 522 and 197 OTUs (ACE) and 1,059, 1,014 and 148 OTUs (Chao1), respectively. Phylogenetic analyses of the sequences obtained revealed a high richness of microorganisms which participate in the carbon cycle, namely, methanogenic archaea and methanotrophic proteobacteria. Most sequences obtained belong to non-culturable prokaryotes. The present study offers the first glimpse of the huge microbial diversity of an anoxic area of a man-made lacustrine environment in the tropics.

Nucleotide sequences of Dictyostelium discoideum developmentally regulated cDNAs rich in (AAC) imply proteins that contain clusters of asparagine, glutamine, or threonine.

PubMed

Shaw, D R; Richter, H; Giorda, R; Ohmachi, T; Ennis, H L

1989-09-01

A Dictyostelium discoideum repetitive element composed of long repeats of the codon (AAC) is found in developmentally regulated transcripts. The concentration of (AAC) sequences is low in mRNA from dormant spores and growing cells and increases markedly during spore germination and multicellular development. The sequence hybridizes to many different sized Dictyostelium DNA restriction fragments indicating that it is scattered throughout the genome. Four cDNA clones isolated contain (AAC) sequences in the deduced coding region. Interestingly, the (AAC)-rich sequences are present in all three reading frames in the deduced proteins, i.e., AAC (asparagine), ACA (threonine) and CAA (glutamine). Three of the clones contain only one of these in-frame so that the individual proteins carry either asparagine, threonine, or glutamine clusters, not mixtures. However, one clone is both glutamine- and asparagine-rich. The (AAC) portion of the transcripts are reiterated 300 times in the haploid genome while the other portions of the cDNAs represent single copy genes, whose sequences show no similarity other than the (AAC) repeats. The repeated sequence is similar to the opa or M sequence found in Drosophila melanogaster notch and homeo box genes and in fly developmentally regulated transcripts. The transcripts are present on polysomes suggesting that they are translated. Although the function of these repeats is unknown, long amino acid repeats are a characteristic feature of extracellular proteins of lower eukaryotes.

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.

Holocentric chromosomes of psocids (Insecta, Psocoptera) analysed by C-banding, silver impregnation and sequence specific fluorochromes CMA3 and DAPI.

PubMed

Golub, Natalia V; Nokkala, Seppo; Kuznetsova, Valentina G

2004-01-01

The pattern of nucleolus attachment and C-heterochromatin distribution and molecular composition in the karyotypes of psocid species Psococerastis gibbosa (2n = 16+X), Blaste conspurcata (2n = 16+X) and Amphipsocus japonicus (2n = 14+neo-XY) were studied by C-banding, silver impregnation and sequence specific fluorochromes CMA3 and DAPI. Every species was found to have a single nucleolus in male meiosis. In P. gibbosa the nucleolus is attached to an autosomal bivalent; in B. conspurcata to the X-chromosome; in A. japonicus to the neo-XY bivalent. The species show a rather small amount of constitutive heterochromatin, C-blocks demonstrating telomeric localization with rare exceptions. P. gibbosa is characterized by a polymorphism for C-blocks occurrence and distribution. In the autosomes of this species, C-heterochromatin consists of AT-rich DNA except for the nucleolus organizing region, which is also GC-rich; the X-chromosome shows both AT- and GC-rich clusters. In A. japonicus and B. conspurcata, C-heterochromatin of the autosomes and sex chromosomes consists of both GC-rich and AT-rich DNA clusters, which are largely co-localized.

A DNA Barcode Library for North American Ephemeroptera: Progress and Prospects

PubMed Central

Webb, Jeffrey M.; Jacobus, Luke M.; Funk, David H.; Zhou, Xin; Kondratieff, Boris; Geraci, Christy J.; DeWalt, R. Edward; Baird, Donald J.; Richard, Barton; Phillips, Iain; Hebert, Paul D. N.

2012-01-01

DNA barcoding of aquatic macroinvertebrates holds much promise as a tool for taxonomic research and for providing the reliable identifications needed for water quality assessment programs. A prerequisite for identification using barcodes is a reliable reference library. We gathered 4165 sequences from the barcode region of the mitochondrial cytochrome c oxidase subunit I gene representing 264 nominal and 90 provisional species of mayflies (Insecta: Ephemeroptera) from Canada, Mexico, and the United States. No species shared barcode sequences and all can be identified with barcodes with the possible exception of some Caenis. Minimum interspecific distances ranged from 0.3–24.7% (mean: 12.5%), while the average intraspecific divergence was 1.97%. The latter value was inflated by the presence of very high divergences in some taxa. In fact, nearly 20% of the species included two or three haplotype clusters showing greater than 5.0% sequence divergence and some values are as high as 26.7%. Many of the species with high divergences are polyphyletic and likely represent species complexes. Indeed, many of these polyphyletic species have numerous synonyms and individuals in some barcode clusters show morphological attributes characteristic of the synonymized species. In light of our findings, it is imperative that type or topotype specimens be sequenced to correctly associate barcode clusters with morphological species concepts and to determine the status of currently synonymized species. PMID:22666447

Integrated spectral study of small angular diameter galactic open clusters

NASA Astrophysics Data System (ADS)

Clariá, J. J.; Ahumada, A. V.; Bica, E.; Pavani, D. B.; Parisi, M. C.

2017-10-01

This paper presents flux-calibrated integrated spectra obtained at Complejo Astronómico El Leoncito (CASLEO, Argentina) for a sample of 9 Galactic open clusters of small angular diameter. The spectra cover the optical range (3800-6800 Å), with a resolution of ˜14 Å. With one exception (Ruprecht 158), the selected clusters are projected into the fourth Galactic quadrant (282o < l < 345o) near the Galactic plane (∣b∣ ≤ 9o). We performed simultaneous estimates of foreground interstellar reddening and age by comparing the continuum distribution and line strenghts of the cluster spectra with those of template cluster spectra with known parameters. We thus provide spectroscopic information independent from that derived through color-magnitude diagram studies. We found three clusters (Collinder 249, NGC 4463 and Ruprecht 122) younger than ˜40 Myr, four moderately young ones (BH 92, Harvard 5, Hogg 14 and Pismis 23) with ages within 200-400 Myr, and two intermediate-age ones (Ruprecht 158 and ESO 065-SC07) with ages within 1.0-2.2 Gyr. The derived foreground E(B - V) color excesses vary from around 0.0 in Ruprecht 158 to ˜1.1 in Pismis 23. In general terms, the results obtained show good agreement with previous photometric results. In Ruprecht 158 and BH 92, however, some differences are found between the parameters here obtained and previous values in the literature. Individual spectra of some comparatively bright stars located in the fields of 5 out of the 9 clusters here studied, allowed us to evaluate their membership status. The current cluster sample complements that of 46 open clusters previously studied by our group in an effort to gather a spectral library with several clusters per age bin. The cluster spectral library that we have been building is an important tool to tie studies of resolved and unresolved stellar content.

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

Nucleotide sequence of a cluster of early and late genes in a conserved segment of the vaccinia virus genome.

PubMed Central

Plucienniczak, A; Schroeder, E; Zettlmeissl, G; Streeck, R E

1985-01-01

The nucleotide sequence of a 7.6 kb vaccinia DNA segment from a genomic region conserved among different orthopox virus has been determined. This segment contains a tight cluster of 12 partly overlapping open reading frames most of which can be correlated with previously identified early and late proteins and mRNAs. Regulatory signals used by vaccinia virus have been studied. Presumptive promoter regions are rich in A, T and carry the consensus sequences TATA and AATAA spaced at 20-24 base pairs. Tandem repeats of a CTATTC consensus sequence are proposed to be involved in the termination of early transcription. PMID:2987815

Genetic Diversity of Bacterial Communities and Gene Transfer Agents in Northern South China Sea

PubMed Central

Sun, Fu-Lin; Wang, You-Shao; Wu, Mei-Lin; Jiang, Zhao-Yu; Sun, Cui-Ci; Cheng, Hao

2014-01-01

Pyrosequencing of the 16S ribosomal RNA gene (rDNA) amplicons was performed to investigate the unique distribution of bacterial communities in northern South China Sea (nSCS) and evaluate community structure and spatial differences of bacterial diversity. Cyanobacteria, Proteobacteria, Actinobacteria, and Bacteroidetes constitute the majority of bacteria. The taxonomic description of bacterial communities revealed that more Chroococcales, SAR11 clade, Acidimicrobiales, Rhodobacterales, and Flavobacteriales are present in the nSCS waters than other bacterial groups. Rhodobacterales were less abundant in tropical water (nSCS) than in temperate and cold waters. Furthermore, the diversity of Rhodobacterales based on the gene transfer agent (GTA) major capsid gene (g5) was investigated. Four g5 gene clone libraries were constructed from samples representing different regions and yielded diverse sequences. Fourteen g5 clusters could be identified among 197 nSCS clones. These clusters were also related to known g5 sequences derived from genome-sequenced Rhodobacterales. The composition of g5 sequences in surface water varied with the g5 sequences in the sampling sites; this result indicated that the Rhodobacterales population could be highly diverse in nSCS. Phylogenetic tree analysis result indicated distinguishable diversity patterns among tropical (nSCS), temperate, and cold waters, thereby supporting the niche adaptation of specific Rhodobacterales members in unique environments. PMID:25364820

Mechanisms of haplotype divergence at the RGA08 nucleotide-binding leucine-rich repeat gene locus in wild banana (Musa balbisiana)

PubMed Central

2010-01-01

Background 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). Results 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. Conclusions 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. PMID:20637079

Gaia-ESO Survey: Global properties of clusters Trumpler 14 and 16 in the Carina nebula ⋆⋆

NASA Astrophysics Data System (ADS)

Damiani, F.; Klutsch, A.; Jeffries, R. D.; Randich, S.; Prisinzano, L.; Maíz Apellániz, J.; Micela, G.; Kalari, V.; Frasca, A.; Zwitter, T.; Bonito, R.; Gilmore, G.; Flaccomio, E.; Francois, P.; Koposov, S.; Lanzafame, A. C.; Sacco, G. G.; Bayo, A.; Carraro, G.; Casey, A. R.; Alfaro, E. J.; Costado, M. T.; Donati, P.; Franciosini, E.; Hourihane, A.; Jofré, P.; Lardo, C.; Lewis, J.; Magrini, L.; Monaco, L.; Morbidelli, L.; Worley, C. C.; Vink, J. S.; Zaggia, S.

2017-07-01

Aims: We present the first extensive spectroscopic study of the global population in star clusters Trumpler 16, Trumpler 14, and Collinder 232 in the Carina nebula, using data from the Gaia-ESO Survey, down to solar-mass stars. Methods: In addition to the standard homogeneous survey data reduction, a special processing was applied here because of the bright nebulosity surrounding Carina stars. Results: We find about 400 good candidate members ranging from OB types down to slightly subsolar masses. About 100 heavily reddened early-type Carina members found here were previously unrecognized or poorly classified, including two candidate O stars and several candidate Herbig Ae/Be stars. Their large brightness makes them useful tracers of the obscured Carina population. The spectroscopically derived temperatures for nearly 300 low-mass members enables the inference of individual extinction values and the study of the relative placement of stars along the line of sight. Conclusions: We find a complex spatial structure with definite clustering of low-mass members around the most massive stars and spatially variable extinction. By combining the new data with existing X-ray data, we obtain a more complete picture of the three-dimensional spatial structure of the Carina clusters and of their connection to bright and dark nebulosity and UV sources. The identification of tens of background giants also enables us to determine the total optical depth of the Carina nebula along many sightlines. We are also able to put constraints on the star formation history of the region with Trumpler 14 stars found to be systematically younger than stars in other subclusters. We find a large percentage of fast-rotating stars among Carina solar-mass members, which provide new constraints on the rotational evolution of pre-main-sequence stars in this mass range. Based on observations collected with the FLAMES spectrograph at VLT/UT2 telescope (Paranal Observatory, ESO, Chile), for the Gaia-ESO Large Public Survey (program 188.B-3002). Full Tables 1, 2, and 7 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/603/A81

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;

Soil pH determines fungal diversity along an elevation gradient in Southwestern China.

PubMed

Liu, Dan; Liu, Guohua; Chen, Li; Wang, Juntao; Zhang, Limei

2018-01-03

Fungi play important roles in ecosystem processes, and the elevational pattern of fungal diversity is still unclear. Here, we examined the diversity of fungi along a 1,000 m elevation gradient on Mount Nadu, Southwestern China. We used MiSeq sequencing to obtain fungal sequences that were clustered into operational taxonomic units (OTUs) and to measure the fungal composition and diversity. Though the species richness and phylogenetic diversity of the fungal community did not exhibit significant trends with increasing altitude, they were significantly lower at mid-altitudinal sites than at the base. The Bray-Curtis distance clustering also showed that the fungal communities varied significantly with altitude. A distance-based linear model multivariate analysis (DistLM) identified that soil pH dominated the explanatory power of the species richness (23.72%), phylogenetic diversity (24.25%) and beta diversity (28.10%) of the fungal community. Moreover, the species richness and phylogenetic diversity of the fungal community increased linearly with increasing soil pH (P<0.05). Our study provides evidence that pH is an important predictor of soil fungal diversity along elevation gradients in Southwestern China.

CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats.

PubMed

Grissa, Ibtissem; Vergnaud, Gilles; Pourcel, Christine

2007-07-01

Clustered regularly interspaced short palindromic repeats (CRISPRs) constitute a particular family of tandem repeats found in a wide range of prokaryotic genomes (half of eubacteria and almost all archaea). They consist of a succession of highly conserved regions (DR) varying in size from 23 to 47 bp, separated by similarly sized unique sequences (spacer) of usually viral origin. A CRISPR cluster is flanked on one side by an AT-rich sequence called the leader and assumed to be a transcriptional promoter. Recent studies suggest that this structure represents a putative RNA-interference-based immune system. Here we describe CRISPRFinder, a web service offering tools to (i) detect CRISPRs including the shortest ones (one or two motifs); (ii) define DRs and extract spacers; (iii) get the flanking sequences to determine the leader; (iv) blast spacers against Genbank database and (v) check if the DR is found elsewhere in prokaryotic sequenced genomes. CRISPRFinder is freely accessible at http://crispr.u-psud.fr/Server/CRISPRfinder.php.

Tyrosine Nitration within the Proline-Rich Region of Tau in Alzheimer's Disease

PubMed Central

Reyes, Juan F.; Fu, Yifan; Vana, Laurel; Kanaan, Nicholas M.; Binder, Lester I.

2011-01-01

A substantial body of evidence suggests that nitrative injury contributes to neurodegeneration in Alzheimer's disease (AD) and other neurodegenerative disorders. Previously, we showed in vitro that within the tau protein the N-terminal tyrosine residues (Y18 and Y29) are more susceptible to nitrative modifications than other tyrosine sites (Y197 and Y394). Using site-specific antibodies to nitrated tau at Y18 and Y29, we identified tau nitrated in both glial (Y18) and neuronal (Y29) tau pathologies. In this study, we report the characterization of two novel monoclonal antibodies, Tau-nY197 and Tau-nY394, recognizing tau nitrated at Y197 and Y394, respectively. By Western blot analysis, Tau-nY197 labeled soluble tau and insoluble paired helical filament proteins (PHF-tau) nitrated at Y197 from control and AD brain samples. Tau-nY394 failed to label soluble tau isolated from control or severe AD samples, but labeled insoluble PHF-tau to a limited extent. Immunohistochemical analysis using Tau-nY197 revealed the hallmark tau pathology associated with AD; Tau-nY394 did not detect any pathological lesions characteristic of the disorder. These data suggest that a subset of the hallmark pathological inclusions of AD contain tau nitrated at Y197. However, nitration at Y197 was also identified in soluble tau from all control samples, including those at Braak stage 0, suggesting that nitration at this site in the proline-rich region of tau may have normal biological functions in the human brain. PMID:21514440

Gapless genome assembly of Colletotrichum higginsianum reveals chromosome structure and association of transposable elements with secondary metabolite gene clusters.

PubMed

Dallery, Jean-Félix; Lapalu, Nicolas; Zampounis, Antonios; Pigné, Sandrine; Luyten, Isabelle; Amselem, Joëlle; Wittenberg, Alexander H J; Zhou, Shiguo; de Queiroz, Marisa V; Robin, Guillaume P; Auger, Annie; Hainaut, Matthieu; Henrissat, Bernard; Kim, Ki-Tae; Lee, Yong-Hwan; Lespinet, Olivier; Schwartz, David C; Thon, Michael R; O'Connell, Richard J

2017-08-29

The ascomycete fungus Colletotrichum higginsianum causes anthracnose disease of brassica crops and the model plant Arabidopsis thaliana. Previous versions of the genome sequence were highly fragmented, causing errors in the prediction of protein-coding genes and preventing the analysis of repetitive sequences and genome architecture. Here, we re-sequenced the genome using single-molecule real-time (SMRT) sequencing technology and, in combination with optical map data, this provided a gapless assembly of all twelve chromosomes except for the ribosomal DNA repeat cluster on chromosome 7. The more accurate gene annotation made possible by this new assembly revealed a large repertoire of secondary metabolism (SM) key genes (89) and putative biosynthetic pathways (77 SM gene clusters). The two mini-chromosomes differed from the ten core chromosomes in being repeat- and AT-rich and gene-poor but were significantly enriched with genes encoding putative secreted effector proteins. Transposable elements (TEs) were found to occupy 7% of the genome by length. Certain TE families showed a statistically significant association with effector genes and SM cluster genes and were transcriptionally active at particular stages of fungal development. All 24 subtelomeres were found to contain one of three highly-conserved repeat elements which, by providing sites for homologous recombination, were probably instrumental in four segmental duplications. The gapless genome of C. higginsianum provides access to repeat-rich regions that were previously poorly assembled, notably the mini-chromosomes and subtelomeres, and allowed prediction of the complete SM gene repertoire. It also provides insights into the potential role of TEs in gene and genome evolution and host adaptation in this asexual pathogen.

Elastic scattering and breakup reactions of the exotic nucleus 8B on nuclear targets

NASA Astrophysics Data System (ADS)

Lukyanov, V. K.; Kadrev, D. N.; Antonov, A. N.; Zemlyanaya, E. V.; Lukyanov, K. V.; Gaidarov, M. K.; Spasova, K.

2018-05-01

Microscopic calculations of the optical potentials (OPs) and elastic scattering cross sections of the proton-rich nucleus 8B on 12C, 58Ni and 208Pb targets are presented. The density distributions of 8B obtained within the variational Monte Carlo (VMC) model and the three-cluster model (3CM) are used to construct the optical potentials (OP). The real part of the hybrid OP (ReOP) is calculated using the folding model with the direct and exchange terms included, while the imaginary part (ImOP) is obtained on the base of the high energy approximation (HEA). In addition, the cluster model, in which 8B consists of a proton halo and a 7Be core is applied to calculate the breakup cross sections of 8B on 9Be, 12C and 197Au targets, as well as the momentum distributions of 7Be fragments. A comparison with the available experimental data is made and a good agreement is obtained.

Clustering of disulfide-rich peptides provides scaffolds for hit discovery by phage display: application to interleukin-23.

PubMed

Barkan, David T; Cheng, Xiao-Li; Celino, Herodion; Tran, Tran T; Bhandari, Ashok; Craik, Charles S; Sali, Andrej; Smythe, Mark L

2016-11-23

Disulfide-rich peptides (DRPs) are found throughout nature. They are suitable scaffolds for drug development due to their small cores, whose disulfide bonds impart extraordinary chemical and biological stability. A challenge in developing a DRP therapeutic is to engineer binding to a specific target. This challenge can be overcome by (i) sampling the large sequence space of a given scaffold through a phage display library and by (ii) panning multiple libraries encoding structurally distinct scaffolds. Here, we implement a protocol for defining these diverse scaffolds, based on clustering structurally defined DRPs according to their conformational similarity. We developed and applied a hierarchical clustering protocol based on DRP structural similarity, followed by two post-processing steps, to classify 806 unique DRP structures into 81 clusters. The 20 most populated clusters comprised 85% of all DRPs. Representative scaffolds were selected from each of these clusters; the representatives were structurally distinct from one another, but similar to other DRPs in their respective clusters. To demonstrate the utility of the clusters, phage libraries were constructed for three of the representative scaffolds and panned against interleukin-23. One library produced a peptide that bound to this target with an IC 50 of 3.3 μM. Most DRP clusters contained members that were diverse in sequence, host organism, and interacting proteins, indicating that cluster members were functionally diverse despite having similar structure. Only 20 peptide scaffolds accounted for most of the natural DRP structural diversity, providing suitable starting points for seeding phage display experiments. Through selection of the scaffold surface to vary in phage display, libraries can be designed that present sequence diversity in architecturally distinct, biologically relevant combinations of secondary structures. We supported this hypothesis with a proof-of-concept experiment in which three phage libraries were constructed and panned against the IL-23 target, resulting in a single-digit μM hit and suggesting that a collection of libraries based on the full set of 20 scaffolds increases the potential to identify efficiently peptide binders to a protein target in a drug discovery program.

From Globular Clusters to Tidal Dwarfs: Structure Formation in the Tidal Tails of Merging Pairs

NASA Astrophysics Data System (ADS)

Knierman, K. A.; Gallagher, S. C.; Charlton, J. C.; Hunsberger, S. D.; Whitmore, B. C.; Kundu, A.; Hibbard, J. E.; Zaritsky, D. F.

2001-05-01

Using V and I images obtained with the Wide Field Planetary Camera 2 (WFPC2) of the Hubble Space Telescope, we investigate compact stellar structures within tidal tails. Six regions of tidal debris in the four classic ``Toomre Sequence'' mergers: NGC 4038/9 (``Antennae''), NGC 3256, NGC 3921, and NGC 7252 (``Atoms for Peace'') have been studied in order to explore how the star formation depends upon the local and global physical conditions. These mergers sample a range of stages in the evolutionary sequence, and include HI--rich and HI--poor environments. The six tails are found to contain a variety of stellar structures, with sizes ranging from those of globular clusters up to those of dwarf galaxies. From V and I WFPC2 images, we measure the luminosities and colors of the star clusters. NGC 3256 is found to have a large population of young clusters lying along both tails, similar to those found in the inner region of the merger. In contrast, NGC 4038/9 has no clusters in the observed region of the tail, only less luminous point sources likely to be individual stars. NGC 3921 and NGC 7252 have small populations of clusters that are concentrated in certain regions of the tail, and particularly in the prominent tidal dwarfs in the eastern and western tails of NGC 7252. The two cluster--rich tails of NGC 3256 are not distinguished from the others by their ages or by their total HI masses. We acknowledge support from NASA through STScI, and from NSF for an REU supplement for Karen Knierman.

Trophic Status Controls Mercury Methylation Pathways in Northern Peats

NASA Astrophysics Data System (ADS)

Hines, M. E.; Zhang, L.; Barkay, T.; Krabbenhoft, D. P.; Schaefer, J.; Hu, H.; Sidelinger, W.; Liu, X.; Wang, Y.

2015-12-01

Methyl mercury (MeHg) can be produced by a variety of microbes including syntrophs, methanogens, acetogens, and fermenters, besides sulfate (SO42-, SRB) and iron- reducing bacteria. Many freshwater wetlands are deficient in electron acceptors that support the traditional respiratory pathways of methylation, yet they accumulate high levels of MeHg. To investigate methylation in these wetlands and to connect these pathways with vegetation and microbial communities, incubation experiments were conducted using peats from 26 sites in Alaska. The sites were clustered using multiple factor analysis based on pH, temp, CH4 and volatile fatty acids production rates, and surface vegetation composition. Three clusters were generated and corresponded to three trophic levels that were manifested by three pH levels (3.5, 4.5, and 5). Hg methylation activity in laboratory incubations was determined using the short-lived radioisotope 197Hg. In the low pH, Sphagnum-dominated cluster, methylation rates were less than 1% day-1 and likely conducted by primary fermenters. Conversely, the high pH trophic cluster dominated by Carex aquatilis and active syntrophy exhibited Hg methylation rates as high as 12% day-1. In intermediate sites, rich in Sphagnum magellanicum with less Carex, a gradient in syntrophy and Hg methylation paths was observed. Amendments with process-stimulators and inhibitors revealed no evidence of SO42- reduction, but suggested that SRB, metabolizing either syntrophically with methanogens and/or by fermentation, likely methylated Hg. While on going metatranscriptomics studies are required to verify the role of syntrophs, fermenters, and methanogens as methylators, these results revealed that Hg methylation pathways change greatly along trophic gradients with a dominance of respiratory pathways in mineral-rich sites, syntrophy dominance in intermediate sites, and fermentation dominance in nutrient-poor sites.

Sequencing rare marine actinomycete genomes reveals high density of unique natural product biosynthetic gene clusters.

PubMed

Schorn, Michelle A; Alanjary, Mohammad M; Aguinaldo, Kristen; Korobeynikov, Anton; Podell, Sheila; Patin, Nastassia; Lincecum, Tommie; Jensen, Paul R; Ziemert, Nadine; Moore, Bradley S

2016-12-01

Traditional natural product discovery methods have nearly exhausted the accessible diversity of microbial chemicals, making new sources and techniques paramount in the search for new molecules. Marine actinomycete bacteria have recently come into the spotlight as fruitful producers of structurally diverse secondary metabolites, and remain relatively untapped. In this study, we sequenced 21 marine-derived actinomycete strains, rarely studied for their secondary metabolite potential and under-represented in current genomic databases. We found that genome size and phylogeny were good predictors of biosynthetic gene cluster diversity, with larger genomes rivalling the well-known marine producers in the Streptomyces and Salinispora genera. Genomes in the Micrococcineae suborder, however, had consistently the lowest number of biosynthetic gene clusters. By networking individual gene clusters into gene cluster families, we were able to computationally estimate the degree of novelty each genus contributed to the current sequence databases. Based on the similarity measures between all actinobacteria in the Joint Genome Institute's Atlas of Biosynthetic gene Clusters database, rare marine genera show a high degree of novelty and diversity, with Corynebacterium, Gordonia, Nocardiopsis, Saccharomonospora and Pseudonocardia genera representing the highest gene cluster diversity. This research validates that rare marine actinomycetes are important candidates for exploration, as they are relatively unstudied, and their relatives are historically rich in secondary metabolites.

Sequencing rare marine actinomycete genomes reveals high density of unique natural product biosynthetic gene clusters

PubMed Central

Schorn, Michelle A.; Alanjary, Mohammad M.; Aguinaldo, Kristen; Korobeynikov, Anton; Podell, Sheila; Patin, Nastassia; Lincecum, Tommie; Jensen, Paul R.; Ziemert, Nadine

2016-01-01

Traditional natural product discovery methods have nearly exhausted the accessible diversity of microbial chemicals, making new sources and techniques paramount in the search for new molecules. Marine actinomycete bacteria have recently come into the spotlight as fruitful producers of structurally diverse secondary metabolites, and remain relatively untapped. In this study, we sequenced 21 marine-derived actinomycete strains, rarely studied for their secondary metabolite potential and under-represented in current genomic databases. We found that genome size and phylogeny were good predictors of biosynthetic gene cluster diversity, with larger genomes rivalling the well-known marine producers in the Streptomyces and Salinispora genera. Genomes in the Micrococcineae suborder, however, had consistently the lowest number of biosynthetic gene clusters. By networking individual gene clusters into gene cluster families, we were able to computationally estimate the degree of novelty each genus contributed to the current sequence databases. Based on the similarity measures between all actinobacteria in the Joint Genome Institute's Atlas of Biosynthetic gene Clusters database, rare marine genera show a high degree of novelty and diversity, with Corynebacterium, Gordonia, Nocardiopsis, Saccharomonospora and Pseudonocardia genera representing the highest gene cluster diversity. This research validates that rare marine actinomycetes are important candidates for exploration, as they are relatively unstudied, and their relatives are historically rich in secondary metabolites. PMID:27902408

A complete, multi-level conformational clustering of antibody complementarity-determining regions

PubMed Central

Nikoloudis, Dimitris; Pitts, Jim E.

2014-01-01

Classification of antibody complementarity-determining region (CDR) conformations is an important step that drives antibody modelling and engineering, prediction from sequence, directed mutagenesis and induced-fit studies, and allows inferences on sequence-to-structure relations. Most of the previous work performed conformational clustering on a reduced set of structures or after application of various structure pre-filtering criteria. In this study, it was judged that a clustering of every available CDR conformation would produce a complete and redundant repertoire, increase the number of sequence examples and allow better decisions on structure validity in the future. In order to cope with the potential increase in data noise, a first-level statistical clustering was performed using structure superposition Root-Mean-Square Deviation (RMSD) as a distance-criterion, coupled with second- and third-level clustering that employed Ramachandran regions for a deeper qualitative classification. The classification of a total of 12,712 CDR conformations is thus presented, along with rich annotation and cluster descriptions, and the results are compared to previous major studies. The present repertoire has procured an improved image of our current CDR Knowledge-Base, with a novel nesting of conformational sensitivity and specificity that can serve as a systematic framework for improved prediction from sequence as well as a number of future studies that would aid in knowledge-based antibody engineering such as humanisation. PMID:25071986

UIT ultraviolet imaging of 30 Doradus

NASA Technical Reports Server (NTRS)

Hintzen, P.; Cheng, K.-P.; Michalitsianos, A.; Bohlin, R.; O'Connell, R.; Cornett, R.; Roberts, M.; Smith, A.; Smith, E.; Stecher, T.

1992-01-01

During the Astro-1 mission, near- and far-UV images of the 30 Doradus region were obtained using the Ultraviolet Imaging Telescope (UIT). These wide-field, 40 min in diameter, high spatial resolution, 2-3 sec, UIT UV images reveal a rich field of luminous UV-bright stars, clusters, and associations. There are 181 stars brighter than m(sub 2558A) = 16.5 and 197 stars brighter than m(sub 1615A) = 16.4 within 3 min diameter of the 30 Doradus central cluster. We have derived UV fluxes emitted from the 30 Doradus central cluster and from its UV bright core, R136. The region within 5 sec of R136 produces approximately 14% of the far-UV flux (lambda = 1892 A) and approximately 16% of the near-UV flux (lambda = 2558 A) emitted from the 3 min diameter central cluster. The derived UV luminosity of R136 at 1892 A is only 7.8 times that of the nearby O6-7 Iaf star, R139, and the m(sub 1892) - m(sub v) colors of R136 are similar to other O or Wolf-Rayet stars in the same region. These UIT data, combined with other published observations at longer wavelengths, indicate that there is no observational evidence for a supermassive star in R136.

UIT ultraviolet imaging of 30 Doradus

NASA Astrophysics Data System (ADS)

Hintzen, P.; Cheng, K.-P.; Michalitsianos, A.; Bohlin, R.; O'Connell, R.; Cornett, R.; Roberts, M.; Smith, A.; Smith, E.; Stecher, T.

During the Astro-1 mission, near- and far-UV images of the 30 Doradus region were obtained using the Ultraviolet Imaging Telescope (UIT). These wide-field, 40 min in diameter, high spatial resolution, 2-3 sec, UIT UV images reveal a rich field of luminous UV-bright stars, clusters, and associations. There are 181 stars brighter than m2558A = 16.5 and 197 stars brighter than m1615A = 16.4 within 3 min diameter of the 30 Doradus central cluster. We have derived UV fluxes emitted from the 30 Doradus central cluster and from its UV bright core, R136. The region within 5 sec of R136 produces approximately 14% of the far-UV flux (lambda = 1892 A) and approximately 16% of the near-UV flux (lambda = 2558 A) emitted from the 3 min diameter central cluster. The derived UV luminosity of R136 at 1892 A is only 7.8 times that of the nearby O6-7 Iaf star, R139, and the m1892 - mv colors of R136 are similar to other O or Wolf-Rayet stars in the same region. These UIT data, combined with other published observations at longer wavelengths, indicate that there is no observational evidence for a supermassive star in R136.

Conserved noncoding sequences (CNSs) in higher plants.

PubMed

Freeling, Michael; Subramaniam, Shabarinath

2009-04-01

Plant conserved noncoding sequences (CNSs)--a specific category of phylogenetic footprint--have been shown experimentally to function. No plant CNS is conserved to the extent that ultraconserved noncoding sequences are conserved in vertebrates. Plant CNSs are enriched in known transcription factor or other cis-acting binding sites, and are usually clustered around genes. Genes that encode transcription factors and/or those that respond to stimuli are particularly CNS-rich. Only rarely could this function involve small RNA binding. Some transcribed CNSs encode short translation products as a form of negative control. Approximately 4% of Arabidopsis gene content is estimated to be both CNS-rich and occupies a relatively long stretch of chromosome: Bigfoot genes (long phylogenetic footprints). We discuss a 'DNA-templated protein assembly' idea that might help explain Bigfoot gene CNSs.

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

NASA Technical Reports Server (NTRS)

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

Nitrous Oxide Reductase (nosZ) Gene Fragments Differ between Native and Cultivated Michigan Soils

PubMed Central

Stres, Blaž; Mahne, Ivan; Avguštin, Gorazd; Tiedje, James M.

2004-01-01

The effect of standard agricultural management on the genetic heterogeneity of nitrous oxide reductase (nosZ) fragments from denitrifying prokaryotes in native and cultivated soil was explored. Thirty-six soil cores were composited from each of the two soil management conditions. nosZ gene fragments were amplified from triplicate samples, and PCR products were cloned and screened by restriction fragment length polymorphism (RFLP). The total nosZ RFLP profiles increased in similarity with soil sample size until triplicate 3-g samples produced visually identical RFLP profiles for each treatment. Large differences in total nosZ profiles were observed between the native and cultivated soils. The fragments representing major groups of clones encountered at least twice and four randomly selected clones with unique RFLP patterns were sequenced to verify nosZ identity. The sequence diversity of nosZ clones from the cultivated field was higher, and only eight patterns were found in clone libraries from both soils among the 182 distinct nosZ RFLP patterns identified from the two soils. A group of clones that comprised 32% of all clones dominated the gene library of native soil, whereas many minor groups were observed in the gene library of cultivated soil. The 95% confidence intervals of the Chao1 nonparametric richness estimator for nosZ RFLP data did not overlap, indicating that the levels of species richness are significantly different in the two soils, the cultivated soil having higher diversity. Phylogenetic analysis of deduced amino acid sequences grouped the majority of nosZ clones into an interleaved Michigan soil cluster whose cultured members are α-Proteobacteria. Only four nosZ sequences from cultivated soil and one from the native soil were related to sequences found in γ-Proteobacteria. Sequences from the native field formed a distinct, closely related cluster (Dmean = 0.16) containing 91.6% of the native clones. Clones from the cultivated field were more distantly related to each other (Dmean = 0.26), and 65% were found outside of the cluster from the native soil, further indicating a difference in the two communities. Overall, there appears to be a relationship between use and richness, diversity, and the phylogenetic position of nosZ sequences, indicating that agricultural use of soil caused a shift to a more diverse denitrifying community. PMID:14711656

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.

Genome sequencing reveals complex secondary metabolome in themarine actinomycete Salinispora tropica

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

Udwary, Daniel W.; Zeigler, Lisa; Asolkar, Ratnakar

2007-05-01

Recent fermentation studies have identified actinomycetes ofthe marine-dwelling genus Salinispora as prolific natural productproducers. To further evaluate their biosynthetic potential, we analyzedall identifiable secondary natural product gene clusters from therecently sequenced 5,184,724 bp S. tropica CNB-440 circular genome. Ouranalysis shows that biosynthetic potential meets or exceeds that shown byprevious Streptomyces genome sequences as well as other naturalproduct-producing actinomycetes. The S. tropica genome features ninepolyketide synthase systems of every known formally classified family,non-ribosomal peptide synthetases and several hybrid clusters. While afew clusters appear to encode molecules previously identified inStreptomyces species,the majority of the 15 biosynthetic loci are novel.Specific chemical information aboutmore » putative and observed natural productmolecules is presented and discussed. In addition, our bioinformaticanalysis was critical for the structure elucidation of the novelpolyenemacrolactam salinilactam A. This study demonstrates the potentialfor genomic analysis to complement and strengthen traditional naturalproduct isolation studies and firmly establishes the genus Salinispora asa rich source of novel drug-like molecules.« less

Weak lensing magnification of SpARCS galaxy clusters

NASA Astrophysics Data System (ADS)

Tudorica, A.; Hildebrandt, H.; Tewes, M.; Hoekstra, H.; Morrison, C. B.; Muzzin, A.; Wilson, G.; Yee, H. K. C.; Lidman, C.; Hicks, A.; Nantais, J.; Erben, T.; van der Burg, R. F. J.; Demarco, R.

2017-12-01

Context. Measuring and calibrating relations between cluster observables is critical for resource-limited studies. The mass-richness relation of clusters offers an observationally inexpensive way of estimating masses. Its calibration is essential for cluster and cosmological studies, especially for high-redshift clusters. Weak gravitational lensing magnification is a promising and complementary method to shear studies, that can be applied at higher redshifts. Aims: We aim to employ the weak lensing magnification method to calibrate the mass-richness relation up to a redshift of 1.4. We used the Spitzer Adaptation of the Red-Sequence Cluster Survey (SpARCS) galaxy cluster candidates (0.2 < z < 1.4) and optical data from the Canada France Hawaii Telescope (CFHT) to test whether magnification can be effectively used to constrain the mass of high-redshift clusters. Methods: Lyman-break galaxies (LBGs) selected using the u-band dropout technique and their colours were used as a background sample of sources. LBG positions were cross-correlated with the centres of the sample of SpARCS clusters to estimate the magnification signal, which was optimally-weighted using an externally-calibrated LBG luminosity function. The signal was measured for cluster sub-samples, binned in both redshift and richness. Results: We measured the cross-correlation between the positions of galaxy cluster candidates and LBGs and detected a weak lensing magnification signal for all bins at a detection significance of 2.6-5.5σ. In particular, the significance of the measurement for clusters with z> 1.0 is 4.1σ; for the entire cluster sample we obtained an average M200 of 1.28 -0.21+0.23 × 1014 M⊙. Conclusions: Our measurements demonstrated the feasibility of using weak lensing magnification as a viable tool for determining the average halo masses for samples of high redshift galaxy clusters. The results also established the success of using galaxy over-densities to select massive clusters at z > 1. Additional studies are necessary for further modelling of the various systematic effects we discussed.

Effects of Vegetation Composition and Trophic Structure on Pathways of Mercury Methylation in Alaskan Peatlands

NASA Astrophysics Data System (ADS)

Hines, M. E.; Zhang, L.; Barkay, T.; Krabbenhoft, D. P.; Liu, X.

2016-12-01

Methyl mercury (MeHg) can be produced by diverse microbes including syntrophs, methanogens, and fermenters, besides sulfate (SO42-, SRB) and iron- reducing bacteria. Many freshwater wetlands are deficient in electron acceptors that support the traditional respiratory pathways of methylation, yet high levels of MeHg can accumulate. To investigate methylation pathways in these wetlands and to connect these pathways with surface vegetation and microbial communities, experiments were conducted using peats from 28 sites in Alaska collected during the summer of 2015. The sites were clustered using multiple factor analysis based on pH, temp, CH4 and volatile fatty acids production rates, and surface vegetation composition. Three clusters were generated and corresponded to three trophic levels that were manifested by three pH levels (4.2, 5.3, and 5.8). Hg methylation activity in laboratory incubations was determined using the short-lived radioisotope 197Hg. In the low pH, Sphagnum fuscum dominated cluster, methylation rates were less than 0.1% day-1. Conversely, the high pH trophic cluster dominated by Carex aquatilis, Carex tenuiflora, and active syntrophy, exhibited Hg methylation rates as high as 10% day-1. In intermediate sites, rich in Sphagnum magellanicum with less Carex, a gradient in syntrophy and Hg methylation paths was observed. Amendments with SO42- showed very active sulfate reduction but no stimulation of methylation; another set of amendments with methanogenic inhibitors greatly reduced methylation rates at intermediate and high trophic clusters. These results suggested that SRB, metabolizing either syntrophically with methanogens and/or by fermentation, likely methylated Hg. While metatranscriptomics studies are being conducted to verify the role of syntrophs, fermenters, and methanogens as methylators, these incubation results revealed that Hg methylation pathways change greatly along trophic gradients with a dominance of respiratory pathways in rich fens, syntrophy dominance in intermediate sites, and fermentation dominance in poor bogs.

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

A multicomponent matched filter cluster confirmation tool for eROSITA: initial application to the RASS and DES-SV data sets

NASA Astrophysics Data System (ADS)

Klein, M.; Mohr, J. J.; Desai, S.; Israel, H.; Allam, S.; Benoit-Lévy, A.; Brooks, D.; Buckley-Geer, E.; Carnero Rosell, A.; Carrasco Kind, M.; Cunha, C. E.; da Costa, L. N.; Dietrich, J. P.; Eifler, T. F.; Evrard, A. E.; Frieman, J.; Gruen, D.; Gruendl, R. A.; Gutierrez, G.; Honscheid, K.; James, D. J.; Kuehn, K.; Lima, M.; Maia, M. A. G.; March, M.; Melchior, P.; Menanteau, F.; Miquel, R.; Plazas, A. A.; Reil, K.; Romer, A. K.; Sanchez, E.; Santiago, B.; Scarpine, V.; Schubnell, M.; Sevilla-Noarbe, I.; Smith, M.; Soares-Santos, M.; Sobreira, F.; Suchyta, E.; Swanson, M. E. C.; Tarle, G.; Collaboration, the DES

2018-03-01

We describe a multicomponent matched filter (MCMF) cluster confirmation tool designed for the study of large X-ray source catalogues produced by the upcoming X-ray all-sky survey mission eROSITA. We apply the method to confirm a sample of 88 clusters with redshifts 0.05 < z < 0.8 in the recently published 2RXS catalogue from the ROSAT All-Sky Survey (RASS) over the 208 deg2 region overlapped by the Dark Energy Survey (DES) Science Verification (DES-SV) data set. In our pilot study, we examine all X-ray sources, regardless of their extent. Our method employs a multicolour red sequence (RS) algorithm that incorporates the X-ray count rate and peak position in determining the region of interest for follow-up and extracts the positionally and colour-weighted optical richness λMCMF as a function of redshift for each source. Peaks in the λMCMF-redshift distribution are identified and used to extract photometric redshifts, richness and uncertainties. The significances of all optical counterparts are characterized using the distribution of richnesses defined along random lines of sight. These significances are used to extract cluster catalogues and to estimate the contamination by random superpositions of unassociated optical systems. The delivered photometric redshift accuracy is δz/(1 + z) = 0.010. We find a well-defined X-ray luminosity-λMCMF relation with an intrinsic scatter of δln (λMCMF|Lx) = 0.21. Matching our catalogue with the DES-SV redMaPPer catalogue yields good agreement in redshift and richness estimates; comparing our catalogue with the South Pole Telescope (SPT) selected clusters shows no inconsistencies. SPT clusters in our data set are consistent with the high-mass extension of the RASS-based λMCMF-mass relation.

The redMaPPer Galaxy Cluster Catalog From DES Science Verification Data

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

Rykoff, E. S.

We describe updates to the redMaPPer algorithm, a photometric red-sequence cluster finder specifically designed for large photometric surveys. The updated algorithm is applied tomore » $$150\\,\\mathrm{deg}^2$$ of Science Verification (SV) data from the Dark Energy Survey (DES), and to the Sloan Digital Sky Survey (SDSS) DR8 photometric data set. The DES SV catalog is locally volume limited, and contains 786 clusters with richness $$\\lambda>20$$ (roughly equivalent to $$M_{\\mathrm{500c}}\\gtrsim10^{14}\\,h_{70}^{-1}\\,M_{\\odot}$$) and 0.2 < $z$ <0.9. The DR8 catalog consists of 26311 clusters with 0.08 < $z$ < 0.6, with a sharply increasing richness threshold as a function of redshift for $$z\\gtrsim 0.35$$. The photometric redshift performance of both catalogs is shown to be excellent, with photometric redshift uncertainties controlled at the $$\\sigma_z/(1+z)\\sim 0.01$$ level for $$z\\lesssim0.7$$, rising to $$\\sim0.02$$ at $$z\\sim0.9$$ in DES SV. We make use of $Chandra$ and $XMM$ X-ray and South Pole Telescope Sunyaev-Zeldovich data to show that the centering performance and mass--richness scatter are consistent with expectations based on prior runs of redMaPPer on SDSS data. We also show how the redMaPPer photo-$z$ and richness estimates are relatively insensitive to imperfect star/galaxy separation and small-scale star masks.« less

Horizontal gene transfer from Bacteria to rumen Ciliates indicates adaptation to their anaerobic, carbohydrates-rich environment

PubMed Central

Ricard, Guénola; McEwan, Neil R; Dutilh, Bas E; Jouany, Jean-Pierre; Macheboeuf, Didier; Mitsumori, Makoto; McIntosh, Freda M; Michalowski, Tadeusz; Nagamine, Takafumi; Nelson, Nancy; Newbold, Charles J; Nsabimana, Eli; Takenaka, Akio; Thomas, Nadine A; Ushida, Kazunari; Hackstein, Johannes HP; Huynen, Martijn A

2006-01-01

Background The horizontal transfer of expressed genes from Bacteria into Ciliates which live in close contact with each other in the rumen (the foregut of ruminants) was studied using ciliate Expressed Sequence Tags (ESTs). More than 4000 ESTs were sequenced from representatives of the two major groups of rumen Cilates: the order Entodiniomorphida (Entodinium simplex, Entodinium caudatum, Eudiplodinium maggii, Metadinium medium, Diploplastron affine, Polyplastron multivesiculatum and Epidinium ecaudatum) and the order Vestibuliferida, previously called Holotricha (Isotricha prostoma, Isotricha intestinalis and Dasytricha ruminantium). Results A comparison of the sequences with the completely sequenced genomes of Eukaryotes and Prokaryotes, followed by large-scale construction and analysis of phylogenies, identified 148 ciliate genes that specifically cluster with genes from the Bacteria and Archaea. The phylogenetic clustering with bacterial genes, coupled with the absence of close relatives of these genes in the Ciliate Tetrahymena thermophila, indicates that they have been acquired via Horizontal Gene Transfer (HGT) after the colonization of the gut by the rumen Ciliates. Conclusion Among the HGT candidates, we found an over-representation (>75%) of genes involved in metabolism, specifically in the catabolism of complex carbohydrates, a rich food source in the rumen. We propose that the acquisition of these genes has greatly facilitated the Ciliates' colonization of the rumen providing evidence for the role of HGT in the adaptation to new niches. PMID:16472398

Horizontal gene transfer from Bacteria to rumen Ciliates indicates adaptation to their anaerobic, carbohydrates-rich environment.

PubMed

Ricard, Guénola; McEwan, Neil R; Dutilh, Bas E; Jouany, Jean-Pierre; Macheboeuf, Didier; Mitsumori, Makoto; McIntosh, Freda M; Michalowski, Tadeusz; Nagamine, Takafumi; Nelson, Nancy; Newbold, Charles J; Nsabimana, Eli; Takenaka, Akio; Thomas, Nadine A; Ushida, Kazunari; Hackstein, Johannes H P; Huynen, Martijn A

2006-02-10

The horizontal transfer of expressed genes from Bacteria into Ciliates which live in close contact with each other in the rumen (the foregut of ruminants) was studied using ciliate Expressed Sequence Tags (ESTs). More than 4000 ESTs were sequenced from representatives of the two major groups of rumen Cilates: the order Entodiniomorphida (Entodinium simplex, Entodinium caudatum, Eudiplodinium maggii, Metadinium medium, Diploplastron affine, Polyplastron multivesiculatum and Epidinium ecaudatum) and the order Vestibuliferida, previously called Holotricha (Isotricha prostoma, Isotricha intestinalis and Dasytricha ruminantium). A comparison of the sequences with the completely sequenced genomes of Eukaryotes and Prokaryotes, followed by large-scale construction and analysis of phylogenies, identified 148 ciliate genes that specifically cluster with genes from the Bacteria and Archaea. The phylogenetic clustering with bacterial genes, coupled with the absence of close relatives of these genes in the Ciliate Tetrahymena thermophila, indicates that they have been acquired via Horizontal Gene Transfer (HGT) after the colonization of the gut by the rumen Ciliates. Among the HGT candidates, we found an over-representation (>75%) of genes involved in metabolism, specifically in the catabolism of complex carbohydrates, a rich food source in the rumen. We propose that the acquisition of these genes has greatly facilitated the Ciliates' colonization of the rumen providing evidence for the role of HGT in the adaptation to new niches.

SOFIA/FORCAST Observations of the Arched Filamentary Region in the Galactic Center

NASA Astrophysics Data System (ADS)

Hankins, Matthew; Lau, Ryan M.; Morris, Mark; Herter, Terry L.

2016-06-01

Abstract: We present 19.7, 25.2, 31.5, and 37.1 μm maps of the Thermal Arched Filament region in the Galactic Center taken with the Faint Object Infrared Camera for the SOFIA Telescope (FORCAST) with an angular resolution of 3.2-3.8". We calculate the integrated infrared luminosity of the Arched Filaments and show that they are consistent with being heated by the nearby Arches cluster. Additionally, using our observations, we infer dust temperatures (75 - 90 K) across the Arched Filaments which are remarkably consistent over large spatial scales (˜ 25 pc). We discuss the possible geometric effects needed to recreate this temperature structure. Additionally, we compare the observed morphology of the Arches in the FORCAST maps with the Paschen-α emission in the region to study what fraction of the infrared emission may be coming from dust in the HII region versus the PDR beneath it. Finally, we use Spitzer/IRAC 8 μm data to look for spatial variations in PAH abundance in the rich UV environment of the young (~2-4 Myr) and massive Arches cluster.

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

antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences.

PubMed

Medema, Marnix H; Blin, Kai; Cimermancic, Peter; de Jager, Victor; Zakrzewski, Piotr; Fischbach, Michael A; Weber, Tilmann; Takano, Eriko; Breitling, Rainer

2011-07-01

Bacterial and fungal secondary metabolism is a rich source of novel bioactive compounds with potential pharmaceutical applications as antibiotics, anti-tumor drugs or cholesterol-lowering drugs. To find new drug candidates, microbiologists are increasingly relying on sequencing genomes of a wide variety of microbes. However, rapidly and reliably pinpointing all the potential gene clusters for secondary metabolites in dozens of newly sequenced genomes has been extremely challenging, due to their biochemical heterogeneity, the presence of unknown enzymes and the dispersed nature of the necessary specialized bioinformatics tools and resources. Here, we present antiSMASH (antibiotics & Secondary Metabolite Analysis Shell), the first comprehensive pipeline capable of identifying biosynthetic loci covering the whole range of known secondary metabolite compound classes (polyketides, non-ribosomal peptides, terpenes, aminoglycosides, aminocoumarins, indolocarbazoles, lantibiotics, bacteriocins, nucleosides, beta-lactams, butyrolactones, siderophores, melanins and others). It aligns the identified regions at the gene cluster level to their nearest relatives from a database containing all other known gene clusters, and integrates or cross-links all previously available secondary-metabolite specific gene analysis methods in one interactive view. antiSMASH is available at http://antismash.secondarymetabolites.org.

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.

Copper Sensing Function of Drosophila Metal-Responsive Transcription Factor-1 Is Mediated By a Tetranuclear Cu(I) Cluster

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

Chen, X.; Hua, H.; Balamurugan, K.

2009-05-12

Drosophila melanogaster MTF-1 (dMTF-1) is a copper-responsive transcriptional activator that mediates resistance to Cu, as well as Zn and Cd. Here, we characterize a novel cysteine-rich domain which is crucial for sensing excess intracellular copper by dMTF-1. Transgenic flies expressing mutant dMTF-1 containing alanine substitutions of two, four or six cysteine residues within the sequence {sup 547}CNCTNCKCDQTKSCHGGDC{sup 565} are significantly or completely impaired in their ability to protect flies from copper toxicity and fail to up-regulate MtnA (metallothionein) expression in response to excess Cu. In contrast, these flies exhibit wild-type survival in response to copper deprivation thus revealing that themore » cysteine cluster domain is required only for sensing Cu load by dMTF-1. Parallel studies show that the isolated cysteine cluster domain is required to protect a copper-sensitive S. cerevisiae ace1 strain from copper toxicity. Cu(I) ligation by a Cys-rich domain peptide fragment drives the cooperative assembly of a polydentate [Cu{sub 4}-S{sub 6}] cage structure, characterized by a core of trigonally S{sub 3} coordinated Cu(I) ions bound by bridging thiolate ligands. While reminiscent of Cu{sub 4}-L{sub 6} (L = ligand) tetranuclear clusters in copper regulatory transcription factors of yeast, the absence of significant sequence homology is consistent with convergent evolution of a sensing strategy particularly well suited for Cu(I).« less

Topology characterization of a benzodiazepine-binding beta-rich domain of the GABAA receptor alpha1 subunit.

PubMed

Xu, Zhiwen; Fang, Shisong; Shi, Haifeng; Li, Hoiming; Deng, Yiqun; Liao, Yinglei; Wu, Jiun-Ming; Zheng, Hui; Zhu, Huaimin; Chen, Hueih-Min; Tsang, Shui Ying; Xue, Hong

2005-10-01

Structural investigation of GABAA receptors has been limited by difficulties imposed by its trans-membrane-complex nature. In the present study, the topology of a membrane-proximal beta-rich (MPB) domain in the C139-L269 segment of the receptor alpha1 subunit was probed by mapping the benzodiazepine (BZ)-binding and epitopic sites, as well as fluorescence resonance energy transfer (FRET) analysis. Ala-scanning and semiconservative substitutions within this segment revealed the contribution of the phenyl rings of Y160 and Y210, the hydroxy group of S186 and the positive charge on R187 to BZ-binding. FRET with the bound BZ ligand indicated the proximity of Y160, S186, R187, and S206 to the BZ-binding site. On the other hand, epitope-mapping using the monoclonal antibodies (mAbs) against the MPB domain established a clustering of T172, R173, E174, Q196, and T197. Based on the lack of FRET between Trp substitutionally placed at R173 or V198 and bound BZ, this epitope-mapped cluster is located on a separate end of the folded protein from the BZ-binding site. Mutations of the five conserved Cys and Trp residues in the MPB domain gave rise to synergistic and rescuing effects on protein secondary structures and unfolding stability that point to a CCWCW-pentad, reminiscent to the CWC-triad "pin" of immunoglobulin (Ig)-like domains, important for the structural maintenance. These findings, together with secondary structure and fold predictions suggest an anti-parallel beta-strand topology with resemblance to Ig-like fold, having the BZ-binding and the epitopic residues being clustered at two different ends of the fold.

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.

[Diversity of beta-proteobacterial ammonia-oxidizing bacteria and ammonia-oxidizing archaea in shrimp farm sediment].

PubMed

Gao, Lihai; Lin, Weitie

2011-01-01

In order to study the diversity of ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) in shrimp farm sediment. Total microbial DNA was directly extracted from the shrimp farm sediment. The clone library of amoA genes were constructed with beta-Proteobacterial-AOB and AOA specific primers. The library was screened by PCR-restriction fragment length polymorphism (RFLP) analysis and clones with unique RFLP patterns were sequenced. Phylogenetic analyses of the amoA gene fragments showed that all AOB sequences from shrimp farm sediment were affiliated with Nitrosomonas (61.54%) or Nitrosomonas-like (38. 46%) species and grouped into Nitrosomonas communis cluster, Nitrosomonas sp. Nm148 cluster, Nitrosomonas oligotropha cluster. All AOA sequences belonged to the kingdom Crenarchaeote except that one Operational Taxa Unit (OTU) sequence was Unclassified-Archaea and fell within cluster S (soil origin). AOB and AOA species composition included 13 OTUs and 9 OTUs. The clone coverage of bacterial and archaeal amoA genes was 73.47% and 90.43%. The Shannon-Wiener index, Evenness index, Simpson index and Richness index of AOB were higher than those of AOA. These findings represent the first detailed examination of archaeal amoA diversity in shrimp farm sediment and demonstrate that diverse communities of Crenarchaeote capable of ammonia oxidation are present within shrimp farm sediment, where they may be actively involved in nitrification.

The white-dwarf cooling sequence of NGC 6791: a unique tool for stellar evolution

NASA Astrophysics Data System (ADS)

García-Berro, E.; Torres, S.; Renedo, I.; Camacho, J.; Althaus, L. G.; Córsico, A. H.; Salaris, M.; Isern, J.

2011-09-01

Context. NGC 6791 is a well-studied, metal-rich open cluster that is so close to us that it can be imaged down to luminosities fainter than that of the termination of its white-dwarf cooling sequence, thus allowing for an in-depth study of its white dwarf population. Aims: White dwarfs carry important information about the history of the cluster. We use observations of the white-dwarf cooling sequence to constrain important properties of the cluster stellar population, such as the existence of a putative population of massive helium-core white dwarfs, and the properties of a large population of unresolved binary white dwarfs. We also investigate the use of white dwarfs to disclose the presence of cluster subpopulations with a different initial chemical composition, and we obtain an upper bound to the fraction of hydrogen-deficient white dwarfs. Methods: We use a Monte Carlo simulator that employs up-to-date evolutionary cooling sequences for white dwarfs with hydrogen-rich and hydrogen-deficient atmospheres, with carbon-oxygen and helium cores. The cooling sequences for carbon-oxygen cores account for the delays introduced by both 22Ne sedimentation in the liquid phase and by carbon-oxygen phase separation upon crystallization. Results: We do not find evidence for a substantial fraction of helium-core white dwarfs, and hence our results support the suggestion that the origin of the bright peak of the white-dwarf luminosity function can only be attributed to a population of unresolved binary white dwarfs. Moreover, our results indicate that if this hypothesis is at the origin of the bright peak, the number distribution of secondary masses of the population of unresolved binaries has to increase with increasing mass ratio between the secondary and primary components of the progenitor system. We also find that the observed cooling sequence appears to be able to constrain the presence of progenitor subpopulations with different chemical compositions and the fraction of hydrogen-deficient white dwarfs. Conclusions: Our simulations place interesting constraints on important characteristics of the stellar populations of NGC 6791. In particular, we find that the fraction of single helium-core white dwarfs must be smaller than 5%, that a subpopulation of stars with zero metallicity must be ≲12%, while if the adopted metallicity of the subpopulation is solar the upper limit is ~8%. Finally, we also find that the fraction of hydrogen-deficient white dwarfs in this particular cluster is surprinsingly small (≲6%).

THE SWIFT AGN AND CLUSTER SURVEY. II. CLUSTER CONFIRMATION WITH SDSS DATA

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

Griffin, Rhiannon D.; Dai, Xinyu; Kochanek, Christopher S.

2016-01-15

We study 203 (of 442) Swift AGN and Cluster Survey extended X-ray sources located in the SDSS DR8 footprint to search for galaxy over-densities in three-dimensional space using SDSS galaxy photometric redshifts and positions near the Swift cluster candidates. We find 104 Swift clusters with a >3σ galaxy over-density. The remaining targets are potentially located at higher redshifts and require deeper optical follow-up observations for confirmation as galaxy clusters. We present a series of cluster properties including the redshift, brightest cluster galaxy (BCG) magnitude, BCG-to-X-ray center offset, optical richness, and X-ray luminosity. We also detect red sequences in ∼85% ofmore » the 104 confirmed clusters. The X-ray luminosity and optical richness for the SDSS confirmed Swift clusters are correlated and follow previously established relations. The distribution of the separations between the X-ray centroids and the most likely BCG is also consistent with expectation. We compare the observed redshift distribution of the sample with a theoretical model, and find that our sample is complete for z ≲ 0.3 and is still 80% complete up to z ≃ 0.4, consistent with the SDSS survey depth. These analysis results suggest that our Swift cluster selection algorithm has yielded a statistically well-defined cluster sample for further study of cluster evolution and cosmology. We also match our SDSS confirmed Swift clusters to existing cluster catalogs, and find 42, 23, and 1 matches in optical, X-ray, and Sunyaev–Zel’dovich catalogs, respectively, and so the majority of these clusters are new detections.« less

K2: A NEW METHOD FOR THE DETECTION OF GALAXY CLUSTERS BASED ON CANADA-FRANCE-HAWAII TELESCOPE LEGACY SURVEY MULTICOLOR IMAGES

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

Thanjavur, Karun; Willis, Jon; Crampton, David, E-mail: karun@uvic.c

2009-11-20

We have developed a new method, K2, optimized for the detection of galaxy clusters in multicolor images. Based on the Red Sequence approach, K2 detects clusters using simultaneous enhancements in both colors and position. The detection significance is robustly determined through extensive Monte Carlo simulations and through comparison with available cluster catalogs based on two different optical methods, and also on X-ray data. K2 also provides quantitative estimates of the candidate clusters' richness and photometric redshifts. Initially, K2 was applied to the two color (gri) 161 deg{sup 2} images of the Canada-France-Hawaii Telescope Legacy Survey Wide (CFHTLS-W) data. Our simulationsmore » show that the false detection rate for these data, at our selected threshold, is only approx1%, and that the cluster catalogs are approx80% complete up to a redshift of z = 0.6 for Fornax-like and richer clusters and to z approx 0.3 for poorer clusters. Based on the g-, r-, and i-band photometric catalogs of the Terapix T05 release, 35 clusters/deg{sup 2} are detected, with 1-2 Fornax-like or richer clusters every 2 deg{sup 2}. Catalogs containing data for 6144 galaxy clusters have been prepared, of which 239 are rich clusters. These clusters, especially the latter, are being searched for gravitational lenses-one of our chief motivations for cluster detection in CFHTLS. The K2 method can be easily extended to use additional color information and thus improve overall cluster detection to higher redshifts. The complete set of K2 cluster catalogs, along with the supplementary catalogs for the member galaxies, are available on request from the authors.« less

THE REDMAPPER GALAXY CLUSTER CATALOG FROM DES SCIENCE VERIFICATION DATA

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

Rykoff, E. S.; Rozo, E.; Hollowood, D.

We describe updates to the redMaPPer algorithm, a photometric red-sequence cluster finder specifically designed for large photometric surveys. The updated algorithm is applied to 150 deg(2) of Science Verification (SV) data from the Dark Energy Survey (DES), and to the Sloan Digital Sky Survey (SDSS) DR8 photometric data set. The DES SV catalog is locally volume limited and contains 786 clusters with richness lambda > 20 (roughly equivalent to M500c greater than or similar to 10(14) h(70)(-1)M(circle dot)) and 0.2 < z < 0.9. The DR8 catalog consists of 26,311 clusters with 0.08 < z < 0.6, with a sharplymore » increasing richness threshold as a function of redshift for z greater than or similar to 0.35. The photometric redshift performance of both catalogs is shown to be excellent, with photometric redshift uncertainties controlled at the sigma(z)/(1+ z) similar to 0.01 level for z greater than or similar to 0.7, rising to similar to 0.02 at z similar to 0.9 in DES SV. We make use of Chandra and XMM X-ray and South Pole Telescope Sunyaev-Zeldovich data to show that the centering performance and mass-richness scatter are consistent with expectations based on prior runs of redMaPPer on SDSS data. We also show how the redMaPPer photo-z and richness estimates are relatively insensitive to imperfect star/galaxy separation and small-scale star masks.« less

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.

Generation and Analysis of Expressed Sequence Tags (ESTs) from Halophyte Atriplex canescens to Explore Salt-Responsive Related Genes

PubMed Central

Li, Jingtao; Sun, Xinhua; Yu, Gang; Jia, Chengguo; Liu, Jinliang; Pan, Hongyu

2014-01-01

Little information is available on gene expression profiling of halophyte A. canescens. To elucidate the molecular mechanism for stress tolerance in A. canescens, a full-length complementary DNA library was generated from A. canescens exposed to 400 mM NaCl, and provided 343 high-quality ESTs. In an evaluation of 343 valid EST sequences in the cDNA library, 197 unigenes were assembled, among which 190 unigenes (83.1% ESTs) were identified according to their significant similarities with proteins of known functions. All the 343 EST sequences have been deposited in the dbEST GenBank under accession numbers JZ535802 to JZ536144. According to Arabidopsis MIPS functional category and GO classifications, we identified 193 unigenes of the 311 annotations EST, representing 72 non-redundant unigenes sharing similarities with genes related to the defense response. The sets of ESTs obtained provide a rich genetic resource and 17 up-regulated genes related to salt stress resistance were identified by qRT-PCR. Six of these genes may contribute crucially to earlier and later stage salt stress resistance. Additionally, among the 343 unigenes sequences, 22 simple sequence repeats (SSRs) were also identified contributing to the study of A. canescens resources. PMID:24960361

"A Richness Study of 14 Distant X-Ray Clusters from the 160 Square Degree Survey"

NASA Technical Reports Server (NTRS)

Jones, Christine; West, Donald (Technical Monitor)

2001-01-01

We have measured the surface density of galaxies toward 14 X-ray-selected cluster candidates at redshifts z(sub i) 0.46, and we show that they are associated with rich galaxy concentrations. These clusters, having X-ray luminosities of Lx(0.5-2 keV) approx. (0.5 - 2.6) x 10(exp 44) ergs/ sec are among the most distant and luminous in our 160 deg(exp 2) ROSAT Position Sensitive Proportional Counter cluster survey. We find that the clusters range between Abell richness classes 0 and 2 and have a most probable richness class of 1. We compare the richness distribution of our distant clusters to those for three samples of nearby clusters with similar X-ray luminosities. We find that the nearby and distant samples have similar richness distributions, which shows that clusters have apparently not evolved substantially in richness since redshift z=0.5. There is, however, a marginal tendency for the distant clusters to be slightly poorer than nearby clusters, although deeper multicolor data for a large sample would be required to confirm this trend. We compare the distribution of distant X-ray clusters in the L(sub X)-richness plane to the distribution of optically selected clusters from the Palomar Distant Cluster Survey. The optically selected clusters appear overly rich for their X-ray luminosities, when compared to X-ray-selected clusters. Apparently, X-ray and optical surveys do not necessarily sample identical mass concentrations at large redshifts. This may indicate the existence of a population of optically rich clusters with anomalously low X-ray emission, More likely, however, it reflects the tendency for optical surveys to select unvirialized mass concentrations, as might be expected when peering along large-scale filaments.

Proteomic analysis of the gamma human papillomavirus type 197 E6 and E7 associated cellular proteins

PubMed Central

Grace, Miranda; Munger, Karl

2016-01-01

Gamma HPV197 was the most frequently identified HPV when human skin cancer specimens were analyzed by deep sequencing. To gain insight into the biological activities of HPV197, we investigated the cellular interactomes of HPV197 E6 and E7. HPV197 E6 protein interacts with a broad spectrum of cellular LXXLL domain proteins, including UBE3A and MAML1. HPV197 E6 also binds and inhibits the TP53 tumor suppressor and interacts with the CCR4-NOT ubiquitin ligase and deadenylation complex. Despite lacking a canonical retinoblastoma (RB1) tumor suppressor binding site, HPV197 E7 binds RB1 and activates E2F transcription. Hence, HPV197 E6 and E7 proteins interact with a similar set of cellular proteins as E6 and E7 proteins encoded by HPVs that have been linked to human carcinogenesis and/or have transforming activities in vitro. PMID:27771561

Long-range comparison of human and mouse Sprr loci to identify conserved noncoding sequences involved in coordinate regulation

PubMed Central

Martin, Natalia; Patel, Satyakam; Segre, Julia A.

2004-01-01

Mammalian epidermis provides a permeability barrier between an organism and its environment. Under homeostatic conditions, epidermal cells produce structural proteins, which are cross-linked in an orderly fashion to form a cornified envelope (CE). However, under genetic or environmental stress, specific genes are induced to rapidly build a temporary barrier. Small proline-rich (SPRR) proteins are the primary constituents of the CE. Under stress the entire family of 14 Sprr genes is upregulated. The Sprr genes are clustered within the larger epidermal differentiation complex on mouse chromosome 3, human chromosome 1q21. The clustering of the Sprr genes and their upregulation under stress suggest that these genes may be coordinately regulated. To identify enhancer elements that regulate this stress response activation of the Sprr locus, we utilized bioinformatic tools and classical biochemical dissection. Long-range comparative sequence analysis identified conserved noncoding sequences (CNSs). Clusters of epidermal-specific DNaseI-hypersensitive sites (HSs) mapped to specific CNSs. Increased prevalence of these HSs in barrier-deficient epidermis provides in vivo evidence of the regulation of the Sprr locus by these conserved sequences. Individual components of these HSs were cloned, and one was shown to have strong enhancer activity specific to conditions when the Sprr genes are coordinately upregulated. PMID:15574822

Cloning and sequencing of a gene encoding a 21-kilodalton outer membrane protein from Bordetella avium and expression of the gene in Salmonella typhimurium.

PubMed Central

Gentry-Weeks, C R; Hultsch, A L; Kelly, S M; Keith, J M; Curtiss, R

1992-01-01

Three gene libraries of Bordetella avium 197 DNA were prepared in Escherichia coli LE392 by using the cosmid vectors pCP13 and pYA2329, a derivative of pCP13 specifying spectinomycin resistance. The cosmid libraries were screened with convalescent-phase anti-B. avium turkey sera and polyclonal rabbit antisera against B. avium 197 outer membrane proteins. One E. coli recombinant clone produced a 56-kDa protein which reacted with convalescent-phase serum from a turkey infected with B. avium 197. In addition, five E. coli recombinant clones were identified which produced B. avium outer membrane proteins with molecular masses of 21, 38, 40, 43, and 48 kDa. At least one of these E. coli clones, which encoded the 21-kDa protein, reacted with both convalescent-phase turkey sera and antibody against B. avium 197 outer membrane proteins. The gene for the 21-kDa outer membrane protein was localized by Tn5seq1 mutagenesis, and the nucleotide sequence was determined by dideoxy sequencing. DNA sequence analysis of the 21-kDa protein revealed an open reading frame of 582 bases that resulted in a predicted protein of 194 amino acids. Comparison of the predicted amino acid sequence of the gene encoding the 21-kDa outer membrane protein with protein sequences in the National Biomedical Research Foundation protein sequence data base indicated significant homology to the OmpA proteins of Shigella dysenteriae, Enterobacter aerogenes, E. coli, and Salmonella typhimurium and to Neisseria gonorrhoeae outer membrane protein III, Haemophilus influenzae protein P6, and Pseudomonas aeruginosa porin protein F. The gene (ompA) encoding the B. avium 21-kDa protein hybridized with 4.1-kb DNA fragments from EcoRI-digested, chromosomal DNA of Bordetella pertussis and Bordetella bronchiseptica and with 6.0- and 3.2-kb DNA fragments from EcoRI-digested, chromosomal DNA of B. avium and B. avium-like DNA, respectively. A 6.75-kb DNA fragment encoding the B. avium 21-kDa protein was subcloned into the Asd+ vector pYA292, and the construct was introduced into the avirulent delta cya delta crp delta asd S. typhimurium chi 3987 for oral immunization of birds. The gene encoding the 21-kDa protein was expressed equivalently in B. avium 197, delta asd E. coli chi 6097, and S. typhimurium chi 3987 and was localized primarily in the cytoplasmic membrane and outer membrane. In preliminary studies on oral inoculation of turkey poults with S. typhimurium chi 3987 expressing the gene encoding the B. avium 21-kDa protein, it was determined that a single dose of the recombinant Salmonella vaccine failed to elicit serum antibodies against the 21-kDa protein and challenge with wild-type B. avium 197 resulted in colonization of the trachea and thymus with B. avium 197. Images PMID:1447140

Chemical-biogeographic survey of secondary metabolism in soil.

PubMed

Charlop-Powers, Zachary; Owen, Jeremy G; Reddy, Boojala Vijay B; Ternei, Melinda A; Brady, Sean F

2014-03-11

In this study, we compare biosynthetic gene richness and diversity of 96 soil microbiomes from diverse environments found throughout the southwestern and northeastern regions of the United States. The 454-pyroseqencing of nonribosomal peptide adenylation (AD) and polyketide ketosynthase (KS) domain fragments amplified from these microbiomes provide a means to evaluate the variation of secondary metabolite biosynthetic diversity in different soil environments. Through soil composition and AD- and KS-amplicon richness analysis, we identify soil types with elevated biosynthetic potential. In general, arid soils show the richest observed biosynthetic diversity, whereas brackish sediments and pine forest soils show the least. By mapping individual environmental amplicon sequences to sequences derived from functionally characterized biosynthetic gene clusters, we identified conserved soil type-specific secondary metabolome enrichment patterns despite significant sample-to-sample sequence variation. These data are used to create chemical biogeographic distribution maps for biomedically valuable families of natural products in the environment that should prove useful for directing the discovery of bioactive natural products in the future.

Diversity of the small subunit ribosomal RNA gene of the arbuscular mycorrhizal fungi colonizing Clintonia borealis from a mixed-wood boreal forest.

PubMed

DeBellis, Tonia; Widden, Paul

2006-11-01

Arbuscular mycorrhizal fungi (AMF) communities in Clintonia borealis roots from a boreal mixed forests in northwestern Québec were investigated. Roots were sampled from 100 m2 plots whose overstory was dominated by either trembling aspen (Populus tremuloides Michx.), white birch (Betula papyrifera Marsh.), or mixed white spruce (Picea glauca (Moench) Voss) and balsam fir (Abies balsamea (L.) Mill.). Part of the 18S ribosomal gene of the AMF was amplified and the resulting PCR products were cloned. Restriction analysis of the 576 resulting clones yielded 92 different restriction patterns which were then sequenced. Fifty-two sequences closely matched other Glomus sequences from Genbank. Phylogenetic analysis revealed 10 different AMF sequence types, most of which clustered with other uncultured AM sequences from plant roots from various field sites. Compared with other AMF communities from comparable studies, richness and diversity were higher than observed in an arable field, but lower than seen in a tropical forest and a temperate wetland. The AMF communities from Clintonia roots under the different canopy types did not differ significantly and the dominant sequence type, which clustered with AM sequences from a variety of environments and hosts at distant geographical locations, represented 66.9% of all the clones analyzed.

Genome sequence of a diabetes-prone rodent reveals a mutation hotspot around the ParaHox gene cluster.

PubMed

Hargreaves, Adam D; Zhou, Long; Christensen, Josef; Marlétaz, Ferdinand; Liu, Shiping; Li, Fang; Jansen, Peter Gildsig; Spiga, Enrico; Hansen, Matilde Thye; Pedersen, Signe Vendelbo Horn; Biswas, Shameek; Serikawa, Kyle; Fox, Brian A; Taylor, William R; Mulley, John Frederick; Zhang, Guojie; Heller, R Scott; Holland, Peter W H

2017-07-18

The sand rat Psammomys obesus is a gerbil species native to deserts of North Africa and the Middle East, and is constrained in its ecology because high carbohydrate diets induce obesity and type II diabetes that, in extreme cases, can lead to pancreatic failure and death. We report the sequencing of the sand rat genome and discovery of an unusual, extensive, and mutationally biased GC-rich genomic domain. This highly divergent genomic region encompasses several functionally essential genes, and spans the ParaHox cluster which includes the insulin-regulating homeobox gene Pdx1. The sequence of sand rat Pdx1 has been grossly affected by GC-biased mutation, leading to the highest divergence observed for this gene across the Bilateria. In addition to genomic insights into restricted caloric intake in a desert species, the discovery of a localized chromosomal region subject to elevated mutation suggests that mutational heterogeneity within genomes could influence the course of evolution.

Constraints on the Mass–Richness Relation from the Abundance and Weak Lensing of SDSS Clusters

NASA Astrophysics Data System (ADS)

Murata, Ryoma; Nishimichi, Takahiro; Takada, Masahiro; Miyatake, Hironao; Shirasaki, Masato; More, Surhud; Takahashi, Ryuichi; Osato, Ken

2018-02-01

We constrain the scaling relation between optical richness (λ) and halo mass (M) for a sample of Sloan Digital Sky Survey (SDSS) red-sequence Matched-filter Probabilistic Percolation (redMaPPer) galaxy clusters within the context of the Planck cosmological model. We use a forward modeling approach where we model the probability distribution of optical richness for a given mass, P({ln}λ | M). To model the abundance and the stacked lensing profiles, we use an emulator specifically built to interpolate the halo mass function and the stacked lensing profile for an arbitrary set of halo mass and redshift, which is calibrated based on a suite of high-resolution N-body simulations. We apply our method to 8312 SDSS redMaPPer clusters with 20 ≤ λ ≤ 100 and 0.10 ≤ z λ ≤ 0.33 and show that the lognormal distribution model for P(λ | M), with four free parameters, well reproduces the measured abundances and lensing profiles simultaneously. The constraints are characterized by the mean relation, < {ln}λ > (M)=A+B{ln}(M/{M}pivot}), with A={3.207}-0.046+0.044 and B={0.993}-0.055+0.041 (68% CL), where the pivot mass scale M pivot = 3 × 1014 h ‑1 M ⊙, and the scatter {σ }lnλ | M}={σ }0+q{ln}(M/{M}pivot}) with {σ }0={0.456}-0.039+0.047 and q=-{0.169}-0.026+0.035. We find that a large scatter in halo masses is required at the lowest-richness bins (20 ≤ λ ≲ 30) in order to reproduce the measurements. Without such a large scatter, the model prediction for the lensing profiles tends to overestimate the measured amplitudes. This might imply a possible contamination of intrinsically low-richness clusters due to the projection effects. Such a low-mass halo contribution is significantly reduced when applying our method to the sample of 30 ≤ λ ≤ 100.

Interaction of Plasmodium vivax Tryptophan-rich Antigen PvTRAg38 with Band 3 on Human Erythrocyte Surface Facilitates Parasite Growth*

PubMed Central

Alam, Mohd. Shoeb; Choudhary, Vandana; Zeeshan, Mohammad; Tyagi, Rupesh K.; Rathore, Sumit; Sharma, Yagya D.

2015-01-01

Plasmodium tryptophan-rich proteins are involved in host-parasite interaction and thus potential drug/vaccine targets. Recently, we have described several P. vivax tryptophan-rich antigens (PvTRAgs), including merozoite expressed PvTRAg38, from this noncultivable human malaria parasite. PvTRAg38 is highly immunogenic in humans and binds to host erythrocytes, and this binding is inhibited by the patient sera. This binding is also affected if host erythrocytes were pretreated with chymotrypsin. Here, Band 3 has been identified as the chymotrypsin-sensitive erythrocyte receptor for this parasite protein. Interaction of PvTRAg38 with Band 3 has been mapped to its three different ectodomains (loops 1, 3, and 6) exposed at the surface of the erythrocyte. The binding region of PvTRAg38 to Band3 has been mapped to its sequence, KWVQWKNDKIRSWLSSEW, present at amino acid positions 197–214. The recombinant PvTRAg38 was able to inhibit the parasite growth in in vitro Plasmodium falciparum culture probably by competing with the ligand(s) of this heterologous parasite for the erythrocyte Band 3 receptor. In conclusion, the host-parasite interaction at the molecular level is much more complicated than known so far and should be considered during the development of anti-malarial therapeutics. PMID:26149684

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}

amoA-based consensus phylogeny of ammonia-oxidizing archaea and deep sequencing of amoA genes from soils of four different geographic regions

PubMed Central

Pester, Michael; Rattei, Thomas; Flechl, Stefan; Gröngröft, Alexander; Richter, Andreas; Overmann, Jörg; Reinhold-Hurek, Barbara; Loy, Alexander; Wagner, Michael

2012-01-01

Ammonia-oxidizing archaea (AOA) play an important role in nitrification and many studies exploit their amoA genes as marker for their diversity and abundance. We present an archaeal amoA consensus phylogeny based on all publicly available sequences (status June 2010) and provide evidence for the diversification of AOA into four previously recognized clusters and one newly identified major cluster. These clusters, for which we suggest a new nomenclature, harboured 83 AOA species-level OTU (using an inferred species threshold of 85% amoA identity). 454 pyrosequencing of amoA amplicons from 16 soils sampled in Austria, Costa Rica, Greenland and Namibia revealed that only 2% of retrieved sequences had no database representative on the species-level and represented 30–37 additional species-level OTUs. With the exception of an acidic soil from which mostly amoA amplicons of the Nitrosotalea cluster were retrieved, all soils were dominated by amoA amplicons from the Nitrososphaera cluster (also called group I.1b), indicating that the previously reported AOA from the Nitrosopumilus cluster (also called group I.1a) are absent or represent minor populations in soils. AOA richness estimates on the species level ranged from 8–83 co-existing AOAs per soil. Presence/absence of amoA OTUs (97% identity level) correlated with geographic location, indicating that besides contemporary environmental conditions also dispersal limitation across different continents and/or historical environmental conditions might influence AOA biogeography in soils. PMID:22141924

From Globular Clusters to Tidal Dwarfs: Structure Formation in Tidal Tails

NASA Astrophysics Data System (ADS)

Knierman, K.; Hunsberger, S.; Gallagher, S.; Charlton, J.; Whitmore, B.; Hibbard, J.; Kundu, A.; Zaritsky, D.

1999-12-01

Galaxy interactions trigger star formation in tidal debris. How does this star formation depend on the local and global physical conditions? Using WFPC2/HST images, we investigate the range of structure within tidal tails of four classic ``Toomre Sequence'' mergers: NGC 4038/9 (``Antennae''), NGC 7252 (``Atoms for Peace''), NGC 3921, and NGC 3256. These tails contain a variety of stellar associations with sizes from globular clusters up to dwarf Irregulars. We explore whether there is a continuum between the two extremes. Our eight fields sample seven tidal tails at a variety of stages in the evolutionary sequence. Some of these tails are rich in HI while others are HI poor. Large tidal dwarfs are embedded in three of the tails. Using V and I WFPC2 images, we measure luminosities and colors of substructures within the tidal tails. The properties of globular cluster candidates in the tails will be contrasted with those of the hundreds of young clusters in the central regions of these mergers. We address whether globular clusters form and survive in the tidal tails and whether tidal dwarfs are composed of only young stars. By comparing the properties of structures in the tails of the four mergers with different ages, we examine systematic evolution of structure along the evolutionary sequence and as a function of HI content. We acknowledge support from NASA through STScI, and from NSF for an REU supplement for Karen Knierman.

Estimating Bacterial Diversity for Ecological Studies: Methods, Metrics, and Assumptions

PubMed Central

Birtel, Julia; Walser, Jean-Claude; Pichon, Samuel; Bürgmann, Helmut; Matthews, Blake

2015-01-01

Methods to estimate microbial diversity have developed rapidly in an effort to understand the distribution and diversity of microorganisms in natural environments. For bacterial communities, the 16S rRNA gene is the phylogenetic marker gene of choice, but most studies select only a specific region of the 16S rRNA to estimate bacterial diversity. Whereas biases derived from from DNA extraction, primer choice and PCR amplification are well documented, we here address how the choice of variable region can influence a wide range of standard ecological metrics, such as species richness, phylogenetic diversity, β-diversity and rank-abundance distributions. We have used Illumina paired-end sequencing to estimate the bacterial diversity of 20 natural lakes across Switzerland derived from three trimmed variable 16S rRNA regions (V3, V4, V5). Species richness, phylogenetic diversity, community composition, β-diversity, and rank-abundance distributions differed significantly between 16S rRNA regions. Overall, patterns of diversity quantified by the V3 and V5 regions were more similar to one another than those assessed by the V4 region. Similar results were obtained when analyzing the datasets with different sequence similarity thresholds used during sequences clustering and when the same analysis was used on a reference dataset of sequences from the Greengenes database. In addition we also measured species richness from the same lake samples using ARISA Fingerprinting, but did not find a strong relationship between species richness estimated by Illumina and ARISA. We conclude that the selection of 16S rRNA region significantly influences the estimation of bacterial diversity and species distributions and that caution is warranted when comparing data from different variable regions as well as when using different sequencing techniques. PMID:25915756

Science from a glimpse: Hubble SNAPshot observations of massive galaxy clusters

NASA Astrophysics Data System (ADS)

Repp, A.; Ebeling, H.

2018-06-01

Hubble Space Telescope SNAPshot surveys of 86 X-ray selected galaxy clusters at 0.3 < z < 0.5 from the MACS sample have proven invaluable for the exploration of a wide range of astronomical research topics. We here present an overview of the four MACS SNAPshot surveys conducted from Cycle 14 to Cycle 20 as part of a long-term effort aimed at identifying exceptional cluster targets for in-depth follow up by the extragalactic community. We also release redshifts and X-ray luminosities of all clusters observed as part of this initiative. To illustrate the power of SNAPshot observations of MACS clusters, we explore several aspects of galaxy evolution illuminated by the images obtained for these programmes. We confirm the high lensing efficiency of X-ray selected clusters at z > 0.3. Examining the evolution of the slope of the cluster red sequence, we observe at best a slight decrease with redshift, indicating minimal age contribution since z ˜ 1. Congruent to previous studies' findings, we note that the two BCGs which are significantly bluer (≥5σ) than their clusters' red sequences reside in relaxed clusters and exhibit pronounced internal structure. Thanks to our targets' high X-ray luminosity, the subset of our sample observed with Chandra adds valuable leverage to the X-ray luminosity-optical richness relation, which, albeit with substantial scatter, is now clearly established from groups to extremely massive clusters of galaxies. We conclude that SNAPshot observations of MACS clusters stand to continue to play a vital pathfinder role for astrophysical investigations across the entire electromagnetic spectrum.

The Richness Dependence of Galaxy Cluster Correlations: Results From A Redshift Survey Of Rich APM Clusters

NASA Technical Reports Server (NTRS)

Croft, R. A. C.; Dalton, G. B.; Efstathiou, G.; Sutherland, W. J.; Maddox, S. J.

1997-01-01

We analyze the spatial clustering properties of a new catalog of very rich galaxy clusters selected from the APM Galaxy Survey. These clusters are of comparable richness and space density to Abell Richness Class greater than or equal to 1 clusters, but selected using an objective algorithm from a catalog demonstrably free of artificial inhomogeneities. Evaluation of the two-point correlation function xi(sub cc)(r) for the full sample and for richer subsamples reveals that the correlation amplitude is consistent with that measured for lower richness APM clusters and X-ray selected clusters. We apply a maximum likelihood estimator to find the best fitting slope and amplitude of a power law fit to x(sub cc)(r), and to estimate the correlation length r(sub 0) (the value of r at which xi(sub cc)(r) is equal to unity). For clusters with a mean space density of 1.6 x 10(exp -6) h(exp 3) MpC(exp -3) (equivalent to the space density of Abell Richness greater than or equal to 2 clusters), we find r(sub 0) = 21.3(+11.1/-9.3) h(exp -1) Mpc (95% confidence limits). This is consistent with the weak richness dependence of xi(sub cc)(r) expected in Gaussian models of structure formation. In particular, the amplitude of xi(sub cc)(r) at all richnesses matches that of xi(sub cc)(r) for clusters selected in N-Body simulations of a low density Cold Dark Matter model.

Complex Routes of Nosocomial Vancomycin-Resistant Enterococcus faecium Transmission Revealed by Genome Sequencing.

PubMed

Raven, Kathy E; Gouliouris, Theodore; Brodrick, Hayley; Coll, Francesc; Brown, Nicholas M; Reynolds, Rosy; Reuter, Sandra; Török, M Estée; Parkhill, Julian; Peacock, Sharon J

2017-04-01

Vancomycin-resistant Enterococcus faecium (VREfm) is a leading cause of nosocomial infection. Here, we describe the utility of whole-genome sequencing in defining nosocomial VREfm transmission. A retrospective study at a single hospital in the United Kingdom identified 342 patients with E. faecium bloodstream infection over 7 years. Of these, 293 patients had a stored isolate and formed the basis for the study. The first stored isolate from each case was sequenced (200 VREfm [197 vanA, 2 vanB, and 1 isolate containing both vanA and vanB], 93 vancomycin-susceptible E. faecium) and epidemiological data were collected. Genomes were also available for E. faecium associated with bloodstream infections in 15 patients in neighboring hospitals, and 456 patients across the United Kingdom and Ireland. The majority of infections in the 293 patients were hospital-acquired (n = 249) or healthcare-associated (n = 42). Phylogenetic analysis showed that 291 of 293 isolates resided in a hospital-associated clade that contained numerous discrete clusters of closely related isolates, indicative of multiple introductions into the hospital followed by clonal expansion associated with transmission. Fine-scale analysis of 6 exemplar phylogenetic clusters containing isolates from 93 patients (32%) identified complex transmission routes that spanned numerous wards and years, extending beyond the detection of conventional infection control. These contained both vancomycin-resistant and -susceptible isolates. We also identified closely related isolates from patients at Cambridge University Hospitals NHS Foundation Trust and regional and national hospitals, suggesting interhospital transmission. These findings provide important insights for infection control practice and signpost areas for interventions. We conclude that sequencing represents a powerful tool for the enhanced surveillance and control of nosocomial E. faecium transmission and infection. © The Author 2017. Published by Oxford University Press for the Infectious Diseases Society of America.

Mass and galaxy distributions of four massive galaxy clusters from Dark Energy Survey Science Verification data

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

Melchior, P.; Suchyta, E.; Huff, E.

2015-03-31

We measure the weak-lensing masses and galaxy distributions of four massive galaxy clusters observed during the Science Verification phase of the Dark Energy Survey. This pathfinder study is meant to 1) validate the DECam imager for the task of measuring weak-lensing shapes, and 2) utilize DECam's large field of view to map out the clusters and their environments over 90 arcmin. We conduct a series of rigorous tests on astrometry, photometry, image quality, PSF modeling, and shear measurement accuracy to single out flaws in the data and also to identify the optimal data processing steps and parameters. We find Sciencemore » Verification data from DECam to be suitable for the lensing analysis described in this paper. The PSF is generally well-behaved, but the modeling is rendered difficult by a flux-dependent PSF width and ellipticity. We employ photometric redshifts to distinguish between foreground and background galaxies, and a red-sequence cluster finder to provide cluster richness estimates and cluster-galaxy distributions. By fitting NFW profiles to the clusters in this study, we determine weak-lensing masses that are in agreement with previous work. For Abell 3261, we provide the first estimates of redshift, weak-lensing mass, and richness. In addition, the cluster-galaxy distributions indicate the presence of filamentary structures attached to 1E 0657-56 and RXC J2248.7-4431, stretching out as far as 1 degree (approximately 20 Mpc), showcasing the potential of DECam and DES for detailed studies of degree-scale features on the sky.« less

Mass and galaxy distributions of four massive galaxy clusters from Dark Energy Survey Science Verification data

DOE PAGES

Melchior, P.; Suchyta, E.; Huff, E.; ...

2015-03-31

We measure the weak-lensing masses and galaxy distributions of four massive galaxy clusters observed during the Science Verification phase of the Dark Energy Survey. This pathfinder study is meant to 1) validate the DECam imager for the task of measuring weak-lensing shapes, and 2) utilize DECam's large field of view to map out the clusters and their environments over 90 arcmin. We conduct a series of rigorous tests on astrometry, photometry, image quality, PSF modelling, and shear measurement accuracy to single out flaws in the data and also to identify the optimal data processing steps and parameters. We find Sciencemore » Verification data from DECam to be suitable for the lensing analysis described in this paper. The PSF is generally well-behaved, but the modelling is rendered difficult by a flux-dependent PSF width and ellipticity. We employ photometric redshifts to distinguish between foreground and background galaxies, and a red-sequence cluster finder to provide cluster richness estimates and cluster-galaxy distributions. By fitting NFW profiles to the clusters in this study, we determine weak-lensing masses that are in agreement with previous work. For Abell 3261, we provide the first estimates of redshift, weak-lensing mass, and richness. Additionally, the cluster-galaxy distributions indicate the presence of filamentary structures attached to 1E 0657-56 and RXC J2248.7-4431, stretching out as far as 1degree (approximately 20 Mpc), showcasing the potential of DECam and DES for detailed studies of degree-scale features on the sky.« less

The skin microbiome in healthy and allergic dogs.

PubMed

Rodrigues Hoffmann, Aline; Patterson, Adam P; Diesel, Alison; Lawhon, Sara D; Ly, Hoai Jaclyn; Elkins Stephenson, Christine; Mansell, Joanne; Steiner, Jörg M; Dowd, Scot E; Olivry, Thierry; Suchodolski, Jan S

2014-01-01

Changes in the microbial populations on the skin of animals have traditionally been evaluated using conventional microbiology techniques. The sequencing of bacterial 16S rRNA genes has revealed that the human skin is inhabited by a highly diverse and variable microbiome that had previously not been demonstrated by culture-based methods. The goals of this study were to describe the microbiome inhabiting different areas of the canine skin, and to compare the skin microbiome of healthy and allergic dogs. DNA extracted from superficial skin swabs from healthy (n = 12) and allergic dogs (n = 6) from different regions of haired skin and mucosal surfaces were used for 454-pyrosequencing of the 16S rRNA gene. Principal coordinates analysis revealed clustering for the different skin sites across all dogs, with some mucosal sites and the perianal regions clustering separately from the haired skin sites. The rarefaction analysis revealed high individual variability between samples collected from healthy dogs and between the different skin sites. Higher species richness and microbial diversity were observed in the samples from haired skin when compared to mucosal surfaces or mucocutaneous junctions. In all examined regions, the most abundant phylum and family identified in the different regions of skin and mucosal surfaces were Proteobacteria and Oxalobacteriaceae. The skin of allergic dogs had lower species richness when compared to the healthy dogs. The allergic dogs had lower proportions of the Betaproteobacteria Ralstonia spp. when compared to the healthy dogs. The study demonstrates that the skin of dogs is inhabited by much more rich and diverse microbial communities than previously thought using culture-based methods. Our sequence data reveal high individual variability between samples collected from different patients. Differences in species richness was also seen between healthy and allergic dogs, with allergic dogs having lower species richness when compared to healthy dogs.

The Skin Microbiome in Healthy and Allergic Dogs

PubMed Central

Rodrigues Hoffmann, Aline; Patterson, Adam P.; Diesel, Alison; Lawhon, Sara D.; Ly, Hoai Jaclyn; Stephenson, Christine Elkins; Mansell, Joanne; Steiner, Jörg M.; Dowd, Scot E.; Olivry, Thierry; Suchodolski, Jan S.

2014-01-01

Background Changes in the microbial populations on the skin of animals have traditionally been evaluated using conventional microbiology techniques. The sequencing of bacterial 16S rRNA genes has revealed that the human skin is inhabited by a highly diverse and variable microbiome that had previously not been demonstrated by culture-based methods. The goals of this study were to describe the microbiome inhabiting different areas of the canine skin, and to compare the skin microbiome of healthy and allergic dogs. Methodology/Principal Findings DNA extracted from superficial skin swabs from healthy (n = 12) and allergic dogs (n = 6) from different regions of haired skin and mucosal surfaces were used for 454-pyrosequencing of the 16S rRNA gene. Principal coordinates analysis revealed clustering for the different skin sites across all dogs, with some mucosal sites and the perianal regions clustering separately from the haired skin sites. The rarefaction analysis revealed high individual variability between samples collected from healthy dogs and between the different skin sites. Higher species richness and microbial diversity were observed in the samples from haired skin when compared to mucosal surfaces or mucocutaneous junctions. In all examined regions, the most abundant phylum and family identified in the different regions of skin and mucosal surfaces were Proteobacteria and Oxalobacteriaceae. The skin of allergic dogs had lower species richness when compared to the healthy dogs. The allergic dogs had lower proportions of the Betaproteobacteria Ralstonia spp. when compared to the healthy dogs. Conclusions/Significance The study demonstrates that the skin of dogs is inhabited by much more rich and diverse microbial communities than previously thought using culture-based methods. Our sequence data reveal high individual variability between samples collected from different patients. Differences in species richness was also seen between healthy and allergic dogs, with allergic dogs having lower species richness when compared to healthy dogs. PMID:24421875

A Definitive Optical Detection of a Supercluster at Z ~ 0.91

NASA Astrophysics Data System (ADS)

Lubin, Lori M.; Brunner, Robert; Metzger, Mark R.; Postman, Marc; Oke, J. B.

2000-03-01

We present the results from a multiband optical imaging program that has definitively confirmed the existence of a supercluster at z~0.91. Two massive clusters of galaxies, Cl 1604+4304 at z=0.897 and Cl 1604+4321 at z=0.924, were originally observed in the high-redshift cluster survey of Oke, Postman, & Lubin. They are separated by 4300 km s-1 in radial velocity and 17' on the plane of the sky. Their physical and redshift proximity suggested a promising supercluster candidate. Deep BRi imaging of the region between the two clusters indicates a large population of red galaxies. This population forms a tight, red sequence in the color-magnitude diagram at (R-i)~1.4. The characteristic color is identical to that of the spectroscopically confirmed early-type galaxies in the two member clusters. The red galaxies are spread throughout the 5 h-1 Mpc region between Cl 1604+4304 and Cl 1604+4321. Their spatial distribution delineates the entire large-scale structure with high concentrations at the cluster centers. In addition, we detect a significant overdensity of red galaxies directly between Cl 1604+4304 and Cl 1604+4321 which is the signature of a third, rich cluster associated with this system. The strong sequence of red galaxies and their spatial distribution clearly indicate that we have discovered a supercluster at z~0.91.

The end of the White Dwarf Cooling Sequence of NGC 6752

NASA Astrophysics Data System (ADS)

Bedin, Luigi

2017-08-01

We propose to study the last HST-accessible white dwarf (WD) cooling sequence (CS) for a nearby globular cluster (GC), the chemically complex, extreme blue horizontal branch cluster NGC 6752. Over 97% of stars end their lives as WDs, and the WD CS provides constraints not only on the age, but also potentially the star formation history of a GC. The CS of WDs also lies in the least-explored region of the color-magnitude diagram of old stellar populations. Recent deep imaging with HST has successfully reached the end of the WD CS in only three classical old GCs, M4, NGC 6397 and 47 Tuc, and reveals an unexpectedly complex, and double-peaked, WD CS in the metal rich old open cluster NGC 6791. One more investigation is in progress on the massive globular Omega Centauri, where over 14 sub-populations are known to exist.While almost every cluster is known to host multiple populations, every single cluster is unique. NGC 6752 is a bridge between the relatively simple globular clusters, and Omega Cen, the most complex globular cluster known. NGC 6752 has an extended blue horizontal branch, a collapsed core and 3 chemically distinct populations. It is our last chance to add diversity to our very limited sample of WD CS, so far containing only 3 globular clusters, one old open cluster, and the complex Omega Cen system. We need to undertake this investigation while HST is still operational, as there is no foreseeable opportunity in the post-HST era to have one extra WD CS in the homogeneus optical photometric system of HST.

Consistency of mist netting and point counts in assessing landbird species richness and relative abundance during migration

Treesearch

Yong Wang; Deborah M. Finch

2002-01-01

We compared consistency of species richness and relative abundance data collected concurrently using mist netting and point counts during migration in riparian habitats along the middle Rio Grande of central New Mexico. Mist netting detected 74% and point counts detected 82% of the 197 species encountered during the study. Species that mist netting failed to capture...

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.

FrameD: A flexible program for quality check and gene prediction in prokaryotic genomes and noisy matured eukaryotic sequences.

PubMed

Schiex, Thomas; Gouzy, Jérôme; Moisan, Annick; de Oliveira, Yannick

2003-07-01

We describe FrameD, a program that predicts coding regions in prokaryotic and matured eukaryotic sequences. Initially targeted at gene prediction in bacterial GC rich genomes, the gene model used in FrameD also allows to predict genes in the presence of frameshifts and partially undetermined sequences which makes it also very suitable for gene prediction and frameshift correction in unfinished sequences such as EST and EST cluster sequences. Like recent eukaryotic gene prediction programs, FrameD also includes the ability to take into account protein similarity information both in its prediction and its graphical output. Its performances are evaluated on different bacterial genomes. The web site (http://genopole.toulouse.inra.fr/bioinfo/FrameD/FD) allows direct prediction, sequence correction and translation and the ability to learn new models for new organisms.

Two hundred passage three-way valve: Fraction collector

NASA Technical Reports Server (NTRS)

Keffer, J. L.

1983-01-01

This paper describes the design and operation of a fraction collector used to direct flow of separated biological materials from 197 capillary tubes to either a collection tray or to a waste tank. This mechanism uses a 28-volt dc gear motor driving twin cams to force 197 needles through a self-sealing silicone rubber septum, where they inject the material in 197 separate pockets in a collection tray. The position of the collector tray is sensed by two optical limit switches. The time sequences are controlled automatically by an electronics control monitoring module.

Neutron-rich rare-isotope production from projectile fission of heavy nuclei near 20 MeV/nucleon beam energy

NASA Astrophysics Data System (ADS)

Vonta, N.; Souliotis, G. A.; Loveland, W.; Kwon, Y. K.; Tshoo, K.; Jeong, S. C.; Veselsky, M.; Bonasera, A.; Botvina, A.

2016-12-01

We investigate the possibilities of producing neutron-rich nuclides in projectile fission of heavy beams in the energy range of 20 MeV/nucleon expected from low-energy facilities. We report our efforts to theoretically describe the reaction mechanism of projectile fission following a multinucleon transfer collision at this energy range. Our calculations are mainly based on a two-step approach: The dynamical stage of the collision is described with either the phenomenological deep-inelastic transfer model (DIT) or with the microscopic constrained molecular dynamics model (CoMD). The de-excitation or fission of the hot heavy projectile fragments is performed with the statistical multifragmentation model (SMM). We compared our model calculations with our previous experimental projectile-fission data of 238U (20 MeV/nucleon) + 208Pb and 197Au (20 MeV/nucleon) + 197Au and found an overall reasonable agreement. Our study suggests that projectile fission following peripheral heavy-ion collisions at this energy range offers an effective route to access very neutron-rich rare isotopes toward and beyond the astrophysical r-process path.

Development of Genomic Microsatellite Markers in Carthamus tinctorius L. (Safflower) Using Next Generation Sequencing and Assessment of Their Cross-Species Transferability and Utility for Diversity Analysis

PubMed Central

Variath, Murali Tottekkad; Joshi, Gopal; Bali, Sapinder; Agarwal, Manu; Kumar, Amar; Jagannath, Arun; Goel, Shailendra

2015-01-01

Background Safflower (Carthamus tinctorius L.), an Asteraceae member, yields high quality edible oil rich in unsaturated fatty acids and is resilient to dry conditions. The crop holds tremendous potential for improvement through concerted molecular breeding programs due to the availability of significant genetic and phenotypic diversity. Genomic resources that could facilitate such breeding programs remain largely underdeveloped in the crop. The present study was initiated to develop a large set of novel microsatellite markers for safflower using next generation sequencing. Principal Findings Low throughput genome sequencing of safflower was performed using Illumina paired end technology providing ~3.5X coverage of the genome. Analysis of sequencing data allowed identification of 23,067 regions harboring perfect microsatellite loci. The safflower genome was found to be rich in dinucleotide repeats followed by tri-, tetra-, penta- and hexa-nucleotides. Primer pairs were designed for 5,716 novel microsatellite sequences with repeat length ≥ 20 bases and optimal flanking regions. A subset of 325 microsatellite loci was tested for amplification, of which 294 loci produced robust amplification. The validated primers were used for assessment of 23 safflower accessions belonging to diverse agro-climatic zones of the world leading to identification of 93 polymorphic primers (31.6%). The numbers of observed alleles at each locus ranged from two to four and mean polymorphism information content was found to be 0.3075. The polymorphic primers were tested for cross-species transferability on nine wild relatives of cultivated safflower. All primers except one showed amplification in at least two wild species while 25 primers amplified across all the nine species. The UPGMA dendrogram clustered C. tinctorius accessions and wild species separately into two major groups. The proposed progenitor species of safflower, C. oxyacantha and C. palaestinus were genetically closer to cultivated safflower and formed a distinct cluster. The cluster analysis also distinguished diploid and tetraploid wild species of safflower. Conclusion Next generation sequencing of safflower genome generated a large set of microsatellite markers. The novel markers developed in this study will add to the existing repertoire of markers and can be used for diversity analysis, synteny studies, construction of linkage maps and marker-assisted selection. PMID:26287743

IMG-ABC: An Atlas of Biosynthetic Gene Clusters to Fuel the Discovery of Novel Secondary Metabolites

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

Chen, I-Min; Chu, Ken; Ratner, Anna

2014-10-28

In the discovery of secondary metabolites (SMs), large-scale analysis of sequence data is a promising exploration path that remains largely underutilized due to the lack of relevant computational resources. We present IMG-ABC (https://img.jgi.doe.gov/abc/) -- An Atlas of Biosynthetic gene Clusters within the Integrated Microbial Genomes (IMG) system1. IMG-ABC is a rich repository of both validated and predicted biosynthetic clusters (BCs) in cultured isolates, single-cells and metagenomes linked with the SM chemicals they produce and enhanced with focused analysis tools within IMG. The underlying scalable framework enables traversal of phylogenetic dark matter and chemical structure space -- serving as a doorwaymore » to a new era in the discovery of novel molecules.« less

Plant diversity and plant identity influence Fusarium communities in soil.

PubMed

LeBlanc, Nicholas; Kinkel, Linda; Kistler, H Corby

2017-01-01

Fusarium communities play important functional roles in soil and in plants as pathogens, endophytes, and saprotrophs. This study tests how rhizosphere Fusarium communities may vary with plant species, changes in the diversity of the surrounding plant community, and soil physiochemical characteristics. Fusarium communities in soil associated with the roots of two perennial prairie plant species maintained as monocultures or growing within polyculture plant communities were characterized using targeted metagenomics. Amplicon libraries targeting the RPB2 locus were generated from rhizosphere soil DNAs and sequenced using pyrosequencing. Sequences were clustered into operational taxonomic units (OTUs) and assigned a taxonomy using the Evolutionary Placement Algorithm. Fusarium community composition was differentiated between monoculture and polyculture plant communities, and by plant species in monoculture, but not in polyculture. Taxonomic classification of the Fusarium OTUs showed a predominance of F. tricinctum and F. oxysporum as well of the presence of a clade previously only found in the Southern Hemisphere. Total Fusarium richness was not affected by changes in plant community richness or correlated with soil physiochemical characteristics. However, OTU richness within two predominant phylogenetic lineages within the genus was positively or negatively correlated with soil physiochemical characteristics among samples within each lineage. This work shows that plant species, plant community richness, and soil physiochemical characteristics may all influence the composition and richness of Fusarium communities in soil.

A comparative hidden Markov model analysis pipeline identifies proteins characteristic of cereal-infecting fungi

PubMed Central

2013-01-01

Background Fungal pathogens cause devastating losses in economically important cereal crops by utilising pathogen proteins to infect host plants. Secreted pathogen proteins are referred to as effectors and have thus far been identified by selecting small, cysteine-rich peptides from the secretome despite increasing evidence that not all effectors share these attributes. Results We take advantage of the availability of sequenced fungal genomes and present an unbiased method for finding putative pathogen proteins and secreted effectors in a query genome via comparative hidden Markov model analyses followed by unsupervised protein clustering. Our method returns experimentally validated fungal effectors in Stagonospora nodorum and Fusarium oxysporum as well as the N-terminal Y/F/WxC-motif from the barley powdery mildew pathogen. Application to the cereal pathogen Fusarium graminearum reveals a secreted phosphorylcholine phosphatase that is characteristic of hemibiotrophic and necrotrophic cereal pathogens and shares an ancient selection process with bacterial plant pathogens. Three F. graminearum protein clusters are found with an enriched secretion signal. One of these putative effector clusters contains proteins that share a [SG]-P-C-[KR]-P sequence motif in the N-terminal and show features not commonly associated with fungal effectors. This motif is conserved in secreted pathogenic Fusarium proteins and a prime candidate for functional testing. Conclusions Our pipeline has successfully uncovered conservation patterns, putative effectors and motifs of fungal pathogens that would have been overlooked by existing approaches that identify effectors as small, secreted, cysteine-rich peptides. It can be applied to any pathogenic proteome data, such as microbial pathogen data of plants and other organisms. PMID:24252298

A new reduction of the blanco cosmology survey: An optically selected galaxy cluster catalog and a

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

Bleem, L. E.; Stalder, B.; Brodwin, M.

2015-01-01

The Blanco Cosmology Survey is a four-band (griz) optical-imaging survey of ≈80 deg2 of the southern sky. The survey consists of two fields centered approximately at (R.A., decl.) = (23h, -55°) and (5h30m, -53°) with imaging sufficient for the detection of Lmore » $$\\star$$ galaxies at redshift z ≤ 1. In this paper, we present our reduction of the survey data and describe a new technique for the separation of stars and galaxies. We search the calibrated source catalogs for galaxy clusters at z ≤ 0.75 by identifying spatial over-densities of red-sequence galaxies and report the coordinates, redshifts, and optical richnesses, λ, for 764 galaxy clusters at z ≤ 0.75. This sample, >85% of which are new discoveries, has a median redshift of z = 0.52 and median richness λ(0.4L$$\\star$$) = 16.4. Accompanying this paper we also release full survey data products including reduced images and calibrated source catalogs. These products are available at http://data.rcc.uchicago.edu/dataset/blanco-cosmology-survey.« less

A NEW REDUCTION OF THE BLANCO COSMOLOGY SURVEY: AN OPTICALLY SELECTED GALAXY CLUSTER CATALOG AND A PUBLIC RELEASE OF OPTICAL DATA PRODUCTS

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

Bleem, L. E.; Stalder, B.; Brodwin, M.

2015-01-01

The Blanco Cosmology Survey is a four-band (griz) optical-imaging survey of ∼80 deg{sup 2} of the southern sky. The survey consists of two fields centered approximately at (R.A., decl.) = (23{sup h}, –55°) and (5{sup h}30{sup m}, –53°) with imaging sufficient for the detection of L {sub *} galaxies at redshift z ≤ 1. In this paper, we present our reduction of the survey data and describe a new technique for the separation of stars and galaxies. We search the calibrated source catalogs for galaxy clusters at z ≤ 0.75 by identifying spatial over-densities of red-sequence galaxies and report the coordinates,more » redshifts, and optical richnesses, λ, for 764 galaxy clusters at z ≤ 0.75. This sample, >85% of which are new discoveries, has a median redshift of z = 0.52 and median richness λ(0.4 L {sub *}) = 16.4. Accompanying this paper we also release full survey data products including reduced images and calibrated source catalogs. These products are available at http://data.rcc.uchicago.edu/dataset/blanco-cosmology-survey.« less

Bacterial diversity in the oxygen minimum zone of the eastern tropical South Pacific.

PubMed

Stevens, Heike; Ulloa, Osvaldo

2008-05-01

The structure and diversity of bacterial communities associated with the oxygen minimum zone (OMZ) of the eastern tropical South Pacific was studied through phylogenetic analysis. Clone libraries of 16S rRNA gene fragments were constructed using environmental DNA collected from the OMZ (60 m and 200 m), the sea surface (10 m), and the deep oxycline (450 m). At the class level, the majority of sequences affiliated to the gamma- (53.7%) and alpha-Proteobacteria (19.7%), and to the Bacteroidetes (11.2%). A vertical partitioning of the bacterial communities was observed, with main differences between the suboxic OMZ and the more oxygenated surface and deep oxycline waters. At the surface, the microbial community was predominantly characterized by SAR86, Loktanella and unclassified Flavobacteriaceae, whereas the deeper layer was dominated by Sulfitobacter and unclassified Alteromonadaceae. In the OMZ, major constituents affiliated to the marine SAR11 clade and to thiotrophic gamma-symbionts (25% of all sequences), a group not commonly found in pelagic waters. Sequences affiliating to the phylum Chloroflexi, to the AGG47 and SAR202 clades, to the delta-Proteobacteria, to the Acidobacteria, and to the 'anammox group' of the Planctomycetes were found exclusively in the OMZ. The bacterial richness in the OMZ was higher than in the oxic surface and deeper oxycline, as revealed by rarefaction analysis and the Chao1 richness estimator (surface: 45 +/- 8, deeper oxycline: 76 +/- 26; OMZ (60 m): 97 +/- 33, OMZ (200 m): 109 +/- 31). OMZ bacterial diversity indices (Fisher's: approximately 30 +/- 5, Shannon's: approximately 3.31, inverse Simpson's: approximately 20) were similar to those found in other pelagic marine environments. Thus, our results indicate a distinct and diverse bacterial community within the OMZ, with presumably novel and yet uncultivated bacterial lineages.

The Hidden Diversity of Flagellated Protists in Soil.

PubMed

Venter, Paul Christiaan; Nitsche, Frank; Arndt, Hartmut

2018-07-01

Protists are among the most diverse and abundant eukaryotes in soil. However, gaps between described and sequenced protist morphospecies still present a pending problem when surveying environmental samples for known species using molecular methods. The number of sequences in the molecular PR 2 database (∼130,000) is limited compared to the species richness expected (>1 million protist species) - limiting the recovery rate. This is important, since high throughput sequencing (HTS) methods are used to find associative patterns between functional traits, taxa and environmental parameters. We performed HTS to survey soil flagellates in 150 grasslands of central Europe, and tested the recovery rate of ten previously isolated and cultivated cercomonad species, among locally found diversity. We recovered sequences for reference soil flagellate species, but also a great number of their phylogenetically evaluated genetic variants, among rare and dominant taxa with presumably own biogeography. This was recorded among dominant (cercozoans, Sandona), rare (apusozoans) and a large hidden diversity of predominantly aquatic protists in soil (choanoflagellates, bicosoecids) often forming novel clades associated with uncultured environmental sequences. Evaluating the reads, instead of the OTUs that individual reads are usually clustered into, we discovered that much of this hidden diversity may be lost due to clustering. Copyright © 2018 Elsevier GmbH. All rights reserved.

Neotropical Bats from Costa Rica harbour Diverse Coronaviruses.

PubMed

Moreira-Soto, A; Taylor-Castillo, L; Vargas-Vargas, N; Rodríguez-Herrera, B; Jiménez, C; Corrales-Aguilar, E

2015-11-01

Bats are hosts of diverse coronaviruses (CoVs) known to potentially cross the host-species barrier. For analysing coronavirus diversity in a bat species-rich country, a total of 421 anal swabs/faecal samples from Costa Rican bats were screened for CoV RNA-dependent RNA polymerase (RdRp) gene sequences by a pancoronavirus PCR. Six families, 24 genera and 41 species of bats were analysed. The detection rate for CoV was 1%. Individuals (n = 4) from four different species of frugivorous (Artibeus jamaicensis, Carollia perspicillata and Carollia castanea) and nectivorous (Glossophaga soricina) bats were positive for coronavirus-derived nucleic acids. Analysis of 440 nt. RdRp sequences allocated all Costa Rican bat CoVs to the α-CoV group. Several CoVs sequences clustered near previously described CoVs from the same species of bat, but were phylogenetically distant from the human CoV sequences identified to date, suggesting no recent spillover events. The Glossophaga soricina CoV sequence is sufficiently dissimilar (26% homology to the closest known bat CoVs) to represent a unique coronavirus not clustering near other CoVs found in the same bat species so far, implying an even higher CoV diversity than previously suspected. © 2015 Blackwell Verlag GmbH.

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.

The X-ray luminosity functions of Abell clusters from the Einstein Cluster Survey

NASA Technical Reports Server (NTRS)

Burg, R.; Giacconi, R.; Forman, W.; Jones, C.

1994-01-01

We have derived the present epoch X-ray luminosity function of northern Abell clusters using luminosities from the Einstein Cluster Survey. The sample is sufficiently large that we can determine the luminosity function for each richness class separately with sufficient precision to study and compare the different luminosity functions. We find that, within each richness class, the range of X-ray luminosity is quite large and spans nearly a factor of 25. Characterizing the luminosity function for each richness class with a Schechter function, we find that the characteristic X-ray luminosity, L(sub *), scales with richness class as (L(sub *) varies as N(sub*)(exp gamma), where N(sub *) is the corrected, mean number of galaxies in a richness class, and the best-fitting exponent is gamma = 1.3 +/- 0.4. Finally, our analysis suggests that there is a lower limit to the X-ray luminosity of clusters which is determined by the integrated emission of the cluster member galaxies, and this also scales with richness class. The present sample forms a baseline for testing cosmological evolution of Abell-like clusters when an appropriate high-redshift cluster sample becomes available.

Natural Time and Nowcasting Earthquakes: Are Large Global Earthquakes Temporally Clustered?

NASA Astrophysics Data System (ADS)

Luginbuhl, Molly; Rundle, John B.; Turcotte, Donald L.

2018-02-01

The objective of this paper is to analyze the temporal clustering of large global earthquakes with respect to natural time, or interevent count, as opposed to regular clock time. To do this, we use two techniques: (1) nowcasting, a new method of statistically classifying seismicity and seismic risk, and (2) time series analysis of interevent counts. We chose the sequences of M_{λ } ≥ 7.0 and M_{λ } ≥ 8.0 earthquakes from the global centroid moment tensor (CMT) catalog from 2004 to 2016 for analysis. A significant number of these earthquakes will be aftershocks of the largest events, but no satisfactory method of declustering the aftershocks in clock time is available. A major advantage of using natural time is that it eliminates the need for declustering aftershocks. The event count we utilize is the number of small earthquakes that occur between large earthquakes. The small earthquake magnitude is chosen to be as small as possible, such that the catalog is still complete based on the Gutenberg-Richter statistics. For the CMT catalog, starting in 2004, we found the completeness magnitude to be M_{σ } ≥ 5.1. For the nowcasting method, the cumulative probability distribution of these interevent counts is obtained. We quantify the distribution using the exponent, β, of the best fitting Weibull distribution; β = 1 for a random (exponential) distribution. We considered 197 earthquakes with M_{λ } ≥ 7.0 and found β = 0.83 ± 0.08. We considered 15 earthquakes with M_{λ } ≥ 8.0, but this number was considered too small to generate a meaningful distribution. For comparison, we generated synthetic catalogs of earthquakes that occur randomly with the Gutenberg-Richter frequency-magnitude statistics. We considered a synthetic catalog of 1.97 × 10^5 M_{λ } ≥ 7.0 earthquakes and found β = 0.99 ± 0.01. The random catalog converted to natural time was also random. We then generated 1.5 × 10^4 synthetic catalogs with 197 M_{λ } ≥ 7.0 in each catalog and found the statistical range of β values. The observed value of β = 0.83 for the CMT catalog corresponds to a p value of p=0.004 leading us to conclude that the interevent natural times in the CMT catalog are not random. For the time series analysis, we calculated the autocorrelation function for the sequence of natural time intervals between large global earthquakes and again compared with data from 1.5 × 10^4 synthetic catalogs of random data. In this case, the spread of autocorrelation values was much larger, so we concluded that this approach is insensitive to deviations from random behavior.

THE STAR FORMATION HISTORY OF BCGs TO z = 1.8 FROM THE SpARCS/SWIRE SURVEY: EVIDENCE FOR SIGNIFICANT IN SITU STAR FORMATION AT HIGH REDSHIFT

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

Webb, Tracy M. A.; Bonaventura, Nina; Muzzin, Adam

2015-12-01

We present the results of an MIPS-24 μm study of the brightest cluster galaxies (BCGs) of 535 high-redshift galaxy clusters. The clusters are drawn from the Spitzer Adaptation of the Red-Sequence Cluster Survey, which effectively provides a sample selected on total stellar mass, over 0.2 < z < 1.8 within the Spitzer Wide-Area Infrared Extragalactic (SWIRE) Survey fields. Twenty percent, or 106 clusters, have spectroscopically confirmed redshifts, and the rest have redshifts estimated from the color of their red sequence. A comparison with the public SWIRE images detects 125 individual BCGs at 24 μm ≳ 100 μJy, or 23%. Themore » luminosity-limited detection rate of BCGs in similar richness clusters (N{sub gal} > 12) increases rapidly with redshift. Above z ∼ 1, an average of ∼20% of the sample have 24 μm inferred infrared luminosities of L{sub IR} > 10{sup 12} L{sub ⊙}, while the fraction below z ∼ 1 exhibiting such luminosities is <1%. The Spitzer-IRAC colors indicate the bulk of the 24 μm detected population is predominantly powered by star formation, with only 7/125 galaxies lying within the color region inhabited by active galactic nuclei (AGNs). Simple arguments limit the star formation activity to several hundred million years and this may therefore be indicative of the timescale for AGN feedback to halt the star formation. Below redshift z ∼ 1, there is not enough star formation to significantly contribute to the overall stellar mass of the BCG population, and therefore BCG growth is likely dominated by dry mergers. Above z ∼ 1, however, the inferred star formation would double the stellar mass of the BCGs and is comparable to the mass assembly predicted by simulations through dry mergers. We cannot yet constrain the process driving the star formation for the overall sample, though a single object studied in detail is consistent with a gas-rich merger.« less

Molecular evidence for a uniform microbial community in sponges from different oceans.

PubMed

Hentschel, Ute; Hopke, Jörn; Horn, Matthias; Friedrich, Anja B; Wagner, Michael; Hacker, Jörg; Moore, Bradley S

2002-09-01

Sponges (class Porifera) are evolutionarily ancient metazoans that populate the tropical oceans in great abundances but also occur in temperate regions and even in freshwater. Sponges contain large numbers of bacteria that are embedded within the animal matrix. The phylogeny of these bacteria and the evolutionary age of the interaction are virtually unknown. In order to provide insights into the species richness of the microbial community of sponges, we performed a comprehensive diversity survey based on 190 sponge-derived 16S ribosomal DNA (rDNA) sequences. The sponges Aplysina aerophoba and Theonella swinhoei were chosen for construction of the bacterial 16S rDNA library because they are taxonomically distantly related and they populate nonoverlapping geographic regions. In both sponges, a uniform microbial community was discovered whose phylogenetic signature is distinctly different from that of marine plankton or marine sediments. Altogether 14 monophyletic, sponge-specific sequence clusters were identified that belong to at least seven different bacterial divisions. By definition, the sequences of each cluster are more closely related to each other than to a sequence from nonsponge sources. These monophyletic clusters comprise 70% of all publicly available sponge-derived 16S rDNA sequences, reflecting the generality of the observed phenomenon. This shared microbial fraction represents the smallest common denominator of the sponges investigated in this study. Bacteria that are exclusively found in certain host species or that occur only transiently would have been missed. A picture emerges where sponges can be viewed as highly concentrated reservoirs of so far uncultured and elusive marine microorganisms.

Modulation of frustration in folding by sequence permutation.

PubMed

Nobrega, R Paul; Arora, Karunesh; Kathuria, Sagar V; Graceffa, Rita; Barrea, Raul A; Guo, Liang; Chakravarthy, Srinivas; Bilsel, Osman; Irving, Thomas C; Brooks, Charles L; Matthews, C Robert

2014-07-22

Folding of globular proteins can be envisioned as the contraction of a random coil unfolded state toward the native state on an energy surface rough with local minima trapping frustrated species. These substructures impede productive folding and can serve as nucleation sites for aggregation reactions. However, little is known about the relationship between frustration and its underlying sequence determinants. Chemotaxis response regulator Y (CheY), a 129-amino acid bacterial protein, has been shown previously to populate an off-pathway kinetic trap in the microsecond time range. The frustration has been ascribed to premature docking of the N- and C-terminal subdomains or, alternatively, to the formation of an unproductive local-in-sequence cluster of branched aliphatic side chains, isoleucine, leucine, and valine (ILV). The roles of the subdomains and ILV clusters in frustration were tested by altering the sequence connectivity using circular permutations. Surprisingly, the stability and buried surface area of the intermediate could be increased or decreased depending on the location of the termini. Comparison with the results of small-angle X-ray-scattering experiments and simulations points to the accelerated formation of a more compact, on-pathway species for the more stable intermediate. The effect of chain connectivity in modulating the structures and stabilities of the early kinetic traps in CheY is better understood in terms of the ILV cluster model. However, the subdomain model captures the requirement for an intact N-terminal domain to access the native conformation. Chain entropy and aliphatic-rich sequences play crucial roles in biasing the early events leading to frustration in the folding of CheY.

Within-population distribution of trimethoprim resistance in Escherichia coli before and after a community-wide intervention on trimethoprim use.

PubMed

Sundqvist, Martin; Granholm, Susanne; Naseer, Umaer; Rydén, Patrik; Brolund, Alma; Sundsfjord, Arnfinn; Kahlmeter, Gunnar; Johansson, Anders

2014-12-01

A 2-year prospective intervention on the prescription of trimethoprim reduced the use by 85% in a health care region with 178,000 inhabitants. Here, we performed before-and-after analyses of the within-population distribution of trimethoprim resistance in Escherichia coli. Phylogenetic and population genetic methods were applied to multilocus sequence typing data of 548 consecutively collected E. coli isolates from clinical urinary specimens. Results were analyzed in relation to antibiotic susceptibility and the presence and genomic location of different trimethoprim resistance gene classes. A total of 163 E. coli sequence types (STs) were identified, of which 68 were previously undescribed. The isolates fell into one of three distinct genetic clusters designated BAPS 1 (E. coli phylogroup B2), BAPS 2 (phylogroup A and B1), and BAPS 3 (phylogroup D), each with a similar frequency before and after the intervention. BAPS 2 and BAPS 3 were positively and BAPS 1 was negatively associated with trimethoprim resistance (odds ratios of 1.97, 3.17, and 0.26, respectively). In before-and-after analyses, trimethoprim resistance frequency increased in BAPS 1 and decreased in BAPS 2. Resistance to antibiotics other than trimethoprim increased in BAPS 2. Analysis of the genomic location of different trimethoprim resistance genes in isolates of ST69, ST58, and ST73 identified multiple independent acquisition events in isolates of the same ST. The results show that despite a stable overall resistance frequency in E. coli before and after the intervention, marked within-population changes occurred. A decrease of resistance in one major genetic cluster was masked by a reciprocal increase in another major cluster. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

Within-Population Distribution of Trimethoprim Resistance in Escherichia coli before and after a Community-Wide Intervention on Trimethoprim Use

PubMed Central

Sundqvist, Martin; Granholm, Susanne; Naseer, Umaer; Rydén, Patrik; Brolund, Alma; Sundsfjord, Arnfinn; Kahlmeter, Gunnar

2014-01-01

A 2-year prospective intervention on the prescription of trimethoprim reduced the use by 85% in a health care region with 178,000 inhabitants. Here, we performed before-and-after analyses of the within-population distribution of trimethoprim resistance in Escherichia coli. Phylogenetic and population genetic methods were applied to multilocus sequence typing data of 548 consecutively collected E. coli isolates from clinical urinary specimens. Results were analyzed in relation to antibiotic susceptibility and the presence and genomic location of different trimethoprim resistance gene classes. A total of 163 E. coli sequence types (STs) were identified, of which 68 were previously undescribed. The isolates fell into one of three distinct genetic clusters designated BAPS 1 (E. coli phylogroup B2), BAPS 2 (phylogroup A and B1), and BAPS 3 (phylogroup D), each with a similar frequency before and after the intervention. BAPS 2 and BAPS 3 were positively and BAPS 1 was negatively associated with trimethoprim resistance (odds ratios of 1.97, 3.17, and 0.26, respectively). In before-and-after analyses, trimethoprim resistance frequency increased in BAPS 1 and decreased in BAPS 2. Resistance to antibiotics other than trimethoprim increased in BAPS 2. Analysis of the genomic location of different trimethoprim resistance genes in isolates of ST69, ST58, and ST73 identified multiple independent acquisition events in isolates of the same ST. The results show that despite a stable overall resistance frequency in E. coli before and after the intervention, marked within-population changes occurred. A decrease of resistance in one major genetic cluster was masked by a reciprocal increase in another major cluster. PMID:25288078

A comprehensive study of the rich open star cluster NGC 2099 based on deep BVI CCD observations

NASA Astrophysics Data System (ADS)

Nilakshi,; Sagar, R.

2002-01-01

The CCD observations of the rich open star cluster NGC 2099 and its surrounding field region have been carried out up to a limiting magnitude of V ~ 22 mag in B, V and I passbands for the first time. A total of ~ 12 000 stars have been observed in the area of about 24arcmin x 34arcmin in the cluster region, as well as ~ 2180 stars in the ~ 12arcmin x 12arcmin area of the field region located ~ 45arcmin away from the cluster center. The cluster parameters determined by fitting the convective core overshoot isochrones in the V, (B-V) and V, (V-I) diagrams are E(B-V) = 0.30+/-0.04 mag, distance = 1360+/- 100 pc, age = 400 Myr and metallicity Z = 0.008. A well-defined cluster main sequence spread over about 8 mag in range is observed for the first time. Its intrinsic spread amounting to ~ 0.06 mag in colour is almost the same over the entire brightness and can be understood in terms of the presence of physical/optical binaries. The core and cluster radii determined from the radial stellar density profiles are 185 arcsec and 1000 arcsec respectively. Only about 22% of cluster members are present in the core region. The effects of mass segregation, most probably due to dynamical evolution, have been observed in the cluster. The mass function slope of the entire cluster is ~ -0.67+/-0.12. It becomes closer to the Salpeter value of -1.35, if flattening in the cluster mass function due to presence of both binaries and a much more extended corona is considered. Full Table 4 is only available in electronic form at the CDS via anonymous ftp to cdsarc.u-strasbg.fr (130.79.128.5) or via http://cdsweb.u-strasbg.fr/cgi-bin/qcat?J/A+A/381/65

Identification and characterization of a NBS–LRR class resistance gene analog in Pistacia atlantica subsp. Kurdica

PubMed Central

Bahramnejad, Bahman

2014-01-01

P. atlantica subsp. Kurdica, with the local name of Baneh, is a wild medicinal plant which grows in Kurdistan, Iran. The identification of resistance gene analogs holds great promise for the development of resistant cultivars. A PCR approach with degenerate primers designed according to conserved NBS-LRR (nucleotide binding site-leucine rich repeat) regions of known disease-resistance (R) genes was used to amplify and clone homologous sequences from P. atlantica subsp. Kurdica. A DNA fragment of the expected 500-bp size was amplified. The nucleotide sequence of this amplicon was obtained through sequencing and the predicted amino acid sequence compared to the amino acid sequences of known R-genes revealed significant sequence similarity. Alignment of the deduced amino acid sequence of P. atlantica subsp. Kurdica resistance gene analog (RGA) showed strong identity, ranging from 68% to 77%, to the non-toll interleukin receptor (non-TIR) R-gene subfamily from other plants. A P-loop motif (GMMGGEGKTT), a conserved and hydrophobic motif GLPLAL, a kinase-2a motif (LLVLDDV), when replaced by IAVFDDI in PAKRGA1 and a kinase-3a (FGPGSRIII) were presented in all RGA. A phylogenetic tree, based on the deduced amino-acid sequences of PAKRGA1 and RGAs from different species indicated that they were separated in two clusters, PAKRGA1 being on cluster II. The isolated NBS analogs can be eventually used as guidelines to isolate numerous R-genes in Pistachio. PMID:27843981

Single Cell Genome Amplification Accelerates Identification of the Apratoxin Biosynthetic Pathway from a Complex Microbial Assemblage

PubMed Central

Grindberg, Rashel V.; Ishoey, Thomas; Brinza, Dumitru; Esquenazi, Eduardo; Coates, R. Cameron; Liu, Wei-ting; Gerwick, Lena; Dorrestein, Pieter C.; Pevzner, Pavel; Lasken, Roger; Gerwick, William H.

2011-01-01

Filamentous marine cyanobacteria are extraordinarily rich sources of structurally novel, biomedically relevant natural products. To understand their biosynthetic origins as well as produce increased supplies and analog molecules, access to the clustered biosynthetic genes that encode for the assembly enzymes is necessary. Complicating these efforts is the universal presence of heterotrophic bacteria in the cell wall and sheath material of cyanobacteria obtained from the environment and those grown in uni-cyanobacterial culture. Moreover, the high similarity in genetic elements across disparate secondary metabolite biosynthetic pathways renders imprecise current gene cluster targeting strategies and contributes sequence complexity resulting in partial genome coverage. Thus, it was necessary to use a dual-method approach of single-cell genomic sequencing based on multiple displacement amplification (MDA) and metagenomic library screening. Here, we report the identification of the putative apratoxin. A biosynthetic gene cluster, a potent cancer cell cytotoxin with promise for medicinal applications. The roughly 58 kb biosynthetic gene cluster is composed of 12 open reading frames and has a type I modular mixed polyketide synthase/nonribosomal peptide synthetase (PKS/NRPS) organization and features loading and off-loading domain architecture never previously described. Moreover, this work represents the first successful isolation of a complete biosynthetic gene cluster from Lyngbya bouillonii, a tropical marine cyanobacterium renowned for its production of diverse bioactive secondary metabolites. PMID:21533272

Enviromental Effects on Internal Color Gradients of Early-Type Galaxies

NASA Astrophysics Data System (ADS)

La Barbera, F.; de Carvalho, R. R.; Gal, R. R.; Busarello, G.; Haines, C. P.; Mercurio, A.; Merluzzi, P.; Capaccioli, M.; Djorgovski, S. G.

2007-05-01

One of the most debated issues of observational and theoretical cosmology is that of how the environment affects the formation and evolution of galaxies. To gain new insight into this subject, we have derived surface photometry for a sample of 3,000 early-type galaxies belonging to 163 clusters with different richness, spanning a redshift range of 0.05 to 0.25. This large data-set is used to analyze how the color distribution inside galaxies depends on several parameters, such as cluster richness, local galaxy density, galaxy luminosity and redshift. We find that the internal color profile of galaxies strongly depends on the environment where galaxies reside. Galaxies in poor and rich clusters are found to follow two distinct trends in the color gradient vs. redshift diagram, with color gradients beeing less steep in rich rather than in poor clusters. No dependence of color gradients on galaxy luminosity is detected both for poor and rich clusters. We find that color gradients strongly depend on local galaxy density, with more shallow gradients in high density regions. Interestingly, this result holds only for low richness clusters, with color gradients of galaxies in rich clusters showing no dependence on local galaxy density. Our results support a reasonable picture whereby young early-type galaxies form in a dissipative collapse process, and then undergo increased (either major or minor) merging activity in richer rather than in poor clusters.

Gas loss in simulated galaxies as they fall into clusters

PubMed Central

Cen, Renyue; Pop, Ana Roxana; Bahcall, Neta A.

2014-01-01

We use high-resolution cosmological hydrodynamic galaxy formation simulations to gain insights into how galaxies lose their cold gas at low redshift as they migrate from the field to the high-density regions of clusters of galaxies. We find that beyond three cluster virial radii, the fraction of gas-rich galaxies is constant, representing the field. Within three cluster-centric radii, the fraction of gas-rich galaxies declines steadily with decreasing radius, reaching <10% near the cluster center. Our results suggest galaxies start to feel the effect of the cluster environment on their gas content well beyond the cluster virial radius. We show that almost all gas-rich galaxies at the cluster virial radius are falling in for the first time at nearly radial orbits. Furthermore, we find that almost no galaxy moving outward at the cluster virial radius is gas-rich (with a gas-to-baryon ratio greater than 1%). These results suggest that galaxies that fall into clusters lose their cold gas within a single radial round-trip. PMID:24843167

Gas loss in simulated galaxies as they fall into clusters.

PubMed

Cen, Renyue; Pop, Ana Roxana; Bahcall, Neta A

2014-06-03

We use high-resolution cosmological hydrodynamic galaxy formation simulations to gain insights into how galaxies lose their cold gas at low redshift as they migrate from the field to the high-density regions of clusters of galaxies. We find that beyond three cluster virial radii, the fraction of gas-rich galaxies is constant, representing the field. Within three cluster-centric radii, the fraction of gas-rich galaxies declines steadily with decreasing radius, reaching <10% near the cluster center. Our results suggest galaxies start to feel the effect of the cluster environment on their gas content well beyond the cluster virial radius. We show that almost all gas-rich galaxies at the cluster virial radius are falling in for the first time at nearly radial orbits. Furthermore, we find that almost no galaxy moving outward at the cluster virial radius is gas-rich (with a gas-to-baryon ratio greater than 1%). These results suggest that galaxies that fall into clusters lose their cold gas within a single radial round-trip.

PRISM 3: expanded prediction of natural product chemical structures from microbial genomes

PubMed Central

Skinnider, Michael A.; Merwin, Nishanth J.; Johnston, Chad W.

2017-01-01

Abstract Microbial natural products represent a rich resource of pharmaceutically and industrially important compounds. Genome sequencing has revealed that the majority of natural products remain undiscovered, and computational methods to connect biosynthetic gene clusters to their corresponding natural products therefore have the potential to revitalize natural product discovery. Previously, we described PRediction Informatics for Secondary Metabolomes (PRISM), a combinatorial approach to chemical structure prediction for genetically encoded nonribosomal peptides and type I and II polyketides. Here, we present a ground-up rewrite of the PRISM structure prediction algorithm to derive prediction of natural products arising from non-modular biosynthetic paradigms. Within this new version, PRISM 3, natural product scaffolds are modeled as chemical graphs, permitting structure prediction for aminocoumarins, antimetabolites, bisindoles and phosphonate natural products, and building upon the addition of ribosomally synthesized and post-translationally modified peptides. Further, with the addition of cluster detection for 11 new cluster types, PRISM 3 expands to detect 22 distinct natural product cluster types. Other major modifications to PRISM include improved sequence input and ORF detection, user-friendliness and output. Distribution of PRISM 3 over a 300-core server grid improves the speed and capacity of the web application. PRISM 3 is available at http://magarveylab.ca/prism/. PMID:28460067

Deep CCD Photometry of the Rich Galaxy Cluster Abel 1656 Characteristics of the Dwarf Elliptical Galaxy Population in the Cluster Core

NASA Astrophysics Data System (ADS)

Secker, Jeffrey Alan

1995-01-01

We have developed a statistically rigorous and automated method to implement the detection, photometry and classification of faint objects on digital images. We use these methods to analyze deep R- and B-band CCD images of the central ~ 700 arcmin ^2 of the Coma cluster core, and an associated control field. We have detected and measured total R magnitudes and (B-R) colors for a sample of 3741 objects on the galaxy cluster fields, and 1164 objects on a remote control field, complete to a limiting magnitude of R = 22.5 mag. The typical uncertainties are +/- 0.06 and +/-0.12 mag in total magnitude and color respectively. The dwarf elliptical (dE) galaxies are confined to a well-defined sequence in the color range given by 0.7<= (B-R)<= 1.9 mag: within this interval there are 2535 dE candidates on our fields in the cluster core, and 694 objects on the control field. With an image scale of 0.53 arcsec/pixel and seeing near 1.2 arcsec, a large fraction of the dE galaxy candidates are resolved. We find a significant metallicity gradient in the radial distribution of the dwarf elliptical galaxies, which goes as Z~ R^{-0.32 } outwards from the cluster center at NGC 4874. As well, there is a strong color-luminosity correlation, in the sense that more luminous dE galaxies are redder in the mean. These effects give rise to a radial variation in the cluster luminosity function. The spatial distribution of the faint dE galaxies is well fit by a standard King model with a central surface density of Sigma _0 = 1.44 dEs arcmin^{ -2}, a core radius R_{ rm c} = 18.7 arcmin (~eq 0.44 Mpc), and a tidal radius of 1.44 deg ( ~eq 2.05 Mpc). This core is significantly larger than R_{rm c} = 12.3 arcmin (~eq 0.29 Mpc) found for the bright cluster galaxies. The composite luminosity function for Coma galaxies is modeled as the sum of a log -normal distribution for the giant galaxies and a Schechter function for the dwarf elliptical galaxies, with a faint -end slope of alpha = -1.41, consistent with known faint-end slopes for the Virgo and Fornax clusters. The early-type dwarf-to-giant ratio for the Coma cluster core is consistent with that of the Virgo cluster, and thus with the rich Coma cluster being formed as the merger of multiple less-rich galaxy clusters.

Fluorescent DNA-templated silver nanoclusters

NASA Astrophysics Data System (ADS)

Lin, Ruoqian

Because of the ultra-small size and biocompatibility of silver nanoclusters, they have attracted much research interest for their applications in biolabeling. Among the many ways of synthesizing silver nanoclusters, DNA templated method is particularly attractive---the high tunability of DNA sequences provides another degree of freedom for controlling the chemical and photophysical properties. However, systematic studies about how DNA sequences and concentrations are controlling the photophysical properties are still lacking. The aim of this thesis is to investigate the binding mechanisms of silver clusters binding and single stranded DNAs. Here in this thesis, we report synthesis and characterization of DNA-templated silver nanoclusters and provide a systematic interrogation of the effects of DNA concentrations and sequences, including lengths and secondary structures. We performed a series of syntheses utilizing five different sequences to explore the optimal synthesis condition. By characterizing samples with UV-vis and fluorescence spectroscopy, we achieved the most proper reactants ratio and synthesis conditions. Two of them were chosen for further concentration dependence studies and sequence dependence studies. We found that cytosine-rich sequences are more likely to produce silver nanoclusters with stronger fluorescence signals; however, sequences with hairpin secondary structures are more capable in stabilizing silver nanoclusters. In addition, the fluorescence peak emission intensities and wavelengths of the DNA templated silver clusters have sequence dependent fingerprints. This potentially can be applied to sequence sensing in the future. However all the current conclusions are not warranted; there is still difficulty in formulating general rules in DNA strand design and silver nanocluster production. Further investigation of more sequences could solve these questions in the future.

Do satellite galaxies trace matter in galaxy clusters?

NASA Astrophysics Data System (ADS)

Wang, Chunxiang; Li, Ran; Gao, Liang; Shan, Huanyuan; Kneib, Jean-Paul; Wang, Wenting; Chen, Gang; Makler, Martin; Pereira, Maria E. S.; Wang, Lin; Maia, Marcio A. G.; Erben, Thomas

2018-04-01

The spatial distribution of satellite galaxies encodes rich information of the structure and assembly history of galaxy clusters. In this paper, we select a red-sequence Matched-filter Probabilistic Percolation cluster sample in SDSS Stripe 82 region with 0.1 ≤ z ≤ 0.33, 20 < λ < 100, and Pcen > 0.7. Using the high-quality weak lensing data from CS82 Survey, we constrain the mass profile of this sample. Then we compare directly the mass density profile with the satellite number density profile. We find that the total mass and number density profiles have the same shape, both well fitted by an NFW profile. The scale radii agree with each other within a 1σ error (r_s,gal=0.34_{-0.03}^{+0.04} Mpc versus r_s=0.37_{-0.10}^{+0.15} Mpc).

Clasificación de asterismos utilizando datos astrométricos

NASA Astrophysics Data System (ADS)

de Biasi, M. S.; Orellana, R. B.

Based on accurate positions and proper motion data up to faint magnitudes, we have studied the regions of twenty three objects known in the literature as asterisms. A parametric method was applied to confirm the nature of these objects. The following objects have been classified: Alessi 11, Alessi 17, Brosch 1, Collinder 21, Dol-Dzim 1, Dolidze 31, Dolidze 43, Dolidze 50, Dolidze 51, NGC 272, NGC2063, NGC 2413, NGC 2664, NGC 5155, NGC 5284, NGC 6222, NGC 6360, NGC 6447, NGC 6476, NGC 6480, NGC 6605, NGC 6659, NGC 6728. FULL TEXT IN SPANISH

Do protein crystals nucleate within dense liquid clusters?

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

Maes, Dominique, E-mail: dommaes@vub.ac.be; Vorontsova, Maria A.; Potenza, Marco A. C.

2015-06-27

The evolution of protein-rich clusters and nucleating crystals were characterized by dynamic light scattering (DLS), confocal depolarized dynamic light scattering (cDDLS) and depolarized oblique illumination dark-field microscopy. Newly nucleated crystals within protein-rich clusters were detected directly. These observations indicate that the protein-rich clusters are locations for crystal nucleation. Protein-dense liquid clusters are regions of high protein concentration that have been observed in solutions of several proteins. The typical cluster size varies from several tens to several hundreds of nanometres and their volume fraction remains below 10{sup −3} of the solution. According to the two-step mechanism of nucleation, the protein-rich clustersmore » serve as locations for and precursors to the nucleation of protein crystals. While the two-step mechanism explained several unusual features of protein crystal nucleation kinetics, a direct observation of its validity for protein crystals has been lacking. Here, two independent observations of crystal nucleation with the proteins lysozyme and glucose isomerase are discussed. Firstly, the evolutions of the protein-rich clusters and nucleating crystals were characterized simultaneously by dynamic light scattering (DLS) and confocal depolarized dynamic light scattering (cDDLS), respectively. It is demonstrated that protein crystals appear following a significant delay after cluster formation. The cDDLS correlation functions follow a Gaussian decay, indicative of nondiffusive motion. A possible explanation is that the crystals are contained inside large clusters and are driven by the elasticity of the cluster surface. Secondly, depolarized oblique illumination dark-field microscopy reveals the evolution from liquid clusters without crystals to newly nucleated crystals contained in the clusters to grown crystals freely diffusing in the solution. Collectively, the observations indicate that the protein-rich clusters in lysozyme and glucose isomerase solutions are locations for crystal nucleation.« less

The weak lensing analysis of the CFHTLS and NGVS RedGOLD galaxy clusters

NASA Astrophysics Data System (ADS)

Parroni, C.; Mei, S.; Erben, T.; Van Waerbeke, L.; Raichoor, A.; Ford, J.; Licitra, R.; Meneghetti, M.; Hildebrandt, H.; Miller, L.; Côté, P.; Covone, G.; Cuillandre, J.-C.; Duc, P.-A.; Ferrarese, L.; Gwyn, S. D. J.; Puzia, T. H.

2017-12-01

An accurate estimation of galaxy cluster masses is essential for their use in cosmological and astrophysical studies. We studied the accuracy of the optical richness obtained by our RedGOLD cluster detection algorithm tep{licitra2016a, licitra2016b} as a mass proxy, using weak lensing and X-ray mass measurements. We measured stacked weak lensing cluster masses for a sample of 1323 galaxy clusters in the Canada-France-Hawaii Telescope Legacy Survey W1 and the Next Generation Virgo Cluster Survey at 0.2

Abundance patterns of evolved stars with Hipparcos parallaxes and ages based on the APOGEE data base

NASA Astrophysics Data System (ADS)

Jia, Y. P.; Chen, Y. Q.; Zhao, G.; Bari, M. A.; Zhao, J. K.; Tan, K. F.

2018-01-01

We investigate the abundance patterns for four groups of stars at evolutionary phases from sub-giant to red clump (RC) and trace the chemical evolution of the disc by taking 21 individual elemental abundances from APOGEE and ages from evolutionary models with the aid of Hipparcos distances. We find that the abundances of six elements (Si, S, K, Ca, Mn and Ni) are similar from the sub-giant phase to the RC phase. In particular, we find that a group of stars with low [C/N] ratios, mainly from the second sequence of RC stars, show that there is a difference in the transfer efficiency of the C-N-O cycle between the main and the secondary RC sequences. We also compare the abundance patterns of C-N, Mg-Al and Na-O with giant stars in globular clusters from APOGEE and find that field stars follow similar patterns as M107, a metal-rich globular cluster with [M/H] ∼- 1.0, which shows that the self-enrichment mechanism represented by strong C-N, Mg-Al and Na-O anti-correlations may not be important as the metallicity reaches [M/H] > -1.0 dex. Based on the abundances of above-mentioned six elements and [Fe/H], we investigate age versus abundance relations and find some old super-metal-rich stars in our sample. Their properties of old age and being rich in metal are evidence for stellar migration. The age versus metallicity relations in low-[α/M] bins show unexpectedly positive slopes. We propose that the fresh metal-poor gas infalling on to the Galactic disc may be the precursor for this unexpected finding.

Structure of the highly repeated, long interspersed DNA family (LINE or L1Rn) of the rat.

PubMed Central

D'Ambrosio, E; Waitzkin, S D; Witney, F R; Salemme, A; Furano, A V

1986-01-01

We present the DNA sequence of a 6.7-kilobase member of the rat long interspersed repeated DNA family (LINE or L1Rn). This member (LINE 3) is flanked by a perfect 14-base-pair (bp) direct repeat and is a full-length, or close-to-full-length, member of this family. LINE 3 contains an approximately 100-bp A-rich right end, a number of long (greater than 400-bp) open reading frames, and a ca. 200-bp G + C-rich (ca. 60%) cluster near each terminus. Comparison of the LINE 3 sequence with the sequence of about one-half of another member, which we also present, as well as restriction enzyme analysis of the genomic copies of this family, indicates that in length and overall structure LINE 3 is quite typical of the 40,000 or so other genomic members of this family which would account for as much as 10% of the rat genome. Therefore, the rat LINE family is relatively homogeneous, which contrasts with the heterogeneous LINE families in primates and mice. Transcripts corresponding to the entire LINE sequence are abundant in the nuclear RNA of rat liver. The characteristics of the rat LINE family are discussed with respect to the possible function and evolution of this family of DNA sequences. Images PMID:3023845

Clustering environments of BL Lac objects

NASA Technical Reports Server (NTRS)

Wurtz, Ronald; Ellingson, Erica; Stocke, John T.; Yee, H. K. C.

1993-01-01

We report measurements of the amplitude of the BL Lac galaxy spatial covariance function, B(gb), for the fields of five BL Lacertae objects. We present evidence for rich clusters around MS 1207+39 and MS 1407+59, and confirm high richness for the cluster containing H0414+009. We discuss the ease of 3C 66 A and find evidence for a poor cluster based on an uncertain redshift of z = 0.444. These data suggest that at least some BL Lac objects are consistent with being FR 1 radio galaxies in rich clusters.

An optical catalog of galaxy clusters obtained from an adaptive matched filter finder applied to SDSS DR9 data

NASA Astrophysics Data System (ADS)

Banerjee, P.; Szabo, T.; Pierpaoli, E.; Franco, G.; Ortiz, M.; Oramas, A.; Tornello, B.

2018-01-01

We present a new galaxy cluster catalog constructed from the Sloan Digital Sky Survey Data Release 9 (SDSS DR9) using an Adaptive Matched Filter (AMF) technique. Our catalog has 46,479 galaxy clusters with richness Λ200 > 20 in the redshift range 0.045 ≤ z < 0.641 in ∼11,500 deg2 of the sky. Angular position, richness, core and virial radii and redshift estimates for these clusters, as well as their error analysis, are provided as part of this catalog. In addition to the main version of the catalog, we also provide an extended version with a lower richness cut, containing 79,368 clusters. This version, in addition to the clusters in the main catalog, also contains those clusters (with richness 10 < Λ200 < 20) which have a one-to-one match in the DR8 catalog developed by Wen et al.(WHL). We obtain probabilities for cluster membership for each galaxy and implement several procedures for the identification and removal of false cluster detections. We cross-correlate the main AMF DR9 catalog with a number of cluster catalogs in different wavebands (Optical, X-ray). We compare our catalog with other SDSS-based ones such as the redMaPPer (26,350 clusters) and the Wen et al. (WHL) (132,684 clusters) in the same area of the sky and in the overlapping redshift range. We match 97% of the richest Abell clusters (Richness group 3), the same as WHL, while redMaPPer matches ∼ 90% of these clusters. Considering AMF DR9 richness bins, redMaPPer does not have one-to-one matches for 70% of our lowest richness clusters (20 < Λ200 < 40), while WHL matches 54% of these missed clusters (not present in redMaPPer). redMaPPer consistently does not possess one-to-one matches for ∼ 20% AMF DR9 clusters with Λ200 > 40, while WHL matches ≥ 70% of these missed clusters on average. For comparisons with X-ray clusters, we match the AMF catalog with BAX, MCXC and a combined catalog from NORAS and REFLEX. We consistently obtain a greater number of one-to-one matches for X-ray clusters across higher luminosity bins (Lx > 6 × 1044 ergs/sec) than redMaPPer while WHL matches the most clusters overall. For the most luminous clusters (Lx > 8), our catalog performs equivalently to WHL. This new catalog provides a wider sample than redMaPPer while retaining many fewer objects than WHL.

Cluster redshifts in five suspected superclusters

NASA Technical Reports Server (NTRS)

Ciardullo, R.; Ford, H.; Harms, R.

1985-01-01

Redshift surveys for rich superclusters were carried out in five regions of the sky containing surface-density enhancements of Abell clusters. While several superclusters are identified, projection effects dominate each field, and no system contains more than five rich clusters. Two systems are found to be especially interesting. The first, field 0136 10, is shown to contain a superposition of at least four distinct superclusters, with the richest system possessing a small velocity dispersion. The second system, 2206 - 22, though a region of exceedingly high Abell cluster surface density, appears to be a remarkable superposition of 23 rich clusters almost uniformly distributed in redshift space between 0.08 and 0.24. The new redshifts significantly increase the three-dimensional information available for the distance class 5 and 6 Abell clusters and allow the spatial correlation function around rich superclusters to be estimated.

Constraining the mass–richness relationship of redMaPPer clusters with angular clustering

DOE PAGES

Baxter, Eric J.; Rozo, Eduardo; Jain, Bhuvnesh; ...

2016-08-04

The potential of using cluster clustering for calibrating the mass–richness relation of galaxy clusters has been recognized theoretically for over a decade. In this paper, we demonstrate the feasibility of this technique to achieve high-precision mass calibration using redMaPPer clusters in the Sloan Digital Sky Survey North Galactic Cap. By including cross-correlations between several richness bins in our analysis, we significantly improve the statistical precision of our mass constraints. The amplitude of the mass–richness relation is constrained to 7 per cent statistical precision by our analysis. However, the error budget is systematics dominated, reaching a 19 per cent total errormore » that is dominated by theoretical uncertainty in the bias–mass relation for dark matter haloes. We confirm the result from Miyatake et al. that the clustering amplitude of redMaPPer clusters depends on galaxy concentration as defined therein, and we provide additional evidence that this dependence cannot be sourced by mass dependences: some other effect must account for the observed variation in clustering amplitude with galaxy concentration. Assuming that the observed dependence of redMaPPer clustering on galaxy concentration is a form of assembly bias, we find that such effects introduce a systematic error on the amplitude of the mass–richness relation that is comparable to the error bar from statistical noise. Finally, the results presented here demonstrate the power of cluster clustering for mass calibration and cosmology provided the current theoretical systematics can be ameliorated.« less

VizieR Online Data Catalog: Clusters of galaxies in SDSS-III (Wen+, 2012)

NASA Astrophysics Data System (ADS)

Wen, Z. L.; Han, J. L.; Liu, F. S.

2012-06-01

Wen et al. (2009, Cat. J/ApJS/183/197) identified 39668 galaxy clusters from the SDSS DR6 by the discrimination of member galaxies of clusters using photometric redshifts of galaxies. Wen & Han (2011ApJ...734...68W) improved the method and successfully identified the high-redshift clusters from the deep fields of the Canada-France-Hawaii Telescope (CFHT) Wide survey, the CHFT Deep survey, the Cosmic Evolution Survey, and the Spitzer Wide-area InfraRed Extragalactic survey. Here, we follow and improve the algorithm to identify clusters from SDSS-III (SDSS Data Release 8; Aihara et al. 2011ApJS..193...29A, see Cat. II/306). (1 data file).

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.

The Richness of Task-Evoked Hemodynamic Responses Defines a Pseudohierarchy of Functionally Meaningful Brain Networks

PubMed Central

Orban, Pierre; Doyon, Julien; Petrides, Michael; Mennes, Maarten; Hoge, Richard; Bellec, Pierre

2015-01-01

Functional magnetic resonance imaging can measure distributed and subtle variations in brain responses associated with task performance. However, it is unclear whether the rich variety of responses observed across the brain is functionally meaningful and consistent across individuals. Here, we used a multivariate clustering approach that grouped brain regions into clusters based on the similarity of their task-evoked temporal responses at the individual level, and then established the spatial consistency of these individual clusters at the group level. We observed a stable pseudohierarchy of task-evoked networks in the context of a delayed sequential motor task, where the fractionation of networks was driven by a gradient of involvement in motor sequence preparation versus execution. In line with theories about higher-level cognitive functioning, this gradient evolved in a rostro-caudal manner in the frontal lobe. In addition, parcellations in the cerebellum and basal ganglia matched with known anatomical territories and fiber pathways with the cerebral cortex. These findings demonstrate that subtle variations in brain responses associated with task performance are systematic enough across subjects to define a pseudohierarchy of task-evoked networks. Such networks capture meaningful functional features of brain organization as shaped by a given cognitive context. PMID:24729172

Distal regulatory regions restrict the expression of cis-linked genes to the tapetal cells.

PubMed

Franco, Luciana O; de O Manes, Carmem Lara; Hamdi, Said; Sachetto-Martins, Gilberto; de Oliveira, Dulce E

2002-04-24

The oleosin glycine-rich protein genes Atgrp-6, Atgrp-7, and Atgrp-8 occur in clusters in the Arabidopsis genome and are expressed specifically in the tapetum cells. The cis-regulatory regions involved in the tissue-specific gene expression were investigated by fusing different segments of the gene cluster to the uidA reporter gene. Common distal regulatory regions were identified that coordinate expression of the sequential genes. At least two of these genes were regulated spatially by proximal and distal sequences. The cis-acting elements (122 bp upstream of the transcriptional start point) drive the uidA expression to floral tissues, whereas distal 5' upstream regions restrict the gene activity to tapetal cells.

Color-magnitude diagrams for six metal-rich, low-latitude globular clusters

NASA Technical Reports Server (NTRS)

Armandroff, Taft E.

1988-01-01

Colors and magnitudes for stars on CCD frames for six metal-rich, low-latitude, previously unstudied globular clusters and one well-studied, metal-rich cluster (47 Tuc) have been derived and color-magnitude diagrams have been constructed. The photometry for stars in 47 Tuc are in good agreement with previous studies, while the V magnitudes of the horizontal-branch stars in the six program clusters do not agree with estimates based on secondary methods. The distances to these clusters are different from prior estimates. Redding values are derived for each program cluster. The horizontal branches of the program clusters all appear to lie entirely redwards of the red edge of the instability strip, as is normal for their metallicities.

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.

Molecular basis of CENP-C association with the CENP-A nucleosome at yeast centromeres

PubMed Central

Xiao, Hua; Wang, Feng; Wisniewski, Jan; Shaytan, Alexey K.; Ghirlando, Rodolfo; FitzGerald, Peter C.; Huang, Yingzi; Wei, Debbie; Li, Shipeng; Landsman, David; Panchenko, Anna R.; Wu, Carl

2017-01-01

Histone CENP-A-containing nucleosomes play an important role in nucleating kinetochores at centromeres for chromosome segregation. However, the molecular mechanisms by which CENP-A nucleosomes engage with kinetochore proteins are not well understood. Here, we report the finding of a new function for the budding yeast Cse4/CENP-A histone-fold domain interacting with inner kinetochore protein Mif2/CENP-C. Strikingly, we also discovered that AT-rich centromere DNA has an important role for Mif2 recruitment. Mif2 contacts one side of the nucleosome dyad, engaging with both Cse4 residues and AT-rich nucleosomal DNA. Both interactions are directed by a contiguous DNA- and histone-binding domain (DHBD) harboring the conserved CENP-C motif, an AT hook, and RK clusters (clusters enriched for arginine–lysine residues). Human CENP-C has two related DHBDs that bind preferentially to DNA sequences of higher AT content. Our findings suggest that a DNA composition-based mechanism together with residues characteristic for the CENP-A histone variant contribute to the specification of centromere identity. PMID:29074736

Aryl-Aryl Interactions in Designed Peptide Folds: Spectroscopic Characteristics and Placement Issues for Optimal Structure Stabilization

PubMed Central

Anderson, Jordan M.; Kier, Brandon; Jurban, Brice; Byrne, Aimee; Shu, Irene; Eidenschink, Lisa A.; Shcherbakov, Alexander A.; Hudson, Mike; Fesinmeyer, R. M.; Andersen, Niels H.

2017-01-01

We have extended our studies of Trp/Trp to other Aryl/Aryl through-space interactions that stabilize hairpins and other small polypeptide folds. Herein we detail the NMR and CD spectroscopic features of these types of interactions. NMR data remains the best diagnostic for characterizing the common T-shape orientation. Designated as an edge-to-face (EtF or FtE) interaction, large ring current shifts are produced at the edge aryl ring hydrogens and, in most cases, large exciton couplets appear in the far UV circular dichroic (CD) spectrum. The preference for the face aryl in FtE clusters is W≫Y≥F (there are some exceptions in the Y/F order); this sequence corresponds to the order of fold stability enhancement and always predicts the amplitude of the lower energy feature of the exciton couplet in the CD spectrum. The CD spectra for FtE W/W, W/Y, Y/W, and Y/Y pairs all include an intense feature at 225–232 nm. An additional couplet feature seen for W/Y, W/F, Y/Y and F/Y clusters, is a negative feature at 197–200 nm. Tyr/Tyr (as well as F/Y and F/F) interactions produce much smaller exciton couplet amplitudes. The Trp-cage fold was employed to search for the CD effects of other Trp/Trp and Trp/Tyr cluster geometries: several were identified. In this account, we provide additional examples of the application of cross-strand aryl/aryl clusters for the design of stable β-sheet models and a scale of fold stability increments associated with all possible FtE Ar/Ar clusters in several structural contexts. PMID:26850220

PRISM 3: expanded prediction of natural product chemical structures from microbial genomes.

PubMed

Skinnider, Michael A; Merwin, Nishanth J; Johnston, Chad W; Magarvey, Nathan A

2017-07-03

Microbial natural products represent a rich resource of pharmaceutically and industrially important compounds. Genome sequencing has revealed that the majority of natural products remain undiscovered, and computational methods to connect biosynthetic gene clusters to their corresponding natural products therefore have the potential to revitalize natural product discovery. Previously, we described PRediction Informatics for Secondary Metabolomes (PRISM), a combinatorial approach to chemical structure prediction for genetically encoded nonribosomal peptides and type I and II polyketides. Here, we present a ground-up rewrite of the PRISM structure prediction algorithm to derive prediction of natural products arising from non-modular biosynthetic paradigms. Within this new version, PRISM 3, natural product scaffolds are modeled as chemical graphs, permitting structure prediction for aminocoumarins, antimetabolites, bisindoles and phosphonate natural products, and building upon the addition of ribosomally synthesized and post-translationally modified peptides. Further, with the addition of cluster detection for 11 new cluster types, PRISM 3 expands to detect 22 distinct natural product cluster types. Other major modifications to PRISM include improved sequence input and ORF detection, user-friendliness and output. Distribution of PRISM 3 over a 300-core server grid improves the speed and capacity of the web application. PRISM 3 is available at http://magarveylab.ca/prism/. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

The insignificant evolution of the richness-mass relation of galaxy clusters

NASA Astrophysics Data System (ADS)

Andreon, S.; Congdon, P.

2014-08-01

We analysed the richness-mass scaling of 23 very massive clusters at 0.15 < z < 0.55 with homogenously measured weak-lensing masses and richnesses within a fixed aperture of 0.5 Mpc radius. We found that the richness-mass scaling is very tight (the scatter is <0.09 dex with 90% probability) and independent of cluster evolutionary status and morphology. This implies a close association between infall and evolution of dark matter and galaxies in the central region of clusters. We also found that the evolution of the richness-mass intercept is minor at most, and, given the minor mass evolution across the studied redshift range, the richness evolution of individual massive clusters also turns out to be very small. Finally, it was paramount to account for the cluster mass function and the selection function. Ignoring them would lead to larger biases than the (otherwise quoted) errors. Our study benefits from: a) weak-lensing masses instead of proxy-based masses thereby removing the ambiguity between a real trend and one induced by an accounted evolution of the used mass proxy; b) the use of projected masses that simplify the statistical analysis thereby not requiring consideration of the unknown covariance induced by the cluster orientation/triaxiality; c) the use of aperture masses as they are free of the pseudo-evolution of mass definitions anchored to the evolving density of the Universe; d) a proper accounting of the sample selection function and of the Malmquist-like effect induced by the cluster mass function; e) cosmological simulations for the computation of the cluster mass function, its evolution, and the mass growth of each individual cluster.

THE MASS-RICHNESS RELATION OF MaxBCG CLUSTERS FROM QUASAR LENSING MAGNIFICATION USING VARIABILITY

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

Bauer, Anne H.; Baltay, Charles; Ellman, Nancy

2012-04-10

Accurate measurement of galaxy cluster masses is an essential component not only in studies of cluster physics but also for probes of cosmology. However, different mass measurement techniques frequently yield discrepant results. The Sloan Digital Sky Survey MaxBCG catalog's mass-richness relation has previously been constrained using weak lensing shear, Sunyaev-Zeldovich (SZ), and X-ray measurements. The mass normalization of the clusters as measured by weak lensing shear is {approx}>25% higher than that measured using SZ and X-ray methods, a difference much larger than the stated measurement errors in the analyses. We constrain the mass-richness relation of the MaxBCG galaxy cluster catalogmore » by measuring the gravitational lensing magnification of type I quasars in the background of the clusters. The magnification is determined using the quasars' variability and the correlation between quasars' variability amplitude and intrinsic luminosity. The mass-richness relation determined through magnification is in agreement with that measured using shear, confirming that the lensing strength of the clusters implies a high mass normalization and that the discrepancy with other methods is not due to a shear-related systematic measurement error. We study the dependence of the measured mass normalization on the cluster halo orientation. As expected, line-of-sight clusters yield a higher normalization; however, this minority of haloes does not significantly bias the average mass-richness relation of the catalog.« less

Nucleotide sequence analysis of the gene encoding the Deinococcus radiodurans surface protein, derived amino acid sequence, and complementary protein chemical studies

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

Peters, J.; Peters, M.; Lottspeich, F.

1987-11-01

The complete nucleotide sequence of the gene encoding the surface (hexagonally packed intermediate (HPI))-layer polypeptide of Deinococcus radiodurans Sark was determined and found to encode a polypeptide of 1036 amino acids. Amino acid sequence analysis of about 30% of the residues revealed that the mature polypeptide consists of at least 978 amino acids. The N terminus was blocked to Edman degradation. The results of proteolytic modification of the HPI layer in situ and M/sub r/ estimations of the HPI polypeptide expressed in Escherichia coli indicated that there is a leader sequence. The N-terminal region contained a very high percentage (29%)more » of threonine and serine, including a cluster of nine consecutive serine or threonine residues, whereas a stretch near the C terminus was extremely rich in aromatic amino acids (29%). The protein contained at least two disulfide bridges, as well as tightly bound reducing sugars and fatty acids.« less

Two distinct Photobacterium populations thrive in ancient Mediterranean sapropels.

PubMed

Süss, Jacqueline; Herrmann, Kerstin; Seidel, Michael; Cypionka, Heribert; Engelen, Bert; Sass, Henrik

2008-04-01

Eastern Mediterranean sediments are characterized by the periodic occurrence of conspicuous, organic matter-rich sapropel layers. Phylogenetic analysis of a large culture collection isolated from these sediments revealed that about one third of the isolates belonged to the genus Photobacterium. In the present study, 22 of these strains were examined with respect to their phylogenetic and metabolic diversity. The strains belonged to two distinct Photobacterium populations (Mediterranean cluster I and II). Strains of cluster I were isolated almost exclusively from organic-rich sapropel layers and were closely affiliated with P. aplysiae (based on their 16S rRNA gene sequences). They possessed almost identical Enterobacterial Repetitive Intergenic Consensus (ERIC) and substrate utilization patterns, even among strains from different sampling sites or from layers differing up to 100,000 years in age. Strains of cluster II originated from sapropels and from the surface and carbon-lean intermediate layers. They were related to Photobacterium frigidiphilum but differed significantly in their fingerprint patterns and substrate spectra, even when these strains were obtained from the same sampling site and layer. Temperature range for growth (4 to 33 degrees C), salinity tolerance (5 to 100 per thousand), pH requirements (5.5-9.3), and the composition of polar membrane lipids were similar for both clusters. All strains grew by fermentation (glucose, organic acids) and all but five by anaerobic respiration (nitrate, dimethyl sulfoxide, anthraquinone disulfonate, or humic acids). These results indicate that the genus Photobacterium forms subsurface populations well adapted to life in the deep biosphere.

An insight into the sialotranscriptome of the seed-feeding bug, Oncopeltus fasciatus.

PubMed

Francischetti, Ivo M B; Lopes, Angela H; Dias, Felipe A; Pham, Van M; Ribeiro, José M C

2007-09-01

The salivary transcriptome of the seed-feeding hemipteran, Oncopeltus fasciatus (milkweed bug), is described following assembly of 1025 expressed sequence tags (ESTs) into 305 clusters of related sequences. Inspection of these sequences reveals abundance of low complexity, putative secreted products rich in the amino acids (aa) glycine, serine or threonine, which might function as silk or mucins and assist food canal lubrication and sealing of the feeding site around the mouthparts. Several protease inhibitors were found, including abundant expression of cystatin transcripts that may inhibit cysteine proteases common in seeds that might injure the insect or induce plant apoptosis. Serine proteases and lipases are described that might assist digestion and liquefaction of seed proteins and oils. Finally, several novel putative proteins are described with no known function that might affect plant physiology or act as antimicrobials.

Immune-Related Transcriptome of Coptotermes formosanus Shiraki Workers: The Defense Mechanism

PubMed Central

Hussain, Abid; Li, Yi-Feng; Cheng, Yu; Liu, Yang; Chen, Chuan-Cheng; Wen, Shuo-Yang

2013-01-01

Formosan subterranean termites, Coptotermes formosanus Shiraki, live socially in microbial-rich habitats. To understand the molecular mechanism by which termites combat pathogenic microbes, a full-length normalized cDNA library and four Suppression Subtractive Hybridization (SSH) libraries were constructed from termite workers infected with entomopathogenic fungi (Metarhizium anisopliae and Beauveria bassiana), Gram-positive Bacillus thuringiensis and Gram-negative Escherichia coli, and the libraries were analyzed. From the high quality normalized cDNA library, 439 immune-related sequences were identified. These sequences were categorized as pattern recognition receptors (47 sequences), signal modulators (52 sequences), signal transducers (137 sequences), effectors (39 sequences) and others (164 sequences). From the SSH libraries, 27, 17, 22 and 15 immune-related genes were identified from each SSH library treated with M. anisopliae, B. bassiana, B. thuringiensis and E. coli, respectively. When the normalized cDNA library was compared with the SSH libraries, 37 immune-related clusters were found in common; 56 clusters were identified in the SSH libraries, and 259 were identified in the normalized cDNA library. The immune-related gene expression pattern was further investigated using quantitative real time PCR (qPCR). Important immune-related genes were characterized, and their potential functions were discussed based on the integrated analysis of the results. We suggest that normalized cDNA and SSH libraries enable us to discover functional genes transcriptome. The results remarkably expand our knowledge about immune-inducible genes in C. formosanus Shiraki and enable the future development of novel control strategies for the management of Formosan subterranean termites. PMID:23874972

Crystal structure of the 3C protease from Southern African Territories type 2 foot-and-mouth disease virus

PubMed Central

Yang, Jingjie; Leen, Eoin N.; Maree, Francois F.

2016-01-01

The replication of foot-and-mouth disease virus (FMDV) is dependent on the virus-encoded 3C protease (3Cpro). As in other picornaviruses, 3Cpro performs most of the proteolytic processing of the polyprotein expressed from the large open reading frame in the RNA genome of the virus. Previous work revealed that the 3Cpro from serotype A—one of the seven serotypes of FMDV—adopts a trypsin-like fold. On the basis of capsid sequence comparisons the FMDV serotypes are grouped into two phylogenetic clusters, with O, A, C, and Asia 1 in one, and the three Southern African Territories serotypes, (SAT-1, SAT-2 and SAT-3) in another, a grouping pattern that is broadly, but not rigidly, reflected in 3Cpro amino acid sequences. We report here the cloning, expression and purification of 3C proteases from four SAT serotype viruses (SAT2/GHA/8/91, SAT1/NIG/5/81, SAT1/UGA/1/97, and SAT2/ZIM/7/83) and the crystal structure at 3.2 Å resolution of 3Cpro from SAT2/GHA/8/91. PMID:27168976

The bovine lactation genome: Insights into the evolution of mammalian milk

USDA-ARS?s Scientific Manuscript database

The newly assembled Bos Taurus genome sequence enables the linkage of bovine milk and lactation data with other mammalian genomes. Using publicly available milk proteome data and mammary expressed sequence tags, 197 milk protein genes and over 6,000 mammary genes were identified in the bovine genome...

Decompression Theory.

DTIC Science & Technology

1980-06-25

vessel- rich group, a vessel-poor group, a fatty group, and so on ( Papper and Kitz 1963). Behnke’s original suggestion, put forth in the first...An examination of the critical released volume concept in decom- pression sickness. Proc. Roy. Soc. Lond. B. 197:299-313, 1977. Papper , E.M., and R.J

X-ray emission from a complete sample of Abell clusters of galaxies

NASA Astrophysics Data System (ADS)

Briel, Ulrich G.; Henry, J. Patrick

1993-11-01

The ROSAT All-Sky Survey (RASS) is used to investigate the X-ray properties of a complete sample of Abell clusters with measured redshifts and accurate positions. The sample comprises the 145 clusters within a 561 square degree region at high galactic latitude. The mean redshift is 0.17. This sample is especially well suited to be studied within the RASS since the mean exposure time is higher than average and the mean galactic column density is very low. These together produce a flux limit of about 4.2 x 10-13 erg/sq cm/s in the 0.5 to 2.5 keV energy band. Sixty-six (46%) individual clusters are detected at a significance level higher than 99.7% of which 7 could be chance coincidences of background or foreground sources. At redshifts greater than 0.3 six clusters out of seven (86%) are detected at the same significance level. The detected objects show a clear X-ray luminosity -- galaxy count relation with a dispersion consistent with other external estimates of the error in the counts. By analyzing the excess of positive fluctuations of the X-ray flux at the cluster positions, compared with the fluctuations of randomly drawn background fields, it is possible to extend these results below the nominal flux limit. We find 80% of richness R greater than or = 0 and 86% of R greater than or = 1 clusters are X-ray emitters with fluxes above 1 x 10-13 erg/sq cm/s. Nearly 90% of the clusters meeting the requirements to be in Abell's statistical sample emit above the same level. We therefore conclude that almost all Abell clusters are real clusters and the Abell catalog is not strongly contaminated by projection effects. We use the Kaplan-Meier product limit estimator to calculate the cumulative X-ray luminosity function. We show that the shape of the luminosity functions are similiar for different richness classes, but the characteristic luminosities of richness 2 clusters are about twice those of richness 1 clusters which are in turn about twice those of richness 0 clusters. This result is another manifestation of the luminosity -- richness elation for Abell clusters.

Heterogeneic dynamics of the structures of multiple gene clusters in two pathogenetically different lines originating from the same phytoplasma.

PubMed

Arashida, Ryo; Kakizawa, Shigeyuki; Hoshi, Ayaka; Ishii, Yoshiko; Jung, Hee-Young; Kagiwada, Satoshi; Yamaji, Yasuyuki; Oshima, Kenro; Namba, Shigetou

2008-04-01

Phytoplasmas are phloem-limited plant pathogens that are transmitted by insect vectors and are associated with diseases in hundreds of plant species. Despite their small sizes, phytoplasma genomes have repeat-rich sequences, which are due to several genes that are encoded as multiple copies. These multiple genes exist in a gene cluster, the potential mobile unit (PMU). PMUs are present at several distinct regions in the phytoplasma genome. The multicopy genes encoded by PMUs (herein named mobile unit genes [MUGs]) and similar genes elsewhere in the genome (herein named fundamental genes [FUGs]) are likely to have the same function based on their annotations. In this manuscript we show evidence that MUGs and FUGs do not cluster together within the same clade. Each MUG is in a cluster with a short branch length, suggesting that MUGs are recently diverged paralogs, whereas the origin of FUGs is different from that of MUGs. We also compared the genome structures around the lplA gene in two derivative lines of the 'Candidatus Phytoplasma asteris' OY strain, the severe-symptom line W (OY-W) and the mild-symptom line M (OY-M). The gene organizations of the nucleotide sequences upstream of the lplA genes of OY-W and OY-M were dramatically different. The tra5 insertion sequence, an element of PMUs, was found only in this region in OY-W. These results suggest that transposition of entire PMUs and PMU sections has occurred frequently in the OY phytoplasma genome. The difference in the pathogenicities of OY-W and OY-M might be caused by the duplication and transposition of PMUs, followed by genome rearrangement.

Constraints on the richness-mass relation and the optical-SZE positional offset distribution for SZE-selected clusters

DOE PAGES

Saro, A.

2015-10-12

In this study, we cross-match galaxy cluster candidates selected via their Sunyaev–Zel'dovich effect (SZE) signatures in 129.1 deg 2 of the South Pole Telescope 2500d SPT-SZ survey with optically identified clusters selected from the Dark Energy Survey science verification data. We identify 25 clusters between 0.1 ≲ z ≲ 0.8 in the union of the SPT-SZ and redMaPPer (RM) samples. RM is an optical cluster finding algorithm that also returns a richness estimate for each cluster. We model the richness λ-mass relation with the following function 500> ∝ B λlnM 500 + C λlnE(z) and use SPT-SZ cluster masses andmore » RM richnesses λ to constrain the parameters. We find B λ = 1.14 +0.21 –0.18 and C λ = 0.73 +0.77 –0.75. The associated scatter in mass at fixed richness is σ lnM|λ = 0.18 +0.08 –0.05 at a characteristic richness λ = 70. We demonstrate that our model provides an adequate description of the matched sample, showing that the fraction of SPT-SZ-selected clusters with RM counterparts is consistent with expectations and that the fraction of RM-selected clusters with SPT-SZ counterparts is in mild tension with expectation. We model the optical-SZE cluster positional offset distribution with the sum of two Gaussians, showing that it is consistent with a dominant, centrally peaked population and a subdominant population characterized by larger offsets. We also cross-match the RM catalogue with SPT-SZ candidates below the official catalogue threshold significance ξ = 4.5, using the RM catalogue to provide optical confirmation and redshifts for 15 additional clusters with ξ ϵ [4, 4.5].« less

High-resolution picture of a venom gland transcriptome: case study with the marine snail Conus consors.

PubMed

Terrat, Yves; Biass, Daniel; Dutertre, Sébastien; Favreau, Philippe; Remm, Maido; Stöcklin, Reto; Piquemal, David; Ducancel, Frédéric

2012-01-01

Although cone snail venoms have been intensively investigated in the past few decades, little is known about the whole conopeptide and protein content in venom ducts, especially at the transcriptomic level. If most of the previous studies focusing on a limited number of sequences have contributed to a better understanding of conopeptide superfamilies, they did not give access to a complete panorama of a whole venom duct. Additionally, rare transcripts were usually not identified due to sampling effect. This work presents the data and analysis of a large number of sequences obtained from high throughput 454 sequencing technology using venom ducts of Conus consors, an Indo-Pacific living piscivorous cone snail. A total of 213,561 Expressed Sequence Tags (ESTs) with an average read length of 218 base pairs (bp) have been obtained. These reads were assembled into 65,536 contiguous DNA sequences (contigs) then into 5039 clusters. The data revealed 11 conopeptide superfamilies representing a total of 53 new isoforms (full length or nearly full-length sequences). Considerable isoform diversity and major differences in transcription level could be noted between superfamilies. A, O and M superfamilies are the most diverse. The A family isoforms account for more than 70% of the conopeptide cocktail (considering all ESTs before clustering step). In addition to traditional superfamilies and families, minor transcripts including both cysteine free and cysteine-rich peptides could be detected, some of them figuring new clades of conopeptides. Finally, several sets of transcripts corresponding to proteins commonly recruited in venom function could be identified for the first time in cone snail venom duct. This work provides one of the first large-scale EST project for a cone snail venom duct using next-generation sequencing, allowing a detailed overview of the venom duct transcripts. This leads to an expanded definition of the overall cone snail venom duct transcriptomic activity, which goes beyond the cysteine-rich conopeptides. For instance, this study enabled to detect proteins involved in common post-translational maturation and folding, and to reveal compounds classically involved in hemolysis and mechanical penetration of the venom into the prey. Further comparison with proteomic and genomic data will lead to a better understanding of conopeptides diversity and the underlying mechanisms involved in conopeptide evolution. Copyright © 2011 Elsevier Ltd. All rights reserved.

STAR - Copperhead Interface.

DTIC Science & Technology

1981-03-01

elements which fall outside the original box initiate new clusters. 65 ELL. CH ECK This routine provides the calculation which determines if a target...US Air Force Project Rand Report 3-152b-PR, March 197 88 INITIAL DISTRIBUTION LIST 1o. Copies 1. Defense Technical Information Center 2 Cameron

Carrier priming with CRM 197 or diphtheria toxoid has a different impact on the immunogenicity of the respective glycoconjugates: biophysical and immunochemical interpretation.

PubMed

Pecetta, S; Lo Surdo, P; Tontini, M; Proietti, D; Zambonelli, C; Bottomley, M J; Biagini, M; Berti, F; Costantino, P; Romano, M R

2015-01-03

Glycoconjugate vaccines play an enormous role in preventing infectious diseases. The main carrier proteins used in commercial conjugate vaccines are the non-toxic mutant of diphtheria toxin (CRM197), diphtheria toxoid (DT) and tetanus toxoid (TT). Modern childhood routine vaccination schedules include the administration of several vaccines simultaneously or in close sequence, increasing the concern that the repeated exposure to conjugates based on these carrier proteins might interfere with the anti-polysaccharide response. Extending previous observations we show here that priming mice with CRM197 or DT does not suppress the response to the carbohydrate moiety of CRM197 meningococcal serogroup A (MenA) conjugates, while priming with DT can suppress the response to DT-MenA conjugates. To explain these findings we made use of biophysical and immunochemical techniques applied mainly to MenA conjugates. Differential scanning calorimetry and circular dichroism data revealed that the CRM197 structure was altered by the chemical conjugation, while DT and the formaldehyde-treated form of CRM197 were less impacted, depending on the degree of glycosylation. Investigating the binding and avidity properties of IgGs induced in mice by non-conjugated carriers, we found that CRM197 induced low levels of anti-carrier antibodies, with decreased avidity for its MenA conjugates and poor binding to DT and respective MenA conjugates. In contrast, DT induced high antibody titers able to bind with comparable avidity both the protein and its conjugates but showing very low avidity for CRM197 and related conjugates. The low intrinsic immunogenicity of CRM197 as compared to DT, the structural modifications induced by glycoconjugation and detoxification processes, resulting in conformational changes in CRM197 and DT epitopes with consequent alteration of the antibody recognition and avidity, might explain the different behavior of CRM197 and DT in a carrier priming context. Copyright © 2014 Elsevier Ltd. All rights reserved.

Evolution of long-lived globular cluster stars. III. Effect of the initial helium spread on the position of stars in a synthetic Hertzsprung-Russell diagram

NASA Astrophysics Data System (ADS)

Chantereau, W.; Charbonnel, C.; Meynet, G.

2016-08-01

Context. Globular clusters host multiple populations of long-lived low-mass stars whose origin remains an open question. Several scenarios have been proposed to explain the associated photometric and spectroscopic peculiarities. They differ, for instance, in the maximum helium enrichment they predict for stars of the second population, which these stars can inherit at birth as the result of the internal pollution of the cluster by different types of stars of the first population. Aims: We present the distribution of helium-rich stars in present-day globular clusters as it is expected in the original framework of the fast-rotating massive stars scenario (FRMS) as first-population polluters. We focus on NGC 6752. Methods: We completed a grid of 330 stellar evolution models for globular cluster low-mass stars computed with different initial chemical compositions corresponding to the predictions of the original FRMS scenario for [Fe/H] = -1.75. Starting from the initial helium-sodium relation that allows reproducing the currently observed distribution of sodium in NGC 6752, we deduce the helium distribution expected in that cluster at ages equal to 9 and 13 Gyr. We distinguish the stars that are moderately enriched in helium from those that are very helium-rich (initial helium mass fraction below and above 0.4, respectively), and compare the predictions of the FRMS framework with other scenarios for globular cluster enrichment. Results: The effect of helium enrichment on the stellar lifetime and evolution reduces the total number of very helium-rich stars that remain in the cluster at 9 and 13 Gyr to only 12% and 10%, respectively, from an initial fraction of 21%. Within this age range, most of the stars still burn their hydrogen in their core, which widens the MS band significantly in effective temperature. The fraction of very helium-rich stars drops in the more advanced evolution phases, where the associated spread in effective temperature strongly decreases. These stars even disappear from the horizontal branch and the asymptotic giant branch at 13 Gyr. Conclusions: The helium constraint is no suitable criterion for clearly distinguishing between the scenarios for GC self-enrichment because only few very helium-rich stars are predicted in the investigated framework and because it is difficult to derive the helium content of GC stars observationally. However, the helium constraint indicates some difficulties of the original FRMS scenario that require the exploration of alternatives. The files containing the relevant evolution characteristics of the complete grid of models from the pre-main sequence up to the end of the stellar life (see Appendix of Chantereau et al. 2015) 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/592/A111 As in Chantereau et al. (2015), we also provide all the tables on the website http://obswww.unige.ch/Recherche/evol/starevol/Globular.php

High-quality draft genome sequence of Rhizobium mesoamericanum strain STM6155, a Mimosa pudica microsymbiont from New Caledonia

DOE PAGES

Klonowska, Agnieszka; López-López, Aline; Moulin, Lionel; ...

2017-01-17

Rhizobium mesoamericanum STM6155 (INSCD=ATYY01000000) is an aerobic, motile, Gram-negative, non-spore-forming rod that can exist as a soil saprophyte or as an effective nitrogen fixing microsymbiont of the legume Mimosa pudica L.. STM6155 was isolated in 2009 from a nodule of the trap host M. pudica grown in nickel-rich soil collected near Mont Dore, New Caledonia. R. mesoamericanum STM6155 was selected as part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) genome sequencing project. Here we describe the symbiotic properties of R. mesoamericanum STM6155, together with its genome sequence information and annotation. Themore » 6,927,906bp high-quality draft genome is arranged into 147 scaffolds of 152 contigs containing 6855 protein-coding genes and 71 RNA-only encoding genes. Strain STM6155 forms an ANI clique (ID 2435) with the sequenced R. mesoamericanum strain STM3625, and the nodulation genes are highly conserved in these strains and the type strain of Rhizobium grahamii CCGE501 T . Within the STM6155 genome, we have identified a chr chromate efflux gene cluster of six genes arranged into two putative operons and we postulate that this cluster is important for the survival of STM6155 in ultramafic soils containing high concentrations of chromate.« less

Distribution and Diversity of Microbial Eukaryotes in Bathypelagic Waters of the South China Sea.

PubMed

Xu, Dapeng; Jiao, Nianzhi; Ren, Rui; Warren, Alan

2017-05-01

Little is known about the biodiversity of microbial eukaryotes in the South China Sea, especially in waters at bathyal depths. Here, we employed SSU rDNA gene sequencing to reveal the diversity and community structure across depth and distance gradients in the South China Sea. Vertically, the highest alpha diversity was found at 75-m depth. The communities of microbial eukaryotes were clustered into shallow-, middle-, and deep-water groups according to the depth from which they were collected, indicating a depth-related diversity and distribution pattern. Rhizaria sequences dominated the microeukaryote community and occurred in all samples except those from less than 50-m deep, being most abundant near the sea floor where they contributed ca. 64-97% and 40-74% of the total sequences and OTUs recovered, respectively. A large portion of rhizarian OTUs has neither a nearest named neighbor nor a nearest neighbor in the GenBank database which indicated the presence of new phylotypes in the South China Sea. Given their overwhelming abundance and richness, further phylogenetic analysis of rhizarians were performed and three new genetic clusters were revealed containing sequences retrieved from the deep waters of the South China Sea. Our results shed light on the diversity and community structure of microbial eukaryotes in this not yet fully explored area. © 2016 The Author(s) Journal of Eukaryotic Microbiology © 2016 International Society of Protistologists.

High-quality draft genome sequence of Rhizobium mesoamericanum strain STM6155, a Mimosa pudica microsymbiont from New Caledonia

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

Klonowska, Agnieszka; López-López, Aline; Moulin, Lionel

Rhizobium mesoamericanum STM6155 (INSCD=ATYY01000000) is an aerobic, motile, Gram-negative, non-spore-forming rod that can exist as a soil saprophyte or as an effective nitrogen fixing microsymbiont of the legume Mimosa pudica L.. STM6155 was isolated in 2009 from a nodule of the trap host M. pudica grown in nickel-rich soil collected near Mont Dore, New Caledonia. R. mesoamericanum STM6155 was selected as part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) genome sequencing project. Here we describe the symbiotic properties of R. mesoamericanum STM6155, together with its genome sequence information and annotation. Themore » 6,927,906bp high-quality draft genome is arranged into 147 scaffolds of 152 contigs containing 6855 protein-coding genes and 71 RNA-only encoding genes. Strain STM6155 forms an ANI clique (ID 2435) with the sequenced R. mesoamericanum strain STM3625, and the nodulation genes are highly conserved in these strains and the type strain of Rhizobium grahamii CCGE501 T . Within the STM6155 genome, we have identified a chr chromate efflux gene cluster of six genes arranged into two putative operons and we postulate that this cluster is important for the survival of STM6155 in ultramafic soils containing high concentrations of chromate.« less

Intrinsic alignment of redMaPPer clusters: cluster shape-matter density correlation

NASA Astrophysics Data System (ADS)

van Uitert, Edo; Joachimi, Benjamin

2017-07-01

We measure the alignment of the shapes of galaxy clusters, as traced by their satellite distributions, with the matter density field using the public redMaPPer catalogue based on Sloan Digital Sky Survey-Data Release 8 (SDSS-DR8), which contains 26 111 clusters up to z ˜ 0.6. The clusters are split into nine redshift and richness samples; in each of them, we detect a positive alignment, showing that clusters point towards density peaks. We interpret the measurements within the tidal alignment paradigm, allowing for a richness and redshift dependence. The intrinsic alignment (IA) amplitude at the pivot redshift z = 0.3 and pivot richness λ = 30 is A_IA^gen=12.6_{-1.2}^{+1.5}. We obtain tentative evidence that the signal increases towards higher richness and lower redshift. Our measurements agree well with results of maxBCG clusters and with dark-matter-only simulations. Comparing our results to the IA measurements of luminous red galaxies, we find that the IA amplitude of galaxy clusters forms a smooth extension towards higher mass. This suggests that these systems share a common alignment mechanism, which can be exploited to improve our physical understanding of IA.

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.

Spectroscopy of dwarf elliptical galaxies in the Fornax cluster

NASA Technical Reports Server (NTRS)

Held, Enrico V.; Mould, Jeremy R.

1994-01-01

We present the results of spectroscopic observations of 10 nucleated dwarf elliptical galaxies (dE's) in the Fornax cluster. The blue spectra of Fornax dE galaxies indicate a wide range of metallicities at a given luminosity, similar to those of intermediate to metal-rich globular clusters. Metal abundances derived in this paper are well correlated with optical colors and agree with previous spectroscopic results. A discrepancy with metallicities inferred from infrared colors is evident; possible causes include an intermediate age population and dilution of spectral features by a blue light excess. Dwarf ellipticals exhibit a wide variation of hydrogen line strength which points to a complex star formation history. Prominent Balmer absorption lines are the signature of a young stellar population in the nuclei of some (but not all) dE's, while moderately strong Balmer lines in relatively metal-rich dE's are more consistent with an extended main sequence. In a few metal-poor dE galaxies, the hydrogen lines are consisent with, or perhaps weaker than, those found in Galactic globulars of similar metallicity. In the limited magnitude range of this sample, there is no apparent correlation of metallicity either with effective and central surface brightness, or with total and nuclear magnitudes. The velocity distribution of the Fornax dwarfs is flatter than that of brighter galaxies at the 75% confidence level, possibly indicating a difference in the kinematics of the two samples.

The cluster-cluster correlation function. [of galaxies

NASA Technical Reports Server (NTRS)

Postman, M.; Geller, M. J.; Huchra, J. P.

1986-01-01

The clustering properties of the Abell and Zwicky cluster catalogs are studied using the two-point angular and spatial correlation functions. The catalogs are divided into eight subsamples to determine the dependence of the correlation function on distance, richness, and the method of cluster identification. It is found that the Corona Borealis supercluster contributes significant power to the spatial correlation function to the Abell cluster sample with distance class of four or less. The distance-limited catalog of 152 Abell clusters, which is not greatly affected by a single system, has a spatial correlation function consistent with the power law Xi(r) = 300r exp -1.8. In both the distance class four or less and distance-limited samples the signal in the spatial correlation function is a power law detectable out to 60/h Mpc. The amplitude of Xi(r) for clusters of richness class two is about three times that for richness class one clusters. The two-point spatial correlation function is sensitive to the use of estimated redshifts.

Melt density and the average composition of basalt

NASA Technical Reports Server (NTRS)

Stolper, E.; Walker, D.

1980-01-01

Densities of residual liquids produced by low pressure fractionation of olivine-rich melts pass through a minimum when pyroxene and plagioclase joint the crystallization sequence. The observation that erupted basalt compositions cluster around the degree of fractionation from picritic liquids corresponding to the density minimum in the liquid line of descent may thus suggest that the earth's crust imposes a density fiber on the liquids that pass through it, favoring the eruption of the light liquids at the density minimum over the eruption of denser more fractionated and less fractionated liquids.

Mining Genomes of Three Marine Sponge-Associated Actinobacterial Isolates for Secondary Metabolism.

PubMed

Horn, Hannes; Hentschel, Ute; Abdelmohsen, Usama Ramadan

2015-10-01

Here, we report the draft genome sequences of three actinobacterial isolates, Micromonospora sp. RV43, Rubrobacter sp. RV113, and Nocardiopsis sp. RV163 that had previously been isolated from Mediterranean sponges. The draft genomes were analyzed for the presence of gene clusters indicative of secondary metabolism using antiSMASH 3.0 and NapDos pipelines. Our findings demonstrated the chemical richness of sponge-associated actinomycetes and the efficacy of genome mining in exploring the genomic potential of sponge-derived actinomycetes. Copyright © 2015 Horn et al.

α-induced reaction cross section measurements on 197Au

NASA Astrophysics Data System (ADS)

Szücs, Tamás; Gyürky, György; Halász, Zoltán; Kiss, Gábor Gy.; Fülöp, Zsolt

2018-01-01

The γ-process is responsible for creating the majority of the isotopes of heavier elements on the proton rich side of the valley of stability. The γ-process simulations fail to reproduce the measured solar system abundance of these isotopes. The problem can lie in the not well known astrophysical scenarios where the process takes place, or in the not sufficiently known nuclear physics input. To improve the latter part, α-induced reaction cross section measurements on 197Au were carried out at Atomki. With this dataset new experimental information will become available, which can be later used as validation of the theoretical cross section calculations used in the γ-process simulations.

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.

Genetic analysis of 430 Chinese Cynodon dactylon accessions using sequence-related amplified polymorphism markers.

PubMed

Huang, Chunqiong; Liu, Guodao; Bai, Changjun; Wang, Wenqiang

2014-10-21

Although Cynodon dactylon (C. dactylon) is widely distributed in China, information on its genetic diversity within the germplasm pool is limited. The objective of this study was to reveal the genetic variation and relationships of 430 C. dactylon accessions collected from 22 Chinese provinces using sequence-related amplified polymorphism (SRAP) markers. Fifteen primer pairs were used to amplify specific C. dactylon genomic sequences. A total of 481 SRAP fragments were generated, with fragment sizes ranging from 260-1800 base pairs (bp). Genetic similarity coefficients (GSC) among the 430 accessions averaged 0.72 and ranged from 0.53-0.96. Cluster analysis conducted by two methods, namely the unweighted pair-group method with arithmetic averages (UPGMA) and principle coordinate analysis (PCoA), separated the accessions into eight distinct groups. Our findings verify that Chinese C. dactylon germplasms have rich genetic diversity, which is an excellent basis for C. dactylon breeding for new cultivars.

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

Old meets new: using interspecies interactions to detect secondary metabolite production in actinomycetes.

PubMed

Seyedsayamdost, Mohammad R; Traxler, Matthew F; Clardy, Jon; Kolter, Roberto

2012-01-01

Actinomycetes, a group of filamentous, Gram-positive bacteria, have long been a remarkable source of useful therapeutics. Recent genome sequencing and transcriptomic studies have shown that these bacteria, responsible for half of the clinically used antibiotics, also harbor a large reservoir of gene clusters, which have the potential to produce novel secreted small molecules. Yet, many of these clusters are not expressed under common culture conditions. One reason why these clusters have not been linked to a secreted small molecule lies in the way that actinomycetes have typically been studied: as pure cultures in nutrient-rich media that do not mimic the complex environments in which these bacteria evolved. New methods based on multispecies culture conditions provide an alternative approach to investigating the products of these gene clusters. We have recently implemented binary interspecies interaction assays to mine for new secondary metabolites and to study the underlying biology of interactinomycete interactions. Here, we describe the detailed biological and chemical methods comprising these studies. Copyright © 2012 Elsevier Inc. All rights reserved.

Molecular diversity of rumen bacterial communities from tannin-rich and fiber-rich forage fed domestic Sika deer (Cervus nippon) in China

PubMed Central

2013-01-01

Background Sika deer (Cervus nippon) have different dietary preferences to other ruminants and are tolerant to tannin-rich plants. Because the rumen bacteria in domestic Sika deer have not been comprehensively studied, it is important to investigate its rumen bacterial population in order to understand its gut health and to improve the productivity of domestic Sika deer. Results The rumen bacterial diversity in domestic Sika deer (Cervus nippon) fed oak leaves- (OL group) and corn stalks-based diets (CS group) were elucidated using 16S rRNA gene libraries and denaturing gradient gel electrophoresis (DGGE). Overall, 239 sequences were examined from the two groups, 139 clones from the OL group were assigned to 57 operational taxonomic units (OTUs) and 100 sequences from the CS group were divided into 50 OTUs. Prevotella-like sequences belonging to the phylum Bacteroidetes were the dominant bacteria in both groups (97.2% OL and 77% CS), and sequences related to Prevotella brevis were present in both groups. However, Prevotella shahii-like, Prevotella veroralis-like, Prevotella albensis-like, and Prevotella salivae-like sequences were abundant in the OL group compared to those in the CS group, while Succinivibrio dextrinosolvens-like and Prevotella ruminicola-like sequences were prevalent in the CS group. PCR-DGGE showed that bacterial communities clustered with respect to diets and the genus Prevotella was the dominant bacteria in the rumen of domestic Sika deer. However, the distribution of genus Prevotella from two groups was apparent. In addition, other fibrolytic bacteria, such as Clostridium populeti and Eubacterium cellulosolvens were found in the rumen of domestic Sika deer. Conclusions The rumen of domestic Sika deer harbored unique bacteria which may represent novel species. The bacterial composition appeared to be affected by diet, and sequences related to Prevotella spp. may represent new species that may be related to the degradation of fiber biomass or tannins. Moreover, the mechanism and biological functions of Prevotella spp. in the rumen ecosystem, and synergistic interactions with other microorganisms should be noticed. PMID:23834656

Molecular diversity of rumen bacterial communities from tannin-rich and fiber-rich forage fed domestic Sika deer (Cervus nippon) in China.

PubMed

Li, Zhi Peng; Liu, Han Lu; Li, Guang Yu; Bao, Kun; Wang, Kai Ying; Xu, Chao; Yang, Yi Feng; Yang, Fu He; Wright, André-Denis G

2013-07-08

Sika deer (Cervus nippon) have different dietary preferences to other ruminants and are tolerant to tannin-rich plants. Because the rumen bacteria in domestic Sika deer have not been comprehensively studied, it is important to investigate its rumen bacterial population in order to understand its gut health and to improve the productivity of domestic Sika deer. The rumen bacterial diversity in domestic Sika deer (Cervus nippon) fed oak leaves- (OL group) and corn stalks-based diets (CS group) were elucidated using 16S rRNA gene libraries and denaturing gradient gel electrophoresis (DGGE). Overall, 239 sequences were examined from the two groups, 139 clones from the OL group were assigned to 57 operational taxonomic units (OTUs) and 100 sequences from the CS group were divided into 50 OTUs. Prevotella-like sequences belonging to the phylum Bacteroidetes were the dominant bacteria in both groups (97.2% OL and 77% CS), and sequences related to Prevotella brevis were present in both groups. However, Prevotella shahii-like, Prevotella veroralis-like, Prevotella albensis-like, and Prevotella salivae-like sequences were abundant in the OL group compared to those in the CS group, while Succinivibrio dextrinosolvens-like and Prevotella ruminicola-like sequences were prevalent in the CS group. PCR-DGGE showed that bacterial communities clustered with respect to diets and the genus Prevotella was the dominant bacteria in the rumen of domestic Sika deer. However, the distribution of genus Prevotella from two groups was apparent. In addition, other fibrolytic bacteria, such as Clostridium populeti and Eubacterium cellulosolvens were found in the rumen of domestic Sika deer. The rumen of domestic Sika deer harbored unique bacteria which may represent novel species. The bacterial composition appeared to be affected by diet, and sequences related to Prevotella spp. may represent new species that may be related to the degradation of fiber biomass or tannins. Moreover, the mechanism and biological functions of Prevotella spp. in the rumen ecosystem, and synergistic interactions with other microorganisms should be noticed.

Mass calibration of galaxy clusters at redshift 0.1–1.0 using weak lensing in the Sloan Digital Sky Survey Stripe 82 co-add

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

Wiesner, Matthew P.; Lin, Huan; Soares-Santos, Marcelle

We present galaxy cluster mass–richness relations found in the Sloan Digital Sky Survey Stripe 82 co-add using clusters found using a Voronoi tessellation cluster finder. These relations were found using stacked weak lensing shear observed in a large sample of galaxy clusters. These mass–richness relations are presented for four redshift bins, 0.1 < z ≤ 0.4, 0.4 < z ≤ 0.7, 0.7 < z ≤ 1.0 and 0.1 < z ≤ 1.0. We describe the sample of galaxy clusters and explain how these clusters were found using a Voronoi tessellation cluster finder. We fit a Navarro-Frenk-White profile to the stackedmore » weak lensing shear signal in redshift and richness bins in order to measure virial mass (M 200). We describe several effects that can bias weak lensing measurements, including photometric redshift bias, the effect of the central BCG, halo miscentering, photometric redshift uncertainty and foreground galaxy contamination. We present mass–richness relations using richness measure N VT with each of these effects considered separately as well as considered altogether. We also examine redshift evolution of the mass–richness relation. As a result, we present measurements of the mass coefficient (M 200|20) and the power-law slope (α) for power-law fits to the mass and richness values in each of the redshift bins. We find values of the mass coefficient of 8.49 ± 0.526, 14.1 ± 1.78, 30.2 ± 8.74 and 9.23 ± 0.525 × 10 13 h –1 M ⊙ for each of the four redshift bins, respectively. As a result, we find values of the power-law slope of 0.905 ± 0.0585, 0.948 ± 0.100, 1.33 ± 0.260 and 0.883 ± 0.0500, respectively.« less

Mass calibration of galaxy clusters at redshift 0.1–1.0 using weak lensing in the Sloan Digital Sky Survey Stripe 82 co-add

DOE PAGES

Wiesner, Matthew P.; Lin, Huan; Soares-Santos, Marcelle

2015-07-08

We present galaxy cluster mass–richness relations found in the Sloan Digital Sky Survey Stripe 82 co-add using clusters found using a Voronoi tessellation cluster finder. These relations were found using stacked weak lensing shear observed in a large sample of galaxy clusters. These mass–richness relations are presented for four redshift bins, 0.1 < z ≤ 0.4, 0.4 < z ≤ 0.7, 0.7 < z ≤ 1.0 and 0.1 < z ≤ 1.0. We describe the sample of galaxy clusters and explain how these clusters were found using a Voronoi tessellation cluster finder. We fit a Navarro-Frenk-White profile to the stackedmore » weak lensing shear signal in redshift and richness bins in order to measure virial mass (M 200). We describe several effects that can bias weak lensing measurements, including photometric redshift bias, the effect of the central BCG, halo miscentering, photometric redshift uncertainty and foreground galaxy contamination. We present mass–richness relations using richness measure N VT with each of these effects considered separately as well as considered altogether. We also examine redshift evolution of the mass–richness relation. As a result, we present measurements of the mass coefficient (M 200|20) and the power-law slope (α) for power-law fits to the mass and richness values in each of the redshift bins. We find values of the mass coefficient of 8.49 ± 0.526, 14.1 ± 1.78, 30.2 ± 8.74 and 9.23 ± 0.525 × 10 13 h –1 M ⊙ for each of the four redshift bins, respectively. As a result, we find values of the power-law slope of 0.905 ± 0.0585, 0.948 ± 0.100, 1.33 ± 0.260 and 0.883 ± 0.0500, respectively.« less

Next Generation Virgo Cluster Survey. XXI. The Weak Lensing Masses of the CFHTLS and NGVS RedGOLD Galaxy Clusters and Calibration of the Optical Richness

NASA Astrophysics Data System (ADS)

Parroni, Carolina; Mei, Simona; Erben, Thomas; Van Waerbeke, Ludovic; Raichoor, Anand; Ford, Jes; Licitra, Rossella; Meneghetti, Massimo; Hildebrandt, Hendrik; Miller, Lance; Côté, Patrick; Covone, Giovanni; Cuillandre, Jean-Charles; Duc, Pierre-Alain; Ferrarese, Laura; Gwyn, Stephen D. J.; Puzia, Thomas H.

2017-10-01

We measured stacked weak lensing cluster masses for a sample of 1323 galaxy clusters detected by the RedGOLD algorithm in the Canada-France-Hawaii Telescope Legacy Survey W1 and the Next Generation Virgo Cluster Survey at 0.2< z< 0.5, in the optical richness range 10< λ < 70. This is the most comprehensive lensing study of a ˜ 100 % complete and ˜ 80 % pure optical cluster catalog in this redshift range. We test different mass models, and our final model includes a basic halo model with a Navarro Frenk and White profile, as well as correction terms that take into account cluster miscentering, non-weak shear, the two-halo term, the contribution of the Brightest Cluster Galaxy, and an a posteriori correction for the intrinsic scatter in the mass-richness relation. With this model, we obtain a mass-richness relation of {log}{M}200/{M}⊙ =(14.46+/- 0.02)+(1.04+/- 0.09){log}(λ /40) (statistical uncertainties). This result is consistent with other published lensing mass-richness relations. We give the coefficients of the scaling relations between the lensing mass and X-ray mass proxies, L X and T X, and compare them with previous results. When compared to X-ray masses and mass proxies, our results are in agreement with most previous results and simulations, and consistent with the expected deviations from self-similarity.

Accumulation of transposable elements in Hox gene clusters during adaptive radiation of Anolis lizards.

PubMed

Feiner, Nathalie

2016-10-12

Transposable elements (TEs) are DNA sequences that can insert elsewhere in the genome and modify genome structure and gene regulation. The role of TEs in evolution is contentious. One hypothesis posits that TE activity generates genomic incompatibilities that can cause reproductive isolation between incipient species. This predicts that TEs will accumulate during speciation events. Here, I tested the prediction that extant lineages with a relatively high rate of speciation have a high number of TEs in their genomes. I sequenced and analysed the TE content of a marker genomic region (Hox clusters) in Anolis lizards, a classic case of an adaptive radiation. Unlike other vertebrates, including closely related lizards, Anolis lizards have high numbers of TEs in their Hox clusters, genomic regions that regulate development of the morphological adaptations that characterize habitat specialists in these lizards. Following a burst of TE activity in the lineage leading to extant Anolis, TEs have continued to accumulate during or after speciation events, resulting in a positive relationship between TE density and lineage speciation rate. These results are consistent with the prediction that TE activity contributes to adaptive radiation by promoting speciation. Although there was no evidence that TE density per se is associated with ecological morphology, the activity of TEs in Hox clusters could have been a rich source for phenotypic variation that may have facilitated the rapid parallel morphological adaptation to microhabitats seen in extant Anolis lizards. © 2016 The Author(s).

Accumulation of transposable elements in Hox gene clusters during adaptive radiation of Anolis lizards

PubMed Central

2016-01-01

Transposable elements (TEs) are DNA sequences that can insert elsewhere in the genome and modify genome structure and gene regulation. The role of TEs in evolution is contentious. One hypothesis posits that TE activity generates genomic incompatibilities that can cause reproductive isolation between incipient species. This predicts that TEs will accumulate during speciation events. Here, I tested the prediction that extant lineages with a relatively high rate of speciation have a high number of TEs in their genomes. I sequenced and analysed the TE content of a marker genomic region (Hox clusters) in Anolis lizards, a classic case of an adaptive radiation. Unlike other vertebrates, including closely related lizards, Anolis lizards have high numbers of TEs in their Hox clusters, genomic regions that regulate development of the morphological adaptations that characterize habitat specialists in these lizards. Following a burst of TE activity in the lineage leading to extant Anolis, TEs have continued to accumulate during or after speciation events, resulting in a positive relationship between TE density and lineage speciation rate. These results are consistent with the prediction that TE activity contributes to adaptive radiation by promoting speciation. Although there was no evidence that TE density per se is associated with ecological morphology, the activity of TEs in Hox clusters could have been a rich source for phenotypic variation that may have facilitated the rapid parallel morphological adaptation to microhabitats seen in extant Anolis lizards. PMID:27733546

In Silico Analysis of Correlations between Protein Disorder and Post-Translational Modifications in Algae

PubMed Central

Kurotani, Atsushi; Sakurai, Tetsuya

2015-01-01

Recent proteome analyses have reported that intrinsically disordered regions (IDRs) of proteins play important roles in biological processes. In higher plants whose genomes have been sequenced, the correlation between IDRs and post-translational modifications (PTMs) has been reported. The genomes of various eukaryotic algae as common ancestors of plants have also been sequenced. However, no analysis of the relationship to protein properties such as structure and PTMs in algae has been reported. Here, we describe correlations between IDR content and the number of PTM sites for phosphorylation, glycosylation, and ubiquitination, and between IDR content and regions rich in proline, glutamic acid, serine, and threonine (PEST) and transmembrane helices in the sequences of 20 algae proteomes. Phosphorylation, O-glycosylation, ubiquitination, and PEST preferentially occurred in disordered regions. In contrast, transmembrane helices were favored in ordered regions. N-glycosylation tended to occur in ordered regions in most of the studied algae; however, it correlated positively with disordered protein content in diatoms. Additionally, we observed that disordered protein content and the number of PTM sites were significantly increased in the species-specific protein clusters compared to common protein clusters among the algae. Moreover, there were specific relationships between IDRs and PTMs among the algae from different groups. PMID:26307970

In Silico Analysis of Correlations between Protein Disorder and Post-Translational Modifications in Algae.

PubMed

Kurotani, Atsushi; Sakurai, Tetsuya

2015-08-20

Recent proteome analyses have reported that intrinsically disordered regions (IDRs) of proteins play important roles in biological processes. In higher plants whose genomes have been sequenced, the correlation between IDRs and post-translational modifications (PTMs) has been reported. The genomes of various eukaryotic algae as common ancestors of plants have also been sequenced. However, no analysis of the relationship to protein properties such as structure and PTMs in algae has been reported. Here, we describe correlations between IDR content and the number of PTM sites for phosphorylation, glycosylation, and ubiquitination, and between IDR content and regions rich in proline, glutamic acid, serine, and threonine (PEST) and transmembrane helices in the sequences of 20 algae proteomes. Phosphorylation, O-glycosylation, ubiquitination, and PEST preferentially occurred in disordered regions. In contrast, transmembrane helices were favored in ordered regions. N-glycosylation tended to occur in ordered regions in most of the studied algae; however, it correlated positively with disordered protein content in diatoms. Additionally, we observed that disordered protein content and the number of PTM sites were significantly increased in the species-specific protein clusters compared to common protein clusters among the algae. Moreover, there were specific relationships between IDRs and PTMs among the algae from different groups.

NOA36 Protein Contains a Highly Conserved Nucleolar Localization Signal Capable of Directing Functional Proteins to the Nucleolus, in Mammalian Cells

PubMed Central

de Melo, Ivan S.; Jimenez-Nuñez, Maria D.; Iglesias, Concepción; Campos-Caro, Antonio; Moreno-Sanchez, David; Ruiz, Felix A.; Bolívar, Jorge

2013-01-01

NOA36/ZNF330 is an evolutionarily well-preserved protein present in the nucleolus and mitochondria of mammalian cells. We have previously reported that the pro-apoptotic activity of this protein is mediated by a characteristic cysteine-rich domain. We now demonstrate that the nucleolar localization of NOA36 is due to a highly-conserved nucleolar localization signal (NoLS) present in residues 1–33. This NoLS is a sequence containing three clusters of two or three basic amino acids. We fused the amino terminal of NOA36 to eGFP in order to characterize this putative NoLS. We show that a cluster of three lysine residues at positions 3 to 5 within this sequence is critical for the nucleolar localization. We also demonstrate that the sequence as found in human is capable of directing eGFP to the nucleolus in several mammal, fish and insect cells. Moreover, this NoLS is capable of specifically directing the cytosolic yeast enzyme polyphosphatase to the target of the nucleolus of HeLa cells, wherein its enzymatic activity was detected. This NoLS could therefore serve as a very useful tool as a nucleolar marker and for directing particular proteins to the nucleolus in distant animal species. PMID:23516598

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

Improved optical mass tracer for galaxy clusters calibrated using weak lensing measurements

NASA Astrophysics Data System (ADS)

Reyes, R.; Mandelbaum, R.; Hirata, C.; Bahcall, N.; Seljak, U.

2008-11-01

We develop an improved mass tracer for clusters of galaxies from optically observed parameters, and calibrate the mass relation using weak gravitational lensing measurements. We employ a sample of ~13000 optically selected clusters from the Sloan Digital Sky Survey (SDSS) maxBCG catalogue, with photometric redshifts in the range 0.1-0.3. The optical tracers we consider are cluster richness, cluster luminosity, luminosity of the brightest cluster galaxy (BCG) and combinations of these parameters. We measure the weak lensing signal around stacked clusters as a function of the various tracers, and use it to determine the tracer with the least amount of scatter. We further use the weak lensing data to calibrate the mass normalization. We find that the best mass estimator for massive clusters is a combination of cluster richness, N200, and the luminosity of the BCG, LBCG: , where is the observed mean BCG luminosity at a given richness. This improved mass tracer will enable the use of galaxy clusters as a more powerful tool for constraining cosmological parameters.

Cluster-cluster clustering

NASA Technical Reports Server (NTRS)

Barnes, J.; Dekel, A.; Efstathiou, G.; Frenk, C. S.

1985-01-01

The cluster correlation function xi sub c(r) is compared with the particle correlation function, xi(r) in cosmological N-body simulations with a wide range of initial conditions. The experiments include scale-free initial conditions, pancake models with a coherence length in the initial density field, and hybrid models. Three N-body techniques and two cluster-finding algorithms are used. In scale-free models with white noise initial conditions, xi sub c and xi are essentially identical. In scale-free models with more power on large scales, it is found that the amplitude of xi sub c increases with cluster richness; in this case the clusters give a biased estimate of the particle correlations. In the pancake and hybrid models (with n = 0 or 1), xi sub c is steeper than xi, but the cluster correlation length exceeds that of the points by less than a factor of 2, independent of cluster richness. Thus the high amplitude of xi sub c found in studies of rich clusters of galaxies is inconsistent with white noise and pancake models and may indicate a primordial fluctuation spectrum with substantial power on large scales.

Characterizing X-ray Sources in the Rich Open Cluster NGC 7789 Using XMM-Newton

NASA Astrophysics Data System (ADS)

Farner, William; Pooley, David

2018-01-01

It is well established that globular clusters exhibit a correlation between their population of exotic binaries and their rate of stellar encounters, but little work has been done to characterize this relationship in rich open clusters. X-ray observations are the most efficient means to find various types of close binaries, and optical (and radio) identifications can provide secure source classifications. We report on an observation of the rich open cluster NGC 7789 using the XMM-Newton observatory. We present the X-ray and optical imaging data, source lists, and preliminary characterization of the sources based on their X-ray and multiwavelength properties.

Special AT-rich sequence binding protein 1 promotes tumor growth and metastasis of esophageal squamous cell carcinoma.

PubMed

Ma, Jun; Wu, Kaiming; Zhao, Zhenxian; Miao, Rong; Xu, Zhe

2017-03-01

Esophageal squamous cell carcinoma is one of the most aggressive malignancies worldwide. Special AT-rich sequence binding protein 1 is a nuclear matrix attachment region binding protein which participates in higher order chromatin organization and tissue-specific gene expression. However, the role of special AT-rich sequence binding protein 1 in esophageal squamous cell carcinoma remains unknown. In this study, western blot and quantitative real-time polymerase chain reaction analysis were performed to identify differentially expressed special AT-rich sequence binding protein 1 in a series of esophageal squamous cell carcinoma tissue samples. The effects of special AT-rich sequence binding protein 1 silencing by two short-hairpin RNAs on cell proliferation, migration, and invasion were assessed by the CCK-8 assay and transwell assays in esophageal squamous cell carcinoma in vitro. Special AT-rich sequence binding protein 1 was significantly upregulated in esophageal squamous cell carcinoma tissue samples and cell lines. Silencing of special AT-rich sequence binding protein 1 inhibited the proliferation of KYSE450 and EC9706 cells which have a relatively high level of special AT-rich sequence binding protein 1, and the ability of migration and invasion of KYSE450 and EC9706 cells was distinctly suppressed. Special AT-rich sequence binding protein 1 could be a potential target for the treatment of esophageal squamous cell carcinoma and inhibition of special AT-rich sequence binding protein 1 may provide a new strategy for the prevention of esophageal squamous cell carcinoma invasion and metastasis.

Alcohol and tobacco consumption affects bacterial richness in oral cavity mucosa biofilms.

PubMed

Thomas, Andrew Maltez; Gleber-Netto, Frederico Omar; Fernandes, Gustavo Ribeiro; Amorim, Maria; Barbosa, Luisa Fernanda; Francisco, Ana Lúcia Noronha; de Andrade, Arthur Guerra; Setubal, João Carlos; Kowalski, Luiz Paulo; Nunes, Diana Noronha; Dias-Neto, Emmanuel

2014-10-03

Today there are more than 2 billion alcohol users and about 1.3 billion tobacco users worldwide. The chronic and heavy use of these two substances is at the heart of numerous diseases and may wreak havoc on the human oral microbiome. This study delves into the changes that alcohol and tobacco may cause on biofilms of the human oral microbiome. To do so, we used swabs to sample the oral biofilm of 22 subjects; including 9 control-individuals with no or very low consumption of alcohol and no consumption of tobacco, 7 who were chronic and heavy users of both substances and 6 active smokers that reported no significant alcohol consumption. DNA was extracted from swabs and the V1 region of the 16S rRNA gene was PCR amplified and sequenced using the Ion Torrent PGM platform, generating 3.7 million high quality reads. DNA sequences were clustered and OTUs were assigned using the ARB SILVA database and Qiime. We found no differences in species diversity and evenness among the groups. However, we found a significant decrease in species richness in only smokers and in smokers/drinkers when compared to controls. We found that Neisseria abundance was significantly decreased in both groups when compared to controls. Smokers had significant increases in Prevotella and Capnocytophaga and reductions in Granulicatella, Staphylococcus, Peptostreptococcus and Gemella when compared to the two other groups. Controls showed higher abundance of Aggregibacter, whilst smokers/drinkers had lower abundances of Fusobacteria. Samples from only smokers clustered closer together than to controls and smokers/drinkers, and also had a significant reduction in inter-group dissimilarity distances, indicating a more homogenous group than controls. Our results indicate that the continued use of tobacco or alcohol plus tobacco significantly reduces bacterial richness, which apparently leads to a reduction in inter-group variability, turning the respective biofilms into a more homogenous microenvironment in terms of bacterial community composition, with possible consequences for human oral diseases.

THE VMC SURVEY. XVIII. RADIAL DEPENDENCE OF THE LOW-MASS, 0.55–0.82 M{sub ⊙} STELLAR MASS FUNCTION IN THE GALACTIC GLOBULAR CLUSTER 47 TUCANAE

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

Zhang, Chaoli; Li, Chengyuan; De Grijs, Richard

2015-12-20

We use near-infrared observations obtained as part of the Visible and Infrared Survey Telescope for Astronomy (VISTA) Survey of the Magellanic Clouds (VMC), as well as two complementary Hubble Space Telescope (HST) data sets, to study the luminosity and mass functions (MFs) as a function of clustercentric radius of the main-sequence stars in the Galactic globular cluster 47 Tucanae. The HST observations indicate a relative deficit in the numbers of faint stars in the central region of the cluster compared with its periphery, for 18.75 ≤ m{sub F606W} ≤ 20.9 mag (corresponding to a stellar mass range of 0.55 < m{sub *}/M{sub ⊙} < 0.73). The stellar numbermore » counts at 6.′7 from the cluster core show a deficit for 17.62 ≤ m{sub F606W} ≤ 19.7 mag (i.e., 0.65 < m{sub *}/M{sub ⊙} < 0.82), which is consistent with expectations from mass segregation. The VMC-based stellar MFs exhibit power-law shapes for masses in the range 0.55 < m{sub *}/M{sub ⊙} < 0.82. These power laws are characterized by an almost constant slope, α. The radial distribution of the power-law slopes α thus shows evidence of the importance of both mass segregation and tidal stripping, for both the first- and second-generation stars in 47 Tuc.« less

Exploring N-Rich Phases in Li(x)N(y) Clusters for Hydrogen Storage at Nanoscale.

PubMed

Bhattacharya, Amrita; Bhattacharya, Saswata

2015-09-17

We have performed cascade genetic algorithm and ab initio atomistic thermodynamics under the framework of first-principles-based hybrid density functional theory to study the (meta-)stability of a wide range of Li(x)N(y) clusters. We found that hybrid xc-functional is essential to address this problem as a local/semilocal functional simply fails even to predict a qualitative prediction. Most importantly, we find that though in bulk lithium nitride, the Li-rich phase, that is, Li3N, is the stable stoichiometry; in small Li(x)N(y) clusters, N-rich phases are more stable at thermodynamic equilibrium. We further show that these N-rich clusters are promising hydrogen storage material because of their easy adsorption and desorption ability at respectively low (≤300 K) and moderately high temperature (≥600 K).

The pH Sensitivity of Murine Heat Shock Protein 47 (HSP47) Binding to Collagen Is Affected by Mutations in the Breach Histidine Cluster*

PubMed Central

Abdul-Wahab, Mohd Firdaus; Homma, Takayuki; Wright, Michael; Olerenshaw, Dee; Dafforn, Timothy R.; Nagata, Kazuhiro; Miller, Andrew D.

2013-01-01

Heat shock protein 47 (HSP47) is a single-substrate molecular chaperone crucial for collagen biosynthesis. Although its function is well established, the molecular mechanisms that govern binding to procollagen peptides and triple helices in the endoplasmic reticulum (followed by controlled release in the Golgi) are unclear. HSP47 binds procollagen at a neutral pH but releases at a pH similar to the pKa of the imidazole side chain of histidine residues. It thus seems likely that these residues are involved in this pH-dependent mechanism. Murine HSP47 has 14 histidine residues grouped into three clusters, known as the breach, gate, and shutter. Here, we report the use of histidine mutagenesis to demonstrate the relative contribution of these three clusters to HSP47 structure and the “pH switch.” Many of the tested mutants are silent; however, breach mutants H197A and H198A show binding but no apparent pH switch and are unable to control release. Another breach mutant, H191A, shows perturbed collagen release characteristics, consistent with observed perturbations in pH-driven trans-conformational changes. Thus, His-198, His-197 and His-191 are important (if not central) to HSP47 mechanism of binding/release to collagen. This is consistent with the breach cluster residues being well conserved across the HSP47 family. PMID:23212911

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.

LITHIUM-RICH GIANTS IN GLOBULAR CLUSTERS

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

Kirby, Evan N.; Cohen, Judith G.; Guhathakurta, Puragra

Although red giants deplete lithium on their surfaces, some giants are Li-rich. Intermediate-mass asymptotic giant branch (AGB) stars can generate Li through the Cameron–Fowler conveyor, but the existence of Li-rich, low-mass red giant branch (RGB) stars is puzzling. Globular clusters are the best sites to examine this phenomenon because it is straightforward to determine membership in the cluster and to identify the evolutionary state of each star. In 72 hours of Keck/DEIMOS exposures in 25 clusters, we found four Li-rich RGB and two Li-rich AGB stars. There were 1696 RGB and 125 AGB stars with measurements or upper limits consistentmore » with normal abundances of Li. Hence, the frequency of Li-richness in globular clusters is (0.2 ± 0.1)% for the RGB, (1.6 ± 1.1)% for the AGB, and (0.3 ± 0.1)% for all giants. Because the Li-rich RGB stars are on the lower RGB, Li self-generation mechanisms proposed to occur at the luminosity function bump or He core flash cannot explain these four lower RGB stars. We propose the following origin for Li enrichment: (1) All luminous giants experience a brief phase of Li enrichment at the He core flash. (2) All post-RGB stars with binary companions on the lower RGB will engage in mass transfer. This scenario predicts that 0.1% of lower RGB stars will appear Li-rich due to mass transfer from a recently Li-enhanced companion. This frequency is at the lower end of our confidence interval.« less

Comparative Genomics of Non-TNL Disease Resistance Genes from Six Plant Species.

PubMed

Nepal, Madhav P; Andersen, Ethan J; Neupane, Surendra; Benson, Benjamin V

2017-09-30

Disease resistance genes (R genes), as part of the plant defense system, have coevolved with corresponding pathogen molecules. The main objectives of this project were to identify non-Toll interleukin receptor, nucleotide-binding site, leucine-rich repeat (nTNL) genes and elucidate their evolutionary divergence across six plant genomes. Using reference sequences from Arabidopsis , we investigated nTNL orthologs in the genomes of common bean, Medicago , soybean, poplar, and rice. We used Hidden Markov Models for sequence identification, performed model-based phylogenetic analyses, visualized chromosomal positioning, inferred gene clustering, and assessed gene expression profiles. We analyzed 908 nTNL R genes in the genomes of the six plant species, and classified them into 12 subgroups based on the presence of coiled-coil (CC), nucleotide binding site (NBS), leucine rich repeat (LRR), resistance to Powdery mildew 8 (RPW8), and BED type zinc finger domains. Traditionally classified CC-NBS-LRR (CNL) genes were nested into four clades (CNL A-D) often with abundant, well-supported homogeneous subclades of Type-II R genes. CNL-D members were absent in rice, indicating a unique R gene retention pattern in the rice genome. Genomes from Arabidopsis , common bean, poplar and soybean had one chromosome without any CNL R genes. Medicago and Arabidopsis had the highest and lowest number of gene clusters, respectively. Gene expression analyses suggested unique patterns of expression for each of the CNL clades. Differential gene expression patterns of the nTNL genes were often found to correlate with number of introns and GC content, suggesting structural and functional divergence.

Comparative Genomics of Non-TNL Disease Resistance Genes from Six Plant Species

PubMed Central

Andersen, Ethan J.; Neupane, Surendra; Benson, Benjamin V.

2017-01-01

Disease resistance genes (R genes), as part of the plant defense system, have coevolved with corresponding pathogen molecules. The main objectives of this project were to identify non-Toll interleukin receptor, nucleotide-binding site, leucine-rich repeat (nTNL) genes and elucidate their evolutionary divergence across six plant genomes. Using reference sequences from Arabidopsis, we investigated nTNL orthologs in the genomes of common bean, Medicago, soybean, poplar, and rice. We used Hidden Markov Models for sequence identification, performed model-based phylogenetic analyses, visualized chromosomal positioning, inferred gene clustering, and assessed gene expression profiles. We analyzed 908 nTNL R genes in the genomes of the six plant species, and classified them into 12 subgroups based on the presence of coiled-coil (CC), nucleotide binding site (NBS), leucine rich repeat (LRR), resistance to Powdery mildew 8 (RPW8), and BED type zinc finger domains. Traditionally classified CC-NBS-LRR (CNL) genes were nested into four clades (CNL A-D) often with abundant, well-supported homogeneous subclades of Type-II R genes. CNL-D members were absent in rice, indicating a unique R gene retention pattern in the rice genome. Genomes from Arabidopsis, common bean, poplar and soybean had one chromosome without any CNL R genes. Medicago and Arabidopsis had the highest and lowest number of gene clusters, respectively. Gene expression analyses suggested unique patterns of expression for each of the CNL clades. Differential gene expression patterns of the nTNL genes were often found to correlate with number of introns and GC content, suggesting structural and functional divergence. PMID:28973974

The Porcelain Crab Transcriptome and PCAD, the Porcelain Crab Microarray and Sequence Database

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

Tagmount, Abderrahmane; Wang, Mei; Lindquist, Erika

2010-01-27

Background: With the emergence of a completed genome sequence of the freshwater crustacean Daphnia pulex, construction of genomic-scale sequence databases for additional crustacean sequences are important for comparative genomics and annotation. Porcelain crabs, genus Petrolisthes, have been powerful crustacean models for environmental and evolutionary physiology with respect to thermal adaptation and understanding responses of marine organisms to climate change. Here, we present a large-scale EST sequencing and cDNA microarray database project for the porcelain crab Petrolisthes cinctipes. Methodology/Principal Findings: A set of ~;;30K unique sequences (UniSeqs) representing ~;;19K clusters were generated from ~;;98K high quality ESTs from a set ofmore » tissue specific non-normalized and mixed-tissue normalized cDNA libraries from the porcelain crab Petrolisthes cinctipes. Homology for each UniSeq was assessed using BLAST, InterProScan, GO and KEGG database searches. Approximately 66percent of the UniSeqs had homology in at least one of the databases. All EST and UniSeq sequences along with annotation results and coordinated cDNA microarray datasets have been made publicly accessible at the Porcelain Crab Array Database (PCAD), a feature-enriched version of the Stanford and Longhorn Array Databases.Conclusions/Significance: The EST project presented here represents the third largest sequencing effort for any crustacean, and the largest effort for any crab species. Our assembly and clustering results suggest that our porcelain crab EST data set is equally diverse to the much larger EST set generated in the Daphnia pulex genome sequencing project, and thus will be an important resource to the Daphnia research community. Our homology results support the pancrustacea hypothesis and suggest that Malacostraca may be ancestral to Branchiopoda and Hexapoda. Our results also suggest that our cDNA microarrays cover as much of the transcriptome as can reasonably be captured in EST library sequencing approaches, and thus represent a rich resource for studies of environmental genomics.« less

Stellar abundances and ages for metal-rich Milky Way globular clusters. Stellar parameters and elemental abundances for 9 HB stars in NGC 6352

NASA Astrophysics Data System (ADS)

Feltzing, S.; Primas, F.; Johnson, R. A.

2009-01-01

Context: Metal-rich globular clusters provide important tracers of the formation of our Galaxy. Moreover, and not less important, they are very important calibrators for the derivation of properties of extra-galactic metal-rich stellar populations. Nonetheless, only a few of the metal-rich globular clusters in the Milky Way have been studied using high-resolution stellar spectra to derive elemental abundances. Additionally, Rosenberg et al. identified a small group of metal-rich globular clusters that appeared to be about 2 billion years younger than the bulk of the Milky Way globular clusters. However, it is unclear if like is compared with like in this dataset as we do not know the enhancement of α-elements in the clusters and the amount of α-elements is well known to influence the derivation of ages for globular clusters. Aims: We derive elemental abundances for the metal-rich globular cluster NGC 6352 and we present our methods to be used in up-coming studies of other metal-rich globular clusters. Methods: We present a study of elemental abundances for α- and iron-peak elements for nine HB stars in the metal-rich globular cluster NGC 6352. The elemental abundances are based on high-resolution, high signal-to-noise spectra obtained with the UVES spectrograph on VLT. The elemental abundances have been derived using standard LTE calculations and stellar parameters have been derived from the spectra themselves by requiring ionizational as well as excitational equilibrium. Results: We find that NGC 6352 has [Fe/H] = -0.55, is enhanced in the α-elements to about +0.2 dex for Ca, Si, and Ti relative to Fe. For the iron-peak elements we find solar values. Based on the spectroscopically derived stellar parameters we find that an E(B-V) = 0.24 and (m-M) ≃ 14.05 better fits the data than the nominal values. An investigation of log gf-values for suitable Fe i lines lead us to the conclusion that the commonly used correction to the May et al. (1974) data should not be employed. Full Table [see full text] are also only available in electronic form at the CDS via anonymous ftp to cdsarc.u-strasbg.fr (130.79.128.5) or via http://cdsweb.u-strasbg.fr/cgi-bin/qcat?J/A+A/493/913 Based on observations collected at the European Southern Observatory, Chile, ESO No. 69.B-0467.

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

Primordial inhomogeneities in the expanding universe. I - Density and velocity distributions of galaxies in the vicinities of rich clusters

NASA Technical Reports Server (NTRS)

Silk, J.; Wilson, M. L.

1979-01-01

The density profiles and Hubble flow deviations in the vicinities of rich galaxy clusters are derived for a variety of models of initial density and velocity perturbations at the recombination epoch. The galaxy correlation function, measured with respect to the Abell clusters, is used to normalize the theoretical models. The angular scales of the required primordial inhomogeneities are calculated. It is found that the resulting density profiles around rich clusters are surprisingly insensitive to the shape of the initial perturbations and also to the cosmological density parameter, Omega. However, it is shown that the distribution of galaxy radial velocities can provide a possible means of deriving Omega.

The HectoMAP Cluster Survey. I. redMaPPer Clusters

NASA Astrophysics Data System (ADS)

Sohn, Jubee; Geller, Margaret J.; Rines, Kenneth J.; Hwang, Ho Seong; Utsumi, Yousuke; Diaferio, Antonaldo

2018-04-01

We use the dense HectoMAP redshift survey to explore the properties of 104 redMaPPer cluster candidates. The redMaPPer systems in HectoMAP cover the full range of richness and redshift (0.08 < z < 0.60). Fifteen of the systems included in the Subaru/Hyper Suprime-Cam public data release are bona fide clusters. The median number of spectroscopic members per cluster is ∼20. We include redshifts of 3547 member candidates listed in the redMaPPer catalog whether they are cluster members or not. We evaluate the redMaPPer membership probability spectroscopically. The purity (number of real systems) in redMaPPer exceeds 90% even at the lowest richness. Three massive galaxy clusters (M ∼ 2 × 1013 M ⊙) associated with X-ray emission in the HectoMAP region are not included in the public redMaPPer catalog with λ rich > 20, because they lie outside the cuts for this catalog.

The HectoMAP Cluster Survey. I. redMaPPer Clusters

DOE PAGES

Sohn, Jubee; Geller, Margaret J.; Rines, Kenneth J.; ...

2018-04-05

We use the dense HectoMAP redshift survey to explore the properties of 104 redMaPPer cluster candidates. The redMaPPer systems in HectoMAP cover the full range of richness and redshift (0.08 < z < 0.60). Fifteen of the systems included in the Subaru/Hyper Suprime-Cam public data release are bona fide clusters. The median number of spectroscopic members per cluster is ~20. We include redshifts of 3547 member candidates listed in the redMaPPer catalog whether they are cluster members or not. Here, we evaluate the redMaPPer membership probability spectroscopically. The purity (number of real systems) in redMaPPer exceeds 90% even at themore » lowest richness. Three massive galaxy clusters (M ~ 2 × 10 13 M ⊙) associated with X-ray emission in the HectoMAP region are not included in the public redMaPPer catalog with λ rich > 20, because they lie outside the cuts for this catalog.« less

The HectoMAP Cluster Survey. I. redMaPPer Clusters

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

Sohn, Jubee; Geller, Margaret J.; Rines, Kenneth J.

We use the dense HectoMAP redshift survey to explore the properties of 104 redMaPPer cluster candidates. The redMaPPer systems in HectoMAP cover the full range of richness and redshift (0.08 < z < 0.60). Fifteen of the systems included in the Subaru/Hyper Suprime-Cam public data release are bona fide clusters. The median number of spectroscopic members per cluster is ~20. We include redshifts of 3547 member candidates listed in the redMaPPer catalog whether they are cluster members or not. Here, we evaluate the redMaPPer membership probability spectroscopically. The purity (number of real systems) in redMaPPer exceeds 90% even at themore » lowest richness. Three massive galaxy clusters (M ~ 2 × 10 13 M ⊙) associated with X-ray emission in the HectoMAP region are not included in the public redMaPPer catalog with λ rich > 20, because they lie outside the cuts for this catalog.« less

Reproducing the local and global morphological segregation between S and S0 galaxies in rich clusters by simple ram-pressure stripping

NASA Astrophysics Data System (ADS)

Solanes, Jose M.; Salvador-Sole, Eduardo

1992-08-01

We calculate the morphological segregation in rich galaxy clusters expected to arise from the possible evolution of S galaxies into S0 galaxies via the gas removal of their disks by ram-pressure stripping. The calculation is run on Monte Carlo simulations by following individual S galaxies in the potential well of a spherical anisotropic cluster making use of Gunn and Gott's (1972) stripping condition. The results are compared with both Dressler's (1980) local type/density relation and a global population-richness correlation inferred from real data in the present work. We find that, contrary to a rather extended opinion, this evolution scheme reproduces very well the observed morphological segregation between S and S0 galaxies in rich clusters provided that the initial populations are close to those i dense loose groups.

Host Specific Diversity in Lactobacillus johnsonii as Evidenced by a Major Chromosomal Inversion and Phage Resistance Mechanisms

PubMed Central

Guinane, Caitriona M.; Kent, Robert M.; Norberg, Sarah; Hill, Colin; Fitzgerald, Gerald F.; Stanton, Catherine; Ross, R. Paul

2011-01-01

Genetic diversity and genomic rearrangements are a driving force in bacterial evolution and niche adaptation. We sequenced and annotated the genome of Lactobacillus johnsonii DPC6026, a strain isolated from the porcine intestinal tract. Although the genome of DPC6026 is similar in size (1.97mbp) and GC content (34.8%) to the sequenced human isolate L. johnsonii NCC 533, a large symmetrical inversion of approximately 750 kb differentiated the two strains. Comparative analysis among 12 other strains of L. johnsonii including 8 porcine, 3 human and 1 poultry isolate indicated that the genome architecture found in DPC6026 is more common within the species than that of NCC 533. Furthermore a number of unique features were annotated in DPC6026, some of which are likely to have been acquired by horizontal gene transfer (HGT) and contribute to protection against phage infection. A putative type III restriction-modification system was identified, as were novel Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) elements. Interestingly, these particular elements are not widely distributed among L. johnsonii strains. Taken together these data suggest intra-species genomic rearrangements and significant genetic diversity within the L. johnsonii species and indicate towards a host-specific divergence of L. johnsonii strains with respect to genome inversion and phage exposure. PMID:21533100

Host specific diversity in Lactobacillus johnsonii as evidenced by a major chromosomal inversion and phage resistance mechanisms.

PubMed

Guinane, Caitriona M; Kent, Robert M; Norberg, Sarah; Hill, Colin; Fitzgerald, Gerald F; Stanton, Catherine; Ross, R Paul

2011-04-20

Genetic diversity and genomic rearrangements are a driving force in bacterial evolution and niche adaptation. We sequenced and annotated the genome of Lactobacillus johnsonii DPC6026, a strain isolated from the porcine intestinal tract. Although the genome of DPC6026 is similar in size (1.97 mbp) and GC content (34.8%) to the sequenced human isolate L. johnsonii NCC 533, a large symmetrical inversion of approximately 750 kb differentiated the two strains. Comparative analysis among 12 other strains of L. johnsonii including 8 porcine, 3 human and 1 poultry isolate indicated that the genome architecture found in DPC6026 is more common within the species than that of NCC 533. Furthermore a number of unique features were annotated in DPC6026, some of which are likely to have been acquired by horizontal gene transfer (HGT) and contribute to protection against phage infection. A putative type III restriction-modification system was identified, as were novel Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) elements. Interestingly, these particular elements are not widely distributed among L. johnsonii strains. Taken together these data suggest intra-species genomic rearrangements and significant genetic diversity within the L. johnsonii species and indicate towards a host-specific divergence of L. johnsonii strains with respect to genome inversion and phage exposure.

Homologues of a single resistance-gene cluster in potato confer resistance to distinct pathogens: a virus and a nematode.

PubMed

van der Vossen, E A; van der Voort, J N; Kanyuka, K; Bendahmane, A; Sandbrink, H; Baulcombe, D C; Bakker, J; Stiekema, W J; Klein-Lankhorst, R M

2000-09-01

The isolation of the nematode-resistance gene Gpa2 in potato is described, and it is demonstrated that highly homologous resistance genes of a single resistance-gene cluster can confer resistance to distinct pathogen species. Molecular analysis of the Gpa2 locus resulted in the identification of an R-gene cluster of four highly homologous genes in a region of approximately 115 kb. At least two of these genes are active: one corresponds to the previously isolated Rx1 gene that confers resistance to potato virus X, while the other corresponds to the Gpa2 gene that confers resistance to the potato cyst nematode Globodera pallida. The proteins encoded by the Gpa2 and the Rx1 genes share an overall homology of over 88% (amino-acid identity) and belong to the leucine-zipper, nucleotide-binding site, leucine-rich repeat (LZ-NBS-LRR)-containing class of plant resistance genes. From the sequence conservation between Gpa2 and Rx1 it is clear that there is a direct evolutionary relationship between the two proteins. Sequence diversity is concentrated in the LRR region and in the C-terminus. The putative effector domains are more conserved suggesting that, at least in this case, nematode and virus resistance cascades could share common components. These findings underline the potential of protein breeding for engineering new resistance specificities against plant pathogens in vitro.

Do X-ray dark or underluminous galaxy clusters exist?

NASA Astrophysics Data System (ADS)

Andreon, S.; Moretti, A.

2011-12-01

We study the X-ray properties of a color-selected sample of clusters at 0.1 < z < 0.3, to quantify the real aboundance of the population of X-ray dark or underluminous clusters and at the same time the spurious detection contamination level of color-selected cluster catalogs. Starting from a local sample of color-selected clusters, we restrict our attention to those with sufficiently deep X-ray observations to probe their X-ray luminosity down to very faint values and without introducing any X-ray bias. This allowed us to have an X-ray- unbiased sample of 33 clusters to measure the LX-richness relation. Swift 1.4 Ms X-ray observations show that at least 89% of the color-detected clusters are real objects with a potential well deep enough to heat and retain an intracluster medium. The percentage rises to 94% when one includes the single spectroscopically confirmed color-selected cluster whose X-ray emission is not secured. Looking at our results from the opposite perspective, the percentage of X-ray dark clusters among color-selected clusters is very low: at most about 11 per cent (at 90% confidence). Supplementing our data with those from literature, we conclude that X-ray- and color- cluster surveys sample the same population and consequently that in this regard we can safely use clusters selected with any of the two methods for cosmological purposes. This is an essential and promising piece of information for upcoming surveys in both the optical/IR (DES, EUCLID) and X-ray (eRosita). Richness correlates with X-ray luminosity with a large scatter, 0.51 ± 0.08 (0.44 ± 0.07) dex in lgLX at a given richness, when Lx is measured in a 500 (1070) kpc aperture. We release data and software to estimate the X-ray flux, or its upper limit, of a source with over-Poisson background fluctuations (found in this work to be ~20% on cluster angular scales) and to fit X-ray luminosity vs richness if there is an intrinsic scatter. These Bayesian applications rigorously account for boundaries (e.g., the X-ray luminosity and the richness cannot be negative).

Whole-Genome Sequence of Coxiella burnetii Nine Mile RSA439 (Phase II, Clone 4), a Laboratory Workhorse Strain

PubMed Central

Beare, Paul A.; Moses, Abraham S.; Martens, Craig A.; Heinzen, Robert A.

2017-01-01

ABSTRACT Here, we report the whole-genome sequence of Coxiella burnetii Nine Mile RSA439 (phase II, clone 4), a laboratory strain used extensively to investigate the biology of this intracellular bacterial pathogen. The genome consists of a 1.97-Mb chromosome and a 37.32-kb plasmid. PMID:28596399

Whole-Genome Sequence of Coxiella burnetii Nine Mile RSA439 (Phase II, Clone 4), a Laboratory Workhorse Strain.

PubMed

Millar, Jess A; Beare, Paul A; Moses, Abraham S; Martens, Craig A; Heinzen, Robert A; Raghavan, Rahul

2017-06-08

Here, we report the whole-genome sequence of Coxiella burnetii Nine Mile RSA439 (phase II, clone 4), a laboratory strain used extensively to investigate the biology of this intracellular bacterial pathogen. The genome consists of a 1.97-Mb chromosome and a 37.32-kb plasmid. Copyright © 2017 Millar et al.

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.

Generation of Hypertension-Associated STK39 Polymorphism Knockin Cell Lines With the Clustered Regularly Interspaced Short Palindromic Repeats/Cas9 System.

PubMed

Mandai, Shintaro; Mori, Takayasu; Sohara, Eisei; Rai, Tatemitsu; Uchida, Shinichi

2015-12-01

Previous genome-wide association studies identified serine threonine kinase 39 (STK39), encoding STE20/SPS1-related proline/alanine-rich kinase, as one of a limited number of hypertension susceptibility genes. A recent meta-analysis confirmed the association of STK39 intronic polymorphism rs3754777 with essential hypertension, among previously reported hypertension-associated STK39 polymorphisms. However, the biochemical function of this polymorphism in the mechanism responsible for hypertension is yet to be clarified. We generated rs3754777G>A knockin human cell lines with clustered regularly interspaced short palindromic repeats-mediated genome engineering. Homozygous (A/A) and heterozygous (G/A) knockin human embryonic kidney cell lines were generated using a double nickase, single-guide RNAs targeting STK39 intron 5 around single-nucleotide polymorphism, and a 100-bp donor single-stranded DNA oligonucleotide. Reverse transcription polymerase chain reaction with sequencing analyses revealed the identical STK39 transcripts among the wild-type and both knockin cell lines. Quantitative reverse transcription polymerase chain reaction showed increased STK39 mRNA expression, and immunoblot analysis revealed increases in total and phosphorylated STE20/SPS1-related proline/alanine-rich kinase with increased phosphorylated Na-K-Cl cotransporter isoform 1 in both knockin cell lines. The largest increases in these molecules were observed in the homozygous cell line. These findings indicated that this intronic polymorphism increases STK39 transcription, leading to activation of the STE20/SPS1-related proline/alanine-rich kinase-solute carrier family 12A signaling cascade. Increased interactions between STE20/SPS1-related proline/alanine-rich kinase and the target cation-chloride cotransporters may be responsible for hypertension susceptibility in individuals with this polymorphism. © 2015 American Heart Association, Inc.

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.

Hepatitis B virus surface protein mutations clustered mainly in CTL immune epitopes in chronic carriers: results of an Iranian nationwide study.

PubMed

Khedive, A; Norouzi, M; Ramezani, F; Karimzadeh, H; Alavian, S M; Malekzadeh, R; Montazeri, G; Nejatizadeh, A; Ziaee, M; Abedi, F; Ataei, B; Yaran, M; Sayad, B; Somi, M H; Sarizadeh, G; Sanei-Moghaddam, I; Mansour-Ghanaei, F; Rafatpanah, H; Pourhosseingholi, M A; Keyvani, H; Kalantari, E; Saberifiroozi, M; Judaki, M A; Ghamari, S; Daram, M; Mahabadi, M; Fazeli, Z; Goodarzi, Z; Poortahmasebi, V; Jazayeri, S M

2013-07-01

Mutations within the coding region of hepatitis B surface antigen (HBsAg) have been found naturally in chronic carriers. To characterize the mutations of HBsAg from Iranian chronic carriers who were vaccine and/or medication naive. The surface genes from 360 patients were amplified and directly sequenced. The distribution of amino acid substitutions was classified according to different immune epitopes of the surface protein. All isolates belonged to genotype D. 222 (61.6%) of 360 patients contained at least one amino acid substitution. 404 (74.5%) of 542 amino acid changes occurred in different immune epitopes of HBsAg, of which 112 (27.7%) in 32 residues of B-cell epitopes (62 in the 'a' determinant); 111 (27.4%) in 32 residues of T helper; and 197 (48.7%) in 32 residues inside cytotoxic T lymphocyte (CTL) epitopes. One Th (186-197) and two CTL (28-51 and 206-215) epitopes were found to be hotspot motifs for the occurrence of 213 (52.7%) substitutions. 20 stop codons were identified in different epitopes. There was a significant association between amino acid substitutions and anti-HBe seropositivity; however, the correlation between such changes with viral load and ALT levels was not significant. In chronic hepatitis B virus(HBV) carriers, positive selection in particular outside the 'a' determinant appeared to exert influence on the surface proteins. These changes could be immune escape mutations naturally occurring due to the host immune surveillance especially at the T-cell level. © 2013 John Wiley & Sons Ltd.

Galaxy evolution in the densest environments: HST imaging

NASA Astrophysics Data System (ADS)

Jorgensen, Inger

2013-10-01

We propose to process in a consistent fashion all available HST/ACS and WFC3 imaging of seven rich clusters of galaxies at z=1.2-1.6. The clusters are part of our larger project aimed at constraining models for galaxy evolution in dense environments from observations of stellar populations in rich z=1.2-2 galaxy clusters. The main objective is to establish the star formation {SF} history and structural evolution over this epoch during which large changes in SF rates and galaxy structure are expected to take place in cluster galaxies.The observational data required to meet our main objective are deep HST imaging and high S/N spectroscopy of individual cluster members. The HST imaging already exists for the seven rich clusters at z=1.2-1.6 included in this archive proposal. However, the data have not been consistently processed to derive colors, magnitudes, sizes and morphological parameters for all potential cluster members bright enough to be suitable for spectroscopic observations with 8-m class telescopes. We propose to carry out this processing and make all derived parameters publicly available. We will use the parameters derived from the HST imaging to {1} study the structural evolution of the galaxies, {2} select clusters and galaxies for spectroscopic observations, and {3} use the photometry and spectroscopy together for a unified analysis aimed at the SF history and structural changes. The analysis will also utilize data from the Gemini/HST Cluster Galaxy Project, which covers rich clusters at z=0.2-1.0 and for which we have similar HST imaging and high S/N spectroscopy available.

New ligand platforms featuring boron-rich clusters as organomimetic substituents*,**

PubMed Central

Spokoyny, Alexander M.

2013-01-01

200 years of research with carbon-rich molecules have shaped the development of modern chemistry. Research pertaining to the chemistry of boron-rich species has historically trailed behind its more distinguished neighbor (carbon) in the periodic table. Notably, a potentially rich and, in many cases, unmatched field of coordination chemistry using boronrich clusters remains fundamentally underdeveloped. Our work has been devoted to examining several basic concepts related to the functionalization of icosahedral boron-rich clusters and their use as ligands, aimed at designing fundamentally new hybrid molecular motifs and materials. Particularly interesting are icosahedral carboranes, which can be regarded as 3D analogs of benzene. These species comprise a class of boron-rich clusters that were discovered in the 1950s during the “space race” while researchers were developing energetic materials for rocket fuels. Ultimately, the unique chemical and physical properties of carborane species, such as rigidity, indefinite stability to air and moisture, and 3D aromaticity, may allow one to access a set of properties not normally available in carbon-based chemistry. While technically these species are considered as inorganic clusters, the chemical properties they possess make these boron-rich species suitable for replacing and/or altering structural and functional features of the organic and organometallic molecules—a phenomenon best described as “organomimetic”. Aside from purely fundamental features associated with the organomimetic chemistry of icosahedral carboranes, their use can also provide new avenues in the development of systems relevant to solving current problems associated with energy production, storage, and conversion. PMID:24311823

Clustering Aspects in Nuclear Structure and Collisions

NASA Astrophysics Data System (ADS)

Horiuchi, H.

Four topics on nuclear clustering are discussed. The first subject is about the cluster formation in dilute matter which we think is now observed in heavy ion collisions at hundreds MeV/nucleon. The second subject is about our new proposal of the existense of alpha condensed states in light nuclei. Two other subjects are both about the clustering in neutron-rich nuclei. One is the cluster structures in neutron-rich Be and B isotopes. In these isotopes, the clustering prevails as fundamental characters of nuclear structure. The other is the report of our recent study about the possible relation of the clustering with the breaking of the neutron magic number N=20 in 32Mg and 30Ne.

Transcriptome wide identification and characterization of starch branching enzyme in finger millet.

PubMed

Tyagi, Rajhans; Tiwari, Apoorv; Garg, Vijay Kumar; Gupta, Sanjay

2017-01-01

Starch-branching enzymes (SBEs) are one of the four major enzyme classes involved in starch biosynthesis in plants and play an important role in determining the structure and physical properties of starch granules. Multiple SBEs are involved in starch biosynthesis in plants. Finger millet is calcium rich important serial crop belongs to grass family and the transcriptome data of developing spikes is available on NCBI. In this study it was try to find out the gene sequence of starch branching enzyme and annotate the sequence and submit the sequence for further use. Rice SBE sequence was taken as reference and for characterization of the sequence different in silico tools were used. Four domains were found in the finger millet Starch branching enzyme like alpha amylase catalytic domain from 925 to2172 with E value 0, N-terminal Early set domain from 634 to 915 with E value 1.62 e-42, Alpha amylase, C-terminal all-beta domain from 2224 to 2511 with E value 5.80e-24 and 1,4-alpha-glucan-branching enzyme from 421 to 2517 with E value 0. Major binding interactions with the GLC (alpha-d-glucose), CA (calcium ion), GOL (glycerol), TRS (2-amino-2-hydroxymethylpropane- 1, 3-diol), MG (magnesium ion) and FLC (citrate anion) are fond with different residues. It was found in the phylogenetic study of the finger millet SBE with the 6 species of grass family that two clusters were form A and B. In cluster A, finger millet showed closeness with Oryzasativa and Setariaitalica, Sorghum bicolour and Zea mays while cluster B was formed with Triticumaestivum and Brachypodium distachyon. The nucleotide sequence of Finger millet SBE was submitted to NCBI with the accession no KY648913 and protein structure of SBE of finger millet was also submitted in PMDB with the PMDB id - PM0080938. This research presents a comparative overview of Finger millet SBE and includes their properties, structural and functional characteristics, and recent developments on their post-translational regulation.

Association of high-risk sexual behaviour with diversity of the vaginal microbiota and abundance of Lactobacillus

PubMed Central

Wessels, Jocelyn M.; Lajoie, Julie; Vitali, Danielle; Omollo, Kenneth; Kimani, Joshua; Oyugi, Julius; Cheruiyot, Juliana; Kimani, Makubo; Mungai, John N.; Akolo, Maureen; Stearns, Jennifer C.; Surette, Michael G.; Fowke, Keith R.

2017-01-01

Objective To compare the vaginal microbiota of women engaged in high-risk sexual behaviour (sex work) with women who are not engaged in high-risk sexual behaviour. Diverse vaginal microbiota, low in Lactobacillus species, like those in bacterial vaginosis (BV), are associated with increased prevalence of sexually transmitted infections (STIs) and human immunodeficiency virus (HIV) acquisition. Although high-risk sexual behaviour increases risk for STIs, the vaginal microbiota of sex workers is understudied. Methods A retrospective cross-sectional study was conducted comparing vaginal microbiota of women who are not engaged in sex work (non-sex worker controls, NSW, N = 19) and women engaged in sex work (female sex workers, FSW, N = 48), using Illumina sequencing (16S rRNA, V3 region). Results Bacterial richness and diversity were significantly less in controls, than FSW. Controls were more likely to have Lactobacillus as the most abundant genus (58% vs. 17%; P = 0.002) and composition of their vaginal microbiota differed from FSW (PERMANOVA, P = 0.001). Six microbiota clusters were detected, including a high diversity cluster with three sub-clusters, and 55% of women with low Nugent Scores fell within this cluster. High diversity was observed by 16S sequencing in FSW, regardless of Nugent Scores, suggesting that Nugent Score may not be capable of capturing the diversity present in the FSW vaginal microbiota. Conclusions High-risk sexual behaviour is associated with diversity of the vaginal microbiota and lack of Lactobacillus. These factors could contribute to increased risk of STIs and HIV in women engaged in high-risk sexual behaviour. PMID:29095928

Association of high-risk sexual behaviour with diversity of the vaginal microbiota and abundance of Lactobacillus.

PubMed

Wessels, Jocelyn M; Lajoie, Julie; Vitali, Danielle; Omollo, Kenneth; Kimani, Joshua; Oyugi, Julius; Cheruiyot, Juliana; Kimani, Makubo; Mungai, John N; Akolo, Maureen; Stearns, Jennifer C; Surette, Michael G; Fowke, Keith R; Kaushic, Charu

2017-01-01

To compare the vaginal microbiota of women engaged in high-risk sexual behaviour (sex work) with women who are not engaged in high-risk sexual behaviour. Diverse vaginal microbiota, low in Lactobacillus species, like those in bacterial vaginosis (BV), are associated with increased prevalence of sexually transmitted infections (STIs) and human immunodeficiency virus (HIV) acquisition. Although high-risk sexual behaviour increases risk for STIs, the vaginal microbiota of sex workers is understudied. A retrospective cross-sectional study was conducted comparing vaginal microbiota of women who are not engaged in sex work (non-sex worker controls, NSW, N = 19) and women engaged in sex work (female sex workers, FSW, N = 48), using Illumina sequencing (16S rRNA, V3 region). Bacterial richness and diversity were significantly less in controls, than FSW. Controls were more likely to have Lactobacillus as the most abundant genus (58% vs. 17%; P = 0.002) and composition of their vaginal microbiota differed from FSW (PERMANOVA, P = 0.001). Six microbiota clusters were detected, including a high diversity cluster with three sub-clusters, and 55% of women with low Nugent Scores fell within this cluster. High diversity was observed by 16S sequencing in FSW, regardless of Nugent Scores, suggesting that Nugent Score may not be capable of capturing the diversity present in the FSW vaginal microbiota. High-risk sexual behaviour is associated with diversity of the vaginal microbiota and lack of Lactobacillus. These factors could contribute to increased risk of STIs and HIV in women engaged in high-risk sexual behaviour.

Pal 12 - A metal-rich globular cluster in the outer halo

NASA Technical Reports Server (NTRS)

Cohen, J. G.; Frogel, J. A.; Persson, S. E.; Zinn, R.

1980-01-01

New optical and infrared observations of several stars in the distant globular cluster Pal 12 show that they have CO strengths and heavy element abundances only slightly less than in M 71, one of the more metal-rich globular clusters. Pal 12 thus has a metal abundance near the high end of the range over which globular clusters exist and lies in the outer galactic halo. Its red horizontal branch is not anomalous in view of the abundance that has been found.

Mouse cysteine-rich secretory protein 4 (CRISP4): a member of the Crisp family exclusively expressed in the epididymis in an androgen-dependent manner.

PubMed

Jalkanen, Jenni; Huhtaniemi, Ilpo; Poutanen, Matti

2005-05-01

The final maturation of spermatozoa produced in the testis takes place during their passage through the epididymis. In this process, the proteins secreted into the epididymal lumen along with changes in the pH and salt composition of the epididymal fluid cause several biochemical changes and remodeling of the sperm plasma membrane. The Crisp family is a group of cysteine-rich secretory proteins that previously consisted of three members, one of which-CRISP1-is an epididymal protein shown to attach to the sperm surface in the epididymal lumen and to inhibit gamete membrane fusion. In the present paper, we introduce a new member of the Crisp protein family, CRISP4. The new gene was discovered through in silico analysis of the epididymal expressed sequence tag library deposited in the UniGene database. The peptide sequence of CRISP4 has a signal sequence suggesting that it is secreted into the epididymal lumen and might thus interact with sperm. Unlike the other members of the family, Crisp4 is located on chromosome 1 in a cluster of genes encoding for cysteine-rich proteins. Crisp4 is expressed in the mouse exclusively in epithelial cells of the epididymis in an androgen-dependent manner, and the expression of the gene starts at puberty along with the onset of sperm maturation. The identified murine CRISP4 peptide has high homology with human CRISP1, and the homology is higher than that between murine and human CRISP1, suggesting that CRISP4 represents the mouse counterpart of human CRISP1 and could have similar effects on sperm membrane as mouse and human CRISP1.

The globular cluster systems of 54 Coma ultra-diffuse galaxies: statistical constraints from HST data

NASA Astrophysics Data System (ADS)

Amorisco, N. C.; Monachesi, A.; Agnello, A.; White, S. D. M.

2018-04-01

We use data from the HST Coma Cluster Treasury program to assess the richness of the globular cluster systems (GCSs) of 54 Coma ultra-diffuse galaxies (UDGs), 18 of which have a half-light radius exceeding 1.5 kpc. We use a hierarchical Bayesian method tested on a large number of mock data sets to account consistently for the high and spatially varying background counts in Coma. These include both background galaxies and intra-cluster globular clusters (ICGCs), which are disentangled from the population of member globular clusters (GCs) in a probabilistic fashion. We find no candidate for a GCS as rich as that of the Milky Way, our sample has GCSs typical of dwarf galaxies. For the standard relation between GCS richness and halo mass, 33 galaxies have a virial mass Mvir ≤ 1011 M⊙ at 90 per cent probability. Only three have Mvir > 1011 M⊙ with the same confidence. The mean colour and spread in colour of the UDG GCs are indistinguishable from those of the abundant population of ICGCs. The majority of UDGs in our sample are consistent with the relation between stellar mass and GC richness of `normal' dwarf galaxies. Nine systems, however, display GCSs that are richer by a factor of 3 or more (at 90 per cent probability). Six of these have sizes ≲1.4 kpc. Our results imply that the physical mechanisms responsible for the extended size of the UDGs and for the enhanced GC richness of some cluster dwarfs are at most weakly correlated.

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.

Expansion of ribosomally produced natural products: a nitrile hydratase- and Nif11-related precursor family

PubMed Central

2010-01-01

Background A new family of natural products has been described in which cysteine, serine and threonine from ribosomally-produced peptides are converted to thiazoles, oxazoles and methyloxazoles, respectively. These metabolites and their biosynthetic gene clusters are now referred to as thiazole/oxazole-modified microcins (TOMM). As exemplified by microcin B17 and streptolysin S, TOMM precursors contain an N-terminal leader sequence and C-terminal core peptide. The leader sequence contains binding sites for the posttranslational modifying enzymes which subsequently act upon the core peptide. TOMM peptides are small and highly variable, frequently missed by gene-finders and occasionally situated far from the thiazole/oxazole forming genes. Thus, locating a substrate for a particular TOMM pathway can be a challenging endeavor. Results Examination of candidate TOMM precursors has revealed a subclass with an uncharacteristically long leader sequence closely related to the enzyme nitrile hydratase. Members of this nitrile hydratase leader peptide (NHLP) family lack the metal-binding residues required for catalysis. Instead, NHLP sequences display the classic Gly-Gly cleavage motif and have C-terminal regions rich in heterocyclizable residues. The NHLP family exhibits a correlated species distribution and local clustering with an ABC transport system. This study also provides evidence that a separate family, annotated as Nif11 nitrogen-fixing proteins, can serve as natural product precursors (N11P), but not always of the TOMM variety. Indeed, a number of cyanobacterial genomes show extensive N11P paralogous expansion, such as Nostoc, Prochlorococcus and Cyanothece, which replace the TOMM cluster with lanthionine biosynthetic machinery. Conclusions This study has united numerous TOMM gene clusters with their cognate substrates. These results suggest that two large protein families, the nitrile hydratases and Nif11, have been retailored for secondary metabolism. Precursors for TOMMs and lanthionine-containing peptides derived from larger proteins to which other functions are attributed, may be widespread. The functions of these natural products have yet to be elucidated, but it is probable that some will display valuable industrial or medical activities. PMID:20500830

Assembly rules for functional groups of North American shrews: effects of geographic range and habitat partitioning

Treesearch

Timothy S. McCay; Matthew J. Lovallo; W. Mark Ford; Michael A. Menzel; Michael A. Menzel

2004-01-01

We examined the representation of shrew species within assemblages at 197 sites in the southern Appalachian Mountains, USA. Assemblages were classified according to representation of functional groups, including fossorial, small epigeal, and large epigeal. Average (9?SD) species richness was 2.99?1.0 and assemblages averaged 0.8 species in the fossorial and large...

Structural Principles or Frequency of Use? An ERP Experiment on the Learnability of Consonant Clusters

PubMed Central

Wiese, Richard; Orzechowska, Paula; Alday, Phillip M.; Ulbrich, Christiane

2017-01-01

Phonological knowledge of a language involves knowledge about which segments can be combined under what conditions. Languages vary in the quantity and quality of licensed combinations, in particular sequences of consonants, with Polish being a language with a large inventory of such combinations. The present paper reports on a two-session experiment in which Polish-speaking adult participants learned nonce words with final consonant clusters. The aim was to study the role of two factors which potentially play a role in the learning of phonotactic structures: the phonological principle of sonority (ordering sound segments within the syllable according to their inherent loudness) and the (non-) existence as a usage-based phenomenon. EEG responses in two different time windows (adversely to behavioral responses) show linguistic processing by native speakers of Polish to be sensitive to both distinctions, in spite of the fact that Polish is rich in sonority-violating clusters. In particular, a general learning effect in terms of an N400 effect was found which was demonstrated to be different for sonority-obeying clusters than for sonority-violating clusters. Furthermore, significant interactions of formedness and session, and of existence and session, demonstrate that both factors, the sonority principle and the frequency pattern, play a role in the learning process. PMID:28119642

A novel family of sequence-specific endoribonucleases associated with the clustered regularly interspaced short palindromic repeats.

PubMed

Beloglazova, Natalia; Brown, Greg; Zimmerman, Matthew D; Proudfoot, Michael; Makarova, Kira S; Kudritska, Marina; Kochinyan, Samvel; Wang, Shuren; Chruszcz, Maksymilian; Minor, Wladek; Koonin, Eugene V; Edwards, Aled M; Savchenko, Alexei; Yakunin, Alexander F

2008-07-18

Clustered regularly interspaced short palindromic repeats (CRISPRs) together with the associated CAS proteins protect microbial cells from invasion by foreign genetic elements using presently unknown molecular mechanisms. All CRISPR systems contain proteins of the CAS2 family, suggesting that these uncharacterized proteins play a central role in this process. Here we show that the CAS2 proteins represent a novel family of endoribonucleases. Six purified CAS2 proteins from diverse organisms cleaved single-stranded RNAs preferentially within U-rich regions. A representative CAS2 enzyme, SSO1404 from Sulfolobus solfataricus, cleaved the phosphodiester linkage on the 3'-side and generated 5'-phosphate- and 3'-hydroxyl-terminated oligonucleotides. The crystal structure of SSO1404 was solved at 1.6A resolution revealing the first ribonuclease with a ferredoxin-like fold. Mutagenesis of SSO1404 identified six residues (Tyr-9, Asp-10, Arg-17, Arg-19, Arg-31, and Phe-37) that are important for enzymatic activity and suggested that Asp-10 might be the principal catalytic residue. Thus, CAS2 proteins are sequence-specific endoribonucleases, and we propose that their role in the CRISPR-mediated anti-phage defense might involve degradation of phage or cellular mRNAs.

Divergent homologs of the predicted small RNA BpCand697 in Burkholderia spp.

NASA Astrophysics Data System (ADS)

Damiri, Nadzirah; Mohd-Padil, Hirzahida; Firdaus-Raih, Mohd

2015-09-01

The small RNA (sRNA) gene candidate, BpCand697 was previously reported to be unique to Burkholderia spp. and is encoded at 3' non-coding region of a putative AraC family transcription regulator gene. This study demonstrates the conservation of BpCand697 sequence across 32 Burkholderia spp. including B. pseudomallei, B. mallei, B. thailandensis and Burkholderia sp. by integrating both sequence homology and secondary structural analyses of BpCand697 within the dataset. The divergent sequence of BpCand697 was also used as a discriminatory power in clustering the dataset according to the potential virulence of Burkholderia spp., showing that B. thailandensis was clearly secluded from the virulent cluster of B. pseudomallei and B. mallei. Finally, the differential co-transcript expression of BpCand697 and its flanking gene, bpsl2391 was detected in Burkholderia pseudomallei D286 after grown under two different culture conditions using nutrient-rich and minimal media. It is hypothesized that the differential expression of BpCand697-bpsl2391 co-transcript between the two standard prepared media might correlate with nutrient availability in the culture media, suggesting that the physical co-localization of BpCand697 in B. pseudomallei D286 might be directly or indirectly involved with the transcript regulation of bpsl2391 under the selected in vitro culture conditions.

Reentrant and Isostructural Transitions in the Cluster-Crystal Forming GEM-4

NASA Astrophysics Data System (ADS)

Zhang, Kai; Charbonneau, Patrick; Mladek, Bianca

2011-03-01

Systems governed by soft, bounded, purely repulsive interactions show two possible equilibrium behaviors under compression: reentrant melting, as in the Gaussian core model (GCM), or clustering, as in the penetrable sphere model (PSM). The generalized exponential model of power 4 (GEM-4), which is the intermedia of the GCM and PSM with a simple isotropic pair interaction u (r) ~e-r4 , is thought to belong to the second family and was indeed found to form clusters at sufficiently high densities at high temperatures. Here, we present the low-temperature behavior of GEM-4 through Monte Carlo simulations using a specially developed free energy integration scheme. We find the phase behavior to be hybrid between the GCM and the PSM limits, showing a surprisingly rich phase behavior in spite of the simplicity of the interaction form. For instance, S- shaped doubly reentrant phase sequences and evidence of a cascade of critical isostructural transitions between crystals of different average lattice site occupancy are observed. The possible annihilation of lattice sites and accompanying clustering moreover leads to an unusual softening upon compression, which suggest that these materials may have interesting mechanical properties. We discuss possible experimental realizations and challenges of this class of materials.

The Hottest Horizontal-Branch Stars in Omega Centauri: Late Hot Flasher vs. Helium Enrichment

NASA Technical Reports Server (NTRS)

Moehler, S.; Dreizler, S.; Lanz, T.; Bono, G.; Sweigart, A V.; Calamida, A.; Monelli, M.; Nonino, M.

2007-01-01

UV observations of some massive globular clusters uncovered a significant population of very hot stars below the hot end of the horizontal branch (HB), the so-called blue hook stars. This feature might be explained either by the late hot flasher scenario here stars experience the helium flash while on the white dwarf cooling curve or by the helium-rich sub-population recently postulated to exist in some clusters. Spectroscopic analyses of blue hook stars in omega Cen and NGC 2808 support the late hot flasher scenario, but the stars contain much less helium than expected and the predicted C, N enrichment could not be verified from existing data. We want to determine effective temperatures, surface gravities and abundances of He, C, N in blue hook and canonical extreme horizontal branch (EHB) star candidates. Moderately high resolution spectra of stars at the hot end of the blue horizontal branch in the globular cluster omega Cen were analysed for atmospheric parameters (T(sub eff), log g) and abundances using LTE and Non-LTE model atmospheres. In the temperature range 30,000 K to 50,000 K we find that 37% of our stars are helium-poor (log nHe/nH less than -2), 49% have solar helium abundance within a factor of 3 (-1.5 less than or equal to log nHe/nH less than or equal to -0.5) and 14% are helium rich (log nHe/nH greater than -0.4). We also find carbon enrichment in step with helium enrichment, with a maximum carbon enrichment of 3% by mass. At least 30% of the hottest HB stars in omega Centauri show helium abundances well above the predictions from the helium enrichment scenario (Y = 0.42 corresponding to log nHe/nH approximately equal to -0.74). In addition the most helium-rich stars show strong carbon enrichment as predicted by the late hot flasher scenario. We conclude that the helium-rich HB stars in omega Cen cannot be explained solely by the helium-enrichment scenario invoked to explain the blue main sequence.

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.

Structural basis for genome wide recognition of 5-bp GC motifs by SMAD transcription factors.

PubMed

Martin-Malpartida, Pau; Batet, Marta; Kaczmarska, Zuzanna; Freier, Regina; Gomes, Tiago; Aragón, Eric; Zou, Yilong; Wang, Qiong; Xi, Qiaoran; Ruiz, Lidia; Vea, Angela; Márquez, José A; Massagué, Joan; Macias, Maria J

2017-12-12

Smad transcription factors activated by TGF-β or by BMP receptors form trimeric complexes with Smad4 to target specific genes for cell fate regulation. The CAGAC motif has been considered as the main binding element for Smad2/3/4, whereas Smad1/5/8 have been thought to preferentially bind GC-rich elements. However, chromatin immunoprecipitation analysis in embryonic stem cells showed extensive binding of Smad2/3/4 to GC-rich cis-regulatory elements. Here, we present the structural basis for specific binding of Smad3 and Smad4 to GC-rich motifs in the goosecoid promoter, a nodal-regulated differentiation gene. The structures revealed a 5-bp consensus sequence GGC(GC)|(CG) as the binding site for both TGF-β and BMP-activated Smads and for Smad4. These 5GC motifs are highly represented as clusters in Smad-bound regions genome-wide. Our results provide a basis for understanding the functional adaptability of Smads in different cellular contexts, and their dependence on lineage-determining transcription factors to target specific genes in TGF-β and BMP pathways.

Tracing Large Scale Structure with a Redshift Survey of Rich Clusters of Galaxies

NASA Astrophysics Data System (ADS)

Batuski, D.; Slinglend, K.; Haase, S.; Hill, J. M.

1993-12-01

Rich clusters of galaxies from Abell's catalog show evidence of structure on scales of 100 Mpc and hold promise of confirming the existence of structure in the more immediate universe on scales corresponding to COBE results (i.e., on the order of 10% or more of the horizon size of the universe). However, most Abell clusters do not as yet have measured redshifts (or, in the case of most low redshift clusters, have only one or two galaxies measured), so present knowledge of their three dimensional distribution has quite large uncertainties. The shortage of measured redshifts for these clusters may also mask a problem of projection effects corrupting the membership counts for the clusters, perhaps even to the point of spurious identifications of some of the clusters themselves. Our approach in this effort has been to use the MX multifiber spectrometer to measure redshifts of at least ten galaxies in each of about 80 Abell cluster fields with richness class R>= 1 and mag10 <= 16.8. This work will result in a somewhat deeper, much more complete (and reliable) sample of positions of rich clusters. Our primary use for the sample is for two-point correlation and other studies of the large scale structure traced by these clusters. We are also obtaining enough redshifts per cluster so that a much better sample of reliable cluster velocity dispersions will be available for other studies of cluster properties. To date, we have collected such data for 40 clusters, and for most of them, we have seven or more cluster members with redshifts, allowing for reliable velocity dispersion calculations. Velocity histograms for several interesting cluster fields are presented, along with summary tables of cluster redshift results. Also, with 10 or more redshifts in most of our cluster fields (30({') } square, just about an `Abell diameter' at z ~ 0.1) we have investigated the extent of projection effects within the Abell catalog in an effort to quantify and understand how this may effect the Abell sample.

Rapidly rotating second-generation progenitors for the 'blue hook' stars of ω Centauri.

PubMed

Tailo, Marco; D'Antona, Francesca; Vesperini, Enrico; Di Criscienzo, Marcella; Ventura, Paolo; Milone, Antonino P; Bellini, Andrea; Dotter, Aaron; Decressin, Thibaut; D'Ercole, Annibale; Caloi, Vittoria; Capuzzo-Dolcetta, Roberto

2015-07-16

Horizontal branch stars belong to an advanced stage in the evolution of the oldest stellar galactic population, occurring either as field halo stars or grouped in globular clusters. The discovery of multiple populations in clusters that were previously believed to have single populations gave rise to the currently accepted theory that the hottest horizontal branch members (the 'blue hook' stars, which had late helium-core flash ignition, followed by deep mixing) are the progeny of a helium-rich 'second generation' of stars. It is not known why such a supposedly rare event (a late flash followed by mixing) is so common that the blue hook of ω Centauri contains approximately 30 per cent of the horizontal branch stars in the cluster, or why the blue hook luminosity range in this massive cluster cannot be reproduced by models. Here we report that the presence of helium core masses up to about 0.04 solar masses larger than the core mass resulting from evolution is required to solve the luminosity range problem. We model this by taking into account the dispersion in rotation rates achieved by the progenitors, whose pre-main-sequence accretion disk suffered an early disruption in the dense environment of the cluster's central regions, where second-generation stars form. Rotation may also account for frequent late-flash-mixing events in massive globular clusters.

Genetic Analysis of 430 Chinese Cynodon dactylon Accessions Using Sequence-Related Amplified Polymorphism Markers

PubMed Central

Huang, Chunqiong; Liu, Guodao; Bai, Changjun; Wang, Wenqiang

2014-01-01

Although Cynodon dactylon (C. dactylon) is widely distributed in China, information on its genetic diversity within the germplasm pool is limited. The objective of this study was to reveal the genetic variation and relationships of 430 C. dactylon accessions collected from 22 Chinese provinces using sequence-related amplified polymorphism (SRAP) markers. Fifteen primer pairs were used to amplify specific C. dactylon genomic sequences. A total of 481 SRAP fragments were generated, with fragment sizes ranging from 260–1800 base pairs (bp). Genetic similarity coefficients (GSC) among the 430 accessions averaged 0.72 and ranged from 0.53–0.96. Cluster analysis conducted by two methods, namely the unweighted pair-group method with arithmetic averages (UPGMA) and principle coordinate analysis (PCoA), separated the accessions into eight distinct groups. Our findings verify that Chinese C. dactylon germplasms have rich genetic diversity, which is an excellent basis for C. dactylon breeding for new cultivars. PMID:25338051

Census of solo LuxR genes in prokaryotic genomes

PubMed Central

Hudaiberdiev, Sanjarbek; Choudhary, Kumari S.; Vera Alvarez, Roberto; Gelencsér, Zsolt; Ligeti, Balázs; Lamba, Doriano; Pongor, Sándor

2015-01-01

luxR genes encode transcriptional regulators that control acyl homoserine lactone-based quorum sensing (AHL QS) in Gram negative bacteria. On the bacterial chromosome, luxR genes are usually found next or near to a luxI gene encoding the AHL signal synthase. Recently, a number of luxR genes were described that have no luxI genes in their vicinity on the chromosome. These so-called solo luxR genes may either respond to internal AHL signals produced by a non-adjacent luxI in the chromosome, or can respond to exogenous signals. Here we present a survey of solo luxR genes found in complete and draft bacterial genomes in the NCBI databases using HMMs. We found that 2698 of the 3550 luxR genes found are solos, which is an unexpectedly high number even if some of the hits may be false positives. We also found that solo LuxR sequences form distinct clusters that are different from the clusters of LuxR sequences that are part of the known luxR-luxI topological arrangements. We also found a number of cases that we termed twin luxR topologies, in which two adjacent luxR genes were in tandem or divergent orientation. Many of the luxR solo clusters were devoid of the sequence motifs characteristic of AHL binding LuxR proteins so there is room to speculate that the solos may be involved in sensing hitherto unknown signals. It was noted that only some of the LuxR clades are rich in conserved cysteine residues. Molecular modeling suggests that some of the cysteines may be involved in disulfide formation, which makes us speculate that some LuxR proteins, including some of the solos may be involved in redox regulation. PMID:25815274

The major resistance gene cluster in lettuce is highly duplicated and spans several megabases.

PubMed Central

Meyers, B C; Chin, D B; Shen, K A; Sivaramakrishnan, S; Lavelle, D O; Zhang, Z; Michelmore, R W

1998-01-01

At least 10 Dm genes conferring resistance to the oomycete downy mildew fungus Bremia lactucae map to the major resistance cluster in lettuce. We investigated the structure of this cluster in the lettuce cultivar Diana, which contains Dm3. A deletion breakpoint map of the chromosomal region flanking Dm3 was saturated with a variety of molecular markers. Several of these markers are components of a family of resistance gene candidates (RGC2) that encode a nucleotide binding site and a leucine-rich repeat region. These motifs are characteristic of plant disease resistance genes. Bacterial artificial chromosome clones were identified by using duplicated restriction fragment length polymorphism markers from the region, including the nucleotide binding site-encoding region of RGC2. Twenty-two distinct members of the RGC2 family were characterized from the bacterial artificial chromosomes; at least two additional family members exist. The RGC2 family is highly divergent; the nucleotide identity was as low as 53% between the most distantly related copies. These RGC2 genes span at least 3.5 Mb. Eighteen members were mapped on the deletion breakpoint map. A comparison between the phylogenetic and physical relationships of these sequences demonstrated that closely related copies are physically separated from one another and indicated that complex rearrangements have shaped this region. Analysis of low-copy genomic sequences detected no genes, including RGC2, in the Dm3 region, other than sequences related to retrotransposons and transposable elements. The related but divergent family of RGC2 genes may act as a resource for the generation of new resistance phenotypes through infrequent recombination or unequal crossing over. PMID:9811791

Census of solo LuxR genes in prokaryotic genomes.

PubMed

Hudaiberdiev, Sanjarbek; Choudhary, Kumari S; Vera Alvarez, Roberto; Gelencsér, Zsolt; Ligeti, Balázs; Lamba, Doriano; Pongor, Sándor

2015-01-01

luxR genes encode transcriptional regulators that control acyl homoserine lactone-based quorum sensing (AHL QS) in Gram negative bacteria. On the bacterial chromosome, luxR genes are usually found next or near to a luxI gene encoding the AHL signal synthase. Recently, a number of luxR genes were described that have no luxI genes in their vicinity on the chromosome. These so-called solo luxR genes may either respond to internal AHL signals produced by a non-adjacent luxI in the chromosome, or can respond to exogenous signals. Here we present a survey of solo luxR genes found in complete and draft bacterial genomes in the NCBI databases using HMMs. We found that 2698 of the 3550 luxR genes found are solos, which is an unexpectedly high number even if some of the hits may be false positives. We also found that solo LuxR sequences form distinct clusters that are different from the clusters of LuxR sequences that are part of the known luxR-luxI topological arrangements. We also found a number of cases that we termed twin luxR topologies, in which two adjacent luxR genes were in tandem or divergent orientation. Many of the luxR solo clusters were devoid of the sequence motifs characteristic of AHL binding LuxR proteins so there is room to speculate that the solos may be involved in sensing hitherto unknown signals. It was noted that only some of the LuxR clades are rich in conserved cysteine residues. Molecular modeling suggests that some of the cysteines may be involved in disulfide formation, which makes us speculate that some LuxR proteins, including some of the solos may be involved in redox regulation.

Turnerbactin, a Novel Triscatecholate Siderophore from the Shipworm Endosymbiont Teredinibacter turnerae T7901

PubMed Central

Han, Andrew W.; Sandy, Moriah; Fishman, Brian; Trindade-Silva, Amaro E.; Soares, Carlos A. G.; Distel, Daniel L.; Butler, Alison; Haygood, Margo G.

2013-01-01

Shipworms are marine bivalve mollusks (Family Teredinidae) that use wood for shelter and food. They harbor a group of closely related, yet phylogenetically distinct, bacterial endosymbionts in bacteriocytes located in the gills. This endosymbiotic community is believed to support the host's nutrition in multiple ways, through the production of cellulolytic enzymes and the fixation of nitrogen. The genome of the shipworm endosymbiont Teredinibacter turnerae T7901 was recently sequenced and in addition to the potential for cellulolytic enzymes and diazotrophy, the genome also revealed a rich potential for secondary metabolites. With nine distinct biosynthetic gene clusters, nearly 7% of the genome is dedicated to secondary metabolites. Bioinformatic analyses predict that one of the gene clusters is responsible for the production of a catecholate siderophore. Here we describe this gene cluster in detail and present the siderophore product from this cluster. Genes similar to the entCEBA genes of enterobactin biosynthesis involved in the production and activation of dihydroxybenzoic acid (DHB) are present in this cluster, as well as a two-module non-ribosomal peptide synthetase (NRPS). A novel triscatecholate siderophore, turnerbactin, was isolated from the supernatant of iron-limited T. turnerae T7901 cultures. Turnerbactin is a trimer of N-(2,3-DHB)-L-Orn-L-Ser with the three monomeric units linked by Ser ester linkages. A monomer, dimer, dehydrated dimer, and dehydrated trimer of 2,3-DHB-L-Orn-L-Ser were also found in the supernatant. A link between the gene cluster and siderophore product was made by constructing a NRPS mutant, TtAH03. Siderophores could not be detected in cultures of TtAH03 by HPLC analysis and Fe-binding activity of culture supernatant was significantly reduced. Regulation of the pathway by iron is supported by identification of putative Fur box sequences and observation of increased Fe-binding activity under iron restriction. Evidence of a turnerbactin fragment was found in shipworm extracts, suggesting the production of turnerbactin in the symbiosis. PMID:24146831

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.

Analyzing multistep homogeneous nucleation in vapor-to-solid transitions using molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Tanaka, Kyoko K.; Diemand, Jürg; Tanaka, Hidekazu; Angélil, Raymond

2017-08-01

In this paper, we present multistep homogeneous nucleations in vapor-to-solid transitions as revealed by molecular dynamics simulations on Lennard-Jones molecules, where liquidlike clusters are created and crystallized. During a long, direct N V E (constant volume, energy, and number of molecules) involving the integration of (1.9 -15 )× 106 molecules in up to 200 million steps (=4.3 μ s ), crystallization in many large, supercooled nanoclusters is observed once the liquid clusters grow to a certain size (˜800 molecules for the case of T ≃0.5 ɛ /k ). In the simulations, we discovered an interesting process associated with crystallization: the solid clusters lost 2-5 % of their mass during crystallization at low temperatures below their melting temperatures. Although the crystallized clusters were heated by latent heat, they were stabilized by cooling due to evaporation. The clusters crystallized quickly and completely except at surface layers. However, they did not have stable crystal structures, rather they had metastable structures such as icosahedral, decahedral, face-centered-cubic-rich (fcc-rich), and hexagonal-close-packed-rich (hcp-rich). Several kinds of cluster structures coexisted in the same size range of ˜1000 -5000 molecules. Our results imply that multistep nucleation is a common first stage of condensation from vapor to solid.

From Globular Clusters to Tidal Dwarfs: Structure Formation in the Tidal Tails of Merging Galaxies

NASA Astrophysics Data System (ADS)

Knierman, Karen A.; Gallagher, Sarah C.; Charlton, Jane C.; Hunsberger, Sally D.; Whitmore, Bradley; Kundu, Arunav; Hibbard, J. E.; Zaritsky, Dennis

2003-09-01

Using V and I images obtained with the Wide Field Planetary Camera 2 (WFPC2) of the Hubble Space Telescope, we investigate compact stellar structures within tidal tails. Six regions of tidal debris in the four classic ``Toomre sequence'' mergers: NGC 4038/39 (``Antennae''), NGC 3256, NGC 3921, and NGC 7252 (``Atoms for Peace'') have been studied in order to explore how the star formation depends on the local and global physical conditions. These mergers sample a range of stages in the evolutionary sequence and tails with and without embedded tidal dwarf galaxies. The six tails are found to contain a variety of stellar structures, with sizes ranging from those of globular clusters up to those of dwarf galaxies. From V and I WFPC2 images, we measure the luminosities and colors of the star clusters. NGC 3256 is found to have a large population of blue clusters (0.2<~V-I<~0.9), particularly in its western tail, similar to those found in the inner region of the merger. In contrast, NGC 4038/39 has no clusters in the observed region of the tail, only less luminous point sources likely to be individual stars. NGC 3921 and NGC 7252 have small populations of clusters along their tails. A significant cluster population is clearly associated with the prominent tidal dwarf candidates in the eastern and western tails of NGC 7252. The cluster-rich western tail of NGC 3256 is not distinguished from the others by its dynamical age or by its total H I mass. However, the mergers that have few clusters in the tail all have tidal dwarf galaxies, while NGC 3256 does not have prominent tidal dwarfs. We speculate that star formation in tidal tails may manifest itself either in small structures like clusters along the tail or in large structures such as dwarf galaxies, but not in both. Also, NGC 3256 has the highest star formation rate of the four mergers studied, which may contribute to the high number of star clusters in its tidal tails. Based in part on observations obtained 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 (AURA), Inc., under NASA contract NAS 5-26555.

Constraints on cold dark matter theories from observations of massive x-ray-luminous clusters of galaxies at high redshift

NASA Technical Reports Server (NTRS)

Luppino, G. A.; Gioia, I. M.

1995-01-01

During the course of a gravitational lensing survey of distant, X-ray selected Einstein Observatory Extended Medium Sensitivity Survey (EMSS) clusters of galaxies, we have studied six X-ray-luminous (L(sub x) greater than 5 x 10(exp 44)(h(sub 50)(exp -2))ergs/sec) clusters at redshifts exceeding z = 0.5. All of these clusters are apparently massive. In addition to their high X-ray luminosity, two of the clusters at z approximately 0.6 exhibit gravitationally lensed arcs. Furthermore, the highest redshift cluster in our sample, MS 1054-0321 at z = 0.826, is both extremely X-ray luminous (L(sub 0.3-3.5keV)=9.3 x 10(exp 44)(h(sub 50)(exp -2))ergs/sec) and exceedingly rich with an optical richness comparable to an Abell Richness Class 4 cluster. In this Letter, we discuss the cosmological implications of the very existence of these clusters for hierarchical structure formation theories such as standard Omega = 1 CDM (cold dark matter), hybrid Omega = 1 C + HDM (hot dark matter), and flat, low-density Lambda + CDM models.

RUBIDIUM ABUNDANCES IN THE GLOBULAR CLUSTERS NGC 6752, NGC 1904, AND NGC 104 (47 Tuc)

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

D'Orazi, Valentina; Lugaro, Maria; Campbell, Simon W.

2013-10-10

Large star-to-star variations of the abundances of proton-capture elements, such as Na and O, in globular clusters (GCs) are interpreted as the effect of internal pollution resulting from the presence of multiple stellar populations. To better constrain this scenario, we investigate the abundance distribution of the heavy element rubidium (Rb) in NGC 6752, NGC 1904, and NGC 104 (47 Tuc). Combining the results from our sample with those in the literature, we found that Rb exhibits no star-to-star variations, regardless of cluster metallicity, with the possible intriguing, although very uncertain, exception of the metal-rich bulge cluster NGC 6388. If nomore » star-to-star variations can be confirmed for all GCs, this finding implies that the stellar source of the proton-capture element variations must not have produced significant amounts of Rb. This element is observed to be enhanced at extremely high levels in intermediate-mass asymptotic giant branch (IM-AGB) stars in the Magellanic Clouds (i.e., at a metallicity similar to 47 Tuc and NGC 6388). This fact may present a challenge to this popular candidate polluter, unless the mass range of the observed IM-AGB stars does not participate in the formation of the second-generation stars in GCs. A number of possible solutions are available to resolve this conundrum, including the fact that the Magellanic Cloud observations are very uncertain and may need to be revised. The fast rotating massive stars scenario would not face this potential problem as the slow mechanical winds of these stars during their main-sequence phase do not carry any Rb enhancements; however, these candidates face even bigger issues such as the production of Li and the close overlap with core-collapse supernova timescales. Observations of Sr, Rb, and Zr in metal-rich clusters such as NGC 6388 and NGC 6441 are sorely needed to clarify the situation.« less

Highlighting Astyanax Species Diversity through DNA Barcoding

PubMed Central

Oliveira, Carlos Alexandre Miranda; de Melo, Filipe Augusto Gonçalves; Bertaco, Vinicius de Araújo; de Astarloa, Juan M. Díaz; Rosso, Juan J.; Foresti, Fausto; Oliveira, Claudio

2016-01-01

DNA barcoding has been used extensively to solve taxonomic questions and identify new species. Neotropical fishes are found in a wide variety of shapes and sizes, with a large number of species yet to be described, many of which are very difficult to identify. Characidae is the most species-rich family of the Characiformes, and many of its genera are affected by taxonomic uncertainties, including the widely-distributed, species-rich genus Astyanax. In this study, we present an extensive analysis of Astyanax covering almost its entire area of occurrence, based on DNA barcoding. The use of different approaches (ABGD, GMYC and BIN) to the clustering of the sequences revealed ample consistency in the results obtained by the initial cutoff value of 2% divergence for putative species in the Neighbor-Joining analysis using the Kimura-2-parameter model. The results indicate the existence of five Astyanax lineages. Some groups, such as that composed by the trans-Andean forms, are mostly composed of well-defined species, and in others a number of nominal species are clustered together, hampering the delimitation of species, which in many cases proved impossible. The results confirm the extreme complexity of the systematics of the genus Astyanax and show that DNA barcoding can be an useful tool to address these complexes questions. PMID:27992537

What is living on your dog's skin? Characterization of the canine cutaneous mycobiota and fungal dysbiosis in canine allergic dermatitis.

PubMed

Meason-Smith, Courtney; Diesel, Alison; Patterson, Adam P; Older, Caitlin E; Mansell, Joanne M; Suchodolski, Jan S; Rodrigues Hoffmann, Aline

2015-12-01

To characterize the skin-associated fungal microbiota (mycobiota) in dogs, and to evaluate the influence of body site, individual dog or health status on the distribution of fungi, next-generation sequencing was performed targeting the internal transcribed spacer region. A total of 10 dogs with no history of skin disease were sampled at 10 distinct body sites consisting of haired and mucosal skin, and 8 dogs with diagnosed skin allergies were sampled at six body sites commonly affected by allergic disease. Analysis of similarities revealed that body site was not an influencing factor on membership or structure of fungal communities in healthy skin; however, the mucosal sites were significantly reduced in fungal richness. The mycobiota from body sites in healthy dogs tended to be similar within a dog, which was visualized in principle coordinates analysis (PCoA) by clustering of all sites from one dog separate from other dogs. The mycobiota of allergic skin was significantly less rich than that of healthy skin, and all sites sampled clustered by health status in PCoA. Interestingly, the most abundant fungi present on canine skin, across all body sites and health statuses, were Alternaria and Cladosporium--two of the most common fungal allergens in human environmental allergies. © FEMS 2015.

What is living on your dog's skin? Characterization of the canine cutaneous mycobiota and fungal dysbiosis in canine allergic dermatitis

PubMed Central

Meason-Smith, Courtney; Diesel, Alison; Patterson, Adam P.; Older, Caitlin E.; Mansell, Joanne M.; Suchodolski, Jan S.; Rodrigues Hoffmann, Aline

2015-01-01

To characterize the skin-associated fungal microbiota (mycobiota) in dogs, and to evaluate the influence of body site, individual dog or health status on the distribution of fungi, next-generation sequencing was performed targeting the internal transcribed spacer region. A total of 10 dogs with no history of skin disease were sampled at 10 distinct body sites consisting of haired and mucosal skin, and 8 dogs with diagnosed skin allergies were sampled at six body sites commonly affected by allergic disease. Analysis of similarities revealed that body site was not an influencing factor on membership or structure of fungal communities in healthy skin; however, the mucosal sites were significantly reduced in fungal richness. The mycobiota from body sites in healthy dogs tended to be similar within a dog, which was visualized in principle coordinates analysis (PCoA) by clustering of all sites from one dog separate from other dogs. The mycobiota of allergic skin was significantly less rich than that of healthy skin, and all sites sampled clustered by health status in PCoA. Interestingly, the most abundant fungi present on canine skin, across all body sites and health statuses, were Alternaria and Cladosporium—two of the most common fungal allergens in human environmental allergies. PMID:26542075

Bacterial community composition in different sediments from the Eastern Mediterranean Sea: a comparison of four 16S ribosomal DNA clone libraries.

PubMed

Polymenakou, Paraskevi N; Bertilsson, Stefan; Tselepides, Anastasios; Stephanou, Euripides G

2005-10-01

The regional variability of sediment bacterial community composition and diversity was studied by comparative analysis of four large 16S ribosomal DNA (rDNA) clone libraries from sediments in different regions of the Eastern Mediterranean Sea (Thermaikos Gulf, Cretan Sea, and South lonian Sea). Amplified rDNA restriction analysis of 664 clones from the libraries indicate that the rDNA richness and evenness was high: for example, a near-1:1 relationship among screened clones and number of unique restriction patterns when up to 190 clones were screened for each library. Phylogenetic analysis of 207 bacterial 16S rDNA sequences from the sediment libraries demonstrated that Gamma-, Delta-, and Alphaproteobacteria, Holophaga/Acidobacteria, Planctomycetales, Actinobacteria, Bacteroidetes, and Verrucomicrobia were represented in all four libraries. A few clones also grouped with the Betaproteobacteria, Nitrospirae, Spirochaetales, Chlamydiae, Firmicutes, and candidate division OPl 1. The abundance of sequences affiliated with Gammaproteobacteria was higher in libraries from shallow sediments in the Thermaikos Gulf (30 m) and the Cretan Sea (100 m) compared to the deeper South Ionian station (2790 m). Most sequences in the four sediment libraries clustered with uncultured 16S rDNA phylotypes from marine habitats, and many of the closest matches were clones from hydrocarbon seeps, benzene-mineralizing consortia, sulfate reducers, sulk oxidizers, and ammonia oxidizers. LIBSHUFF statistics of 16S rDNA gene sequences from the four libraries revealed major differences, indicating either a very high richness in the sediment bacterial communities or considerable variability in bacterial community composition among regions, or both.

Absolute parameters of young stars: QZ Carinae

NASA Astrophysics Data System (ADS)

Walker, W. S. G.; Blackford, M.; Butland, R.; Budding, E.

2017-09-01

New high-resolution spectroscopy and BVR photometry together with literature data on the complex massive quaternary star QZ Car are collected and analysed. Absolute parameters are found as follows. System A: M1 = 43 (±3), M2 = 19 (+3 -7), R1 = 28 (±2), R2 = 6 (±2), (⊙); T1 ˜ 28 000, T2 ˜ 33 000 K; System B: M1 = 30 (±3), M2 = 20 (±3), R1 = 10 (±0.5), R2 = 20 (±1), (⊙); T1 ˜ 36 000, T2 ˜ 30 000 K (model dependent temperatures). The wide system AB: Period = 49.5 (±1) yr, Epochs, conjunction = 1984.8 (±1), periastron = 2005.3 (±3) yr, mean separation = 65 (±3), (au); orbital inclination = 85 (+5 -15) deg, photometric distance ˜2700 (±300) pc, age = 4 (±1) Myr. Other new contributions concern: (a) analysis of the timing of minima differences (O - C)s for the eclipsing binary (System B); (b) the width of the eclipses, pointing to relatively large effects of radiation pressure; (c) inferences from the rotational widths of lines for both Systems A and B; and (d) implications for theoretical models of early-type stars. While feeling greater confidence on the quaternary's general parametrization, observational complications arising from strong wind interactions or other, unclear, causes still inhibit precision and call for continued multiwavelength observations. Our high-inclination value for the AB system helps to explain failures to resolve the wide binary in the previous years. The derived young age independently confirms membership of QZ Car to the open cluster Collinder 228.

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.

In silico Analysis of 3′-End-Processing Signals in Aspergillus oryzae Using Expressed Sequence Tags and Genomic Sequencing Data

PubMed Central

Tanaka, Mizuki; Sakai, Yoshifumi; Yamada, Osamu; Shintani, Takahiro; Gomi, Katsuya

2011-01-01

To investigate 3′-end-processing signals in Aspergillus oryzae, we created a nucleotide sequence data set of the 3′-untranslated region (3′ UTR) plus 100 nucleotides (nt) sequence downstream of the poly(A) site using A. oryzae expressed sequence tags and genomic sequencing data. This data set comprised 1065 sequences derived from 1042 unique genes. The average 3′ UTR length in A. oryzae was 241 nt, which is greater than that in yeast but similar to that in plants. The 3′ UTR and 100 nt sequence downstream of the poly(A) site is notably U-rich, while the region located 15–30 nt upstream of the poly(A) site is markedly A-rich. The most frequently found hexanucleotide in this A-rich region is AAUGAA, although this sequence accounts for only 6% of all transcripts. These data suggested that A. oryzae has no highly conserved sequence element equivalent to AAUAAA, a mammalian polyadenylation signal. We identified that putative 3′-end-processing signals in A. oryzae, while less well conserved than those in mammals, comprised four sequence elements: the furthest upstream U-rich element, A-rich sequence, cleavage site, and downstream U-rich element flanking the cleavage site. Although these putative 3′-end-processing signals are similar to those in yeast and plants, some notable differences exist between them. PMID:21586533

Differences between the bacterial community structures of first- and multi-year Arctic sea ice in the Lincoln Sea.

NASA Astrophysics Data System (ADS)

Hatam, I.; Beckers, J. F.; Haas, C.; Lanoil, B. D.

2014-12-01

The Arctic sea ice composition is shifting from predominantly thick perennial ice (multiyear ice -MYI) to thinner, seasonal ice (first year ice -FYI). The effects of the shift on the Arctic ecosystem and macro-organisms of the Arctic Ocean have been the focus of many studies and have also been extensively debated in the public domain. The effect of this shift on the microbial constituents of the Arctic sea ice has been grossly understudied, although it is a vast habitat for a microbial community that plays a key role in the biogeochemical cycles and energy flux of the Arctic Ocean. MYI and FYI differ in many chemical and physical attributes (e.g. bulk salinity, brine volume, thickness and age), therefore comparing and contrasting the structure and composition of microbial communities from both ice types will be crucial to our understanding of the challenges that the Arctic Ocean ecosystem faces as MYI cover continues to decline. Here, we contend that due to the differences in abiotic conditions, differences in bacterial community structure will be greater between samples from different ice types than within samples from the same ice type. We also argue that since FYI is younger, its community structure will be closer to that of the surface sea water (SW). To test this hypotheses, we extracted DNA and used high throughput sequencing to sequence V1-V3 regions of the bacterial 16s rRNA gene from 10 sea ice samples (5 for each ice type) and 4 surface sea water (SW) collected off the shore of Northern Ellesmere Island, NU, CAN, during the month of May from 2010-2012. Our results showed that observed richness was higher in FYI than MYI. FYI and MYI shared 26% and 36% of their observed richness respectively. While FYI shared 23% of its observed richness with SW, MYI only shared 17%. Both ice types showed similar levels of endemism (61% of the observed richness). This high level of endemism results in the grouping of microbial communities from MYI, FYI, and SW to three distinct groups when looking at membership (jclass dissimilarity index, tested by AMOVA). However, when looking at composition (θYC dissimilarity index) while communities from MYI and SW samples still clustered as two distinct groups, communities from FYI samples show no significant clustering (tested by AMOVA).

Variable Stars In the Unusual, Metal-Rich Globular Cluster

NASA Technical Reports Server (NTRS)

Pritzl, Barton J.; Smith, Horace A.; Catelan, Marcio; Sweigart, Allen V.; Oegerle, William R. (Technical Monitor)

2002-01-01

We have undertaken a search for variable stars in the metal-rich globular cluster NGC 6388 using time-series BV photometry. Twenty-eight new variables were found in this survey, increasing the total number of variables found near NGC 6388 to approx. 57. A significant number of the variables are RR Lyrae (approx. 14), most of which are probable cluster members. The periods of the fundamental mode RR Lyrae are shown to be unusually long compared to metal-rich field stars. The existence of these long period RRab stars suggests that the horizontal branch of NGC 6388 is unusually bright. This implies that the metallicity-luminosity relationship for RR Lyrae stars is not universal if the RR Lyrae in NGC 6388 are indeed metal-rich. We consider the alternative possibility that the stars in NGC 6388 may span a range in [Fe/H]. Four candidate Population II Cepheids were also found. If they are members of the cluster, NGC 6388 would be the most metal-rich globular cluster to contain Population II Cepheids. The mean V magnitude of the RR Lyrae is found to be 16.85 +/- 0.05 resulting in a distance of 9.0 to 10.3 kpc, for a range of assumed values of (M(sub V)) for RR Lyrae. We determine the reddening of the cluster to be E(B - V) = 0.40 +/- 0.03 mag, with differential reddening across the face of the cluster. We discuss the difficulty in determining the Oosterhoff classification of NGC 6388 and NGC 6441 due to the unusual nature of their RR Lyrae, and address evolutionary constraints on a recent suggestion that they are of Oosterhoff type II.

Final Report for "Non-Accelerator Physics – Research in High Energy Physics: Dark Energy Research on DES"

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

Ritz, Steve; Jeltema, Tesla

One of the greatest mysteries in modern cosmology is the fact that the expansion of the universe is observed to be accelerating. This acceleration may stem from dark energy, an additional energy component of the universe, or may indicate that the theory of general relativity is incomplete on cosmological scales. The growth rate of large-scale structure in the universe and particularly the largest collapsed structures, clusters of galaxies, is highly sensitive to the underlying cosmology. Clusters will provide one of the single most precise methods of constraining dark energy with the ongoing Dark Energy Survey (DES). The accuracy of themore » cosmological constraints derived from DES clusters necessarily depends on having an optimized and well-calibrated algorithm for selecting clusters as well as an optical richness estimator whose mean relation and scatter compared to cluster mass are precisely known. Calibrating the galaxy cluster richness-mass relation and its scatter was the focus of the funded work. Specifically, we employ X-ray observations and optical spectroscopy with the Keck telescopes of optically-selected clusters to calibrate the relationship between optical richness (the number of galaxies in a cluster) and underlying mass. This work also probes aspects of cluster selection like the accuracy of cluster centering which are critical to weak lensing cluster studies.« less

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.

Structure and substructure analysis of DAFT/FADA galaxy clusters in the [0.4–0.9] redshift range

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

Guennou, L.; et al.

2014-01-17

Context. The DAFT/FADA survey is based on the study of ~90 rich(masses found in the literature >2 x 10^14 M_⊙)and moderately distant clusters (redshifts 0.4 < z < 0.9), all withHST imaging data available. This survey has two main objectives: to constrain dark energy(DE) using weak lensing tomography on galaxy clusters and to build a database (deepmulti-band imaging allowing photometric redshift estimates, spectroscopic data, X-raydata) of rich distant clusters to study their properties.

Comparative Study of IS6110 Restriction Fragment Length Polymorphism and Variable-Number Tandem-Repeat Typing of Mycobacterium tuberculosis Isolates in the Netherlands, Based on a 5-Year Nationwide Survey

PubMed Central

de Beer, Jessica L.; van Ingen, Jakko; de Vries, Gerard; Erkens, Connie; Sebek, Maruschka; Mulder, Arnout; Sloot, Rosa; van den Brandt, Anne-Marie; Enaimi, Mimount; Kremer, Kristin; Supply, Philip

2013-01-01

In order to switch from IS6110 and polymorphic GC-rich repetitive sequence (PGRS) restriction fragment length polymorphism (RFLP) to 24-locus variable-number tandem-repeat (VNTR) typing of Mycobacterium tuberculosis complex isolates in the national tuberculosis control program in The Netherlands, a detailed evaluation on discriminatory power and agreement with findings in a cluster investigation was performed on 3,975 tuberculosis cases during the period of 2004 to 2008. The level of discrimination of the two typing methods did not differ substantially: RFLP typing yielded 2,733 distinct patterns compared to 2,607 in VNTR typing. The global concordance, defined as isolates labeled unique or identically distributed in clusters by both methods, amounted to 78.5% (n = 3,123). Of the remaining 855 cases, 12% (n = 479) of the cases were clustered only by VNTR, 7.7% (n = 305) only by RFLP typing, and 1.8% (n = 71) revealed different cluster compositions in the two approaches. A cluster investigation was performed for 87% (n = 1,462) of the cases clustered by RFLP. For the 740 cases with confirmed or presumed epidemiological links, 92% were concordant with VNTR typing. In contrast, only 64% of the 722 cases without an epidemiological link but clustered by RFLP typing were also clustered by VNTR typing. We conclude that VNTR typing has a discriminatory power equal to IS6110 RFLP typing but is in better agreement with findings in a cluster investigation performed on an RFLP-clustering-based cluster investigation. Both aspects make VNTR typing a suitable method for tuberculosis surveillance systems. PMID:23363841

Culture-independent discovery of natural products from soil metagenomes.

PubMed

Katz, Micah; Hover, Bradley M; Brady, Sean F

2016-03-01

Bacterial natural products have proven to be invaluable starting points in the development of many currently used therapeutic agents. Unfortunately, traditional culture-based methods for natural product discovery have been deemphasized by pharmaceutical companies due in large part to high rediscovery rates. Culture-independent, or "metagenomic," methods, which rely on the heterologous expression of DNA extracted directly from environmental samples (eDNA), have the potential to provide access to metabolites encoded by a large fraction of the earth's microbial biosynthetic diversity. As soil is both ubiquitous and rich in bacterial diversity, it is an appealing starting point for culture-independent natural product discovery efforts. This review provides an overview of the history of soil metagenome-driven natural product discovery studies and elaborates on the recent development of new tools for sequence-based, high-throughput profiling of environmental samples used in discovering novel natural product biosynthetic gene clusters. We conclude with several examples of these new tools being employed to facilitate the recovery of novel secondary metabolite encoding gene clusters from soil metagenomes and the subsequent heterologous expression of these clusters to produce bioactive small molecules.

CHEMICAL TAGGING OF THREE DISTINCT POPULATIONS OF RED GIANTS IN THE GLOBULAR CLUSTER NGC 6752

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

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

2012-05-01

We present aluminum, magnesium, and silicon abundances in the metal-poor globular cluster NGC 6752 for a sample of more than 130 red giants with homogeneous oxygen and sodium abundances. We find that [Al/Fe] shows a spread of about 1.4 dex among giants in NGC 6752 and is anticorrelated with [Mg/Fe] and [O/Fe] and correlated with [Na/Fe] and [Si/Fe]. These relations are not continuous in nature, but the distribution of stars is clearly clustered around three distinct Al values, low, intermediate, and high. These three groups nicely correspond to the three distinct sequences previously detected using Stroemgren photometry along the redmore » giant branch. These two independent findings strongly indicate the existence of three distinct stellar populations in NGC 6752. Comparing the abundances of O and Mg, we find that the population with intermediate chemical abundances cannot originate from material with the same composition of the most O- and Mg-poor population, diluted by material with that of the most O- and Mg-rich one. This calls for different polluters.« less

Regulation of specialised metabolites in Actinobacteria - expanding the paradigms.

PubMed

Hoskisson, Paul A; Fernández-Martínez, Lorena T

2018-06-01

The increase in availability of actinobacterial whole genome sequences has revealed huge numbers of specialised metabolite biosynthetic gene clusters, encoding a range of bioactive molecules such as antibiotics, antifungals, immunosuppressives and anticancer agents. Yet the majority of these clusters are not expressed under standard laboratory conditions in rich media. Emerging data from studies of specialised metabolite biosynthesis suggest that the diversity of regulatory mechanisms is greater than previously thought and these act at multiple levels, through a range of signals such as nutrient limitation, intercellular signalling and competition with other organisms. Understanding the regulation and environmental cues that lead to the production of these compounds allows us to identify the role that these compounds play in their natural habitat as well as provide tools to exploit this untapped source of specialised metabolites for therapeutic uses. Here, we provide an overview of novel regulatory mechanisms that act in physiological, global and cluster-specific regulatory manners on biosynthetic pathways in Actinobacteria and consider these alongside their ecological and evolutionary implications. © 2018 The Authors. Environmental Microbiology published by Society for Applied Microbiology and JohnWiley & Sons Ltd.

Transcription blockage by homopurine DNA sequences: role of sequence composition and single-strand breaks

PubMed Central

Belotserkovskii, Boris P.; Neil, Alexander J.; Saleh, Syed Shayon; Shin, Jane Hae Soo; Mirkin, Sergei M.; Hanawalt, Philip C.

2013-01-01

The ability of DNA to adopt non-canonical structures can affect transcription and has broad implications for genome functioning. We have recently reported that guanine-rich (G-rich) homopurine-homopyrimidine sequences cause significant blockage of transcription in vitro in a strictly orientation-dependent manner: when the G-rich strand serves as the non-template strand [Belotserkovskii et al. (2010) Mechanisms and implications of transcription blockage by guanine-rich DNA sequences., Proc. Natl Acad. Sci. USA, 107, 12816–12821]. We have now systematically studied the effect of the sequence composition and single-stranded breaks on this blockage. Although substitution of guanine by any other base reduced the blockage, cytosine and thymine reduced the blockage more significantly than adenine substitutions, affirming the importance of both G-richness and the homopurine-homopyrimidine character of the sequence for this effect. A single-strand break in the non-template strand adjacent to the G-rich stretch dramatically increased the blockage. Breaks in the non-template strand result in much weaker blockage signals extending downstream from the break even in the absence of the G-rich stretch. Our combined data support the notion that transcription blockage at homopurine-homopyrimidine sequences is caused by R-loop formation. PMID:23275544

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.

An Analysis of Rich Cluster Redshift Survey Data for Large Scale Structure Studies

NASA Astrophysics Data System (ADS)

Slinglend, K.; Batuski, D.; Haase, S.; Hill, J.

1994-12-01

The results from the COBE satellite show the existence of structure on scales on the order of 10% or more of the horizon scale of the universe. Rich clusters of galaxies from Abell's catalog show evidence of structure on scales of 100 Mpc and may hold the promise of confirming structure on the scale of the COBE result. However, many Abell clusters have zero or only one measured redshift, so present knowledge of their three dimensional distribution has quite large uncertainties. The shortage of measured redshifts for these clusters may also mask a problem of projection effects corrupting the membership counts for the clusters. Our approach in this effort has been to use the MX multifiber spectrometer on the Steward 2.3m to measure redshifts of at least ten galaxies in each of 80 Abell cluster fields with richness class R>= 1 and mag10 <= 16.8 (estimated z<= 0.12) and zero or one measured redshifts. This work will result in a deeper, more complete (and reliable) sample of positions of rich clusters. Our primary intent for the sample is for two-point correlation and other studies of the large scale structure traced by these clusters in an effort to constrain theoretical models for structure formation. We are also obtaining enough redshifts per cluster so that a much better sample of reliable cluster velocity dispersions will be available for other studies of cluster properties. To date, we have collected such data for 64 clusters, and for most of them, we have seven or more cluster members with redshifts, allowing for reliable velocity dispersion calculations. Velocity histograms and stripe density plots for several interesting cluster fields are presented, along with summary tables of cluster redshift results. Also, with 10 or more redshifts in most of our cluster fields (30({') } square, just about an `Abell diameter' at z ~ 0.1) we have investigated the extent of projection effects within the Abell catalog in an effort to quantify and understand how this may effect the Abell sample.

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

The X-CLASS-redMaPPer galaxy cluster comparison. I. Identification procedures

NASA Astrophysics Data System (ADS)

Sadibekova, T.; Pierre, M.; Clerc, N.; Faccioli, L.; Gastaud, R.; Le Fevre, J.-P.; Rozo, E.; Rykoff, E.

2014-11-01

Context. This paper is the first in a series undertaking a comprehensive correlation analysis between optically selected and X-ray-selected cluster catalogues. The rationale of the project is to develop a holistic picture of galaxy clusters utilising optical and X-ray-cluster-selected catalogues with well-understood selection functions. Aims: Unlike most of the X-ray/optical cluster correlations to date, the present paper focuses on the non-matching objects in either waveband. We investigate how the differences observed between the optical and X-ray catalogues may stem from (1) a shortcoming of the detection algorithms; (2) dispersion in the X-ray/optical scaling relations; or (3) substantial intrinsic differences between the cluster populations probed in the X-ray and optical bands. The aim is to inventory and elucidate these effects in order to account for selection biases in the further determination of X-ray/optical cluster scaling relations. Methods: We correlated the X-CLASS serendipitous cluster catalogue extracted from the XMM archive with the redMaPPer optical cluster catalogue derived from the Sloan Digital Sky Survey (DR8). We performed a detailed and, in large part, interactive analysis of the matching output from the correlation. The overlap between the two catalogues has been accurately determined and possible cluster positional errors were manually recovered. The final samples comprise 270 and 355 redMaPPer and X-CLASS clusters, respectively. X-ray cluster matching rates were analysed as a function of optical richness. In the second step, the redMaPPer clusters were correlated with the entire X-ray catalogue, containing point and uncharacterised sources (down to a few 10-15 erg s-1 cm-2 in the [0.5-2] keV band). A stacking analysis was performed for the remaining undetected optical clusters. Results: We find that all rich (λ ≥ 80) clusters are detected in X-rays out to z = 0.6. Below this redshift, the richness threshold for X-ray detection steadily decreases with redshift. Likewise, all X-ray bright clusters are detected by redMaPPer. After correcting for obvious pipeline shortcomings (about 10% of the cases both in optical and X-ray), ~50% of the redMaPPer (down to a richness of 20) are found to coincide with an X-CLASS cluster; when considering X-ray sources of any type, this fraction increases to ~80%; for the remaining objects, the stacking analysis finds a weak signal within 0.5 Mpc around the cluster optical centres. The fraction of clusters totally dominated by AGN-type emission appears to be a few percent. Conversely, ~40% of the X-CLASS clusters are identified with a redMaPPer (down to a richness of 20) - part of the non-matches being due to the X-CLASS sample extending further out than redMaPPer (z< 1.5 vs. z< 0.6), but extending the correlation down to a richness of 5 raises the matching rate to ~65%. Conclusions: This state-of-the-art study involving two well-validated cluster catalogues has shown itself to be complex, and it points to a number of issues inherent to blind cross-matching, owing both to pipeline shortcomings and cluster peculiar properties. These can only been accounted for after a manual check. The combined X-ray and optical scaling relations will be presented in a subsequent article.

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

A Cysteine-Rich CCG Domain Contains a Novel [4Fe-4S] Cluster Binding Motif As Deduced From Studies With Subunit B of Heterodisulfide Reductase From Methanothermobacter Marburgensis

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

Hamann, N.; Mander, G.J.; Shokes, J.E.

Heterodisulfide reductase (HDR) of methanogenic archaea with its active-site [4Fe-4S] cluster catalyzes the reversible reduction of the heterodisulfide (CoM-S-S-CoB) of the methanogenic coenzyme M (CoM-SH) and coenzyme B (CoB-SH). CoM-HDR, a mechanistic-based paramagnetic intermediate generated upon half-reaction of the oxidized enzyme with CoM-SH, is a novel type of [4Fe-4S]{sup 3+} cluster with CoM-SH as a ligand. Subunit HdrB of the Methanothermobacter marburgensis HdrABC holoenzyme contains two cysteine-rich sequence motifs (CX{sub 31-39}CCX{sub 35-36}CXXC), designated as CCG domain in the Pfam database and conserved in many proteins. Here we present experimental evidence that the C-terminal CCG domain of HdrB binds this unusualmore » [4Fe-4S] cluster. HdrB was produced in Escherichia coli, and an iron-sulfur cluster was subsequently inserted by in vitro reconstitution. In the oxidized state the cluster without the substrate exhibited a rhombic EPR signal (g{sub zyx} = 2.015, 1.995, and 1.950) reminiscent of the CoM-HDR signal. {sup 57}Fe ENDOR spectroscopy revealed that this paramagnetic species is a [4Fe-4S] cluster with {sup 57}Fe hyperfine couplings very similar to that of CoM-HDR. CoM-{sup 33}SH resulted in a broadening of the EPR signal, and upon addition of CoM-SH the midpoint potential of the cluster was shifted to values observed for CoM-HDR, both indicating binding of CoM-SH to the cluster. Site-directed mutagenesis of all 12 cysteine residues in HdrB identified four cysteines of the C-terminal CCG domain as cluster ligands. Combined with the previous detection of CoM-HDR-like EPR signals in other CCG domain-containing proteins our data indicate a general role of the C-terminal CCG domain in coordination of this novel [4Fe-4S] cluster. In addition, Zn K-edge X-ray absorption spectroscopy identified an isolated Zn site with an S{sub 3}(O/N){sub 1} geometry in HdrB and the HDR holoenzyme. The N-terminal CCG domain is suggested to provide ligands to the Zn site.« less

Lithium-rich Giants in Globular Clusters

NASA Astrophysics Data System (ADS)

Kirby, Evan N.; Guhathakurta, Puragra; Zhang, Andrew J.; Hong, Jerry; Guo, Michelle; Guo, Rachel; Cohen, Judith G.; Cunha, Katia

2016-03-01

Although red giants deplete lithium on their surfaces, some giants are Li-rich. Intermediate-mass asymptotic giant branch (AGB) stars can generate Li through the Cameron-Fowler conveyor, but the existence of Li-rich, low-mass red giant branch (RGB) stars is puzzling. Globular clusters are the best sites to examine this phenomenon because it is straightforward to determine membership in the cluster and to identify the evolutionary state of each star. In 72 hours of Keck/DEIMOS exposures in 25 clusters, we found four Li-rich RGB and two Li-rich AGB stars. There were 1696 RGB and 125 AGB stars with measurements or upper limits consistent with normal abundances of Li. Hence, the frequency of Li-richness in globular clusters is (0.2 ± 0.1)% for the RGB, (1.6 ± 1.1)% for the AGB, and (0.3 ± 0.1)% for all giants. Because the Li-rich RGB stars are on the lower RGB, Li self-generation mechanisms proposed to occur at the luminosity function bump or He core flash cannot explain these four lower RGB stars. We propose the following origin for Li enrichment: (1) All luminous giants experience a brief phase of Li enrichment at the He core flash. (2) All post-RGB stars with binary companions on the lower RGB will engage in mass transfer. This scenario predicts that 0.1% of lower RGB stars will appear Li-rich due to mass transfer from a recently Li-enhanced companion. This frequency is at the lower end of our confidence interval. The data presented herein were obtained at the W. M. Keck Observatory, which is operated as a scientific partnership among the California Institute of Technology, the University of California and the National Aeronautics and Space Administration. The Observatory was made possible by the generous financial support of the W. M. Keck Foundation.

Clear Evidence for the Presence of Second-generation Asymptotic Giant Branch Stars in Metal-poor Galactic Globular Clusters

NASA Astrophysics Data System (ADS)

García-Hernández, D. A.; Mészáros, Sz.; Monelli, M.; Cassisi, S.; Stetson, P. B.; Zamora, O.; Shetrone, M.; Lucatello, S.

2015-12-01

Galactic globular clusters (GCs) are known to host multiple stellar populations: a first generation (FG) with a chemical pattern typical of halo field stars and a second generation (SG) enriched in Na and Al and depleted in O and Mg. Both stellar generations are found at different evolutionary stages (e.g., the main-sequence turnoff, the subgiant branch, and the red giant branch (RGB)). The non detection of SG asymptotic giant branch (AGB) stars in several metal-poor ([Fe/H] < -1) GCs suggests that not all SG stars ascend the AGB phase, and that failed AGB stars may be very common in metal-poor GCs. This observation represents a serious problem for stellar evolution and GC formation/evolution theories. We report fourteen SG-AGB stars in four metal-poor GCs (M13, M5, M3, and M2) with different observational properties: horizontal branch (HB) morphology, metallicity, and age. By combining the H-band Al abundances obtained by the Apache Point Observatory Galactic Evolution Experiment survey with ground-based optical photometry, we identify SG Al-rich AGB stars in these four GCs and show that Al-rich RGB/AGB GC stars should be Na-rich. Our observations provide strong support for present, standard stellar models, i.e., without including a strong mass-loss efficiency, for low-mass HB stars. In fact, current empirical evidence is in agreement with the predicted distribution of FG and SG stars during the He-burning stages based on these standard stellar models.

Multi-temporal clustering of continental floods and associated atmospheric circulations

NASA Astrophysics Data System (ADS)

Liu, Jianyu; Zhang, Yongqiang

2017-12-01

Investigating clustering of floods has important social, economic and ecological implications. This study examines the clustering of Australian floods at different temporal scales and its possible physical mechanisms. Flood series with different severities are obtained by peaks-over-threshold (POT) sampling in four flood thresholds. At intra-annual scale, Cox regression and monthly frequency methods are used to examine whether and when the flood clustering exists, respectively. At inter-annual scale, dispersion indices with four-time variation windows are applied to investigate the inter-annual flood clustering and its variation. Furthermore, the Kernel occurrence rate estimate and bootstrap resampling methods are used to identify flood-rich/flood-poor periods. Finally, seasonal variation of horizontal wind at 850 hPa and vertical wind velocity at 500 hPa are used to investigate the possible mechanisms causing the temporal flood clustering. Our results show that: (1) flood occurrences exhibit clustering at intra-annual scale, which are regulated by climate indices representing the impacts of the Pacific and Indian Oceans; (2) the flood-rich months occur from January to March over northern Australia, and from July to September over southwestern and southeastern Australia; (3) stronger inter-annual clustering takes place across southern Australia than northern Australia; and (4) Australian floods are characterised by regional flood-rich and flood-poor periods, with 1987-1992 identified as the flood-rich period across southern Australia, but the flood-poor period across northern Australia, and 2001-2006 being the flood-poor period across most regions of Australia. The intra-annual and inter-annual clustering and temporal variation of flood occurrences are in accordance with the variation of atmospheric circulation. These results provide relevant information for flood management under the influence of climate variability, and, therefore, are helpful for developing flood hazard mitigation schemes.

Biofilm formation and cellulose expression by Bordetella avium 197N, the causative agent of bordetellosis in birds and an opportunistic respiratory pathogen in humans.

PubMed

McLaughlin, Kimberley; Folorunso, Ayorinde O; Deeni, Yusuf Y; Foster, Dona; Gorbatiuk, Oksana; Hapca, Simona M; Immoor, Corinna; Koza, Anna; Mohammed, Ibrahim U; Moshynets, Olena; Rogalsky, Sergii; Zawadzki, Kamil; Spiers, Andrew J

2017-06-01

Although bacterial cellulose synthase (bcs) operons are widespread within the Proteobacteria phylum, subunits required for the partial-acetylation of the polymer appear to be restricted to a few γ-group soil, plant-associated and phytopathogenic pseudomonads, including Pseudomonas fluorescens SBW25 and several Pseudomonas syringae pathovars. However, a bcs operon with acetylation subunits has also been annotated in the unrelated β-group respiratory pathogen, Bordetella avium 197N. Our comparison of subunit protein sequences and GC content analyses confirms the close similarity between the B. avium 197N and pseudomonad operons and suggests that, in both cases, the cellulose synthase and acetylation subunits were acquired as a single unit. Using static liquid microcosms, we can confirm that B. avium 197N expresses low levels of cellulose in air-liquid interface biofilms and that biofilm strength and attachment levels could be increased by elevating c-di-GMP levels like the pseudomonads, but cellulose was not required for biofilm formation itself. The finding that B. avium 197N is capable of producing cellulose from a highly-conserved, but relatively uncommon bcs operon raises the question of what functional role this modified polymer plays during the infection of the upper respiratory tract or survival between hosts, and what environmental signals control its production. Copyright © 2017 Institut Pasteur. All rights reserved.

Improving the neutral phytase activity from Bacillus amyloliquefaciens DSM 1061 by site-directed mutagenesis.

PubMed

Xu, Wei; Shao, Rong; Wang, Zupeng; Yan, Xiuhua

2015-03-01

Neutral phytase is used as a feed additive for degradation of anti-nutritional phytate in aquatic feed industry. Site-directed mutagenesis of Bacillus amyloliquefaciens DSM 1061 phytase was performed with an aim to increase its activity. Mutation residues were chosen based on multiple sequence alignments and structure analysis of neutral phytsaes from different microorganisms. The mutation sites on surface (D148E, S197E and N156E) and around the active site (D52E) of phytase were selected. Analysis of the phytase variants showed that the specific activities of mutants D148E and S197E remarkably increased by about 35 and 13% over a temperature range of 40-75 °C at pH 7.0, respectively. The k cat of mutants D148E and S197E were 1.50 and 1.25 times than that of the wild-type phytase, respectively. Both D148E and S197E showed much higher thermostability than that of the wild-type phytase. However, mutants N156E and D52E led to significant loss of specific activity of the enzyme. Structural analysis revealed that these mutations may affect conformation of the active site of phytase. The present mutant phytases D148E and S197E with increased activities and thermostabilities have application potential as additives in aquaculture feed.

KONAGAbase: a genomic and transcriptomic database for the diamondback moth, Plutella xylostella.

PubMed

Jouraku, Akiya; Yamamoto, Kimiko; Kuwazaki, Seigo; Urio, Masahiro; Suetsugu, Yoshitaka; Narukawa, Junko; Miyamoto, Kazuhisa; Kurita, Kanako; Kanamori, Hiroyuki; Katayose, Yuichi; Matsumoto, Takashi; Noda, Hiroaki

2013-07-09

The diamondback moth (DBM), Plutella xylostella, is one of the most harmful insect pests for crucifer crops worldwide. DBM has rapidly evolved high resistance to most conventional insecticides such as pyrethroids, organophosphates, fipronil, spinosad, Bacillus thuringiensis, and diamides. Therefore, it is important to develop genomic and transcriptomic DBM resources for analysis of genes related to insecticide resistance, both to clarify the mechanism of resistance of DBM and to facilitate the development of insecticides with a novel mode of action for more effective and environmentally less harmful insecticide rotation. To contribute to this goal, we developed KONAGAbase, a genomic and transcriptomic database for DBM (KONAGA is the Japanese word for DBM). KONAGAbase provides (1) transcriptomic sequences of 37,340 ESTs/mRNAs and 147,370 RNA-seq contigs which were clustered and assembled into 84,570 unigenes (30,695 contigs, 50,548 pseudo singletons, and 3,327 singletons); and (2) genomic sequences of 88,530 WGS contigs with 246,244 degenerate contigs and 106,455 singletons from which 6,310 de novo identified repeat sequences and 34,890 predicted gene-coding sequences were extracted. The unigenes and predicted gene-coding sequences were clustered and 32,800 representative sequences were extracted as a comprehensive putative gene set. These sequences were annotated with BLAST descriptions, Gene Ontology (GO) terms, and Pfam descriptions, respectively. KONAGAbase contains rich graphical user interface (GUI)-based web interfaces for easy and efficient searching, browsing, and downloading sequences and annotation data. Five useful search interfaces consisting of BLAST search, keyword search, BLAST result-based search, GO tree-based search, and genome browser are provided. KONAGAbase is publicly available from our website (http://dbm.dna.affrc.go.jp/px/) through standard web browsers. KONAGAbase provides DBM comprehensive transcriptomic and draft genomic sequences with useful annotation information with easy-to-use web interfaces, which helps researchers to efficiently search for target sequences such as insect resistance-related genes. KONAGAbase will be continuously updated and additional genomic/transcriptomic resources and analysis tools will be provided for further efficient analysis of the mechanism of insecticide resistance and the development of effective insecticides with a novel mode of action for DBM.

[Characteristics of arthropod community in alpine cabbage fields].

PubMed

Wang, Xiang-ping; Zhang, Zhong-ning

2007-01-01

The study on the community structure of arthropod in the alpine cabbage fields of Hubei Province showed that the dominant pests were Brevicoryne brassicae, Mamestra brassicae and Plutella xylostella, while the dominant natural enemies were Diaeretiella rapae, Cotesia plutella, Erigonidum gramiaicolum and Syrphus corollae. The richness, diversity index, evenness index and dominance index of pest and natural enemy sub-communities all changed with time. The dominance index of pest sub-community was higher, while its diversity and evenness indices were lower than those of natural enemy sub-community. Based on fuzzy clustering analysis, the pest and natural enemy subcommunities of 14 time sequences were grouped into 4 and 3 sorts, respectively.

Intrinsic alignments in redMaPPer clusters - I. Central galaxy alignments and angular segregation of satellites

NASA Astrophysics Data System (ADS)

Huang, Hung-Jin; Mandelbaum, Rachel; Freeman, Peter E.; Chen, Yen-Chi; Rozo, Eduardo; Rykoff, Eli; Baxter, Eric J.

2016-11-01

The shapes of cluster central galaxies are not randomly oriented, but rather exhibit coherent alignments with the shapes of their parent clusters as well as with the surrounding large-scale structures. In this work, we aim to identify the galaxy and cluster quantities that most strongly predict the central galaxy alignment phenomenon among a large parameter space with a sample of 8237 clusters and 94 817 members within 0.1 < z < 0.35, based on the red-sequence Matched-filter Probabilistic Percolation cluster catalogue constructed from the Sloan Digital Sky Survey. We first quantify the alignment between the projected central galaxy shapes and the distribution of member satellites, to understand what central galaxy and cluster properties most strongly correlate with these alignments. Next, we investigate the angular segregation of satellites with respect to their central galaxy major axis directions, to identify the satellite properties that most strongly predict their angular segregation. We find that central galaxies are more aligned with their member galaxy distributions in clusters that are more elongated and have higher richness, and for central galaxies with larger physical size, higher luminosity and centring probability, and redder colour. Satellites with redder colour, higher luminosity, located closer to the central galaxy, and with smaller ellipticity show a stronger angular segregation towards their central galaxy major axes. Finally, we provide physical explanations for some of the identified correlations, and discuss the connection to theories of central galaxy alignments, the impact of primordial alignments with tidal fields, and the importance of anisotropic accretion.

Intrinsic alignments in redMaPPer clusters – I. Central galaxy alignments and angular segregation of satellites

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

Huang, Hung -Jin; Mandelbaum, Rachel; Freeman, Peter E.

The shapes of cluster central galaxies are not randomly oriented, but rather exhibit coherent alignments with the shapes of their parent clusters as well as with the surrounding large-scale structures. In this work, we aim to identify the galaxy and cluster quantities that most strongly predict the central galaxy alignment phenomenon among a large parameter space with a sample of 8237 clusters and 94 817 members within 0.1 < z < 0.35, based on the red-sequence Matched-filter Probabilistic Percolation cluster catalogue constructed from the Sloan Digital Sky Survey. We first quantify the alignment between the projected central galaxy shapes andmore » the distribution of member satellites, to understand what central galaxy and cluster properties most strongly correlate with these alignments. Next, we investigate the angular segregation of satellites with respect to their central galaxy major axis directions, to identify the satellite properties that most strongly predict their angular segregation. We find that central galaxies are more aligned with their member galaxy distributions in clusters that are more elongated and have higher richness, and for central galaxies with larger physical size, higher luminosity and centring probability, and redder colour. Satellites with redder colour, higher luminosity, located closer to the central galaxy, and with smaller ellipticity show a stronger angular segregation towards their central galaxy major axes. Lastly, we provide physical explanations for some of the identified correlations, and discuss the connection to theories of central galaxy alignments, the impact of primordial alignments with tidal fields, and the importance of anisotropic accretion.« less

Intrinsic alignments in redMaPPer clusters – I. Central galaxy alignments and angular segregation of satellites

DOE PAGES

Huang, Hung -Jin; Mandelbaum, Rachel; Freeman, Peter E.; ...

2016-08-11

The shapes of cluster central galaxies are not randomly oriented, but rather exhibit coherent alignments with the shapes of their parent clusters as well as with the surrounding large-scale structures. In this work, we aim to identify the galaxy and cluster quantities that most strongly predict the central galaxy alignment phenomenon among a large parameter space with a sample of 8237 clusters and 94 817 members within 0.1 < z < 0.35, based on the red-sequence Matched-filter Probabilistic Percolation cluster catalogue constructed from the Sloan Digital Sky Survey. We first quantify the alignment between the projected central galaxy shapes andmore » the distribution of member satellites, to understand what central galaxy and cluster properties most strongly correlate with these alignments. Next, we investigate the angular segregation of satellites with respect to their central galaxy major axis directions, to identify the satellite properties that most strongly predict their angular segregation. We find that central galaxies are more aligned with their member galaxy distributions in clusters that are more elongated and have higher richness, and for central galaxies with larger physical size, higher luminosity and centring probability, and redder colour. Satellites with redder colour, higher luminosity, located closer to the central galaxy, and with smaller ellipticity show a stronger angular segregation towards their central galaxy major axes. Lastly, we provide physical explanations for some of the identified correlations, and discuss the connection to theories of central galaxy alignments, the impact of primordial alignments with tidal fields, and the importance of anisotropic accretion.« less

High-Resolution Whole-Genome Sequencing Reveals That Specific Chromatin Domains from Most Human Chromosomes Associate with Nucleoli

PubMed Central

van Koningsbruggen, Silvana; Gierliński, Marek; Schofield, Pietá; Martin, David; Barton, Geoffey J.; Ariyurek, Yavuz; den Dunnen, Johan T.

2010-01-01

The nuclear space is mostly occupied by chromosome territories and nuclear bodies. Although this organization of chromosomes affects gene function, relatively little is known about the role of nuclear bodies in the organization of chromosomal regions. The nucleolus is the best-studied subnuclear structure and forms around the rRNA repeat gene clusters on the acrocentric chromosomes. In addition to rDNA, other chromatin sequences also surround the nucleolar surface and may even loop into the nucleolus. These additional nucleolar-associated domains (NADs) have not been well characterized. We present here a whole-genome, high-resolution analysis of chromatin endogenously associated with nucleoli. We have used a combination of three complementary approaches, namely fluorescence comparative genome hybridization, high-throughput deep DNA sequencing and photoactivation combined with time-lapse fluorescence microscopy. The data show that specific sequences from most human chromosomes, in addition to the rDNA repeat units, associate with nucleoli in a reproducible and heritable manner. NADs have in common a high density of AT-rich sequence elements, low gene density and a statistically significant enrichment in transcriptionally repressed genes. Unexpectedly, both the direct DNA sequencing and fluorescence photoactivation data show that certain chromatin loci can specifically associate with either the nucleolus, or the nuclear envelope. PMID:20826608

High-resolution whole-genome sequencing reveals that specific chromatin domains from most human chromosomes associate with nucleoli.

PubMed

van Koningsbruggen, Silvana; Gierlinski, Marek; Schofield, Pietá; Martin, David; Barton, Geoffey J; Ariyurek, Yavuz; den Dunnen, Johan T; Lamond, Angus I

2010-11-01

The nuclear space is mostly occupied by chromosome territories and nuclear bodies. Although this organization of chromosomes affects gene function, relatively little is known about the role of nuclear bodies in the organization of chromosomal regions. The nucleolus is the best-studied subnuclear structure and forms around the rRNA repeat gene clusters on the acrocentric chromosomes. In addition to rDNA, other chromatin sequences also surround the nucleolar surface and may even loop into the nucleolus. These additional nucleolar-associated domains (NADs) have not been well characterized. We present here a whole-genome, high-resolution analysis of chromatin endogenously associated with nucleoli. We have used a combination of three complementary approaches, namely fluorescence comparative genome hybridization, high-throughput deep DNA sequencing and photoactivation combined with time-lapse fluorescence microscopy. The data show that specific sequences from most human chromosomes, in addition to the rDNA repeat units, associate with nucleoli in a reproducible and heritable manner. NADs have in common a high density of AT-rich sequence elements, low gene density and a statistically significant enrichment in transcriptionally repressed genes. Unexpectedly, both the direct DNA sequencing and fluorescence photoactivation data show that certain chromatin loci can specifically associate with either the nucleolus, or the nuclear envelope.

Diverse and Abundant Secondary Metabolism Biosynthetic Gene Clusters in the Genomes of Marine Sponge Derived Streptomyces spp. Isolates.

PubMed

Jackson, Stephen A; Crossman, Lisa; Almeida, Eduardo L; Margassery, Lekha Menon; Kennedy, Jonathan; Dobson, Alan D W

2018-02-20

The genus Streptomyces produces secondary metabolic compounds that are rich in biological activity. Many of these compounds are genetically encoded by large secondary metabolism biosynthetic gene clusters (smBGCs) such as polyketide synthases (PKS) and non-ribosomal peptide synthetases (NRPS) which are modular and can be highly repetitive. Due to the repeats, these gene clusters can be difficult to resolve using short read next generation datasets and are often quite poorly predicted using standard approaches. We have sequenced the genomes of 13 Streptomyces spp. strains isolated from shallow water and deep-sea sponges that display antimicrobial activities against a number of clinically relevant bacterial and yeast species. Draft genomes have been assembled and smBGCs have been identified using the antiSMASH (antibiotics and Secondary Metabolite Analysis Shell) web platform. We have compared the smBGCs amongst strains in the search for novel sequences conferring the potential to produce novel bioactive secondary metabolites. The strains in this study recruit to four distinct clades within the genus Streptomyces . The marine strains host abundant smBGCs which encode polyketides, NRPS, siderophores, bacteriocins and lantipeptides. The deep-sea strains appear to be enriched with gene clusters encoding NRPS. Marine adaptations are evident in the sponge-derived strains which are enriched for genes involved in the biosynthesis and transport of compatible solutes and for heat-shock proteins. Streptomyces spp. from marine environments are a promising source of novel bioactive secondary metabolites as the abundance and diversity of smBGCs show high degrees of novelty. Sponge derived Streptomyces spp. isolates appear to display genomic adaptations to marine living when compared to terrestrial strains.

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...

The peculiar velocities of rich clusters in the hot and cold dark matter scenarios

NASA Technical Reports Server (NTRS)

Rhee, George F.; West, Michael J.; Villumsen, Jens V.

1993-01-01

We present the results of a study of the peculiar velocities of rich clusters of galaxies. The peculiar motion of rich clusters in various cosmological scenarios is of interest for a number of reasons. Observationally, one can measure the peculiar motion of clusters to greater distances than galaxies because cluster peculiar motions can be determined to greater accuracy. One can also test the slope of distance indicator relations using clusters to see if galaxy properties vary with environment. We have used N-body simulations to measure the amplitude and rms cluster peculiar velocity as a function of bias parameter in the hot and cold dark matter scenarios. In addition to measuring the mean and rms peculiar velocity of clusters in the two models, we determined whether the peculiar velocity vector of a given cluster is well aligned with the gravity vector due to all the particles in the simulation and the gravity vector due to the particles present only in the clusters. We have investigated the peculiar velocities of rich clusters of galaxies in the cold dark matter and hot dark matter galaxy formation scenarios. We have derived peculiar velocities and associated errors for the scenarios using four values of the bias parameter ranging from b = 1 to b = 2.5. The growth of the mean peculiar velocity with scale factor has been determined and compared to that predicted by linear theory. In addition, we have compared the orientation of force and velocity in these simulations to see if a program such as that proposed by Bertschinger and Dekel (1989) for elliptical galaxy peculiar motions can be applied to clusters. The method they describe enables one to recover the density field from large scale redshift distance samples. The method makes it possible to do this when only radial velocities are known by assuming that the velocity field is curl free. Our analysis suggests that this program if applied to clusters is only realizable for models with a low value of the bias parameter, i.e., models in which the peculiar velocities of clusters are large enough that the errors do not render the analysis impracticable.

Planck/SDSS Cluster Mass and Gas Scaling Relations for a Volume-Complete redMaPPer Sample

NASA Astrophysics Data System (ADS)

Jimeno, Pablo; Diego, Jose M.; Broadhurst, Tom; De Martino, I.; Lazkoz, Ruth

2018-04-01

Using Planck satellite data, we construct Sunyaev-Zel'dovich (SZ) gas pressure profiles for a large, volume-complete sample of optically selected clusters. We have defined a sample of over 8,000 redMaPPer clusters from the Sloan Digital Sky Survey (SDSS), within the volume-complete redshift region 0.100 < z < 0.325, for which we construct SZ effect maps by stacking Planck data over the full range of richness. Dividing the sample into richness bins we simultaneously solve for the mean cluster mass in each bin together with the corresponding radial pressure profile parameters, employing an MCMC analysis. These profiles are well detected over a much wider range of cluster mass and radius than previous work, showing a clear trend towards larger break radius with increasing cluster mass. Our SZ-based masses fall ˜16% below the mass-richness relations from weak lensing, in a similar fashion as the "hydrostatic bias" related with X-ray derived masses. Finally, we derive a tight Y500-M500 relation over a wide range of cluster mass, with a power law slope equal to 1.70 ± 0.07, that agrees well with the independent slope obtained by the Planck team with an SZ-selected cluster sample, but extends to lower masses with higher precision.

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

Innate Immune Complexity in the Purple Sea Urchin: Diversity of the Sp185/333 System

PubMed Central

Smith, L. Courtney

2012-01-01

The California purple sea urchin, Strongylocentrotus purpuratus, is a long-lived echinoderm with a complex and sophisticated innate immune system. There are several large gene families that function in immunity in this species including the Sp185/333 gene family that has ∼50 (±10) members. The family shows intriguing sequence diversity and encodes a broad array of diverse yet similar proteins. The genes have two exons of which the second encodes the mature protein and has repeats and blocks of sequence called elements. Mosaics of element patterns plus single nucleotide polymorphisms-based variants of the elements result in significant sequence diversity among the genes yet maintains similar structure among the members of the family. Sequence of a bacterial artificial chromosome insert shows a cluster of six, tightly linked Sp185/333 genes that are flanked by GA microsatellites. The sequences between the GA microsatellites in which the Sp185/333 genes and flanking regions are located, are much more similar to each other than are the sequences outside the microsatellites suggesting processes such as gene conversion, recombination, or duplication. However, close linkage does not correspond with greater sequence similarity compared to randomly cloned and sequenced genes that are unlikely to be linked. There are three segmental duplications that are bounded by GAT microsatellites and include three almost identical genes plus flanking regions. RNA editing is detectible throughout the mRNAs based on comparisons to the genes, which, in combination with putative post-translational modifications to the proteins, results in broad arrays of Sp185/333 proteins that differ among individuals. The mature proteins have an N-terminal glycine-rich region, a central RGD motif, and a C-terminal histidine-rich region. The Sp185/333 proteins are localized to the cell surface and are found within vesicles in subsets of polygonal and small phagocytes. The coelomocyte proteome shows full-length and truncated proteins, including some with missense sequence. Current results suggest that both native Sp185/333 proteins and a recombinant protein bind bacteria and are likely important in sea urchin innate immunity. PMID:22566951

Messier 35 (NGC 2168) DANCe. I. Membership, proper motions, and multiwavelength photometry

NASA Astrophysics Data System (ADS)

Bouy, H.; Bertin, E.; Barrado, D.; Sarro, L. M.; Olivares, J.; Moraux, E.; Bouvier, J.; Cuillandre, J.-C.; Ribas, Á.; Beletsky, Y.

2015-03-01

Context. Messier 35 (NGC 2168) is an important young nearby cluster. Its age, richness and relative proximity make it an ideal target for stellar evolution studies. The Kepler K2 mission recently observed it and provided a high accuracy photometric time series of a large number of sources in this area of the sky. Identifying the cluster's members is therefore of high importance to optimize the interpretation and analysis of the Kepler K2 data. Aims: We aim to identify the cluster's members by deriving membership probabilities for the sources within 1° of the cluster's center, which is farther away than equivalent previous studies. Methods: We measure accurate proper motions and multiwavelength (optical and near-infrared) photometry using ground-based archival images of the cluster. We use these measurements to compute membership probabilities. The list of candidate members from the literature is used as a training set to identify the cluster's locus in a multidimensional space made of proper motions, luminosities, and colors. Results: The final catalog includes 338 892 sources with multiwavelength photometry. Approximately half (194 452) were detected at more than two epochs and we measured their proper motion and used it to derive membership probability. A total of 4349 candidate members with membership probabilities greater than 50% are found in this sample in the luminosity range between 10 mag and 22 mag. The slow proper motion of the cluster and the overlap of its sequence with the field and background sequences in almost all color-magnitude and color-color diagrams complicate the analysis and the contamination level is expected to be significant. Our study, nevertheless, provides a coherent and quantitative membership analysis of Messier 35 based on a large fraction of the best ground-based data sets obtained over the past 18 years. As such, it represents a valuable input for follow-up studies using, in particular, the Kepler K2 photometric time series. Table 3 is only available at the CDS via anonymous ftp to http://cdsarc.u-strasbg.fr (ftp://130.79.128.5) or via http://cdsarc.u-strasbg.fr/viz-bin/qcat?J/A+A/575/A120

Catalytic properties of the isolated diaphorase fragment of the NAD-reducing [NiFe]-hydrogenase from Ralstonia eutropha.

PubMed

Lauterbach, Lars; Idris, Zulkifli; Vincent, Kylie A; Lenz, Oliver

2011-01-01

The NAD+-reducing soluble hydrogenase (SH) from Ralstonia eutropha H16 catalyzes the H₂-driven reduction of NAD+, as well as reverse electron transfer from NADH to H+, in the presence of O₂. It comprises six subunits, HoxHYFUI₂, and incorporates a [NiFe] H+/H₂ cycling catalytic centre, two non-covalently bound flavin mononucleotide (FMN) groups and an iron-sulfur cluster relay for electron transfer. This study provides the first characterization of the diaphorase sub-complex made up of HoxF and HoxU. Sequence comparisons with the closely related peripheral subunits of Complex I in combination with UV/Vis spectroscopy and the quantification of the metal and FMN content revealed that HoxFU accommodates a [2Fe2S] cluster, FMN and a series of [4Fe4S] clusters. Protein film electrochemistry (PFE) experiments show clear electrocatalytic activity for both NAD+ reduction and NADH oxidation with minimal overpotential relative to the potential of the NAD+/NADH couple. Michaelis-Menten constants of 56 µM and 197 µM were determined for NADH and NAD+, respectively. Catalysis in both directions is product inhibited with K(I) values of around 0.2 mM. In PFE experiments, the electrocatalytic current was unaffected by O₂, however in aerobic solution assays, a moderate superoxide production rate of 54 nmol per mg of protein was observed, meaning that the formation of reactive oxygen species (ROS) observed for the native SH can be attributed mainly to HoxFU. The results are discussed in terms of their implications for aerobic functioning of the SH and possible control mechanism for the direction of catalysis.

Transcriptome Analysis Revealed Highly Expressed Genes Encoding Secondary Metabolite Pathways and Small Cysteine-Rich Proteins in the Sclerotium of Lignosus rhinocerotis

PubMed Central

Yap, Hui-Yeng Y.; Chooi, Yit-Heng; Fung, Shin-Yee; Ng, Szu-Ting; Tan, Chon-Seng; Tan, Nget-Hong

2015-01-01

Lignosus rhinocerotis (Cooke) Ryvarden (tiger milk mushroom) has long been known for its nutritional and medicinal benefits among the local communities in Southeast Asia. However, the molecular and genetic basis of its medicinal and nutraceutical properties at transcriptional level have not been investigated. In this study, the transcriptome of L. rhinocerotis sclerotium, the part with medicinal value, was analyzed using high-throughput Illumina HiSeqTM platform with good sequencing quality and alignment results. A total of 3,673, 117, and 59,649 events of alternative splicing, novel transcripts, and SNP variation were found to enrich its current genome database. A large number of transcripts were expressed and involved in the processing of gene information and carbohydrate metabolism. A few highly expressed genes encoding the cysteine-rich cerato-platanin, hydrophobins, and sugar-binding lectins were identified and their possible roles in L. rhinocerotis were discussed. Genes encoding enzymes involved in the biosynthesis of glucans, six gene clusters encoding four terpene synthases and one each of non-ribosomal peptide synthetase and polyketide synthase, and 109 transcribed cytochrome P450 sequences were also identified in the transcriptome. The data from this study forms a valuable foundation for future research in the exploitation of this mushroom in pharmacological and industrial applications. PMID:26606395

Development and Characterization of 1,906 EST-SSR Markers from Unigenes in Jute (Corchorus spp.)

PubMed Central

Zhang, Liwu; Li, Yanru; Tao, Aifen; Fang, Pingping; Qi, Jianmin

2015-01-01

Jute, comprising white and dark jute, is the second important natural fiber crop after cotton worldwide. However, the lack of expressed sequence tag-derived simple sequence repeat (EST-SSR) markers has resulted in a large gap in the improvement of jute. Previously, de novo 48,914 unigenes from white jute were assembled. In this study, 1,906 EST-SSRs were identified from these assembled uingenes. Among these markers, di-, tri- and tetra-nucleotide repeat types were the abundant types (12.0%, 56.9% and 21.6% respectively). The AG-rich or GA-rich nucleotide repeats were the predominant. Subsequently, a sample of 116 SSRs, located in genes encoding transcription factors and cellulose synthases, were selected to survey polymorphisms among12 diverse jute accessions. Of these, 83.6% successfully amplified at least one fragment and detected polymorphism among the 12diverse genotypes, indicating that the newly developed SSRs are of good quality. Furthermore, the genetic similarity coefficients of all the 12 accessions were evaluated using 97 polymorphic SSRs. The cluster analysis divided the jute accessions into two main groups with genetic similarity coefficient of 0.61. These EST-SSR markers not only enrich molecular markers of jute genome, but also facilitate genetic and genomic researches in jute. PMID:26512891

STELLAR MEMBERSHIP AND DUSTY DEBRIS DISKS IN THE {alpha} PERSEI CLUSTER

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

Zuckerman, B.; Melis, Carl; Rhee, Joseph H.

2012-06-10

Because of its proximity to the Galactic plane, reliable identification of members of the {alpha} Persei cluster is often problematic. Based primarily on membership evaluations contained in six published papers, we constructed a mostly complete list of high-fidelity members of spectral type G and earlier that lie within 3 arc degrees of the cluster center. {alpha} Persei was the one nearby, rich, young open cluster not surveyed with the Spitzer Space Telescope. We examined the first and final data releases of the Wide-field Infrared Survey Explorer and found 11, or perhaps 12, {alpha} Per cluster members that have excess mid-infraredmore » emission above the stellar photosphere attributable to an orbiting dusty debris disk. The most unusual of these is V488 Per, a K-type star with an excess IR luminosity 16% (or more) of the stellar luminosity; this is a larger excess fraction than that of any other known dusty main-sequence star. Much of the dust that orbits V488 Per is at a temperature of {approx}800 K; if these grains radiate like blackbodies, then they lie only {approx}0.06 AU from the star. The dust is probably the aftermath of a collision of two planetary embryos or planets with small semimajor axes; such orbital radii are similar to those of many of the transiting planets discovered by the Kepler satellite.« less

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

Cluster-transfer reactions with radioactive beams: A spectroscopic tool for neutron-rich nuclei

DOE PAGES

Bottoni, S.; Leoni, S.; Fornal, B.; ...

2015-08-27

An exploratory experiment performed at REX-ISOLDE to investigate cluster-transfer reactions with radioactive beams in inverse kinematics is presented. The aim of the experiment was to test the potential of cluster-transfer reactions at the Coulomb barrier as a mechanism to explore the structure of exotic neutron-rich nuclei. The reactions 7Li( 98Rb,αxn) and 7Li( 98Rb,txn) were studied through particle-γ coincidence measurements, and the results are presented in terms of the observed excitation energies and spins. Moreover, the reaction mechanism is qualitatively discussed as a transfer of a clusterlike particle within a distorted-wave Born approximation framework. The results indicate that cluster-transfer reactions canmore » be described well as a direct process and that they can be an efficient method to investigate the structure of neutron-rich nuclei at medium-high excitation energies and spins.« less

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.

Prospecting for pig single nucleotide polymorphisms in the human genome: have we struck gold?

PubMed

Grapes, L; Rudd, S; Fernando, R L; Megy, K; Rocha, D; Rothschild, M F

2006-06-01

Gene-to-gene variation in the frequency of single nucleotide polymorphisms (SNPs) has been observed in humans, mice, rats, primates and pigs, but a relationship across species in this variation has not been described. Here, the frequency of porcine coding SNPs (cSNPs) identified by in silico methods, and the frequency of murine cSNPs, were compared with the frequency of human cSNPs across homologous genes. From 150,000 porcine expressed sequence tag (EST) sequences, a total of 452 SNP-containing sequence clusters were found, totalling 1394 putative SNPs. All the clustered porcine EST annotations and SNP data have been made publicly available at http://sputnik.btk.fi/project?name=swine. Human and murine cSNPs were identified from dbSNP and were characterized as either validated or total number of cSNPs (validated plus non-validated) for comparison purposes. The correlation between in silico pig cSNP and validated human cSNP densities was found to be 0.77 (p < 0.00001) for a set of 25 homologous genes, while a correlation of 0.48 (p < 0.0005) was found for a primarily random sample of 50 homologous human and mouse genes. This is the first evidence of conserved gene-to-gene variability in cSNP frequency across species and indicates that site-directed screening of porcine genes that are homologous to cSNP-rich human genes may rapidly advance cSNP discovery in pigs.

Short-term evolution of Shiga toxin-producing Escherichia coli O157:H7 between two food-borne outbreaks.

PubMed

Cowley, Lauren A; Dallman, Timothy J; Fitzgerald, Stephen; Irvine, Neil; Rooney, Paul J; McAteer, Sean P; Day, Martin; Perry, Neil T; Bono, James L; Jenkins, Claire; Gally, David L

2016-09-01

Shiga toxin-producing Escherichia coli (STEC) O157:H7 is a public health threat and outbreaks occur worldwide. Here, we investigate genomic differences between related STEC O157:H7 that caused two outbreaks, eight weeks apart, at the same restaurant. Short-read genome sequencing divided the outbreak strains into two sub-clusters separated by only three single-nucleotide polymorphisms in the core genome while traditional typing identified them as separate phage types, PT8 and PT54. Isolates did not cluster with local strains but with those associated with foreign travel to the Middle East/North Africa. Combined long-read sequencing approaches and optical mapping revealed that the two outbreak strains had undergone significant microevolution in the accessory genome with prophage gain, loss and recombination. In addition, the PT54 sub-type had acquired a 240 kbp multi-drug resistance (MDR) IncHI2 plasmid responsible for the phage type switch. A PT54 isolate had a general fitness advantage over a PT8 isolate in rich medium, including an increased capacity to use specific amino acids and dipeptides as a nitrogen source. The second outbreak was considerably larger and there were multiple secondary cases indicative of effective human-to-human transmission. We speculate that MDR plasmid acquisition and prophage changes have adapted the PT54 strain for human infection and transmission. Our study shows the added insights provided by combining whole-genome sequencing approaches for outbreak investigations.

Short-term evolution of Shiga toxin-producing Escherichia coli O157:H7 between two food-borne outbreaks

PubMed Central

Dallman, Timothy J.; Fitzgerald, Stephen; Irvine, Neil; Rooney, Paul J.; McAteer, Sean P.; Day, Martin; Perry, Neil T.; Bono, James L.; Jenkins, Claire; Gally, David L.

2016-01-01

Shiga toxin-producing Escherichia coli (STEC) O157:H7 is a public health threat and outbreaks occur worldwide. Here, we investigate genomic differences between related STEC O157:H7 that caused two outbreaks, eight weeks apart, at the same restaurant. Short-read genome sequencing divided the outbreak strains into two sub-clusters separated by only three single-nucleotide polymorphisms in the core genome while traditional typing identified them as separate phage types, PT8 and PT54. Isolates did not cluster with local strains but with those associated with foreign travel to the Middle East/North Africa. Combined long-read sequencing approaches and optical mapping revealed that the two outbreak strains had undergone significant microevolution in the accessory genome with prophage gain, loss and recombination. In addition, the PT54 sub-type had acquired a 240 kbp multi-drug resistance (MDR) IncHI2 plasmid responsible for the phage type switch. A PT54 isolate had a general fitness advantage over a PT8 isolate in rich medium, including an increased capacity to use specific amino acids and dipeptides as a nitrogen source. The second outbreak was considerably larger and there were multiple secondary cases indicative of effective human-to-human transmission. We speculate that MDR plasmid acquisition and prophage changes have adapted the PT54 strain for human infection and transmission. Our study shows the added insights provided by combining whole-genome sequencing approaches for outbreak investigations. PMID:28348875

Challenges And Results of the Applications of Fuzzy Logic in the Classification of Rich Galaxy Clusters

NASA Astrophysics Data System (ADS)

Santiago Girola Schneider, Rafael

2015-08-01

The fuzzy logic is a branch of the artificial intelligence founded on the concept that 'everything is a matter of degree.' It intends to create mathematical approximations on the resolution of certain types of problems. In addition, it aims to produce exact results obtained from imprecise data, for which it is particularly useful for electronic and computer applications. This enables it to handle vague or unspecific information when certain parts of a system are unknown or ambiguous and, therefore, they cannot be measured in a reliable manner. Also, when the variation of a variable can produce an alteration on the others.The main focus of this paper is to prove the importance of these techniques formulated from a theoretical analysis on its application on ambiguous situations in the field of the rich clusters of galaxies. The purpose is to show its applicability in the several classification systems proposed for the rich clusters, which are based on criteria such as the level of richness of the cluster, the distribution of the brightest galaxies, whether there are signs of type-cD galaxies or not or the existence of sub-clusters.Fuzzy logic enables the researcher to work with “imprecise” information implementing fuzzy sets and combining rules to define actions. The control systems based on fuzzy logic join input variables that are defined in terms of fuzzy sets through rule groups that produce one or several output values of the system under study. From this context, the application of the fuzzy logic’s techniques approximates the solution of the mathematical models in abstractions about the rich galaxy cluster classification of physical properties in order to solve the obscurities that must be confronted by an investigation group in order to make a decision.

Challenges And Results of the Applications of Fuzzy Logic in the Classification of Rich Galaxy Clusters

NASA Astrophysics Data System (ADS)

Girola Schneider, R.

2017-07-01

The fuzzy logic is a branch of the artificial intelligence founded on the concept that everything is a matter of degree. It intends to create mathematical approximations on the resolution of certain types of problems. In addition, it aims to produce exact results obtained from imprecise data, for which it is particularly useful for electronic and computer applications. This enables it to handle vague or unspecific information when certain parts of a system are unknown or ambiguous and, therefore, they cannot be measured in a reliable manner. Also, when the variation of a variable can produce an alteration on the others The main focus of this paper is to prove the importance of these techniques formulated from a theoretical analysis on its application on ambiguous situations in the field of the rich clusters of galaxies. The purpose is to show its applicability in the several classification systems proposed for the rich clusters, which are based on criteria such as the level of richness of the cluster, the distribution of the brightest galaxies, whether there are signs of type-cD galaxies or not or the existence of sub-clusters. Fuzzy logic enables the researcher to work with "imprecise" information implementing fuzzy sets and combining rules to define actions. The control systems based on fuzzy logic join input variables that are defined in terms of fuzzy sets through rule groups that produce one or several output values of the system under study. From this context, the application of the fuzzy logic's techniques approximates the solution of the mathematical models in abstractions about the rich galaxy cluster classification of physical properties in order to solve the obscurities that must be confronted by an investigation group in order to make a decision.

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

Intensive management affects composition of betaproteobacterial ammonia oxidizers in turfgrass systems.

PubMed

Dell, Emily A; Bowman, Daniel; Rufty, Thomas; Shi, Wei

2008-07-01

Turfgrass is a highly managed ecosystem subject to frequent fertilization, mowing, irrigation, and application of pesticides. Turf management practices may create a perturbed environment for ammonia oxidizers, a key microbial group responsible for nitrification. To elucidate the long-term effects of turf management on these bacteria, we assessed the composition of betaproteobacterial ammonia oxidizers in a chronosequence of turfgrass systems (i.e., 1, 6, 23, and 95 years old) and the adjacent native pines by using both 16S rRNA and amoA gene fragments specific to ammonia oxidizers. Based on the Shannon-Wiener diversity index of denaturing gradient gel electrophoresis patterns and the rarefaction curves of amoA clones, turf management did not change the relative diversity and richness of ammonia oxidizers in turf soils as compared to native pine soils. Ammonia oxidizers in turfgrass systems comprised a suite of phylogenetic clusters common to other terrestrial ecosystems. Nitrosospira clusters 0, 2, 3, and 4; Nitrosospira sp. Nsp65-like sequences; and Nitrosomonas clusters 6 and 7 were detected in the turfgrass chronosequence with Nitrosospira clusters 3 and 4 being dominant. However, both turf age and land change (pine to turf) effected minor changes in ammonia oxidizer composition. Nitrosospira cluster 0 was observed only in older turfgrass systems (i.e., 23 and 95 years old); fine-scale differences within Nitrosospira cluster 3 were seen between native pines and turf. Further investigations are needed to elucidate the ecological implications of the compositional differences.

Integrated Light Chemical Abundance Analyses of 7 M31 Outer Halo Globular Clusters from the Pan-Andromeda Archaeological Survey

NASA Astrophysics Data System (ADS)

Sakari, Charli; Venn, Kim; Mackey, Dougal; Shetrone, Matthew D.; Dotter, Aaron L.; Wallerstein, George

2015-01-01

Detailed chemical abundances of globular clusters provide insight into the formation and evolution of galaxies and their globular cluster systems. This talk presents detailed chemical abundances for seven M31 outer halo globular clusters (with projected radii greater than 30 kpc), as derived from high resolution integrated light spectra. Five of these clusters were recently discovered in the Pan-Andromeda Archaeological Survey (PAndAS). The integrated abundances show that 4 of these clusters are metal-poor ([Fe/H] < -1.5) while the other 3 are more metal-rich. The most metal-poor globular clusters are α-enhanced, though 3 of the 4 are possibly less α-enhanced than MW stars (at the 1σ level). Other chemical abundance ratios ([Ba/Eu], [Eu/Ca], and [Ni/Fe]) are consistent with origins in low mass dwarf galaxies (similar to Fornax). The most metal-rich cluster ([Fe/H] ~ -1) stands out as being chemically distinct from Milky Way field stars of the same metallicity---its chemical abundance ratios agree best with the stars and clusters in the Large Magellanic Cloud (LMC) and the Sagittarius dwarf spheroidal (Sgr) than with the Milky Way field stars. The other metal-rich clusters, H10 and H23, look similar to the LMC and Milky Way field stars in all abundance ratios. These results indicate that M31's outer halo is being at least partially built up by the accretion of dwarf satellites, in agreement with previous observations.

A Novel Family of Sequence-specific Endoribonucleases Associated with the Clustered Regularly Interspaced Short Palindromic Repeats

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

Beloglazova, Natalia; Brown, Greg; Zimmerman, Matthew D.

Clustered regularly interspaced short palindromic repeats (CRISPRs) together with the associated CAS proteins protect microbial cells from invasion by foreign genetic elements using presently unknown molecular mechanisms. All CRISPR systems contain proteins of the CAS2 family, suggesting that these uncharacterized proteins play a central role in this process. Here we show that the CAS2 proteins represent a novel family of endoribonucleases. Six purified CAS2 proteins from diverse organisms cleaved single-stranded RNAs preferentially within U-rich regions. A representative CAS2 enzyme, SSO1404 from Sulfolobus solfataricus, cleaved the phosphodiester linkage on the 3'-side and generated 5'-phosphate- and 3'-hydroxyl-terminated oligonucleotides. The crystal structure ofmore » SSO1404 was solved at 1.6{angstrom} resolution revealing the first ribonuclease with a ferredoxin-like fold. Mutagenesis of SSO1404 identified six residues (Tyr-9, Asp-10, Arg-17, Arg-19, Arg-31, and Phe-37) that are important for enzymatic activity and suggested that Asp-10 might be the principal catalytic residue. Thus, CAS2 proteins are sequence-specific endoribonucleases, and we propose that their role in the CRISPR-mediated anti-phage defense might involve degradation of phage or cellular mRNAs.« less

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.

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.

Molecular characteristics of insect vitellogenins and vitellogenin receptors.

PubMed

Sappington, T W; Raikhel, A S

1998-01-01

The recent cloning and sequencing of several insect vitellogenins (Vg), the major yolk protein precursor of most oviparous animals, and the mosquito Vg receptor (VgR) has brought the study of insect vitellogenesis to a new plane. Insect Vgs are homologous to nematode and vertebrate Vgs. All but one of the insect Vgs for which we know the primary structure are cleaved into two subunits at a site [(R/K)X(R/K)R or RXXR with an adjacent beta-turn] recognized by subtilisin-like proprotein convertases. In four of the Vgs, the cleavage site is near the N-terminus, but in one insect species, it is near the C-terminus of the Vg precursor. Multiple alignments of these Vg sequences indicate that the variation in cleavage location has not arisen through exon shuffling, but through local modifications of the amino acid sequences. A wasp Vg precursor is not cleaved, apparently because the sequence at the presumed ancestral cleavage site has been mutated from RXRR to LYRR and is no longer recognized by convertases. Some insect Vgs contain polyserine domains which are reminiscent of, but not homologous to, the phosvitin domain in vertebrate Vgs. The sequence of the mosquito VgR revealed that it is a member of the low-density lipoprotein receptor (LDLR) family. Though resembling chicken and frog VgRs, which are also members of the LDLR family, it is twice as big, carrying two clusters of cysteine-rich complement-type (Class A) repeats (implicated in ligand-binding) instead of one like vertebrate VgRs and LDLRs. It is very similar in sequence and domain arrangement to the Drosophila yolk protein receptor (YPR), despite a non-vitellogenin ligand for the latter. Though vertebrate VgRs, insect VgR/YPRs, and LDLR-related proteins/megalins all accommodate one cluster of eight Class A repeats, fingerprint analysis of the repeats in these clusters indicate they are not directly homologous with one another, but have undergone differing histories of duplications, deletions, and exon shuffling so that their apparent similarity is superficial. The so-called epidermal growth factor precursor region contains two types of motifs (cysteine-rich Class B repeats and YWXD repeats) which occur independently of one another in diverse proteins, and are often involved in protein-protein interactions, suggesting that they potentially are involved in dimerization of VgRs and other LDLR-family proteins. Like the LDLR, but unlike vertebrate VgRs and the Drosophila YPR, the mosquito VgR contains a putative O-linked sugar region on the extra-cellular side of the transmembrane domain. Its function is unclear, but may protect the receptor from membrane-bound proteases. The cytoplasmic tail of insect VgR/YPRs contains a di-leucine (or leucine-isoleucine) internalization signal, unlike the tight-turn tyrosine motif of other LDLR-family proteins. The importance of understanding the details of yolk protein uptake by oocytes lies in its potential for exploitation in novel insect control strategies, and the molecular characterization of the proteins involved has made the development of such strategies a realistic possibility.

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

Characterisation of secretory calcium-binding phosphoprotein-proline-glutamine-rich 1: a novel basal lamina component expressed at cell-tooth interfaces.

PubMed

Moffatt, Pierre; Wazen, Rima M; Dos Santos Neves, Juliana; Nanci, Antonio

2014-12-01

Functional genomic screening of the rat enamel organ (EO) has led to the identification of a number of secreted proteins expressed during the maturation stage of amelogenesis, including amelotin (AMTN) and odontogenic ameloblast-associated (ODAM). In this study, we characterise the gene, protein and pattern of expression of a related protein called secretory calcium-binding phosphoprotein-proline-glutamine-rich 1 (SCPPPQ1). The Scpppq1 gene resides within the secretory calcium-binding phosphoprotein (Scpp) cluster. SCPPPQ1 is a highly conserved, 75-residue, secreted protein rich in proline, leucine, glutamine and phenylalanine. In silico data mining has revealed no correlation to any known sequences. Northern blotting of various rat tissues suggests that the expression of Scpppq1 is restricted to tooth and associated tissues. Immunohistochemical analyses show that the protein is expressed during the late maturation stage of amelogenesis and in the junctional epithelium where it localises to an atypical basal lamina at the cell-tooth interface. This discrete localisation suggests that SCPPPQ1, together with AMTN and ODAM, participates in structuring the basal lamina and in mediating attachment of epithelia cells to mineralised tooth surfaces.

Molecular Characterization and Comparative Sequence Analysis of Defense-Related Gene, Oryza rufipogon Receptor-Like Protein Kinase 1

PubMed Central

Law, Yee-Song; Gudimella, Ranganath; Song, Beng-Kah; Ratnam, Wickneswari; Harikrishna, Jennifer Ann

2012-01-01

Many of the plant leucine rich repeat receptor-like kinases (LRR-RLKs) have been found to regulate signaling during plant defense processes. In this study, we selected and sequenced an LRR-RLK gene, designated as Oryza rufipogon receptor-like protein kinase 1 (OrufRPK1), located within yield QTL yld1.1 from the wild rice Oryza rufipogon (accession IRGC105491). A 2055 bp coding region and two exons were identified. Southern blotting determined OrufRPK1 to be a single copy gene. Sequence comparison with cultivated rice orthologs (OsI219RPK1, OsI9311RPK1 and OsJNipponRPK1, respectively derived from O. sativa ssp. indica cv. MR219, O. sativa ssp. indica cv. 9311 and O. sativa ssp. japonica cv. Nipponbare) revealed the presence of 12 single nucleotide polymorphisms (SNPs) with five non-synonymous substitutions, and 23 insertion/deletion sites. The biological role of the OrufRPK1 as a defense related LRR-RLK is proposed on the basis of cDNA sequence characterization, domain subfamily classification, structural prediction of extra cellular domains, cluster analysis and comparative gene expression. PMID:22942769

Weak lensing measurement of the mass–richness relation of SDSS redMaPPer clusters

DOE PAGES

Simet, Melanie; McClintock, Tom; Mandelbaum, Rachel; ...

2016-12-15

Here, we perform a measurement of the mass–richness relation of the redMaPPer galaxy cluster catalogue using weak lensing data from the Sloan Digital Sky Survey. We carefully characterized a broad range of systematic uncertainties, including shear calibration errors, photo-zz biases, dilution by member galaxies, source obscuration, magnification bias, incorrect assumptions about cluster mass profiles, cluster centering, halo triaxiality, and projection effects. We then compare measurements of the lensing signal from two independently-produced shear and photometric redshift catalogues to characterize systematic errors in the lensing signal itself. Using a sample of 5,570 clusters from 0.1 ≤ zz ≤ 0.33, the normalization of our power-law mass vs. λ relation is log 10[M 200m/h -1 M ⊙] = 14.344 ± 0.021 (statistical) ±0.023 (systematic) at a richness λ = 40, a 7 per cent calibration uncertainty, with a power-law index of 1.33+0.09-0.101.33more » $$+0.09\\atop{-0.10}$$ (1σ). Finally, the detailed systematics characterization in this work renders it the definitive weak lensing mass calibration for SDSS redMaPPer clusters at this time.« less

Correction of Hydrostatic Cluster Masses through Power Ratios and Weak Lensing

NASA Astrophysics Data System (ADS)

Mahdavi, Andisheh

2009-09-01

The evolution of rich, X-ray emitting clusters of galaxies has given us precise measurements of the cosmological parameters, with dramatic constraints on the dark energy equation of state. Built into these measurements are wholesale corrections for the infamous "X-ray mass underestimate"---the fact that X-ray masses are systematically low due to the incomplete thermalization of the intracluster plasma. We seek to refine the mass correction for cosmological use through morphological power ratios. Power ratios deliver more accurate correction factors because they take into account variations in substructure from cluster to cluster. We will test their ability to correct X-ray masses by comparing hydrostatic and weak lensing mass profiles for a sample of 44 rich clusters of galaxies.

A Segment of the Apospory-Specific Genomic Region Is Highly Microsyntenic Not Only between the Apomicts Pennisetum squamulatum and Buffelgrass, But Also with a Rice Chromosome 11 Centromeric-Proximal Genomic Region1[W

PubMed Central

Gualtieri, Gustavo; Conner, Joann A.; Morishige, Daryl T.; Moore, L. David; Mullet, John E.; Ozias-Akins, Peggy

2006-01-01

Bacterial artificial chromosome (BAC) clones from apomicts Pennisetum squamulatum and buffelgrass (Cenchrus ciliaris), isolated with the apospory-specific genomic region (ASGR) marker ugt197, were assembled into contigs that were extended by chromosome walking. Gene-like sequences from contigs were identified by shotgun sequencing and BLAST searches, and used to isolate orthologous rice contigs. Additional gene-like sequences in the apomicts' contigs were identified by bioinformatics using fully sequenced BACs from orthologous rice contigs as templates, as well as by interspecies, whole-contig cross-hybridizations. Hierarchical contig orthology was rapidly assessed by constructing detailed long-range contig molecular maps showing the distribution of gene-like sequences and markers, and searching for microsyntenic patterns of sequence identity and spatial distribution within and across species contigs. We found microsynteny between P. squamulatum and buffelgrass contigs. Importantly, this approach also enabled us to isolate from within the rice (Oryza sativa) genome contig Rice A, which shows the highest microsynteny and is most orthologous to the ugt197-containing C1C buffelgrass contig. Contig Rice A belongs to the rice genome database contig 77 (according to the current September 12, 2003, rice fingerprint contig build) that maps proximal to the chromosome 11 centromere, a feature that interestingly correlates with the mapping of ASGR-linked BACs proximal to the centromere or centromere-like sequences. Thus, relatedness between these two orthologous contigs is supported both by their molecular microstructure and by their centromeric-proximal location. Our discoveries promote the use of a microsynteny-based positional-cloning approach using the rice genome as a template to aid in constructing the ASGR toward the isolation of genes underlying apospory. PMID:16415213

A segment of the apospory-specific genomic region is highly microsyntenic not only between the apomicts Pennisetum squamulatum and buffelgrass, but also with a rice chromosome 11 centromeric-proximal genomic region.

PubMed

Gualtieri, Gustavo; Conner, Joann A; Morishige, Daryl T; Moore, L David; Mullet, John E; Ozias-Akins, Peggy

2006-03-01

Bacterial artificial chromosome (BAC) clones from apomicts Pennisetum squamulatum and buffelgrass (Cenchrus ciliaris), isolated with the apospory-specific genomic region (ASGR) marker ugt197, were assembled into contigs that were extended by chromosome walking. Gene-like sequences from contigs were identified by shotgun sequencing and BLAST searches, and used to isolate orthologous rice contigs. Additional gene-like sequences in the apomicts' contigs were identified by bioinformatics using fully sequenced BACs from orthologous rice contigs as templates, as well as by interspecies, whole-contig cross-hybridizations. Hierarchical contig orthology was rapidly assessed by constructing detailed long-range contig molecular maps showing the distribution of gene-like sequences and markers, and searching for microsyntenic patterns of sequence identity and spatial distribution within and across species contigs. We found microsynteny between P. squamulatum and buffelgrass contigs. Importantly, this approach also enabled us to isolate from within the rice (Oryza sativa) genome contig Rice A, which shows the highest microsynteny and is most orthologous to the ugt197-containing C1C buffelgrass contig. Contig Rice A belongs to the rice genome database contig 77 (according to the current September 12, 2003, rice fingerprint contig build) that maps proximal to the chromosome 11 centromere, a feature that interestingly correlates with the mapping of ASGR-linked BACs proximal to the centromere or centromere-like sequences. Thus, relatedness between these two orthologous contigs is supported both by their molecular microstructure and by their centromeric-proximal location. Our discoveries promote the use of a microsynteny-based positional-cloning approach using the rice genome as a template to aid in constructing the ASGR toward the isolation of genes underlying apospory.

Quantifying the Earthquake Clustering that Independent Sources with Stationary Rates (as Included in Current Risk Models) Can Produce.

NASA Astrophysics Data System (ADS)

Fitzenz, D. D.; Nyst, M.; Apel, E. V.; Muir-Wood, R.

2014-12-01

The recent Canterbury earthquake sequence (CES) renewed public and academic awareness concerning the clustered nature of seismicity. Multiple event occurrence in short time and space intervals is reminiscent of aftershock sequences, but aftershock is a statistical definition, not a label one can give an earthquake in real-time. Aftershocks are defined collectively as what creates the Omori event rate decay after a large event or are defined as what is taken away as "dependent events" using a declustering method. It is noteworthy that depending on the declustering method used on the Canterbury earthquake sequence, the number of independent events varies a lot. This lack of unambiguous definition of aftershocks leads to the need to investigate the amount of clustering inherent in "declustered" risk models. This is the task we concentrate on in this contribution. We start from a background source model for the Canterbury region, in which 1) centroids of events of given magnitude are distributed using a latin-hypercube lattice, 2) following the range of preferential orientations determined from stress maps and focal mechanism, 3) with length determined using the local scaling relationship and 4) rates from a and b values derived from the declustered pre-2010 catalog. We then proceed to create tens of thousands of realizations of 6 to 20 year periods, and we define criteria to identify which successions of events in the region would be perceived as a sequence. Note that the spatial clustering expected is a lower end compared to a fully uniform distribution of events. Then we perform the same exercise with rates and b-values determined from the catalog including the CES. If the pre-2010 catalog was long (or rich) enough, then the computed "stationary" rates calculated from it would include the CES declustered events (by construction, regardless of the physical meaning of or relationship between those events). In regions of low seismicity rate (e.g., Canterbury before 2010), it is hard to know how long is long enough. Using simulations, we can look at the apparent activity rate for the region over a few years (for example for events above M5.8), see how often it exceeds some level and also long those high activity rate periods last on average.

Photometric binary stars in Praesepe and the search for globular cluster binaries

NASA Technical Reports Server (NTRS)

Bolte, Michael

1991-01-01

A radial velocity study of the stars which are located on a second sequence above the single-star zero-age main sequence at a given color in the color-magnitude diagram of the open cluster Praesepe, (NGC 2632) shows that 10, and possibly 11, of 17 are binary systems. Of the binary systems, five have full amplitudes for their velocity variations that are greater than 50 km/s. To the extent that they can be applied to globular clusters, these results suggests that (1) observations of 'second-sequence' stars in globular clusters would be an efficient way of finding main-sequence binary systems in globulars, and (2) current instrumentation on large telescopes is sufficient for establishing unambiguously the existence of main-sequence binary systems in nearby globular clusters.

Planck/SDSS cluster mass and gas scaling relations for a volume-complete redMaPPer sample

NASA Astrophysics Data System (ADS)

Jimeno, Pablo; Diego, Jose M.; Broadhurst, Tom; De Martino, I.; Lazkoz, Ruth

2018-07-01

Using Planck satellite data, we construct Sunyaev-Zel'dovich (SZ) gas pressure profiles for a large, volume-complete sample of optically selected clusters. We have defined a sample of over 8000 redMaPPer clusters from the Sloan Digital Sky Survey, within the volume-complete redshift region 0.100

Dissemination and genetic diversity of chlamydial agents in Polish wildfowl: Isolation and molecular characterisation of avian Chlamydia abortus strains.

PubMed

Szymańska-Czerwińska, Monika; Mitura, Agata; Niemczuk, Krzysztof; Zaręba, Kinga; Jodełko, Agnieszka; Pluta, Aneta; Scharf, Sabine; Vitek, Bailey; Aaziz, Rachid; Vorimore, Fabien; Laroucau, Karine; Schnee, Christiane

2017-01-01

Wild birds are considered as a reservoir for avian chlamydiosis posing a potential infectious threat to domestic poultry and humans. Analysis of 894 cloacal or fecal swabs from free-living birds in Poland revealed an overall Chlamydiaceae prevalence of 14.8% (n = 132) with the highest prevalence noted in Anatidae (19.7%) and Corvidae (13.4%). Further testing conducted with species-specific real-time PCR showed that 65 samples (49.2%) were positive for C. psittaci whereas only one was positive for C. avium. To classify the non-identified chlamydial agents and to genotype the C. psittaci and C. avium-positive samples, specimens were subjected to ompA-PCR and sequencing (n = 83). The ompA-based NJ dendrogram revealed that only 23 out of 83 sequences were assigned to C. psittaci, in particular to four clades representing the previously described C. psittaci genotypes B, C, Mat116 and 1V. Whereas the 59 remaining sequences were assigned to two new clades named G1 and G2, each one including sequences recently obtained from chlamydiae detected in Swedish wetland birds. G1 (18 samples from Anatidae and Rallidae) grouped closely together with genotype 1V and in relative proximity to several C. abortus isolates, and G2 (41 samples from Anatidae and Corvidae) grouped closely to C. psittaci strains of the classical ABE cluster, Matt116 and M56. Finally, deep molecular analysis of four representative isolates of genotypes 1V, G1 and G2 based on 16S rRNA, IGS and partial 23S rRNA sequences as well as MLST clearly classify these isolates within the C. abortus species. Consequently, we propose an expansion of the C. abortus species to include not only the classical isolates of mammalian origin, but also avian isolates so far referred to as atypical C. psittaci or C. psittaci/C. abortus intermediates.

Dissemination and genetic diversity of chlamydial agents in Polish wildfowl: Isolation and molecular characterisation of avian Chlamydia abortus strains

PubMed Central

Szymańska-Czerwińska, Monika; Mitura, Agata; Niemczuk, Krzysztof; Zaręba, Kinga; Jodełko, Agnieszka; Pluta, Aneta; Scharf, Sabine; Vitek, Bailey; Aaziz, Rachid; Vorimore, Fabien; Laroucau, Karine; Schnee, Christiane

2017-01-01

Wild birds are considered as a reservoir for avian chlamydiosis posing a potential infectious threat to domestic poultry and humans. Analysis of 894 cloacal or fecal swabs from free-living birds in Poland revealed an overall Chlamydiaceae prevalence of 14.8% (n = 132) with the highest prevalence noted in Anatidae (19.7%) and Corvidae (13.4%). Further testing conducted with species-specific real-time PCR showed that 65 samples (49.2%) were positive for C. psittaci whereas only one was positive for C. avium. To classify the non-identified chlamydial agents and to genotype the C. psittaci and C. avium-positive samples, specimens were subjected to ompA-PCR and sequencing (n = 83). The ompA-based NJ dendrogram revealed that only 23 out of 83 sequences were assigned to C. psittaci, in particular to four clades representing the previously described C. psittaci genotypes B, C, Mat116 and 1V. Whereas the 59 remaining sequences were assigned to two new clades named G1 and G2, each one including sequences recently obtained from chlamydiae detected in Swedish wetland birds. G1 (18 samples from Anatidae and Rallidae) grouped closely together with genotype 1V and in relative proximity to several C. abortus isolates, and G2 (41 samples from Anatidae and Corvidae) grouped closely to C. psittaci strains of the classical ABE cluster, Matt116 and M56. Finally, deep molecular analysis of four representative isolates of genotypes 1V, G1 and G2 based on 16S rRNA, IGS and partial 23S rRNA sequences as well as MLST clearly classify these isolates within the C. abortus species. Consequently, we propose an expansion of the C. abortus species to include not only the classical isolates of mammalian origin, but also avian isolates so far referred to as atypical C. psittaci or C. psittaci/C. abortus intermediates. PMID:28350846

Microbial methane formation in deep aquifers of a coal-bearing sedimentary basin, Germany

PubMed Central

Gründger, Friederike; Jiménez, Núria; Thielemann, Thomas; Straaten, Nontje; Lüders, Tillmann; Richnow, Hans-Hermann; Krüger, Martin

2015-01-01

Coal-bearing sediments are major reservoirs of organic matter potentially available for methanogenic subsurface microbial communities. In this study the specific microbial community inside lignite-bearing sedimentary basin in Germany and its contribution to methanogenic hydrocarbon degradation processes was investigated. The stable isotope signature of methane measured in groundwater and coal-rich sediment samples indicated methanogenic activity. Analysis of 16S rRNA gene sequences showed the presence of methanogenic Archaea, predominantly belonging to the orders Methanosarcinales and Methanomicrobiales, capable of acetoclastic or hydrogenotrophic methanogenesis. Furthermore, we identified fermenting, sulfate-, nitrate-, and metal-reducing, or acetogenic Bacteria clustering within the phyla Proteobacteria, complemented by members of the classes Actinobacteria, and Clostridia. The indigenous microbial communities found in the groundwater as well as in the coal-rich sediments are able to degrade coal-derived organic components and to produce methane as the final product. Lignite-bearing sediments may be an important nutrient and energy source influencing larger compartments via groundwater transport. PMID:25852663

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.

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

Physical mapping of repetitive DNA suggests 2n reduction in Amazon turtles Podocnemis (Testudines: Podocnemididae)

PubMed Central

Cavalcante, Manoella Gemaque; Bastos, Carlos Eduardo Matos Carvalho; Nagamachi, Cleusa Yoshiko; Pieczarka, Julio Cesar; Vicari, Marcelo Ricardo; Noronha, Renata Coelho Rodrigues

2018-01-01

Cytogenetic studies show that there is great karyotypic diversity in order Testudines (2n = 26–68), and that this may be mainly attributed to the presence/absence of microchromosomes. Members of the Podocnemididae family have the smallest diploid numbers of this order (2n = 26–28), which may be a derived condition of the group. Diverse studies suggest that repetitive-DNA-rich sites generally act as hotspots for double-strand breaks and chromosomal reorganization. In this context, we used fluorescent in situ hybridization (FISH) to map telomeric sequences (TTAGGG)n, 45S rDNA, and the genes encoding histones H1 and H3 in two species of genus Podocnemis. We also observed conservation of the 45S rDNA and H1 histone sequences (probable case of conserved synteny), but multiple conserved and non-conserved clusters of H3 genes, which colocalized with the interstitial telomeric sequences in the Podocnemis genome. Our results suggest that fusions have occurred between macro and microchromosomes or between microchromosomes, leading to the observed reduction in diploid number in the family Podocnemididae. PMID:29813087

Physical mapping of repetitive DNA suggests 2n reduction in Amazon turtles Podocnemis (Testudines: Podocnemididae).

PubMed

Cavalcante, Manoella Gemaque; Bastos, Carlos Eduardo Matos Carvalho; Nagamachi, Cleusa Yoshiko; Pieczarka, Julio Cesar; Vicari, Marcelo Ricardo; Noronha, Renata Coelho Rodrigues

2018-01-01

Cytogenetic studies show that there is great karyotypic diversity in order Testudines (2n = 26-68), and that this may be mainly attributed to the presence/absence of microchromosomes. Members of the Podocnemididae family have the smallest diploid numbers of this order (2n = 26-28), which may be a derived condition of the group. Diverse studies suggest that repetitive-DNA-rich sites generally act as hotspots for double-strand breaks and chromosomal reorganization. In this context, we used fluorescent in situ hybridization (FISH) to map telomeric sequences (TTAGGG)n, 45S rDNA, and the genes encoding histones H1 and H3 in two species of genus Podocnemis. We also observed conservation of the 45S rDNA and H1 histone sequences (probable case of conserved synteny), but multiple conserved and non-conserved clusters of H3 genes, which colocalized with the interstitial telomeric sequences in the Podocnemis genome. Our results suggest that fusions have occurred between macro and microchromosomes or between microchromosomes, leading to the observed reduction in diploid number in the family Podocnemididae.

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.

Infalling groups and galaxy transformations in the cluster A2142

NASA Astrophysics Data System (ADS)

Einasto, Maret; Deshev, Boris; Lietzen, Heidi; Kipper, Rain; Tempel, Elmo; Park, Changbom; Gramann, Mirt; Heinämäki, Pekka; Saar, Enn; Einasto, Jaan

2018-03-01

Context. Superclusters of galaxies provide dynamical environments for the study of the formation and evolution of structures in the cosmic web from galaxies, to the richest galaxy clusters, and superclusters themselves. Aims: We study galaxy populations and search for possible merging substructures in the rich galaxy cluster A2142 in the collapsing core of the supercluster SCl A2142, which may give rise to radio and X-ray structures in the cluster, and affect galaxy properties of this cluster. Methods: We used normal mixture modelling to select substructure of the cluster A2142. We compared alignments of the cluster, its brightest galaxies (hereafter BCGs), subclusters, and supercluster axes. The projected phase space (PPS) diagram and clustercentric distributions are used to analyse the dynamics of the cluster and study the distribution of various galaxy populations in the cluster and subclusters. Results: We find several infalling galaxy groups and subclusters. The cluster, supercluster, BCGs, and one infalling subcluster are all aligned. Their orientation is correlated with the alignment of the radio and X-ray haloes of the cluster. Galaxy populations in the main cluster and in the outskirts subclusters are different. Galaxies in the centre of the main cluster at the clustercentric distances 0.5 h-1 Mpc (Dc/Rvir < 0.5, Rvir = 0.9 h-1 Mpc) have older stellar populations (with the median age of 10-11 Gyr) than galaxies at larger clustercentric distances. Star-forming and recently quenched galaxies are located mostly at the clustercentric distances Dc ≈ 1.8 h-1 Mpc, where subclusters fall into the cluster and the properties of galaxies change rapidly. In this region the median age of stellar populations of galaxies is about 2 Gyr. Galaxies in A2142 on average have higher stellar masses, lower star formation rates, and redder colours than galaxies in rich groups. The total mass in infalling groups and subclusters is M ≈ 6 × 1014 h-1 M⊙, that is approximately half of the mass of the cluster. This mass is sufficient for the mass growth of the cluster from redshift z = 0.5 (half-mass epoch) to the present. Conclusions: Our analysis suggests that the cluster A2142 has formed as a result of past and present mergers and infallen groups, predominantly along the supercluster axis. Mergers cause complex radio and X-ray structure of the cluster and affect the properties of galaxies in the cluster, especially at the boundaries of the cluster in the infall region. Explaining the differences between galaxy populations, mass, and richness of A2142, and other groups and clusters may lead to better insight about the formation and evolution of rich galaxy clusters.

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

Identification of significantly mutated regions across cancer types highlights a rich landscape of functional molecular alterations

PubMed Central

Araya, Carlos L.; Cenik, Can; Reuter, Jason A.; Kiss, Gert; Pande, Vijay S.; Snyder, Michael P.; Greenleaf, William J.

2015-01-01

Cancer sequencing studies have primarily identified cancer-driver genes by the accumulation of protein-altering mutations. An improved method would be annotation-independent, sensitive to unknown distributions of functions within proteins, and inclusive of non-coding drivers. We employed density-based clustering methods in 21 tumor types to detect variably-sized significantly mutated regions (SMRs). SMRs reveal recurrent alterations across a spectrum of coding and non-coding elements, including transcription factor binding sites and untranslated regions mutated in up to ∼15% of specific tumor types. SMRs reveal spatial clustering of mutations at molecular domains and interfaces, often with associated changes in signaling. Mutation frequencies in SMRs demonstrate that distinct protein regions are differentially mutated among tumor types, as exemplified by a linker region of PIK3CA in which biophysical simulations suggest mutations affect regulatory interactions. The functional diversity of SMRs underscores both the varied mechanisms of oncogenic misregulation and the advantage of functionally-agnostic driver identification. PMID:26691984

Regulation of specialised metabolites in Actinobacteria – expanding the paradigms

PubMed Central

Hoskisson, Paul A.

2018-01-01

Summary The increase in availability of actinobacterial whole genome sequences has revealed huge numbers of specialised metabolite biosynthetic gene clusters, encoding a range of bioactive molecules such as antibiotics, antifungals, immunosuppressives and anticancer agents. Yet the majority of these clusters are not expressed under standard laboratory conditions in rich media. Emerging data from studies of specialised metabolite biosynthesis suggest that the diversity of regulatory mechanisms is greater than previously thought and these act at multiple levels, through a range of signals such as nutrient limitation, intercellular signalling and competition with other organisms. Understanding the regulation and environmental cues that lead to the production of these compounds allows us to identify the role that these compounds play in their natural habitat as well as provide tools to exploit this untapped source of specialised metabolites for therapeutic uses. Here, we provide an overview of novel regulatory mechanisms that act in physiological, global and cluster‐specific regulatory manners on biosynthetic pathways in Actinobacteria and consider these alongside their ecological and evolutionary implications. PMID:29457705

Measuring the scatter in the cluster optical richness-mass relation with machine learning

NASA Astrophysics Data System (ADS)

Boada, Steven Alvaro

The distribution of massive clusters of galaxies depends strongly on the total cosmic mass density, the mass variance, and the dark energy equation of state. As such, measures of galaxy clusters can provide constraints on these parameters and even test models of gravity, but only if observations of clusters can lead to accurate estimates of their total masses. Here, we carry out a study to investigate the ability of a blind spectroscopic survey to recover accurate galaxy cluster masses through their line-of- sight velocity dispersions (LOSVD) using probability based and machine learning methods. We focus on the Hobby Eberly Telescope Dark Energy Experiment (HETDEX), which will employ new Visible Integral-Field Replicable Unit Spectrographs (VIRUS), over 420 degree2 on the sky with a 1/4.5 fill factor. VIRUS covers the blue/optical portion of the spectrum (3500 - 5500 A), allowing surveys to measure redshifts for a large sample of galaxies out to z < 0.5 based on their absorption or emission (e.g., [O II], Mg II, Ne V) features. We use a detailed mock galaxy catalog from a semi-analytic model to simulate surveys observed with VIRUS, including: (1) Survey, a blind, HETDEX-like survey with an incomplete but uniform spectroscopic selection function; and (2) Targeted, a survey which targets clusters directly, obtaining spectra of all galaxies in a VIRUS-sized field. For both surveys, we include realistic uncertainties from galaxy magnitude and line-flux limits. We benchmark both surveys against spectroscopic observations with perfect" knowledge of galaxy line-of-sight velocities. With Survey observations, we can recover cluster masses to ˜ 0.1 dex which can be further improved to < 0.1 dex with Targeted observations. This level of cluster mass recovery provides important measurements of the intrinsic scatter in the optical richness-cluster mass relation, and enables constraints on the key cosmological parameter, sigma 8, to < 20%. As a demonstration of the methods developed previously, we present a pilot survey with integral field spectroscopy of ten galaxy clusters optically selected from the Sloan Digital Sky Survey's DR8 at z = 0.2 - 0.3. Eight of the clusters are rich (lambda > 60) systems with total inferred masses (1.58 -17.37) x1014 M (M 200c), and two are poor (lambda < 15) systems with inferred total masses ˜ 0.5 x 1014 M? (M200c ). We use the Mitchell Spectrograph, (formerly the VIRUS-P spectrograph, a prototype of the HETDEX VIRUS instrument) located on the McDonald Observatory 2.7m telescope, to measure spectroscopic redshifts and line-of-sight velocities of the galaxies in and around each cluster, determine cluster membership and derive LOSVDs. We test both a LOSVD-cluster mass scaling relation and a machine learning based approach to infer total cluster mass. After comparing the cluster mass estimates to the literature, we use these independent cluster mass measurements to estimate the absolute cluster mass scale, and intrinsic scatter in the optical richness-mass relationship. We measure the intrinsic scatter in richness at fixed cluster mass to be sigmaM/lambda = 0.27 +/- 0.07 dex in excellent agreement with previous estimates of sigmaM/lambda ˜ 0.2 - 0.3 dex. We discuss the importance of the data used to train the machine learning methods and suggest various strategies to import the accuracy of the bias (offset) and scatter in the optical richness-cluster mass relation. This demonstrates the power of blind spectroscopic surveys such as HETDEX to provide robust cluster mass estimates which can aid in the determination of cosmological parameters and help to calibrate the observable-mass relation for future photometric large area-sky surveys.

Large Scale Structure Studies: Final Results from a Rich Cluster Redshift Survey

NASA Astrophysics Data System (ADS)

Slinglend, K.; Batuski, D.; Haase, S.; Hill, J.

1995-12-01

The results from the COBE satellite show the existence of structure on scales on the order of 10% or more of the horizon scale of the universe. Rich clusters of galaxies from the Abell-ACO catalogs show evidence of structure on scales of 100 Mpc and hold the promise of confirming structure on the scale of the COBE result. Unfortunately, until now, redshift information has been unavailable for a large percentage of these clusters, so present knowledge of their three dimensional distribution has quite large uncertainties. Our approach in this effort has been to use the MX multifiber spectrometer on the Steward 2.3m to measure redshifts of at least ten galaxies in each of 88 Abell cluster fields with richness class R>= 1 and mag10 <= 16.8 (estimated z<= 0.12) and zero or one measured redshifts. This work has resulted in a deeper, 95% complete and more reliable sample of 3-D positions of rich clusters. The primary intent of this survey has been to constrain theoretical models for the formation of the structure we see in the universe today through 2-pt. spatial correlation function and other analyses of the large scale structures traced by these clusters. In addition, we have obtained enough redshifts per cluster to greatly improve the quality and size of the sample of reliable cluster velocity dispersions available for use in other studies of cluster properties. This new data has also allowed the construction of an updated and more reliable supercluster candidate catalog. Our efforts have resulted in effectively doubling the volume traced by these clusters. Presented here is the resulting 2-pt. spatial correlation function, as well as density plots and several other figures quantifying the large scale structure from this much deeper and complete sample. Also, with 10 or more redshifts in most of our cluster fields, we have investigated the extent of projection effects within the Abell catalog in an effort to quantify and understand how this may effect the Abell sample.

The evolution of resistance genes in multi-protein plant resistance systems.

PubMed

Friedman, Aaron R; Baker, Barbara J

2007-12-01

The genomic perspective aids in integrating the analysis of single resistance (R-) genes into a higher order model of complex plant resistance systems. The majority of R-genes encode a class of proteins with nucleotide binding (NB) and leucine-rich repeat (LRR) domains. Several R-proteins act in multi-protein R-complexes that mediate interaction with pathogen effectors to induce resistance signaling. The complexity of these systems seems to have resulted from multiple rounds of plant-pathogen co-evolution. R-gene evolution is thought to be facilitated by the formation of R-gene clusters, which permit sequence exchanges via recombinatorial mispairing and generate high haplotypic diversity. This pattern of evolution may also generate diversity at other loci that contribute to the R-complex. The rate of recombination at R-clusters is not necessarily homogeneous or consistent over evolutionary time: recent evidence suggests that recombination at R-clusters is increased following pathogen infection, suggesting a mechanism that induces temporary genome instability in response to extreme stress. DNA methylation and chromatin modifications may allow this instability to be conditionally regulated and targeted to specific genome regions. Knowledge of natural R-gene evolution may contribute to strategies for artificial evolution of novel resistance specificities.

WIYN OPEN CLUSTER STUDY. LXXI. SPECTROSCOPIC MEMBERSHIP AND ORBITS OF NGC 6791 SUB-SUBGIANTS

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

Milliman, Katelyn E.; Leiner, Emily; Mathieu, Robert D.

2016-06-01

In an optical color–magnitude diagram, sub-subgiants (SSGs) lie redward of the main sequence and fainter than the base of the red giant branch in a region not easily populated by standard stellar-evolution pathways. In this paper, we present multi-epoch radial velocities for five SSG candidates in the old and metal-rich open cluster NGC 6791 (8 Gyr, [Fe/H] = +0.30). From these data, we are able to make three-dimensional kinematic membership determinations and confirm four SSG candidates as likely cluster members. We also identify three member SSGs as short-period binary systems and present their orbital solutions. These are the first SSGsmore » with known three-dimensional kinematic membership, binary status, and orbital parameters since the two SSGs in M67 studied by Mathieu et al. We also remark on the other properties of these stars including photometric variability, H α emission, and X-ray luminosity. The membership confirmation of these SSGs in NGC 6791 strengthens the case that SSGs are a new class of nonstandard stellar evolution products, and that a physical mechanism must be found that explains the evolutionary paths of these stars.« less

High-Efficiency Genome Editing of Streptomyces Species by an Engineered CRISPR/Cas System.

PubMed

Wang, Y; Cobb, R E; Zhao, H

2016-01-01

Next-generation sequencing technologies have rapidly expanded the genomic information of numerous organisms and revealed a rich reservoir of natural product gene clusters from microbial genomes, especially from Streptomyces, the largest genus of known actinobacteria at present. However, genetic engineering of these bacteria is often time consuming and labor intensive, if even possible. In this chapter, we describe the design and construction of pCRISPomyces, an engineered Type II CRISPR/Cas system, for targeted multiplex gene deletions in Streptomyces lividans, Streptomyces albus, and Streptomyces viridochromogenes with editing efficiency ranging from 70% to 100%. We demonstrate pCRISPomyces as a powerful tool for genome editing in Streptomyces. © 2016 Elsevier Inc. All rights reserved.

Einstein x ray observations of the core of the Shapley Supercluster in northern Centaurus

NASA Technical Reports Server (NTRS)

Breen, Jeffrey; Raychaudhury, Somak; Forman, William; Jones, Christine

1994-01-01

We present Einstein x ray observations of the core of the Shapley Supercluster, one of the richest and densest known mass concentrations in the local (z less than 0.1) universe. We used Imaging Proportional Counter (IPC) observations supplemented with data from the Einstein Slew Survey to determine the locations and structure of mass concentrations in the region. An x ray map composed of IPC observations of the central (10 deg x 10 deg) region of the Shapley Supercluster is presented. We present evidence that the X-ray clusters observed within 5 deg of the core of the supercluster are on average brighter than those of corresponding richness class distributed throughout the sky. However, we measure no significant difference in the galaxy formation efficiency of these cluster of galaxies compared to other, more isolated clusters. We also find one previously uncataloged cluster-sized mass concentration in the core of the Shapley Supercluster. This new cluster, 'SC 1327-312', is relatively x ray bright (F(sub x) = 1.1 + or - 0.2 x 10(exp -11) erg sec(exp -1) cm(exp -2)) and L(sub x) = 1.1 + or - 0.2 x 10(exp 44) erg sec(exp -1) within 10 minutes, assuming z = 0.0477, H(sub 0) = 50, q(sub 0) = 0). As SC 1327-312 lies well within an Abell radius of the richness R = 4 cluster Shapley 8 (A3558), we suggest it may contribute to an artificially high galaxy count and richness classification for shapley 8. From slew data, we estimate an x ray luminosity for Shapley 8 which is just half the mean luminosity of the four other R = 4 clusters observed by the IPC, further suggesting the richness classification to be an overestimate.

Exploring Genetic Divergence in a Species-Rich Insect Genus Using 2790 DNA Barcodes

PubMed Central

Lin, Xiaolong; Stur, Elisabeth; Ekrem, Torbjørn

2015-01-01

DNA barcoding using a fragment of the mitochondrial cytochrome c oxidase subunit 1 gene (COI) has proven to be successful for species-level identification in many animal groups. However, most studies have been focused on relatively small datasets or on large datasets of taxonomically high-ranked groups. We explore the quality of DNA barcodes to delimit species in the diverse chironomid genus Tanytarsus (Diptera: Chironomidae) by using different analytical tools. The genus Tanytarsus is the most species-rich taxon of tribe Tanytarsini (Diptera: Chironomidae) with more than 400 species worldwide, some of which can be notoriously difficult to identify to species-level using morphology. Our dataset, based on sequences generated from own material and publicly available data in BOLD, consist of 2790 DNA barcodes with a fragment length of at least 500 base pairs. A neighbor joining tree of this dataset comprises 131 well separated clusters representing 121 morphological species of Tanytarsus: 77 named, 16 unnamed and 28 unidentified theoretical species. For our geographically widespread dataset, DNA barcodes unambiguously discriminate 94.6% of the Tanytarsus species recognized through prior morphological study. Deep intraspecific divergences exist in some species complexes, and need further taxonomic studies using appropriate nuclear markers as well as morphological and ecological data to be resolved. The DNA barcodes cluster into 120–242 molecular operational taxonomic units (OTUs) depending on whether Objective Clustering, Automatic Barcode Gap Discovery (ABGD), Generalized Mixed Yule Coalescent model (GMYC), Poisson Tree Process (PTP), subjective evaluation of the neighbor joining tree or Barcode Index Numbers (BINs) are used. We suggest that a 4–5% threshold is appropriate to delineate species of Tanytarsus non-biting midges. PMID:26406595

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.

IMG-ABC. A knowledge base to fuel discovery of biosynthetic gene clusters and novel secondary metabolites

DOE PAGES

Hadjithomas, Michalis; Chen, I-Min Amy; Chu, Ken; ...

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 asmore » 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 lphaproteobacteria. 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.« less

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

Ichthyoplankton assemblages in the Gulf of Nicoya and Golfo Dulce embayments, Pacific coast of Costa Rica.

PubMed

Molina-Ureña, H

1996-12-01

Ichthyoplankton surveys were conducted in December (rainy season), 1993 and February (dry season), 1994, during the RV Victor Hensen German-Costa Rican Expedition to the Gulf of Nicoya and Gulfo Dulce, Costa Rica. Samples from the inner, central, and outer areas of each gulf were collected in oblique tows with a bongo net of 0.6 m mouth diameter, 2.5 m long and 1000-micron mesh. A total of 416 fish larvae of 22 families were sorted out of 14 samples. Stations of both the maximum (11) and the minimum (1) family richness were located in Golfo Dulce. Mean total larval abundances were 124.9 and 197.2 individuals 10 m-2 for the Gulf of Nicoya and Golfo Dulce, respectively, while mean larval densities ranged from 95.3 larvae 10 m-2 in December to 236.7 larvae 10 m-2 in February. However, no statistical differences between gulfs or seasons were detected, due to the high within-group variability. Cluster Analysis, Multi-Dimensional Scaling (MDS), and non-parametric tests showed two well-defined major groups: (1) the Gulf of Nicoya neritic assemblage, represented by Engraulids, Sciaenids, and Gobiids (inner and central stations), and (2) the oceanic assemblage, dominated by Myctophids, Bregmacerotids, Ophiidids, and Trichiurids (outer stations off the Gulf of Nicoya and Golfo Dulce). A third, although less defined group, was an Ophichthid-dominated assemblage (typical in areas nearby coral or rocky reefs). These assemblages closely resemble the clusters based upon adult fish data of the beamtrawl catches of the same cruise. This publication is the first to report on the ichthyoplankton community of Golfo Dulce.

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.

VizieR Online Data Catalog: Collinder 261 Chandra sources & optical counterparts (Vats+, 2017)

NASA Astrophysics Data System (ADS)

Vats, S.; van den Berg, M.

2017-10-01

Cr 261 was observed with the Advanced CCD Imaging Spectrometer (ACIS) on board Chandra starting 2009 November 9 14:50 UTC, for a total exposure time of 53.8ks (ObsID 11308). We retrieved optical images of Cr 261 in the B and V bands from the ESO public archive. These data were taken as part of the ESO Imaging Survey (EIS; program ID 164.O-0561). The observations of Cr 261 were made using the Wide Field Imager (WFI), mounted on the 2.2m MPG/ESO telescope at La Silla, Chile. The Cr 261 data were taken from 2001 June 27 23:55 UTC to 2001 June 28 00:38 UTC, with a total exposure time of 510s in the B and V filter each. (2 data files).

VizieR Online Data Catalog: NGC 6802 dwarf cluster members and non-members (Tang+, 2017)

NASA Astrophysics Data System (ADS)

Tang, B.; Geisler, D.; Friel, E.; Villanova, S.; Smiljanic, R.; Casey, A. R.; Randich, S.; Magrini, L.; San, Roman I.; Munoz, C.; Cohen, R. E.; Mauro, F.; Bragaglia, A.; Donati, P.; Tautvaisiene, G.; Drazdauskas, A.; Zenoviene, R.; Snaith, O.; Sousa, S.; Adibekyan, V.; Costado, M. T.; Blanco-Cuaresma, S.; Jimenez-Esteban, F.; Carraro, G.; Zwitter, T.; Francois, P.; Jofre, P.; Sordo, R.; Gilmore, G.; Flaccomio, E.; Koposov, S.; Korn, A. J.; Lanzafame, A. C.; Pancino, E.; Bayo, A.; Damiani, F.; Franciosini, E.; Hourihane, A.; Lardo, C.; Lewis, J.; Monaco, L.; Morbidelli, L.; Prisinzano, L.; Sacco, G.; Worley, C. C.; Zaggia, S.

2016-11-01

The dwarf stars in NGC 6802 observed by GIRAFFE spectrograph are separated into four tables: 1. cluster members in the lower main sequence; 2. cluster members in the upper main sequence; 3. non-member dwarfs in the lower main sequence; 4. non-member dwarfs in the upper main sequence. The star coordinates, V band magnitude, V-I color, and radial velocity are given. (4 data files).

Joint scaling properties of Sunyaev-Zel'dovich and optical richness observables in an optically-selected galaxy cluster sample

NASA Astrophysics Data System (ADS)

Greer, Christopher Holland

Galaxy cluster abundance measurements are an important tool used to study the universe as a whole. The advent of multiple large-area galaxy cluster surveys across multiple ensures that cluster measurements will play a key role in understanding the dark energy currently thought to be accelerating the universe. The main systematic limitation at the moment is the understanding of the observable-mass relation. Recent theoretical work has shown that combining samples of clusters from surveys at different wavelengths can mitigate this systematic limitation. Precise measurements of the scatter in the observable-mass relation can lead to further improvements. We present Combined Array for Research in Millimeter-wave Astronomy (CARMA) observations of the Sunyaev-Zel'dovich (SZ) signal for 28 galaxy clusters selected from the Sloan Digital Sky Survey (SDSS) maxBCG catalog. This cluster sample represents a complete, volume-limited sample of the richest galaxy clusters in the SDSS between redshifts 0.2 ≥ z ≥ 0.3, as measured by the RedMaPPer algorithm being developed for the Dark Energy Survey (DES; Rykoff et al. 2012). We develop a formalism that uses the cluster abundance in tandem with the galaxy richness measurements from SDSS and the SZ signal measurements from CARMA to calibrate the SZ and optical observable-mass relations. We find that the scatter in richness at fixed mass is σlog λ| M = 0.24+0.09-0.07 using SZ signal calculated by integrating a cluster pressure profile to a radius of 1 Mpc at the redshift of the cluster. We also calculate the SZ signal at R500 and find that the choice of scaling relation used to determined R500 has a non-trivial effect on the constraints of the observable-mass relationship. Finally, we investigate the source of disagreement between the positions of the SZ signal and SDSS Brightest Cluster Galaxies (BCGs). Improvements to the richness calculator that account for blue BCGs in the cores of cool-core X-ray clusters, as well as multiple BCGs in merger situations will help reduce σ log λ|M further. This work is the first independent calibration of the RedMaPPer algorithm that is being designed for the Dark Energy Survey.

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

Formation of Cool Cores in Galaxy Clusters via Hierarchical Mergers

NASA Astrophysics Data System (ADS)

Motl, Patrick M.; Burns, Jack O.; Loken, Chris; Norman, Michael L.; Bryan, Greg

2004-05-01

We present a new scenario for the formation of cool cores in rich galaxy clusters, based on results from recent high spatial dynamic range, adaptive mesh Eulerian hydrodynamic simulations of large-scale structure formation. We find that cores of cool gas, material that would be identified as a classical cooling flow on the basis of its X-ray luminosity excess and temperature profile, are built from the accretion of discrete stable subclusters. Any ``cooling flow'' present is overwhelmed by the velocity field within the cluster; the bulk flow of gas through the cluster typically has speeds up to about 2000 km s-1, and significant rotation is frequently present in the cluster core. The inclusion of consistent initial cosmological conditions for the cluster within its surrounding supercluster environment is crucial when the evolution of cool cores in rich galaxy clusters is simulated. This new model for the hierarchical assembly of cool gas naturally explains the high frequency of cool cores in rich galaxy clusters, despite the fact that a majority of these clusters show evidence of substructure that is believed to arise from recent merger activity. Furthermore, our simulations generate complex cluster cores in concordance with recent X-ray observations of cool fronts, cool ``bullets,'' and filaments in a number of galaxy clusters. Our simulations were computed with a coupled N-body, Eulerian, adaptive mesh refinement, hydrodynamics cosmology code that properly treats the effects of shocks and radiative cooling by the gas. We employ up to seven levels of refinement to attain a peak resolution of 15.6 kpc within a volume 256 Mpc on a side and assume a standard ΛCDM cosmology.

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

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

Paleomagnetic and rock magnetic results from Koko Seamount (ODP Leg 197, Site 1206): Implications for hotspot motion

NASA Astrophysics Data System (ADS)

Olton, G.; Cottrell, R. D.; Tarduno, J. A.; Carvallo, C.; Torii, M.; Doubrovine, P. V.

2002-12-01

ODP Leg 197 sought to test whether the Hawaiian hotspot was fixed in the mantle during Late Cretaceous to Early Tertiary times. The principal goal was the recovery of basalt sequences from several of the Emperor seamounts and the main tool to be applied was paleomagnetism. Koko Seamount, near the bend in the Hawaiian-Emperor Seamounts, was the southernmost site drilled during Leg 197. Fifteen basalt units separated by thick volcaniclastic units were recovered in 278 m of penetration. Based on nannofossil stratigraphy of the sediments above basalt, the top of the volcanic section is 43.5-49.7 m.y.-old. Shipboard geochemical analyses (Initial Reports, Leg 197) indicate the lavas include tholeiites, suggesting that the age of the sequence recovered is similar to that of the major phase of shield building. Detailed, stepwise alternating field demagnetization experiments, and subsequent principal component analysis (all conducted aboard the JOIDES Resolution) yielded 14 inclination groups suggesting a mean paleolatitude of 21.7o N, slightly steeper than that the present-day latitude of Hawaii. Shore-based hysteresis measurements of basalt samples indicate single to pseudo-single domain behavior (mean Hc = 170 Oe, Hcr = 309 Oe, Mr/Ms = 0.274), whereas unblocking temperatures range from 200-300 oC and 550-600 oC. These data suggest the presence of high titanium titanomagnetite and magnetite. Shore-based thermal demagnetization inclinations are similar to the shipboard alternating field demagnetization data. The paleomagnetic data from Koko Seamount, together with results from Detroit, Suiko and Nintoku Seamounts form a southward decreasing series of paleolatitudes that appear to track motion of the Hawaiian ``hotspot" in the mantle. Rates of motion based on paleolatitudes of the Emperor Seamounts range from 30-50 mm/yr, similar to that observed for some continental plates.

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.

Origin of the high velocity gas in NGC 6231

NASA Astrophysics Data System (ADS)

Massa, Derck

2017-08-01

It is well known that clusters of massive stars are influenced by the presence of strong winds, that they are sources of diffuse X-rays from shocked gas, and that this gas can be vented into the surrounding region or the halo, forming a critical element in the process of galactic feedback. However, the details of how these different environments interact and evolve are far from complete. Recently, Massa (2017) showed that the peculiar C IV 1550 Ang absorption seen in several otherwise normal main sequence B stars in NGC 6231 is not intrinsic to the stars. Instead, this absorption, which extends to more than -2000 km/s, is due to intervening carbon rich, high speed gas in the cluster environment. In this proposal, we seek to identify the origin of the high speed gas. The proposed observations will enable us to determine whether it is due to the outer wind of the WC star WR79, or to a collective cluster wind, enriched by carbon from the wind of WR79. If it is due to the wind of WR79, then the new data will furnish a novel, less model dependent estimate of the mass loss rate of a WC star. If it is due to a collective wind from the cluster, then we could be witnessing an important stage of galactic feedback. In either case, the proposed observations will provide a unique and significant insight on how massive, open clusters evolve - insight that can only be obtained through UV spectroscopy.

Multiwavelength Studies of Young OB Associations

NASA Astrophysics Data System (ADS)

Feigelson, Eric D.

We discuss how contemporary multiwavelength observations of young OB-dominated clusters address long-standing astrophysical questions: Do clusters form rapidly or slowly with an age spread? When do clusters expand and disperse to constitute the field star population? Do rich clusters form by amalgamation of smaller subclusters? What is the pattern and duration of cluster formation in massive star forming regions (MSFRs)? Past observational difficulties in obtaining good stellar censuses of MSFRs have been alleviated in recent studies that combine X-ray and infrared surveys to obtain rich, though still incomplete, censuses of young stars in MSFRs. We describe here one of these efforts, the MYStIX project, that produced a catalog of 31,784 probable members of 20 MSFRs. We find that age spread within clusters is real in the sense that the stars in the core formed after the cluster halo. This is consistent with some recent astrophysical models involving merging star-forming filaments. Cluster expansion is seen in the ensemble of (sub)clusters, and older dispersing populations are found across MSFRs. Long-lived, asynchronous star formation is pervasive across MSFRs.

Differences in the methanogen population exist in sika deer (Cervus nippon) fed different diets in China.

PubMed

Li, Zhi Peng; Liu, Han Lu; Jin, Chun Ai; Cui, Xue Zhe; Jing, Yi; Yang, Fu He; Li, Guang Yu; Wright, André-Denis G

2013-11-01

Understanding the methanogen structure from sika deer (Cervus nippon) in China may be beneficial to methane mitigation. In the present preliminary study, we investigated the methanogen community in the rumen of domesticated sika deer fed either tannin-rich plants (oak leaf, OL group) or corn stalk (CS group) using 16S rRNA gene clone libraries. Overall, we obtained 197 clone sequences, revealing 146 unique phylotypes, which were assigned to 36 operational taxonomic units at the species level (98 % identity). Methanogens related to the genus Methanobrevibacter were the predominant phylotypes representing 83.9 % (OL library) and 85.9 % (CS library) of the clones. Methanobrevibacter millerae was the most abundant species in both libraries, but the proportion of M. millerae-related clones in the CS library was higher than in the OL library (69.5 and 51.4 %, respectively). Moreover, Methanobrevibacter wolinii-related clones (32.5 %) were predominant in the OL library. Methanobrevibacter smithii-related clones and Methanobrevibacter ruminantium-related clones accounted for 6.5 and 6.6 % in the CS library, respectively. However, these clones were absent from the OL library. The concentrations of butyrate and total short-chain fatty acids (SCFAs) were significantly higher in the OL group, but the concentrations of acetate, propionate, and valerate and the acetate to propionate ratio in the OL group were not significantly different between the two groups. Tannin-rich plants may have affected the distribution of genus Methanobrevibacter phylotypes at the species level and the concentration and composition of SCFAs.

Using Cluster Analysis to Examine Husband-Wife Decision Making

ERIC Educational Resources Information Center

Bonds-Raacke, Jennifer M.

2006-01-01

Cluster analysis has a rich history in many disciplines and although cluster analysis has been used in clinical psychology to identify types of disorders, its use in other areas of psychology has been less popular. The purpose of the current experiments was to use cluster analysis to investigate husband-wife decision making. Cluster analysis was…

Deep CO(1-0) Observations of z = 1.62 Cluster Galaxies with Substantial Molecular Gas Reservoirs and Normal Star Formation Efficiencies

NASA Astrophysics Data System (ADS)

Rudnick, Gregory; Hodge, Jacqueline; Walter, Fabian; Momcheva, Ivelina; Tran, Kim-Vy; Papovich, Casey; da Cunha, Elisabete; Decarli, Roberto; Saintonge, Amelie; Willmer, Christopher; Lotz, Jennifer; Lentati, Lindley

2017-11-01

We present an extremely deep CO(1-0) observation of a confirmed z = 1.62 galaxy cluster. We detect two spectroscopically confirmed cluster members in CO(1-0) with signal-to-noise ratio > 5. Both galaxies have log({{ M }}\\star /{{ M }}⊙ ) > 11 and are gas rich, with {{ M }}{mol}/({{ M }}\\star +{{ M }}{mol}) ˜ 0.17-0.45. One of these galaxies lies on the star formation rate (SFR)-{{ M }}\\star sequence, while the other lies an order of magnitude below. We compare the cluster galaxies to other SFR-selected galaxies with CO measurements and find that they have CO luminosities consistent with expectations given their infrared luminosities. We also find that they have gas fractions and star formation efficiencies (SFE) comparable to what is expected from published field galaxy scaling relations. The galaxies are compact in their stellar light distribution, at the extreme end for all high-redshift star-forming galaxies. However, their SFE is consistent with other field galaxies at comparable compactness. This is similar to two other sources selected in a blind CO survey of the HDF-N. Despite living in a highly quenched protocluster core, the molecular gas properties of these two galaxies, one of which may be in the process of quenching, appear entirely consistent with field scaling relations between the molecular gas content, stellar mass, star formation rate, and redshift. We speculate that these cluster galaxies cannot have any further substantive gas accretion if they are to become members of the dominant passive population in z< 1 clusters.

Weak-lensing mass calibration of redMaPPer galaxy clusters in Dark Energy Survey Science Verification data

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

Melchior, P.; Gruen, D.; McClintock, T.

We use weak-lensing shear measurements to determine the mean mass of optically selected galaxy clusters in Dark Energy Survey Science Verification data. In a blinded analysis, we split the sample of more than 8,000 redMaPPer clusters into 15 subsets, spanning ranges in the richness parametermore » $$5 \\leq \\lambda \\leq 180$$ and redshift $$0.2 \\leq z \\leq 0.8$$, and fit the averaged mass density contrast profiles with a model that accounts for seven distinct sources of systematic uncertainty: shear measurement and photometric redshift errors; cluster-member contamination; miscentering; deviations from the NFW halo profile; halo triaxiality; and line-of-sight projections. We combine the inferred cluster masses to estimate the joint scaling relation between mass, richness and redshift, $$\\mathcal{M}(\\lambda,z) \\varpropto M_0 \\lambda^{F} (1+z)^{G}$$. We find $$M_0 \\equiv \\langle M_{200\\mathrm{m}}\\,|\\,\\lambda=30,z=0.5\\rangle=\\left[ 2.35 \\pm 0.22\\ \\rm{(stat)} \\pm 0.12\\ \\rm{(sys)} \\right] \\cdot 10^{14}\\ M_\\odot$$, with $$F = 1.12\\,\\pm\\,0.20\\ \\rm{(stat)}\\, \\pm\\, 0.06\\ \\rm{(sys)}$$ and $$G = 0.18\\,\\pm\\, 0.75\\ \\rm{(stat)}\\, \\pm\\, 0.24\\ \\rm{(sys)}$$. The amplitude of the mass-richness relation is in excellent agreement with the weak-lensing calibration of redMaPPer clusters in SDSS by Simet et al. (2016) and with the Saro et al. (2015) calibration based on abundance matching of SPT-detected clusters. Our results extend the redshift range over which the mass-richness relation of redMaPPer clusters has been calibrated with weak lensing from $$z\\leq 0.3$$ to $$z\\leq0.8$$. Calibration uncertainties of shear measurements and photometric redshift estimates dominate our systematic error budget and require substantial improvements for forthcoming studies.« less

Computational prediction of CRISPR cassettes in gut metagenome samples from Chinese type-2 diabetic patients and healthy controls.

PubMed

Mangericao, Tatiana C; Peng, Zhanhao; Zhang, Xuegong

2016-01-11

CRISPR has been becoming a hot topic as a powerful technique for genome editing for human and other higher organisms. The original CRISPR-Cas (Clustered Regularly Interspaced Short Palindromic Repeats coupled with CRISPR-associated proteins) is an important adaptive defence system for prokaryotes that provides resistance against invading elements such as viruses and plasmids. A CRISPR cassette contains short nucleotide sequences called spacers. These unique regions retain a history of the interactions between prokaryotes and their invaders in individual strains and ecosystems. One important ecosystem in the human body is the human gut, a rich habitat populated by a great diversity of microorganisms. Gut microbiomes are important for human physiology and health. Metagenome sequencing has been widely applied for studying the gut microbiomes. Most efforts in metagenome study has been focused on profiling taxa compositions and gene catalogues and identifying their associations with human health. Less attention has been paid to the analysis of the ecosystems of microbiomes themselves especially their CRISPR composition. We conducted a preliminary analysis of CRISPR sequences in a human gut metagenomic data set of Chinese individuals of type-2 diabetes patients and healthy controls. Applying an available CRISPR-identification algorithm, PILER-CR, we identified 3169 CRISPR cassettes in the data, from which we constructed a set of 1302 unique repeat sequences and 36,709 spacers. A more extensive analysis was made for the CRISPR repeats: these repeats were submitted to a more comprehensive clustering and classification using the web server tool CRISPRmap. All repeats were compared with known CRISPRs in the database CRISPRdb. A total of 784 repeats had matches in the database, and the remaining 518 repeats from our set are potentially novel ones. The computational analysis of CRISPR composition based contigs of metagenome sequencing data is feasible. It provides an efficient approach for finding potential novel CRISPR arrays and for analysing the ecosystem and history of human microbiomes.

Strong transcription blockage mediated by R-loop formation within a G-rich homopurine–homopyrimidine sequence localized in the vicinity of the promoter

PubMed Central

Soo Shin, Jane Hae

2017-01-01

Abstract Guanine-rich (G-rich) homopurine–homopyrimidine nucleotide sequences can block transcription with an efficiency that depends upon their orientation, composition and length, as well as the presence of negative supercoiling or breaks in the non-template DNA strand. We report that a G-rich sequence in the non-template strand reduces the yield of T7 RNA polymerase transcription by more than an order of magnitude when positioned close (9 bp) to the promoter, in comparison to that for a distal (∼250 bp) location of the same sequence. This transcription blockage is much less pronounced for a C-rich sequence, and is not significant for an A-rich sequence. Remarkably, the blockage is not pronounced if transcription is performed in the presence of RNase H, which specifically digests the RNA strands within RNA–DNA hybrids. The blockage also becomes less pronounced upon reduced RNA polymerase concentration. Based upon these observations and those from control experiments, we conclude that the blockage is primarily due to the formation of stable RNA–DNA hybrids (R-loops), which inhibit successive rounds of transcription. Our results could be relevant to transcription dynamics in vivo (e.g. transcription ‘bursting’) and may also have practical implications for the design of expression vectors. PMID:28498974

Strong transcription blockage mediated by R-loop formation within a G-rich homopurine-homopyrimidine sequence localized in the vicinity of the promoter.

PubMed

Belotserkovskii, Boris P; Soo Shin, Jane Hae; Hanawalt, Philip C

2017-06-20

Guanine-rich (G-rich) homopurine-homopyrimidine nucleotide sequences can block transcription with an efficiency that depends upon their orientation, composition and length, as well as the presence of negative supercoiling or breaks in the non-template DNA strand. We report that a G-rich sequence in the non-template strand reduces the yield of T7 RNA polymerase transcription by more than an order of magnitude when positioned close (9 bp) to the promoter, in comparison to that for a distal (∼250 bp) location of the same sequence. This transcription blockage is much less pronounced for a C-rich sequence, and is not significant for an A-rich sequence. Remarkably, the blockage is not pronounced if transcription is performed in the presence of RNase H, which specifically digests the RNA strands within RNA-DNA hybrids. The blockage also becomes less pronounced upon reduced RNA polymerase concentration. Based upon these observations and those from control experiments, we conclude that the blockage is primarily due to the formation of stable RNA-DNA hybrids (R-loops), which inhibit successive rounds of transcription. Our results could be relevant to transcription dynamics in vivo (e.g. transcription 'bursting') and may also have practical implications for the design of expression vectors. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Coma cluster of galaxies

NASA Image and Video Library

1999-12-02

Atlas Image mosaic, covering 34 x 34 on the sky, of the Coma cluster, aka Abell 1656. This is a particularly rich cluster of individual galaxies over 1000 members, most prominently the two giant ellipticals, NGC 4874 right and NGC 4889 left.

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

Bacterial microbiome in the nose of healthy cats and in cats with nasal disease

PubMed Central

Tress, Barbara; Suchodolski, Jan S.; Nisar, Tariq; Ravindran, Prajesh; Weber, Karin; Hartmann, Katrin; Schulz, Bianka S.

2017-01-01

Background Traditionally, changes in the microbial population of the nose have been assessed using conventional culture techniques. Sequencing of bacterial 16S rRNA genes demonstrated that the human nose is inhabited by a rich and diverse bacterial microbiome that cannot be detected using culture-based methods. The goal of this study was to describe the nasal microbiome of healthy cats, cats with nasal neoplasia, and cats with feline upper respiratory tract disease (FURTD). Methodology/Principal findings DNA was extracted from nasal swabs of healthy cats (n = 28), cats with nasal neoplasia (n = 16), and cats with FURTD (n = 15), and 16S rRNA genes were sequenced. High species richness was observed in all samples. Rarefaction analysis revealed that healthy cats living indoors had greater species richness (observed species p = 0.042) and Shannon diversity (p = 0.003) compared with healthy cats living outdoors. Higher species richness (observed species p = 0.001) and Shannon diversity (p<0.001) were found in middle-aged cats in comparison to healthy cats in different age groups. Principal coordinate analysis revealed separate clustering based on similarities in bacterial molecular phylogenetic trees of 16S rRNA genes for indoor and outdoor cats. In all groups examined, the most abundant phyla identified were Proteobacteria, Firmicutes, and Bacteroidetes. At the genus level, 375 operational taxonomic units (OTUs) were identified. In healthy cats and cats with FURTD, Moraxella spp. was the most common genus, while it was unclassified Bradyrhizobiaceae in cats with nasal neoplasia. High individual variability was observed. Conclusion This study demonstrates that the nose of cats is inhabited by much more variable and diverse microbial communities than previously shown. Future research in this field might help to develop new diagnostic tools to easily identify nasal microbial changes, relate them to certain disease processes, and help clinicians in the decision process of antibiotic selection for individual patients. PMID:28662139

Characterization of two genes encoding leucine-rich repeat-containing proteins in grass carp Ctenopharyngodon idellus.

PubMed

Chang, M X; Nie, P; Xie, H X; Sun, B J; Gao, Q

2005-01-01

The cDNAs and genes of two different types of leucine-rich repeat-containing proteins from grass carp (Ctenopharyngodon idellus) were cloned. Homology search revealed that the two genes, designated as GC-GARP and GC-LRG, have 37% and 32% deduced amino-acid sequence similarities with human glycoprotein A repetitions predominant precursor (GARP) and leucine-rich alpha2-glycoprotein (LRG), respectively. The cDNAs of GC-GARP and GC-LRG encoded 664 and 339 amino acid residues, respectively. GC-GARP and GC-LRG contain many distinct structural and/or functional motifs of the leucine-rich repeat (LRR) subfamily, such as multiple conserved 11-residue segments with the consensus sequence LxxLxLxxN/CxL (x can be any amino acid). The genes GC-GARP and GC-LRG consist of two exons, with 4,782 bp and 2,119 bp in total length, respectively. The first exon of each gene contains a small 5'-untranslated region and partial open reading frame. The putative promoter region of GC-GARP was found to contain transcription factor binding sites for GATA-1, IRF4, Oct-1, IRF-7, IRF-1, AP1, GATA-box and NFAT, and the promoter region of GC-LRG for MYC-MAX, MEIS1, ISRE, IK3, HOXA9 and C/EBP alpha. Phylogenetic analysis showed that GC-GARP and mammalian GARPs were clustered into one branch, while GC-LRG and mammalian LRGs were in another branch. The GC-GARP gene was only detected in head kidney, and GC-LRG in the liver, spleen and heart in the copepod (Sinergasilus major)-infected grass carp, indicating the induction of gene expression by the parasite infection. The results obtained in the present study provide insight into the structure of fish LRR genes, and further study should be carried out to understand the importance of LRR proteins in host-pathogen interactions.

Genomics-driven discovery of the pneumocandin biosynthetic gene cluster in the fungus Glarea lozoyensis

PubMed Central

2013-01-01

Background The antifungal therapy caspofungin is a semi-synthetic derivative of pneumocandin B0, a lipohexapeptide produced by the fungus Glarea lozoyensis, and was the first member of the echinocandin class approved for human therapy. The nonribosomal peptide synthetase (NRPS)-polyketide synthases (PKS) gene cluster responsible for pneumocandin biosynthesis from G. lozoyensis has not been elucidated to date. In this study, we report the elucidation of the pneumocandin biosynthetic gene cluster by whole genome sequencing of the G. lozoyensis wild-type strain ATCC 20868. Results The pneumocandin biosynthetic gene cluster contains a NRPS (GLNRPS4) and a PKS (GLPKS4) arranged in tandem, two cytochrome P450 monooxygenases, seven other modifying enzymes, and genes for L-homotyrosine biosynthesis, a component of the peptide core. Thus, the pneumocandin biosynthetic gene cluster is significantly more autonomous and organized than that of the recently characterized echinocandin B gene cluster. Disruption mutants of GLNRPS4 and GLPKS4 no longer produced the pneumocandins (A0 and B0), and the Δglnrps4 and Δglpks4 mutants lost antifungal activity against the human pathogenic fungus Candida albicans. In addition to pneumocandins, the G. lozoyensis genome encodes a rich repertoire of natural product-encoding genes including 24 PKSs, six NRPSs, five PKS-NRPS hybrids, two dimethylallyl tryptophan synthases, and 14 terpene synthases. Conclusions Characterization of the gene cluster provides a blueprint for engineering new pneumocandin derivatives with improved pharmacological properties. Whole genome estimation of the secondary metabolite-encoding genes from G. lozoyensis provides yet another example of the huge potential for drug discovery from natural products from the fungal kingdom. PMID:23688303

Nucleation of Hydrogen Deficient Carbon Clusters in Circumstellar Envelopes of Carbon Stars

NASA Astrophysics Data System (ADS)

Chiong, C. C.; Asvany, O.; Balucani, N.; Lee, Y. T.; Kaiser, R. I.

2001-04-01

Hydrogen deficient carbon clusters HCn and H2Cn are thought to resemble the crucial link between naked carbon clusters such as C2/C3, polycyclic aromatic hydrocarbons, and carbon rich interstellar/circumstellar grains. To fully understand the astrophysical significance of these grain nuclei condensation processes, it is of paramount significance to elucidate first detailed mechanism how these simple precursors are formed in outflow of carbon rich stars. Due to this importance, we initiated in our laboratory a systematic research program to investigate reactions of C2 and C3 clusters in their singlet X1Σg+ ground state with unsaturated hydrocarbons C2H2 and C2H4 employing the crossed molecular beam technique. These experiments yield the first doubly differential reactive cross section on the cluster versus H/H2 exchange and supply valuable information on the stepwise growth of carbon rich structures in extraterrestrial environments. Preliminary data analyses identify the CCCCH, CCCCH, and CCCCH2 isomers which were identified in the circumstellar shell of IRC+10216 together with hitherto unobserved interstellar n-C4H3, n-C5H3, and CCCCCH2 radicals.

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.

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

Handali, Melody; Neupane, Durga P.; Roychowdhury, Hridindu

Here, ATP-binding cassette (ABC) transporters of the cluster 9 family are ubiquitous among bacteria and essential for acquiring Zn 2+ and Mn 2+ from the environment or, in the case of pathogens, from the host. These rely on a substrate-binding protein (SBP) to coordinate the relevant metal with high affinity and specificity and subsequently release it to a membrane permease for translocation into the cytoplasm. Although a number of cluster 9 SBP structures have been determined, the structural attributes conferring Zn 2+ or Mn 2+ specificity remain ambiguous. Here we describe the gene expression profile, in vitro metal binding properties,more » and crystal structure of a new cluster 9 SBP from Paracoccus denitrificans we have called AztC. Although all of our results strongly indicate Zn 2+ over Mn 2+ specificity, the Zn 2+ ion is coordinated by a conserved Asp residue only observed to date as a metal ligand in Mn 2+-specific SBPs. The unusual sequence properties of this protein are shared among close homologues, including members from the human pathogens Klebsiella pneumonia and Enterobacter aerogenes, and would seem to suggest a subclass of Zn 2+-specific transporters among the cluster 9 family. In any case, the unusual coordination environment of AztC expands the already considerable range of those available to Zn 2+-specific SBPs and highlights the presence of a His-rich loop as the most reliable indicator of Zn 2+ specificity.« less

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.

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.

26 CFR 1.197-2 - Amortization of goodwill and certain other intangibles.

Code of Federal Regulations, 2014 CFR

2014-04-01

..., process, design, pattern, know-how, format, package design, computer software (as defined in paragraph (c... agreement that provides one of the parties to the agreement with the right to distribute, sell, or provide... any program or routine (that is, any sequence of machine-readable code) that is designed to cause a...

Cluster expansion modeling and Monte Carlo simulation of alnico 5–7 permanent magnets

DOE PAGES

Nguyen, Manh Cuong; Zhao, Xin; Wang, Cai -Zhuang; ...

2015-03-05

The concerns about the supply and resource of rare earth (RE) metals have generated a lot of interests in searching for high performance RE-free permanent magnets. Alnico alloys are traditional non-RE permanent magnets and have received much attention recently due their good performance at high temperature. In this paper, we develop an accurate and efficient cluster expansion energy model for alnico 5–7. Monte Carlo simulations using the cluster expansion method are performed to investigate the structure of alnico 5–7 at atomistic and nano scales. The alnico 5–7 master alloy is found to decompose into FeCo-rich and NiAl-rich phases at lowmore » temperature. The boundary between these two phases is quite sharp (~2 nm) for a wide range of temperature. The compositions of the main constituents in these two phases become higher when the temperature gets lower. Both FeCo-rich and NiAl-rich phases are in B2 ordering with Fe and Al on α-site and Ni and Co on β-site. The degree of order of the NiAl-rich phase is much higher than that of the FeCo-rich phase. In addition, a small magnetic moment is also observed in NiAl-rich phase but the moment reduces as the temperature is lowered, implying that the magnetic properties of alnico 5–7 could be improved by lowering annealing temperature to diminish the magnetism in NiAl-rich phase. Furthermore, the results from our Monte Carlo simulations are consistent with available experimental results.« less

Cluster expansion modeling and Monte Carlo simulation of alnico 5-7 permanent magnets

NASA Astrophysics Data System (ADS)

Nguyen, Manh Cuong; Zhao, Xin; Wang, Cai-Zhuang; Ho, Kai-Ming

2015-03-01

The concerns about the supply and resource of rare earth (RE) metals have generated a lot of interests in searching for high performance RE-free permanent magnets. Alnico alloys are traditional non-RE permanent magnets and have received much attention recently due their good performance at high temperature. In this paper, we develop an accurate and efficient cluster expansion energy model for alnico 5-7. Monte Carlo simulations using the cluster expansion method are performed to investigate the structure of alnico 5-7 at atomistic and nano scales. The alnico 5-7 master alloy is found to decompose into FeCo-rich and NiAl-rich phases at low temperature. The boundary between these two phases is quite sharp (˜2 nm) for a wide range of temperature. The compositions of the main constituents in these two phases become higher when the temperature gets lower. Both FeCo-rich and NiAl-rich phases are in B2 ordering with Fe and Al on α-site and Ni and Co on β-site. The degree of order of the NiAl-rich phase is much higher than that of the FeCo-rich phase. A small magnetic moment is also observed in NiAl-rich phase but the moment reduces as the temperature is lowered, implying that the magnetic properties of alnico 5-7 could be improved by lowering annealing temperature to diminish the magnetism in NiAl-rich phase. The results from our Monte Carlo simulations are consistent with available experimental results.

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

Long-period oxygen-rich optical Miras in the solar neighborhood

NASA Technical Reports Server (NTRS)

Jura, M.; Yamamoto, A.; Kleinmann, S. G.

1993-01-01

The spatial distribution of the oxygen-rich Miras with periods longer than 400 days in the neighborhood of the sun were determined using available survey and the K-band period luminosity relationship. It is found that the exponential scale height of these stars is near 240 pc. There is a marked contrast between the Mira population at about 1 kpc from the Galactic center where there are nearly as many long-period oxygen-rich Miras as intermediate-period oxygen-rich Miras. It is hypothesized that, at about 1 kpc from the Galactic center, the main sequence stars with masses larger than 1 solar mass have higher metallicities than main-sequence stars with the same masses in the solar neighborhood. In the solar neighborhood such main sequence stars become carbon-rich on the AGB and in the region near the Galactic center they become long-period oxygen-rich Miras.

Ages of intermediate-age Magellanic Cloud star clusters

NASA Technical Reports Server (NTRS)

Flower, P. J.

1984-01-01

Ages of intermediate-age Large Magellanic Cloud star clusters have been estimated without locating the faint, unevolved portion of cluster main sequences. Six clusters with established color-magnitude diagrams were selected for study: SL 868, NGC 1783, NGC 1868, NGC 2121, NGC 2209, and NGC 2231. Since red giant photometry is more accurate than the necessarily fainter main-sequence photometry, the distributions of red giants on the cluster color-magnitude diagrams were compared to a grid of 33 stellar evolutionary tracks, evolved from the main sequence through core-helium exhaustion, spanning the expected mass and metallicity range for Magellanic Cloud cluster red giants. The time-dependent behavior of the luminosity of the model red giants was used to estimate cluster ages from the observed cluster red giant luminosities. Except for the possibility of SL 868 being an old globular cluster, all clusters studied were found to have ages less than 10 to the 9th yr. It is concluded that there is currently no substantial evidence for a major cluster population of large, populous clusters greater than 10 to the 9th yr old in the Large Magellanic Cloud.

Species richness and composition of epiphytic bryophytes in flooded forests of Caxiuanã National Forest, Eastern Amazon, Brazil.

PubMed

Cerqueira, Gabriela R; Ilkiu-Borges, Anna Luiza; Ferreira, Leandro V

2017-01-01

This study aimed to compare the richness and composition of the epiphytic bryoflora between várzea and igapó forests in Caxiuanã National Forest, Brazilian Amazon. Bryophytes were collected on 502 phorophytes of Virola surinamensis. Average richness per phorophyte and composition between forests and between dry and rainy periods was tested by two-way analysis and by cluster analysis, respectively. In total, 54 species of 13 families were identified. Richness was greater in igapó forest (44 species) compared to várzea forest (38 species). There was no significant difference in the number of species between the studied periods. Cluster analysis showed the bryoflora composition was different between várzea and igapó, but not between dry and rainy periods. Results did not corroborate the hypothesis that várzea forests harbor higher species richness than igapó forests.

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.

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

The immunoglobulin heavy chain locus of the duck. Genomic organization and expression of D, J, and C region genes.

PubMed

Lundqvist, M L; Middleton, D L; Hazard, S; Warr, G W

2001-12-14

The region of the duck IgH locus extending from upstream of the proximal diversity (D) segment to downstream of the constant gene cluster has been cloned and mapped. A sequence contig of 48,796 base pairs established that the organization of the genes is D-J(H)-mu-alpha-upsilon. No evidence for a functional homologue (or remnant) of a delta gene was found. The alpha gene is in inverted transcriptional orientation; class switch to IgA expression thus requires inversion of the approximately 27-kilobase pair region that includes both mu and alpha genes. The secreted forms of duck alpha and mu are each encoded by 4 constant region exons, and the hydrophobic C-terminal regions of the membrane receptor forms of alpha and mu are encoded by one and two transmembrane exons, respectively. Putative switch (S) regions were identified for duck mu and upsilon by comparison with chicken Smu and Supsilon sequences and for duck alpha by comparison with mouse Salpha. The duck IgH locus is rich in complex variable number tandem repeats, which occupy approximately 60% of the sequenced region, and occur at a much higher frequency in the IgH locus than in other sequenced regions of the duck genome.

Molecular Analysis of Methanogen Richness in Landfill and Marshland Targeting 16S rDNA Sequences

PubMed Central

Yadav, Shailendra; Kundu, Sharbadeb; Ghosh, Sankar K.; Maitra, S. S.

2015-01-01

Methanogens, a key contributor in global carbon cycling, methane emission, and alternative energy production, generate methane gas via anaerobic digestion of organic matter. The methane emission potential depends upon methanogenic diversity and activity. Since they are anaerobes and difficult to isolate and culture, their diversity present in the landfill sites of Delhi and marshlands of Southern Assam, India, was analyzed using molecular techniques like 16S rDNA sequencing, DGGE, and qPCR. The sequencing results indicated the presence of methanogens belonging to the seventh order and also the order Methanomicrobiales in the Ghazipur and Bhalsawa landfill sites of Delhi. Sequences, related to the phyla Crenarchaeota (thermophilic) and Thaumarchaeota (mesophilic), were detected from marshland sites of Southern Assam, India. Jaccard analysis of DGGE gel using Gel2K showed three main clusters depending on the number and similarity of band patterns. The copy number analysis of hydrogenotrophic methanogens using qPCR indicates higher abundance in landfill sites of Delhi as compared to the marshlands of Southern Assam. The knowledge about “methanogenic archaea composition” and “abundance” in the contrasting ecosystems like “landfill” and “marshland” may reorient our understanding of the Archaea inhabitants. This study could shed light on the relationship between methane-dynamics and the global warming process. PMID:26568700

Profiling the resting venom gland of the scorpion Tityus stigmurus through a transcriptomic survey.

PubMed

Almeida, Diego D; Scortecci, Katia C; Kobashi, Leonardo S; Agnez-Lima, Lucymara F; Medeiros, Silvia R B; Silva-Junior, Arnóbio A; Junqueira-de-Azevedo, Inácio de L M; Fernandes-Pedrosa, Matheus de F

2012-08-01

The scorpion Tityus stigmurus is widely distributed in Northeastern Brazil and known to cause severe human envenoming, inducing pain, hyposthesia, edema, erythema, paresthesia, headaches and vomiting. The present study uses a transcriptomic approach to characterize the gene expression profile from the non-stimulated venom gland of Tityus stigmurus scorpion. A cDNA library was constructed and 540 clones were sequenced and grouped into 153 clusters, with one or more ESTs (expressed sequence tags). Forty-one percent of ESTs belong to recognized toxin-coding sequences, with transcripts encoding antimicrobial toxins (AMP-like) being the most abundant, followed by alfa KTx- like, beta KTx-like, beta NaTx-like and alfa NaTx-like. Our analysis indicated that 34% of the transcripts encode "other possible venom molecules", which correspond to anionic peptides, hypothetical secreted peptides, metalloproteinases, cystein-rich peptides and lectins. Fifteen percent of ESTs are similar to cellular transcripts. Sequences without good matches corresponded to 11%. This investigation provides the first global view of gene expression of the venom gland from Tityus stigmurus under resting conditions. This approach enables characterization of a large number of venom gland component molecules, which belong either to known or non yet described types of venom peptides and proteins from the Buthidae family.

Deep-branching Novel Lineages and High Diversity of Haptophytes in the Skagerrak (Norway) Uncovered by 454 Pyrosequencing

PubMed Central

Egge, Elianne S; Eikrem, Wenche; Edvardsen, Bente

2015-01-01

Microalgae in the division Haptophyta may be difficult to identify to species by microscopy because they are small and fragile. Here, we used high-throughput sequencing to explore the diversity of haptophytes in outer Oslofjorden, Skagerrak, and supplemented this with electron microscopy. Nano- and picoplanktonic subsurface samples were collected monthly for 2 yr, and the haptophytes were targeted by amplification of RNA/cDNA with Haptophyta-specific 18S ribosomal DNA V4 primers. Pyrosequencing revealed higher species richness of haptophytes than previously observed in the Skagerrak by microscopy. From ca. 400,000 reads we obtained 156 haptophyte operational taxonomic units (OTUs) after rigorous filtering and 99.5% clustering. The majority (84%) of the OTUs matched environmental sequences not linked to a morphological species, most of which were affiliated with the order Prymnesiales. Phylogenetic analyses including Oslofjorden OTUs and available cultured and environmental haptophyte sequences showed that several of the OTUs matched sequences forming deep-branching lineages, potentially representing novel haptophyte classes. Pyrosequencing also retrieved cultured species not previously reported by microscopy in the Skagerrak. Electron microscopy revealed species not yet genetically characterised and some potentially novel taxa. This study contributes to linking genotype to phenotype within this ubiquitous and ecologically important protist group, and reveals great, unknown diversity. PMID:25099994

Cluster richness-mass calibration with cosmic microwave background lensing

NASA Astrophysics Data System (ADS)

Geach, James E.; Peacock, John A.

2017-11-01

Identifying galaxy clusters through overdensities of galaxies in photometric surveys is the oldest1,2 and arguably the most economical and mass-sensitive detection method3,4, compared with X-ray5-7 and Sunyaev-Zel'dovich effect8 surveys that detect the hot intracluster medium. However, a perennial problem has been the mapping of optical `richness' measurements onto total cluster mass3,9-12. Emitted at a conformal distance of 14 gigaparsecs, the cosmic microwave background acts as a backlight to all intervening mass in the Universe, and therefore has been gravitationally lensed13-15. Experiments such as the Atacama Cosmology Telescope16, South Pole Telescope17-19 and the Planck20 satellite have now detected gravitational lensing of the cosmic microwave background and produced large-area maps of the foreground deflecting structures. Here we present a calibration of cluster optical richness at the 10% level by measuring the average cosmic microwave background lensing measured by Planck towards the positions of large numbers of optically selected clusters, detecting the deflection of photons by structures of total mass of order 1014 M⊙. Although mainly aimed at the study of larger-scale structures, the Planck estimate of the cosmic microwave background lensing field can be used to recover a nearly unbiased lensing signal for stacked clusters on arcminute scales15,21. This approach offers a clean measure of total cluster masses over most of cosmic history, largely independent of baryon physics.

Genomic and transcriptomic analysis of the endophytic fungus Pestalotiopsis fici reveals its lifestyle and high potential for synthesis of natural products.

PubMed

Wang, Xiuna; Zhang, Xiaoling; Liu, Ling; Xiang, Meichun; Wang, Wenzhao; Sun, Xiang; Che, Yongsheng; Guo, Liangdong; Liu, Gang; Guo, Liyun; Wang, Chengshu; Yin, Wen-Bing; Stadler, Marc; Zhang, Xinyu; Liu, Xingzhong

2015-01-27

In recent years, the genus Pestalotiopsis is receiving increasing attention, not only because of its economic impact as a plant pathogen but also as a commonly isolated endophyte which is an important source of bioactive natural products. Pestalotiopsis fici Steyaert W106-1/CGMCC3.15140 as an endophyte of tea produces numerous novel secondary metabolites, including chloropupukeananin, a derivative of chlorinated pupukeanane that is first discovered in fungi. Some of them might be important as the drug leads for future pharmaceutics. Here, we report the genome sequence of the endophytic fungus of tea Pestalotiopsis fici W106-1/CGMCC3.15140. The abundant carbohydrate-active enzymes especially significantly expanding pectinases allow the fungus to utilize the limited intercellular nutrients within the host plants, suggesting adaptation of the fungus to endophytic lifestyle. The P. fici genome encodes a rich set of secondary metabolite synthesis genes, including 27 polyketide synthases (PKSs), 12 non-ribosomal peptide synthases (NRPSs), five dimethylallyl tryptophan synthases, four putative PKS-like enzymes, 15 putative NRPS-like enzymes, 15 terpenoid synthases, seven terpenoid cyclases, seven fatty-acid synthases, and five hybrids of PKS-NRPS. The majority of these core enzymes distributed into 74 secondary metabolite clusters. The putative Diels-Alderase genes have undergone expansion. The significant expansion of pectinase encoding genes provides essential insight in the life strategy of endophytes, and richness of gene clusters for secondary metabolites reveals high potential of natural products of endophytic fungi.

Liver Ischemic Preconditioning (IPC) Improves Intestinal Microbiota Following Liver Transplantation in Rats through 16s rDNA-Based Analysis of Microbial Structure Shift

PubMed Central

Lu, Haifeng; Chen, Xinhua; Jiang, Jianwen; Liu, Hui; He, Yong; Ding, Songming; Hu, Zhenhua; Wang, Weilin; Zheng, Shusen

2013-01-01

Background Ischemia-reperfusion (I/R) injury is associated with intestinal microbial dysbiosis. The “gut-liver axis” closely links gut function and liver function in health and disease. Ischemic preconditioning (IPC) has been proven to reduce I/R injury in the surgery. This study aims to explore the effect of IPC on intestinal microbiota and to analyze characteristics of microbial structure shift following liver transplantation (LT). Methods The LT animal models of liver and gut IPC were established. Hepatic graft function was assessed by histology and serum ALT/AST. Intestinal barrier function was evaluated by mucosal ultrastructure, serum endotoxin, bacterial translocation, fecal sIgA content and serum TNF-α. Intestinal bacterial populations were determined by quantitative PCR. Microbial composition was characterized by DGGE and specific bacterial species were determined by sequence analysis. Principal Findings Liver IPC improved hepatic graft function expressed as ameliorated graft structure and reduced ALT/AST levels. After administration of liver IPC, intestinal mucosal ultrastructure improved, serum endotoxin and bacterial translocation mildly decreased, fecal sIgA content increased, and serum TNF-α decreased. Moreover, liver IPC promoted microbial restorations mainly through restoring Bifidobacterium spp., Clostridium clusters XI and Clostridium cluster XIVab on bacterial genus level. DGGE profiles indicated that liver IPC increased microbial diversity and species richness, and cluster analysis demonstrated that microbial structures were similar and clustered together between the NC group and Liver-IPC group. Furthermore, the phylogenetic tree of band sequences showed key bacteria corresponding to 10 key band classes of microbial structure shift induced by liver IPC, most of which were assigned to Bacteroidetes phylum. Conclusion Liver IPC cannot only improve hepatic graft function and intestinal barrier function, but also promote restorations of intestinal microbiota following LT, which may further benefit hepatic graft by positive feedback of the “gut-liver axis”. PMID:24098410

Sexuality Generates Diversity in the Aflatoxin Gene Cluster: Evidence on a Global Scale

PubMed Central

Moore, Geromy G.; Elliott, Jacalyn L.; Singh, Rakhi; Horn, Bruce W.; Dorner, Joe W.; Stone, Eric A.; Chulze, Sofia N.; Barros, German G.; Naik, Manjunath K.; Wright, Graeme C.; Hell, Kerstin; Carbone, Ignazio

2013-01-01

Aflatoxins are produced by Aspergillus flavus and A. parasiticus in oil-rich seed and grain crops and are a serious problem in agriculture, with aflatoxin B1 being the most carcinogenic natural compound known. Sexual reproduction in these species occurs between individuals belonging to different vegetative compatibility groups (VCGs). We examined natural genetic variation in 758 isolates of A. flavus, A. parasiticus and A. minisclerotigenes sampled from single peanut fields in the United States (Georgia), Africa (Benin), Argentina (Córdoba), Australia (Queensland) and India (Karnataka). Analysis of DNA sequence variation across multiple intergenic regions in the aflatoxin gene clusters of A. flavus, A. parasiticus and A. minisclerotigenes revealed significant linkage disequilibrium (LD) organized into distinct blocks that are conserved across different localities, suggesting that genetic recombination is nonrandom and a global occurrence. To assess the contributions of asexual and sexual reproduction to fixation and maintenance of toxin chemotype diversity in populations from each locality/species, we tested the null hypothesis of an equal number of MAT1-1 and MAT1-2 mating-type individuals, which is indicative of a sexually recombining population. All samples were clone-corrected using multi-locus sequence typing which associates closely with VCG. For both A. flavus and A. parasiticus, when the proportions of MAT1-1 and MAT1-2 were significantly different, there was more extensive LD in the aflatoxin cluster and populations were fixed for specific toxin chemotype classes, either the non-aflatoxigenic class in A. flavus or the B1-dominant and G1-dominant classes in A. parasiticus. A mating type ratio close to 1∶1 in A. flavus, A. parasiticus and A. minisclerotigenes was associated with higher recombination rates in the aflatoxin cluster and less pronounced chemotype differences in populations. This work shows that the reproductive nature of the population (more sexual versus more asexual) is predictive of aflatoxin chemotype diversity in these agriculturally important fungi. PMID:24009506

Liver ischemic preconditioning (IPC) improves intestinal microbiota following liver transplantation in rats through 16s rDNA-based analysis of microbial structure shift.

PubMed

Ren, Zhigang; Cui, Guangying; Lu, Haifeng; Chen, Xinhua; Jiang, Jianwen; Liu, Hui; He, Yong; Ding, Songming; Hu, Zhenhua; Wang, Weilin; Zheng, Shusen

2013-01-01

Ischemia-reperfusion (I/R) injury is associated with intestinal microbial dysbiosis. The "gut-liver axis" closely links gut function and liver function in health and disease. Ischemic preconditioning (IPC) has been proven to reduce I/R injury in the surgery. This study aims to explore the effect of IPC on intestinal microbiota and to analyze characteristics of microbial structure shift following liver transplantation (LT). The LT animal models of liver and gut IPC were established. Hepatic graft function was assessed by histology and serum ALT/AST. Intestinal barrier function was evaluated by mucosal ultrastructure, serum endotoxin, bacterial translocation, fecal sIgA content and serum TNF-α. Intestinal bacterial populations were determined by quantitative PCR. Microbial composition was characterized by DGGE and specific bacterial species were determined by sequence analysis. Liver IPC improved hepatic graft function expressed as ameliorated graft structure and reduced ALT/AST levels. After administration of liver IPC, intestinal mucosal ultrastructure improved, serum endotoxin and bacterial translocation mildly decreased, fecal sIgA content increased, and serum TNF-α decreased. Moreover, liver IPC promoted microbial restorations mainly through restoring Bifidobacterium spp., Clostridium clusters XI and Clostridium cluster XIVab on bacterial genus level. DGGE profiles indicated that liver IPC increased microbial diversity and species richness, and cluster analysis demonstrated that microbial structures were similar and clustered together between the NC group and Liver-IPC group. Furthermore, the phylogenetic tree of band sequences showed key bacteria corresponding to 10 key band classes of microbial structure shift induced by liver IPC, most of which were assigned to Bacteroidetes phylum. Liver IPC cannot only improve hepatic graft function and intestinal barrier function, but also promote restorations of intestinal microbiota following LT, which may further benefit hepatic graft by positive feedback of the "gut-liver axis".

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.

The two-point correlation function for groups of galaxies in the Center for Astrophysics redshift survey

NASA Technical Reports Server (NTRS)

Ramella, Massimo; Geller, Margaret J.; Huchra, John P.

1990-01-01

The large-scale distribution of groups of galaxies selected from complete slices of the CfA redshift survey extension is examined. The survey is used to reexamine the contribution of group members to the galaxy correlation function. The relationship between the correlation function for groups and those calculated for rich clusters is discussed, and the results for groups are examined as an extension of the relation between correlation function amplitude and richness. The group correlation function indicates that groups and individual galaxies are equivalent tracers of the large-scale matter distribution. The distribution of group centers is equivalent to random sampling of the galaxy distribution. The amplitude of the correlation function for groups is consistent with an extrapolation of the amplitude-richness relation for clusters. The amplitude scaled by the mean intersystem separation is also consistent with results for richer clusters.

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 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

Molecular markers shared by diverse apomictic Pennisetum species.

PubMed

Lubbers, E L; Arthur, L; Hanna, W W; Ozias-Akins, P

1994-11-01

Two molecular markers, a RAPD (randomly amplified polymorphic DNA) and a RFLP/STS (restriction fragment length polymorphism/sequence-tagged site), previously were found associated with apomictic reproductive behavior in a backcross population produced to transfer apomixis from Pennisetum squamulatum to pearl millet. The occurrence of these molecular markers in a range of 29 accessions of Pennisetum comprising 11 apomictic and 8 sexual species was investigated. Both markers were specific for apomictic species in Pennisetum. The RFLP/STS marker, UGT 197, was found to be associated with all taxa that displayed apomictic reproductive behavior except those in section Brevivalvula. Neither UGT197 nor the cloned RAPD fragment OPC-04600 hybridized with any sexually reproducing representatives of the genus. The cloned C04600 was associated with 3 of the 11 apomictic species, P. ciliare, P. massaicum, and P. squamulatum. UGT197 was more consistently associated with apomictic reproductive behavior than OPC04600 or cloned C04600, thus it could be inferred that UGT197 is more closely linked to the gene(s) for apomixis than the cloned C04600. The successful use of these probes to survey other Pennisetum species indicates that apomixis is a trait that can be followed across species by using molecular means. This technique of surveying species within a genus will be useful in determining the relative importance of newly isolated markers and may facilitate the identification of the apomixis gene(s).

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

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.

Early Results from Swift AGN and Cluster Survey

NASA Astrophysics Data System (ADS)

Dai, Xinyu; Griffin, Rhiannon; Nugent, Jenna; Kochanek, Christopher S.; Bregman, Joel N.

2016-04-01

The Swift AGN and Cluster Survey (SACS) uses 125 deg^2 of Swift X-ray Telescope serendipitous fields with variable depths surrounding gamma-ray bursts to provide a medium depth (4 × 10^-15 erg cm^-2 s^-1) and area survey filling the gap between deep, narrow Chandra/XMM-Newton surveys and wide, shallow ROSAT surveys. Here, we present the first two papers in a series of publications for SACS. In the first paper, we introduce our method and catalog of 22,563 point sources and 442 extended sources. SACS provides excellent constraints on the AGN and cluster number counts at the bright end with negligible uncertainties due to cosmic variance, and these constraints are consistent with previous measurements. The depth and areal coverage of SACS is well suited for galaxy cluster surveys outside the local universe, reaching z > 1 for massive clusters. In the second paper, we use SDSS DR8 data to study the 203 extended SACS sources that are located within the SDSS footprint. We search for galaxy over-densities in 3-D space using SDSS galaxies and their photometric redshifts near the Swift galaxy cluster candidates. We find 103 Swift clusters with a > 3σ over-density. The remaining targets are potentially located at higher redshifts and require deeper optical follow-up observations for confirmations as galaxy clusters. We present a series of cluster properties including the redshift, BCG magnitude, BCG-to-X-ray center offset, optical richness, X-ray luminosity and red sequences. We compare the observed redshift distribution of the sample with a theoretical model, and find that our sample is complete for z ≤ 0.3 and 80% complete for z ≤ 0.4, consistent with the survey depth of SDSS. These analysis results suggest that our Swift cluster selection algorithm presented in our first paper has yielded a statistically well-defined cluster sample for further studying cluster evolution and cosmology. In the end, we will discuss our ongoing optical identification of z>0.5 cluster sample, using MDM, KPNO, CTIO, and Magellan data, and discuss SACS as a pilot for eROSITA deep surveys.

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

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

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

2013-05-10

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

A 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

Observations of rich clusters of galaxies at metre wavelengths

NASA Technical Reports Server (NTRS)

Cane, H. V.; Erickson, W. C.; Hanisch, R. J.; Turner, P. J.

1981-01-01

Observations have been made at 10 frequencies between 50 and 120 MHz of 17 rich, X-ray emitting clusters of galaxies with the 78 x 156 m dipole array al Llanherne. The observed flux densities were compared to the flux densities expected on the basis of the known discrete sources in the fields. In no case was a significant flux excess found that might have indicated the presence of a diffuse halo component of radio emission in the cluster. For those clusters in which spectral indices could be determined, the spectra all tend to be much steeper than is normal for extragalactic radio sources, although a strict correlation between the X-ray luminosity and the low-frequency radio luminosity or spectral index is not found. The occurrence of large halo sources such as that which is present in the Coma cluster seems to be quite unusual.

Human ribosomal RNA gene: nucleotide sequence of the transcription initiation region and comparison of three mammalian genes.

PubMed Central

Financsek, I; Mizumoto, K; Mishima, Y; Muramatsu, M

1982-01-01

The transcription initiation site of the human ribosomal RNA gene (rDNA) was located by using the single-strand specific nuclease protection method and by determining the first nucleotide of the in vitro capped 45S preribosomal RNA. The sequence of 1,211 nucleotides surrounding the initiation site was determined. The sequenced region was found to consist of 75% G and C and to contain a number of short direct and inverted repeats and palindromes. By comparison of the corresponding initiation regions of three mammalian species, several conserved sequences were found upstream and downstream from the transcription starting point. Two short A + T-rich sequences are present on human, mouse, and rat ribosomal RNA genes between the initiation site and 40 nucleotides upstream, and a C + T cluster is located at a position around -60. At and downstream from the initiation site, a common sequence, T-AG-C-T-G-A-C-A-C-G-C-T-G-T-C-C-T-CT-T, was found in the three genes from position -1 through +18. The strong conservation of these sequences suggests their functional significance in rDNA. The S1 nuclease protection experiments with cloned rDNA fragments indicated the presence in human 45S RNA of molecules several hundred nucleotides shorter than the supposed primary transcript. The first 19 nucleotides of these molecules appear identical--except for one mismatch--to the nucleotide sequence of the 5' end of a supposed early processing product of the mouse 45S RNA. Images PMID:6954460

Complete mitochondrial genome of the larch hawk moth, Sphinx morio (Lepidoptera: Sphingidae).

PubMed

Kim, Min Jee; Choi, Sei-Woong; Kim, Iksoo

2013-12-01

The larch hawk moth, Sphinx morio, belongs to the lepidopteran family Sphingidae that has long been studied as a family of model insects in a diverse field. In this study, we describe the complete mitochondrial genome (mitogenome) sequences of the species in terms of general genomic features and characteristic short repetitive sequences found in the A + T-rich region. The 15,299-bp-long genome consisted of a typical set of genes (13 protein-coding genes, 2 rRNA genes, and 22 tRNA genes) and one major non-coding A + T-rich region, with the typical arrangement found in Lepidoptera. The 316-bp-long A + T-rich region located between srRNA and tRNA(Met) harbored the conserved sequence blocks that are typically found in lepidopteran insects. Additionally, the A + T-rich region of S. morio contained three characteristic repeat sequences that are rarely found in Lepidoptera: two identical 12-bp repeat, three identical 5-bp-long tandem repeat, and six nearly identical 5-6 bp long repeat sequences.

Electron-Rich Carboranes. Studies of a Stereochemically Novel System, (CH3)4C4B7H9, and 11-Vertex Arachno Cluster.

DTIC Science & Technology

1981-01-01

FINSTER , R N GRIMES NOGOIR-75C-0305 UNCLASSIFIED TR-37 NL EOMEEEhE OFFICE OF NAVAL RESEARCH CONTRACT NO. i14.-7-C-31 q,4 TECHNICAL REPORT NO. 37L" 0...Electron-Rich Carboranes. Studies of a Stereochemically Novel System, (CH") 4C4 BH 9 , an 11-Vertex Arachno Cluster. .) David C./ Finster aad Russell N...System, (CH3 )4C4B7H9 , an l-Vertex Arachno Cluster 1 David C. Finster and Russell N. Grimes* Contribution from the Department of Chemistry University of

Gas cluster ion beam assisted NiPt germano-silicide formation on SiGe

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

Ozcan, Ahmet S., E-mail: asozcan@us.ibm.com; Lavoie, Christian; Jordan-Sweet, Jean

We report the formation of very uniform and smooth Ni(Pt)Si on epitaxially grown SiGe using Si gas cluster ion beam treatment after metal-rich silicide formation. The gas cluster ion implantation process was optimized to infuse Si into the metal-rich silicide layer and lowered the NiSi nucleation temperature significantly according to in situ X-ray diffraction measurements. This novel method which leads to more uniform films can also be used to control silicide depth in ultra-shallow junctions, especially for high Ge containing devices, where silicidation is problematic as it leads to much rougher interfaces.

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.

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.

Obesigenic families: parents’ physical activity and dietary intake patterns predict girls’ risk of overweight

PubMed Central

Davison, K Krahnstoever; Birch, L Lipps

2008-01-01

OBJECTIVE To determine whether obesigenic families can be identified based on mothers’ and fathers’ dietary and activity patterns. METHODS A total of 197 girls and their parents were assessed when girls were 5 y old; 192 families were reassessed when girls were 7 y old. Measures of parents’ physical activity and dietary intake were obtained and entered into a cluster analysis to assess whether distinct family clusters could be identified. Girls’ skinfold thickness and body mass index (BMI) were also assessed and were used to examine the predictive validity of the clusters. RESULTS Obesigenic and a non-obesigenic family clusters were identified. Mothers and fathers in the obesigenic cluster reported high levels of dietary intake and low levels of physical activity, while mothers and fathers in the non-obesigenic cluster reported low levels of dietary intake and high levels of activity. Girls from families in the obesigenic cluster had significantly higher BMI and skinfold thickness values at age 7 and showed significantly greater increases in BMI and skinfold thickness from ages 5 to 7 y than girls from non-obesigenic families; differences were reduced but not eliminated after controlling for parents’ BMI. CONCLUSIONS Obesigenic families, defined in terms of parents’ activity and dietary patterns, can be used predict children’s risk of obesity. PMID:12187395

The SpTransformer Gene Family (Formerly Sp185/333) in the Purple Sea Urchin and the Functional Diversity of the Anti-Pathogen rSpTransformer-E1 Protein

PubMed Central

Smith, L. Courtney; Lun, Cheng Man

2017-01-01

The complex innate immune system of sea urchins is underpinned by several multigene families including the SpTransformer family (SpTrf; formerly Sp185/333) with estimates of ~50 members, although the family size is likely variable among individuals of Strongylocentrotus purpuratus. The genes are small with similar structure, are tightly clustered, and have several types of repeats in the second of two exons and that surround each gene. The density of repeats suggests that the genes are positioned within regions of genomic instability, which may be required to drive sequence diversification. The second exon encodes the mature protein and is composed of blocks of sequence called elements that are present in mosaics of defined element patterns and are the major source of sequence diversity. The SpTrf genes respond swiftly to immune challenge, but only a single gene is expressed per phagocyte. Many of the mRNAs appear to be edited and encode proteins with altered and/or missense sequence that are often truncated, of which some may be functional. The standard SpTrf protein structure is an N-terminal glycine-rich region, a central RGD motif, a histidine-rich region, and a C-terminal region. Function is predicted from a recombinant protein, rSpTransformer-E1 (rSpTrf-E1), which binds to Vibrio and Saccharomyces, but not to Bacillus, and binds tightly to lipopolysaccharide, β-1,3-glucan, and flagellin, but not to peptidoglycan. rSpTrf-E1 is intrinsically disordered but transforms to α helical structure in the presence of binding targets including lipopolysaccharide, which may underpin the characteristics of binding to multiple targets. SpTrf proteins associate with coelomocyte membranes, and rSpTrf-E1 binds specifically to phosphatidic acid (PA). When rSpTrf-E1 is bound to PA in liposome membranes, it induces morphological changes in liposomes that correlate with PA clustering and leakage of luminal contents, and it extracts or removes PA from the bilayer. The multitasking activities of rSpTrf-E1 infer multiple and perhaps overlapping activities for the hundreds of native SpTrf proteins that are produced by individual sea urchins. This likely generates a flexible and highly protective immune system for the sea urchin in its marine habitat that it shares with broad arrays of microbes that may be pathogens and opportunists. PMID:28713368

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

Genome sequence of an enhancin gene-rich nucleopolyhedrovirus (NPV) from Agrotis segetum: collinearity with Spodoptera exigua multiple NPV.

PubMed

Jakubowska, Agata K; Peters, Sander A; Ziemnicka, Jadwiga; Vlak, Just M; van Oers, Monique M

2006-03-01

The genome sequence of a Polish isolate of Agrotis segetum nucleopolyhedrovirus (AgseNPV-A) was determined and analysed. The circular genome is composed of 147,544 bp and has a G+C content of 45.7 mol%. It contains 153 putative, non-overlapping open reading frames (ORFs) encoding predicted proteins of more than 50 aa, together making up 89.8 % of the genome. The remaining 10.2 % of the DNA constitutes non-coding regions and homologous-repeat regions. One hundred and forty-three AgseNPV-A ORFs are homologues of previously reported baculovirus gene sequences. There are ten unique ORFs and they account for 3 % of the genome in total. All 62 lepidopteran baculovirus genes, including the 29 core baculovirus genes, were found in the AgseNPV-A genome. The gene content and gene order of AgseNPV-A are most similar to those of Spodoptera exigua (Se) multiple NPV and their shared homologous genes are 100 % collinear. Three putative enhancin genes were identified in the AgseNPV-A genome. In phylogenetic analysis, the AgseNPV-A enhancins form a cluster separated from enhancins of the Mamestra species NPVs.

Phylogenetic characterization of culturable bacteria and fungi associated with tarballs from Betul beach, Goa, India.

PubMed

Shinde, Varsha Laxman; Meena, Ram Murti; Shenoy, Belle Damodara

2018-03-01

Tarballs are semisolid blobs of crude oil, normally formed due to weathering of crude-oil in the sea after any kind of oil spills. Microorganisms are believed to thrive on hydrocarbon-rich tarballs and possibly assist in biodegradation. The taxonomy of ecologically and economically important tarball-associated microbes, however, needs improvement as DNA-based identification and phylogenetic characterization have been scarcely incorporated into it. In this study, bacteria and fungi associated with tarballs from touristic Betul beach in Goa, India were isolated, followed by phylogenetic analyses of 16S rRNA gene and the ITS sequence-data to decipher their clustering patterns with closely-related taxa. The gene-sequence analyses identified phylogenetically diverse 20 bacterial genera belonging to the phyla Proteobacteria (14), Actinobacteria (3), Firmicutes (2) and Bacteroidetes (1), and 8 fungal genera belonging to the classes Eurotiomycetes (6), Sordariomycetes (1) and Leotiomycetes (1) associated with the Betul tarball samples. Future studies employing a polyphasic approach, including multigene sequence-data, are needed for species-level identification of culturable tarball-associated microbes. This paper also discusses potentials of tarball-associated microbes to degrade hydrocarbons. Copyright © 2018 Elsevier Ltd. All rights reserved.

Subspace K-means clustering.

PubMed

Timmerman, Marieke E; Ceulemans, Eva; De Roover, Kim; Van Leeuwen, Karla

2013-12-01

To achieve an insightful clustering of multivariate data, we propose subspace K-means. Its central idea is to model the centroids and cluster residuals in reduced spaces, which allows for dealing with a wide range of cluster types and yields rich interpretations of the clusters. We review the existing related clustering methods, including deterministic, stochastic, and unsupervised learning approaches. To evaluate subspace K-means, we performed a comparative simulation study, in which we manipulated the overlap of subspaces, the between-cluster variance, and the error variance. The study shows that the subspace K-means algorithm is sensitive to local minima but that the problem can be reasonably dealt with by using partitions of various cluster procedures as a starting point for the algorithm. Subspace K-means performs very well in recovering the true clustering across all conditions considered and appears to be superior to its competitor methods: K-means, reduced K-means, factorial K-means, mixtures of factor analyzers (MFA), and MCLUST. The best competitor method, MFA, showed a performance similar to that of subspace K-means in easy conditions but deteriorated in more difficult ones. Using data from a study on parental behavior, we show that subspace K-means analysis provides a rich insight into the cluster characteristics, in terms of both the relative positions of the clusters (via the centroids) and the shape of the clusters (via the within-cluster residuals).

Enacs Survey of Southern Galaxies Indicates Open Universe

NASA Astrophysics Data System (ADS)

1996-02-01

New Light on Rich Clusters of Galaxies and their Formation History In the context of a comprehensive Key-Programme , carried out with telescopes at the ESO La Silla Observatory, a team of European astronomers [1]. has recently obtained radial velocities for more than 5600 galaxies in about 100 rich clusters of galaxies. With this programme the amount of information about the motions of galaxies (the kinematical data) in such clusters has almost been doubled. This has allowed the team to study the distribution of the cluster masses, and also the dynamical state of clusters in new and interesting ways. An important result of this programme is that the derived masses of the investigated clusters of galaxies indicate that the mean density of the Universe is insufficient to halt the current expansion; we may therefore be living in an open Universe that will expand forever. Clusters of galaxies as tracers of large-scale structure About 40 years ago, American astronomer George Abell, working at the Palomar Observatory in California, was the first to perform a systematic study of rich clusters of galaxies , that is clusters with particularly many member galaxies located within a relatively restricted region in the sky. He identified several thousands of such clusters, and he numbered and described them; they are now known to astronomers as `Abell clusters'. More than twenty years earlier, Swiss-American astronomer Fritz Zwicky, using the famous 100-inch Mount Wilson telescope above Los Angeles, concluded that the total mass of a rich cluster of galaxies is probably much larger than the combined mass of the individual galaxies we can observe in it. This phenomenon is now known as the `Missing Dark Matter' , and many attempts have since been made to understand its true nature. Although the existence of this Dark Matter is generally accepted, it has been very difficult to prove its existence in a direct way. Rich clusters have several components: in addition to several hundreds, in some cases even thousands of galaxies (each with many billions of stars and much interstellar matter), they also contain hot gas (with a temperature of several million degrees) which is best visible in X-rays, as well as the invisible dark matter just mentioned. In fact, these clusters are the largest and most massive objects that are known today, and a detailed study of their properties can therefore provide insight into the way in which large-scale structures in the Universe have formed. This unique information is encoded into the distribution of the clusters' total masses, of their physical shapes, and not the least in the way they are distributed in space. The need for a `complete' cluster sample Several of these fundamental questions can be studied by observing a few, or at the most several tens of well-chosen clusters. However, if the goal is to discriminate between the various proposed theories of formation of their spatial distribution and thus the Universe's large-scale structure, it is essential that uniform data is collected for a sample of clusters that is complete in a statistical sense. Only then will it be possible to determine reliably the distribution of cluster masses and shapes, etc. For such comprehensive investigations, `complete' samples of clusters (that is, brighter than a certain magnitude and located within a given area in the sky) can be compiled either by means of catalogues like the one published by Abell and his collaborators and based on the distribution of optically selected galaxies, or from large-scale surveys of X-ray sources. However, in both cases, it is of paramount importance to verify the physical reality of the presumed clusters. Sometimes several galaxies are seen in nearly the same direction and therefore appear to form a cluster, but it later turns out that they are at very different distances and do not form a physical entity. This control must be performed through spectroscopic observations of the galaxies in the candidate clusters. Such observations are crucial, as they not only prove the existence of a cluster, but also determine its distance and provide information about the motion of the individual galaxies within the cluster. The ESO Nearby Abell Cluster Survey (ENACS) Until recently, there existed no large cluster sample with extensive and uniform data on the motions of the individual galaxies. But now, in the context of an ESO Key-Programme known as the ESO Nearby Abell Cluster Survey or ENACS , the team of European astronomers has collected spectroscopic and photometric data for a substantial sample of more than one-hundred, rich and relatively nearby southern clusters from the Abell catalogue [2]. The extensive observations were carried out with the OPTOPUS multi-fibre spectrograph attached to the ESO 3.6-metre telescope at the La Silla Observatory, during 35 nights in the period from September 1989 to October 1993. With this very efficient spectrograph, the spectra of about 50 galaxies could be recorded simultaneously, dramatically reducing the necessary observing time. In total, the programme has yielded reliable radial velocities for more than 5600 galaxies in the direction of about 100 rich clusters. The velocities were derived from a comparison of the observed wavelengths of absorption and emission lines with their rest wavelengths (the galaxy `redshifts'). Assuming a particular value of the `Hubble constant' (the proportionality factor between the velocity of a galaxy and its distance, due to the general expansion of the Universe), the distances of the galaxies can then be derived directly from the measured velocities. The new observations approximately double the amount of data available for rich clusters of galaxies. In combination with earlier data, the ENACS has produced a `complete' sample of 128 rich Abell clusters in a region centered near the south galactic pole (the direction which is perpendicular to the main plane of the Milky Way galaxy), and comprising about one-fifth of the entire sky. The sample extends out to a cluster distance of almost 1,000 million light-years (300 Mpc) The space density of the 128 clusters is constant within the investigated volume, so that this sample is well suited to study, among others, the distribution of cluster masses. For a representative subset of 80 clusters, accurate information on the internal motions of galaxies in the clusters is available. Most nearby and rich Abell clusters are real In their pioneering work, Abell and his collaborators identified the clusters from visual inspection of photographic plates obtained with the Palomar telescopes [3]. Some concern has frequently been expressed that an important fraction of the rich Abell clusters may not be real, but rather the result of chance superpositions in the sky of several smaller groups of galaxies. However, the data of the ENACS now prove conclusively that 90 percent of the rich, nearby Abell clusters are real: i.e. many of the galaxies observed in each of these clusters are indeed at the same distance and they form a physical entity. Nevertheless, about one-quarter of the galaxies in the ENACS do not belong to the main clusters and reside in much smaller galaxy groups or are located in the vast space in between. This can be clearly seen in the distribution of the radial velocities in the direction of each of the clusters, shown in the diagramme (click here to get the [GIF,35k] or [Postscript,544k] version and the caption ) attached to this Press Release. When studying this distribution, it must be kept in mind, that the velocities of the galaxies in the clusters contain two components. The first is due to the general expansion of the Universe and depends only on the distance of the cluster; it is therefore the same for all galaxies in the cluster. The other reflects the individual motions of the galaxies within the cluster. Cluster masses and the mean density of the Universe The motions of the galaxies within a cluster makes it possible to estimate the total mass of the cluster: the greater the mass, the faster the motions must be in order to prevent the cluster from collapsing [4]. Using the data for the full sample of 128 clusters, the distribution of cluster masses has been derived. This distribution has been compared with predictions based on several models for the formation of large-scale structures in the Universe. A very important result of the current work is that the observations do not support scenarios which are based on the assumption that the mean density of the Universe is equal to the `critical' value, i.e. the one which would correspond to a so-called `flat' Universe. The observed cluster masses are systematically smaller than those predicted in such models. Instead, the observed distribution of cluster masses seems to indicate that the mean density of the Universe is probably only a fairly small fraction of the critical value. This points to the Universe being `open' and ever-expanding. Cluster formation may still be going on The galaxies observed during the ENACS programme may be divided into two groups on the basis of their optical spectra, those that show clear emission lines and those that do not. The former are almost all late-type galaxies, that is spiral galaxies with ionized gas in their disks which gives rise to the emission lines. It appears that both the distribution within the cluster, as well as the velocities, of the galaxies with emission lines are significantly different from those of the galaxies without emission lines. It seems that the emission-line galaxies have a tendency to avoid the central regions of their clusters, and their average radial velocities are about 20 percent larger than those of the non-emission galaxies. A plausible interpretation of these results is that a large part of the emission-line galaxies have not yet `mixed' with the other galaxies, and that they are approaching the central regions of their respective clusters for the first time. This may imply that the formation of at least a good fraction of the nearby, rich clusters is still going on. If the mean density of the Universe is indeed much smaller than the critical density, as indicated by the cluster masses determined during this survey, then this is a quite unexpected result. One explanation may be that many clusters have only started to form fairly recently. Notes: [1] The team is headed by Peter Katgert (Leiden Observatory, The Netherlands) and Alain Mazure (Laboratoire d'Astronomie Spatiale, Marseille, France); other members are Andrea Biviano and Roland den Hartog (Leiden Observatory, The Netherlands), Pierre Dubath (Observatoire de Geneve, Switzerland), Eric Escalera (SISSA, Trieste, Italy), Paola Focardi (Bologna University, Italy), Daniel Gerbal (Institut d'Astrophysique, Paris, France), Guilano Giuricin (SISSA, Trieste, Italy), Bernard Jones (Theoretical Astrophysics Centre, Copenhagen, Denmark), Olivier Le Fevre (Meudon Observatory, Paris, France), Mariano Moles and Jaime Perea (Astrophysics Institute of Andalucia, Granada, Spain), and George Rhee (University of Nevada, Las Vegas, U.S.A.). [2] The detailed results will soon be published in two comprehensive articles to appear in the European journal Astronomy & Astrophysics. [3] This Press Release is accompanied by ESO Press Photo 07/96, (click here to get the image [GIF,45k] and caption ) showing one of the rich clusters, as observed with the ESO 1-metre Schmidt telescope. [4] The masses of the planets in the solar system are determined in a similar way from the motions of their moons. The faster the moon moves around the planet at a given distance, the heavier is the planet.

Star clusters in the Magellanic Clouds - I. Parametrization and classification of 1072 clusters in the LMC

NASA Astrophysics Data System (ADS)

Nayak, P. K.; Subramaniam, A.; Choudhury, S.; Indu, G.; Sagar, Ram

2016-12-01

We have introduced a semi-automated quantitative method to estimate the age and reddening of 1072 star clusters in the Large Magellanic Cloud (LMC) using the Optical Gravitational Lensing Experiment III survey data. This study brings out 308 newly parametrized clusters. In a first of its kind, the LMC clusters are classified into groups based on richness/mass as very poor, poor, moderate and rich clusters, similar to the classification scheme of open clusters in the Galaxy. A major cluster formation episode is found to happen at 125 ± 25 Myr in the inner LMC. The bar region of the LMC appears prominently in the age range 60-250 Myr and is found to have a relatively higher concentration of poor and moderate clusters. The eastern and the western ends of the bar are found to form clusters initially, which later propagates to the central part. We demonstrate that there is a significant difference in the distribution of clusters as a function of mass, using a movie based on the propagation (in space and time) of cluster formation in various groups. The importance of including the low-mass clusters in the cluster formation history is demonstrated. The catalogue with parameters, classification, and cleaned and isochrone fitted colour-magnitude diagrams of 1072 clusters, which are available as online material, can be further used to understand the hierarchical formation of clusters in selected regions of the LMC.

26 CFR 1.197-2 - Amortization of goodwill and certain other intangibles.

Code of Federal Regulations, 2011 CFR

2011-04-01

..., process, design, pattern, know-how, format, package design, computer software (as defined in paragraph (c... section 1253(b)(1) and includes any agreement that provides one of the parties to the agreement with the... any program or routine (that is, any sequence of machine-readable code) that is designed to cause a...

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.

Average and local atomic-scale structure in BaZrxTi(1-x)O3 (x = 0. 10, 0.20, 0.40) ceramics by high-energy x-ray diffraction and Raman spectroscopy.

PubMed

Buscaglia, Vincenzo; Tripathi, Saurabh; Petkov, Valeri; Dapiaggi, Monica; Deluca, Marco; Gajović, Andreja; Ren, Yang

2014-02-12

High-resolution x-ray diffraction (XRD), Raman spectroscopy and total scattering XRD coupled to atomic pair distribution function (PDF) analysis studies of the atomic-scale structure of archetypal BaZrxTi(1-x)O3 (x = 0.10, 0.20, 0.40) ceramics are presented over a wide temperature range (100-450 K). For x = 0.1 and 0.2 the results reveal, well above the Curie temperature, the presence of Ti-rich polar clusters which are precursors of a long-range ferroelectric order observed below TC. Polar nanoregions (PNRs) and relaxor behaviour are observed over the whole temperature range for x = 0.4. Irrespective of ceramic composition, the polar clusters are due to locally correlated off-centre displacement of Zr/Ti cations compatible with local rhombohedral symmetry. Formation of Zr-rich clusters is indicated by Raman spectroscopy for all compositions. Considering the isovalent substitution of Ti with Zr in BaZrxTi1-xO3, the mechanism of formation and growth of the PNRs is not due to charge ordering and random fields, but rather to a reduction of the local strain promoted by the large difference in ion size between Zr(4+) and Ti(4+). As a result, non-polar or weakly polar Zr-rich clusters and polar Ti-rich clusters are randomly distributed in a paraelectric lattice and the long-range ferroelectric order is disrupted with increasing Zr concentration.

Recent progress in understanding the eruptions of classical novae

NASA Technical Reports Server (NTRS)

Shara, Michael M.

1988-01-01

Dramatic progress has occurred in the last two decades in understanding the physical processes and events leading up to, and transpiring during the eruption of a classical nova. The mechanism whereby a white dwarf accreting hydrogen-rich matter from a low-mass main-sequence companion produces a nova eruption has been understood since 1970. The mass-transferring binary stellar configuration leads inexorably to thermonuclear runaways detected at distances of megaparsecs. Summarized here are the efforts of many researchers in understanding the physical processes which generate nova eruptions; the effects upon nova eruptions of different binary-system parameters (e.g., chemical composition or mass of the white dwarf, different mass accretion rates); the possible metamorphosis from dwarf to classical novae and back again; and observational diagnostics of novae, including x ray and gamma ray emission, and the characteristics and distributions of novae in globular clusters and in extragalactic systems. While the thermonuclear-runaway model remains the successful cornerstone of nova simulation, it is now clear that a wide variety of physical processes, and three-dimensional hydrodynamic simulations, will be needed to explain the rich spectrum of behavior observed in erupting novae.

The complete mitochondrial genome of Rondotia menciana (Lepidoptera: Bombycidae)

PubMed Central

Kong, Weiqing; Yang, Jinhong

2015-01-01

The mulberry white caterpillar, Rondotia menciana Moore (Lepidoptera: Bombycidae) is a species with closest relationship with Bombyx mori and Bombyx mandarina, and the genetic information of R. menciana is important for understanding the diversity of the Bombycidae. In this study, the mitochondrial genome (mitogenome) of R. menciana was amplified by polymerase chain reaction and sequenced. The mitogenome of R. menciana was determined to be 15,301 bp, including 13 protein-coding genes (PCGs), 2 ribosomal RNA genes, 22 transfer RNA genes, and an AT-rich region. The A+T content (78.87%) was lower than that observed for other Bombycidae insects. All PCGs were initiated by ATN codons and terminated with the canonical stop codons, except for coxII, which was terminated by a single T. All the tRNA genes displayed a typical clover-leaf structure of mitochondrial tRNA. The length of AT-rich region (360 bp) of R. menciana mitogenome is shorter than that of other Bombycidae species. Phylogenetic analysis showed that the R. menciana was clustered on one branch with B. mori and B. mandarina from Bombycidae. PMID:25888706

Research and Project Activities in Astrophysics

NASA Technical Reports Server (NTRS)

Harnden, F. Rick, Jr.; Kaluzienski, Louis J. (Technical Monitor)

2002-01-01

In collaboration with G Micela, S. Sciortino, and others at the Osservatorio Astronomico di Palermo G. S. Valens, we conducted studies of X-ray emission from normal stars, primarily via observations of several open star clusters and star forming regions (viz. the Pleiades, NBC 2516, NBC 2264, and the Orion Nebula Cluster). Our work was based on combined data from several X-ray observatories, Einstein, ROSAT, XMM-Newton and Chandra, as well as ground-based optical and radio data. Preliminary results were presented at several meetings: HEAD/AAS, November, 1997 a 195th AAS Meeting, January 2000 a Three Islands Conference, April 2000 a X-ray Astronomy 2000, September 2000 a 197th AAS Meeting, January 2001 Two Years of Science with Chandra, September 2001

Galaxy Population Properties in the Rich Clusters MS 0839.8+2938, MS 1224.7+2007, and MS 1231.3+1542

NASA Astrophysics Data System (ADS)

Hutchings, J. B.; Edwards, L.

2000-03-01

This paper discusses the galaxy populations of three rich clusters, with redshifts 0.19 (0839+29), 0.24 (1231+15), and 0.32 (1224+20), from the database of the CNOC1 consortium. The data consist of spectra of 52 cluster members for 0839+29, 30 members for 1224+15, and 82 members for 1231+15, and there are comparable numbers of field galaxy spectra. Cluster 0839+29 is compact with no strong radial gradients, and possibly dusty. Cluster 1224+20 is isolated in redshift and has low velocity dispersion around the cD galaxy and low 4000 Å break. Cluster 1231+15 is asymmetric, and we discuss the possibility that it may be a recent merger of two old clusters. We find few galaxies in 0839+29 and 1231+15 with ongoing or recently truncated star formation. Based on observations with the Canada-France-Hawaii-Telescope, which is operated by the National Research Council of Canada, the Centre National de la Recherche Scientifique of France, and the University of Hawaii.

Radio emission in the directions of cD and related galaxies in poor clusters. III. VLA observations at 20 cm

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

Burns, J.O.; White, R.A.; Hough, D.H.

1981-01-01

VLA radio maps and optical identifications of a sample of sources in the directions of 21 Yerkes poor cluster fields are presented. The majority of the cluster radio sources are associated with the dominant D or cD galaxies (approx.70%). Our analysis of dominant galaxies in rich and poor clusters indicates that these giant galaxies are much more often radio emitters (approx.25% of cD's are radio active in the poor clusters), have steeper radio spectra, and have simpler radio morphologies (i.e., double or other linear structure) than other less bright ellipticals. A strong continuum of radio properties in cD galaxies ismore » seen from rich to poor clusters. We speculate that the location of these dominant galaxies at the cluster centers (i.e., at the bottom of a deep, isolated gravitational potential well) is the crucial factor in explaining their multifrequency activity. We briefly discuss galaxy cannibalism and gas infall models as fueling mechanisms for the observed radio and x-ray emission.« less

Radio emission in the directions of cD and related galaxies in poor clusters. III - VLA observations at 20 cm

NASA Technical Reports Server (NTRS)

Burns, J. O.; White, R. A.; Hough, D. H.

1981-01-01

VLA radio maps and optical identifications of a sample of sources in the directions of 21 Yerkes poor cluster fields are presented. The majority of the cluster radio sources are associated with the dominant D or cD galaxies (approximately 70 percent). Our analysis of dominant galaxies in rich and poor clusters indicates that these giant galaxies are much more often radio emitters (approximately 25 percent of cD's are radio active in the poor clusters), have steeper radio spectra, and have simpler radio morphologies (i.e., double or other linear structure) than other less bright ellipticals. A strong continuum of radio properties in cD galaxies is seen from rich to poor clusters. It is speculated that the location of these dominant galaxies at the cluster centers (i.e., at the bottom of a deep, isolated gravitational potential well) is the crucial factor in explaining their multifrequency activity. Galaxy cannibalism and gas infall models as fueling mechanisms for the observed radio and X-ray emission are discussed

[Genetic diversity of wild Cynodon dactylon germplasm detected by SRAP markers].

PubMed

Yi, Yang-Jie; Zhang, Xin-Quan; Huang, Lin-Kai; Ling, Yao; Ma, Xiao; Liu, Wei

2008-01-01

Sequence-related amplified polymorphism (SRAP) molecular markers were used to detect the genetic diversity of 32 wild accessions of Cynodon dactylon collected from Sichuan, Chongqing, Guizhou and Tibet, China. The following results were obtained. (1) Fourteen primer pairs produced 132 polymorphic bands, averaged 9.4 bands per primer pair. The percentage of polymorphic bands in average was 79.8%. The Nei's genetic similarity coefficient of the tested accessions ranged from 0.591 to 0.957, and the average Nei's coefficient was 0.759. These results suggested that there was rich genetic diversity among the wild resources of Cynodon dactylon tested. (2) Thirty two wild accessions were clustered into four groups. Moreover, the accessions from the same origin frequently clustered into one group. The findings implied that a correlation among the wild resources, geographical and ecological environment. (3) Genetic differentiation between and within six eco-geographical groups of C. dactylon was estimated by Shannon's diversity index, which showed that 65.56% genetic variance existed within group, and 34.44% genetic variance was among groups. (4) Based on Nei's unbiased measures of genetic identity, UPGMA cluster analysis measures of six eco-geographical groups of Cynodon dactylon, indicated that there was a correlation between genetic differentiation and eco-geographical habits among the groups.

Genetic differentiation and geographical Relationship of Asian barley landraces using SSRs

PubMed Central

Naeem, Rehan; Dahleen, Lynn; Mirza, Bushra

2011-01-01

Genetic diversity in 403 morphologically distinct landraces of barley (Hordeum vulgare L. subsp. vulgare) originating from seven geographical zones of Asia was studied using simple sequence repeat (SSR) markers from regions of medium to high recombination in the barley genome. The seven polymorphic SSR markers representing each of the chromosomes chosen for the study revealed a high level of allelic diversity among the landraces. Genetic richness was highest in those from India, followed by Pakistan while it was lowest for Uzbekistan and Turkmenistan. Out of the 50 alleles detected, 15 were unique to a geographic region. Genetic diversity was highest for landraces from Pakistan (0.70 ± 0.06) and lowest for those from Uzbekistan (0.18 ± 0.17). Likewise, polymorphic information content (PIC) was highest for Pakistan (0.67 ± 0.06) and lowest for Uzbekistan (0.15 ± 0.17). Diversity among groups was 40% compared to 60% within groups. Principal component analysis clustered the barley landraces into three groups to predict their domestication patterns. In total 51.58% of the variation was explained by the first two principal components of the barley germplasm. Pakistan landraces were clustered separately from those of India, Iran, Nepal and Iraq, whereas those from Turkmenistan and Uzbekistan were clustered together into a separate group. PMID:21734828

Growth rate regulation of Escherichia coli acetyl coenzyme A carboxylase, which catalyzes the first committed step of lipid biosynthesis.

PubMed Central

Li, S J; Cronan, J E

1993-01-01

Acetyl coenzyme A (CoA) carboxylase catalyzes the synthesis of malonyl-CoA, the first intermediate of fatty acid synthesis. The Escherichia coli enzyme is encoded by four subunits located at three different positions on the E. coli chromosome. The accBC genes lie in a small operon at min 72, whereas accA and accD are located at min 4.3 and 50, respectively. We examined the expression of the genes that encode the E. coli acetyl-CoA carboxylase subunits (accA, accBC, and accD) under a variety of growth conditions by quantitative Northern (RNA) blot analysis. We found a direct correlation between the levels of transcription of the acc genes and the rate of cellular growth. Consistent results were also obtained upon nutritional upshift and downshift experiments and upon dilution of stationary-phase cultures into fresh media. We also determined the 5' end of the accA and accD mRNAs by primer extension and did transcriptional fusion analysis of the previously reported accBC promoter. Several interesting features were found in the promoter regions of these genes, including a bent DNA sequence and an open reading frame within the unusually long leader mRNA of the accBC operon, potential stem-loop structures in the accA and accD mRNA leader regions, and a stretch of GC-rich sequences followed by AT-rich sequences common to all three promoters. In addition, both accA and accD are located in complex gene clusters. For example, the accA promoter was localized within the upstream polC gene (which encodes the DNA polymerase III catalytic subunit), suggesting that additional regulatory mechanisms exist. Images PMID:7678242

Seasonal diversity and dynamics of haptophytes in the Skagerrak, Norway, explored by high-throughput sequencing

PubMed Central

Egge, Elianne Sirnæs; Johannessen, Torill Vik; Andersen, Tom; Eikrem, Wenche; Bittner, Lucie; Larsen, Aud; Sandaa, Ruth-Anne; Edvardsen, Bente

2015-01-01

Microalgae in the division Haptophyta play key roles in the marine ecosystem and in global biogeochemical processes. Despite their ecological importance, knowledge on seasonal dynamics, community composition and abundance at the species level is limited due to their small cell size and few morphological features visible under the light microscope. Here, we present unique data on haptophyte seasonal diversity and dynamics from two annual cycles, with the taxonomic resolution and sampling depth obtained with high-throughput sequencing. From outer Oslofjorden, S Norway, nano- and picoplanktonic samples were collected monthly for 2 years, and the haptophytes targeted by amplification of RNA/cDNA with Haptophyta-specific 18S rDNA V4 primers. We obtained 156 operational taxonomic units (OTUs), from c. 400.000 454 pyrosequencing reads, after rigorous bioinformatic filtering and clustering at 99.5%. Most OTUs represented uncultured and/or not yet 18S rDNA-sequenced species. Haptophyte OTU richness and community composition exhibited high temporal variation and significant yearly periodicity. Richness was highest in September–October (autumn) and lowest in April–May (spring). Some taxa were detected all year, such as Chrysochromulina simplex, Emiliania huxleyi and Phaeocystis cordata, whereas most calcifying coccolithophores only appeared from summer to early winter. We also revealed the seasonal dynamics of OTUs representing putative novel classes (clades HAP-3–5) or orders (clades D, E, F). Season, light and temperature accounted for 29% of the variation in OTU composition. Residual variation may be related to biotic factors, such as competition and viral infection. This study provides new, in-depth knowledge on seasonal diversity and dynamics of haptophytes in North Atlantic coastal waters. PMID:25893259

Seasonal diversity and dynamics of haptophytes in the Skagerrak, Norway, explored by high-throughput sequencing.

PubMed

Egge, Elianne Sirnaes; Johannessen, Torill Vik; Andersen, Tom; Eikrem, Wenche; Bittner, Lucie; Larsen, Aud; Sandaa, Ruth-Anne; Edvardsen, Bente

2015-06-01

Microalgae in the division Haptophyta play key roles in the marine ecosystem and in global biogeochemical processes. Despite their ecological importance, knowledge on seasonal dynamics, community composition and abundance at the species level is limited due to their small cell size and few morphological features visible under the light microscope. Here, we present unique data on haptophyte seasonal diversity and dynamics from two annual cycles, with the taxonomic resolution and sampling depth obtained with high-throughput sequencing. From outer Oslofjorden, S Norway, nano- and picoplanktonic samples were collected monthly for 2 years, and the haptophytes targeted by amplification of RNA/cDNA with Haptophyta-specific 18S rDNA V4 primers. We obtained 156 operational taxonomic units (OTUs), from c. 400.000 454 pyrosequencing reads, after rigorous bioinformatic filtering and clustering at 99.5%. Most OTUs represented uncultured and/or not yet 18S rDNA-sequenced species. Haptophyte OTU richness and community composition exhibited high temporal variation and significant yearly periodicity. Richness was highest in September-October (autumn) and lowest in April-May (spring). Some taxa were detected all year, such as Chrysochromulina simplex, Emiliania huxleyi and Phaeocystis cordata, whereas most calcifying coccolithophores only appeared from summer to early winter. We also revealed the seasonal dynamics of OTUs representing putative novel classes (clades HAP-3-5) or orders (clades D, E, F). Season, light and temperature accounted for 29% of the variation in OTU composition. Residual variation may be related to biotic factors, such as competition and viral infection. This study provides new, in-depth knowledge on seasonal diversity and dynamics of haptophytes in North Atlantic coastal waters. © 2015 The Authors. Molecular Ecology Published by John Wiley & Sons Ltd.

A Martian origin for the Mars Trojan asteroids

NASA Astrophysics Data System (ADS)

Polishook, D.; Jacobson, S. A.; Morbidelli, A.; Aharonson, O.

2017-08-01

Seven of the nine known Mars Trojan asteroids belong to an orbital cluster1,2 named after its largest member, (5261) Eureka. Eureka is probably the progenitor of the whole cluster, which formed at least 1 Gyr ago3. It has been suggested3 that the thermal YORP (Yarkovsky-O'Keefe-Radzievskii-Paddack) effect spun up Eureka, resulting in fragments being ejected by the rotational-fission mechanism. Eureka's spectrum exhibits a broad and deep absorption band around 1 μm, indicating an olivine-rich composition4. Here we show evidence that the Trojan Eureka cluster progenitor could have originated as impact debris excavated from the Martian mantle. We present new near-infrared observations of two Trojans ((311999) 2007 NS2 and (385250) 2001 DH47) and find that both exhibit an olivine-rich reflectance spectrum similar to Eureka's. These measurements confirm that the progenitor of the cluster has an achondritic composition4. Olivine-rich reflectance spectra are rare amongst asteroids5 but are seen around the largest basins on Mars6. They are also consistent with some Martian meteorites (for example, Chassigny7) and with the material comprising much of the Martian mantle8,9. Using numerical simulations, we show that the Mars Trojans are more likely to be impact ejecta from Mars than captured olivine-rich asteroids transported from the main belt. This result directly links specific asteroids to debris from the forming planets.

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 novel class of plant-specific zinc-dependent DNA-binding protein that binds to A/T-rich DNA sequences

PubMed Central

Nagano, Yukio; Furuhashi, Hirofumi; Inaba, Takehito; Sasaki, Yukiko

2001-01-01

Complementary DNA encoding a DNA-binding protein, designated PLATZ1 (plant AT-rich sequence- and zinc-binding protein 1), was isolated from peas. The amino acid sequence of the protein is similar to those of other uncharacterized proteins predicted from the genome sequences of higher plants. However, no paralogous sequences have been found outside the plant kingdom. Multiple alignments among these paralogous proteins show that several cysteine and histidine residues are invariant, suggesting that these proteins are a novel class of zinc-dependent DNA-binding proteins with two distantly located regions, C-x2-H-x11-C-x2-C-x(4–5)-C-x2-C-x(3–7)-H-x2-H and C-x2-C-x(10–11)-C-x3-C. In an electrophoretic mobility shift assay, the zinc chelator 1,10-o-phenanthroline inhibited DNA binding, and two distant zinc-binding regions were required for DNA binding. A protein blot with 65ZnCl2 showed that both regions are required for zinc-binding activity. The PLATZ1 protein non-specifically binds to A/T-rich sequences, including the upstream region of the pea GTPase pra2 and plastocyanin petE genes. Expression of the PLATZ1 repressed those of the reporter constructs containing the coding sequence of luciferase gene driven by the cauliflower mosaic virus (CaMV) 35S90 promoter fused to the tandem repeat of the A/T-rich sequences. These results indicate that PLATZ1 is a novel class of plant-specific zinc-dependent DNA-binding protein responsible for A/T-rich sequence-mediated transcriptional repression. PMID:11600698

The impact of radiation feedback on the assembly of star clusters in a galactic context

NASA Astrophysics Data System (ADS)

Guillard, Nicolas; Emsellem, Eric; Renaud, Florent

2018-07-01

Massive star clusters are observed in galaxies spanning a broad range of luminosities and types, and are assumed to form in dense gas-rich environments. Using a parsec-resolution hydrodynamical simulation of an isolated gas-rich low-mass galaxy, we discuss here the non-linear effects of stellar feedback on the properties of star clusters with a focus on the progenitors of nuclear clusters. Our simulation shows two categories of star clusters: those for which feedback expels gas leftovers associated with their formation sites, and those, in a denser environment, around which feedback fails to totally clear the gas. We confirm that radiation feedback (photoionization and radiative pressure) plays a more important role than Type II supernovae in destroying dense gas structures, and in altering or quenching the subsequent cluster formation. Radiation feedback also disturbs the cluster mass growth, by increasing the internal energy of the gas component to the point at which radiation pressure overcomes the cluster gravity. We discuss how these effects may depend on the local properties of the interstellar medium, and also on the details of the subgrid recipes, which can affect the available cluster gas reservoirs, the evolution of potential nuclear cluster progenitors, and the overall galaxy morphology.

RNA sequencing uncovers antisense RNAs and novel small RNAs in Streptococcus pyogenes.

PubMed

Le Rhun, Anaïs; Beer, Yan Yan; Reimegård, Johan; Chylinski, Krzysztof; Charpentier, Emmanuelle

2016-01-01

Streptococcus pyogenes is a human pathogen responsible for a wide spectrum of diseases ranging from mild to life-threatening infections. During the infectious process, the temporal and spatial expression of pathogenicity factors is tightly controlled by a complex network of protein and RNA regulators acting in response to various environmental signals. Here, we focus on the class of small RNA regulators (sRNAs) and present the first complete analysis of sRNA sequencing data in S. pyogenes. In the SF370 clinical isolate (M1 serotype), we identified 197 and 428 putative regulatory RNAs by visual inspection and bioinformatics screening of the sequencing data, respectively. Only 35 from the 197 candidates identified by visual screening were assigned a predicted function (T-boxes, ribosomal protein leaders, characterized riboswitches or sRNAs), indicating how little is known about sRNA regulation in S. pyogenes. By comparing our list of predicted sRNAs with previous S. pyogenes sRNA screens using bioinformatics or microarrays, 92 novel sRNAs were revealed, including antisense RNAs that are for the first time shown to be expressed in this pathogen. We experimentally validated the expression of 30 novel sRNAs and antisense RNAs. We show that the expression profile of 9 sRNAs including 2 predicted regulatory elements is affected by the endoribonucleases RNase III and/or RNase Y, highlighting the critical role of these enzymes in sRNA regulation.

Shorebird abundance and distribution on the coastal plain of the Arctic National Wildlife Refuge

USGS Publications Warehouse

Brown, S.; Bart, J.; Lanctot, Richard B.; Johnson, J.A.; Kendall, S.; Payer, D.; Johnson, J.

2007-01-01

The coastal plain of the Arctic National Wildlife Refuge hosts seven species of migratory shorebirds listed as highly imperiled or high priority by the U.S. Shorebird Conservation Plan and five species listed as Birds of Conservation Concern by the U.S. Fish and Wildlife Service. During the first comprehensive shorebird survey of the 674 000 ha "1002 Area" on the coastal plain, we recorded 14 species of breeding shorebirds at 197 rapidly surveyed plots during June 2002 and 2004. We also estimated detection ratios with a double counting technique, using data collected at 37 intensively studied plots located on the North Slope of Alaska and northern Canada. We stratified the study area by major habitat types, including wetlands, moist areas, uplands, and riparian areas, using previously classified Landsat imagery. We developed population estimates with confidence limits by species, and estimated the total number of shorebirds in the study area to be 230 000 (95% CI: 104 000-363 000), which exceeds the biological criterion for classification as both a Western Hemisphere Shorebird Reserve Network Site of International Importance (100 000 birds) and a Ramsar Wetland of International Importance (20 000 birds), even when conservatively estimated. Species richness and the density of many species were highest in wetland or riparian habitats, which are clustered along the coast. ?? The Cooper Ornithological Society 2007.

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

Not-so-simple stellar populations in the intermediate-age Large Magellanic Cloud star clusters NGC 1831 and NGC 1868

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

Li, Chengyuan; De Grijs, Richard; Deng, Licai, E-mail: joshuali@pku.edu.cn, E-mail: grijs@pku.edu.cn

2014-04-01

Using a combination of high-resolution Hubble Space Telescope/Wide-Field and Planetary Camera-2 observations, we explore the physical properties of the stellar populations in two intermediate-age star clusters, NGC 1831 and NGC 1868, in the Large Magellanic Cloud based on their color-magnitude diagrams. We show that both clusters exhibit extended main-sequence turn offs. To explain the observations, we consider variations in helium abundance, binarity, age dispersions, and the fast rotation of the clusters' member stars. The observed narrow main sequence excludes significant variations in helium abundance in both clusters. We first establish the clusters' main-sequence binary fractions using the bulk of themore » clusters' main-sequence stellar populations ≳ 1 mag below their turn-offs. The extent of the turn-off regions in color-magnitude space, corrected for the effects of binarity, implies that age spreads of order 300 Myr may be inferred for both clusters if the stellar distributions in color-magnitude space were entirely due to the presence of multiple populations characterized by an age range. Invoking rapid rotation of the population of cluster members characterized by a single age also allows us to match the observed data in detail. However, when taking into account the extent of the red clump in color-magnitude space, we encounter an apparent conflict for NGC 1831 between the age dispersion derived from that based on the extent of the main-sequence turn off and that implied by the compact red clump. We therefore conclude that, for this cluster, variations in stellar rotation rate are preferred over an age dispersion. For NGC 1868, both models perform equally well.« less

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

Van den Bergh, Sidney

It is widely believed that lenticular (S0) galaxies were initially spirals from which the gas has been removed by interactions with hot cluster gas, or by ram pressure stripping of cool gas from spirals that are orbiting within rich clusters of galaxies. However, problems with this interpretation are that (1) some lenticulars, such as NGC 3115, are isolated field galaxies rather than cluster members. (2) The distribution of flattening values of S0 galaxies in clusters, in groups, and in the field are statistically indistinguishable. This is surprising because one might have expected most of the progenitors of field S0 galaxiesmore » to have been flattened late-type galaxies, whereas lenticulars in clusters are thought to have mostly been derived from bulge-dominated early-type galaxies. (3) It should be hardest for ram pressure to strip massive luminous galaxies with deep potential wells. However, no statistically significant differences are seen between the luminosity distributions of early-type Shapley-Ames galaxies in clusters, groups, and in the field. (4) Finally both ram pressure stripping and evaporation by hot intracluster gas would be most efficient in rich clusters. However, the small number of available data in the Shapley-Ames sample appears to show no statistically significant differences between the relative frequencies of dust-poor S0{sub 1} and dust-rich S0{sub 3} galaxies in clusters, groups, and in the field. It is tentatively concluded that ram pressure stripping and heating by intracluster gas, may not be the only evolutionary channels that lead to the formation of lenticular galaxies. It is speculated that gas starvation, or gas ejection by active nuclei, may have played a major role in the formation of a significant fraction of all S0 galaxies.« less

Galaxy Cluster Mass Reconstruction Project - II. Quantifying scatter and bias using contrasting mock catalogues

DOE PAGES

Old, L.; Wojtak, R.; Mamon, G. A.; ...

2015-03-26

Our paper is the second in a series in which we perform an extensive comparison of various galaxy-based cluster mass estimation techniques that utilize the positions, velocities and colours of galaxies. Our aim is to quantify the scatter, systematic bias and completeness of cluster masses derived from a diverse set of 25 galaxy-based methods using two contrasting mock galaxy catalogues based on a sophisticated halo occupation model and a semi-analytic model. Analysing 968 clusters, we find a wide range in the rms errors in log M200c delivered by the different methods (0.18–1.08 dex, i.e. a factor of ~1.5–12), with abundance-matchingmore » and richness methods providing the best results, irrespective of the input model assumptions. In addition, certain methods produce a significant number of catastrophic cases where the mass is under- or overestimated by a factor greater than 10. Given the steeply falling high-mass end of the cluster mass function, we recommend that richness- or abundance-matching-based methods are used in conjunction with these methods as a sanity check for studies selecting high-mass clusters. We also see a stronger correlation of the recovered to input number of galaxies for both catalogues in comparison with the group/cluster mass, however, this does not guarantee that the correct member galaxies are being selected. Finally, we did not observe significantly higher scatter for either mock galaxy catalogues. These results have implications for cosmological analyses that utilize the masses, richnesses, or abundances of clusters, which have different uncertainties when different methods are used.« less

Microbial colonization of basaltic glasses in hydrothermal organic-rich sediments at Guaymas Basin

PubMed Central

Callac, Nolwenn; Rommevaux-Jestin, Céline; Rouxel, Olivier; Lesongeur, Françoise; Liorzou, Céline; Bollinger, Claire; Ferrant, Antony; Godfroy, Anne

2013-01-01

Oceanic basalts host diverse microbial communities with various metabolisms involved in C, N, S, and Fe biogeochemical cycles which may contribute to mineral and glass alteration processes at, and below the seafloor. In order to study the microbial colonization on basaltic glasses and their potential biotic/abiotic weathering products, two colonization modules called AISICS (“Autonomous in situ Instrumented Colonization System”) were deployed in hydrothermal deep-sea sediments at the Guaymas Basin for 8 days and 22 days. Each AISICS module contained 18 colonizers (including sterile controls) filled with basaltic glasses of contrasting composition. Chemical analyses of ambient fluids sampled through the colonizers showed a greater contribution of hydrothermal fluids (maximum temperature 57.6°C) for the module deployed during the longer time period. For each colonizer, the phylogenetic diversity and metabolic function of bacterial and archaeal communities were explored using a molecular approach by cloning and sequencing. Results showed large microbial diversity in all colonizers. The bacterial distribution was primarily linked to the deployment duration, as well as the depth for the short deployment time module. Some 16s rRNA sequences formed a new cluster of Epsilonproteobacteria. Within the Archaea the retrieved diversity could not be linked to either duration, depth or substrata. However, mcrA gene sequences belonging to the ANME-1 mcrA-guaymas cluster were found sometimes associated with their putative sulfate-reducers syntrophs depending on the colonizers. Although no specific glass alteration texture was identified, nano-crystals of barite and pyrite were observed in close association with organic matter, suggesting a possible biological mediation. This study gives new insights into the colonization steps of volcanic rock substrates and the capability of microbial communities to exploit new environmental conditions. PMID:23986754

GenomeVista

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

Poliakov, Alexander; Couronne, Olivier

2002-11-04

Aligning large vertebrate genomes that are structurally complex poses a variety of problems not encountered on smaller scales. Such genomes are rich in repetitive elements and contain multiple segmental duplications, which increases the difficulty of identifying true orthologous SNA segments in alignments. The sizes of the sequences make many alignment algorithms designed for comparing single proteins extremely inefficient when processing large genomic intervals. We integrated both local and global alignment tools and developed a suite of programs for automatically aligning large vertebrate genomes and identifying conserved non-coding regions in the alignments. Our method uses the BLAT local alignment program tomore » find anchors on the base genome to identify regions of possible homology for a query sequence. These regions are postprocessed to find the best candidates which are then globally aligned using the AVID global alignment program. In the last step conserved non-coding segments are identified using VISTA. Our methods are fast and the resulting alignments exhibit a high degree of sensitivity, covering more than 90% of known coding exons in the human genome. The GenomeVISTA software is a suite of Perl programs that is built on a MySQL database platform. The scheduler gets control data from the database, builds a queve of jobs, and dispatches them to a PC cluster for execution. The main program, running on each node of the cluster, processes individual sequences. A Perl library acts as an interface between the database and the above programs. The use of a separate library allows the programs to function independently of the database schema. The library also improves on the standard Perl MySQL database interfere package by providing auto-reconnect functionality and improved error handling.« less

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.

Characterization of intronic uridine-rich sequence elements acting as possible targets for nuclear proteins during pre-mRNA splicing in Nicotiana plumbaginifolia.

PubMed

Gniadkowski, M; Hemmings-Mieszczak, M; Klahre, U; Liu, H X; Filipowicz, W

1996-02-15

Introns of nuclear pre-mRNAs in dicotyledonous plants, unlike introns in vertebrates or yeast, are distinctly rich in A+U nucleotides and this feature is essential for their processing. In order to define more precisely sequence elements important for intron recognition in plants, we investigated the effects of short insertions, either U-rich or A-rich, on splicing of synthetic introns in transfected protoplast of Nicotiana plumbaginifolia. It was found that insertions of U-rich (sequence UUUUUAU) but not A-rich (AUAAAAA) segments can activate splicing of a GC-rich synthetic infron, and that U-rich segments, or multimers thereof, can function irrespective of the site of insertion within the intron. Insertions of multiple U-rich segments, either at the same or different locations, generally had an additive, stimulatory effect on splicing. Mutational analysis showed that replacement of one or two U residues in the UUUUUAU sequence with A or C residues had only a small effect on splicing, but replacement with G residues was strongly inhibitory. Proteins that interact with fragments of natural and synthetic pre-mRNAs in vitro were identified in nuclear extracts of N.plumbaginifolia by UV cross- linking. The profile of cross-linked plant proteins was considerably less complex than that obtained with a HeLa cell nuclear extract. Two major cross-linkable plant proteins had apparent molecular mass of 50 and 54 kDa and showed affinity for oligouridilates present in synGC introns or for poly(U).

Characterization of intronic uridine-rich sequence elements acting as possible targets for nuclear proteins during pre-mRNA splicing in Nicotiana plumbaginifolia.

PubMed Central

Gniadkowski, M; Hemmings-Mieszczak, M; Klahre, U; Liu, H X; Filipowicz, W

1996-01-01

Introns of nuclear pre-mRNAs in dicotyledonous plants, unlike introns in vertebrates or yeast, are distinctly rich in A+U nucleotides and this feature is essential for their processing. In order to define more precisely sequence elements important for intron recognition in plants, we investigated the effects of short insertions, either U-rich or A-rich, on splicing of synthetic introns in transfected protoplast of Nicotiana plumbaginifolia. It was found that insertions of U-rich (sequence UUUUUAU) but not A-rich (AUAAAAA) segments can activate splicing of a GC-rich synthetic infron, and that U-rich segments, or multimers thereof, can function irrespective of the site of insertion within the intron. Insertions of multiple U-rich segments, either at the same or different locations, generally had an additive, stimulatory effect on splicing. Mutational analysis showed that replacement of one or two U residues in the UUUUUAU sequence with A or C residues had only a small effect on splicing, but replacement with G residues was strongly inhibitory. Proteins that interact with fragments of natural and synthetic pre-mRNAs in vitro were identified in nuclear extracts of N.plumbaginifolia by UV cross- linking. The profile of cross-linked plant proteins was considerably less complex than that obtained with a HeLa cell nuclear extract. Two major cross-linkable plant proteins had apparent molecular mass of 50 and 54 kDa and showed affinity for oligouridilates present in synGC introns or for poly(U). PMID:8604302

Nucleotide sequence of the gene for the Mr 32,000 thylakoid membrane protein from Spinacia oleracea and Nicotiana debneyi predicts a totally conserved primary translation product of Mr 38,950

PubMed Central

Zurawski, Gerard; Bohnert, Hans J.; Whitfeld, Paul R.; Bottomley, Warwick

1982-01-01

The gene for the so-called Mr 32,000 rapidly labeled photosystem II thylakoid membrane protein (here designated psbA) of spinach (Spinacia oleracea) chloroplasts is located on the chloroplast DNA in the large single-copy region immediately adjacent to one of the inverted repeat sequences. In this paper we show that the size of the mRNA for this protein is ≈ 1.25 kilobases and that the direction of transcription is towards the inverted repeat unit. The nucleotide sequence of the gene and its flanking regions is presented. The only large open reading frame in the sequence codes for a protein of Mr 38,950. The nucleotide sequence of psbA from Nicotiana debneyi also has been determined, and comparison of the sequences from the two species shows them to be highly conserved (>95% homology) throughout the entire reading frame. Conservation of the amino acid sequence is absolute, there being no changes in a total of 353 residues. This leads us to conclude that the primary translation product of psbA must be a protein of Mr 38,950. The protein is characterized by the complete absence of lysine residues and is relatively rich in hydrophobic amino acids, which tend to be clustered. Transcription of spinach psbA starts about 86 base pairs before the first ATG codon. Immediately upstream from this point there is a sequence typical of that found in E. coli promoters. An almost identical sequence occurs in the equivalent region of N. debneyi DNA. Images PMID:16593262

Sensitive detection of mercury and copper ions by fluorescent DNA/Ag nanoclusters in guanine-rich DNA hybridization

NASA Astrophysics Data System (ADS)

Peng, Jun; Ling, Jian; Zhang, Xiu-Qing; Bai, Hui-Ping; Zheng, Liyan; Cao, Qiu-E.; Ding, Zhong-Tao

2015-02-01

In this work, we designed a new fluorescent oligonucleotides-stabilized silver nanoclusters (DNA/AgNCs) probe for sensitive detection of mercury and copper ions. This probe contains two tailored DNA sequence. One is a signal probe contains a cytosine-rich sequence template for AgNCs synthesis and link sequence at both ends. The other is a guanine-rich sequence for signal enhancement and link sequence complementary to the link sequence of the signal probe. After hybridization, the fluorescence of hybridized double-strand DNA/AgNCs is 200-fold enhanced based on the fluorescence enhancement effect of DNA/AgNCs in proximity of guanine-rich DNA sequence. The double-strand DNA/AgNCs probe is brighter and stable than that of single-strand DNA/AgNCs, and more importantly, can be used as novel fluorescent probes for detecting mercury and copper ions. Mercury and copper ions in the range of 6.0-160.0 and 6-240 nM, can be linearly detected with the detection limits of 2.1 and 3.4 nM, respectively. Our results indicated that the analytical parameters of the method for mercury and copper ions detection are much better than which using a single-strand DNA/AgNCs.

Superplasticity - A Fundamental Investigation on Deformation Mechanism and Cavitation Phenomena.

DTIC Science & Technology

1988-02-15

NI-MODIFIED SUPERPLASTIC Ti- 6Al - 4V ALLOY, B. Hidalgo-Prada and A.K. Mukherjee, Proc. of Intnl. Conf. of Strength of Metals and AlloyS-7, Montreal...features, e.g., initial porosity (15 to 500 pm diam.), stringers (of Fe-rich particles, 5-30 pm diam.), and small (0.3-3 pm) copper- rich particles...500% or greater, porosity between grains was observed. Some grains as well as grain clusters are visible in Fig. 6. The grain clusters are believed to

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

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.

Magnetic analysis of a melt-spun Fe-dilute Cu60Ag35Fe5 alloy

NASA Astrophysics Data System (ADS)

Kondo, Shin-ichiro; Kaneko, Kazuhiro; Morimura, Takao; Nakashima, Hiromichi; Kobayashi, Shin-Taro; Michioka, Chishiro; Yoshimura, Kazuyoshi

2015-04-01

The magnetic properties of a melt-spun Fe-dilute Cu60Ag35Fe5 alloy are examined by X-ray diffraction, magnetic measurements, and transmission electron microscopy (TEM). The X-ray diffraction patterns show that the as-spun and annealed (773 K×36 ks) samples contain Cu and Ag phases and no Fe phases; thus, most Fe atoms are dispersed as clusters. Magnetic measurements indicate that the as-spun and annealed samples exhibit superparamagnetic behavior at 300 K, whereas ferromagnetic and superparamagnetic behaviors coexist at 4.2 K. The magnetic moments of small clusters at 300 K are determined by the nonlinear least squares method as 5148 and 4671 μB for as-spun and annealed samples, respectively, whereas those at 300 K are experimentally determined as 3500 and 3200 μB. This decrease in magnetic moments may imply the formation of anti-ferromagnetic coupling by annealing. TEM observation of the melt-spun sample suggests that there are three regions with different compositions: Cu-rich, Ag-rich, and Fe-rich with no precipitation in the matrix. In addition, these regions have obscure interfaces. The magnetic clusters are attributed to the Fe-rich regions.

Transcriptome-Wide Changes in Chlamydomonas reinhardtii Gene Expression Regulated by Carbon Dioxide and the CO2-Concentrating Mechanism Regulator CIA5/CCM1[W][OA

PubMed Central

Fang, Wei; Si, Yaqing; Douglass, Stephen; Casero, David; Merchant, Sabeeha S.; Pellegrini, Matteo; Ladunga, Istvan; Liu, Peng; Spalding, Martin H.

2012-01-01

We used RNA sequencing to query the Chlamydomonas reinhardtii transcriptome for regulation by CO2 and by the transcription regulator CIA5 (CCM1). Both CO2 and CIA5 are known to play roles in acclimation to low CO2 and in induction of an essential CO2-concentrating mechanism (CCM), but less is known about their interaction and impact on the whole transcriptome. Our comparison of the transcriptome of a wild type versus a cia5 mutant strain under three different CO2 conditions, high CO2 (5%), low CO2 (0.03 to 0.05%), and very low CO2 (<0.02%), provided an entry into global changes in the gene expression patterns occurring in response to the interaction between CO2 and CIA5. We observed a massive impact of CIA5 and CO2 on the transcriptome, affecting almost 25% of all Chlamydomonas genes, and we discovered an array of gene clusters with distinctive expression patterns that provide insight into the regulatory interaction between CIA5 and CO2. Several individual clusters respond primarily to either CIA5 or CO2, providing access to genes regulated by one factor but decoupled from the other. Three distinct clusters clearly associated with CCM-related genes may represent a rich source of candidates for new CCM components, including a small cluster of genes encoding putative inorganic carbon transporters. PMID:22634760

Transcriptional Regulation, Metal Binding Properties and Structure of Pden1597, an Unusual Zinc Transport Protein from Paracoccus denitrificans*

PubMed Central

Handali, Melody; Neupane, Durga P.; Roychowdhury, Hridindu; Yukl, Erik T.

2015-01-01

ATP-binding cassette (ABC) transporters of the cluster 9 family are ubiquitous among bacteria and essential for acquiring Zn2+ and Mn2+ from the environment or, in the case of pathogens, from the host. These rely on a substrate-binding protein (SBP) to coordinate the relevant metal with high affinity and specificity and subsequently release it to a membrane permease for translocation into the cytoplasm. Although a number of cluster 9 SBP structures have been determined, the structural attributes conferring Zn2+ or Mn2+ specificity remain ambiguous. Here we describe the gene expression profile, in vitro metal binding properties, and crystal structure of a new cluster 9 SBP from Paracoccus denitrificans we have called AztC. Although all of our results strongly indicate Zn2+ over Mn2+ specificity, the Zn2+ ion is coordinated by a conserved Asp residue only observed to date as a metal ligand in Mn2+-specific SBPs. The unusual sequence properties of this protein are shared among close homologues, including members from the human pathogens Klebsiella pneumonia and Enterobacter aerogenes, and would seem to suggest a subclass of Zn2+-specific transporters among the cluster 9 family. In any case, the unusual coordination environment of AztC expands the already considerable range of those available to Zn2+-specific SBPs and highlights the presence of a His-rich loop as the most reliable indicator of Zn2+ specificity. PMID:25787075

Transcriptional regulation, metal binding properties and structure of Pden1597, an unusual zinc transport protein from Paracoccus denitrificans

DOE PAGES

Handali, Melody; Neupane, Durga P.; Roychowdhury, Hridindu; ...

2015-03-18

Here, ATP-binding cassette (ABC) transporters of the cluster 9 family are ubiquitous among bacteria and essential for acquiring Zn 2+ and Mn 2+ from the environment or, in the case of pathogens, from the host. These rely on a substrate-binding protein (SBP) to coordinate the relevant metal with high affinity and specificity and subsequently release it to a membrane permease for translocation into the cytoplasm. Although a number of cluster 9 SBP structures have been determined, the structural attributes conferring Zn 2+ or Mn 2+ specificity remain ambiguous. Here we describe the gene expression profile, in vitro metal binding properties,more » and crystal structure of a new cluster 9 SBP from Paracoccus denitrificans we have called AztC. Although all of our results strongly indicate Zn 2+ over Mn 2+ specificity, the Zn 2+ ion is coordinated by a conserved Asp residue only observed to date as a metal ligand in Mn 2+-specific SBPs. The unusual sequence properties of this protein are shared among close homologues, including members from the human pathogens Klebsiella pneumonia and Enterobacter aerogenes, and would seem to suggest a subclass of Zn 2+-specific transporters among the cluster 9 family. In any case, the unusual coordination environment of AztC expands the already considerable range of those available to Zn 2+-specific SBPs and highlights the presence of a His-rich loop as the most reliable indicator of Zn 2+ specificity.« less

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.

Human CST Facilitates Genome-wide RAD51 Recruitment to GC-Rich Repetitive Sequences in Response to Replication Stress.

PubMed

Chastain, Megan; Zhou, Qing; Shiva, Olga; Fadri-Moskwik, Maria; Whitmore, Leanne; Jia, Pingping; Dai, Xueyu; Huang, Chenhui; Ye, Ping; Chai, Weihang

2016-08-02

The telomeric CTC1/STN1/TEN1 (CST) complex has been implicated in promoting replication recovery under replication stress at genomic regions, yet its precise role is unclear. Here, we report that STN1 is enriched at GC-rich repetitive sequences genome-wide in response to hydroxyurea (HU)-induced replication stress. STN1 deficiency exacerbates the fragility of these sequences under replication stress, resulting in chromosome fragmentation. We find that upon fork stalling, CST proteins form distinct nuclear foci that colocalize with RAD51. Furthermore, replication stress induces physical association of CST with RAD51 in an ATR-dependent manner. Strikingly, CST deficiency diminishes HU-induced RAD51 foci formation and reduces RAD51 recruitment to telomeres and non-telomeric GC-rich fragile sequences. Collectively, our findings establish that CST promotes RAD51 recruitment to GC-rich repetitive sequences in response to replication stress to facilitate replication restart, thereby providing insights into the mechanism underlying genome stability maintenance. Copyright © 2016 The Author(s). Published by Elsevier Inc. All rights reserved.

Evolution of the cluster optical galaxy luminosity function in the CFHTLS: breaking the degeneracy between mass and redshift

NASA Astrophysics Data System (ADS)

Sarron, F.; Martinet, N.; Durret, F.; Adami, C.

2018-06-01

Obtaining large samples of galaxy clusters is important for cosmology: cluster counts as a function of redshift and mass can constrain the parameters of our Universe. They are also useful in order to understand the formation and evolution of clusters. We develop an improved version of the Adami & MAzure Cluster FInder (AMACFI), now the Adami, MAzure & Sarron Cluster FInder (AMASCFI), and apply it to the 154 deg2 of the Canada-France-Hawaii Telescope Legacy Survey (CFHTLS) to obtain a large catalogue of 1371 cluster candidates with mass M200 > 1014 M⊙ and redshift z ≤ 0.7. We derive the selection function of the algorithm from the Millennium simulation, and cluster masses from a richness-mass scaling relation built from matching our candidates with X-ray detections. We study the evolution of these clusters with mass and redshift by computing the i'-band galaxy luminosity functions (GLFs) for the early-type (ETGs) and late-type galaxies (LTGs). This sample is 90% pure and 70% complete, and therefore our results are representative of a large fraction of the cluster population in these redshift and mass ranges. We find an increase in both the ETG and LTG faint populations with decreasing redshift (with Schechter slopes αETG = -0.65 ± 0.03 and αLTG = -0.95 ± 0.04 at z = 0.6, and αETG = -0.79 ± 0.02 and αLTG = -1.26 ± 0.03 at z = 0.2) and also a decrease in the LTG (but not the ETG) bright end. Our large sample allows us to break the degeneracy between mass and redshift, finding that the redshift evolution is more pronounced in high-mass clusters, but that there is no significant dependence of the faint end on mass for a given redshift. These results show that the cluster red sequence is mainly formed at redshift z > 0.7, and that faint ETGs continue to enrich the red sequence through quenching of brighter LTGs at z ≤ 0.7. The efficiency of this quenching is higher in large-mass clusters, while the accretion rate of faint LTGs is lower as the more massive clusters have already emptied most of their environment at higher redshifts. Based on observations obtained with MegaPrime/MegaCam, a joint project of CFHT and CEA/IRFU, 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. This work is based in part on data products produced at Terapix available at the Canadian Astronomy Data Centre as part of the Canada-France-Hawaii Telescope Legacy Survey, a collaborative project of NRC and CNRS.The candidate cluster catalog is only available at the CDS via anonymous ftp to http://cdsarc.u-strasbg.fr (ftp://130.79.128.5) or via http://cdsarc.u-strasbg.fr/viz-bin/qcat?J/A+A/613/A67

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.

Antimicrobial Peptides from Plants

PubMed Central

Tam, James P.; Wang, Shujing; Wong, Ka H.; Tan, Wei Liang

2015-01-01

Plant antimicrobial peptides (AMPs) have evolved differently from AMPs from other life forms. They are generally rich in cysteine residues which form multiple disulfides. In turn, the disulfides cross-braced plant AMPs as cystine-rich peptides to confer them with extraordinary high chemical, thermal and proteolytic stability. The cystine-rich or commonly known as cysteine-rich peptides (CRPs) of plant AMPs are classified into families based on their sequence similarity, cysteine motifs that determine their distinctive disulfide bond patterns and tertiary structure fold. Cystine-rich plant AMP families include thionins, defensins, hevein-like peptides, knottin-type peptides (linear and cyclic), lipid transfer proteins, α-hairpinin and snakins family. In addition, there are AMPs which are rich in other amino acids. The ability of plant AMPs to organize into specific families with conserved structural folds that enable sequence variation of non-Cys residues encased in the same scaffold within a particular family to play multiple functions. Furthermore, the ability of plant AMPs to tolerate hypervariable sequences using a conserved scaffold provides diversity to recognize different targets by varying the sequence of the non-cysteine residues. These properties bode well for developing plant AMPs as potential therapeutics and for protection of crops through transgenic methods. This review provides an overview of the major families of plant AMPs, including their structures, functions, and putative mechanisms. PMID:26580629

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.

The Swift AGN and Cluster Survey

NASA Astrophysics Data System (ADS)

Danae Griffin, Rhiannon; Dai, Xinyu; Kochanek, Christopher S.; Bregman, Joel N.; Nugent, Jenna

2016-01-01

The Swift active galactic nucleus (AGN) and Cluster Survey (SACS) uses 125 deg^2 of Swift X-ray Telescope serendipitous fields with variable depths surrounding X-ray bursts to provide a medium depth (4 × 10^-15 erg cm^-2 s^-1) and area survey filling the gap between deep, narrow Chandra/XMM-Newton surveys and wide, shallow ROSAT surveys. Here, we present the first two papers in a series of publications for SACS. In the first paper, we introduce our method and catalog of 22,563 point sources and 442 extended sources. We examine the number counts of the AGN and galaxy cluster populations. SACS provides excellent constraints on the AGN number counts at the bright end with negligible uncertainties due to cosmic variance, and these constraints are consistent with previous measurements. The depth and areal coverage of SACS is well suited for galaxy cluster surveys outside the local universe, reaching z ˜ 1 for massive clusters. In the second paper, we use Sloan Digital Sky Survey (SDSS) DR8 data to study the 203 extended SACS sources that are located within the SDSS footprint. We search for galaxy over-densities in 3-D space using SDSS galaxies and their photometric redshifts near the Swift galaxy cluster candidates. We find 103 Swift clusters with a > 3σ over-density. The remaining targets are potentially located at higher redshifts and require deeper optical follow-up observations for confirmations as galaxy clusters. We present a series of cluster properties including the redshift, BCG magnitude, BCG-to-X-ray center offset, optical richness, X-ray luminosity and red sequences. We compare the observed redshift distribution of the sample with a theoretical model, and find that our sample is complete for z ≤ 0.3 and 80% complete for z ≤ 0.4, consistent with the survey depth of SDSS. We also match our SDSS confirmed Swift clusters to existing cluster catalogs, and find 42, 2 and 1 matches in optical, X-ray and SZ catalogs, respectively, so the majority of these clusters are new detections. These analysis results suggest that our Swift cluster selection algorithm presented in our first paper has yielded a statistically well-defined cluster sample for further studying cluster evolution and cosmology.

The X-ray structure of a galaxy cluster at z = 0.54 - Implications for cluster evolution and cosmology

NASA Technical Reports Server (NTRS)

White, S. D. M.; Silk, J.; Henry, J. P.

1981-01-01

High-resolution X-ray observations of the rich cluster 0016+16 at a redshift of 0.541 are presented. The emitting gas in this cluster is hot and extremely luminous, and its structure resembles that seen in the brightest nearby cluster sources. In most of its properties, 0016+16 resembles a richer version of the Coma cluster, and it offers little support to the hypothesis that clusters at z greater than 0.5 differ fundamentally from nearer objects.

Natural-product-derived fragments for fragment-based ligand discovery

NASA Astrophysics Data System (ADS)

Over, Björn; Wetzel, Stefan; Grütter, Christian; Nakai, Yasushi; Renner, Steffen; Rauh, Daniel; Waldmann, Herbert

2013-01-01

Fragment-based ligand and drug discovery predominantly employs sp2-rich compounds covering well-explored regions of chemical space. Despite the ease with which such fragments can be coupled, this focus on flat compounds is widely cited as contributing to the attrition rate of the drug discovery process. In contrast, biologically validated natural products are rich in stereogenic centres and populate areas of chemical space not occupied by average synthetic molecules. Here, we have analysed more than 180,000 natural product structures to arrive at 2,000 clusters of natural-product-derived fragments with high structural diversity, which resemble natural scaffolds and are rich in sp3-configured centres. The structures of the cluster centres differ from previously explored fragment libraries, but for nearly half of the clusters representative members are commercially available. We validate their usefulness for the discovery of novel ligand and inhibitor types by means of protein X-ray crystallography and the identification of novel stabilizers of inactive conformations of p38α MAP kinase and of inhibitors of several phosphatases.

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.

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.

Cosmological constraints from X-ray all sky surveys, from CODEX to eROSITA

NASA Astrophysics Data System (ADS)

Finoguenov, A.

2017-10-01

Large area cluster cosmology has long become a multiwavelength discipline. Understanding the effect of various selections is currently the main path to improving on the validity of cluster cosmological results. Many of these results are based on the large area sample derived from RASS data. We perform wavelet detection of X-ray sources and make extensive simulations of the detection of clusters in the RASS data. We assign an optical richness to each of the 25,000 detected X-ray sources in the 10,000 square degrees of SDSS BOSS area. We show that there is no obvious separation of sources on galaxy clusters and AGN, based on distribution of systems on their richness. We conclude that previous catalogs, such as MACS, REFLEX are all subject to a complex optical selection function, in addition to an X-ray selection. We provide a complete model of identification of cluster counts are galaxy clusters, which includes chance identification, effect of AGN halo occupation distribution and the thermal emission of ICM. Finally we present the cosmological results obtained using this sample.

Synthesis efficiency of heavy carbon clusters from ETFE ablated by different numbers of laser pulse in vacuum

NASA Astrophysics Data System (ADS)

Shibagaki, K.; Takada, N.; Sasaki, K.; Kadota, K.

2002-09-01

We have carried out mass spectral analysis of positive ions produced by laser ablation of a copolymer of ethylene and tetrafluoroethylene (ETFE: [CH 2CH 2CF 2CF 2] n) in vacuum using time-of-flight mass spectrometry (TOF-MS). The surfaces of the ETFE targets irradiated by different numbers of laser pulse were analyzed by X-ray photoelectron spectroscopy (XPS) and scanning electron microscopy (SEM). Heavy carbon cluster ions C n+ with n≥30 were observed in the mass spectra. The fractional abundance of heavy clusters in the mass spectrum decreased with the number of laser pulse. On the other hand, carbon became rich in the atomic composition of the laser-irradiated surface, and the eroded area on the surface increased with the number of laser pulse. From these results, it is suggested that the carbon-rich material surface results in the less efficient production of heavy carbon clusters. In addition, it is also suggested that clustering reactions in eroded craters do not contribute to the synthesis of heavy clusters.

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.

Dark Energy Survey Year 1 Results: Weak Lensing Mass Calibration of redMaPPer Galaxy Clusters

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

McClintock, T.; et al.

We constrain the mass--richness scaling relation of redMaPPer galaxy clusters identified in the Dark Energy Survey Year 1 data using weak gravitational lensing. We split clusters intomore » $$4\\times3$$ bins of richness $$\\lambda$$ and redshift $z$ for $$\\lambda\\geq20$$ and $$0.2 \\leq z \\leq 0.65$$ and measure the mean masses of these bins using their stacked weak lensing signal. By modeling the scaling relation as $$\\langle M_{\\rm 200m}|\\lambda,z\\rangle = M_0 (\\lambda/40)^F ((1+z)/1.35)^G$$, we constrain the normalization of the scaling relation at the 5.0 per cent level as $$M_0 = [3.081 \\pm 0.075 ({\\rm stat}) \\pm 0.133 ({\\rm sys})] \\cdot 10^{14}\\ {\\rm M}_\\odot$$ at $$\\lambda=40$$ and $z=0.35$. The richness scaling index is constrained to be $$F=1.356 \\pm 0.051\\ ({\\rm stat})\\pm 0.008\\ ({\\rm sys})$$ and the redshift scaling index $$G=-0.30\\pm 0.30\\ ({\\rm stat})\\pm 0.06\\ ({\\rm sys})$$. These are the tightest measurements of the normalization and richness scaling index made to date. We use a semi-analytic covariance matrix to characterize the statistical errors in the recovered weak lensing profiles. Our analysis accounts for the following sources of systematic error: shear and photometric redshift errors, cluster miscentering, cluster member dilution of the source sample, systematic uncertainties in the modeling of the halo--mass correlation function, halo triaxiality, and projection effects. We discuss prospects for reducing this systematic error budget, which dominates the uncertainty on $$M_0$$. Our result is in excellent agreement with, but has significantly smaller uncertainties than, previous measurements in the literature, and augurs well for the power of the DES cluster survey as a tool for precision cosmology and upcoming galaxy surveys such as LSST, Euclid and WFIRST.« less

Processes and subdivisions in diogenites, a multivariate statistical analysis

NASA Technical Reports Server (NTRS)

Harriott, T. A.; Hewins, R. H.

1984-01-01

Multivariate statistical techniques used on diogenite orthopyroxene analyses show the relationships that occur within diogenites and the two orthopyroxenite components (class I and II) in the polymict diogenite Garland. Cluster analysis shows that only Peckelsheim is similar to Garland class I (Fe-rich) and the other diogenites resemble Garland class II. The unique diogenite Y 75032 may be related to type I by fractionation. Factor analysis confirms the subdivision and shows that Fe does not correlate with the weakly incompatible elements across the entire pyroxene composition range, indicating that igneous fractionation is not the process controlling total diogenite composition variation. The occurrence of two groups of diogenites is interpreted as the result of sampling or mixing of two main sequences of orthopyroxene cumulates with slightly different compositions.

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

Photometry and spectroscopy in the open cluster Alpha Persei, 2

NASA Technical Reports Server (NTRS)

Prosser, Charles F.

1993-01-01

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

Analysis of Transcriptional Regulation of the Human miR-17-92 Cluster; Evidence for Involvement of Pim-1

PubMed Central

Thomas, Maren; Lange-Grünweller, Kerstin; Hartmann, Dorothee; Golde, Lara; Schlereth, Julia; Streng, Dennis; Aigner, Achim; Grünweller, Arnold; Hartmann, Roland K.

2013-01-01

The human polycistronic miRNA cluster miR-17-92 is frequently overexpressed in hematopoietic malignancies and cancers. Its transcription is in part controlled by an E2F-regulated host gene promoter. An intronic A/T-rich region directly upstream of the miRNA coding region also contributes to cluster expression. Our deletion analysis of the A/T-rich region revealed a strong dependence on c-Myc binding to the functional E3 site. Yet, constructs lacking the 5′-proximal ~1.3 kb or 3′-distal ~0.1 kb of the 1.5 kb A/T-rich region still retained residual specific promoter activity, suggesting multiple transcription start sites (TSS) in this region. Furthermore, the protooncogenic kinase, Pim-1, its phosphorylation target HP1γ and c-Myc colocalize to the E3 region, as inferred from chromatin immunoprecipitation. Analysis of pri-miR-17-92 expression levels in K562 and HeLa cells revealed that silencing of E2F3, c-Myc or Pim-1 negatively affects cluster expression, with a synergistic effect caused by c-Myc/Pim-1 double knockdown in HeLa cells. Thus, we show, for the first time, that the protooncogene Pim-1 is part of the network that regulates transcription of the human miR-17-92 cluster. PMID:23749113

Reduction and analysis of VLA maps for 281 radio-loud quasars using the UNLV Cray Y-MP supercomputer

NASA Technical Reports Server (NTRS)

Ding, Ailian; Hintzen, Paul; Weistrop, Donna; Owen, Frazer

1993-01-01

The identification of distorted radio-loud quasars provides a potentially very powerful tool for basic cosmological studies. If large morphological distortions are correlated with membership of the quasars in rich clusters of galaxies, optical observations can be used to identify rich clusters of galaxies at large redshifts. Hintzen, Ulvestad, and Owen (1983, HUO) undertook a VLA A array snapshot survey at 20 cm of 123 radio-loud quasars, and they found that among triple sources in their sample, 17 percent had radio axes which were bent more than 20 deg and 5 percent were bent more than 40 deg. Their subsequent optical observations showed that excess galaxy densities within 30 arcsec of 6 low-redshift distorted quasars were on average 3 times as great as those around undistorted quasars (Hintzen 1984). At least one of the distorted quasars observed, 3C275.1, apparently lies in the first-ranked galaxy at the center of a rich cluster of galaxies (Hintzen and Romanishin, 1986). Although their sample was small, these results indicated that observations of distorted quasars could be used to identify clusters of galaxies at large redshifts. The purpose of this project is to increase the available sample of distorted quasars to allow optical detection of a significant sample of quasar-associated clusters of galaxies at large redshifts.

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

A partial list of southern clusters of galaxies

NASA Technical Reports Server (NTRS)

Quintana, H.; White, R. A.

1990-01-01

An inspection of 34 SRC/ESO J southern sky fields is the basis of the present list of clusters of galaxies and their approximate classifications in terms of cluster concentration, defined independently of richness and shape-symmetry. Where possible, an estimate of the cluster morphological population is provided. The Bautz-Morgan classification was applied using a strict comparison with clusters on the Palomar Sky Survey. Magnitudes were estimated on the basis of galaxies with photoelectric or photographic magnitudes.

YSOVAR II: Mapping YSO Inner Disk Structure in NGC 2264 with Simultaneous Spitzer and CoRoT Time Series Photometry

NASA Astrophysics Data System (ADS)

Stauffer, John; Morales-Calderon, Maria; Rebull, Luisa; Affer, Laura; Alencar, Sylvia; Allen, Lori; Barrado, David; Bouvier, Jerome; Calvet, Nuria; Carey, Sean; Carpenter, John; Ciardi, David; Covey, Kevin; D'Alessio, Paola; Espaillat, Catherine; Favata, Fabio; Flaccomio, Ettore; Forbrich, Jan; Furesz, Gabor; Hartman, Lee; Herbst, William; Hillenbrand, Lynne; Holtzman, Jon; Hora, Joe; Marchis, Franck; McCaughrean, Mark; Micela, Giusi; Mundt, Reinhard; Plavchan, Peter; Turner, Neal; Skrutzkie, Mike; Smith, Howard; Song, Inseok; Szentgyorgi, Andy; Terebey, Susan; Vrba, Fred; Wasserman, Lawrence; Watson, Alan; Whitney, Barbara; Winston, Elaine; Wood, Kenny

2011-05-01

We propose a simultaneous, continuous 30 day observation of the star forming region NGC2264 with Spitzer and CoRoT. NGC2264 is the only nearby, rich star-forming region which can be observed with CoRoT; it is by definition then the only nearby, rich star-forming region where a simultaneous Spitzer/CoRoT campaign is possible. Fortunately, the visibility windows for the two spacecraft overlap, allowing this program to be done in the Nov. 25, 2011 to Jan. 4, 2012 time period. For 10 days, we propose to map the majority of the cluster (a 35'x35' region) to a depth of 48 seconds per point, with each epoch taking 1.7 hours, allowing of order 12 epochs per day. For the other 20 days, we propose to obtaining staring-mode data for two positions in the cluster having a high density of cluster members. We also plan to propose for a variety of other ground and space-based data, most of which would also be simultaneous with the Spitzer and CoRoT observing. These data will allow us to address many astrophysical questions related to the structure and evolution of the disks of young stars and the interaction of those disks with the forming star. The data may also help inform models of planet formation since planets form and migrate through the pre-main sequence disks during the 0.5-5 Myr age range of stars in NGC2264. The data we collect will also provide an archive of the variability properties of young stars that is unmatched in its accuracy, sensitivity, cadence and duration and which therefore could inspire investigation of phenomena which we cannot now imagine. The CoRoT observations have been approved, contingent on approval of a simultaneous Spitzer observing program (this proposal).

Physical properties of star clusters in the outer LMC as observed by the DES

DOE PAGES

Pieres, A.; Santiago, B.; Balbinot, E.; ...

2016-05-26

The Large Magellanic Cloud (LMC) harbors a rich and diverse system of star clusters, whose ages, chemical abundances, and positions provide information about the LMC history of star formation. We use Science Verification imaging data from the Dark Energy Survey to increase the census of known star clusters in the outer LMC and to derive physical parameters for a large sample of such objects using a spatially and photometrically homogeneous data set. Our sample contains 255 visually identified cluster candidates, of which 109 were not listed in any previous catalog. We quantify the crowding effect for the stellar sample producedmore » by the DES Data Management pipeline and conclude that the stellar completeness is < 10% inside typical LMC cluster cores. We therefore develop a pipeline to sample and measure stellar magnitudes and positions around the cluster candidates using DAOPHOT. We also implement a maximum-likelihood method to fit individual density profiles and colour-magnitude diagrams. For 117 (from a total of 255) of the cluster candidates (28 uncatalogued clusters), we obtain reliable ages, metallicities, distance moduli and structural parameters, confirming their nature as physical systems. The distribution of cluster metallicities shows a radial dependence, with no clusters more metal-rich than [Fe/H] ~ -0.7 beyond 8 kpc from the LMC center. Furthermore, the age distribution has two peaks at ≃ 1.2 Gyr and ≃ 2.7 Gyr.« less