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Sample records for high-density phylogenetic 16s

  1. 16S rRNA gene sequence and phylogenetic tree of lactobacillus ...

    African Journals Online (AJOL)

    ... processed by denaturing gradient gel electrophoresis (DGGE). Phylogenetic tree was constructed with the sequences of the V2-V3 region of 16S rRNA gene. Results show two distinct divisions among the Lactobacillus species. The study presents a new understanding of the nature of the Lactobacillus vaginal microbiota ...

  2. Phylogenetic relatedness determined between antibiotic resistance and 16S rRNA genes in actinobacteria.

    Science.gov (United States)

    Sagova-Mareckova, Marketa; Ulanova, Dana; Sanderova, Petra; Omelka, Marek; Kamenik, Zdenek; Olsovska, Jana; Kopecky, Jan

    2015-04-01

    Distribution and evolutionary history of resistance genes in environmental actinobacteria provide information on intensity of antibiosis and evolution of specific secondary metabolic pathways at a given site. To this day, actinobacteria producing biologically active compounds were isolated mostly from soil but only a limited range of soil environments were commonly sampled. Consequently, soil remains an unexplored environment in search for novel producers and related evolutionary questions. Ninety actinobacteria strains isolated at contrasting soil sites were characterized phylogenetically by 16S rRNA gene, for presence of erm and ABC transporter resistance genes and antibiotic production. An analogous analysis was performed in silico with 246 and 31 strains from Integrated Microbial Genomes (JGI_IMG) database selected by the presence of ABC transporter genes and erm genes, respectively. In the isolates, distances of erm gene sequences were significantly correlated to phylogenetic distances based on 16S rRNA genes, while ABC transporter gene distances were not. The phylogenetic distance of isolates was significantly correlated to soil pH and organic matter content of isolation sites. In the analysis of JGI_IMG datasets the correlation between phylogeny of resistance genes and the strain phylogeny based on 16S rRNA genes or five housekeeping genes was observed for both the erm genes and ABC transporter genes in both actinobacteria and streptomycetes. However, in the analysis of sequences from genomes where both resistance genes occurred together the correlation was observed for both ABC transporter and erm genes in actinobacteria but in streptomycetes only in the erm gene. The type of erm resistance gene sequences was influenced by linkage to 16S rRNA gene sequences and site characteristics. The phylogeny of ABC transporter gene was correlated to 16S rRNA genes mainly above the genus level. The results support the concept of new specific secondary metabolite

  3. 16S ribosomal RNA sequence analysis for determination of phylogenetic relationship among methylotrophs.

    Science.gov (United States)

    Tsuji, K; Tsien, H C; Hanson, R S; DePalma, S R; Scholtz, R; LaRoche, S

    1990-01-01

    16S ribosomal RNAs (rRNA) of 12 methylotrophic bacteria have been almost completely sequenced to establish their phylogenetic relationships. Methylotrophs that are physiologically related are phylogenetically diverse and are scattered among the purple eubacteria (class Proteobacteria). Group I methylotrophs can be classified in the beta- and the gamma-subdivisions and group II methylotrophs in the alpha-subdivision of the purple eubacteria, respectively. Pink-pigmented facultative and non-pigmented obligate group II methylotrophs form two distinctly separate branches within the alpha-subdivision. The secondary structures of the 16S rRNA sequences of 'Methylocystis parvus' strain OBBP, 'Methylosinus trichosporium' strain OB3b, 'Methylosporovibrio methanica' strain 81Z and Hyphomicrobium sp. strain DM2 are similar, and these non-pigmented obligate group II methylotrophs form one tight cluster in the alpha-subdivision. The pink-pigmented facultative methylotrophs, Methylobacterium extorquens strain AM1, Methylobacterium sp. strain DM4 and Methylobacterium organophilum strain XX form another cluster within the alpha-subdivision. Although similar in phenotypic characteristics, Methylobacterium organophilum strain XX and Methylobacterium extorquens strain AM1 are clearly distinguishable by their 16S rRNA sequences. The group I methylotrophs, Methylophilus methylotrophus strain AS1 and methylotrophic species DM11, which do not utilize methane, are similar in 16S rRNA sequence to bacteria in the beta-subdivision. The methane-utilizing, obligate group I methanotrophs, Methylococcus capsulatus strain BATH and Methylomonas methanica, are placed in the gamma-subdivision. The results demonstrate that it is possible to distinguish and classify the methylotrophic bacteria using 16S rRNA sequence analysis.

  4. Phylogenetic Analysis of Pasteuria penetrans by 16S rRNA Gene Cloning and Sequencing.

    Science.gov (United States)

    Anderson, J M; Preston, J F; Dickson, D W; Hewlett, T E; Williams, N H; Maruniak, J E

    1999-09-01

    Pasteuria penetrans is an endospore-forming bacterial parasite of Meloidogyne spp. This organism is among the most promising agents for the biological control of root-knot nematodes. In order to establish the phylogenetic position of this species relative to other endospore-forming bacteria, the 16S ribosomal genes from two isolates of P. penetrans, P-20, which preferentially infects M. arenaria race 1, and P-100, which preferentially infects M. incognita and M. javanica, were PCR-amplified from a purified endospore extraction. Universal primers for the 16S rRNA gene were used to amplify DNA which was cloned, and a nucleotide sequence was obtained for 92% of the gene (1,390 base pairs) encoding the 16S rDNA from each isolate. Comparison of both isolates showed identical sequences that were compared to 16S rDNA sequences of 30 other endospore-forming bacteria obtained from GenBank. Parsimony analyses indicated that P. penetrans is a species within a clade that includes Alicyclobacillus acidocaldarius, A. cycloheptanicus, Sulfobacillus sp., Bacillus tusciae, B. schlegelii, and P. ramosa. Its closest neighbor is P. ramosa, a parasite of Daphnia spp. (water fleas). This study provided a genomic basis for the relationship of species assigned to the genus Pasteuria, and for comparison of species that are parasites of different phytopathogenic nematodes.

  5. CORE: a phylogenetically-curated 16S rDNA database of the core oral microbiome.

    Directory of Open Access Journals (Sweden)

    Ann L Griffen

    2011-04-01

    Full Text Available Comparing bacterial 16S rDNA sequences to GenBank and other large public databases via BLAST often provides results of little use for identification and taxonomic assignment of the organisms of interest. The human microbiome, and in particular the oral microbiome, includes many taxa, and accurate identification of sequence data is essential for studies of these communities. For this purpose, a phylogenetically curated 16S rDNA database of the core oral microbiome, CORE, was developed. The goal was to include a comprehensive and minimally redundant representation of the bacteria that regularly reside in the human oral cavity with computationally robust classification at the level of species and genus. Clades of cultivated and uncultivated taxa were formed based on sequence analyses using multiple criteria, including maximum-likelihood-based topology and bootstrap support, genetic distance, and previous naming. A number of classification inconsistencies for previously named species, especially at the level of genus, were resolved. The performance of the CORE database for identifying clinical sequences was compared to that of three publicly available databases, GenBank nr/nt, RDP and HOMD, using a set of sequencing reads that had not been used in creation of the database. CORE offered improved performance compared to other public databases for identification of human oral bacterial 16S sequences by a number of criteria. In addition, the CORE database and phylogenetic tree provide a framework for measures of community divergence, and the focused size of the database offers advantages of efficiency for BLAST searching of large datasets. The CORE database is available as a searchable interface and for download at http://microbiome.osu.edu.

  6. Phylogenetic analysis of Demodex caprae based on mitochondrial 16S rDNA sequence.

    Science.gov (United States)

    Zhao, Ya-E; Hu, Li; Ma, Jun-Xian

    2013-11-01

    Demodex caprae infests the hair follicles and sebaceous glands of goats worldwide, which not only seriously impairs goat farming, but also causes a big economic loss. However, there are few reports on the DNA level of D. caprae. To reveal the taxonomic position of D. caprae within the genus Demodex, the present study conducted phylogenetic analysis of D. caprae based on mt16S rDNA sequence data. D. caprae adults and eggs were obtained from a skin nodule of the goat suffering demodicidosis. The mt16S rDNA sequences of individual mite were amplified using specific primers, and then cloned, sequenced, and aligned. The sequence divergence, genetic distance, and transition/transversion rate were computed, and the phylogenetic trees in Demodex were reconstructed. Results revealed the 339-bp partial sequences of six D. caprae isolates were obtained, and the sequence identity was 100% among isolates. The pairwise divergences between D. caprae and Demodex canis or Demodex folliculorum or Demodex brevis were 22.2-24.0%, 24.0-24.9%, and 22.9-23.2%, respectively. The corresponding average genetic distances were 2.840, 2.926, and 2.665, and the average transition/transversion rates were 0.70, 0.55, and 0.54, respectively. The divergences, genetic distances, and transition/transversion rates of D. caprae versus the other three species all reached interspecies level. The five phylogenetic trees all presented that D. caprae clustered with D. brevis first, and then with D. canis, D. folliculorum, and Demodex injai in sequence. In conclusion, D. caprae is an independent species, and it is closer to D. brevis than to D. canis, D. folliculorum, or D. injai.

  7. Linear programming model to construct phylogenetic network for 16S rRNA sequences of photosynthetic organisms and influenza viruses.

    Science.gov (United States)

    Mathur, Rinku; Adlakha, Neeru

    2014-06-01

    Phylogenetic trees give the information about the vertical relationships of ancestors and descendants but phylogenetic networks are used to visualize the horizontal relationships among the different organisms. In order to predict reticulate events there is a need to construct phylogenetic networks. Here, a Linear Programming (LP) model has been developed for the construction of phylogenetic network. The model is validated by using data sets of chloroplast of 16S rRNA sequences of photosynthetic organisms and Influenza A/H5N1 viruses. Results obtained are in agreement with those obtained by earlier researchers.

  8. Phylogenetic Relationship of Phosphate Solubilizing Bacteria according to 16S rRNA Genes

    Directory of Open Access Journals (Sweden)

    Mohammad Bagher Javadi Nobandegani

    2015-01-01

    Full Text Available Phosphate solubilizing bacteria (PSB can convert insoluble form of phosphorous to an available form. Applications of PSB as inoculants increase the phosphorus uptake by plant in the field. In this study, isolation and precise identification of PSB were carried out in Malaysian (Serdang oil palm field (University Putra Malaysia. Identification and phylogenetic analysis of 8 better isolates were carried out by 16S rRNA gene sequencing in which as a result five isolates belong to the Beta subdivision of Proteobacteria, one isolate was related to the Gama subdivision of Proteobacteria, and two isolates were related to the Firmicutes. Bacterial isolates of 6upmr, 2upmr, 19upmnr, 10upmr, and 24upmr were identified as Alcaligenes faecalis. Also, bacterial isolates of 20upmnr and 17upmnr were identified as Bacillus cereus and Vagococcus carniphilus, respectively, and bacterial isolates of 31upmr were identified as Serratia plymuthica. Molecular identification and characterization of oil palm strains as the specific phosphate solubilizer can reduce the time and cost of producing effective inoculate (biofertilizer in an oil palm field.

  9. Phylogenetic relationships in Demodex mites (Acari: Demodicidae) based on mitochondrial 16S rDNA partial sequences.

    Science.gov (United States)

    Zhao, Ya-E; Wu, Li-Ping

    2012-09-01

    To confirm phylogenetic relationships in Demodex mites based on mitochondrial 16S rDNA partial sequences, mtDNA 16S partial sequences of ten isolates of three Demodex species from China were amplified, recombined, and sequenced and then analyzed with two Demodex folliculorum isolates from Spain. Lastly, genetic distance was computed, and phylogenetic tree was reconstructed. MEGA 4.0 analysis showed high sequence identity among 16S rDNA partial sequences of three Demodex species, which were 95.85 % in D. folliculorum, 98.53 % in Demodex canis, and 99.71 % in Demodex brevis. The divergence, genetic distance, and transition/transversions of the three Demodex species reached interspecies level, whereas there was no significant difference of the divergence (1.1 %), genetic distance (0.011), and transition/transversions (3/1) of the two geographic D. folliculorum isolates (Spain and China). Phylogenetic trees reveal that the three Demodex species formed three separate branches of one clade, where D. folliculorum and D. canis gathered first, and then gathered with D. brevis. The two Spain and five China D. folliculorum isolates did not form sister clades. In conclusion, 16S mtDNA are suitable for phylogenetic relationship analysis in low taxa (genus or species), but not for intraspecies determination of Demodex. The differentiation among the three Demodex species has reached interspecies level.

  10. Phylogenetic relatedness determined between antibiotic resistance and 16S rRNA genes in actinobacteria

    Czech Academy of Sciences Publication Activity Database

    Ságová-Marečková, M.; Ulanová, Dana; Šanderová, P.; Omelka, M.; Kameník, Zdeněk; Olšovská, J.; Kopecký, J.

    2015-01-01

    Roč. 15, APR 2015 (2015) ISSN 1471-2180 Institutional support: RVO:61388971 Keywords : Actinobacteria * 16S rRNA diversity * Resistance genes Subject RIV: EH - Ecology, Behaviour Impact factor: 2.581, year: 2015

  11. 16S rRNA phylogenetic analysis of actinomycetes isolated from ...

    African Journals Online (AJOL)

    Subsequently, phylogenetic tree was constructed using suitable bioinformatics tools to identify the similarity which showed 97% similarity between strains. Moreover, all the selected strains of actinomycetes were subjected to study the protein and plasmid DNA expression profiles which showed prominent bands with ...

  12. Phylogenetic analysis of Fusobacterium prausnitzii based upon the 16S rRNA gene sequence and PCR confirmation.

    Science.gov (United States)

    Wang, R F; Cao, W W; Cerniglia, C E

    1996-01-01

    In order to develop a PCR method to detect Fusobacterium prausnitzii in human feces and to clarify the phylogenetic position of this species, its 16S rRNA gene sequence was determined. The sequence described in this paper is different from the 16S rRNA gene sequence is specific for F. prausnitzii, and the results of this assay confirmed that F. prausnitzii is the most common species in human feces. However, a PCR assay based on the original GenBank sequence was negative when it was performed with two strains of F. prausnitzii obtained from the American Type Culture Collection. A phylogenetic tree based on the new 16S rRNA gene sequence was constructed. On this tree F. prausnitzii was not a member of the Fusobacterium group but was closer to some Eubacterium spp. and located between Clostridium "clusters III and IV" (M.D. Collins, P.A. Lawson, A. Willems, J.J. Cordoba, J. Fernandez-Garayzabal, P. Garcia, J. Cai, H. Hippe, and J.A.E. Farrow, Int. J. Syst. Bacteriol. 44:812-826, 1994).

  13. Phylogenetic inference of Coxiella burnetii by 16S rRNA gene sequencing.

    Directory of Open Access Journals (Sweden)

    Heather P McLaughlin

    Full Text Available Coxiella burnetii is a human pathogen that causes the serious zoonotic disease Q fever. It is ubiquitous in the environment and due to its wide host range, long-range dispersal potential and classification as a bioterrorism agent, this microorganism is considered an HHS Select Agent. In the event of an outbreak or intentional release, laboratory strain typing methods can contribute to epidemiological investigations, law enforcement investigation and the public health response by providing critical information about the relatedness between C. burnetii isolates collected from different sources. Laboratory cultivation of C. burnetii is both time-consuming and challenging. Availability of strain collections is often limited and while several strain typing methods have been described over the years, a true gold-standard method is still elusive. Building upon epidemiological knowledge from limited, historical strain collections and typing data is essential to more accurately infer C. burnetii phylogeny. Harmonization of auspicious high-resolution laboratory typing techniques is critical to support epidemiological and law enforcement investigation. The single nucleotide polymorphism (SNP -based genotyping approach offers simplicity, rapidity and robustness. Herein, we demonstrate SNPs identified within 16S rRNA gene sequences can differentiate C. burnetii strains. Using this method, 55 isolates were assigned to six groups based on six polymorphisms. These 16S rRNA SNP-based genotyping results were largely congruent with those obtained by analyzing restriction-endonuclease (RE-digested DNA separated by SDS-PAGE and by the high-resolution approach based on SNPs within multispacer sequence typing (MST loci. The SNPs identified within the 16S rRNA gene can be used as targets for the development of additional SNP-based genotyping assays for C. burnetii.

  14. Phylogenetic relationships of true butterflies (Lepidoptera: Papilionoidea) inferred from COI, 16S rRNA and EF-1α sequences.

    Science.gov (United States)

    Kim, Man Il; Wan, Xinlong; Kim, Min Jee; Jeong, Heon Cheon; Ahn, Neung-Ho; Kim, Ki-Gyoung; Han, Yeon Soo; Kim, Iksoo

    2010-11-01

    The molecular phylogenetic relationships among true butterfly families (superfamily Papilionoidea) have been a matter of substantial controversy; this debate has led to several competing hypotheses. Two of the most compelling of those hypotheses involve the relationships of (Nymphalidae + Lycaenidae) + (Pieridae + Papilionidae) and (((Nymphalidae + Lycaenidae) + Pieridae) + Papilionidae). In this study, approximately 3,500 nucleotide sequences from cytochrome oxidase subunit I (COI), 16S ribosomal RNA (16S rRNA), and elongation factor-1 alpha (EF-1α) were sequenced from 83 species belonging to four true butterfly families, along with those of three outgroup species belonging to three lepidopteran superfamilies. These sequences were subjected to phylogenetic reconstruction via Bayesian Inference (BI), Maximum Likelihood (ML), and Maximum Parsimony (MP) algorithms. The monophyletic Pieridae and monophyletic Papilionidae evidenced good recovery in all analyses, but in some analyses, the monophylies of the Lycaenidae and Nymphalidae were hampered by the inclusion of single species of the lycaenid subfamily Miletinae and the nymphalid subfamily Danainae. Excluding those singletons, all phylogenetic analyses among the four true butterfly families clearly identified the Nymphalidae as the sister to the Lycaenidae and identified this group as a sister to the Pieridae, with the Papilionidae identified as the most basal linage to the true butterfly, thus supporting the hypothesis: (Papilionidae + (Pieridae + (Nymphalidae + Lycaenidae))).

  15. Phylogenetic diversity of lactic acid bacteria associated with paddy rice silage as determined by 16S ribosomal DNA analysis.

    Science.gov (United States)

    Ennahar, Saïd; Cai, Yimin; Fujita, Yasuhito

    2003-01-01

    A total of 161 low-G+C-content gram-positive bacteria isolated from whole-crop paddy rice silage were classified and subjected to phenotypic and genetic analyses. Based on morphological and biochemical characters, these presumptive lactic acid bacterium (LAB) isolates were divided into 10 groups that included members of the genera Enterococcus, Lactobacillus, Lactococcus, Leuconostoc, Pediococcus, and WEISSELLA: Analysis of the 16S ribosomal DNA (rDNA) was used to confirm the presence of the predominant groups indicated by phenotypic analysis and to determine the phylogenetic affiliation of representative strains. The virtually complete 16S rRNA gene was PCR amplified and sequenced. The sequences from the various LAB isolates showed high degrees of similarity to those of the GenBank reference strains (between 98.7 and 99.8%). Phylogenetic trees based on the 16S rDNA sequence displayed high consistency, with nodes supported by high bootstrap values. With the exception of one species, the genetic data was in agreement with the phenotypic identification. The prevalent LAB, predominantly homofermentative (66%), consisted of Lactobacillus plantarum (24%), Lactococcus lactis (22%), Leuconostoc pseudomesenteroides (20%), Pediococcus acidilactici (11%), Lactobacillus brevis (11%), Enterococcus faecalis (7%), Weissella kimchii (3%), and Pediococcus pentosaceus (2%). The present study, the first to fully document rice-associated LAB, showed a very diverse community of LAB with a relatively high number of species involved in the fermentation process of paddy rice silage. The comprehensive 16S rDNA-based approach to describing LAB community structure was valuable in revealing the large diversity of bacteria inhabiting paddy rice silage and enabling the future design of appropriate inoculants aimed at improving its fermentation quality.

  16. 16S rRNA gene-based phylogenetic microarray for simultaneous identification of members of the genus Burkholderia.

    Science.gov (United States)

    Schönmann, Susan; Loy, Alexander; Wimmersberger, Céline; Sobek, Jens; Aquino, Catharine; Vandamme, Peter; Frey, Beat; Rehrauer, Hubert; Eberl, Leo

    2009-04-01

    For cultivation-independent and highly parallel analysis of members of the genus Burkholderia, an oligonucleotide microarray (phylochip) consisting of 131 hierarchically nested 16S rRNA gene-targeted oligonucleotide probes was developed. A novel primer pair was designed for selective amplification of a 1.3 kb 16S rRNA gene fragment of Burkholderia species prior to microarray analysis. The diagnostic performance of the microarray for identification and differentiation of Burkholderia species was tested with 44 reference strains of the genera Burkholderia, Pandoraea, Ralstonia and Limnobacter. Hybridization patterns based on presence/absence of probe signals were interpreted semi-automatically using the novel likelihood-based strategy of the web-tool Phylo- Detect. Eighty-eight per cent of the reference strains were correctly identified at the species level. The evaluated microarray was applied to investigate shifts in the Burkholderia community structure in acidic forest soil upon addition of cadmium, a condition that selected for Burkholderia species. The microarray results were in agreement with those obtained from phylogenetic analysis of Burkholderia 16S rRNA gene sequences recovered from the same cadmiumcontaminated soil, demonstrating the value of the Burkholderia phylochip for determinative and environmental studies.

  17. Phylogenetic relationships in three species of canine Demodex mite based on partial sequences of mitochondrial 16S rDNA.

    Science.gov (United States)

    Sastre, Natalia; Ravera, Ivan; Villanueva, Sergio; Altet, Laura; Bardagí, Mar; Sánchez, Armand; Francino, Olga; Ferrer, Lluís

    2012-12-01

    The historical classification of Demodex mites has been based on their hosts and morphological features. Genome sequencing has proved to be a very effective taxonomic tool in phylogenetic studies and has been applied in the classification of Demodex. Mitochondrial 16S rDNA has been demonstrated to be an especially useful marker to establish phylogenetic relationships. To amplify and sequence a segment of the mitochondrial 16S rDNA from Demodex canis and Demodex injai, as well as from the short-bodied mite called, unofficially, D. cornei and to determine their genetic proximity. Demodex mites were examined microscopically and classified as Demodex folliculorum (one sample), D. canis (four samples), D. injai (two samples) or the short-bodied species D. cornei (three samples). DNA was extracted, and a 338 bp fragment of the 16S rDNA was amplified and sequenced. The sequences of the four D. canis mites were identical and shared 99.6 and 97.3% identity with two D. canis sequences available at GenBank. The sequences of the D. cornei isolates were identical and showed 97.8, 98.2 and 99.6% identity with the D. canis isolates. The sequences of the two D. injai isolates were also identical and showed 76.6% identity with the D. canis sequence. Demodex canis and D. injai are two different species, with a genetic distance of 23.3%. It would seem that the short-bodied Demodex mite D. cornei is a morphological variant of D. canis. © 2012 The Authors. Veterinary Dermatology © 2012 ESVD and ACVD.

  18. Phylogenetic characterization of a biogas plant microbial community integrating clone library 16S-rDNA sequences and metagenome sequence data obtained by 454-pyrosequencing.

    Science.gov (United States)

    Kröber, Magdalena; Bekel, Thomas; Diaz, Naryttza N; Goesmann, Alexander; Jaenicke, Sebastian; Krause, Lutz; Miller, Dimitri; Runte, Kai J; Viehöver, Prisca; Pühler, Alfred; Schlüter, Andreas

    2009-06-01

    The phylogenetic structure of the microbial community residing in a fermentation sample from a production-scale biogas plant fed with maize silage, green rye and liquid manure was analysed by an integrated approach using clone library sequences and metagenome sequence data obtained by 454-pyrosequencing. Sequencing of 109 clones from a bacterial and an archaeal 16S-rDNA amplicon library revealed that the obtained nucleotide sequences are similar but not identical to 16S-rDNA database sequences derived from different anaerobic environments including digestors and bioreactors. Most of the bacterial 16S-rDNA sequences could be assigned to the phylum Firmicutes with the most abundant class Clostridia and to the class Bacteroidetes, whereas most archaeal 16S-rDNA sequences cluster close to the methanogen Methanoculleus bourgensis. Further sequences of the archaeal library most probably represent so far non-characterised species within the genus Methanoculleus. A similar result derived from phylogenetic analysis of mcrA clone sequences. The mcrA gene product encodes the alpha-subunit of methyl-coenzyme-M reductase involved in the final step of methanogenesis. BLASTn analysis applying stringent settings resulted in assignment of 16S-rDNA metagenome sequence reads to 62 16S-rDNA amplicon sequences thus enabling frequency of abundance estimations for 16S-rDNA clone library sequences. Ribosomal Database Project (RDP) Classifier processing of metagenome 16S-rDNA reads revealed abundance of the phyla Firmicutes, Bacteroidetes and Euryarchaeota and the orders Clostridiales, Bacteroidales and Methanomicrobiales. Moreover, a large fraction of 16S-rDNA metagenome reads could not be assigned to lower taxonomic ranks, demonstrating that numerous microorganisms in the analysed fermentation sample of the biogas plant are still unclassified or unknown.

  19. Phylogenetic study of Geitlerinema and Microcystis (Cyanobacteria) using PC-IGS and 16S-23S ITS as markers: investigation of horizontal gene transfer.

    Science.gov (United States)

    Piccin-Santos, Viviane; Brandão, Marcelo Mendes; Bittencourt-Oliveira, Maria Do Carmo

    2014-08-01

    Selection of genes that have not been horizontally transferred for prokaryote phylogenetic inferences is regarded as a challenging task. The markers internal transcribed spacer of ribosomal genes (16S-23S ITS) and phycocyanin intergenic spacer (PC-IGS), based on the operons of ribosomal and phycocyanin genes respectively, are among the most used markers in cyanobacteria. The region of the ribosomal genes has been considered stable, whereas the phycocyanin operon may have undergone horizontal transfer. To investigate the occurrence of horizontal transfer of PC-IGS, phylogenetic trees of Geitlerinema and Microcystis strains were generated using PC-IGS and 16S-23S ITS and compared. Phylogenetic trees based on the two markers were mostly congruent for Geitlerinema and Microcystis, indicating a common evolutionary history among ribosomal and phycocyanin genes with no evidence for horizontal transfer of PC-IGS. Thus, PC-IGS is a suitable marker, along with 16S-23S ITS for phylogenetic studies of cyanobacteria. © 2014 Phycological Society of America.

  20. Phylogenetic analysis of Thai oyster (Ostreidae) based on partial sequences of the mitochondrial 16S rDNA gene

    DEFF Research Database (Denmark)

    Bussarawit, Somchai; Gravlund, Peter; Glenner, Henrik

    2006-01-01

    Ten oyster species of the family Ostreidae (Subfamilies Crassostreinae and Lophinae) from Thailand were studied using morphological data and mitochondrial 16S rDNA gene sequences. Additional sequence data from five specimens of Ostreidae and one specimen of Tridacna gigas were downloaded from Gen...

  1. Variation in secondary structure of the 16S rRNA molecule in cyanobacteria with implications for phylogenetic analysis

    Czech Academy of Sciences Publication Activity Database

    Řeháková, Klára; Johansen, J. R.; Bowen, M.B.; Martin, M.P.; Sheil, C.A.

    2014-01-01

    Roč. 14, č. 2 (2014), s. 161-178 ISSN 1802-5439 Institutional support: RVO:60077344 Keywords : 16S rRNA secondary structure * cyanobacteria * phylogeny Subject RIV: EE - Microbiology, Virology Impact factor: 1.930, year: 2014

  2. Phylogenetic Diversity of Lactic Acid Bacteria Associated with Paddy Rice Silage as Determined by 16S Ribosomal DNA Analysis

    OpenAIRE

    Ennahar, Saïd; Cai, Yimin; Fujita, Yasuhito

    2003-01-01

    A total of 161 low-G+C-content gram-positive bacteria isolated from whole-crop paddy rice silage were classified and subjected to phenotypic and genetic analyses. Based on morphological and biochemical characters, these presumptive lactic acid bacterium (LAB) isolates were divided into 10 groups that included members of the genera Enterococcus, Lactobacillus, Lactococcus, Leuconostoc, Pediococcus, and Weissella. Analysis of the 16S ribosomal DNA (rDNA) was used to confirm the presence of the ...

  3. Metagenomic and near full-length 16S rRNA sequence data in support of the phylogenetic analysis of the rumen bacterial community in steers

    Directory of Open Access Journals (Sweden)

    Phillip R. Myer

    2016-09-01

    Full Text Available Amplicon sequencing utilizing next-generation platforms has significantly transformed how research is conducted, specifically microbial ecology. However, primer and sequencing platform biases can confound or change the way scientists interpret these data. The Pacific Biosciences RSII instrument may also preferentially load smaller fragments, which may also be a function of PCR product exhaustion during sequencing. To further examine theses biases, data is provided from 16S rRNA rumen community analyses. Specifically, data from the relative phylum-level abundances for the ruminal bacterial community are provided to determine between-sample variability. Direct sequencing of metagenomic DNA was conducted to circumvent primer-associated biases in 16S rRNA reads and rarefaction curves were generated to demonstrate adequate coverage of each amplicon. PCR products were also subjected to reduced amplification and pooling to reduce the likelihood of PCR product exhaustion during sequencing on the Pacific Biosciences platform. The taxonomic profiles for the relative phylum-level and genus-level abundance of rumen microbiota as a function of PCR pooling for sequencing on the Pacific Biosciences RSII platform were provided. For more information, see “Evaluation of 16S rRNA amplicon sequencing using two next-generation sequencing technologies for phylogenetic analysis of the rumen bacterial community in steers” P.R. Myer, M. Kim, H.C. Freetly, T.P.L. Smith (2016 [1]. Keywords: 16S rRNA gene, MiSeq, Pacific Biosciences, Rumen microbiome

  4. Phylogenetic position of the North American isolate of Pasteuria that parasitizes the soybean cyst nematode, Heterodera glycines, as inferred from 16S rDNA sequence analysis.

    Science.gov (United States)

    Atibalentja, N; Noel, G R; Domier, L L

    2000-03-01

    A 1341 bp sequence of the 16S rDNA of an undescribed species of Pasteuria that parasitizes the soybean cyst nematode, Heterodera glycines, was determined and then compared with a homologous sequence of Pasteuria ramosa, a parasite of cladoceran water fleas of the family Daphnidae. The two Pasteuria sequences, which diverged from each other by a dissimilarity index of 7%, also were compared with the 16S rDNA sequences of 30 other bacterial species to determine the phylogenetic position of the genus Pasteuria among the Gram-positive eubacteria. Phylogenetic analyses using maximum-likelihood, maximum-parsimony and neighbour-joining methods showed that the Heterodera glycines-infecting Pasteuria and its sister species, P. ramosa, form a distinct line of descent within the Alicyclobacillus group of the Bacillaceae. These results are consistent with the view that the genus Pasteuria is a deeply rooted member of the Clostridium-Bacillus-Streptococcus branch of the Gram-positive eubacteria, neither related to the actinomycetes nor closely related to true endospore-forming bacteria.

  5. From learning taxonomies to phylogenetic learning: Integration of 16S rRNA gene data into FAME-based bacterial classification

    Directory of Open Access Journals (Sweden)

    Dawyndt Peter

    2010-01-01

    Full Text Available Abstract Background Machine learning techniques have shown to improve bacterial species classification based on fatty acid methyl ester (FAME data. Nonetheless, FAME analysis has a limited resolution for discrimination of bacteria at the species level. In this paper, we approach the species classification problem from a taxonomic point of view. Such a taxonomy or tree is typically obtained by applying clustering algorithms on FAME data or on 16S rRNA gene data. The knowledge gained from the tree can then be used to evaluate FAME-based classifiers, resulting in a novel framework for bacterial species classification. Results In view of learning in a taxonomic framework, we consider two types of trees. First, a FAME tree is constructed with a supervised divisive clustering algorithm. Subsequently, based on 16S rRNA gene sequence analysis, phylogenetic trees are inferred by the NJ and UPGMA methods. In this second approach, the species classification problem is based on the combination of two different types of data. Herein, 16S rRNA gene sequence data is used for phylogenetic tree inference and the corresponding binary tree splits are learned based on FAME data. We call this learning approach 'phylogenetic learning'. Supervised Random Forest models are developed to train the classification tasks in a stratified cross-validation setting. In this way, better classification results are obtained for species that are typically hard to distinguish by a single or flat multi-class classification model. Conclusions FAME-based bacterial species classification is successfully evaluated in a taxonomic framework. Although the proposed approach does not improve the overall accuracy compared to flat multi-class classification, it has some distinct advantages. First, it has better capabilities for distinguishing species on which flat multi-class classification fails. Secondly, the hierarchical classification structure allows to easily evaluate and visualize the

  6. From learning taxonomies to phylogenetic learning: integration of 16S rRNA gene data into FAME-based bacterial classification.

    Science.gov (United States)

    Slabbinck, Bram; Waegeman, Willem; Dawyndt, Peter; De Vos, Paul; De Baets, Bernard

    2010-01-30

    Machine learning techniques have shown to improve bacterial species classification based on fatty acid methyl ester (FAME) data. Nonetheless, FAME analysis has a limited resolution for discrimination of bacteria at the species level. In this paper, we approach the species classification problem from a taxonomic point of view. Such a taxonomy or tree is typically obtained by applying clustering algorithms on FAME data or on 16S rRNA gene data. The knowledge gained from the tree can then be used to evaluate FAME-based classifiers, resulting in a novel framework for bacterial species classification. In view of learning in a taxonomic framework, we consider two types of trees. First, a FAME tree is constructed with a supervised divisive clustering algorithm. Subsequently, based on 16S rRNA gene sequence analysis, phylogenetic trees are inferred by the NJ and UPGMA methods. In this second approach, the species classification problem is based on the combination of two different types of data. Herein, 16S rRNA gene sequence data is used for phylogenetic tree inference and the corresponding binary tree splits are learned based on FAME data. We call this learning approach 'phylogenetic learning'. Supervised Random Forest models are developed to train the classification tasks in a stratified cross-validation setting. In this way, better classification results are obtained for species that are typically hard to distinguish by a single or flat multi-class classification model. FAME-based bacterial species classification is successfully evaluated in a taxonomic framework. Although the proposed approach does not improve the overall accuracy compared to flat multi-class classification, it has some distinct advantages. First, it has better capabilities for distinguishing species on which flat multi-class classification fails. Secondly, the hierarchical classification structure allows to easily evaluate and visualize the resolution of FAME data for the discrimination of bacterial

  7. From learning taxonomies to phylogenetic learning: Integration of 16S rRNA gene data into FAME-based bacterial classification

    Science.gov (United States)

    2010-01-01

    Background Machine learning techniques have shown to improve bacterial species classification based on fatty acid methyl ester (FAME) data. Nonetheless, FAME analysis has a limited resolution for discrimination of bacteria at the species level. In this paper, we approach the species classification problem from a taxonomic point of view. Such a taxonomy or tree is typically obtained by applying clustering algorithms on FAME data or on 16S rRNA gene data. The knowledge gained from the tree can then be used to evaluate FAME-based classifiers, resulting in a novel framework for bacterial species classification. Results In view of learning in a taxonomic framework, we consider two types of trees. First, a FAME tree is constructed with a supervised divisive clustering algorithm. Subsequently, based on 16S rRNA gene sequence analysis, phylogenetic trees are inferred by the NJ and UPGMA methods. In this second approach, the species classification problem is based on the combination of two different types of data. Herein, 16S rRNA gene sequence data is used for phylogenetic tree inference and the corresponding binary tree splits are learned based on FAME data. We call this learning approach 'phylogenetic learning'. Supervised Random Forest models are developed to train the classification tasks in a stratified cross-validation setting. In this way, better classification results are obtained for species that are typically hard to distinguish by a single or flat multi-class classification model. Conclusions FAME-based bacterial species classification is successfully evaluated in a taxonomic framework. Although the proposed approach does not improve the overall accuracy compared to flat multi-class classification, it has some distinct advantages. First, it has better capabilities for distinguishing species on which flat multi-class classification fails. Secondly, the hierarchical classification structure allows to easily evaluate and visualize the resolution of FAME data for

  8. Secondary Structural Models (16S rRNA of Polyhydroxyalkanoates Producing Bacillus Species Isolated from Different Rhizospheric Soil: Phylogenetics and Chemical Analysis

    Directory of Open Access Journals (Sweden)

    Swati Mohapatra

    2016-09-01

    Full Text Available Polyhydroxyalkanoates (PHAs producing bacterial isolates are gaining more importance over the world due to the synthesis of a biodegradable polymer which is extremely desirable to substitute synthetic plastics. PHAs are produced by various microorganisms under certain stress conditions. In this study, sixteen bacterial isolates characterized previously by partial 16S rRNA gene sequencing (NCBI Accession No. KF626466 to KF626481 were again stained by Nile red after three years of preservation in order to confirm their ability to accumulate PHAs. Also, phylogenetic analysis carried out in the present investigation evidenced that the bacterial species belonging to genus Bacillus are the dominant flora of the rhizospheric region, with a potentiality of biodegradable polymer (PHAs production. Again, RNA secondary structure prediction hypothesized that there is no direct correlation between RNA folding pattern stability with a rate of PHAs production among the selected isolates of genus Bacillus.

  9. Diversity of 16S-23S rDNA internal transcribed spacer (ITS reveals phylogenetic relationships in Burkholderia pseudomallei and its near-neighbors.

    Directory of Open Access Journals (Sweden)

    Andrew P Liguori

    Full Text Available Length polymorphisms within the 16S-23S ribosomal DNA internal transcribed spacer (ITS have been described as stable genetic markers for studying bacterial phylogenetics. In this study, we used these genetic markers to investigate phylogenetic relationships in Burkholderia pseudomallei and its near-relative species. B. pseudomallei is known as one of the most genetically recombined bacterial species. In silico analysis of multiple B. pseudomallei genomes revealed approximately four homologous rRNA operons and ITS length polymorphisms therein. We characterized ITS distribution using PCR and analyzed via a high-throughput capillary electrophoresis in 1,191 B. pseudomallei strains. Three major ITS types were identified, two of which were commonly found in most B. pseudomallei strains from the endemic areas, whereas the third one was significantly correlated with worldwide sporadic strains. Interestingly, mixtures of the two common ITS types were observed within the same strains, and at a greater incidence in Thailand than Australia suggesting that genetic recombination causes the ITS variation within species, with greater recombination frequency in Thailand. In addition, the B. mallei ITS type was common to B. pseudomallei, providing further support that B. mallei is a clone of B. pseudomallei. Other B. pseudomallei near-neighbors possessed unique and monomorphic ITS types. Our data shed light on evolutionary patterns of B. pseudomallei and its near relative species.

  10. The phylogenetic position of Lygodactylus angularis and the utility of using the 16S rDNA gene for delimiting species in Lygodactylus (Squamata, Gekkonidae

    Directory of Open Access Journals (Sweden)

    Riccardo Castiglia

    2011-06-01

    Full Text Available The African genus Lygodactylus Gray, is composed of roughly 60 species of diurnal geckos that inhabit tropical and temperate Africa, Madagascar, and South America. In this study, we assessed the phylogenetic position of L. angularis, for which molecular data were so far lacking, by means of sequence analysis of the mitochondrial 16S rDNA gene. We also compared intraspecific vs. interspecific genetic divergences using an extended data set (34 species, 153 sequences, to determine whether a fragment of this gene can be useful for species identification and to reveal the possible existence of new cryptic species in the genus. The analysis placed L. angularis in a monophyletic group together with members of “fischeri” and “picturatus” groups. Nevertheless, the independence of the “angularis” lineage is supported by the high genetic divergence. Comparison of intraspecific vs. interspecific genetic distances highlights that, assuming an equal molecular rate of evolution among the studied species for the used gene, the threshold value useful for recognising a candidate new species can be tentatively placed at 7%. We identified four species that showed an intraspecific divergence higher than, or close to, the 7% threshold: L. capensis (8.7%, L. gutturalis (9.3%, L. madagascariensis (6.5% and L. picturatus (8.1%. Moreover, two species, L. mombasicus and L. verticillatus, are paraphyletic in terms of gene genealogy. Thus, the study shows that a short fragment of the 16S rDNA gene can be an informative tool for species-level taxonomy in the genus Lygodactylus.

  11. Assessment of prey overlap between a native (Polistes humilis) and an introduced (Vespula germanica) social wasp using morphology and phylogenetic analyses of 16S rDNA.

    Science.gov (United States)

    Kasper, Marta L; Reeson, Andrew F; Cooper, Steven J B; Perry, Kym D; Austin, Andrew D

    2004-07-01

    Abstract In newly invaded communities, interspecific competition is thought to play an important role in determining the success of the invader and its impact on the native community. In southern Australia, the native Polistes humilis was the predominant social wasp prior to the arrival of the exotic Vespula germanica (Hymenoptera: Vespidae). Both species forage for similar resources (water, pulp, carbohydrate and protein prey), and concerns have arisen about potential competition between them. The aim of this study was to identify the protein foods that these wasps feed on. As many prey items are masticated by these wasps to the degree that they cannot be identified using conventional means, morphological identification was complemented by sequencing fragments of the mitochondrial 16S rRNA gene. GenBank searches using blast and phylogenetic analyses were used to identify prey items to at least order level. The results were used to construct complete prey inventories for the two species. These indicate that while P. humilis is restricted to feeding on lepidopteran larvae, V. germanica collects a variety of prey of invertebrate and vertebrate origin. Calculated values of prey overlap between the two species are used to discuss the implications of V. germanica impacting on P. humilis. Results obtained are compared to those gained by solely 'conventional' methods, and the advantages of using DNA-based taxonomy in ecological studies are emphasized.

  12. When molecules support morphology: Phylogenetic reconstruction of the family Onuphidae (Eunicida, Annelida) based on 16S rDNA and 18S rDNA.

    Science.gov (United States)

    Budaeva, Nataliya; Schepetov, Dmitry; Zanol, Joana; Neretina, Tatiana; Willassen, Endre

    2016-01-01

    Onuphid polychaetes are tubicolous marine worms commonly reported worldwide from intertidal areas to hadal depths. They often dominate in benthic communities and have economic importance in aquaculture and recreational fishing. Here we report the phylogeny of the family Onuphidae based on the combined analyses of nuclear (18S rDNA) and mitochondrial (16S rDNA) genes. Results of Bayesian and Maximum Likelihood analyses supported the monophyly of Onuphidae and its traditional subdivision into two monophyletic subfamilies: Onuphinae and Hyalinoeciinae. Ten of 22 recognized genera were monophyletic with strong node support; four more genera included in this study were either monotypic or represented by a single species. None of the genera appeared para- or polyphyletic and this indicates a strong congruence between the traditional morphology-based systematics of the family and the newly obtained molecular-based phylogenetic reconstructions. Intergeneric relationships within Hyalinoeciinae were not resolved. Two strongly supported monophyletic groups of genera were recovered within Onuphinae: ((Onuphis, Aponuphis), Diopatra, Paradiopatra) and (Hirsutonuphis, (Paxtonia, (Kinbergonuphis, Mooreonuphis))). A previously accepted hypothesis on the subdivision of Onuphinae into the Onuphis group of genera and the Diopatra group of genera was largely rejected. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

  13. Phylogenetic systematics of Barn Owl (Tyto alba (Scopoli, 1769 complex inferred from mitochondrial rDNA (16S rRNA taxonomic implication

    Directory of Open Access Journals (Sweden)

    Mansour Aliabadian

    2012-09-01

    Full Text Available The Barn owl, Tyto alba (Scopoli, 1769, occurs worldwide and shows a considerable amount of morphological and geographical variations, leading to the recognition of many subspecies throughout the world. Yet, no comprehensive study has not been done on this species. Data from mitochondrial gene (16S Ribosomal RNA (16S with 569 bp length were analyzed for 41 individuals around the world. Maximum likelihood (ML, maximum parsimony (MP and Bayesian analysis showed two distinct clades including alba clad (old world and furcata clad (new world. The amount of genetic variation within each of these clades ranged from 0.5-1.7 but variation between clades was 3.7. This data may suggest that Barn owls of the Old World may be a separate species from those of the New World.

  14. The phylogenetic position of Lygodactylus angularis and the utility of the 16S rDNA gene for delimiting species in Lygodactylus (Squamata, Gekkonidae

    Directory of Open Access Journals (Sweden)

    Riccardo Castiglia

    2011-06-01

    ="EN-US">, the phylogenetic position of one species for which molecular data are lacking, L. angularis. Moreover, we compared the intraspecific vs interspecific genetic divergence using an extended dataset (37 species, 160 haplotypes, to determine whether a fragment of the same gene can be useful for species identification and to reveal the possible presence of new cryptic species in the genus. Lygodactylus angularis resulted in a monophyletic group together with members of the “fisheri” group and of the “picturatus” group. Nevertheless, the independence of the “angularis” lineage is supported by the high genetic divergence. Comparison of intraspecific vs interpecific genetic distances highlights that the threshold values useful for recognising a candidate new species can be tentatively placed at 7%. We identified four species that showed an intraspecific divergence higher than or near the 7% threshold: L. capensis (8.7%, L. gutturalis (9.3%, L. madagascariensis (6.5% and L. picturatus (8.1%. Moreover two species, L. mombasicus and L. verticillatus are paraphyletic in terms of gene genealogy. This study shows that a short fragment of the 16S rDNA gene

  15. Phylogenetic analysis of the fecal microbial community in herbivorous land and marine iguanas of the Galápagos Islands using 16S rRNA-based pyrosequencing.

    Science.gov (United States)

    Hong, Pei-Ying; Wheeler, Emily; Cann, Isaac K O; Mackie, Roderick I

    2011-09-01

    Herbivorous reptiles depend on complex gut microbial communities to effectively degrade dietary polysaccharides. The composition of these fermentative communities may vary based on dietary differences. To explore the role of diet in shaping gut microbial communities, we evaluated the fecal samples from two related host species--the algae-consuming marine iguana (Amblyrhynchus cristatus) and land iguanas (LI) (genus Conolophus) that consume terrestrial vegetation. Marine and LI fecal samples were collected from different islands in the Galápagos archipelago. High-throughput 16S rRNA-based pyrosequencing was used to provide a comparative analysis of fecal microbial diversity. At the phylum level, the fecal microbial community in iguanas was predominated by Firmicutes (69.5±7.9%) and Bacteroidetes (6.2±2.8%), as well as unclassified Bacteria (20.6±8.6%), suggesting that a large portion of iguana fecal microbiota is novel and could be involved in currently unknown functions. Host species differed in the abundance of specific bacterial groups. Bacteroides spp., Lachnospiraceae and Clostridiaceae were significantly more abundant in the marine iguanas (MI) (P-value>1E-9). In contrast, Ruminococcaceae were present at >5-fold higher abundance in the LI than MI (P-value>6E-14). Archaea were only detected in the LI. The number of operational taxonomic units (OTUs) in the LI (356-896 OTUs) was >2-fold higher than in the MI (112-567 OTUs), and this increase in OTU diversity could be related to the complexity of the resident bacterial population and their gene repertoire required to breakdown the recalcitrant polysaccharides prevalent in terrestrial plants. Our findings suggest that dietary differences contribute to gut microbial community differentiation in herbivorous lizards. Most importantly, this study provides a better understanding of the microbial diversity in the iguana gut; therefore facilitating future efforts to discover novel bacterial-associated enzymes that

  16. Phylogenetic diversity and spatial distribution of the microbial community associated with the Caribbean deep-water sponge Polymastia cf. corticata by 16S rRNA, aprA, and amoA gene analysis.

    Science.gov (United States)

    Meyer, Birte; Kuever, Jan

    2008-08-01

    Denaturing gradient gel electrophoresis (DGGE)-based analyses of 16S rRNA, aprA, and amoA genes demonstrated that a phylogenetically diverse and complex microbial community was associated with the Caribbean deep-water sponge Polymastia cf. corticata Ridley and Dendy, 1887. From the 38 archaeal and bacterial 16S rRNA phylotypes identified, 53% branched into the sponge-specific, monophyletic sequence clusters determined by previous studies (considering predominantly shallow-water sponge species), whereas 26% appeared to be P. cf. corticata specifically associated microorganisms ("specialists"); 21% of the phylotypes were confirmed to represent seawater- and sediment-derived proteobacterial species ("contaminants") acquired by filtration processes from the host environment. Consistently, the aprA and amoA gene-based analyses indicated the presence of environmentally derived sulfur- and ammonia-oxidizers besides putative sponge-specific sulfur-oxidizing Gammaproteobacteria and Alphaproteobacteria and a sulfate-reducing archaeon. A sponge-specific, endosymbiotic sulfur cycle as described for marine oligochaetes is proposed to be also present in P. cf. corticata. Overall, the results of this work support the recent studies that demonstrated the sponge species specificity of the associated microbial community while the biogeography of the host collection site has only a minor influence on the composition. In P. cf. corticata, the specificity of the sponge-microbe associations is even extended to the spatial distribution of the microorganisms within the sponge body; distinct bacterial populations were associated with the different tissue sections, papillae, outer and inner cortex, and choanosome. The local distribution of a phylotype within P. cf. corticata correlated with its (1) phylogenetic affiliation, (2) classification as sponge-specific or nonspecifically associated microorganism, and (3) potential ecological role in the host sponge.

  17. Phylogenetic relationships of Chilean leptodactylids: a molecular approach based on mitochondrial genes 12S and 16S Relaciones filogenéticas de los leptodactílidos chilenos: una aproximación molecular basada en los genes mitocondriales 12S y 16S

    Directory of Open Access Journals (Sweden)

    CLAUDIO CORREA

    2006-12-01

    Full Text Available Most Chilean amphibians belong to the subfamily Telmatobiinae (Anura, Leptodactylidae. Several phylogenetic studies of Leptodactylidae and Telmatobiinae, based principally on morphological characters, have implicitly suggested closer relationships of some species of the Telmatobiinae with members of other subfamilies of leptodactylids, including the leptodactyline genus Pleurodema which is present in Chile. Furthermore, a growing number of molecular studies suggest a non monophyletic status for Telmatobiinae, although none of these studies have investigated the phylogenetic relationships of this subfamily. We compared partial sequences of the ribosomal mitochondrial genes 12S and 16S to determine the phylogenetic relationships of Chilean leptodactylids and its position within the modern anurans (Neobatrachia. We included 22 species from nine of the 10 genera of telmatobiines present in Chile (Alsodes, Atelognathus, Batrachyla, Caudiverbera, Eupsophus, Hylorina, Insuetophrynus, Telmatobufo and Telmatobius, two species of the genus Pleurodema, and one species of Rhinodermatidae, which is considered a leptodactylid derivative family by some authors. We also included 51 species representing most of the families that compose Neobatrachia. Phylogenetic reconstructions were performed using the methods of maximum parsimony, maximum likelihood and Bayesian inference. The topologies obtained in all the analyses indicate that Telmatobiinae is a polyphyletic assemblage, composed by species belonging to Hyloidea (most of the genera and species more related to Australasian taxa (the clade Caudiverbera + Telmatobufo, defined as the tribe Calyptocephalellini. These molecular data support groups based on other kinds of evidence (Caudiverbera + Telmatobufo, Alsodes + Eupsophus and Batrachyla + Hylorina and raise new phylogenetic hypotheses for several genera of telmatobiines (Atelognathus with Batrachyla and Hylorina, Insuetophrynus + Rhinoderma. The phylogenetic

  18. Evaluation of haplotype diversity of Achatina fulica (Lissachatina) [Bowdich] from Indian sub-continent by means of 16S rDNA sequence and its phylogenetic relationships with other global populations.

    Science.gov (United States)

    Ayyagari, Vijaya Sai; Sreerama, Krupanidhi

    2017-08-01

    Achatina fulica (Lissachatina fulica) is one of the most invasive species found across the globe causing a significant damage to crops, vegetables, and horticultural plants. This terrestrial snail is native to east Africa and spread to different parts of the world by introductions. India, a hot spot for biodiversity of several endemic gastropods, has witnessed an outburst of this snail population in several parts of the country posing a serious threat to crop loss and also to human health. With an objective to evaluate the genetic diversity of this snail, we have sampled this snail from different parts of India and analyzed its haplotype diversity by means of 16S rDNA sequence information. Apart from this, we have studied the phylogenetic relationships of the isolates sequenced in the present study in relation with other global populations by Bayesian and Maximum-likelihood approaches. Of the isolates sequenced, haplotype 'C' is the predominant one. A new haplotype 'S' from the state of Odisha was observed. The isolates sequenced in the present study clustered with its conspecifics from the Indian sub-continent. Haplotype network analyses were also carried out for studying the evolution of different haplotypes. It was observed that haplotype 'S' was associated with a Mauritius haplotype 'H', indicating the possibility of multiple introductions of A. fulica to India.

  19. High density, genome-wide markers and intra-specific replication yield an unprecedented phylogenetic reconstruction of a globally significant, speciose lineage of Eucalyptus.

    Science.gov (United States)

    Jones, Rebecca C; Nicolle, Dean; Steane, Dorothy A; Vaillancourt, René E; Potts, Brad M

    2016-12-01

    We used genome-wide markers and an unprecedented scale of sampling to construct a phylogeny for a globally significant Eucalyptus lineage that has been impacted by hybridisation, recent radiation and morphological convergence. Our approach, using 3109 DArT markers distributed throughout the genome and 540 samples covering 185 terminal taxa in sections Maidenaria, Exsertaria, Latoangulatae and related smaller sections, with multiple geographically widespread samples per terminal taxon, produced a phylogeny that largely matched the morphological treatment of sections, though sections Exsertaria and Latoangulatae were polyphyletic. At lower levels there were numerous inconsistencies between the morphological treatment and the molecular phylogeny, and taxa within the three main sections were generally not monophyletic at the series (at least 62% polyphyly) or species (at least 52% polyphyly) level. Some of the discrepancies appear to be the result of morphological convergence or misclassifications, and we propose some taxonomic reassessments to address this. However, many inconsistencies appear to be the products of incomplete speciation and/or hybridisation. Our analysis represents a significant advance on previous phylogenies of these important eucalypt sections (which have mainly used single samples to represent each species), thus providing a robust phylogenetic framework for evolutionary and ecological studies. Copyright © 2016 Elsevier Inc. All rights reserved.

  20. 'Candidatus mycoplasma haemodidelphidis' sp. nov., 'Candidatus mycoplasma haemolamae' sp. nov. and Mycoplasma haemocanis comb. nov., haemotrophic parasites from a naturally infected opossum (Didelphis virginiana), alpaca (Lama pacos) and dog (Canis familiaris): phylogenetic and secondary structural relatedness of their 16S rRNA genes to other mycoplasmas.

    Science.gov (United States)

    Messick, Joanne B; Walker, Pamela G; Raphael, William; Berent, Linda; Shi, Xun

    2002-05-01

    The 16S rRNA sequence of newly characterized haemotrophic bacteria in an opossum (Didelphis virginiana) and alpaca (Lama pacos) was determined. In addition, the 16S rRNA sequence of a haemotrophic parasite in the dog (Canis familiaris) was determined. Sequence alignment and evolutionary analysis as well as secondary structural similarity and signature nucleotide sequence motifs of their 16S rRNA genes, positioned these organisms in the genus Mycoplasma. The highest scoring sequence similarities were 16S rRNA genes from haemotrophic mycoplasma species (Haemobartonella and Eperythrozoon spp.). However, the lack of several higher-order structural idiosyncrasies used to define the pneumoniae group, suggests that these organisms and related haemotrophic mycoplasmas represent a new group of mycoplasmas. It is recommended that the organisms be named 'Candidatus Mycoplasma haemodidelphidis', 'Candidatus Mycoplasma haemolamae' and Mycoplasma haemocanis comb. nov., to provide some indication of the target cell and host species of these parasites, and to reflect their phylogenetic affiliation.

  1. High density dispersion fuel

    International Nuclear Information System (INIS)

    Hofman, G.L.

    1996-01-01

    A fuel development campaign that results in an aluminum plate-type fuel of unlimited LEU burnup capability with an uranium loading of 9 grams per cm 3 of meat should be considered an unqualified success. The current worldwide approved and accepted highest loading is 4.8 g cm -3 with U 3 Si 2 as fuel. High-density uranium compounds offer no real density advantage over U 3 Si 2 and have less desirable fabrication and performance characteristics as well. Of the higher-density compounds, U 3 Si has approximately a 30% higher uranium density but the density of the U 6 X compounds would yield the factor 1.5 needed to achieve 9 g cm -3 uranium loading. Unfortunately, irradiation tests proved these peritectic compounds have poor swelling behavior. It is for this reason that the authors are turning to uranium alloys. The reason pure uranium was not seriously considered as a dispersion fuel is mainly due to its high rate of growth and swelling at low temperatures. This problem was solved at least for relatively low burnup application in non-dispersion fuel elements with small additions of Si, Fe, and Al. This so called adjusted uranium has nearly the same density as pure α-uranium and it seems prudent to reconsider this alloy as a dispersant. Further modifications of uranium metal to achieve higher burnup swelling stability involve stabilization of the cubic γ phase at low temperatures where normally α phase exists. Several low neutron capture cross section elements such as Zr, Nb, Ti and Mo accomplish this in various degrees. The challenge is to produce a suitable form of fuel powder and develop a plate fabrication procedure, as well as obtain high burnup capability through irradiation testing

  2. Photoionization and High Density Gas

    Science.gov (United States)

    Kallman, T.; Bautista, M.; White, Nicholas E. (Technical Monitor)

    2002-01-01

    We present results of calculations using the XSTAR version 2 computer code. This code is loosely based on the XSTAR v.1 code which has been available for public use for some time. However it represents an improvement and update in several major respects, including atomic data, code structure, user interface, and improved physical description of ionization/excitation. In particular, it now is applicable to high density situations in which significant excited atomic level populations are likely to occur. We describe the computational techniques and assumptions, and present sample runs with particular emphasis on high density situations.

  3. High-density multicore fibers

    DEFF Research Database (Denmark)

    Takenaga, K.; Matsuo, S.; Saitoh, K.

    2016-01-01

    High-density single-mode multicore fibers were designed and fabricated. A heterogeneous 30-core fiber realized a low crosstalk of −55 dB. A quasi-single-mode homogeneous 31-core fiber attained the highest core count as a single-mode multicore fiber.......High-density single-mode multicore fibers were designed and fabricated. A heterogeneous 30-core fiber realized a low crosstalk of −55 dB. A quasi-single-mode homogeneous 31-core fiber attained the highest core count as a single-mode multicore fiber....

  4. [TYPING OF LEPTOSPIRA SPP. STRAINS BASED ON 16S rRNA].

    Science.gov (United States)

    Ostankova, Yu V; Semenov, A V; Stoyanova, N A; Tokarevich, N K; Lyubimova, N E; Petrova, O A; Ananina, Yu V; Petrov, E M

    2016-01-01

    Comparative typing of Leptospira spp. strain collection based on analysis of 16S RNA fragment. 2 pairs of primers were used for PCR, that jointly flank 1423b.p. sized fragment. Sequences of Leptospira spp. strain 16S rRNA, presented in the international database, were used for phylogenetic analysis. A high similarity, including interspecies, of the 16S fragment in Leptospira spp. strains was shown independently of the source, serovar and serogroup. Heterogeneity of the primary matrix, spontaneous mutations of hotspots and erroneous nucleotide couplings, characteristic for 16S sequence of pathogenic Leptospira spp. strains, are discussed. Molecular-genetic characteristic of certain reference Leptospira spp. strains by 16S sequence is obtained. Results of the studies give evidence on expedience of introduction into clinical practice of identification of Leptospira spp. by 16S sequence directly from the clinical material, that would allow to significantly reduce identification time, dismiss complex type-specific sera and other labor-intensive methods.

  5. Analysis of 16S libraries of mouse gastrointestinal microflora reveals a large new group of mouse intestinal bacteria

    NARCIS (Netherlands)

    Salzman, NH; de Jong, H; Paterson, Y; Harmsen, HJM; Welling, GW; Bos, NA

    2002-01-01

    Total genomic DNA from samples of intact mouse small intestine, large intestine, caecum and faeces was used as template for PCR amplification of 16S rRNA gene sequences with conserved bacterial primers. Phylogenetic analysis of the amplification products revealed 40 unique 16S rDNA sequences. Of

  6. Comparative performance of the 16S rRNA gene in DNA barcoding of amphibians

    Directory of Open Access Journals (Sweden)

    Chiari Ylenia

    2005-03-01

    Full Text Available Abstract Background Identifying species of organisms by short sequences of DNA has been in the center of ongoing discussions under the terms DNA barcoding or DNA taxonomy. A C-terminal fragment of the mitochondrial gene for cytochrome oxidase subunit I (COI has been proposed as universal marker for this purpose among animals. Results Herein we present experimental evidence that the mitochondrial 16S rRNA gene fulfills the requirements for a universal DNA barcoding marker in amphibians. In terms of universality of priming sites and identification of major vertebrate clades the studied 16S fragment is superior to COI. Amplification success was 100% for 16S in a subset of fresh and well-preserved samples of Madagascan frogs, while various combination of COI primers had lower success rates.COI priming sites showed high variability among amphibians both at the level of groups and closely related species, whereas 16S priming sites were highly conserved among vertebrates. Interspecific pairwise 16S divergences in a test group of Madagascan frogs were at a level suitable for assignment of larval stages to species (1–17%, with low degrees of pairwise haplotype divergence within populations (0–1%. Conclusion We strongly advocate the use of 16S rRNA as standard DNA barcoding marker for vertebrates to complement COI, especially if samples a priori could belong to various phylogenetically distant taxa and false negatives would constitute a major problem.

  7. Molecular Characterization and Analysis of 16S Ribosomal DNA in Some Isolates of Demodex folicullorum.

    Science.gov (United States)

    Daneshparvar, Afrooz; Mowlavi, Gholamreza; Mirjalali, Hamed; Hajjaran, Homa; Mobedi, Iraj; Naddaf, Saeed Reza; Shidfar, Mohammadreza; Sadat Makki, Mahsa

    2017-01-01

    Demodicosis is one of the most prevalent skin diseases resulting from infestation by Demodex mites. This parasite usually inhabits in follicular infundibulum or sebaceous duct and transmits through close contact with an infested host. This study was carried from September 2014 to January 2016 at Tehran University of Medical Sciences, Tehran, Iran. DNA extraction and amplification of 16S ribosomal RNA was performed on four isolates, already obtained from four different patients and identified morphologically though clearing with 10% Potassium hydroxide (KOH) and microscopical examination. Amplified fragments from the isolates were compared with GeneBank database and phylogenetic analysis was carried out using MEGA6 software. A 390 bp fragment of 16S rDNA was obtained in all isolates and analysis of generated sequences showed high similarity with those submitted to GenBank, previously. Intra-species similarity and distance also showed 99.983% and 0.017, respectively, for the studied isolates. Multiple alignments of the isolates showed Single Nucleotide Polymorphisms (SNPs) in 16S rRNA fragment. Phylogenetic analysis revealed that all 4 isolates clustered with other D. folliculorum, recovered from GenBank database. Our accession numbers KF875587 and KF875589 showed more similarity together in comparison with two other studied isolates. Mitochondrial 16S rDNA is one of the most suitable molecular barcodes for identification D. folliculorum and this fragment can use for intra-species characterization of the most human-infected mites.

  8. Molecular Characterization and Analysis of 16S Ribosomal DNA in some Isolates of Demodex folliculorum

    Directory of Open Access Journals (Sweden)

    Afrooz DANESHPARVAR

    2017-06-01

    Full Text Available Background: Demodicosis is one of the most prevalent skin diseases resulting from infestation by Demodex mites. This parasite usually inhabits in follicular infundibulum or sebaceous duct transmitted through close contact with an infested host.Methods: This study was carried from September 2014 to January 2016 at Tehran University of Medical Sciences, Tehran, Iran. DNA extraction and amplification of 16S ribosomal RNA was performed on four isolates, obtained from four patients and identified morphologically through clearing with 10% Potassium hydroxide (KOH and microscopical examination. Amplified fragments from the isolates were compared with GenBank database and phylogenetic analysis was carried out using MEGA6 software.Results: A 390 bp fragment of 16S rDNA was obtained in all isolates and analysis of generated sequences showed high similarity with those submitted to GenBank, previously. Intra-species similarity and distance also showed 99.983% and 0.017, respectively, for the studied isolates. Multiple alignments of the isolates showed Single Nucleotide Polymorphisms (SNPs in 16S rRNA fragment. Phylogenetic analysis revealed that all 4 isolates clustered with other D. folliculorum, recovered from GenBank database. Our accession numbers KF875587 and KF875589 showed more similarity together in comparison with two other studied isolates. Conclusion: Mitochondrial 16S rDNA is one of the most suitable molecular barcodes for identification D. folliculorum and this fragment can use for intra-species characterization of the most human-infected mites.

  9. High density harp for SSCL linac

    International Nuclear Information System (INIS)

    Fritsche, C.T.; Krogh, M.L.; Crist, C.E.

    1993-01-01

    AlliedSignal Inc., Kansas City Division, and the Superconducting Super Collider Laboratory (SSCL) are collaboratively developing a high density harp for the SSCL linac. This harp is designed using hybrid microcircuit (HMC) technology to obtain a higher wire density than previously available. The developed harp contains one hundred twenty-eight 33-micron-diameter carbon wires on 0.38-mm centers. The harp features an onboard broken wire detection circuit. Carbon wire preparation and attachment processes were developed. High density surface mount connectors were located. The status of high density harp development will be presented along with planned future activities

  10. High density harp for SSCL linac

    International Nuclear Information System (INIS)

    Fritsche, C.T.; Krogh, M.L.

    1993-05-01

    AlliedSignal Inc., Kansas City Division, and the Superconducting Super Collider Laboratory (SSCL) are collaboratively developing a high density harp for the SSCL linac. This harp is designed using hybrid microcircuit (HMC) technology to obtain a higher wire density than previously available. The developed harp contains one hundred twenty-eight 33-micron-diameter carbon wires on 0.38-mm centers. The harp features an onboard broken wire detection circuit. Carbon wire preparation and attachment processes were developed. High density surface mount connectors were located. The status of high density harp development will be presented along with planned future activities

  11. Extensive 16S rRNA gene sequence diversity in Campylobacter hyointestinalis strains: taxonomic and applied implications

    DEFF Research Database (Denmark)

    Harrington, C.S.; On, Stephen L.W.

    1999-01-01

    Phylogenetic relationships of Campylobacter hyointestinalis subspecies were examined by means of 16S rRNA gene sequencing. Sequence similarities among C. hyointestinalis subsp. lawsonii strains exceeded 99.0 %, but values among C. hyointestinalis subsp. hyointestinalis strains ranged from 96...... of the genus Campylobacter, emphasizing the need for multiple strain analysis when using 16S rRNA gene sequence comparisons for taxonomic investigations........4 to 100 %. Sequence similarites between strains representing the two different subspecies ranged from 95.7 to 99.0 %. An intervening sequence was identified in certain of the C. hyointestinalis subsp. lawsonii strains. C. hyointestinalis strains occupied two distinct branches in a phylogenetic analysis...

  12. The distribution, diversity, and importance of 16S rRNA gene introns in the order Thermoproteales.

    Science.gov (United States)

    Jay, Zackary J; Inskeep, William P

    2015-07-09

    Intron sequences are common in 16S rRNA genes of specific thermophilic lineages of Archaea, specifically the Thermoproteales (phylum Crenarchaeota). Environmental sequencing (16S rRNA gene and metagenome) from geothermal habitats in Yellowstone National Park (YNP) has expanded the available datasets for investigating 16S rRNA gene introns. The objectives of this study were to characterize and curate archaeal 16S rRNA gene introns from high-temperature habitats, evaluate the conservation and distribution of archaeal 16S rRNA introns in geothermal systems, and determine which "universal" archaeal 16S rRNA gene primers are impacted by the presence of intron sequences. Several new introns were identified and their insertion loci were constrained to thirteen locations across the 16S rRNA gene. Many of these introns encode homing endonucleases, although some introns were short or partial sequences. Pyrobaculum, Thermoproteus, and Caldivirga 16S rRNA genes contained the most abundant and diverse intron sequences. Phylogenetic analysis of introns revealed that sequences within the same locus are distributed biogeographically. The most diverse set of introns were observed in a high-temperature, circumneutral (pH 6) sulfur sediment environment, which also contained the greatest diversity of different Thermoproteales phylotypes. The widespread presence of introns in the Thermoproteales indicates a high probability of misalignments using different "universal" 16S rRNA primers employed in environmental microbial community analysis.

  13. Analysis of bacterial genetic diversity in biofloc by using ARDRA 16S-rRNA gene

    Directory of Open Access Journals (Sweden)

    , Widanarni

    2015-05-01

    Full Text Available ABSTRACT This study aimed to analyze the genetic diversity of bacteria associated in bioflocs using 16S-rRNA polymerase chain reaction (PCR with ARDRA technique. A total of 38 dominant bacterial isolates was obtained from bioflocs samples and of these isolates, 16S-rRNA gene was then isolated and amplified using PCR. The 16S-rRNA gene of the isolates was then cut using HaeIII (5’-GG↓CC and HhaI (5’-GCG↓C restriction enzymes resulting an ARDRA pattern which was further used as the binary data for the construction of phylogenetics tree that was used to estimate the group of bacteria. The result with HaeIII cut restriction enzyme from biofloc-associated bacteria gave 11 ARDRA patterns, while with the restriction enzyme HhaI gave eight ARDRA patterns. Phylogenetics of bacterial populations from biofloc-based cultivation system water consisted of at least 13 different bacterial species. Result of sequencing from two gene sample 16S-rRNA were identified as Microbacterium foliorumand and Pseudomonas putida. Keywords: bacterial diversity, ARDRA, biofloc, phylogeny  ABSTRAK Penelitian ini bertujuan untuk menganalisis keragaman genetika bakteri bioflok menggunakan metode polymerase chain reaction (PCR 16S-rRNA dengan teknik ARDRA. Sebanyak 38 isolat bakteri dominan yang diperoleh diamplifikasi gen 16S-rRNAnya dengan PCR, kemudian dipotong dengan enzim restriksi HaeIII (5’-GG↓CC dan HhaI (5’-GCG↓C. Pola ARDRA ini dijadikan data biner sebagai input untuk konstruksi pohon filogenetika yang dapat digunakan untuk memerkirakan jenis bakteri yang ada. Gen 16S-rRNA hasil PCR setelah dipotong dengan enzim restriksi HaeIII didapatkan 11 pola ARDRA, sedangkan dengan enzim restriksi HhaI menghasilkan delapan pola ARDRA. Berdasarkan pohon filogenetika, diketahui populasi bakteri pada air sistem budidaya bioflok sedikitnya terdiri atas 13 jenis bakteri. Berdasarkan sekuensing dari dua sampel gen 16S-rRNA teridentifikasi jenis bakteri Microbacterium

  14. Genotypic Characterization of Bradyrhizobium Strains Nodulating Endemic Woody Legumes of the Canary Islands by PCR-Restriction Fragment Length Polymorphism Analysis of Genes Encoding 16S rRNA (16S rDNA) and 16S-23S rDNA Intergenic Spacers, Repetitive Extragenic Palindromic PCR Genomic Fingerprinting, and Partial 16S rDNA Sequencing

    Science.gov (United States)

    Vinuesa, Pablo; Rademaker, Jan L. W.; de Bruijn, Frans J.; Werner, Dietrich

    1998-01-01

    We present a phylogenetic analysis of nine strains of symbiotic nitrogen-fixing bacteria isolated from nodules of tagasaste (Chamaecytisus proliferus) and other endemic woody legumes of the Canary Islands, Spain. These and several reference strains were characterized genotypically at different levels of taxonomic resolution by computer-assisted analysis of 16S ribosomal DNA (rDNA) PCR-restriction fragment length polymorphisms (PCR-RFLPs), 16S-23S rDNA intergenic spacer (IGS) RFLPs, and repetitive extragenic palindromic PCR (rep-PCR) genomic fingerprints with BOX, ERIC, and REP primers. Cluster analysis of 16S rDNA restriction patterns with four tetrameric endonucleases grouped the Canarian isolates with the two reference strains, Bradyrhizobium japonicum USDA 110spc4 and Bradyrhizobium sp. strain (Centrosema) CIAT 3101, resolving three genotypes within these bradyrhizobia. In the analysis of IGS RFLPs with three enzymes, six groups were found, whereas rep-PCR fingerprinting revealed an even greater genotypic diversity, with only two of the Canarian strains having similar fingerprints. Furthermore, we show that IGS RFLPs and even very dissimilar rep-PCR fingerprints can be clustered into phylogenetically sound groupings by combining them with 16S rDNA RFLPs in computer-assisted cluster analysis of electrophoretic patterns. The DNA sequence analysis of a highly variable 264-bp segment of the 16S rRNA genes of these strains was found to be consistent with the fingerprint-based classification. Three different DNA sequences were obtained, one of which was not previously described, and all belonged to the B. japonicum/Rhodopseudomonas rDNA cluster. Nodulation assays revealed that none of the Canarian isolates nodulated Glycine max or Leucaena leucocephala, but all nodulated Acacia pendula, C. proliferus, Macroptilium atropurpureum, and Vigna unguiculata. PMID:9603820

  15. High Density Digital Data Storage System

    Science.gov (United States)

    Wright, Kenneth D., II; Gray, David L.; Rowland, Wayne D.

    1991-01-01

    The High Density Digital Data Storage System was designed to provide a cost effective means for storing real-time data from the field-deployable digital acoustic measurement system. However, the high density data storage system is a standalone system that could provide a storage solution for many other real time data acquisition applications. The storage system has inputs for up to 20 channels of 16-bit digital data. The high density tape recorders presently being used in the storage system are capable of storing over 5 gigabytes of data at overall transfer rates of 500 kilobytes per second. However, through the use of data compression techniques the system storage capacity and transfer rate can be doubled. Two tape recorders have been incorporated into the storage system to produce a backup tape of data in real-time. An analog output is provided for each data channel as a means of monitoring the data as it is being recorded.

  16. Improved taxonomic assignment of human intestinal 16S rRNA sequences by a dedicated reference database

    NARCIS (Netherlands)

    Ritari, Jarmo; Salojärvi, Jarkko; Lahti, Leo; Vos, de Willem M.

    2015-01-01

    Background: Current sequencing technology enables taxonomic profiling of microbial ecosystems at high resolution and depth by using the 16S rRNA gene as a phylogenetic marker. Taxonomic assignation of newly acquired data is based on sequence comparisons with comprehensive reference databases to

  17. IDENTIFICATION OF ACTIVE BACTERIAL COMMUNITIES IN A MODEL DRINKING WATER BIOFILM SYSTEM USING 16S RRNA-BASED CLONE LIBRARIES

    Science.gov (United States)

    Recent phylogenetic studies have used DNA as the target molecule for the development of environmental 16S rDNA clone libraries. As DNA may persist in the environment, DNA-based libraries cannot be used to identify metabolically active bacteria in water systems. In this study, a...

  18. Magnetization of High Density Hadronic Fluid

    DEFF Research Database (Denmark)

    Bohr, Henrik; Providencia, Constanca; da Providencia, João

    2012-01-01

    In the present paper the magnetization of a high density relativistic fluid of elementary particles is studied. At very high densities, such as may be found in the interior of a neutron star, when the external magnetic field is gradually increased, the energy of the normal phase of the fluid...... in the particle fluid. For nuclear densities above 2 to 3 rho(0), where rho(0) is the equilibrium nuclear density, the resulting magnetic field turns out to be rather huge, of the order of 10(17) Gauss....

  19. Supernovae and high density nuclear matter

    International Nuclear Information System (INIS)

    Kahana, S.

    1986-01-01

    The role of the nuclear equation of state (EOS) in producing prompt supernova explosions is examined. Results of calculations of Baron, Cooperstein, and Kahana incorporating general relativity and a new high density EOS are presented, and the relevance of these calculations to laboratory experiments with heavy ions considered. 31 refs., 6 figs., 2 tabs

  20. Supernovae and high density nuclear matter

    Energy Technology Data Exchange (ETDEWEB)

    Kahana, S.

    1986-01-01

    The role of the nuclear equation of state (EOS) in producing prompt supernova explosions is examined. Results of calculations of Baron, Cooperstein, and Kahana incorporating general relativity and a new high density EOS are presented, and the relevance of these calculations to laboratory experiments with heavy ions considered. 31 refs., 6 figs., 2 tabs.

  1. High Density GEOSAT/GM Altimeter Data

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The high density Geosat/GM altimeter data south of 30 S have finally arrived. In addition, ERS-1 has completed more than 6 cycles of its 35-day repeat track. These...

  2. High density aseismic spent fuel storage racks

    International Nuclear Information System (INIS)

    Louvat, J.P.

    1985-05-01

    After the reasons of the development of high density aseismic spent fuel racks by FRAMATOME and LEMER, a description is presented, as also the codes, standards and regulations used to design this FRAMATOME storage rack. Tests have been carried out concerning criticality, irradiation of Cadminox, corrosion of the cell, and the seismic behaviour

  3. 16S rRNA phylogenetic analysis of actinomycetes isolated from ...

    African Journals Online (AJOL)

    SNPK

    2012-07-26

    Jul 26, 2012 ... Marine mangroves and eastern Ghats of Indian eco- systems facilitate the .... U of Ex Taq polymerase chain reaction (PCR). Conditions consisted of ... its building blocks of amino acids in the cell wall. (Fredimoses, 2010).

  4. Some recent efforts toward high density implosions

    International Nuclear Information System (INIS)

    McClellan, G.E.

    1980-01-01

    Some recent Livermore efforts towards achieving high-density implosions are presented. The implosion dynamics necessary to compress DT fuel to 10 to 100 times liquid density are discussed. Methods of diagnosing the maximum DT density for a specific design are presented along with results to date. The dynamics of the double-shelled target with an exploding outer shell are described, and some preliminary experimental results are presented

  5. Framatome offers new high density Cadminox racks

    International Nuclear Information System (INIS)

    Anon.

    1985-01-01

    Framatome have developed a new material called Cadminox for use in high density spent fuel storage racks. It is claimed that Cadminox will remain stable stable in pond storage when racks submerged in boronated water are irradiated by the spent fuel they contain. A brief description of the storage module is given, including the aseismic bearing device which minimises loads on pond walls, racks and fuel assemblies. (UK)

  6. Spin polarization in high density quark matter

    DEFF Research Database (Denmark)

    Bohr, Henrik; Panda, Prafulla K.; Providênci, Constanca

    2013-01-01

    We investigate the occurrence of a ferromagnetic phase transition in high density hadronic matter (e.g., in the interior of a neutron star). This could be induced by a four-fermion interaction analogous to the one which is responsible for chiral symmetry breaking in the Nambu-Jona-Lasinio model, ...... the so-called 2 flavor super-conducting phase to the ferromagnetic phase arises. The color-flavor-locked phase may be completely hidden by the FP....

  7. The car parking problem at high densities

    Science.gov (United States)

    Burgos, E.; Bonadeo, H.

    1989-04-01

    The radial distribution functions of random 1-D systems of sequential hard rods have been studied in the range of very high densities. It is found that as the number of samples rejected before completion increases, anomalies in the pairwise distribution functions arise. These are discussed using analytical solutions for systems of three rods and numerical simulations with twelve rods. The probabilities of different spatial orderings with respect to the sequential order are examined.

  8. Structure of E. coli 16S RNA elucidated by psoralen crosslinking

    International Nuclear Information System (INIS)

    Thompson, J.F.; Hearst, J.E.

    1983-01-01

    E. coli 16S RNA in solution was photoreacted with hydroxymethyltrimethylpsoralen and long wave ultraviolet light. Positions of crosslinks were determined to high resolution by partially digesting the RNA with T 1 RNase, separating the crosslinked fragments by two-dimensional gel electrophoresis, reversing the crosslink, and sequencing the separated fragments. This method yielded the locations of crosslinks to +/-15 nucleotides. Even finer placement has been made on the basis of our knowledge of psoralen reactivity. Thirteen unique crosslinks were mapped. Seven crosslinks confirmed regions of secondary structure which had been predicted in published phylogenetic models, three crosslinks discriminated between phylogenetic models, and three proved the existence of new structures. The new structures were all long-range interactions which appear to be in dynamic equilibrium with local secondary structure. Because this technique yields direct information about the secondary structure of large RNAs, it should prove invaluable in studying the structure of other RNAs of all sizes

  9. Sekuensing 16S DNA Bakteri Selulolitik Asal Limbah Cairan Rumen Sapi Peranakan Ongole (SEQUENCING OF 16S DNA OF CELLULOLYTIC BACTERIA FROM BOVINE RUMEN FLUID WASTE ONGOLE CROSSBREED

    Directory of Open Access Journals (Sweden)

    Widya Paramita Lokapirnasari

    2017-04-01

    Full Text Available This study aimed to identified cellulolytic inoculant code WPL 214 isolated from bovine rumen fluid waste of Ongole Cross Breed of Surabaya Slaughter house. A single colony of isolates celulolytic grown on 5 mL of liquid media Luria Bertani (LB consist of 1 % NaCl , 1% tripton , 0.5 % yeast extract, containing1 % carboxymethyl cellulose (CMC at temperature 37°C, using a shaker of incubator during 16-18 hours. That isolate determined by 16S DNA gen analysis using High Fidelity Platinum Taq DNA Polymerase with primer forward PB36 5’-AGR GTT TGA TCM TGG CTC AG-3’ and primer reverse PB38 5’-GMT ACCTTG TTA CGA CTT-3’ for PCR. Nucleotide sequence of 16S DNA fragment was determined through the sequencing method. The result was then compared with GenBank database to recognize the type of the sample bacteria. DNA isolation and 16S DNA coding genes amplification were carried out using Kit High Fidelity Platinum Taq DNA Polymerase. Afterward, BLAST was applied to identify the phylogenetic tree. The bacteria was capable of indicating the existence of clear zone in a media CMC by congo red staining. The existence of the clear zone associated with the activity of microbes to degrade cellulose. The conclusión of this research based on the results was the sequencing nucleotides genome 16S DNA showed that cellulolytic inoculant was identified as Enterobacter cloacae WPL 214. ABSTRAK Penelitian ini bertujuan untuk mengidentifikasi lebih lanjut isolat selulolitik kode WPL 214 yang telah diisolasi dari cairan rumen sapi peranakan ongole dari limbah Rumah Potong Hewan Surabaya. Koloni tunggal dari isolat selulolitik ditumbuhkan pada 5 mL media cair Luria Bertani (LB dengan komposisisi 1% NaCl, 1% tripton, 0,5% yeast ekstrak, yang mengandung 1% substrat carboxymethyl cellulose (CMC pada suhu 37°C, dengan pengocokan menggunakan shaker incubator selama ±16-18 jam. Penelitian ini terdiri dari dua tahap, tahap pertama dilakukan isolasi DNA, tahap kedua

  10. High density data recording for SSCL linac

    International Nuclear Information System (INIS)

    VanDeusen, A.L.; Crist, C.

    1993-01-01

    The Superconducting Super Collider Laboratory and AlliedSignal Aerospace have collaboratively developed a high density data monitoring system for beam diagnostic activities. The 128 channel data system is based on a custom multi-channel high speed digitizer card for the VXI bus. The card is referred to as a Modular Input VXI (MIX) digitizer. Multiple MIX cards are used in the complete system to achieve the necessary high channel density requirements. Each MIX digitizer card also contains programmable signal conditioning, and enough local memory to complete an entire beam scan without assistance from the host processor

  11. Plasma Diagnostics in High Density Reactors

    International Nuclear Information System (INIS)

    Daltrini, A. M.; Moshkalyov, S.; Monteiro, M. J. R.; Machida, M.; Kostryukov, A.; Besseler, E.; Biasotto, C.; Diniz, J. A.

    2006-01-01

    Langmuir electric probes and optical emission spectroscopy diagnostics were developed for applications in high density plasmas. These diagnostics were employed in two plasma sources: an electron cyclotron resonance (ECR) plasma and an RF driven inductively coupled plasma (ICP) plasma. Langmuir probes were tested using a number of probing dimensions, probe tip materials, circuits for probe bias and filters. Then, the results were compared with the optical spectroscopy measurements. With these diagnostics, analyses of various plasma processes were performed in both reactors. For example, it has been shown that species like NH radicals generated in gas phase can have critical impact on films deposited by ECR plasmas. In the ICP source, plasmas in atomic and molecular gases were shown to have different spatial distributions, likely due to nonlocal electron heating. The low-to-high density transitions in the ICP plasma were also studied. The role of metastables is shown to be significant in Ar plasmas, in contrast to plasmas with additions of molecular gases

  12. Models for Experimental High Density Housing

    Science.gov (United States)

    Bradecki, Tomasz; Swoboda, Julia; Nowak, Katarzyna; Dziechciarz, Klaudia

    2017-10-01

    The article presents the effects of research on models of high density housing. The authors present urban projects for experimental high density housing estates. The design was based on research performed on 38 examples of similar housing in Poland that have been built after 2003. Some of the case studies show extreme density and that inspired the researchers to test individual virtual solutions that would answer the question: How far can we push the limits? The experimental housing projects show strengths and weaknesses of design driven only by such indexes as FAR (floor attenuation ratio - housing density) and DPH (dwellings per hectare). Although such projects are implemented, the authors believe that there are reasons for limits since high index values may be in contradiction to the optimum character of housing environment. Virtual models on virtual plots presented by the authors were oriented toward maximising the DPH index and DAI (dwellings area index) which is very often the main driver for developers. The authors also raise the question of sustainability of such solutions. The research was carried out in the URBAN model research group (Gliwice, Poland) that consists of academic researchers and architecture students. The models reflect architectural and urban regulations that are valid in Poland. Conclusions might be helpful for urban planners, urban designers, developers, architects and architecture students.

  13. Identification and characterization of rhizospheric microbial diversity by 16S ribosomal RNA gene sequencing

    Directory of Open Access Journals (Sweden)

    Muhammad Naveed

    2014-09-01

    Full Text Available In the present study, samples of rhizosphere and root nodules were collected from different areas of Pakistan to isolate plant growth promoting rhizobacteria. Identification of bacterial isolates was made by 16S rRNA gene sequence analysis and taxonomical confirmation on EzTaxon Server. The identified bacterial strains were belonged to 5 genera i.e. Ensifer, Bacillus, Pseudomona, Leclercia and Rhizobium. Phylogenetic analysis inferred from 16S rRNA gene sequences showed the evolutionary relationship of bacterial strains with the respective genera. Based on phylogenetic analysis, some candidate novel species were also identified. The bacterial strains were also characterized for morphological, physiological, biochemical tests and glucose dehydrogenase (gdh gene that involved in the phosphate solublization using cofactor pyrroloquinolone quinone (PQQ. Seven rhizoshperic and 3 root nodulating stains are positive for gdh gene. Furthermore, this study confirms a novel association between microbes and their hosts like field grown crops, leguminous and non-leguminous plants. It was concluded that a diverse group of bacterial population exist in the rhizosphere and root nodules that might be useful in evaluating the mechanisms behind plant microbial interactions and strains QAU-63 and QAU-68 have sequence similarity of 97 and 95% which might be declared as novel after further taxonomic characterization.

  14. Phylogenetic trees

    OpenAIRE

    Baños, Hector; Bushek, Nathaniel; Davidson, Ruth; Gross, Elizabeth; Harris, Pamela E.; Krone, Robert; Long, Colby; Stewart, Allen; Walker, Robert

    2016-01-01

    We introduce the package PhylogeneticTrees for Macaulay2 which allows users to compute phylogenetic invariants for group-based tree models. We provide some background information on phylogenetic algebraic geometry and show how the package PhylogeneticTrees can be used to calculate a generating set for a phylogenetic ideal as well as a lower bound for its dimension. Finally, we show how methods within the package can be used to compute a generating set for the join of any two ideals.

  15. Comparing the potential for identification of lactobacillus spp. of 16s rDNA variable regions

    International Nuclear Information System (INIS)

    Riano Pachon, Diego Mauricio; Vanegas Lopez, Maria Consuelo; Gonzalez Garcia, Laura Natalia

    2013-01-01

    16s rDNA is used for bacterial identification because its variation rate between species allows differentiation. The gene for this ribosomal subunit has 9 variable regions and some of them give more information than others. We were interested in evaluating the potential for species identification of each region and their combinations. We extracted the V1 to V8 regions of 16s rDNA from different strains and species of Lactobacillus and analyzed them using STAP (ss-RNA Taxonomy Assigning Pipeline) and RDP (Ribosomal Database Project) multiclassifier packages. Phylogenetic trees obtained by maximum likelihood analyses were compared. Classification results show that many regions give the correct genus classification using RDP and STAP; however they are not enough to classify up to the level of species. V5V6 region presents the highest quantity of informative fragments but also present the highest rate of false negatives. V1V3 region presents the highest rate of true positives (species) using STAP and the region V5V8 in RDP (genus).The phylogenetic result shows that the reference topology could be obtained using different combination of regions as V1V3 and V1V8.The experimental validation was done using commercial strains from a probiotic tampon. Sequencing analysis show that the V1V3 region gives the same information and result as the complete 16s rDNA; the three isolated strains correspond to the strains indicated in the product. We conclude that the V1V3 region is the minimum required region to classify Lactobacillus spp. in the correct way and this region is useful in metagenomics to analyze probiotics samples.

  16. The effectiveness of 28S and 16S molecular regions in resolving phylogeny of Malaysian microgastrinae (Hymenoptera: Braconidae)

    Science.gov (United States)

    Zuki, Ameyra Aman; Mohammed, Muhamad Azmi; Md-Zain, Badrul Munir; Yaakop, Salmah

    2018-04-01

    The phylogenetic relationships of Microgastrinae remains unclear though some studies have been conducted to resolve it. The function of Microgastrinae as endoparasitoids of Lepidopteran larvae makes this subfamily an ideal and potential species to be applied as biological control agent of infesting crops. In this study, a total of 13 microgastrine samples under 13 genera were collected from nine localities throughout Peninsular Malaysia. Two molecular regions, 28S nuclear marker and 16S mitochondrial marker were utilized in this study to examine the effectiveness of those regions in resolving the relationships within Microgastrinae. Total of 36 sequences were implemented in the analyses of NJ, MP and Bayesian for both markers. Results obtained from this study were supported by morphological and biological characters. Henceforth, the outcome from this study provides a proof of effectiveness of 28S and 16S molecular markers in studying the phylogenetic relationships of Microgastrinae from Malaysia exclusively and Oriental generally.

  17. Nanotechnology for Synthetic High Density Lipoproteins

    Science.gov (United States)

    Luthi, Andrea J.; Patel, Pinal C.; Ko, Caroline H.; Mutharasan, R. Kannan; Mirkin, Chad A.; Thaxton, C. Shad

    2014-01-01

    Atherosclerosis is the disease mechanism responsible for coronary heart disease (CHD), the leading cause of death worldwide. One strategy to combat atherosclerosis is to increase the amount of circulating high density lipoproteins (HDL), which transport cholesterol from peripheral tissues to the liver for excretion. The process, known as reverse cholesterol transport, is thought to be one of the main reasons for the significant inverse correlation observed between HDL blood levels and the development of CHD. This article highlights the most common strategies for treating atherosclerosis using HDL. We further detail potential treatment opportunities that utilize nanotechnology to increase the amount of HDL in circulation. The synthesis of biomimetic HDL nanostructures that replicate the chemical and physical properties of natural HDL provides novel materials for investigating the structure-function relationships of HDL and for potential new therapeutics to combat CHD. PMID:21087901

  18. Ground state of high-density matter

    Science.gov (United States)

    Copeland, ED; Kolb, Edward W.; Lee, Kimyeong

    1988-01-01

    It is shown that if an upper bound to the false vacuum energy of the electroweak Higgs potential is satisfied, the true ground state of high-density matter is not nuclear matter, or even strange-quark matter, but rather a non-topological soliton where the electroweak symmetry is exact and the fermions are massless. This possibility is examined in the standard SU(3) sub C tensor product SU(2) sub L tensor product U(1) sub Y model. The bound to the false vacuum energy is satisfied only for a narrow range of the Higgs boson masses in the minimal electroweak model (within about 10 eV of its minimum allowed value of 6.6 GeV) and a somewhat wider range for electroweak models with a non-minimal Higgs sector.

  19. High Density Lipoprotein and it's Dysfunction.

    Science.gov (United States)

    Eren, Esin; Yilmaz, Necat; Aydin, Ozgur

    2012-01-01

    Plasma high-density lipoprotein cholesterol(HDL-C) levels do not predict functionality and composition of high-density lipoprotein(HDL). Traditionally, keeping levels of low-density lipoprotein cholesterol(LDL-C) down and HDL-C up have been the goal of patients to prevent atherosclerosis that can lead to coronary vascular disease(CVD). People think about the HDL present in their cholesterol test, but not about its functional capability. Up to 65% of cardiovascular death cannot be prevented by putative LDL-C lowering agents. It well explains the strong interest in HDL increasing strategies. However, recent studies have questioned the good in using drugs to increase level of HDL. While raising HDL is a theoretically attractive target, the optimal approach remains uncertain. The attention has turned to the quality, rather than the quantity, of HDL-C. An alternative to elevations in HDL involves strategies to enhance HDL functionality. The situation poses an opportunity for clinical chemists to take the lead in the development and validation of such biomarkers. The best known function of HDL is the capacity to promote cellular cholesterol efflux from peripheral cells and deliver cholesterol to the liver for excretion, thereby playing a key role in reverse cholesterol transport (RCT). The functions of HDL that have recently attracted attention include anti-inflammatory and anti-oxidant activities. High antioxidant and anti-inflammatory activities of HDL are associated with protection from CVD.This review addresses the current state of knowledge regarding assays of HDL functions and their relationship to CVD. HDL as a therapeutic target is the new frontier with huge potential for positive public health implications.

  20. Bacterial diversity analysis of Huanglongbing pathogen-infected citrus, using PhyloChip and 16S rRNA gene clone library sequencing

    Energy Technology Data Exchange (ETDEWEB)

    Shankar Sagaram, U.; DeAngelis, K.M.; Trivedi, P.; Andersen, G.L.; Lu, S.-E.; Wang, N.

    2009-03-01

    The bacterial diversity associated with citrus leaf midribs was characterized 1 from citrus groves that contained the Huanglongbing (HLB) pathogen, which has yet to be cultivated in vitro. We employed a combination of high-density phylogenetic 16S rDNA microarray and 16S rDNA clone library sequencing to determine the microbial community composition of symptomatic and asymptomatic citrus midribs. Our results revealed that citrus leaf midribs can support a diversity of microbes. PhyloChip analysis indicated that 47 orders of bacteria from 15 phyla were present in the citrus leaf midribs while 20 orders from phyla were observed with the cloning and sequencing method. PhyloChip arrays indicated that nine taxa were significantly more abundant in symptomatic midribs compared to asymptomatic midribs. Candidatus Liberibacter asiaticus (Las) was detected at a very low level in asymptomatic plants, but was over 200 times more abundant in symptomatic plants. The PhyloChip analysis was further verified by sequencing 16S rDNA clone libraries, which indicated the dominance of Las in symptomatic leaves. These data implicate Las as the pathogen responsible for HLB disease. Citrus is the most important commercial fruit crop in Florida. In recent years, citrus Huanglongbing (HLB), also called citrus greening, has severely affected Florida's citrus production and hence has drawn an enormous amount of attention. HLB is one of the most devastating diseases of citrus (6,13), characterized by blotchy mottling with green islands on leaves, as well as stunting, fruit decline, and small, lopsided fruits with poor coloration. The disease tends to be associated with a phloem-limited fastidious {alpha}-proteobacterium given a provisional Candidatus status (Candidatus Liberobacter spp. later changed to Candidatus Liberibacter spp.) in nomenclature (18,25,34). Previous studies indicate that HLB infection causes disorder in the phloem and severely impairs the translocation of assimilates in

  1. Sequence analysis of mitochondrial 16S ribosomal RNA gene ...

    Indian Academy of Sciences (India)

    Unknown

    For the understanding of their vectorial capacity, identification of disease carrying and refractory strains is essential. ... been widely used for phylogenetic studies and sequence differences in ... In order to fill up the internal gap, a new set.

  2. High-density lipoprotein cholesterol: How High

    Directory of Open Access Journals (Sweden)

    G Rajagopal

    2012-01-01

    Full Text Available The high-density lipoprotein cholesterol (HDL-C is considered anti-atherogenic good cholesterol. It is involved in reverse transport of lipids. Epidemiological studies have found inverse relationship of HDL-C and coronary heart disease (CHD risk. When grouped according to HDL-C, subjects having HDL-C more than 60 mg/dL had lesser risk of CHD than those having HDL-C of 40-60 mg/dL, who in turn had lesser risk than those who had HDL-C less than 40 mg/dL. No upper limit for beneficial effect of HDL-C on CHD risk has been identified. The goals of treating patients with low HDL-C have not been firmly established. Though many drugs are known to improve HDL-C concentration, statins are proven to improve CHD risk and mortality. Cholesteryl ester transfer protein (CETP is involved in metabolism of HDL-C and its inhibitors are actively being screened for clinical utility. However, final answer is still awaited on CETP-inhibitors.

  3. High-density hybrid interconnect methodologies

    International Nuclear Information System (INIS)

    John, J.; Zimmermann, L.; Moor, P.De; Hoof, C.Van

    2003-01-01

    Full text: The presentation gives an overview of the state-of-the-art of hybrid integration and in particular the IMEC technological approaches that will be able to address future hybrid detector needs. The dense hybrid flip-chip integration of an array of detectors and its dedicated readout electronics can be achieved with a variety of solderbump techniques such as pure Indium or Indium alloys, Ph-In, Ni/PbSn, but also conducting polymers... Particularly for cooled applications or ultra-high density applications, Indium solderbump technology (electroplated or evaporated) is the method of choice. The state-of-the-art of solderbump technologies that are to a high degree independent of the underlying detector material will be presented and examples of interconnect densities between 5x1E4cm-2 and 1x1E6 cm-2 will be demonstrated. For several classes of detectors, flip-chip integration is not allowed since the detectors have to be illuminated from the top. This applies to image sensors for EUV applications such as GaN/AlGaN based detectors and to MEMS-based sensors. In such cases, the only viable interconnection method has to be through the (thinned) detector wafer followed by a solderbump-based integration. The approaches for dense and ultra-dense through-the-wafer interconnect 'vias' will be presented and wafer thinning approaches will be shown

  4. HIGH DENSITY QCD WITH HEAVY-IONS

    CERN Multimedia

    The Addendum 1 to Volume 2 of the CMS Physics TDR has been published The Heavy-Ion analysis group completed the writing of a TDR summarizing the CMS plans in using heavy ion collisions to study high density QCD. The document was submitted to the LHCC in March and presented in the Open Session of the LHCC on May 9th. The study of heavy-ion physics at the LHC is promising to be very exciting. LHC will open a new energy frontier in ultra-relativistic heavy-ion physics. The collision energy of heavy nuclei at sNN = 5.5 TeV will be thirty times larger than what is presently available at RHIC. We will certainly probe quark and gluon matter at unprecedented values of energy density. The prime goal of this research programme is to study the fundamental theory of the strong interaction - Quantum Chromodynamics (QCD) - in extreme conditions of temperature, density and parton momentum fraction (low-x). Such studies, with impressive experimental and theoretical advances in recent years thanks to the wealth of high-qua...

  5. High-density oxidized porous silicon

    International Nuclear Information System (INIS)

    Gharbi, Ahmed; Souifi, Abdelkader; Remaki, Boudjemaa; Halimaoui, Aomar; Bensahel, Daniel

    2012-01-01

    We have studied oxidized porous silicon (OPS) properties using Fourier transform infraRed (FTIR) spectroscopy and capacitance–voltage C–V measurements. We report the first experimental determination of the optimum porosity allowing the elaboration of high-density OPS insulators. This is an important contribution to the research of thick integrated electrical insulators on porous silicon based on an optimized process ensuring dielectric quality (complete oxidation) and mechanical and chemical reliability (no residual pores or silicon crystallites). Through the measurement of the refractive indexes of the porous silicon (PS) layer before and after oxidation, one can determine the structural composition of the OPS material in silicon, air and silica. We have experimentally demonstrated that a porosity approaching 56% of the as-prepared PS layer is required to ensure a complete oxidation of PS without residual silicon crystallites and with minimum porosity. The effective dielectric constant values of OPS materials determined from capacitance–voltage C–V measurements are discussed and compared to FTIR results predictions. (paper)

  6. Intra-Genomic Heterogeneity in 16S rRNA Genes in Strictly Anaerobic Clinical Isolates from Periodontal Abscesses.

    Science.gov (United States)

    Chen, Jiazhen; Miao, Xinyu; Xu, Meng; He, Junlin; Xie, Yi; Wu, Xingwen; Chen, Gang; Yu, Liying; Zhang, Wenhong

    2015-01-01

    Members of the genera Prevotella, Veillonella and Fusobacterium are the predominant culturable obligate anaerobic bacteria isolated from periodontal abscesses. When determining the cumulative number of clinical anaerobic isolates from periodontal abscesses, ambiguous or overlapping signals were frequently encountered in 16S rRNA gene sequencing chromatograms, resulting in ambiguous identifications. With the exception of the genus Veillonella, the high intra-chromosomal heterogeneity of rrs genes has not been reported. The 16S rRNA genes of 138 clinical, strictly anaerobic isolates and one reference strain were directly sequenced, and the chromatograms were carefully examined. Gene cloning was performed for 22 typical isolates with doublet sequencing signals for the 16S rRNA genes, and four copies of the rrs-ITS genes of 9 Prevotella intermedia isolates were separately amplified by PCR, sequenced and compared. Five conserved housekeeping genes, hsp60, recA, dnaJ, gyrB1 and rpoB from 89 clinical isolates of Prevotella were also amplified by PCR and sequenced for identification and phylogenetic analysis along with 18 Prevotella reference strains. Heterogeneity of 16S rRNA genes was apparent in clinical, strictly anaerobic oral bacteria, particularly in the genera Prevotella and Veillonella. One hundred out of 138 anaerobic strains (72%) had intragenomic nucleotide polymorphisms (SNPs) in multiple locations, and 13 strains (9.4%) had intragenomic insertions or deletions in the 16S rRNA gene. In the genera Prevotella and Veillonella, 75% (67/89) and 100% (19/19) of the strains had SNPs in the 16S rRNA gene, respectively. Gene cloning and separate amplifications of four copies of the rrs-ITS genes confirmed that 2 to 4 heterogeneous 16S rRNA copies existed. Sequence alignment of five housekeeping genes revealed that intra-species nucleotide similarities were very high in the genera Prevotella, ranging from 94.3-100%. However, the inter-species similarities were

  7. High throughput 16S rRNA gene amplicon sequencing

    DEFF Research Database (Denmark)

    Nierychlo, Marta; Larsen, Poul; Jørgensen, Mads Koustrup

    S rRNA gene amplicon sequencing has been developed over the past few years and is now ready to use for more comprehensive studies related to plant operation and optimization thanks to short analysis time, low cost, high throughput, and high taxonomic resolution. In this study we show how 16S r......RNA gene amplicon sequencing can be used to reveal factors of importance for the operation of full-scale nutrient removal plants related to settling problems and floc properties. Using optimized DNA extraction protocols, indexed primers and our in-house Illumina platform, we prepared multiple samples...... be correlated to the presence of the species that are regarded as “strong” and “weak” floc formers. In conclusion, 16S rRNA gene amplicon sequencing provides a high throughput approach for a rapid and cheap community profiling of activated sludge that in combination with multivariate statistics can be used...

  8. A framework for establishing predictive relationships between specific bacterial 16S rRNA sequence abundances and biotransformation rates.

    Science.gov (United States)

    Helbling, Damian E; Johnson, David R; Lee, Tae Kwon; Scheidegger, Andreas; Fenner, Kathrin

    2015-03-01

    The rates at which wastewater treatment plant (WWTP) microbial communities biotransform specific substrates can differ by orders of magnitude among WWTP communities. Differences in taxonomic compositions among WWTP communities may predict differences in the rates of some types of biotransformations. In this work, we present a novel framework for establishing predictive relationships between specific bacterial 16S rRNA sequence abundances and biotransformation rates. We selected ten WWTPs with substantial variation in their environmental and operational metrics and measured the in situ ammonia biotransformation rate constants in nine of them. We isolated total RNA from samples from each WWTP and analyzed 16S rRNA sequence reads. We then developed multivariate models between the measured abundances of specific bacterial 16S rRNA sequence reads and the ammonia biotransformation rate constants. We constructed model scenarios that systematically explored the effects of model regularization, model linearity and non-linearity, and aggregation of 16S rRNA sequences into operational taxonomic units (OTUs) as a function of sequence dissimilarity threshold (SDT). A large percentage (greater than 80%) of model scenarios resulted in well-performing and significant models at intermediate SDTs of 0.13-0.14 and 0.26. The 16S rRNA sequences consistently selected into the well-performing and significant models at those SDTs were classified as Nitrosomonas and Nitrospira groups. We then extend the framework by applying it to the biotransformation rate constants of ten micropollutants measured in batch reactors seeded with the ten WWTP communities. We identified phylogenetic groups that were robustly selected into all well-performing and significant models constructed with biotransformation rates of isoproturon, propachlor, ranitidine, and venlafaxine. These phylogenetic groups can be used as predictive biomarkers of WWTP microbial community activity towards these specific

  9. Retrieval of a million high-quality, full-length microbial 16S and 18S rRNA gene sequences without primer bias

    DEFF Research Database (Denmark)

    Karst, Søren Michael; Dueholm, Morten Simonsen; McIlroy, Simon Jon

    2018-01-01

    Small subunit ribosomal RNA (SSU rRNA) genes, 16S in bacteria and 18S in eukaryotes, have been the standard phylogenetic markers used to characterize microbial diversity and evolution for decades. However, the reference databases of full-length SSU rRNA gene sequences are skewed to well-studied e...

  10. 16S rRNA Gene Sequence Analysis of Drinking Water Using RNA and DNA Extracts as Targets for Clone Library Development

    Science.gov (United States)

    The bacterial composition of chlorinated drinking water was analyzed using 16S rRNA gene clone libraries derived from DNA extracts of 12 samples and compared to clone libraries previously generated using RNA extracts from the same samples. Phylogenetic analysis of 761 DNA-based ...

  11. 16S rRNA Gene Sequence Analysis of Drinking Water Using RNA and DNA Extracts as Targets for Clone Library Development - Poster

    Science.gov (United States)

    We examined the bacterial composition of chlorinated drinking water using 16S rRNA gene clone libraries derived from RNA and DNA extracted from twelve water samples collected in three different months (June, August, and September of 2007). Phylogenetic analysis of 1234 and 1117 ...

  12. Enhanced radiative Auger emission from lithiumlike 16S13+

    International Nuclear Information System (INIS)

    Bernstein, E.M.; Clark, M.W.; Oglesby, C.S.; Tanis, J.A.; Graham, W.G.; McFarland, R.H.; Morgan, T.J.; Johnson, B.M.; Jones, K.W.

    1990-01-01

    The radiative Auger emission (RAE) from 0.94--6.25-MeV/u 16 S 13+ (lithiumlike) projectiles excited in collisions with He target atoms has been measured. For these highly stripped ions the intensity of RAE photons relative to Kα x-ray emission is enhanced by about a factor of five compared with theoretical calculations and an earlier experimental measurement for S ions with few electron vacancies. The enhancement of RAE for S 13+ is qualitatively similar to results reported previously for lithiumlike 23 V 20+ ; however, some differences between S and V are evident

  13. Analysis of 16S libraries of mouse gastrointestinal microflora reveals a large new group of mouse intestinal bacteria.

    Science.gov (United States)

    Salzman, Nita H; de Jong, Hendrik; Paterson, Yvonne; Harmsen, Hermie J M; Welling, Gjalt W; Bos, Nicolaas A

    2002-11-01

    Total genomic DNA from samples of intact mouse small intestine, large intestine, caecum and faeces was used as template for PCR amplification of 16S rRNA gene sequences with conserved bacterial primers. Phylogenetic analysis of the amplification products revealed 40 unique 16S rDNA sequences. Of these sequences, 25% (10/40) corresponded to described intestinal organisms of the mouse, including Lactobacillus spp., Helicobacter spp., segmented filamentous bacteria and members of the altered Schaedler flora (ASF360, ASF361, ASF502 and ASF519); 75% (30/40) represented novel sequences. A large number (11/40) of the novel sequences revealed a new operational taxonomic unit (OTU) belonging to the Cytophaga-Flavobacter-Bacteroides phylum, which the authors named 'mouse intestinal bacteria'. 16S rRNA probes were developed for this new OTU. Upon analysis of the novel sequences, eight were found to cluster within the Eubacterium rectale-Clostridium coccoides group and three clustered within the Bacteroides group. One of the novel sequences was distantly related to Verrucomicrobium spinosum and one was distantly related to Bacillus mycoides. Oligonucleotide probes specific for the 16S rRNA of these novel clones were generated. Using a combination of four previously described and four newly designed probes, approximately 80% of bacteria recovered from the murine large intestine and 71% of bacteria recovered from the murine caecum could be identified by fluorescence in situ hybridization (FISH).

  14. Exploring internal features of 16S rRNA gene for identification of clinically relevant species of the genus Streptococcus

    Science.gov (United States)

    2011-01-01

    Background Streptococcus is an economically important genus as a number of species belonging to this genus are human and animal pathogens. The genus has been divided into different groups based on 16S rRNA gene sequence similarity. The variability observed among the members of these groups is low and it is difficult to distinguish them. The present study was taken up to explore 16S rRNA gene sequence to develop methods that can be used for preliminary identification and can supplement the existing methods for identification of clinically-relevant isolates of the genus Streptococcus. Methods 16S rRNA gene sequences belonging to the isolates of S. dysgalactiae, S. equi, S. pyogenes, S. agalactiae, S. bovis, S. gallolyticus, S. mutans, S. sobrinus, S. mitis, S. pneumoniae, S. thermophilus and S. anginosus were analyzed with the purpose to define genetic variability within each species to generate a phylogenetic framework, to identify species-specific signatures and in-silico restriction enzyme analysis. Results The framework based analysis was used to segregate Streptococcus spp. previously identified upto genus level. This segregation was validated using species-specific signatures and in-silico restriction enzyme analysis. 43 uncharacterized Streptococcus spp. could be identified using this approach. Conclusions The markers generated exploring 16S rRNA gene sequences provided useful tool that can be further used for identification of different species of the genus Streptococcus. PMID:21702978

  15. Conus pennaceus : a phylogenetic analysis of the Mozambican ...

    African Journals Online (AJOL)

    The genus Conus has over 500 species and is the most species-rich taxon of marine invertebrates. Based on mitochondrial DNA, this study focuses on the phylogenetics of Conus, particularly the pennaceus complex collected along the Mozambican coast. Phylogenetic trees based on both the 16S and the 12S ribosomal ...

  16. Improved GAMMA 10 tandem mirror confinement in high density plasma

    International Nuclear Information System (INIS)

    Yatsu, K.; Cho, T.; Higaki, H.; Hirata, M.; Hojo, H.; Ichimura, M.; Ishii, K.; Ishimoto, Y.; Itakura, A.; Katanuma, I.; Kohagura, J.; Minami, R.; Nakashima, Y.; Numakura, T.; Saito, T.; Saosaki, S.; Takemura, Y.; Tatematsu, Y.; Yoshida, M.; Yoshikawa, M.

    2003-01-01

    GAMMA 10 experiments have advanced in high density experiments after the last IAEA fusion energy conference in 2000 where we reported the production of the high density plasma through use of ion cyclotron range of frequency heating at a high harmonic frequency and neutral beam injection in the anchor cells. However, the diamagnetic signal of the plasma decreased when electron cyclotron resonance heating was applied for the potential formation. Recently a high density plasma has been obtained without degradation of the diamagnetic signal and with much improved reproducibility than before. The high density plasma was attained through adjustment of the spacing of the conducting plates installed in the anchor transition regions. The potential confinement of the plasma has been extensively studied. Dependences of the ion confinement time, ion-energy confinement time and plasma confining potential on plasma density were obtained for the first time in the high density region up to a density of 4x10 18 m -3 . (author)

  17. Plastid 16S rRNA gene diversity among eukaryotic picophytoplankton sorted by flow cytometry from the South Pacific Ocean.

    Directory of Open Access Journals (Sweden)

    Xiao Li Shi

    Full Text Available The genetic diversity of photosynthetic picoeukaryotes was investigated in the South East Pacific Ocean. Genetic libraries of the plastid 16S rRNA gene were constructed on picoeukaryote populations sorted by flow cytometry, using two different primer sets, OXY107F/OXY1313R commonly used to amplify oxygenic organisms, and PLA491F/OXY1313R, biased towards plastids of marine algae. Surprisingly, the two sets revealed quite different photosynthetic picoeukaryote diversity patterns, which were moreover different from what we previously reported using the 18S rRNA nuclear gene as a marker. The first 16S primer set revealed many sequences related to Pelagophyceae and Dictyochophyceae, the second 16S primer set was heavily biased toward Prymnesiophyceae, while 18S sequences were dominated by Prasinophyceae, Chrysophyceae and Haptophyta. Primer mismatches with major algal lineages is probably one reason behind this discrepancy. However, other reasons, such as DNA accessibility or gene copy numbers, may be also critical. Based on plastid 16S rRNA gene sequences, the structure of photosynthetic picoeukaryotes varied along the BIOSOPE transect vertically and horizontally. In oligotrophic regions, Pelagophyceae, Chrysophyceae, and Prymnesiophyceae dominated. Pelagophyceae were prevalent at the DCM depth and Chrysophyceae at the surface. In mesotrophic regions Pelagophyceae were still important but Chlorophyta contribution increased. Phylogenetic analysis revealed a new clade of Prasinophyceae (clade 16S-IX, which seems to be restricted to hyper-oligotrophic stations. Our data suggest that a single gene marker, even as widely used as 18S rRNA, provides a biased view of eukaryotic communities and that the use of several markers is necessary to obtain a complete image.

  18. Polynucleotide probes that target a hypervariable region of 16S rRNA genes to identify bacterial isolates corresponding to bands of community fingerprints.

    Science.gov (United States)

    Heuer, H; Hartung, K; Wieland, G; Kramer, I; Smalla, K

    1999-03-01

    Temperature gradient gel electrophoresis (TGGE) is well suited for fingerprinting bacterial communities by separating PCR-amplified fragments of 16S rRNA genes (16S ribosomal DNA [rDNA]). A strategy was developed and was generally applicable for linking 16S rDNA from community fingerprints to pure culture isolates from the same habitat. For this, digoxigenin-labeled polynucleotide probes were generated by PCR, using bands excised from TGGE community fingerprints as a template, and applied in hybridizations with dot blotted 16S rDNA amplified from bacterial isolates. Within 16S rDNA, the hypervariable V6 region, corresponding to positions 984 to 1047 (Escherichia coli 16S rDNA sequence), which is a subset of the region used for TGGE (positions 968 to 1401), best met the criteria of high phylogenetic variability, required for sufficient probe specificity, and closely flanking conserved priming sites for amplification. Removal of flanking conserved bases was necessary to enable the differentiation of closely related species. This was achieved by 5' exonuclease digestion, terminated by phosphorothioate bonds which were synthesized into the primers. The remaining complementary strand was removed by single-strand-specific digestion. Standard hybridization with truncated probes allowed differentiation of bacteria which differed by only two bases within the probe target site and 1.2% within the complete 16S rDNA. However, a truncated probe, derived from an excised TGGE band of a rhizosphere community, hybridized with three phylogenetically related isolates with identical V6 sequences. Only one of the isolates comigrated with the excised band in TGGE, which was shown to be due to identical sequences, demonstrating the utility of a combined TGGE and V6 probe approach.

  19. Phenomenology of high density disruptions in the TFTR tokamak

    International Nuclear Information System (INIS)

    Fredrickson, E.D.; McGuire, K.M.; Bell, M.G.

    1993-01-01

    Studies of high density disruptions on TFTR, including a comparison of minor and major disruptions at high density, provide important new information regarding the nature of the disruption mechanism. Further, for the first time, an (m,n)=(1,1) 'cold bubble' precursor to high density disruptions has been experimentally observed in the electron temperature profile. The precursor to major disruptions resembles the 'vacuum bubble' model of disruptions first proposed by B.B. Kadomtsev and O.P. Pogutse (Sov. Phys. - JETP 38 (1974) 283). (author). Letter-to-the-editor. 25 refs, 3 figs

  20. Diversity of thermophiles in a Malaysian hot spring determined using 16S rRNA and shotgun metagenome sequencing.

    Science.gov (United States)

    Chan, Chia Sing; Chan, Kok-Gan; Tay, Yea-Ling; Chua, Yi-Heng; Goh, Kian Mau

    2015-01-01

    The Sungai Klah (SK) hot spring is the second hottest geothermal spring in Malaysia. This hot spring is a shallow, 150-m-long, fast-flowing stream, with temperatures varying from 50 to 110°C and a pH range of 7.0-9.0. Hidden within a wooded area, the SK hot spring is continually fed by plant litter, resulting in a relatively high degree of total organic content (TOC). In this study, a sample taken from the middle of the stream was analyzed at the 16S rRNA V3-V4 region by amplicon metagenome sequencing. Over 35 phyla were detected by analyzing the 16S rRNA data. Firmicutes and Proteobacteria represented approximately 57% of the microbiome. Approximately 70% of the detected thermophiles were strict anaerobes; however, Hydrogenobacter spp., obligate chemolithotrophic thermophiles, represented one of the major taxa. Several thermophilic photosynthetic microorganisms and acidothermophiles were also detected. Most of the phyla identified by 16S rRNA were also found using the shotgun metagenome approaches. The carbon, sulfur, and nitrogen metabolism within the SK hot spring community were evaluated by shotgun metagenome sequencing, and the data revealed diversity in terms of metabolic activity and dynamics. This hot spring has a rich diversified phylogenetic community partly due to its natural environment (plant litter, high TOC, and a shallow stream) and geochemical parameters (broad temperature and pH range). It is speculated that symbiotic relationships occur between the members of the community.

  1. High regression rate, high density hybrid fuels, Phase I

    Data.gov (United States)

    National Aeronautics and Space Administration — This SBIR program will investigate high energy density novel nanofuels combined with high density binders for use with an N2O oxidizer. Terves has developed...

  2. The Influence of Decreased Levels of High Density Lipoprotein ...

    African Journals Online (AJOL)

    very low density lipoprotein cholesterol, and triglyceride were assayed. ... Abiodun and Gwarzo: Association of high density lipoprotein cholesterol with haemolysis in sickle cell disease ... analyses were carried out to determine the correlation.

  3. High density UO2 powder preparation for HWR fuel

    International Nuclear Information System (INIS)

    Hwang, S. T.; Chang, I. S.; Choi, Y. D.; Cho, B. R.; Kwon, S. W.; Kim, B. H.; Moon, B. H.; Kim, S. D.; Phyu, K. M.; Lee, K. A.

    1992-01-01

    The objective of this project is to study on the preparation of method high density UO 2 powder for HWR Fuel. Accordingly, it is necessary to character ize the AUC processed UO 2 powder and to search method for the preparation of high density UO 2 powder for HWR Fuel. Therefore, it is expected that the results of this study can effect the producing of AUC processed UO 2 powder having sinterability. (Author)

  4. The high density effects in the Drell-Yan process

    International Nuclear Information System (INIS)

    Betemps, M.A.; Gay Ducati, M.B.; Ayala Filho, A.L.

    2003-01-01

    The high density effects in the Drell-Yan process (q q-bar → γ * →l + l - ) are investigated for pA collisions at RHIC and LHC energies. In particular, we use a set of nuclear parton distributions that describes the present nuclear eA and pA data in the DGLAP approach including the high density effects introduced in the perturbative Glauber-Mueller approach. (author)

  5. Microbial Dark Matter: Unusual intervening sequences in 16S rRNA genes of candidate phyla from the deep subsurface

    Energy Technology Data Exchange (ETDEWEB)

    Jarett, Jessica; Stepanauskas, Ramunas; Kieft, Thomas; Onstott, Tullis; Woyke, Tanja

    2014-03-17

    The Microbial Dark Matter project has sequenced genomes from over 200 single cells from candidate phyla, greatly expanding our knowledge of the ecology, inferred metabolism, and evolution of these widely distributed, yet poorly understood lineages. The second phase of this project aims to sequence an additional 800 single cells from known as well as potentially novel candidate phyla derived from a variety of environments. In order to identify whole genome amplified single cells, screening based on phylogenetic placement of 16S rRNA gene sequences is being conducted. Briefly, derived 16S rRNA gene sequences are aligned to a custom version of the Greengenes reference database and added to a reference tree in ARB using parsimony. In multiple samples from deep subsurface habitats but not from other habitats, a large number of sequences proved difficult to align and therefore to place in the tree. Based on comparisons to reference sequences and structural alignments using SSU-ALIGN, many of these ?difficult? sequences appear to originate from candidate phyla, and contain intervening sequences (IVSs) within the 16S rRNA genes. These IVSs are short (39 - 79 nt) and do not appear to be self-splicing or to contain open reading frames. IVSs were found in the loop regions of stem-loop structures in several different taxonomic groups. Phylogenetic placement of sequences is strongly affected by IVSs; two out of three groups investigated were classified as different phyla after their removal. Based on data from samples screened in this project, IVSs appear to be more common in microbes occurring in deep subsurface habitats, although the reasons for this remain elusive.

  6. 16S partial gene mitochondrial DNA and internal transcribed spacers ribosomal DNA as differential markers of Trichuris discolor populations.

    Science.gov (United States)

    Callejón, R; Halajian, A; de Rojas, M; Marrugal, A; Guevara, D; Cutillas, C

    2012-05-25

    Comparative morphological, biometrical and molecular studies of Trichuris discolor isolated from Bos taurus from Spain and Iran was carried out. Furthermore, Trichuris ovis isolated from B. taurus and Capra hircus from Spain has been, molecularly, analyzed. Morphological studies revealed clear differences between T. ovis and T. discolor isolated from B. taurus but differences were not observed between populations of T. discolor isolated from different geographical regions. Nevertheless, the molecular studies based on the amplification and sequencing of the internal transcribed spacers 1 and 2 ribosomal DNA and 16S partial gene mitochondrial DNA showed clear differences between both populations of T. discolor from Spain and Iran suggesting two cryptic species. Phylogenetic studies corroborated these data. Thus, phylogenetic trees based on ITS1, ITS2 and 16S partial gene sequences showed that individuals of T. discolor from B. taurus from Iran clustered together and separated, with high bootstrap values, of T. discolor isolated from B. taurus from Spain, while populations of T. ovis from B. taurus and C. hircus from Spain clustered together but separated with high bootstrap values of both populations of T. discolor. Furthermore, a comparative phylogenetic study has been carried out with the ITS1and ITS2 sequences of Trichuris species from different hosts. Three clades were observed: the first clustered all the species of Trichuris parasitizing herbivores (T. discolor, T. ovis, Trichuris leporis and Trichuris skrjabini), the second clustered all the species of Trichuris parasitizing omnivores (Trichuris trichiura and Trichuris suis) and finally, the third clustered species of Trichuris parasitizing carnivores (Trichuris muris, Trichuris arvicolae and Trichuris vulpis). Copyright © 2011 Elsevier B.V. All rights reserved.

  7. Combined Analyses of the ITS Loci and the Corresponding 16S rRNA Genes Reveal High Micro- and Macrodiversity of SAR11 Populations in the Red Sea

    Science.gov (United States)

    Ngugi, David Kamanda; Stingl, Ulrich

    2012-01-01

    Bacteria belonging to the SAR11 clade are among the most abundant prokaryotes in the pelagic zone of the ocean. 16S rRNA gene-based analyses indicate that they constitute up to 60% of the bacterioplankton community in the surface waters of the Red Sea. This extremely oligotrophic water body is further characterized by an epipelagic zone, which has a temperature above 24°C throughout the year, and a remarkable uniform temperature (∼22°C) and salinity (∼41 psu) from the mixed layer (∼200 m) to the bottom at over 2000 m depth. Despite these conditions that set it apart from other marine environments, the microbiology of this ecosystem is still vastly understudied. Prompted by the limited phylogenetic resolution of the 16S rRNA gene, we extended our previous study by sequencing the internal transcribed spacer (ITS) region of SAR11 in different depths of the Red Sea’s water column together with the respective 16S fragment. The overall diversity captured by the ITS loci was ten times higher than that of the corresponding 16S rRNA genes. Moreover, species estimates based on the ITS showed a highly diverse population of SAR11 in the mixed layer that became diminished in deep isothermal waters, which was in contrast to results of the related 16S rRNA genes. While the 16S rRNA gene-based sequences clustered into three phylogenetic subgroups, the related ITS fragments fell into several phylotypes that showed clear depth-dependent shifts in relative abundances. Blast-based analyses not only documented the observed vertical partitioning and universal co-occurrence of specific phylotypes in five other distinct oceanic provinces, but also highlighted the influence of ecosystem-specific traits (e.g., temperature, nutrient availability, and concentration of dissolved oxygen) on the population dynamics of this ubiquitous marine bacterium. PMID:23185592

  8. Combined analyses of the ITS loci and the corresponding 16S rRNA genes reveal high micro- and macrodiversity of SAR11 populations in the Red Sea.

    KAUST Repository

    Ngugi, David

    2012-11-20

    Bacteria belonging to the SAR11 clade are among the most abundant prokaryotes in the pelagic zone of the ocean. 16S rRNA gene-based analyses indicate that they constitute up to 60% of the bacterioplankton community in the surface waters of the Red Sea. This extremely oligotrophic water body is further characterized by an epipelagic zone, which has a temperature above 24 °C throughout the year, and a remarkable uniform temperature (~22 °C) and salinity (~41 psu) from the mixed layer (~200 m) to the bottom at over 2000 m depth. Despite these conditions that set it apart from other marine environments, the microbiology of this ecosystem is still vastly understudied. Prompted by the limited phylogenetic resolution of the 16S rRNA gene, we extended our previous study by sequencing the internal transcribed spacer (ITS) region of SAR11 in different depths of the Red Sea\\'s water column together with the respective 16S fragment. The overall diversity captured by the ITS loci was ten times higher than that of the corresponding 16S rRNA genes. Moreover, species estimates based on the ITS showed a highly diverse population of SAR11 in the mixed layer that became diminished in deep isothermal waters, which was in contrast to results of the related 16S rRNA genes. While the 16S rRNA gene-based sequences clustered into three phylogenetic subgroups, the related ITS fragments fell into several phylotypes that showed clear depth-dependent shifts in relative abundances. Blast-based analyses not only documented the observed vertical partitioning and universal co-occurrence of specific phylotypes in five other distinct oceanic provinces, but also highlighted the influence of ecosystem-specific traits (e.g., temperature, nutrient availability, and concentration of dissolved oxygen) on the population dynamics of this ubiquitous marine bacterium.

  9. Phylogenetic analysis of the kenaf fiber microbial retting community by semiconductor sequencing of 16S rDNA amplicons

    Science.gov (United States)

    Kenaf, hemp, and jute have been used for cordage and fiber production since prehistory. To obtain the fibers, harvested plants are soaked in ponds where indigenous microflora digests pectins and other heteropolysaccharides, releasing fibers in a process called retting. Renewed interest in “green” ...

  10. High-density-plasma diagnostics in magnetic-confinement fusion

    International Nuclear Information System (INIS)

    Jahoda, F.C.

    1982-01-01

    The lectures will begin by defining high density in the context of magnetic confinement fusion research and listing some alternative reactor concepts, ranging from n/sub e/ approx. 2 x 10 14 cm -3 to several orders of magnitude greater, that offer potential advantages over the main-line, n/sub e/ approx. 1 x 10 14 cm -3 , Tokamak reactor designs. The high density scalings of several major diagnostic techniques, some favorable and some disadvantageous, will be discussed. Special emphasis will be given to interferometric methods, both electronic and photographic, for which integral n/sub e/dl measurements and associated techniques are accessible with low wavelength lasers. Reactor relevant experience from higher density, smaller dimension devices exists. High density implies high β, which implies economies of scale. The specialized features of high β diagnostics will be discussed

  11. High-resolution phylogenetic microbial community profiling

    Energy Technology Data Exchange (ETDEWEB)

    Singer, Esther; Coleman-Derr, Devin; Bowman, Brett; Schwientek, Patrick; Clum, Alicia; Copeland, Alex; Ciobanu, Doina; Cheng, Jan-Fang; Gies, Esther; Hallam, Steve; Tringe, Susannah; Woyke, Tanja

    2014-03-17

    The representation of bacterial and archaeal genome sequences is strongly biased towards cultivated organisms, which belong to merely four phylogenetic groups. Functional information and inter-phylum level relationships are still largely underexplored for candidate phyla, which are often referred to as microbial dark matter. Furthermore, a large portion of the 16S rRNA gene records in the GenBank database are labeled as environmental samples and unclassified, which is in part due to low read accuracy, potential chimeric sequences produced during PCR amplifications and the low resolution of short amplicons. In order to improve the phylogenetic classification of novel species and advance our knowledge of the ecosystem function of uncultivated microorganisms, high-throughput full length 16S rRNA gene sequencing methodologies with reduced biases are needed. We evaluated the performance of PacBio single-molecule real-time (SMRT) sequencing in high-resolution phylogenetic microbial community profiling. For this purpose, we compared PacBio and Illumina metagenomic shotgun and 16S rRNA gene sequencing of a mock community as well as of an environmental sample from Sakinaw Lake, British Columbia. Sakinaw Lake is known to contain a large age of microbial species from candidate phyla. Sequencing results show that community structure based on PacBio shotgun and 16S rRNA gene sequences is highly similar in both the mock and the environmental communities. Resolution power and community representation accuracy from SMRT sequencing data appeared to be independent of GC content of microbial genomes and was higher when compared to Illumina-based metagenome shotgun and 16S rRNA gene (iTag) sequences, e.g. full-length sequencing resolved all 23 OTUs in the mock community, while iTags did not resolve closely related species. SMRT sequencing hence offers various potential benefits when characterizing uncharted microbial communities.

  12. Identification of active methanotrophs in a landfill cover soil through detection of expression of 16S rRNA and functional genes.

    Science.gov (United States)

    Chen, Yin; Dumont, Marc G; Cébron, Aurélie; Murrell, J Colin

    2007-11-01

    Active methanotrophs in a landfill soil were revealed by detecting the 16S rRNA of methanotrophs and the mRNA transcripts of key genes involved in methane oxidation. New 16S rRNA primers targeting type I and type II methanotrophs were designed and optimized for analysis by denaturing gradient gel electrophoresis. Direct extraction of RNA from soil enabled the analysis of the expression of the functional genes: mmoX, pmoA and mxaF, which encode subunits of soluble methane monooxygenase, particulate methane monooxygenase and methanol dehydrogenase respectively. The 16S rRNA polymerase chain reaction (PCR) primers for type I methanotrophs detected Methylomonas, Methylosarcina and Methylobacter sequences from both soil DNA and cDNA which was generated from RNA extracted directly from the landfill cover soil. The 16S rRNA primers for type II methanotrophs detected primarily Methylocella and some Methylocystis 16S rRNA genes. Phylogenetic analysis of mRNA recovered from the soil indicated that Methylobacter, Methylosarcina, Methylomonas, Methylocystis and Methylocella were actively expressing genes involved in methane and methanol oxidation. Transcripts of pmoA but not mmoX were readily detected by reverse transcription polymerase chain reaction (RT-PCR), indicating that particulate methane monooxygenase may be largely responsible for methane oxidation in situ.

  13. Molecular phylogeny of the neritidae (Gastropoda: Neritimorpha) based on the mitochondrial genes cytochrome oxidase I (COI) and 16S rRNA

    International Nuclear Information System (INIS)

    Quintero Galvis, Julian Fernando; Castro, Lyda Raquel

    2013-01-01

    The family Neritidae has representatives in tropical and subtropical regions that occur in a variety of environments, and its known fossil record dates back to the late Cretaceous. However there have been few studies of molecular phylogeny in this family. We performed a phylogenetic reconstruction of the family Neritidae using the COI (722 bp) and the 16S rRNA (559 bp) regions of the mitochondrial genome. Neighbor-joining, maximum parsimony and Bayesian inference were performed. The best phylogenetic reconstruction was obtained using the COI region, and we consider it an appropriate marker for phylogenetic studies within the group. Consensus analysis (COI +16S rRNA) generally obtained the same tree topologies and confirmed that the genus Nerita is monophyletic. The consensus analysis using parsimony recovered a monophyletic group consisting of the genera Neritina, Septaria, Theodoxus, Puperita, and Clithon, while in the Bayesian analyses Theodoxus is separated from the other genera. The phylogenetic status of the species from the genus Nerita from the Colombian Caribbean generated in this study was consistent with that reported for the genus in previous studies. In the resulting consensus tree obtained using maximum parsimony, we included information on habitat type for each species, to map the evolution by habitat. Species of the family Neritidae possibly have their origin in marine environments, which is consistent with conclusions from previous reports based on anatomical studies.

  14. Phylogenetic and chemical diversity of MAR4 streptomycete lineage

    Directory of Open Access Journals (Sweden)

    Marisa Paulino

    2014-06-01

    To date, phylogenetic characterization of 6 representative isolates, based on partial sequence of gene encoding 16S rRNA, confirm that these strains belong to the specie Streptomyces aculeolatus. Figure 2. Neighbour-joining phylogenetic tree created from 6 partial 16S rRNA gene sequence from Streptomyces aculeolatus strains cultured from Madeira Archipelago, based on 1000 bootstrap replicates. BLAST matches (deposited in GenBank are included with species and strain name followed by accession number. Verrucosispora maris and Micromonospora aurantiaca were used as outgroups.

  15. Conservative fragments in bacterial 16S rRNA genes and primer design for 16S ribosomal DNA amplicons in metagenomic studies

    KAUST Repository

    Wang, Yong; Qian, Pei-Yuan

    2009-01-01

    Bacterial 16S ribosomal DNA (rDNA) amplicons have been widely used in the classification of uncultured bacteria inhabiting environmental niches. Primers targeting conservative regions of the rDNAs are used to generate amplicons of variant regions

  16. BCS Theory of Hadronic Matter at High Densities

    DEFF Research Database (Denmark)

    Bohr, Henrik; Panda, Prafulla K.; Providencia, Constanca

    2012-01-01

    The equilibrium between the so-called 2SC and CFL phases of strange quark matter at high densities is investigated in the framework of a simple schematic model of the NJL type. Equal densities are assumed for quarks u, d and s. The 2SC phase is here described by a color-flavor symmetric state, in...

  17. Antioxidant activity of high-density lipoprotein (HDL) using different ...

    African Journals Online (AJOL)

    HDL is a potent antioxidant in terms of inhibition of lipid peroxidation, ROS production and LDL oxidation. These may to some extent add to the antiatherogenic beyond reverse-cholesterol transport properties of HDL. Keywords: high-density lipoprotein; reverse cholesterol transport; apolipoprotein A1; antioxidant; in vitro.

  18. Morphodynamics of supercritical high-density turbidity currents

    NARCIS (Netherlands)

    Cartigny, M.

    2012-01-01

    Seafloor and outcrop observations combined with numerical and physical experiments show that turbidity currents are likely 1) to be in a supercritical flow state and 2) to carry high sediment concentrations (being of high-density). The thesis starts with an experimental study of bedforms

  19. Fluorescent Fe K Emission from High Density Accretion Disks

    Science.gov (United States)

    Bautista, Manuel; Mendoza, Claudio; Garcia, Javier; Kallman, Timothy R.; Palmeri, Patrick; Deprince, Jerome; Quinet, Pascal

    2018-06-01

    Iron K-shell lines emitted by gas closely orbiting black holes are observed to be grossly broadened and skewed by Doppler effects and gravitational redshift. Accordingly, models for line profiles are widely used to measure the spin (i.e., the angular momentum) of astrophysical black holes. The accuracy of these spin estimates is called into question because fitting the data requires very high iron abundances, several times the solar value. Meanwhile, no plausible physical explanation has been proffered for why these black hole systems should be so iron rich. The most likely explanation for the super-solar iron abundances is a deficiency in the models, and the leading candidate cause is that current models are inapplicable at densities above 1018 cm-3. We study the effects of high densities on the atomic parameters and on the spectral models for iron ions. At high densities, Debye plasma can affect the effective atomic potential of the ions, leading to observable changes in energy levels and atomic rates with respect to the low density case. High densities also have the effec of lowering energy the atomic continuum and reducing the recombination rate coefficients. On the spectral modeling side, high densities drive level populations toward a Boltzman distribution and very large numbers of excited atomic levels, typically accounted for in theoretical spectral models, may contribute to the K-shell spectrum.

  20. Sputtered thin films for high density tape recording

    NARCIS (Netherlands)

    Nguyen, L.T.

    This thesis describes the investigation of sputtered thin film media for high density tape recording. As discussed in Chapter 1, to meet the tremendous demand of data storage, the density of recording tape has to be increased continuously. For further increasing the bit density the key factors are:

  1. Ultra-stretchable Interconnects for high-density stretchable electronics

    NARCIS (Netherlands)

    Shafqat, S.; Hoefnagels, J.P.M.; Savov, A.; Joshi, S.; Dekker, R.; Geers, M.G.D.

    2017-01-01

    The exciting field of stretchable electronics (SE) promises numerous novel applications, particularly in-body and medical diagnostics devices. However, future advanced SE miniature devices will require high-density, extremely stretchable interconnects with micron-scale footprints, which calls for

  2. Positron camera with high-density avalanche chambers

    International Nuclear Information System (INIS)

    Manfrass, D.; Enghardt, W.; Fromm, W.D.; Wohlfarth, D.; Hennig, K.

    1988-01-01

    The results of an extensive investigation of the properties of high-density avalanche chambers (HIDAC) are presented. This study has been performed in order to optimize the layout of HIDAC detectors, since they are intended to be applied as position sensitive detectors for annihilation radiation in a positron emission tomograph being under construction. (author)

  3. Role of Lipids in Spheroidal High Density Lipoproteins

    NARCIS (Netherlands)

    Vuorela, Timo; Catte, Andrea; Niemela, Perttu S.; Hall, Anette; Hyvonen, Marja T.; Marrink, Siewert-Jan; Karttunen, Mikko; Vattulainen, Ilpo

    2010-01-01

    We study the structure and dynamics of spherical high density lipoprotein (HDL) particles through coarse-grained multi-microsecond molecular dynamics simulations. We simulate both a lipid droplet without the apolipoprotein A-I (apoA-I) and the full HDL particle including two apoA-I molecules

  4. Role of lipids in spheroidal high density lipoproteins

    NARCIS (Netherlands)

    Vuorela, T.A.; Catte, A.; Niemelä, P.S.; Hall, A.; Hyvönen, M.T.; Marrink, S.J.; Karttunen, M.E.J.; Vattulainen, I.

    2010-01-01

    We study the structure and dynamics of spherical high density lipoprotein (HDL) particles through coarse-grained multi-microsecond molecular dynamics simulations. We simulate both a lipid droplet without the apolipoprotein A-I (apoA-I) and the full HDL particle including two apoA-I molecules

  5. Interfacial stick–slip transition in hydroxyapatite filled high density ...

    Indian Academy of Sciences (India)

    Unknown

    flow curves of composites and that of unfilled system remain identical. Filler addition lowers the .... Injection moulding grade high density polyethylene,. HD6070EA, was ... rheometer (Rosand Precision Ltd., UK) using version. 6⋅10 software. .... Bagley E B, Cabbot I M and West D C 1958 J. Appl. Phys. 29. 109. Blyler L L and ...

  6. Spontaneous magnetization in high-density quark matter

    DEFF Research Database (Denmark)

    Tsue, Yasuhiko; da Providência, João; Providência, Constanca

    2015-01-01

    It is shown that spontaneous magnetization occurs due to the anomalous magnetic moments of quarks in high-density quark matter under the tensor-type four-point interaction. The spin polarized condensate for each flavor of quark appears at high baryon density, which leads to the spontaneous magnet...

  7. The Influence of Decreased Levels of High Density Lipoprotein ...

    African Journals Online (AJOL)

    Background: Changes in lipoproteins levels in sickle cell disease (SCD) patients are well.known, but the physiological ramifications of the low levels observed have not been entirely resolved. Aim: The aim of this study is to evaluate the impact of decreased levels of high density lipoprotein cholesterol (HDL.c) on ...

  8. Identification of pathogenic Nocardia species by reverse line blot hybridization targeting the 16S rRNA and 16S-23S rRNA gene spacer regions.

    Science.gov (United States)

    Xiao, Meng; Kong, Fanrong; Sorrell, Tania C; Cao, Yongyan; Lee, Ok Cha; Liu, Ying; Sintchenko, Vitali; Chen, Sharon C A

    2010-02-01

    Although 16S rRNA gene sequence analysis is employed most often for the definitive identification of Nocardia species, alternate molecular methods and polymorphisms in other gene targets have also enabled species determinations. We evaluated a combined Nocardia PCR-based reverse line blot (RLB) hybridization assay based on 16S and 16S-23S rRNA gene spacer region polymorphisms to identify 12 American Type Culture Collection and 123 clinical Nocardia isolates representing 14 species; results were compared with results from 16S rRNA gene sequencing. Thirteen 16S rRNA gene-based (two group-specific and 11 species-specific) and five 16S-23S spacer-targeted (two taxon-specific and three species-specific) probes were utilized. 16S rRNA gene-based probes correctly identified 124 of 135 isolates (sensitivity, 92%) but were unable to identify Nocardia paucivorans strains (n = 10 strains) and a Nocardia asteroides isolate with a novel 16S rRNA gene sequence. Nocardia farcinica and Nocardia cyriacigeorgica strains were identified by the sequential use of an N. farcinica-"negative" probe and a combined N. farcinica/N. cyriacigeorgica probe. The assay specificity was high (99%) except for weak cross-reactivity between the Nocardia brasiliensis probe with the Nocardia thailandica DNA product; however, cross-hybridization with closely related nontarget species may occur. The incorporation of 16S-23S rRNA gene spacer-based probes enabled the identification of all N. paucivorans strains. The overall sensitivity using both probe sets was >99%. Both N. farcinica-specific 16S-23S rRNA gene spacer-directed probes were required to identify all N. farcinica stains by using this probe set. The study demonstrates the utility of a combined PCR/RLB assay for the identification of clinically relevant Nocardia species and its potential for studying subtypes of N. farcinica. Where species assignment is ambiguous or not possible, 16S rRNA gene sequencing is recommended.

  9. Polybacterial community analysis in human conjunctiva through 16S rRNA gene libraries.

    Science.gov (United States)

    Deepthi, KrishnanNair Geetha; Jayasudha, Rajagopalaboopathi; Girish, Rameshan Nair; Manikandan, Palanisamy; Ram, Rammohan; Narendran, Venkatapathy; Prabagaran, Solai Ramatchandirane

    2018-05-14

    The conjunctival sac of healthy human harbours a variety of microorganisms. When the eye is compromised, an occasional inadvertent spread happens to the adjacent tissue, resulting in bacterial ocular infections. Microbiological investigation of the conjunctival swab is one of the broadly used modality to study the aetiological agent of conjunctiva. However, most of the time such methods yield unsatisfactory results. Hence, the present study intends to identify the bacterial community in human conjunctiva of pre-operative subjects through 16S rRNA gene libraries. Out of 45 samples collected from preoperative patients undergoing cataract surgery, 36 libraries were constructed with bacterial nested-PCR-positive samples. The representative clones with unique restriction pattern were generated through Amplified Ribosomal DNA Restriction Analysis (ARDRA) which were sequenced for phylogenetic affiliation. A total of 211 representative clones were obtained which were distributed in phyla Actinobacteria, Firmicutes, α-Proteobacteria, β-Proteobacteria, γ-Proteobacteria, Bacteroidetes, and Deinococcus-Thermus. Findings revealed the presence of polybacterial community, especially in some cases even though no bacterium or a single bacterium alone was identified through cultivable method. Remarkably, we identified 17 species which have never been reported in any ocular infections. The sequencing data reported 6 unidentified bacteria suggesting the possibility of novel organisms in the sample. Since, polybacterial community has been identified consisting of both gram positive and gram negative bacteria, a broad spectrum antibiotic therapy is advisable to the patients who are undergoing cataract surgery. Consolidated effort would significantly improve a clear understanding of the nature of microbial community in the human conjunctiva which will promote administration of appropriate antibiotic regimen and also help in the development of oligonucleotide probes to screen the

  10. Identification of Bacillus Probiotics Isolated from Soil Rhizosphere Using 16S rRNA, recA, rpoB Gene Sequencing and RAPD-PCR.

    Science.gov (United States)

    Mohkam, Milad; Nezafat, Navid; Berenjian, Aydin; Mobasher, Mohammad Ali; Ghasemi, Younes

    2016-03-01

    Some Bacillus species, especially Bacillus subtilis and Bacillus pumilus groups, have highly similar 16S rRNA gene sequences, which are hard to identify based on 16S rDNA sequence analysis. To conquer this drawback, rpoB, recA sequence analysis along with randomly amplified polymorphic (RAPD) fingerprinting was examined as an alternative method for differentiating Bacillus species. The 16S rRNA, rpoB and recA genes were amplified via a polymerase chain reaction using their specific primers. The resulted PCR amplicons were sequenced, and phylogenetic analysis was employed by MEGA 6 software. Identification based on 16S rRNA gene sequencing was underpinned by rpoB and recA gene sequencing as well as RAPD-PCR technique. Subsequently, concatenation and phylogenetic analysis showed that extent of diversity and similarity were better obtained by rpoB and recA primers, which are also reinforced by RAPD-PCR methods. However, in one case, these approaches failed to identify one isolate, which in combination with the phenotypical method offsets this issue. Overall, RAPD fingerprinting, rpoB and recA along with concatenated genes sequence analysis discriminated closely related Bacillus species, which highlights the significance of the multigenic method in more precisely distinguishing Bacillus strains. This research emphasizes the benefit of RAPD fingerprinting, rpoB and recA sequence analysis superior to 16S rRNA gene sequence analysis for suitable and effective identification of Bacillus species as recommended for probiotic products.

  11. Diversity of thermophiles in a Malaysian hot spring determined using 16S rRNA and shotgun metagenome sequencing

    Directory of Open Access Journals (Sweden)

    Chia Sing eChan

    2015-03-01

    Full Text Available The Sungai Klah (SK hot spring is the second hottest geothermal spring in Malaysia. This hot spring is a shallow, 150-meter-long, fast-flowing stream, with temperatures varying from 50 to 110°C and a pH range of 7.0 to 9.0. Hidden within a wooded area, the SK hot spring is continually fed by plant litter, resulting in a relatively high degree of total organic content (TOC. In this study, a sample taken from the middle of the stream was analyzed at the 16S rRNA V3−V4 region by amplicon metagenome sequencing. Over 35 phyla were detected by analyzing the 16S rRNA data. Firmicutes and Proteobacteria represented approximately 57% of the microbiome. Approximately 70% of the detected thermophiles were strict anaerobes; however, Hydrogenobacter spp., obligate chemolithotrophic thermophiles, represented one of the major taxa. Several thermophilic photosynthetic microorganisms and acidothermophiles were also detected. Most of the phyla identified by 16S rRNA were also found using the shotgun metagenome approaches. The carbon, sulfur, and nitrogen metabolism within the SK hot spring community were evaluated by shotgun metagenome sequencing, and the data revealed diversity in terms of metabolic activity and dynamics. This hot spring has a rich diversified phylogenetic community partly due to its natural environment (plant litter, high TOC, and a shallow stream and geochemical parameters (broad temperature and pH range. It is speculated that symbiotic relationships occur between the members of the community.

  12. High density plasmas formation in Inertial Confinement Fusion and Astrophysics

    International Nuclear Information System (INIS)

    Martinez-Val, J. M.; Minguez, E.; Velarde, P.; Perlado, J. M.; Velarde, G.; Bravo, E.; Eliezer, S.; Florido, R.; Garcia Rubiano, J.; Garcia-Senz, D.; Gil de la Fe, J. M.; Leon, P. T.; Martel, P.; Ogando, F.; Piera, M.; Relano, A.; Rodriguez, R.; Garcia, C.; Gonzalez, E.; Lachaise, M.; Oliva, E.

    2005-01-01

    In inertially confined fusion (ICF), high densities are required to obtain high gains. In Fast Ignition, a high density, low temperature plasma can be obtained during the compression. If the final temperature reached is low enough, the electrons of the plasma can be degenerate. In degenerate plasmas. Bremsstrahlung emission is strongly suppressed an ignition temperature becomes lower than in classical plasmas, which offers a new design window for ICF. The main difficulty of degenerate plasmas in the compression energy needed for high densities. Besides that, the low specific heat of degenerate electrons (as compared to classical values) is also a problem because of the rapid heating of the plasma. Fluid dynamic evolution of supernovae remnants is a very interesting problem in order to predict the thermodynamical conditions achieved in their collision regions. Those conditions have a strong influence in the emission of light and therefore the detection of such events. A laboratory scale system has been designed reproducing the fluid dynamic field in high energy experiments. The evolution of the laboratory system has been calculated with ARWEN code, 2D Radiation CFD that works with Adaptive Mesh Refinement. Results are compared with simulations on the original system obtained with a 3D SPH astrophysical code. New phenomena at the collision plane and scaling of the laboratory magnitudes will be described. Atomic physics for high density plasmas has been studied with participation in experiments to obtain laser produced high density plasmas under NLTE conditions, carried out at LULI. A code, ATOM3R, has been developed which solves rate equations for optically thin plasmas as well as for homogeneous optically thick plasmas making use of escape factors. New improvements in ATOM3R are been done to calculate level populations and opacities for non homogeneous thick plasmas in NLTE, with emphasis in He and H lines for high density plasma diagnosis. Analytical expression

  13. High density data storage principle, technology, and materials

    CERN Document Server

    Zhu, Daoben

    2009-01-01

    The explosive increase in information and the miniaturization of electronic devices demand new recording technologies and materials that combine high density, fast response, long retention time and rewriting capability. As predicted, the current silicon-based computer circuits are reaching their physical limits. Further miniaturization of the electronic components and increase in data storage density are vital for the next generation of IT equipment such as ultra high-speed mobile computing, communication devices and sophisticated sensors. This original book presents a comprehensive introduction to the significant research achievements on high-density data storage from the aspects of recording mechanisms, materials and fabrication technologies, which are promising for overcoming the physical limits of current data storage systems. The book serves as an useful guide for the development of optimized materials, technologies and device structures for future information storage, and will lead readers to the fascin...

  14. Noise reduction in muon tomography for detecting high density objects

    International Nuclear Information System (INIS)

    Benettoni, M; Checchia, P; Cossutta, L; Furlan, M; Gonella, F; Pegoraro, M; Garola, A Rigoni; Ronchese, P; Vanini, S; Viesti, G; Bettella, G; Bonomi, G; Donzella, A; Subieta, M; Zenoni, A; Calvagno, G; Cortelazzo, G; Zanuttigh, P; Calvini, P; Squarcia, S

    2013-01-01

    The muon tomography technique, based on multiple Coulomb scattering of cosmic ray muons, has been proposed as a tool to detect the presence of high density objects inside closed volumes. In this paper a new and innovative method is presented to handle the density fluctuations (noise) of reconstructed images, a well known problem of this technique. The effectiveness of our method is evaluated using experimental data obtained with a muon tomography prototype located at the Legnaro National Laboratories (LNL) of the Istituto Nazionale di Fisica Nucleare (INFN). The results reported in this paper, obtained with real cosmic ray data, show that with appropriate image filtering and muon momentum classification, the muon tomography technique can detect high density materials, such as lead, albeit surrounded by light or medium density material, in short times. A comparison with algorithms published in literature is also presented

  15. Operation and control of high density tokamak reactors

    International Nuclear Information System (INIS)

    Attenberger, S.E.; McAlees, D.G.

    1976-01-01

    The incentive for high density operation of a tokamak reactor is discussed. The plasma size required to attain ignition is determined. Ignition is found to be possible in a relatively small system provided other design criteria are met. These criteria are described and the technology developments and operating procedures required by them are outlined. The parameters for such a system and its dynamic behavior during the operating cycle are also discussed

  16. Volume generation of negative ions in high density hydrogen discharges

    International Nuclear Information System (INIS)

    Hiskes, J.R.; Karo, A.M.

    1983-01-01

    A parametric survey is made of a high-density tandem two-chamber hydrogen negative ion system. The optimum extracted negative ion current densities are sensitive to the atom concentration in the discharge and to the system scale length. For scale lengths ranging from 10 cm to 0.1 cm optimum current densities range from of order 1 to 100 mA cm -2 , respectively

  17. Apparatus and method for generating high density pulses of electrons

    International Nuclear Information System (INIS)

    Lee, C.; Oettinger, P.E.

    1981-01-01

    An apparatus and method are described for the production of high density pulses of electrons using a laser energized emitter. Caesium atoms from a low pressure vapour atmosphere are absorbed on and migrate from a metallic target rapidly heated by a laser to a high temperature. Due to this heating time being short compared with the residence time of the caesium atoms adsorbed on the target surface, copious electrons are emitted which form a high current density pulse. (U.K.)

  18. High-Resolution Melting Curve Analysis of the 16S Ribosomal Gene to Detect and Identify Pathogenic and Saprophytic Leptospira Species in Colombian Isolates.

    Science.gov (United States)

    Peláez Sánchez, Ronald G; Quintero, Juan Álvaro López; Pereira, Martha María; Agudelo-Flórez, Piedad

    2017-05-01

    AbstractIt is important to identify the circulating Leptospira agent to enhance the performance of serodiagnostic tests by incorporating specific antigens of native species, develop vaccines that take into account the species/serovars circulating in different regions, and optimize prevention and control strategies. The objectives of this study were to develop a polymerase chain reaction (PCR)-high-resolution melting (HRM) assay for differentiating between species of the genus Leptospira and to verify its usefulness in identifying unknown samples to species level. A set of primers from the initial region of the 16S ribosomal gene was designed to detect and differentiate the 22 species of Leptospira . Eleven reference strains were used as controls to establish the reference species and differential melting curves. Twenty-five Colombian Leptospira isolates were studied to evaluate the usefulness of the PCR-HRM assay in identifying unknown samples to species level. This identification was confirmed by sequencing and phylogenetic analysis of the 16S ribosomal gene. Eleven Leptospira species were successfully identified, except for Leptospira meyeri / Leptospira yanagawae because the sequences were 100% identical. The 25 isolates from humans, animals, and environmental water sources were identified as Leptospira santarosai (twelve), Leptospira interrogans (nine), and L. meyeri / L. yanagawae (four). The species verification was 100% concordant between PCR-HRM and phylogenetic analysis of the 16S ribosomal gene. The PCR-HRM assay designed in this study is a useful tool for identifying Leptospira species from isolates.

  19. Relativistic many-body theory of high density matter

    International Nuclear Information System (INIS)

    Chin, S.A.

    1977-01-01

    A fully relativistic quantum many-body theory is applied to the study of high-density matter. The latter is identified with the zero-temperature ground state of a system of interacting baryons. In accordance with the observed short-range repulsive and long-range attractive character of the nucleon--nucleon force, baryons are described as interacting with each other via a massive scalar and a massive vector meson exchange. In the Hartree approximation, the theory yields the same result as the mean-field theory, but with additional vacuum fluctuation corrections. The resultant equation of state for neutron matter is used to determine properties of neutron stars. The relativistic exchange energy, its corresponding single-particle excitation spectrum, and its effect on the neutron matter equation of state, are calculated. The correlation energy from summing the set of ring diagrams is derived directly from the energy-momentum tensor, with renormalization carried out by adding counterterms to the original Lagrangian and subtracting purely vacuum expectation values. Terms of order g 4 lng 2 are explicitly given. Effects of scalar-vector mixing are discussed. Collective modes corresponding to macroscopic density fluctuation are investigated. Two basic modes are found, a plasma-like mode and zero sound, with the latter dominant at high density. The stability and damping of these modes are studied. Last, the effect of vacuum polarization in high-density matter is examined

  20. Operation and control of high density tokamak reactors

    International Nuclear Information System (INIS)

    Attenberger, S.E.; McAlees, D.G.

    1976-01-01

    The incentive for high density operation of a tokamak reactor was discussed. It is found that high density permits ignition in a relatively small, moderately elongated plasma with a moderate magnetic field strength. Under these conditions, neutron wall loadings approximately 4 MW/m 2 must be tolerated. The sensitivity analysis with respect to impurity effects shows that impurity control will most likely be necessary to achieve the desired plasma conditions. The charge exchange sputtered impurities are found to have an important effect so that maintaining a low neutral density in the plasma is critical. If it is assumed that neutral beams will be used to heat the plasma to ignition, high energy injection is required (approximately 250 keV) when heating is accompished at full density. A scenario is outlined where the ignition temperature is established at low density and then the fueling rate is increased to attain ignition. This approach may permit beams with energies being developed for use in TFTR to be successfully used to heat a high density device of the type described here to ignition

  1. Evaporation of carbon using electrons of a high density plasma

    International Nuclear Information System (INIS)

    Muhl, S.; Camps, E.; Escobar A, L.; Garcia E, J.L.; Olea, O.

    1999-01-01

    The high density plasmas are used frequently in the preparation of thin films or surface modification, for example to nitridation. In these processes, are used mainly the ions and the neutrals which compose the plasma. However, the electrons present in the plasma are not used, except in the case of chemical reactions induced by collisions, although the electron bombardment usually get hot the work piece. Through the adequate polarization of a conductor material, it is possible to extract electrons from a high density plasma at low pressure, that could be gotten the evaporation of this material. As result of the interaction between the plasma and the electron flux with the vapor produced, this last will be ionized. In this work, it is reported the use of this novelty arrangement to prepare carbon thin films using a high density argon plasma and a high purity graphite bar as material to evaporate. It has been used substrates outside plasma and immersed in the plasma. Also it has been reported the plasma characteristics (temperature and electron density, energy and ions flux), parameters of the deposit process (deposit rate and ion/neutral rate) as well as the properties of the films obtained (IR absorption spectra and UV/Vis, elemental analysis, hardness and refractive index. (Author)

  2. Microbiological and 16S rRNA analysis of sulphite-reducing clostridia from river sediments in central Italy

    Directory of Open Access Journals (Sweden)

    Marcheggiani Stefania

    2008-10-01

    Full Text Available Abstract Background Microbiological indicators are commonly used in the assessment of public health risks associated with fecal contamination of freshwater ecosystems. Sediments are a reservoir of microorganisms, and can thus provide information on past pollution events, not obtainable through the testing of surface water. Moreover, pathogens present in sediment may represent future threats to human health. Clostridium perfringens, a typical colonizer of sediments, has been suggested as an alternative indicator of fecal pollution. In order to be suitable for such purpose, the microorganism should be widely distributed in contaminated environments. The objective of this study was thus to determine the composition of the anaerobic community in sediment samples of the lower Tiber basin, in central Italy, through a combined approach involving granulometric analysis of sediment samples, as well as a microbiological and molecular (16S rRNA analysis of strains. Results Granulometry showed a similar, clayey sediment composition, in most sampling sites. The microbiological method, employing, an adaptation of the standard method, proved to be effective in isolating anaerobic bacteria from the environmental matrix for the purpose of genetic analysis. Eighty-three strains of bacteria were isolated and the partial 16S rRNA gene sequenced. While biochemical analysis detected only C. perfringens strains, phylogenetic analysis indicated the presence of three clusters: C. perfringens, C. bifermentans and B. cereus, comprising eight taxa. C. perfringens, the commonest in almost all sediment sampling sites, was present in all sites, and in both seasons (seasonal sampling was carried out only along the Tiber and Aniene rivers. None of the described genetic profiles showed complete similarity with GenBank sequences. Conclusion The study underlines the value of C. perfringens as an alternative microbial indicator of fecal contamination in river sediments. This is

  3. Microbiological and 16S rRNA analysis of sulphite-reducing clostridia from river sediments in central Italy.

    Science.gov (United States)

    Marcheggiani, Stefania; Iaconelli, Marcello; D'angelo, Annamaria; Pierdominici, Elio; La Rosa, Giuseppina; Muscillo, Michele; Equestre, Michele; Mancini, Laura

    2008-10-08

    Microbiological indicators are commonly used in the assessment of public health risks associated with fecal contamination of freshwater ecosystems. Sediments are a reservoir of microorganisms, and can thus provide information on past pollution events, not obtainable through the testing of surface water. Moreover, pathogens present in sediment may represent future threats to human health. Clostridium perfringens, a typical colonizer of sediments, has been suggested as an alternative indicator of fecal pollution. In order to be suitable for such purpose, the microorganism should be widely distributed in contaminated environments. The objective of this study was thus to determine the composition of the anaerobic community in sediment samples of the lower Tiber basin, in central Italy, through a combined approach involving granulometric analysis of sediment samples, as well as a microbiological and molecular (16S rRNA) analysis of strains. Granulometry showed a similar, clayey sediment composition, in most sampling sites. The microbiological method, employing, an adaptation of the standard method, proved to be effective in isolating anaerobic bacteria from the environmental matrix for the purpose of genetic analysis. Eighty-three strains of bacteria were isolated and the partial 16S rRNA gene sequenced. While biochemical analysis detected only C. perfringens strains, phylogenetic analysis indicated the presence of three clusters: C. perfringens, C. bifermentans and B. cereus, comprising eight taxa. C. perfringens, the commonest in almost all sediment sampling sites, was present in all sites, and in both seasons (seasonal sampling was carried out only along the Tiber and Aniene rivers). None of the described genetic profiles showed complete similarity with GenBank sequences. The study underlines the value of C. perfringens as an alternative microbial indicator of fecal contamination in river sediments. This is supported by the bacterium's presence in all sampling sites

  4. Bacterial diversity of soil under eucalyptus assessed by 16S rDNA sequencing analysis Diversidade bacteriana de solo sob eucaliptos obtida por seqüenciamento do 16S rDNA

    Directory of Open Access Journals (Sweden)

    Érico Leandro da Silveira

    2006-10-01

    Full Text Available Studies on the impact of Eucalyptus spp. on Brazilian soils have focused on soil chemical properties and isolating interesting microbial organisms. Few studies have focused on microbial diversity and ecology in Brazil due to limited coverage of traditional cultivation and isolation methods. Molecular microbial ecology methods based on PCR amplified 16S rDNA have enriched the knowledge of soils microbial biodiversity. The objective of this work was to compare and estimate the bacterial diversity of sympatric communities within soils from two areas, a native forest (NFA and an eucalyptus arboretum (EAA. PCR primers, whose target soil metagenomic 16S rDNA were used to amplify soil DNA, were cloned using pGEM-T and sequenced to determine bacterial diversity. From the NFA soil 134 clones were analyzed, while 116 clones were analyzed from the EAA soil samples. The sequences were compared with those online at the GenBank. Phylogenetic analyses revealed differences between the soil types and high diversity in both communities. Soil from the Eucalyptus spp. arboretum was found to have a greater bacterial diversity than the soil investigated from the native forest area.Estudos sobre impacto do Eucalyptus spp. em solos brasileiros têm focalizado propriedades químicas do solo e isolamento de microrganismos de interesse. No Brasil há pouco enfoque em ecologia e diversidade microbiana, devido às limitações dos métodos tradicionais de cultivo e isolamento. A utilização de métodos moleculares no estudo da ecologia microbiana baseados na amplificação por PCR do 16S rDNA têm enriquecido o conhecimento da biodiversidade microbiana dos solos. O objetivo deste trabalho foi comparar e estimar a diversidade bacteriana de comunidades simpátricas em solos de duas áreas: uma floresta nativa (NFA e outra adjacente com arboreto de eucaliptos (EAA. Oligonucleotídeos iniciadores foram utilizados para amplificar o 16S rDNA metagenômico do solo, o qual foi

  5. High-density cervical ureaplasma urealyticum colonization in pregnant women

    Directory of Open Access Journals (Sweden)

    Ranđelović Gordana

    2006-01-01

    Full Text Available Background/aim: Ureaplasma urealyticum, a common commensal of the female lower genital tract, has been observed as an important opportunistic pathogen during pregnancy. The aims of this study were to determine the degree of cervical colonization with U. urealyticum in pregnant women with risk pregnancy and in pregnant women with normal term delivery and to evaluate the correlation between high-density cervical U. urealyticum colonization and premature rupture of membranes (PROM as well. Methods. This research was conducted on the samples comprising 130 hospitalized pregnant women with threatening preterm delivery and premature rupture of membranes. The control group consisted of 39 pregnant women with term delivery without PROM. In addition to standard bacteriological examination and performing direct immunofluorescence test to detect Chlamydia trachomatis, cervical swabs were also examined for the presence of U. urealyticum and Mycoplasma hominis by commercially available Mycofast Evolution 2 test (International Microbio, France. Results. The number of findings with isolated high-density U. urealyticum in the target group was 69 (53.08%, while in the control group was 14 (35.90%. Premature rupture of membranes (PROM occurred in 43 (33.08% examinees: 29 were pPROM, and 14 were PROM. The finding of U.urealyticum ≥104 was determined in 25 (58.14% pregnant women with rupture, 17 were pPROM, and 8 were PROM. There was statistically significant difference in the finding of high-density U. urealyticum between the pregnant women with PROM and the control group (χ² = 4.06, p < 0.05. U. urealyticum was predominant bacterial species found in 62.79% of isolates in the PROM cases, while in 32.56% it was isolated alone. Among the 49 pregnant women with preterm delivery, pPROM occurred in 29 (59.18% examinees, and in 70.83% of pregnant women with findings of high-density U. urealyticum pPROM was observed. Conclusion. Cervical colonization with U

  6. Utility of 16S rRNA PCR performed on clinical specimens in patient management

    Directory of Open Access Journals (Sweden)

    A. Akram

    2017-04-01

    Conclusions: Despite the low diagnostic yield, results of 16S rRNA PCR can still have a significant impact on patient management due to rationalization or cessation of the antimicrobial therapy. The yield of 16S rRNA PCR was highest for heart valves.

  7. Prevalence of 16S rRNA methylase genes among b-lactamase ...

    African Journals Online (AJOL)

    2014-07-07

    Jul 7, 2014 ... School of Life Sciences, Pondicherry University, Pondicherry, India ... Methods: To study co existence of 16S rRNA methylases (armA, rmtA, rmtB, rmtC, rmtD, and .... Isolates positive for bla or 16S rRNA methylase genes.

  8. Characterization of the high density plasma etching process of CCTO thin films for the fabrication of very high density capacitors

    International Nuclear Information System (INIS)

    Altamore, C; Tringali, C; Sparta', N; Marco, S Di; Grasso, A; Ravesi, S

    2010-01-01

    In this work the feasibility of CCTO (Calcium Copper Titanate) patterning by etching process is demonstrated and fully characterized in a hard to etch materials etcher. CCTO sintered in powder shows a giant relative dielectric constant (10 5 ) measured at 1 MHz at room temperature. This feature is furthermore coupled with stability from 10 1 Hz to 10 6 Hz in a wide temperature range (100K - 600K). In principle, this property can allow to fabricate very high capacitance density condenser. Due to its perovskite multi-component structure, CCTO can be considered a hard to etch material. For high density capacitor fabrication, CCTO anisotropic etching is requested by using high density plasma. The behavior of etched CCTO was studied in a HRe- (High Density Reflected electron) plasma etcher using Cl 2 /Ar chemistry. The relationship between the etch rate and the Cl 2 /Ar ratio was also studied. The effects of RF MHz, KHz Power and pressure variation, the impact of HBr addiction to the Cl 2 /Ar chemistry on the CCTO etch rate and on its selectivity to Pt and photo resist was investigated.

  9. Characterization of the high density plasma etching process of CCTO thin films for the fabrication of very high density capacitors

    Energy Technology Data Exchange (ETDEWEB)

    Altamore, C; Tringali, C; Sparta' , N; Marco, S Di; Grasso, A; Ravesi, S [STMicroelectronics, Industial and Multi-segment Sector R and D, Catania (Italy)

    2010-02-15

    In this work the feasibility of CCTO (Calcium Copper Titanate) patterning by etching process is demonstrated and fully characterized in a hard to etch materials etcher. CCTO sintered in powder shows a giant relative dielectric constant (10{sup 5}) measured at 1 MHz at room temperature. This feature is furthermore coupled with stability from 10{sup 1} Hz to 10{sup 6} Hz in a wide temperature range (100K - 600K). In principle, this property can allow to fabricate very high capacitance density condenser. Due to its perovskite multi-component structure, CCTO can be considered a hard to etch material. For high density capacitor fabrication, CCTO anisotropic etching is requested by using high density plasma. The behavior of etched CCTO was studied in a HRe- (High Density Reflected electron) plasma etcher using Cl{sub 2}/Ar chemistry. The relationship between the etch rate and the Cl{sub 2}/Ar ratio was also studied. The effects of RF MHz, KHz Power and pressure variation, the impact of HBr addiction to the Cl{sub 2}/Ar chemistry on the CCTO etch rate and on its selectivity to Pt and photo resist was investigated.

  10. Bacterial Diversity Studies Using the 16S rRNA Gene Provide a Powerful Research-Based Curriculum for Molecular Biology Laboratory

    Directory of Open Access Journals (Sweden)

    Bryan E. Dutton

    2002-12-01

    Full Text Available We have developed a ten-week curriculum for molecular biology that uses 16S ribosomal RNA genes to characterize and compare novel bacteria from hot spring communities in Yellowstone National Park. The 16S rRNA approach bypasses selective culture-based methods. Our molecular biology course offered the opportunity for students to learn broadly applicable methods while contributing to a long-term research project. Specifically, students isolated and characterized clones that contained novel 16S rRNA inserts using restriction enzyme, DNA sequencing, and computer-based phylogenetic methods. In both classes, students retrieved novel bacterial 16S rRNA genes, several of which were most similar to Green Nonsulfur bacterial isolates. During class, we evaluated student performance and mastery of skills and concepts using quizzes, formal lab notebooks, and a broad project assignment. For this report, we also assessed student performance alongside data quality and discussed the significance, our goal being to improve both research and teaching methods.

  11. 16S/18S ribosomal DNA clone library analysis of rumen microbial diversity

    International Nuclear Information System (INIS)

    Wright, A.G.; Kiyoshi Tajima; Aminov, R.I.

    2005-01-01

    The rumen contains a complex ecosystem where billions of bacteria, archaea, protozoa and fungi reside. This diverse microbiota is well adapted to live in the rumen and play an important role in the digestion of feed and nutrient supply to the host in the form of microbial protein and volatile fatty acids. It is estimated that the rumen microbial population consists of about 10 6 protozoa/ml, 10 3 -10 7 fungi/ml, 10 10 bacteria/ml, and 10 9 methanogens/ml. To better understand the complex relationships in the rumen, it is necessary to gain an insight into the diversity of the rumen microbes and how the quantity and composition of rumen micro-organisms are altered by a number of different host factors such as age, genetics and diet. In the past, the diversity of micro-organisms from the digestive tracts of domesticated ruminants has been identified by classical microbiological techniques. However, given the fastidious growth requirements of rumen micro-organisms, it is reasonable to concede that the culture-dependent methods may select against some species, or taxonomic groups, leading researchers to underestimate the microbial diversity that is actually present in the rumen. In fact, it has been speculated that 90% of micro-organisms in nature have escaped traditional cultivation methods. Therefore, a major challenge in microbial ecology has been to assess the diversity and structure of natural microbial communities. The field of molecular biology has advanced with many innovative technological breakthroughs. The ability to extract and to isolate high-molecular weight DNA from rumen digesta, PCR amplify genes from specific microbial groups and obtain gene sequence data is now a routine event. The small subunit ribosomal RNA (SSU-rRNA) gene, called 16S in prokaryotes and 18S in eukaryotes, is the most widely used molecular marker to presumptively identify morphologically indistinguishable species, to infer their phylogenetic relationships, and to elucidate microbial

  12. Biomimetic High Density Lipoprotein Nanoparticles For Nucleic Acid Delivery

    Science.gov (United States)

    McMahon, Kaylin M.; Mutharasan, R. Kannan; Tripathy, Sushant; Veliceasa, Dorina; Bobeica, Mariana; Shumaker, Dale K.; Luthi, Andrea J.; Helfand, Brian T.; Ardehali, Hossein; Mirkin, Chad A.; Volpert, Olga; Thaxton, C. Shad

    2014-01-01

    We report a gold nanoparticle-templated high density lipoprotein (HDL AuNP) platform for gene therapy which combines lipid-based nucleic acid transfection strategies with HDL biomimicry. For proof-of-concept, HDL AuNPs are shown to adsorb antisense cholesterylated DNA. The conjugates are internalized by human cells, can be tracked within cells using transmission electron microscopy (TEM), and regulate target gene expression. Overall, the ability to directly image the AuNP core within cells, the chemical tailorability of the HDL AuNP platform, and the potential for cell-specific targeting afforded by HDL biomimicry make this platform appealing for nucleic acid delivery. PMID:21319839

  13. High Density Thermal Energy Storage with Supercritical Fluids

    Science.gov (United States)

    Ganapathi, Gani B.; Wirz, Richard

    2012-01-01

    A novel approach to storing thermal energy with supercritical fluids is being investigated, which if successful, promises to transform the way thermal energy is captured and utilized. The use of supercritical fluids allows cost-affordable high-density storage with a combination of latent heat and sensible heat in the two-phase as well as the supercritical state. This technology will enhance penetration of several thermal power generation applications and high temperature water for commercial use if the overall cost of the technology can be demonstrated to be lower than the current state-of-the-art molten salt using sodium nitrate and potassium nitrate eutectic mixtures.

  14. Optically Addressed Nanostructures for High Density Data Storage

    Science.gov (United States)

    2005-10-14

    beam to sub-wavelength resolutions. X. Refereed Journal Publications I. M. D. Stenner , D. J. Gauthier, and M. A. Neifeld, "The speed of information in a...profiles for high-density optical data storage," Optics Communications, Vol.253, pp.56-69, 2005. 5. M. D. Stenner , D. J. Gauthier, and M. A. Neifeld, "Fast...causal information transmission in a medium with a slow group velocity," Physical Review Letters, Vol.94, February 2005. 6. M. D. Stenner , M. A

  15. Viscosity and attenuation of sound wave in high density deuterium

    International Nuclear Information System (INIS)

    Inoue, Kazuko; Ariyasu, Tomio

    1985-01-01

    The penetration of low frequency sound wave into the fuel deuterium is discussed as for laser fusion. The sound velocity and the attenuation constant due to viscosity are calculated for high density (n = 10 24 -- 10 27 cm -3 , T = 10 -1 -- 10 4 eV) deuterium. The shear viscosity of free electron gas and the bulk viscosity due to ion-ion interaction mainly contribute to the attenuation of sound wave. The sound wave of the frequency below 10 10 Hz can easily penetrate through the compressed fuel deuterium of diameter 1 -- 10 3 μm. (author)

  16. Low-frequency oscillations at high density in JFT-2

    International Nuclear Information System (INIS)

    Maeno, Masaki; Katagiri, Masaki; Suzuki, Norio; Fujisawa, Noboru

    1977-12-01

    Low-frequency oscillations in a plasma were measured with magnetic probes and Si surface-barrier detectors, and behaviour of the high density plasmas was studied. The plasma current profile in the phase of decreasing density after the interruption of gas input is more peaked than during gas input. The introduction of hydrogen during a discharge results in a reduction of the impurities flux. The increase of density by fast gas input is limited with a negative voltage spike. Immediately before a negative voltage spike, oscillations of m=1,2 grow, leading to the spike. (auth.)

  17. Possible new form of matter at high density

    International Nuclear Information System (INIS)

    Lee, T.D.

    1974-01-01

    As a preliminary to discussion of the possibility of new forms of matter at high density, questions relating to the vacuum and vacuum excitation are considered. A quasi-classical approach to the development of abnormal nuclear states is undertaken using a Fermi gas of nucleons of uniform density. Discontinuous transitions are considered in the sigma model (tree approximation) followed by brief consideration of higher order loop diagrams. Production and detection of abnormal nuclear states are discussed in the context of high energy heavy ion collisions. Remarks are made on motivation for such research. 8 figures

  18. Characterization of composite high density polyethylene and layered zirconium phosphate

    International Nuclear Information System (INIS)

    Lino, Adan S.; Silva, Daniela F.; Mendes, Luis C.

    2011-01-01

    Zirconium phosphate (ZrP) (2 w%), synthesized by direct precipitation method, was used in the preparation of composite with high density polyethylene (HDPE), through extrusion processing in the molten state. Wide angle x-ray diffraction (WAXD), stress-strain mechanical analysis and scanning electron microscopy (SEM) techniques were used for ZrP, neat polymer and composite mechanical and morphologic characterization. Although there was a slight increase in the Young modulus, WAXD and SEM analysis showed that the intercalation of the HDPE matrix in the filler galleries did not occur, probably due to the insufficient lamellae spacing to intercalate the polymer chains. Then, a microcomposite was achieved. (author)

  19. Structure of high-density amorphous ice under pressure

    International Nuclear Information System (INIS)

    Klotz, S.; Hamel, G.; Loveday, J.S.; Nelmes, R.J.; Guthrie, M.; Soper, A.K.

    2002-01-01

    We report in situ neutron diffraction studies of high-density amorphous ice (HDA) at 100 K at pressures up to 2.2 GPa. We find that the compression is achieved by a strong contraction (∼20%) of the second neighbor coordination shell, so that at 2.2 GPa it closely approaches the first coordination shell, which itself remains intact in both structure and size. The hydrogen bond orientations suggest an absence of hydrogen bonding between first and second shells and that HDA has increasingly interpenetrating hydrogen bond networks under pressure

  20. Behavior of high-density spent-fuel storage racks

    International Nuclear Information System (INIS)

    Bailey, W.J.

    1986-08-01

    Included in this report is a summary of information on neutron-absorbing materials such as B 4 C in an aluminum matrix or organic binder material, stainless steel-boron and aluminum-boron alloys, and stainless steetl-clad cadmium that are used in high-density spent fuel storage racks. A list of the types of neutron-absorbing materials being used in spent fuel storage racks at domestic commercial plants is provided. Recent cases at several domestic plants where swelling of rack side plates (where the B 4 C in an aluminum matrix and B 4 C in an organic binder material were located) occurred are reviewed

  1. [Phylogenetic analysis of closely related Leuconostoc citreum species based on partial housekeeping genes].

    Science.gov (United States)

    Lv, Qiang; Chen, Ming; Xu, Haiyan; Song, Yuqin; Sun, Zhihong; Dan, Tong; Sun, Tiansong

    2013-07-04

    Using the 16S rRNA, dnaA, murC and pyrG gene sequences, we identified the phylogenetic relationship among closely related Leuconostoc citreum species. Seven Leu. citreum strains originally isolated from sourdough were characterized by PCR methods to amplify the dnaA, murC and pyrG gene sequences, which were determined to assess the suitability as phylogenetic markers. Then, we estimated the genetic distance and constructed the phylogenetic trees including 16S rRNA and above mentioned three housekeeping genes combining with published corresponding sequences. By comparing the phylogenetic trees, the topology of three housekeeping genes trees were consistent with that of 16S rRNA gene. The homology of closely related Leu. citreum species among dnaA, murC, pyrG and 16S rRNA gene sequences were different, ranged from75.5% to 97.2%, 50.2% to 99.7%, 65.0% to 99.8% and 98.5% 100%, respectively. The phylogenetic relationship of three housekeeping genes sequences were highly consistent with the results of 16S rRNA gene sequence, while the genetic distance of these housekeeping genes were extremely high than 16S rRNA gene. Consequently, the dnaA, murC and pyrG gene are suitable for classification and identification closely related Leu. citreum species.

  2. Multiplexed, high density electrophysiology with nanofabricated neural probes.

    Directory of Open Access Journals (Sweden)

    Jiangang Du

    Full Text Available Extracellular electrode arrays can reveal the neuronal network correlates of behavior with single-cell, single-spike, and sub-millisecond resolution. However, implantable electrodes are inherently invasive, and efforts to scale up the number and density of recording sites must compromise on device size in order to connect the electrodes. Here, we report on silicon-based neural probes employing nanofabricated, high-density electrical leads. Furthermore, we address the challenge of reading out multichannel data with an application-specific integrated circuit (ASIC performing signal amplification, band-pass filtering, and multiplexing functions. We demonstrate high spatial resolution extracellular measurements with a fully integrated, low noise 64-channel system weighing just 330 mg. The on-chip multiplexers make possible recordings with substantially fewer external wires than the number of input channels. By combining nanofabricated probes with ASICs we have implemented a system for performing large-scale, high-density electrophysiology in small, freely behaving animals that is both minimally invasive and highly scalable.

  3. Mixing of high density solution in vertical upward flow

    International Nuclear Information System (INIS)

    Kumamaru, Hiroshige; Hosogi, Nobuyoshi; Komada, Toshiaki; Fujiwara, Yoshiki

    1999-01-01

    Experimental and analytical studies have been performed in order to provide fundamental data and a numerical calculation model on the mixing of boric acid solution, injected from the standby liquid control system (SLCS), under a low natural circulation flow during an ATWS in a BWR. First, fundamental experiments on the mixing of high-density solution in vertically-upward water flow have been performed by using a small apparatus. Mixing patterns observed in the experiments have been classified to two groups, i.e. complete mixing (entrainment) and incomplete mixing (entrainment). In the complete mixing, the injected high-density solution is mixed (entrained) completely into the vertically-upward water flow. From the experiments, the minimum water flow rates in which the complete mixing (entrainment) is achieved have been obtained for various solution densities and solution injection rates. Secondly, two-dimensional numerical calculations have been performed. A continuity equation for total fluid, momentum equations in two directions and a continuity equation for solute are solved by using the finite difference method for discretization method and by following the MAC method for solution procedure. The calculations have predicted nearly the minimum water flow rate in which the complete mixing is achieved, while the calculations have been performed only for one combination of the solution density and solution injection rate until now. (author)

  4. Ultra-Stretchable Interconnects for High-Density Stretchable Electronics

    Directory of Open Access Journals (Sweden)

    Salman Shafqat

    2017-09-01

    Full Text Available The exciting field of stretchable electronics (SE promises numerous novel applications, particularly in-body and medical diagnostics devices. However, future advanced SE miniature devices will require high-density, extremely stretchable interconnects with micron-scale footprints, which calls for proven standardized (complementary metal-oxide semiconductor (CMOS-type process recipes using bulk integrated circuit (IC microfabrication tools and fine-pitch photolithography patterning. Here, we address this combined challenge of microfabrication with extreme stretchability for high-density SE devices by introducing CMOS-enabled, free-standing, miniaturized interconnect structures that fully exploit their 3D kinematic freedom through an interplay of buckling, torsion, and bending to maximize stretchability. Integration with standard CMOS-type batch processing is assured by utilizing the Flex-to-Rigid (F2R post-processing technology to make the back-end-of-line interconnect structures free-standing, thus enabling the routine microfabrication of highly-stretchable interconnects. The performance and reproducibility of these free-standing structures is promising: an elastic stretch beyond 2000% and ultimate (plastic stretch beyond 3000%, with <0.3% resistance change, and >10 million cycles at 1000% stretch with <1% resistance change. This generic technology provides a new route to exciting highly-stretchable miniature devices.

  5. Manufacture of sintered bricks of high density from beryllium oxide

    International Nuclear Information System (INIS)

    Pointud, R.; Rispal, Ch.; Le Garec, M.

    1959-01-01

    Beryllium oxide bricks of nuclear purity 100 x 100 x 50 and 100 x 100 x 100 mm of very high density (between 2.85 and 3.00) are manufactured by sintering under pressure in graphite moulds at temperatures between 1,750 and 1,850 deg. C, and under a pressure of 150 kg/cm 2 . The physico-chemical state of the saw material is of considerable importance with regard to the success of the sintering operation. In addition, a study of the sintering of a BeO mixture with 3 to 5 per cent of boron introduced in the form of boric acid, boron carbide or elementary boron shows that high densities can only be obtained by sintering under pressure. For technical reasons of manufacture, only the mixture based on boron carbide is used. The sintering is carried out in graphite moulds at 1500 deg. C under 150 kg/cm 2 pressure, and bricks can be obtained with density between 2,85 and 2,90. Laboratory studies and the industrial manufacture of various sinters are described in detail. (author) [fr

  6. Development of technology of high density LEU dispersion fuel fabrication

    International Nuclear Information System (INIS)

    Wiencek, T.; Totev, T.

    2007-01-01

    Advanced Materials Fabrication Facilities at Argonne National Laboratory have been involved in development of LEU dispersion fuel for research and test reactors from the beginning of RERTR program. This paper presents development of technology of high density LEU dispersion fuel fabrication for full size plate type fuel elements. A brief description of Advanced Materials Fabrication Facilities where development of the technology was carried out is given. A flow diagram of the manufacturing process is presented. U-Mo powder was manufactured by the rotating electrode process. The atomization produced a U-Mo alloy powder with a relatively uniform size distribution and a nearly spherical shape. Test plates were fabricated using tungsten and depleted U-7 wt.% Mo alloy, 4043 Al and Al-2 wt% Si matrices with Al 6061 aluminum alloy for the cladding. During the development of the technology of manufacturing of full size high density LEU dispersion fuel plates special attention was paid to meet the required homogeneity, bonding, dimensions, fuel out of zone and other mechanical characteristics of the plates.

  7. Inhibition of Escherichia coli precursor-16S rRNA processing by mouse intestinal contents

    DEFF Research Database (Denmark)

    Licht, Tine Rask; Tolker-Nielsen, Tim; Holmstrøm, Kim

    1999-01-01

    . We have applied fluorescence in situ hybridization of pre-16S rRNA to Escherichia coli cells growing in vitro in extracts from two different compartments of the mouse intestine: the caecal mucus layer, where E. coli grew rapidly, and the contents of the caecum, which supported much slower bacterial...... content of pre-16S rRNA than cultures of the same strain growing rapidly in rich media. We present results suggesting that the mouse intestinal contents contain an agent that inhibits the growth of E. coli by disturbing its ability to process pre-16S rRNA....

  8. Unrealistic phylogenetic trees may improve phylogenetic footprinting.

    Science.gov (United States)

    Nettling, Martin; Treutler, Hendrik; Cerquides, Jesus; Grosse, Ivo

    2017-06-01

    The computational investigation of DNA binding motifs from binding sites is one of the classic tasks in bioinformatics and a prerequisite for understanding gene regulation as a whole. Due to the development of sequencing technologies and the increasing number of available genomes, approaches based on phylogenetic footprinting become increasingly attractive. Phylogenetic footprinting requires phylogenetic trees with attached substitution probabilities for quantifying the evolution of binding sites, but these trees and substitution probabilities are typically not known and cannot be estimated easily. Here, we investigate the influence of phylogenetic trees with different substitution probabilities on the classification performance of phylogenetic footprinting using synthetic and real data. For synthetic data we find that the classification performance is highest when the substitution probability used for phylogenetic footprinting is similar to that used for data generation. For real data, however, we typically find that the classification performance of phylogenetic footprinting surprisingly increases with increasing substitution probabilities and is often highest for unrealistically high substitution probabilities close to one. This finding suggests that choosing realistic model assumptions might not always yield optimal predictions in general and that choosing unrealistically high substitution probabilities close to one might actually improve the classification performance of phylogenetic footprinting. The proposed PF is implemented in JAVA and can be downloaded from https://github.com/mgledi/PhyFoo. : martin.nettling@informatik.uni-halle.de. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press.

  9. Rapid diagnosis of virulent Pasteurella multocida isolated from farm animals with clinical manifestation of pneumonia respiratory infection using 16S rDNA and KMT1 gene

    Directory of Open Access Journals (Sweden)

    Gamal Mohamedin Hassan

    2016-01-01

    Full Text Available Objective: To characterize intra-isolates variation between clinical isolates of Pasteurella multocida (P. multocida isolated from sheep, cattle and buffalo at molecular level to check the distribution of pneumonia and hemorrhagic septicemia in some regions of Fayoum, Egypt. Methods: These isolates were obtained from various locations in the Fayoum Governorate, Egypt and they were identified by amplifying 16S rDNA and KMT1 genes using their DNA as a template in PCR reaction. Results: The results demonstrated that the five selective isolates of P. multocida had similar size of PCR products that generated one band of 16S rDNA having 1 471 bp and KMT1 gene having 460 bp. The phylogenetic tree and similarity of the five selective isolates of P. multocida which were collected from GenBank database were calculated and analyzed for the nucleotide sequence of 16S rDNA and KMT1 genes. The sequencing result of 16S rRNA gene product (1 471 bp for the five selective isolates of P. multocida showed that the isolates of sheep (FUP2 shared 94.08%, 88.10% homology with the buffalo isolate (FUP8 and cattle isolate (FUP9 respectively, whereas, the buffalo isolate (FUP5 shared 98.18% and 94.40% homology with the cattle isolates (FUP12 and FUP9. Conclusions: The results indicated the relationships of P. multocida isolated from buffalo and cattle rather than the close relationships between P. multocida isolated from cattle and sheep. Diagnosis of P. multocida by 16S rDNA and KMT1 gene sequences was important to determine the antigen that is responsible for protective cover within the same group of animals and to help for the production of new vaccines for the control of microbial infection for domestic animals.

  10. Prevalence of 16S rRNA methylase genes among β-lactamase ...

    African Journals Online (AJOL)

    Background: Co production of 16S rRNA methylases gene and β-Lactamase gene among Enterobacteriaceae isolates conferring resistance to both therapeutic options has serious implications for clinicians worldwide. Methods: To study co existence of 16S rRNA methylases (armA, rmtA, rmtB, rmtC, rmtD, and npmA) and ...

  11. Utility of 16S rDNA Sequencing for Identification of Rare Pathogenic Bacteria.

    Science.gov (United States)

    Loong, Shih Keng; Khor, Chee Sieng; Jafar, Faizatul Lela; AbuBakar, Sazaly

    2016-11-01

    Phenotypic identification systems are established methods for laboratory identification of bacteria causing human infections. Here, the utility of phenotypic identification systems was compared against 16S rDNA identification method on clinical isolates obtained during a 5-year study period, with special emphasis on isolates that gave unsatisfactory identification. One hundred and eighty-seven clinical bacteria isolates were tested with commercial phenotypic identification systems and 16S rDNA sequencing. Isolate identities determined using phenotypic identification systems and 16S rDNA sequencing were compared for similarity at genus and species level, with 16S rDNA sequencing as the reference method. Phenotypic identification systems identified ~46% (86/187) of the isolates with identity similar to that identified using 16S rDNA sequencing. Approximately 39% (73/187) and ~15% (28/187) of the isolates showed different genus identity and could not be identified using the phenotypic identification systems, respectively. Both methods succeeded in determining the species identities of 55 isolates; however, only ~69% (38/55) of the isolates matched at species level. 16S rDNA sequencing could not determine the species of ~20% (37/187) of the isolates. The 16S rDNA sequencing is a useful method over the phenotypic identification systems for the identification of rare and difficult to identify bacteria species. The 16S rDNA sequencing method, however, does have limitation for species-level identification of some bacteria highlighting the need for better bacterial pathogen identification tools. © 2016 Wiley Periodicals, Inc.

  12. Detecting 16S rRNA Methyltransferases in Enterobacteriaceae by Use of Arbekacin.

    Science.gov (United States)

    McGann, Patrick; Chahine, Sarah; Okafor, Darius; Ong, Ana C; Maybank, Rosslyn; Kwak, Yoon I; Wilson, Kerry; Zapor, Michael; Lesho, Emil; Hinkle, Mary

    2016-01-01

    16S rRNA methyltransferases confer resistance to most aminoglycosides, but discriminating their activity from that of aminoglycoside-modifying enzymes (AMEs) is challenging using phenotypic methods. We demonstrate that arbekacin, an aminoglycoside refractory to most AMEs, can rapidly detect 16S methyltransferase activity in Enterobacteriaceae with high specificity using the standard disk susceptibility test. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

  13. A distributed current stimulator ASIC for high density neural stimulation.

    Science.gov (United States)

    Jeong Hoan Park; Chaebin Kim; Seung-Hee Ahn; Tae Mok Gwon; Joonsoo Jeong; Sang Beom Jun; Sung June Kim

    2016-08-01

    This paper presents a novel distributed neural stimulator scheme. Instead of a single stimulator ASIC in the package, multiple ASICs are embedded at each electrode site for stimulation with a high density electrode array. This distributed architecture enables the simplification of wiring between electrodes and stimulator ASIC that otherwise could become too complex as the number of electrode increases. The individual ASIC chip is designed to have a shared data bus that independently controls multiple stimulating channels. Therefore, the number of metal lines is determined by the distributed ASICs, not by the channel number. The function of current steering is also implemented within each ASIC in order to increase the effective number of channels via pseudo channel stimulation. Therefore, the chip area can be used more efficiently. The designed chip was fabricated with area of 0.3 mm2 using 0.18 μm BCDMOS process, and the bench-top test was also conducted to validate chip performance.

  14. Automatic Calibration of High Density Electric Muscle Stimulation

    DEFF Research Database (Denmark)

    Knibbe, Jarrod; Strohmeier, Paul; Boring, Sebastian

    2017-01-01

    . (2) EMS requires time consuming, expert calibration -- confining these interaction techniques to the lab. EMS arrays have been shown to increase stimulation resolution, but as calibration complexity increases exponentially as more electrodes are used, we require heuristics or automated procedures......Electric muscle stimulation (EMS) can enable mobile force feedback, support pedestrian navigation, or confer object affordances. To date, however, EMS is limited by two interlinked problems. (1) EMS is low resolution -- achieving only coarse movements and constraining opportunities for exploration...... for successful calibration. We explore the feasibility of using electromyography (EMG) to auto-calibrate high density EMS arrays. We determine regions of muscle activity during human-performed gestures, to inform stimulation patterns for EMS-performed gestures. We report on a study which shows that auto...

  15. A high-density lipoprotein-mediated drug delivery system.

    Science.gov (United States)

    Mo, Zhong-Cheng; Ren, Kun; Liu, Xing; Tang, Zhen-Li; Yi, Guang-Hui

    2016-11-15

    High-density lipoprotein (HDL) is a comparatively dense and small lipoprotein that can carry lipids as a multifunctional aggregate in plasma. Several studies have shown that increasing the levels or improving the functionality of HDL is a promising target for treating a wide variety of diseases. Among lipoproteins, HDL particles possess unique physicochemical properties, including naturally synthesized physiological components, amphipathic apolipoproteins, lipid-loading and hydrophobic agent-incorporating characteristics, specific protein-protein interactions, heterogeneity, nanoparticles, and smaller size. Recently, the feasibility and superiority of using HDL particles as drug delivery vehicles have been of great interest. In this review, we summarize the structure, constituents, biogenesis, remodeling, and reconstitution of HDL drug delivery systems, focusing on their delivery capability, characteristics, applications, manufacturing, and drug-loading and drug-targeting characteristics. Finally, the future prospects are presented regarding the clinical application and challenges of using HDL as a pharmacodelivery carrier. Copyright © 2016 Elsevier B.V. All rights reserved.

  16. Single-Readout High-Density Memristor Crossbar

    KAUST Repository

    Zidan, M. A.

    2016-01-07

    High-density memristor-crossbar architecture is a very promising technology for future computing systems. The simplicity of the gateless-crossbar structure is both its principal advantage and the source of undesired sneak-paths of current. This parasitic current could consume an enormous amount of energy and ruin the readout process. We introduce new adaptive-threshold readout techniques that utilize the locality and hierarchy properties of the computer-memory system to address the sneak-paths problem. The proposed methods require a single memory access per pixel for an array readout. Besides, the memristive crossbar consumes an order of magnitude less power than state-of-the-art readout techniques.

  17. High-Density Lipoproteins and the Immune System

    Directory of Open Access Journals (Sweden)

    Hidesuke Kaji

    2013-01-01

    Full Text Available High-density lipoprotein (HDL plays a major role in vasodilation and in the reduction of low-density lipoprotein (LDL oxidation, inflammation, apoptosis, thrombosis, and infection; however, HDL is now less functional in these roles under certain conditions. This paper focuses on HDL, its anti-inflammation behavior, and the mechanisms by which HDL interacts with components of the innate and adaptive immune systems. Genome-wide association studies (GWAS and proteomic studies have elucidated important molecules involved in the interaction between HDL and the immune system. An understanding of these mechanisms is expected to be useful for the prevention and treatment of chronic inflammation due to metabolic syndrome, atherosclerosis, or various autoimmune diseases.

  18. Reaction of unirradiated high-density fuel with aluminum

    International Nuclear Information System (INIS)

    Wiencek, T.C.; Meyer, M.K.; Prokofiev, I.G.; Keiser, D.D.

    1997-01-01

    Excellent dispersion fuel performance requires that fuel particles remain stable and do not react significantly with the surrounding aluminum matrix. A series of high-density fuels, which contain uranium densities >12 g/cm 3 , have been fabricated into plates. As part of standard processing, all of these fuels were subjected to a blister anneal of 1 h at 485 deg. C. Changes in plate thickness were measured and evaluated. From these results, suppositions about the probable irradiation properties of these fuels have been proposed. In addition, two fuels, U-10 wt% Mo and U 2 Mo, were subjected to various heat treatments and were found to be very stable in an aluminum matrix. On the basis of the experimental data, hypotheses of the irradiation behavior of these fuels are presented. (author)

  19. High-current discharge channel contraction in high density gas

    International Nuclear Information System (INIS)

    Rutberg, Ph. G.; Bogomaz, A. A.; Pinchuk, M. E.; Budin, A. V.; Leks, A. G.; Pozubenkov, A. A.

    2011-01-01

    Research results for discharges at current amplitudes of 0.5-1.6 MA and current rise rate of ∼10 10 A/s are presented. The discharge is performed in the hydrogen environment at the initial pressure of 5-35 MPa. Initiation is implemented by a wire explosion. The time length of the first half-period of the discharge current is 70-150 μs. Under such conditions, discharge channel contraction is observed; the contraction is followed by soft x-ray radiation. The phenomena are discussed, which are determined by high density of the gas surrounding the discharge channel. These phenomena are increase of the current critical value, where the channel contraction begins and growth of temperature in the axis region of the channel, where the initial density of the gas increases.

  20. Diquark Bose Condensates in High Density Matter and Instantons

    International Nuclear Information System (INIS)

    Rapp, R.; Shuryak, E.; Schaefer, T.; Velkovsky, M.

    1998-01-01

    Instantons lead to strong correlations between up and down quarks with spin zero and antisymmetric color wave functions. In cold and dense matter, n b >n c ≅1 fm -3 and T c ∼50 thinspthinspMeV, these pairs Bose condense, replacing the usual left-angle bar qq right-angle condensate and restoring chiral symmetry. At high density, the ground state is a color superconductor in which diquarks play the role of Cooper pairs. An interesting toy model is provided by QCD with two colors: it has a particle-antiparticle symmetry which relates left-angle bar qq right-angle and left-angle qq right-angle condensates. copyright 1998 The American Physical Society

  1. High-Density Near-Field Optical Disc Recording

    Science.gov (United States)

    Shinoda, Masataka; Saito, Kimihiro; Ishimoto, Tsutomu; Kondo, Takao; Nakaoki, Ariyoshi; Ide, Naoki; Furuki, Motohiro; Takeda, Minoru; Akiyama, Yuji; Shimouma, Takashi; Yamamoto, Masanobu

    2005-05-01

    We developed a high-density near-field optical recording disc system using a solid immersion lens. The near-field optical pick-up consists of a solid immersion lens with a numerical aperture of 1.84. The laser wavelength for recording is 405 nm. In order to realize the near-field optical recording disc, we used a phase-change recording media and a molded polycarbonate substrate. A clear eye pattern of 112 GB capacity with 160 nm track pitch and 50 nm bit length was observed. The equivalent areal density is 80.6 Gbit/in2. The bottom bit error rate of 3 tracks-write was 4.5× 10-5. The readout power margin and the recording power margin were ± 30.4% and ± 11.2%, respectively.

  2. EVALUATION OF SOME PLUM CULTIVARS IN A HIGH DENSITY SYSTEM

    Directory of Open Access Journals (Sweden)

    Madalina Butac

    2014-12-01

    Full Text Available Three plum cultivars bred in Romania (‘Carpatin’, ‘Centenar’ and ‘Tita’ were tested together with several standards (‘Cacanska Rodna’ and ‘Stanley’ in a high density experimental orchard established at Pitesti - Maracineni in the spring of 2009, with spacing 4 x 2.25 m. Trees were trained as spindles, grafted on ‘Saint Julian’ rootstock. In the orchard the following characteristics were evaluated: tree vigour based upon measuring of trunk-diameter, yields in kg/tree, time of fruit ripening and basic parameters of fruit quality. All Romanian varieties were characterized by earliness and large fruit, but production was relatively small. Instead, foreign varieties were characterized by high productivity in the 4th year after planting.

  3. High density thermite mixture for shaped charge ordnance disposal

    Directory of Open Access Journals (Sweden)

    Tamer Elshenawy

    2017-10-01

    Full Text Available The effect of thermite mixture based on aluminum and ferric oxides for ammunition neutralization has been studied and tested. Thermochemical calculations have been carried out for different percentage of Al using Chemical Equilibrium Code to expect the highest performance thermite mixture used for shaped charge ordnance disposal. Densities and enthalpy of different formulations have been calculated and demonstrated. The optimized thermite formulation has been prepared experimentally using cold iso-static pressing technique, which exhibited relatively high density and high burning rate thermite mixture. The produced green product compacted powder mixture was tested against small caliber shaped charge bomblet for neutralization. Theoretical and experimental results showed that the prepared thermite mixture containing 33% of aluminum as a fuel with ferric oxide can be successfully used for shaped charge ordnance disposal.

  4. The stability of the High-Density Z-Pinch

    International Nuclear Information System (INIS)

    Glasser, A.H.; Nebel, R.A.

    1989-01-01

    Fiber-initiated High Density Z-Pinches at Los Alamos, NRL, and Karlsruhe have shown anomalously good stability. Kink modes are never seen, and sausage modes are at least delayed until late in the discharge. The success of these devices in reaching fusion conditions may depend on maintaining and understanding this anomalous stability. We have developed two numerical methods to study the stability in the regime where fluid theory is valid. While our methods are applicable to all modes, we will describe them only for the m = 0 sausage mode. The appearance of sausage modes late in the discharge and the total absence of kink modes suggest that an understanding of sausage modes is more urgent, and it is also simpler. 14 refs., 8 figs

  5. The stability of the high-density z-pinch

    International Nuclear Information System (INIS)

    Glasser, A.H.; Nebel, R.A.

    1989-01-01

    Fiber-initiated High Density Z-Pinches at Los Alamos, NRL, and Karlsruhe have shown anomalously good stability. Kink modes are never seen, and sausage modes are at least delayed until late in the discharge. The success of these devices in reaching fusion conditions may depend on maintaining and understanding this anomalous stability. We have developed two numerical methods to study the stability in the regime where fluid theory is valid. While our methods are applicable to all modes, we will describe them only for the m=0 sausage mode. The appearance of sausage modes late in the discharge and the total absence of kink modes suggest that an understanding of sausage modes is more urgent, and it is also simpler

  6. Corrosion of high-density sintered tungsten alloys. Part 2

    International Nuclear Information System (INIS)

    Batten, J.J.; Moore, B.T.

    1988-12-01

    The behaviour of four high-density sintered tungsten alloys has been evluated and compared with that of pure tungsten. Rates of corrosion during the cyclic humidity and the salt mist tests were ascertained from weight loss measurements. Insight into the corrosion mechanism was gained from the nature of the corrosion products and an examination of the corroded surfaces. In the tests, the alloy 95% W, 2.5% Ni, 1.5% Fe was the most corrosion resistant. The data showed that copper as an alloying element accelerates corrosion of tungsten alloys. Both attack on the tungsten particles and the binder phase were observed together with tungsten grain loss. 6 refs., 3 tabs.,

  7. High density high-TC ceramic superconductors by hot pressing

    International Nuclear Information System (INIS)

    Mak, S.; Chaklader, A.C.D.

    1989-01-01

    High density and high T C superconductor specimens, YBa 2 Cu 3 O x , have been produced by hot-pressing. The factors studied are the effect of hot pressing on the density, the oxygen stoichiometry, the crystal structure, and the critical temperature. Hot pressing followed by heat treatment increased the density of the specimen to 93%. The hot pressing itself did not significantly affect the oxygen content in the specimen, and although the crystal structure appeared to be orthorhombic, the specimens were not superconducting above liquid nitrogen temperature. The superconductivity was restored after head treatment in oxygen. The highest critical temperature (T C ) of the hot pressed pellets was 82K, which was slightly lower than the T C that could be obtained with the cold pressed/sintered pellets. (6 refs., 5 figs., tab.)

  8. Evaluation of the radiation resistance of high-density polyethylene

    International Nuclear Information System (INIS)

    Dougherty, D.R.; Adams, J.W.; Barletta, R.R.

    1984-03-01

    Mechanical tests following gamma irradiation and creep tests during irradiation have been conducted on high-density polyethylene (HDPE) to provide data to help assess the adequacy of this material for use in high integrity containers (HICs). Two types of HDPE, a highly cross-linked rotationally molded material and a non-cross-linked blow molded material, were used in these tests. Gamma-ray irradiations were performed at several dose rates in environments of air, Barnwell and Hanford backfill soils, and ion-exchange resins. The results of tensile and bend tests on these materials following irradiation are presented along with results on creep during irradiation. 8 references, 9 figures, 2 tables

  9. The Pulsed High Density Experiment (PHDX) Final Report

    Energy Technology Data Exchange (ETDEWEB)

    Slough, John P. [Univ. of Washington, Seattle, WA (United States); Andreason, Samuel [Univ. of Washington, Seattle, WA (United States)

    2017-04-27

    The purpose of this paper is to present the conclusions that can be drawn from the Field Reversed Configuration (FRC) formation experiments conducted on the Pulsed High Density experiment (PHD) at the University of Washington. The experiment is ongoing. The experimental goal for this first stage of PHD was to generate a stable, high flux (>10 mWb), high energy (>10 KJ) target FRC. Such results would be adequate as a starting point for several later experiments. This work focuses on experimental implementation and the results of the first four month run. Difficulties were encountered due to the initial on-axis plasma ionization source. Flux trapping with this ionization source acting alone was insufficient to accomplish experimental objectives. Additional ionization methods were utilized to overcome this difficulty. A more ideal plasma source layout is suggested and will be explored during a forthcoming work.

  10. High-Density Stacked Ru Nanocrystals for Nonvolatile Memory Application

    International Nuclear Information System (INIS)

    Ping, Mao; Zhi-Gang, Zhang; Li-Yang, Pan; Jun, Xu; Pei-Yi, Chen

    2009-01-01

    Stacked ruthenium (Ru) nanocrystals (NCs) are formed by rapid thermal annealing for the whole gate stacks and embedded in memory structure, which is compatible with conventional CMOS technology. Ru NCs with high density (3 × 10 12 cm −2 ), small size (2–4 nm) and good uniformity both in aerial distribution and morphology are formed. Attributed to the higher surface trap density, a memory window of 5.2 V is obtained with stacked Ru NCs in comparison to that of 3.5 V with single-layer samples. The stacked Ru NCs device also exhibits much better retention performance because of Coulomb blockade and vertical uniformity between stacked Ru NCs

  11. Single-Readout High-Density Memristor Crossbar

    KAUST Repository

    Zidan, M. A.; Omran, Hesham; Naous, Rawan; Salem, Ahmed Sultan; Fahmy, H. A. H.; Lu, W. D.; Salama, Khaled N.

    2016-01-01

    High-density memristor-crossbar architecture is a very promising technology for future computing systems. The simplicity of the gateless-crossbar structure is both its principal advantage and the source of undesired sneak-paths of current. This parasitic current could consume an enormous amount of energy and ruin the readout process. We introduce new adaptive-threshold readout techniques that utilize the locality and hierarchy properties of the computer-memory system to address the sneak-paths problem. The proposed methods require a single memory access per pixel for an array readout. Besides, the memristive crossbar consumes an order of magnitude less power than state-of-the-art readout techniques.

  12. High density submicron magnetoresistive random access memory (invited)

    Science.gov (United States)

    Tehrani, S.; Chen, E.; Durlam, M.; DeHerrera, M.; Slaughter, J. M.; Shi, J.; Kerszykowski, G.

    1999-04-01

    Various giant magnetoresistance material structures were patterned and studied for their potential as memory elements. The preferred memory element, based on pseudo-spin valve structures, was designed with two magnetic stacks (NiFeCo/CoFe) of different thickness with Cu as an interlayer. The difference in thickness results in dissimilar switching fields due to the shape anisotropy at deep submicron dimensions. It was found that a lower switching current can be achieved when the bits have a word line that wraps around the bit 1.5 times. Submicron memory elements integrated with complementary metal-oxide-semiconductor (CMOS) transistors maintained their characteristics and no degradation to the CMOS devices was observed. Selectivity between memory elements in high-density arrays was demonstrated.

  13. The alterations in high density polyethylene properties with gamma irradiation

    Science.gov (United States)

    Zaki, M. F.; Elshaer, Y. H.; Taha, Doaa. H.

    2017-10-01

    In the present investigation, high density polyethylene (HDPE) polymer has been used to study the alterations in its properties under gamma-irradiation. Physico-chemical properties have been investigated with different spectroscopy techniques, Fourier Transform Infrared spectroscopy (FTIR), X-ray diffraction (XRD), biocompatibility properties, as well as, mechanical properties change. The FT-IR analysis shows the formation of new band at 1716 cm-1 that is attributed to the oxidation of irradiated polymer chains, which is due to the formation of carbonyl groups (C˭O). XRD patterns show that a decrease in the crystallite size and increase in the Full Width at Half Maximum (FWHM). This means that the crystallinity of irradiated samples is decreased with increase in gamma dose. The contact angle measurements show an increase in the surface free energy as the gamma irradiation increases. The measurements of mechanical properties of irradiated HDPE samples were discussed.

  14. Relaxation Time of High-Density Amorphous Ice

    Science.gov (United States)

    Handle, Philip H.; Seidl, Markus; Loerting, Thomas

    2012-06-01

    Amorphous water plays a fundamental role in astrophysics, cryoelectron microscopy, hydration of matter, and our understanding of anomalous liquid water properties. Yet, the characteristics of the relaxation processes taking place in high-density amorphous ice (HDA) are unknown. We here reveal that the relaxation processes in HDA at 110-135 K at 0.1-0.2 GPa are of collective and global nature, resembling the alpha relaxation in glassy material. Measured relaxation times suggest liquid-like relaxation characteristics in the vicinity of the crystallization temperature at 145 K. By carefully relaxing pressurized HDA for several hours at 135 K, we produce a state that is closer to the ideal glass state than all HDA states discussed so far in literature.

  15. High-density amorphous ice: A path-integral simulation

    Science.gov (United States)

    Herrero, Carlos P.; Ramírez, Rafael

    2012-09-01

    Structural and thermodynamic properties of high-density amorphous (HDA) ice have been studied by path-integral molecular dynamics simulations in the isothermal-isobaric ensemble. Interatomic interactions were modeled by using the effective q-TIP4P/F potential for flexible water. Quantum nuclear motion is found to affect several observable properties of the amorphous solid. At low temperature (T = 50 K) the molar volume of HDA ice is found to increase by 6%, and the intramolecular O-H distance rises by 1.4% due to quantum motion. Peaks in the radial distribution function of HDA ice are broadened with respect to their classical expectancy. The bulk modulus, B, is found to rise linearly with the pressure, with a slope ∂B/∂P = 7.1. Our results are compared with those derived earlier from classical and path-integral simulations of HDA ice. We discuss similarities and discrepancies with those earlier simulations.

  16. Characterization of High Density Concrete by Ultrasonic Goniometer

    International Nuclear Information System (INIS)

    Suhairy Sani; Mohamad Pauzi Ismail; Noor Azreen Masenwat; Nasharuddin Isa; Mohamad Haniza Mahmud

    2014-01-01

    This paper described the results of ultrasonic goniometer measurements on concrete containing hematite. Local hematite stones were used as aggregates to produce high density concrete for application in X-and gamma shielding. Concrete cube samples (150 mm x 150 mm x 150 mm) containing hematite as coarse aggregates were prepared by changing mix ratio, water to cement ratio (w/ c) and types of fine aggregate. All samples were cured in water for 7 days. After 28 days of casting, the concrete cubes were then cut into small size of about 10 mm x 20 mm x 30 mm so that it can be fitted into goniometer specimen holder. From this measurement, longitudinal, shear and surface Rayleigh waves in the concrete can be determined. The measurement results are explained and discussed. (author)

  17. Microelectromechanical high-density energy storage/rapid release system

    Science.gov (United States)

    Rodgers, M. Steven; Allen, James J.; Meeks, Kent D.; Jensen, Brian D.; Miller, Samuel L.

    1999-08-01

    One highly desirable characteristic of electrostatically driven microelectromechanical systems (MEMS) is that they consume very little power. The corresponding drawback is that the force they produce may be inadequate for many applications. It has previously been demonstrated that gear reduction units or microtransmissions can substantially increase the torque generated by microengines. Operating speed, however, is also reduced by the transmission gear ratio. Some applications require both high speed and high force. If this output is only required for a limited period of time, then energy could be stored in a mechanical system and rapidly released upon demand. We have designed, fabricated, and demonstrated a high-density energy storage/rapid release system that accomplishes this task. Built using a 5-level surface micromachining technology, the assembly closely resembles a medieval crossbow. Energy releases on the order of tens of nanojoules have already been demonstrated, and significantly higher energy systems are under development.

  18. Preparations of high density (Th,U)O2 pellets

    International Nuclear Information System (INIS)

    Akabori, Mitsuo; Ikawa, Katsuichi

    1986-07-01

    Preparations of high density and homogeneous (Th,U)O 2 pellets by a powder metallurgy method were examined. (Th,U)O 2 powders were prepared by calcining coprecipitates of ammonium uranate and thorium hydroxide derived from nitrates and mixed sols, and by calcining mixed oxalates precipitated from nitrates. (Th,U)O 2 pellets were characterized with respect to sinterability, lattice parameter, microstructure, homogeneity and stoichiometry. Sintering atmospheres had a significant effect upon all the properties of the derived pellets. The sinterability of (Th,U)O 2 was most favourable in oxidizing and reducing atmospheres for ThO 2 -rich and UO 2 -rich compositions, respectively, and can be enhanced by presence of water vapour in sintering atmospheres. In addition, highly homogeneous (Th,U)O 2 pellets with 99 % in theoretical density were derived from the sol powders. (author)

  19. Neutron shielding properties of a borated high-density glass

    Directory of Open Access Journals (Sweden)

    Saeed Aly Abdallah

    2017-01-01

    Full Text Available The neutron shielding properties of a borated high density glass system was characterized experimentally. The total removal macroscopic cross-section of fast neutrons, slow neutrons as well as the linear attenuation coefficient of total gamma rays, primary in addition to secondary, were measured experimentally under good geometric condition to characterize the attenuation properties of (75-x B2O3-1Li2O-5MgO-5ZnO-14Na2O-xBaO glassy system. Slabs of different thicknesses from the investigated glass system were exposed to a collimated beam of neutrons emitted from 252Cf and 241Am-Be neutron sources in order to measure the attenuation properties of fast and slow neutrons as well as total gamma rays. Results confirmed that barium borate glass was suitable for practical use in the field of radiation shielding.

  20. Homogeneity of the 16S rDNA sequence among geographically disparate isolates of Taylorella equigenitalis

    Directory of Open Access Journals (Sweden)

    Moore JE

    2006-01-01

    Full Text Available Abstract Background At present, six accessible sequences of 16S rDNA from Taylorella equigenitalis (T. equigenitalis are available, whose sequence differences occur at a few nucleotide positions. Thus it is important to determine these sequences from additional strains in other countries, if possible, in order to clarify any anomalies regarding 16S rDNA sequence heterogeneity. Here, we clone and sequence the approximate full-length 16S rDNA from additional strains of T. equigenitalis isolated in Japan, Australia and France and compare these sequences to the existing published sequences. Results Clarification of any anomalies regarding 16S rDNA sequence heterogeneity of T. equigenitalis was carried out. When cloning, sequencing and comparison of the approximate full-length 16S rDNA from 17 strains of T. equigenitalis isolated in Japan, Australia and France, nucleotide sequence differences were demonstrated at the six loci in the 1,469 nucleotide sequence. Moreover, 12 polymorphic sites occurred among 23 sequences of the 16S rDNA, including the six reference sequences. Conclusion High sequence similarity (99.5% or more was observed throughout, except from nucleotide positions 138 to 501 where substitutions and deletions were noted.

  1. Homogeneity of the 16S rDNA sequence among geographically disparate isolates of Taylorella equigenitalis

    Science.gov (United States)

    Matsuda, M; Tazumi, A; Kagawa, S; Sekizuka, T; Murayama, O; Moore, JE; Millar, BC

    2006-01-01

    Background At present, six accessible sequences of 16S rDNA from Taylorella equigenitalis (T. equigenitalis) are available, whose sequence differences occur at a few nucleotide positions. Thus it is important to determine these sequences from additional strains in other countries, if possible, in order to clarify any anomalies regarding 16S rDNA sequence heterogeneity. Here, we clone and sequence the approximate full-length 16S rDNA from additional strains of T. equigenitalis isolated in Japan, Australia and France and compare these sequences to the existing published sequences. Results Clarification of any anomalies regarding 16S rDNA sequence heterogeneity of T. equigenitalis was carried out. When cloning, sequencing and comparison of the approximate full-length 16S rDNA from 17 strains of T. equigenitalis isolated in Japan, Australia and France, nucleotide sequence differences were demonstrated at the six loci in the 1,469 nucleotide sequence. Moreover, 12 polymorphic sites occurred among 23 sequences of the 16S rDNA, including the six reference sequences. Conclusion High sequence similarity (99.5% or more) was observed throughout, except from nucleotide positions 138 to 501 where substitutions and deletions were noted. PMID:16398935

  2. Comparison of two approaches for the classification of 16S rRNA gene sequences.

    Science.gov (United States)

    Chatellier, Sonia; Mugnier, Nathalie; Allard, Françoise; Bonnaud, Bertrand; Collin, Valérie; van Belkum, Alex; Veyrieras, Jean-Baptiste; Emler, Stefan

    2014-10-01

    The use of 16S rRNA gene sequences for microbial identification in clinical microbiology is accepted widely, and requires databases and algorithms. We compared a new research database containing curated 16S rRNA gene sequences in combination with the lca (lowest common ancestor) algorithm (RDB-LCA) to a commercially available 16S rDNA Centroid approach. We used 1025 bacterial isolates characterized by biochemistry, matrix-assisted laser desorption/ionization time-of-flight MS and 16S rDNA sequencing. Nearly 80 % of isolates were identified unambiguously at the species level by both classification platforms used. The remaining isolates were mostly identified correctly at the genus level due to the limited resolution of 16S rDNA sequencing. Discrepancies between both 16S rDNA platforms were due to differences in database content and the algorithm used, and could amount to up to 10.5 %. Up to 1.4 % of the analyses were found to be inconclusive. It is important to realize that despite the overall good performance of the pipelines for analysis, some inconclusive results remain that require additional in-depth analysis performed using supplementary methods. © 2014 The Authors.

  3. Biominetic High Density Lipoproteins for the Delivery of Therapeutic Oligonucleotides

    Science.gov (United States)

    Tripathy, Sushant

    Advances in nanotechnology have brought about novel inorganic and hybrid nanoparticles with unique physico-chemical properties that make them suitable for a broad range of applications---from nano-circuitry to drug delivery. A significant part of those advancements have led to ground-breaking discoveries that have changed the approaches to formulation of therapeutics against diseases, such as cancer. Now-a-days the focus does not lie solely on finding a candidate small-molecule therapeutic with minimal adverse effects, but researchers are looking up to nanoparticles to improve biodistribution and biocompatibility profile of clinically proven therapeutics. The plethora of conjugation chemistries offered by currently extant inorganic nanoparticles have, in recent years, led to great leaps in the field of biomimicry---a modality that promises high biocompatibility. Further, in the pursuit of highly specific therapeutic molecules, researchers have turned to silencing oligonucleotides and some have already brought together the strengths of nanoparticles and silencing oligonucleotides in search of an efficacious therapy for cancer with minimal adverse effects. This dissertation work focuses on such a biomimetic platform---a gold nanoparticle based high density lipoprotein biomimetic (HDL NP), for the delivery of therapeutic oligonucleotides. The first chapter of this body of work introduces the molecular target of the silencing oligonucleotides---VEGFR2, and its role in the progression of solid tumor cancers. The background information also covers important aspects of natural high density lipoproteins (HDL), especially their innate capacity to bind and deliver exogenous and endogenous silencing oligonucleotides to tissues that express their high affinity receptor SRB1. We subsequently describe the synthesis of the biomimetic HDL NP and its oligonucleotide conjugates, and establish their biocompatibility. Further on, experimental data demonstrate the efficacy of silencing

  4. Rethinking reverse cholesterol transport and dysfunctional high-density lipoproteins.

    Science.gov (United States)

    Gillard, Baiba K; Rosales, Corina; Xu, Bingqing; Gotto, Antonio M; Pownall, Henry J

    2018-04-12

    Human plasma high-density lipoprotein cholesterol concentrations are a negative risk factor for atherosclerosis-linked cardiovascular disease. Pharmacological attempts to reduce atherosclerotic cardiovascular disease by increasing plasma high-density lipoprotein cholesterol have been disappointing so that recent research has shifted from HDL quantity to HDL quality, that is, functional vs dysfunctional HDL. HDL has varying degrees of dysfunction reflected in impaired reverse cholesterol transport (RCT). In the context of atheroprotection, RCT occurs by 2 mechanisms: one is the well-known trans-hepatic pathway comprising macrophage free cholesterol (FC) efflux, which produces early forms of FC-rich nascent HDL (nHDL). Lecithin:cholesterol acyltransferase converts HDL-FC to HDL-cholesteryl ester while converting nHDL from a disc to a mature spherical HDL, which transfers its cholesteryl ester to the hepatic HDL receptor, scavenger receptor B1 for uptake, conversion to bile salts, or transfer to the intestine for excretion. Although widely cited, current evidence suggests that this is a minor pathway and that most HDL-FC and nHDL-FC rapidly transfer directly to the liver independent of lecithin:cholesterol acyltransferase activity. A small fraction of plasma HDL-FC enters the trans-intestinal efflux pathway comprising direct FC transfer to the intestine. SR-B1 -/- mice, which have impaired trans-hepatic FC transport, are characterized by high plasma levels of a dysfunctional FC-rich HDL that increases plasma FC bioavailability in a way that produces whole-body hypercholesterolemia and multiple pathologies. The design of future therapeutic strategies to improve RCT will have to be formulated in the context of these dual RCT mechanisms and the role of FC bioavailability. Copyright © 2018 National Lipid Association. Published by Elsevier Inc. All rights reserved.

  5. Properties of matter at ultra-high densities

    International Nuclear Information System (INIS)

    Banerjee, B.; Chitre, S.M.

    1975-01-01

    The recent discovery of pulsars and their subsequent identification with neutron stars has given a great impetus to the study of the behaviour of matter at ultra high densities. The object of these studies is to calculate the equation of state as a function of density. In this paper, the properties of electrically neutral, cold (T=0) matter at unusually high densities has been reviewed. The physics of the equation of state of such matter divides quite naturally in four density ranges. (i) At the very lowest densities the state of minimum energy is a lattice of 56 Fe atoms. This state persists upto 10 7 g/cm 3 . (ii) In the next density region the nuclei at the lattice sites become neutron rich because the high electron Fermi energy makes inverse beta decay possible. (iii) At a density 4.3 x 10 11 the nuclei become so neutron rich that the neutrons start 'dripping' out of the nuclei and form a gas. This density range is characterised by large, neutron-rich nuclei immersed in a neutron gas. (iv) At a density 2.4 x 10 14 g/cm 3 , the nuclei disappear and a fluid of uniform neutron matter with a small percentage of protons and electrons results. The above four density ranges have been discussed in detail as the equation of state is now well established upto the nuclear density 3 x 10 14 g/cm 3 . The problems of extending the equation of state beyond this density are also touched upon. (author)

  6. Pulsed high-density plasmas for advanced dry etching processes

    International Nuclear Information System (INIS)

    Banna, Samer; Agarwal, Ankur; Cunge, Gilles; Darnon, Maxime; Pargon, Erwine; Joubert, Olivier

    2012-01-01

    Plasma etching processes at the 22 nm technology node and below will have to satisfy multiple stringent scaling requirements of microelectronics fabrication. To satisfy these requirements simultaneously, significant improvements in controlling key plasma parameters are essential. Pulsed plasmas exhibit considerable potential to meet the majority of the scaling challenges, while leveraging the broad expertise developed over the years in conventional continuous wave plasma processing. Comprehending the underlying physics and etching mechanisms in pulsed plasma operation is, however, a complex undertaking; hence the full potential of this strategy has not yet been realized. In this review paper, we first address the general potential of pulsed plasmas for plasma etching processes followed by the dynamics of pulsed plasmas in conventional high-density plasma reactors. The authors reviewed more than 30 years of academic research on pulsed plasmas for microelectronics processing, primarily for silicon and conductor etch applications, highlighting the potential benefits to date and challenges in extending the technology for mass-production. Schemes such as source pulsing, bias pulsing, synchronous pulsing, and others in conventional high-density plasma reactors used in the semiconductor industry have demonstrated greater flexibility in controlling critical plasma parameters such as ion and radical densities, ion energies, and electron temperature. Specifically, plasma pulsing allows for independent control of ion flux and neutral radicals flux to the wafer, which is key to eliminating several feature profile distortions at the nanometer scale. However, such flexibility might also introduce some difficulty in developing new etching processes based on pulsed plasmas. Therefore, the main characteristics of continuous wave plasmas and different pulsing schemes are compared to provide guidelines for implementing different schemes in advanced plasma etching processes based on

  7. The glass transition in high-density amorphous ice.

    Science.gov (United States)

    Loerting, Thomas; Fuentes-Landete, Violeta; Handle, Philip H; Seidl, Markus; Amann-Winkel, Katrin; Gainaru, Catalin; Böhmer, Roland

    2015-01-01

    There has been a long controversy regarding the glass transition in low-density amorphous ice (LDA). The central question is whether or not it transforms to an ultraviscous liquid state above 136 K at ambient pressure prior to crystallization. Currently, the most widespread interpretation of the experimental findings is in terms of a transformation to a superstrong liquid above 136 K. In the last decade some work has also been devoted to the study of the glass transition in high-density amorphous ice (HDA) which is in the focus of the present review. At ambient pressure HDA is metastable against both ice I and LDA, whereas at > 0.2 GPa HDA is no longer metastable against LDA, but merely against high-pressure forms of crystalline ice. The first experimental observation interpreted as the glass transition of HDA was made using in situ methods by Mishima, who reported a glass transition temperature T g of 160 K at 0.40 GPa. Soon thereafter Andersson and Inaba reported a much lower glass transition temperature of 122 K at 1.0 GPa. Based on the pressure dependence of HDA's T g measured in Innsbruck, we suggest that they were in fact probing the distinct glass transition of very high-density amorphous ice (VHDA). Very recently the glass transition in HDA was also observed at ambient pressure at 116 K. That is, LDA and HDA show two distinct glass transitions, clearly separated by about 20 K at ambient pressure. In summary, this suggests that three glass transition lines can be defined in the p-T plane for LDA, HDA, and VHDA.

  8. Propofol Anesthesia and Sleep: A High-Density EEG Study

    Science.gov (United States)

    Murphy, Michael; Bruno, Marie-Aurelie; Riedner, Brady A.; Boveroux, Pierre; Noirhomme, Quentin; Landsness, Eric C.; Brichant, Jean-Francois; Phillips, Christophe; Massimini, Marcello; Laureys, Steven; Tononi, Giulio; Boly, Melanie

    2011-01-01

    Study Objectives: The electrophysiological correlates of anesthetic sedation remain poorly understood. We used high-density electroencephalography (hd-EEG) and source modeling to investigate the cortical processes underlying propofol anesthesia and compare them to sleep. Design: 256-channel EEG recordings in humans during propofol anesthesia. Setting: Hospital operating room. Patients or Participants: 8 healthy subjects (4 males) Interventions: N/A Measurements and Results: Initially, propofol induced increases in EEG power from 12–25 Hz. Loss of consciousness (LOC) was accompanied by the appearance of EEG slow waves that resembled the slow waves of NREM sleep. We compared slow waves in propofol to slow waves recorded during natural sleep and found that both populations of waves share similar cortical origins and preferentially propagate along the mesial components of the default network. However, propofol slow waves were spatially blurred compared to sleep slow waves and failed to effectively entrain spindle activity. Propofol also caused an increase in gamma (25–40 Hz) power that persisted throughout LOC. Source modeling analysis showed that this increase in gamma power originated from the anterior and posterior cingulate cortices. During LOC, we found increased gamma functional connectivity between these regions compared to the wakefulness. Conclusions: Propofol anesthesia is a sleep-like state and slow waves are associated with diminished consciousness even in the presence of high gamma activity. Citation: Murphy M; Bruno MA; Riedner BA; Boveroux P; Noirhomme Q; Landsness EC; Brichant JF; Phillips C; Massimini M; Laureys S; Tononi G; Boly M. Propofol anesthesia and sleep: a high-density EEG study. SLEEP 2011;34(3):283-291. PMID:21358845

  9. Radiation effect test on ADC/DAC and high density memory devices with 60Co γ-rays

    International Nuclear Information System (INIS)

    Xing Kefei; Wang Yueke; Pan Huafeng

    2006-01-01

    A test platform was constructed for 60 Co γ-ray irradiation experiment of microelectronics, with the aid of computer and a FPGA module. The tested sample devices included analog-to-digital converter AD10465, digital-to-analog converter AD9857, high density Flash memory MEF64M16 and anti-fused PROM XQR17V16, which are used in signal processing module in spaceborne systems. Evaluations were made on their ability of resisting the total dose based on the proper function criterion of the devices. The results showed that AD10465 and AD9857 ran properly after 1.59 kGy(Si) irradiation, but errors were found when MEF64M16 and XQR17V16's total ionizing dose is 0.13 kGy(Si) and 0.99 kGy(Si), respectively. (authors)

  10. Effects of gamma irradiation on polypropylene, polypropylene + high density polyethylene and polypropylene + high density polyethylene + wood flour

    Energy Technology Data Exchange (ETDEWEB)

    Reyes, J.; Albano, C.; Davidson, E.; Poleo, R. [Universidad Central de Venezuela, Caracas (Venezuela). Escuela de Quimica; Gonzalez, J.; Ichazo, M. [Universidad Simon Bolivar, Dept. de Mecanica, Caracas (Venezuela); Chipara, M. [Research Institute for Electrotechnics, Bucharest (Romania)

    2001-04-01

    The effect of the gamma-irradiation on the mechanical properties of the composites, Polypropylene (PP), PP+high density Polyethylene (HDPE), PP+ HDPE+wood flour, where HDPE is virgin and recycled, was studied. This paper discusses the behavior of the composites after exposure to various doses of gamma irradiation (1-7 MRads) in the presence of oxygen. The dependence of mechanical properties on the integral dose for a constant dose rate of 0.48 MRads/h confirms the influence of the irradiation. Strong effects on the elongation at break and break strength is noticed. The mathematical analysis suggests for the PP+r-HDPE a bimolecular process of the elongation at break. On the order hand, for the PP+HDPE a complex process is represented for a three exponential equation. (orig.)

  11. Effects of gamma irradiation on polypropylene, polypropylene + high density polyethylene and polypropylene + high density polyethylene + wood flour

    International Nuclear Information System (INIS)

    Reyes, J.; Albano, C.; Davidson, E.; Poleo, R.; Chipara, M.

    2001-01-01

    The effect of the gamma-irradiation on the mechanical properties of the composites, Polypropylene (PP), PP+high density Polyethylene (HDPE), PP+ HDPE+wood flour, where HDPE is virgin and recycled, was studied. This paper discusses the behavior of the composites after exposure to various doses of gamma irradiation (1-7 MRads) in the presence of oxygen. The dependence of mechanical properties on the integral dose for a constant dose rate of 0.48 MRads/h confirms the influence of the irradiation. Strong effects on the elongation at break and break strength is noticed. The mathematical analysis suggests for the PP+r-HDPE a bimolecular process of the elongation at break. On the order hand, for the PP+HDPE a complex process is represented for a three exponential equation. (orig.)

  12. Wake High-Density Electroencephalographic Spatiospectral Signatures of Insomnia

    Science.gov (United States)

    Colombo, Michele A.; Ramautar, Jennifer R.; Wei, Yishul; Gomez-Herrero, Germán; Stoffers, Diederick; Wassing, Rick; Benjamins, Jeroen S.; Tagliazucchi, Enzo; van der Werf, Ysbrand D.; Cajochen, Christian; Van Someren, Eus J.W.

    2016-01-01

    Study Objectives: Although daytime complaints are a defining characteristic of insomnia, most EEG studies evaluated sleep only. We used high-density electroencephalography to investigate wake resting state oscillations characteristic of insomnia disorder (ID) at a fine-grained spatiospectral resolution. Methods: A case-control assessment during eyes open (EO) and eyes closed (EC) was performed in a laboratory for human physiology. Participants (n = 94, 74 female, 21–70 y) were recruited through www.sleepregistry.nl: 51 with ID, according to DSM-5 and 43 matched controls. Exclusion criteria were any somatic, neurological or psychiatric condition. Group differences in the spectral power topographies across multiple frequencies (1.5 to 40 Hz) were evaluated using permutation-based inference with Threshold-Free Cluster-Enhancement, to correct for multiple comparisons. Results: As compared to controls, participants with ID showed less power in a narrow upper alpha band (11–12.7 Hz, peak: 11.7 Hz) over bilateral frontal and left temporal regions during EO, and more power in a broad beta frequency range (16.3–40 Hz, peak: 19 Hz) globally during EC. Source estimates suggested global rather than cortically localized group differences. Conclusions: The widespread high power in a broad beta band reported previously during sleep in insomnia is present as well during eyes closed wakefulness, suggestive of a round-the-clock hyperarousal. Low power in the upper alpha band during eyes open is consistent with low cortical inhibition and attentional filtering. The fine-grained HD-EEG findings suggest that, while more feasible than PSG, wake EEG of short duration with a few well-chosen electrodes and frequency bands, can provide valuable features of insomnia. Citation: Colombo MA, Ramautar JR, Wei Y, Gomez-Herrero G, Stoffers D, Wassing R, Benjamins JS, Tagliazucchi E, van der Werf YD, Cajochen C, Van Someren EJW. Wake high-density electroencephalographic spatiospectral

  13. Mitochondrial 16S ribosomal RNA gene for forensic identification of crocodile species.

    Science.gov (United States)

    Naga Jogayya, K; Meganathan, P R; Dubey, Bhawna; Haque, I

    2013-05-01

    All crocodilians are under various threats due to over exploitation and these species have been listed in Appendix I or II of CITES. Lack of molecular techniques for the forensic identification of confiscated samples makes it difficult to enforce the law. Therefore, we herein present a molecular method developed on the basis on 16S rRNA gene of mitochondrial DNA for identification of crocodile species. We have developed a set of 16S rRNA primers for PCR based identification of crocodilian species. These novel primers amplify partial 16S rRNA sequences of six crocodile species which can be later combined to obtain a larger region (1290 bp) of 16S rRNA gene. This 16S rRNA gene could be used as an effective tool for forensic authentication of crocodiles. The described primers hold great promise in forensic identification of crocodile species, which can aid in the effective enforcement of law and conservation of these species. Copyright © 2012 Elsevier Ltd and Faculty of Forensic and Legal Medicine. All rights reserved.

  14. The Human Microbiome and Understanding the 16S rRNA Gene in Translational Nursing Science.

    Science.gov (United States)

    Ames, Nancy J; Ranucci, Alexandra; Moriyama, Brad; Wallen, Gwenyth R

    As more is understood regarding the human microbiome, it is increasingly important for nurse scientists and healthcare practitioners to analyze these microbial communities and their role in health and disease. 16S rRNA sequencing is a key methodology in identifying these bacterial populations that has recently transitioned from use primarily in research to having increased utility in clinical settings. The objectives of this review are to (a) describe 16S rRNA sequencing and its role in answering research questions important to nursing science; (b) provide an overview of the oral, lung, and gut microbiomes and relevant research; and (c) identify future implications for microbiome research and 16S sequencing in translational nursing science. Sequencing using the 16S rRNA gene has revolutionized research and allowed scientists to easily and reliably characterize complex bacterial communities. This type of research has recently entered the clinical setting, one of the best examples involving the use of 16S sequencing to identify resistant pathogens, thereby improving the accuracy of bacterial identification in infection control. Clinical microbiota research and related requisite methods are of particular relevance to nurse scientists-individuals uniquely positioned to utilize these techniques in future studies in clinical settings.

  15. Highly divergent 16S rRNA sequences in ribosomal operons of Scytonema hyalinum (Cyanobacteria.

    Directory of Open Access Journals (Sweden)

    Jeffrey R Johansen

    Full Text Available A highly divergent 16S rRNA gene was found in one of the five ribosomal operons present in a species complex currently circumscribed as Scytonema hyalinum (Nostocales, Cyanobacteria using clone libraries. If 16S rRNA sequence macroheterogeneity among ribosomal operons due to insertions, deletions or truncation is excluded, the sequence heterogeneity observed in S. hyalinum was the highest observed in any prokaryotic species thus far (7.3-9.0%. The secondary structure of the 16S rRNA molecules encoded by the two divergent operons was nearly identical, indicating possible functionality. The 23S rRNA gene was examined for a few strains in this complex, and it was also found to be highly divergent from the gene in Type 2 operons (8.7%, and likewise had nearly identical secondary structure between the Type 1 and Type 2 operons. Furthermore, the 16S-23S ITS showed marked differences consistent between operons among numerous strains. Both operons have promoter sequences that satisfy consensus requirements for functional prokaryotic transcription initiation. Horizontal gene transfer from another unknown heterocytous cyanobacterium is considered the most likely explanation for the origin of this molecule, but does not explain the ultimate origin of this sequence, which is very divergent from all 16S rRNA sequences found thus far in cyanobacteria. The divergent sequence is highly conserved among numerous strains of S. hyalinum, suggesting adaptive advantage and selective constraint of the divergent sequence.

  16. Using NEG-pumping near a high density internal target

    Energy Technology Data Exchange (ETDEWEB)

    Gruber, Alexander; Marton, Johann; Widmann, Eberhard; Zmeskal, Johann [Stefan Meyer Institut fuer Subatomare Physik, OeAW (Germany); Orth, Herbert [GSI, Helmholtzzentrum fuer Schwerionenforschung, Darmstadt (Germany)

    2009-07-01

    The universal detector PANDA will be constructed at the future high-energy antiproton storage ring HESR at FAIR (Facility for Antiproton and Ion Research, GSI/Darmstadt). It will use antiproton beams (1.5 to 15 GeV/c) for hadron physics in the charmonium region. The Stefan Meyer Institut (SMI) contributes to major parts of the PANDA detector like the hydrogen cluster-jet target and the vacuum system of the antiproton - target interaction zone. To ensure low background, the residual gas load in the interaction zone and in the antiproton beam-pipe has to be minimised. Most of the gas load will come from the high density internal hydrogen target. As the detector will cover almost the full solid angle, the installation of pumps near the interaction zone is impossible. Therefore the use of NEG (non-evaporative-getter) coated beam pipes has been considered as an alternative. Two setups with NEG coated tubes have been installed at SMI as prototypes of the PANDA interaction zone. General parameters of the NEG-film, its outgassing behaviour, the pumping speed and the pumping capacity for hydrogen have been tested. The results of the studies on the PANDA-interaction region are presented.

  17. Statistical mechanics of high-density bond percolation

    Science.gov (United States)

    Timonin, P. N.

    2018-05-01

    High-density (HD) percolation describes the percolation of specific κ -clusters, which are the compact sets of sites each connected to κ nearest filled sites at least. It takes place in the classical patterns of independently distributed sites or bonds in which the ordinary percolation transition also exists. Hence, the study of series of κ -type HD percolations amounts to the description of classical clusters' structure for which κ -clusters constitute κ -cores nested one into another. Such data are needed for description of a number of physical, biological, and information properties of complex systems on random lattices, graphs, and networks. They range from magnetic properties of semiconductor alloys to anomalies in supercooled water and clustering in biological and social networks. Here we present the statistical mechanics approach to study HD bond percolation on an arbitrary graph. It is shown that the generating function for κ -clusters' size distribution can be obtained from the partition function of the specific q -state Potts-Ising model in the q →1 limit. Using this approach we find exact κ -clusters' size distributions for the Bethe lattice and Erdos-Renyi graph. The application of the method to Euclidean lattices is also discussed.

  18. Low fasting low high-density lipoprotein and postprandial lipemia

    Directory of Open Access Journals (Sweden)

    Sorodila Konstandina

    2004-07-01

    Full Text Available Abstract Background Low levels of high density lipoprotein (HDL cholesterol and disturbed postprandial lipemia are associated with coronary heart disease. In the present study, we evaluated the variation of triglyceride (TG postprandially in respect to serum HDL cholesterol levels. Results Fifty two Greek men were divided into 2 main groups: a the low HDL group (HDL p = 0.002. The low HDL group had significantly higher TG at 4, 6 and 8 h postprandially compared to the controls (p = 0.006, p = 0.002, and p p = 0.017 compared to the matched-control group. ROC analysis showed that fasting TG ≥ 121 mg/dl have 100% sensitivity and 81% specificity for an abnormal TG response (auc = 0.962, p Conclusions The delayed TG clearance postprandially seems to result in low HDL cholesterol even in subjects with low fasting TG. The fasting TG > 121 mg/dl are predictable for abnormal response to fatty meal.

  19. High density turbulent plasma processes from a shock tube

    International Nuclear Information System (INIS)

    Oyedeji, O.; Johnson, J.A. III

    1991-01-01

    We have finished the first stages of our experimental and theoretical investigations on models for energy and momentum transport and for photon-particle collision processes in a turbulent quasi-stationary high density plasma. The system is explored by beginning to determine the turbulence phenomenology associated with an ionizing shock wave. The theoretical underpinnings are explored for phonon particle collisions by determining the collisional redistribution function, using Lioville Space Green's Function, which will characterize the inelastic scattering of the radiation from one frequency to another. We have observed that a weak magnetic field tends to increase the apparent random-like behaviors in a collisional turbulent plasma. On the theoretical side, we have been able to achieve a form for the collisional redistribution function. It remains to apply these concepts to a stationary turbulent plasma in the reflected ionizing shock wave and to exercise the implications of evaluations of the collisional redistribution function for such a system when it is probed by a strong radiation source. These results are discussed in detail in the publications, which have resulted from the this effort, cited at the end of the report

  20. Irradiation testing of high density uranium alloy dispersion fuels

    International Nuclear Information System (INIS)

    Hayes, S.L.; Trybus, C.L.; Meyer, M.K.

    1997-10-01

    Two irradiation test vehicles have been designed, fabricated, and inserted into the Advanced Test Reactor in Idaho. Irradiation of these experiments began in August 1997. These irradiation tests were designed to obtain irradiation performance information on a variety of potential new, high-density dispersion fuels. Each of the two irradiation vehicles contains 32 microplates. Each microplate is aluminum clad, having an aluminum matrix phase and containing one of the following compositions as the fuel phase: U-10Mo, U-8Mo, U-6Mo, U-4Mo, U-9Nb-3Zr, U-6Nb-4Zr, U-5Nb-3Zr, U-6Mo-1Pt, U-6Mo-0.6Ru, U-10Mo-0.05Sn, U 2 Mo, or U 3 Si 2 . These experiments will be discharged at peak fuel burnups of 40% and 80%. Of particular interest is the fission gas retention/swelling characteristics of these new fuel alloys. This paper presents the design of the irradiation vehicles and the irradiation conditions

  1. High-field, high-density tokamak power reactor

    International Nuclear Information System (INIS)

    Cohn, D.R.; Cook, D.L.; Hay, R.D.; Kaplan, D.; Kreischer, K.; Lidskii, L.M.; Stephany, W.; Williams, J.E.C.; Jassby, D.L.; Okabayashi, M.

    1977-11-01

    A conceptual design of a compact (R 0 = 6.0 m) high power density (average P/sub f/ = 7.7 MW/m 3 ) tokamak demonstration power reactor has been developed. High magnetic field (B/sub t/ = 7.4 T) and moderate elongation (b/a = 1.6) permit operation at the high density (n(0) approximately 5 x 10 14 cm -3 ) needed for ignition in a relatively small plasma, with a spatially-averaged toroidal beta of only 4%. A unique design for the Nb 3 Sn toroidal-field magnet system reduces the stress in the high-field trunk region, and allows modularization for simpler disassembly. The modest value of toroidal beta permits a simple, modularized plasma-shaping coil system, located inside the TF coil trunk. Heating of the dense central plasma is attained by the use of ripple-assisted injection of 120-keV D 0 beams. The ripple-coil system also affords dynamic control of the plasma temperature during the burn period. A FLIBE-lithium blanket is designed especially for high-power-density operation in a high-field environment, and gives an overall tritium breeding ratio of 1.05 in the slowly pumped lithium

  2. [Residual risk: The roles of triglycerides and high density lipoproteins].

    Science.gov (United States)

    Grammer, Tanja; Kleber, Marcus; Silbernagel, Günther; Scharnagl, Hubert; März, Winfried

    2016-06-01

    In clinical trials, the reduction of LDL-cholesterol (LDL-C) with statins reduces the incidence rate of cardiovascular events by approximately one third. This means, that a sizeable "residual risk" remains. Besides high lipoprotein (a), disorders in the metabolism of triglyceride-rich lipoproteins and high density liproteins have been implicated as effectors of the residual risk. Both lipoprotein parameters correlate inversely with each other. Therefore, the etiological contributions of triglycerides and / or of HDL for developing cardiovascular disease can hardly be estimated from either observational studies or from intervention studies. The largely disappointing results of intervention studies with inhibitors of the cholesteryl ester transfer protein and in particular the available set of genetically-epidemiological studies suggest that in the last decade, the importance of HDL cholesterol has been overvalued, while the importance of triglycerides has been underestimated. High triglycerides not always atherogenic, but only if they are associated with the accumulation relatively cholesterol-enriched, incompletely catabolized remnants of chylomicrons and very low density lipoproteins (familial type III hyperlipidemia, metabolic syndrome, diabetes mellitus). The normalization of the concentration of triglycerides and remnants by inhibiting the expression of apolipoprotein C3 is hence a new, promising therapeutic target. © Georg Thieme Verlag KG Stuttgart · New York.

  3. Silicon micromachining using a high-density plasma source

    International Nuclear Information System (INIS)

    McAuley, S.A.; Ashraf, H.; Atabo, L.; Chambers, A.; Hall, S.; Hopkins, J.; Nicholls, G.

    2001-01-01

    Dry etching of Si is critical in satisfying the demands of the micromachining industry. The micro-electro-mechanical systems (MEMS) community requires etches capable of high aspect ratios, vertical profiles, good feature size control and etch uniformity along with high throughput to satisfy production requirements. Surface technology systems' (STS's) high-density inductively coupled plasma (ICP) etch tool enables a wide range of applications to be realized whilst optimizing the above parameters. Components manufactured from Si using an STS ICP include accelerometers and gyroscopes for military, automotive and domestic applications. STS's advanced silicon etch (ASE TM ) has also allowed the first generation of MEMS-based optical switches and attenuators to reach the marketplace. In addition, a specialized application for fabricating the next generation photolithography exposure masks has been optimized for 200 mm diameter wafers, to depths of ∼750 μm. Where the profile is not critical, etch rates of greater than 8 μm min -1 have been realized to replace previous methods such as wet etching. This is also the case for printer applications. Specialized applications that require etching down to pyrex or oxide often result in the loss of feature size control at the interface; this is an industry wide problem. STS have developed a technique to address this. The rapid progression of the industry has led to development of the STS ICP etch tool, as well as the process. (author)

  4. High-Density Infrared Surface Treatments of Refractories

    Energy Technology Data Exchange (ETDEWEB)

    Tiegs, T.N.

    2005-03-31

    Refractory materials play a crucial role in all energy-intensive industries and are truly a crosscutting technology for the Industries of the Future (IOF). One of the major mechanisms for the degradation of refractories and a general decrease in their performance has been the penetration and corrosion by molten metals or glass. Methods and materials that would reduce the penetration, wetting, and corrosive chemistry would significantly improve refractory performance and also maintain the quality of the processed liquid, be it metal or glass. This report presents the results of an R&D project aimed at investigating the use of high-density infrared (HDI) heating to surface treat refractories to improve their performance. The project was a joint effort between Oak Ridge National Laboratory (ORNL) and the University of Missouri-Rolla (UMR). HDI is capable of heating the near-surface region of materials to very high temperatures where sintering, diffusion, and melting can occur. The intended benefits of HDI processing of refractories were to (1) reduce surface porosity (by essentially sealing the surface to prevent liquid penetration), (2) allow surface chemistry changes to be performed by bonding an adherent coating onto the underlying refractory (in order to inhibit wetting and/or improve corrosion resistance), and (3) produce noncontact refractories with high-emissivity surface coatings.

  5. Postirradiation examination of high-density uranium alloy dispersion fuels

    International Nuclear Information System (INIS)

    Hayes, S.L.; Meyer, M.K.; Hofman, G.L.; Strain, R.V.

    1998-01-01

    Two irradiation test vehicles, designated RERTR-2, were inserted into the Advanced Test reactor in Idaho in August 1997. These tests were designed to obtain irradiation performance information on a variety of potential new, high-density uranium alloy dispersion fuels, including U-10Mo, U-8Mo, U-6Mo, U-4Mo, U-9Nb-3Zr, U-6Nb-4Zr, U-5Nb-3Zr, U-6Mo-1Pt, U-6Mo-0.6Ru and U-10Mo-0.05Sn: the intermetallic compounds U 2 Mo and U-10Mo-0.-5Sn; the intermetallic compounds U 2 Mo and U 3 Si 2 were also included in the fuel test matrix. These fuels are included in the experiments as microplates (76 mm x 22 mm x 1.3mm outer dimensions) with a nominal fuel volume loading of 25% and irradiated at relatively low temperature (∼100 deg C). RERTR-1 and RERTR-2 were discharged from the reactor in November 1997 and July 1998, respectively at calculated peak fuel burnups of 45 and 71 at %-U 235 Both experiments are currently under examination at the Alpha Gamma Hot Cell Facility at Argonne National Laboratory in Chicago. This paper presents the postirradiation examination results available to date from these experiments. (author)

  6. High-density polyethylene dosimetry by transvinylene FTIR analysis

    DEFF Research Database (Denmark)

    McLaughlin, W.L.; Silverman, J.; Al-Sheikhly, M.

    1999-01-01

    and electrons. The useful dose range of 0.053 cm thick high-density polyethylene film (rho = 0.961 g cm(-3); melt index = 0.8 dg min(-1)), for irradiations by (60)Co gamma radiation and 2.0 and 0.4 MeV electron beams in deaerated atmosphere (Na gas), is about 50-10(3) kGy for FTIR transvinylene......The formation of transvinylene unsaturation, -CH=CH-, due to free-radical or cationic-initiated dehydrogenation by irradiation, is a basic reaction in polyethylene and is useful for dosimetry at high absorbed doses. The radiation-enhanced infrared absorption having a maximum at nu = 965 cm......(-l) (lambda = 10.36 mu m) is stable in air and can be measured by Fourier-transform infrared (FTIR) spectrophotometry. The quantitative analysis is a useful means of product end-point dosimetry for radiation processing with gamma rays and electrons, where polyethylene is a component of the processed product...

  7. High Density Lipoprotein: A Therapeutic Target in Type 2 Diabetes

    Directory of Open Access Journals (Sweden)

    Philip J. Barter

    2013-09-01

    Full Text Available High density lipoproteins (HDLs have a number of properties that have the potential to inhibit the development of atherosclerosis and thus reduce the risk of having a cardiovascular event. These protective effects of HDLs may be reduced in patients with type 2 diabetes, a condition in which the concentration of HDL cholesterol is frequently low. In addition to their potential cardioprotective properties, HDLs also increase the uptake of glucose by skeletal muscle and stimulate the synthesis and secretion of insulin from pancreatic β cells and may thus have a beneficial effect on glycemic control. This raises the possibility that a low HDL concentration in type 2 diabetes may contribute to a worsening of diabetic control. Thus, there is a double case for targeting HDLs in patients with type 2 diabetes: to reduce cardiovascular risk and also to improve glycemic control. Approaches to raising HDL levels include lifestyle factors such as weight reduction, increased physical activity and stopping smoking. There is an ongoing search for HDL-raising drugs as agents to use in patients with type 2 diabetes in whom the HDL level remains low despite lifestyle interventions.

  8. High-density matter: current status and future challenges

    Directory of Open Access Journals (Sweden)

    Stone J. R.

    2015-01-01

    Full Text Available There are many fascinating processes in the Universe which we observe in more and more in detail thanks to increasingly sophisticated technology. One of the most interesting phenomena is the life cycle of stars, their birth, evolution and death. If the stars are massive enough, they end their lives in the core-collapse supernova explosion, the one of the most violent events in the Universe. As the result, the densest objects in the Universe, neutron stars and/or black holes are created. Naturally, the physical basis of these events should be understood in line with observation. The current status of our knowledge of processes in the life of stars is far from adequate for their true understanding. We show that although many models have been constructed their detailed ability to describe observations is limited or non-existent. Furthermore the general failure of all models means that we cannot tell which are heading in the right direction. A possible way forward in modeling of high-density matter is outlined, exemplified by the quark-meson-coupling model (QMC. This model has a natural explanation for the saturation of nuclear forces and depends on very few adjustable parameters, strongly constrained by the underlying physics. Latest QMC results for compact objects and finite nuclei are presented.

  9. High-Density Quantum Sensing with Dissipative First Order Transitions.

    Science.gov (United States)

    Raghunandan, Meghana; Wrachtrup, Jörg; Weimer, Hendrik

    2018-04-13

    The sensing of external fields using quantum systems is a prime example of an emergent quantum technology. Generically, the sensitivity of a quantum sensor consisting of N independent particles is proportional to sqrt[N]. However, interactions invariably occurring at high densities lead to a breakdown of the assumption of independence between the particles, posing a severe challenge for quantum sensors operating at the nanoscale. Here, we show that interactions in quantum sensors can be transformed from a nuisance into an advantage when strong interactions trigger a dissipative phase transition in an open quantum system. We demonstrate this behavior by analyzing dissipative quantum sensors based upon nitrogen-vacancy defect centers in diamond. Using both a variational method and a numerical simulation of the master equation describing the open quantum many-body system, we establish the existence of a dissipative first order transition that can be used for quantum sensing. We investigate the properties of this phase transition for two- and three-dimensional setups, demonstrating that the transition can be observed using current experimental technology. Finally, we show that quantum sensors based on dissipative phase transitions are particularly robust against imperfections such as disorder or decoherence, with the sensitivity of the sensor not being limited by the T_{2} coherence time of the device. Our results can readily be applied to other applications in quantum sensing and quantum metrology where interactions are currently a limiting factor.

  10. High density operation on the HT-7 superconducting tokamak

    International Nuclear Information System (INIS)

    Xiang Gao

    2000-01-01

    The structure of the operation region has been studied in the HT-7 superconducting tokamak, and progress on the extension of the HT-7 ohmic discharge operation region is reported. A density corresponding to 1.2 times the Greenwald limit was achieved by RF boronization. The density limit appears to be connected to the impurity content and the edge parameters, so the best results are obtained with very clean plasmas and peaked electron density profiles. The peaking factors of electron density profiles for different current and line averaged densities were observed. The density behaviour and the fuelling efficiency for gas puffing (20-30%), pellet injection (70-80%) and molecular beam injection (40-50%) were studied. The core crash sawteeth and MHD behaviour, which were induced by an injected pellet, were observed and the events correlated with the change of current profile and reversed magnetic shear. The MARFE phenomena on HT-7 are summarized. The best correlation has been found between the total input ohmic power and the product of the edge line averaged density and Z eff . HT-7 could be easily operated in the high density region MARFE-free using RF boronization. (author)

  11. The physics of the high density Z-pinch

    International Nuclear Information System (INIS)

    Glasser, A.H.; Hammel, J.E.; Lewis, H.R.

    1988-01-01

    The fiber-initiated High-Density Z-Pinch (HDZP) is a novel concept in which fusion plasma could be produced by applying 2 MV along a thin filament of frozen deuterium, 20-30 μm in diameter, 5-10 cm long. The megamp-range currents that result would ohmically heat the fiber to fusion temperatures in 100 ns while maintaining nearly constant radius. The plasma pressure would be held stably by the self-magnetic field for many radial sound transit times during the current-rise phase while, in the case of D-T, a significant fraction of the fiber undergoes thermonuclear fusion. This paper presents results of Los Alamos HDZP studies. Existing and new experiments are described. A succession of theoretical studies, including 1D self-similar and numerical studies of the hot plasma phase, 1D and 2D numerical studies of the cold startup phase, and 3D numerical studies of stability in the hot regime, are then presented. 9 refs., 4 figs

  12. High-density housing that works for all

    Energy Technology Data Exchange (ETDEWEB)

    Hasan, Arif

    2010-03-15

    In an urbanising world, the way people fit into cities is vastly important - socially, economically, environmentally, even psychologically. So density, or the number of people living in a given area, is central to urban design and planning. Both governments and markets tend to get density wrong, leading to overcrowding, urban sprawl or often both. A case in point are the high-rise buildings springing up throughtout urban Asia - perceived as key features of that widely touted concept, the 'world-class city'. While some may offer a viable solution to land pressures and density requirements, many built to house evicted or resettled 'slum' dwellers are a social and economic nightmare - inconveniently sited, overcrowded and costly. New evidence from Karachi, Pakistan, reveals a real alternative. Poor people can create liveable high-density settlements as long as community control, the right technical assistance and flexible designs are in place. A city is surely 'world-class' only when it is cosmopolitan – built to serve all, including the poorest.

  13. High-Density Superconducting Cables for Advanced ACTPol

    Science.gov (United States)

    Pappas, C. G.; Austermann, J.; Beall, J. A.; Duff, S. M.; Gallardo, P. A.; Grace, E.; Henderson, S. W.; Ho, S. P.; Koopman, B. J.; Li, D.; McMahon, J.; Nati, F.; Niemack, M. D.; Niraula, P.; Salatino, M.; Schillaci, A.; Schmitt, B. L.; Simon, S. M.; Staggs, S. T.; Stevens, J. R.; Vavagiakis, E. M.; Ward, J. T.; Wollack, E. J.

    2016-07-01

    Advanced ACTPol (AdvACT) is an upcoming Atacama Cosmology Telescope (ACT) receiver upgrade, scheduled to deploy in 2016, that will allow measurement of the cosmic microwave background polarization and temperature to the highest precision yet with ACT. The AdvACT increase in sensitivity is partly provided by an increase in the number of transition-edge sensors (TESes) per array by up to a factor of two over the current ACTPol receiver detector arrays. The high-density AdvACT TES arrays require 70 \\upmu m pitch superconducting flexible cables (flex) to connect the detector wafer to the first-stage readout electronics. Here, we present the flex fabrication process and test results. For the flex wiring layer, we use a 400-nm-thick sputtered aluminum film. In the center of the cable, the wiring is supported by a polyimide substrate, which smoothly transitions to a bare (uncoated with polyimide) silicon substrate at the ends of the cable for a robust wedge wire-bonding interface. Tests on the first batch of flex made for the first AdvACT array show that the flex will meet the requirements for AdvACT, with a superconducting critical current above 1 mA at 500 mK, resilience to mechanical and cryogenic stress, and a room temperature yield of 97 %.

  14. High-Density Quantum Sensing with Dissipative First Order Transitions

    Science.gov (United States)

    Raghunandan, Meghana; Wrachtrup, Jörg; Weimer, Hendrik

    2018-04-01

    The sensing of external fields using quantum systems is a prime example of an emergent quantum technology. Generically, the sensitivity of a quantum sensor consisting of N independent particles is proportional to √{N }. However, interactions invariably occurring at high densities lead to a breakdown of the assumption of independence between the particles, posing a severe challenge for quantum sensors operating at the nanoscale. Here, we show that interactions in quantum sensors can be transformed from a nuisance into an advantage when strong interactions trigger a dissipative phase transition in an open quantum system. We demonstrate this behavior by analyzing dissipative quantum sensors based upon nitrogen-vacancy defect centers in diamond. Using both a variational method and a numerical simulation of the master equation describing the open quantum many-body system, we establish the existence of a dissipative first order transition that can be used for quantum sensing. We investigate the properties of this phase transition for two- and three-dimensional setups, demonstrating that the transition can be observed using current experimental technology. Finally, we show that quantum sensors based on dissipative phase transitions are particularly robust against imperfections such as disorder or decoherence, with the sensitivity of the sensor not being limited by the T2 coherence time of the device. Our results can readily be applied to other applications in quantum sensing and quantum metrology where interactions are currently a limiting factor.

  15. LTCC magnetic components for high density power converter

    Science.gov (United States)

    Lebourgeois, Richard; Labouré, Eric; Lembeye, Yves; Ferrieux, Jean-Paul

    2018-04-01

    This paper deals with multilayer magnetic components for power electronics application and specifically for high frequency switching. New formulations based on nickel-zinc-copper spinel ferrites were developed for high power and high frequency applications. These ferrites can be sintered at low temperature (around 900°C) which makes them compatible with the LTCC (Low Temperature Co-fired Ceramics) technology. Metallic parts of silver or gold can be fully integrated inside the ferrite while guaranteeing the integrity of both the ferrite and the metal. To make inductors or transformers with the required properties, it is mandatory to have nonmagnetic parts between the turns of the winding. Then it is essential to find a dielectric material, which can be co-sintered both with the ferrite and the metal. We will present the solution we found to this problem and we will describe the results we obtained for a multilayer co-sintered transformer. We will see that these new components have good performance compared with the state of the art and are very promising for developing high density switching mode power supplies.

  16. Properties of recycled high density polyethylene and coffee dregs composites

    Directory of Open Access Journals (Sweden)

    Sibele Piedade Cestari

    2013-01-01

    Full Text Available Composites of recycled high density polyethylene (HDPE-R and coffee dregs (COFD were elaborated. The blends were made at the proportions of 100-0, 90-10, 80-20, 70-30, 60-40, 50-50 and 40-60% polymer-filler ratio. The materials were evaluated through scanning electron microscopy (SEM, differential scanning calorimetry (DSC, thermogravimetry/derivative thermogravimetry (TGA, and compressive resistance test. The compounding was done using a two-stage co-kneader system extruder, and then cylindrical specimens were injection molded. All composites had a fine dispersion of the COFD into the polymeric matrix. The composites degraded in two steps. The first one was in a temperature lower than the neat HDPE, but higher than the average processing temperature of the polymer. The melting temperature and the degree of crystallinity of the composites resulted similar to the neat HDPE ones. The compressive moduli of the composites resulted similar to the neat polymer one. The results show that these composites have interesting properties as a building material.

  17. Acrolein impairs the cholesterol transport functions of high density lipoproteins.

    Science.gov (United States)

    Chadwick, Alexandra C; Holme, Rebecca L; Chen, Yiliang; Thomas, Michael J; Sorci-Thomas, Mary G; Silverstein, Roy L; Pritchard, Kirkwood A; Sahoo, Daisy

    2015-01-01

    High density lipoproteins (HDL) are considered athero-protective, primarily due to their role in reverse cholesterol transport, where they transport cholesterol from peripheral tissues to the liver for excretion. The current study was designed to determine the impact of HDL modification by acrolein, a highly reactive aldehyde found in high abundance in cigarette smoke, on the cholesterol transport functions of HDL. HDL was chemically-modified with acrolein and immunoblot and mass spectrometry analyses confirmed apolipoprotein crosslinking, as well as acrolein adducts on apolipoproteins A-I and A-II. The ability of acrolein-modified HDL (acro-HDL) to serve as an acceptor of free cholesterol (FC) from COS-7 cells transiently expressing SR-BI was significantly decreased. Further, in contrast to native HDL, acro-HDL promotes higher neutral lipid accumulation in murine macrophages as judged by Oil Red O staining. The ability of acro-HDL to mediate efficient selective uptake of HDL-cholesteryl esters (CE) into SR-BI-expressing cells was reduced compared to native HDL. Together, the findings from our studies suggest that acrolein modification of HDL produces a dysfunctional particle that may ultimately promote atherogenesis by impairing functions that are critical in the reverse cholesterol transport pathway.

  18. Irradiation testing of high-density uranium alloy dispersion fuels

    International Nuclear Information System (INIS)

    Hayes, S.L.; Trybus, C.L.; Meyer, M.K.

    1997-01-01

    Two irradiation test vehicles have been designed, fabricated, and inserted into the Advanced Test Reactor in Idaho. Irradiation of these experiments began in August 1997. These irradiation tests were designed to obtain irradiation performance information on a variety of potential new, high-density dispersion fuels. Each of the two irradiation vehicles contains 32 'microplates'. Each microplate is aluminum clad, having an aluminum matrix phase and containing one of the following compositions as the fuel phase: U-10Mo, U-8Mo, U-6Mo, U-4Mo, U-9Nb-3Zr, U-6Nb-4Zr, U-5Nb-3Zr, U-6Mo-1Pt, U-6Mo-0.6Ru, U10Mo-0.05Sn, U2Mo, or U 3 Si 2 . These experiments will be discharged at peak fuel burnups of approximately 40 and 80 at.% U 235 . Of particular interest are the extent of reaction of the fuel and matrix phases and the fission gas retention/swelling characteristics of these new fuel alloys. This paper presents the design of the irradiation vehicles and the irradiation conditions. (author)

  19. High-Density Superconducting Cables for Advanced ACTPol

    Science.gov (United States)

    Pappas, C. G.; Austermann, J.; Beall, J. A.; Duff, S. M.; Gallardo, P. A.; Grace, E.; Henderson, S. W.; Ho, S. P.; Koopman, B. J.; Li, D.; hide

    2016-01-01

    Advanced ACTPol (AdvACT) is an upcoming Atacama Cosmology Telescope (ACT) receiver upgrade, scheduled to deploy in 2016, that will allow measure- ment of the cosmic microwave background polarization and temperature to the highest precision yet with ACT. The AdvACT increase in sensitivity is partly provided by an increase in the number of transition-edge sensors (TESes) per array by up to a factor of two over the current ACTPol receiver detector arrays. The high-density AdvACT TES arrays require 70 µ m pitch superconducting flexible cables (flex) to connect the detec- tor wafer to the first-stage readout electronics. Here, we present the flex fabrication process and test results. For the flex wiring layer, we use a 400-nm-thick sputtered alu- minum film. In the center of the cable, the wiring is supported by a polyimide substrate, which smoothly transitions to a bare (uncoated with polyimide) silicon substrate at the ends of the cable for a robust wedge wire-bonding interface. Tests on the first batch of flex made for the first AdvACT array show that the flex will meet the requirements for AdvACT, with a superconducting critical current above 1 mA at 500 mK, resilience to mechanical and cryogenic stress, and a room temperature yield of 97%.

  20. Inelastic neutron scattering from high-density fcc 4He

    International Nuclear Information System (INIS)

    Thomlinson, W.; Eckert, J.; Shirane, G.

    1978-01-01

    The phonon dispersion relations in high-density crystals of fcc 4 He have been measured along high-symmetry directions by the neutron-inelastic-scattering technique. A recent study of the lattice dynamics of fcc 4 He by Eckert et al. has been extended to cover the fcc phase diagram at pressures below 5 kbar. Molar volumes of 9.03, 9.43, and 9.97 cm 3 /mole have been studied in the temperature range from near the melting curve to near the fcc-hcp transition line. The phonon dispersion relations are in good agreement with a first-order self-consistent phonon theory calculation by Goldman. The observed phonon-group line shapes at large energy and momentum transfers show evidence for multiphonon scattering in agreement with calculations by Glyde. Eckert et al. reported extremely large anharmonic isochoric temperature shifts of the phonon energies. The present work studied the shifts as a function of molar volume and temperature. Mode-Grueneisen-parameter dispersion curves have been measured using the present data and earlier measurements at lower density in the fcc phase by Traylor et al. Macroscopic Grueneisen parameters have been calculated from the phonon density of states obtained from the data

  1. The infant mirror neuron system studied with high density EEG.

    Science.gov (United States)

    Nyström, Pär

    2008-01-01

    The mirror neuron system has been suggested to play a role in many social capabilities such as action understanding, imitation, language and empathy. These are all capabilities that develop during infancy and childhood, but the human mirror neuron system has been poorly studied using neurophysiological measures. This study measured the brain activity of 6-month-old infants and adults using a high-density EEG net with the aim of identifying mirror neuron activity. The subjects viewed both goal-directed movements and non-goal-directed movements. An independent component analysis was used to extract the sources of cognitive processes. The desynchronization of the mu rhythm in adults has been shown to be a marker for activation of the mirror neuron system and was used as a criterion to categorize independent components between subjects. The results showed significant mu desynchronization in the adult group and significantly higher ERP activation in both adults and 6-month-olds for the goal-directed action observation condition. This study demonstrate that infants as young as 6 months display mirror neuron activity and is the first to present a direct ERP measure of the mirror neuron system in infants.

  2. High-Density Stretchable Electrode Grids for Chronic Neural Recording.

    Science.gov (United States)

    Tybrandt, Klas; Khodagholy, Dion; Dielacher, Bernd; Stauffer, Flurin; Renz, Aline F; Buzsáki, György; Vörös, János

    2018-04-01

    Electrical interfacing with neural tissue is key to advancing diagnosis and therapies for neurological disorders, as well as providing detailed information about neural signals. A challenge for creating long-term stable interfaces between electronics and neural tissue is the huge mechanical mismatch between the systems. So far, materials and fabrication processes have restricted the development of soft electrode grids able to combine high performance, long-term stability, and high electrode density, aspects all essential for neural interfacing. Here, this challenge is addressed by developing a soft, high-density, stretchable electrode grid based on an inert, high-performance composite material comprising gold-coated titanium dioxide nanowires embedded in a silicone matrix. The developed grid can resolve high spatiotemporal neural signals from the surface of the cortex in freely moving rats with stable neural recording quality and preserved electrode signal coherence during 3 months of implantation. Due to its flexible and stretchable nature, it is possible to minimize the size of the craniotomy required for placement, further reducing the level of invasiveness. The material and device technology presented herein have potential for a wide range of emerging biomedical applications. © 2018 The Authors. Published by WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  3. Using NEG-pumping near a high density internal target

    International Nuclear Information System (INIS)

    Gruber, A.; Marton, J.; Widmann, E.; Zmeskal, J.; Orth, H.

    2008-01-01

    Full text: The Stefan Meyer Institut (SMI) is part of the international PANDA collaboration. The universal detector will be constructed at the future high-energy antiproton storage ring HESR at FAIR (Facility for Antiproton and Ion Research, GSI/Darmstadt). PANDA will use antiproton beams (1.5 to 15 GeV/c) for hadron physics in the charmonium region. SMI contributes to major parts of the PANDA detector like the hydrogen cluster-jet target and the vacuum system of the antiproton - target interaction zone. To ensure low background, the residual gas load in the interaction zone and in the antiproton beam-pipe has to be minimized. Most of the gas load, of course will come from the high density internal hydrogen target. Since the PANDA detector will cover almost the full solid angle, the installation of pumps near the interaction zone is impossible. Therefore, the use of NEG (non-evaporative-getter) coated beam pipes has been considered as an alternative. Two setups with NEG coated tubes have been installed at SMI as prototypes of the PANDA interaction zone. The outgassing behavior, the pumping speed and the pumping capacity for hydrogen have been tested. The status of the studies of the interaction region will be presented. (author)

  4. Improved group-specific primers based on the full SILVA 16S rRNA gene reference database.

    Science.gov (United States)

    Pfeiffer, Stefan; Pastar, Milica; Mitter, Birgit; Lippert, Kathrin; Hackl, Evelyn; Lojan, Paul; Oswald, Andreas; Sessitsch, Angela

    2014-08-01

    Quantitative PCR (qPCR) and community fingerprinting methods, such as the Terminal Restriction Fragment Length Polymorphism (T-RFLP) analysis,are well-suited techniques for the examination of microbial community structures. The use of phylum and class-specific primers can provide enhanced sensitivity and phylogenetic resolution as compared with domain-specific primers. To date, several phylum- and class-specific primers targeting the 16S ribosomal RNA gene have been published. However, many of these primers exhibit low discriminatory power against non-target bacteria in PCR. In this study, we evaluated the precision of certain published primers in silico and via specific PCR. We designed new qPCR and T-RFLP primer pairs (for the classes Alphaproteobacteria and Betaproteobacteria, and the phyla Bacteroidetes, Firmicutes and Actinobacteria) by combining the sequence information from a public dataset (SILVA SSU Ref 102 NR) with manual primer design. We evaluated the primer pairs via PCR using isolates of the above-mentioned groups and via screening of clone libraries from environmental soil samples and human faecal samples. As observed through theoretical and practical evaluation, the primers developed in this study showed a higher level of precision than previously published primers, thus allowing a deeper insight into microbial community dynamics.

  5. Isolation of temperature-sensitive mutants of 16 S rRNA in Escherichia coli

    DEFF Research Database (Denmark)

    Triman, K; Becker, E; Dammel, C

    1989-01-01

    Temperature-sensitive mutants have been isolated following hydroxylamine mutagenesis of a plasmid containing Escherichia coli rRNA genes carrying selectable markers for spectinomycin resistance (U1192 in 16 S rRNA) and erythromycin resistance (G2058 in 23 S rRNA). These antibiotic resistance....... The mutations were localized by in vitro restriction fragment replacement followed by in vivo marker rescue and were identified by DNA sequence analysis. We report here seven single-base alterations in 16 S rRNA (A146, U153, A350, A359, A538, A1292 and U1293), five of which produce temperature......-sensitive spectinomycin resistance and two that produce unconditional loss of resistance. In each case, loss of ribosomal function can be accounted for by disruption of base-pairing in the secondary structure of 16 S rRNA. For the temperature-sensitive mutants, there is a lag period of about two generations between...

  6. Cross-linking of streptomycin to the 16S ribosomal RNA of Escherichia coli

    International Nuclear Information System (INIS)

    Gravel, M.; Melancon, P.; Barkier-Gingras, L.

    1987-01-01

    [ 3 H]Dihydrostreptomycin was cross-linked to the 30S ribosomal subunit from Escherichia coli with the bifunctional reagent nitrogen mustard. The cross-linking primarily involved the 16S RNA. To localize the site of cross-linking of streptomycin to the 16S RNA, the authors hybridized RNA labeled with streptomycin to restriction fragments of the 16S RNA gene. Labeled RNA hybridized to DNA fragments corresponding to bases 892-917 and bases 1394-1415. These two segments of the ribosomal RNA must by juxtaposed in the ribosome, since there is a single binding site for streptomycin. This region has been implicated both in the decoding site and in the binding of initiation factor IF-3, indicating its functional importance

  7. Experimental study of high density foods for the Space Operations Center

    Science.gov (United States)

    Ahmed, S. M.

    1981-01-01

    The experimental study of high density foods for the Space Operations Center is described. A sensory evaluation of the high density foods was conducted first to test the acceptability of the products. A shelf-life study of the high density foods was also conducted for three different time lengths at three different temperatures. The nutritional analysis of the high density foods is at present incomplete.

  8. The effects of alignment quality, distance calculation method, sequence filtering, and region on the analysis of 16S rRNA gene-based studies.

    Directory of Open Access Journals (Sweden)

    Patrick D Schloss

    Full Text Available Pyrosequencing of PCR-amplified fragments that target variable regions within the 16S rRNA gene has quickly become a powerful method for analyzing the membership and structure of microbial communities. This approach has revealed and introduced questions that were not fully appreciated by those carrying out traditional Sanger sequencing-based methods. These include the effects of alignment quality, the best method of calculating pairwise genetic distances for 16S rRNA genes, whether it is appropriate to filter variable regions, and how the choice of variable region relates to the genetic diversity observed in full-length sequences. I used a diverse collection of 13,501 high-quality full-length sequences to assess each of these questions. First, alignment quality had a significant impact on distance values and downstream analyses. Specifically, the greengenes alignment, which does a poor job of aligning variable regions, predicted higher genetic diversity, richness, and phylogenetic diversity than the SILVA and RDP-based alignments. Second, the effect of different gap treatments in determining pairwise genetic distances was strongly affected by the variation in sequence length for a region; however, the effect of different calculation methods was subtle when determining the sample's richness or phylogenetic diversity for a region. Third, applying a sequence mask to remove variable positions had a profound impact on genetic distances by muting the observed richness and phylogenetic diversity. Finally, the genetic distances calculated for each of the variable regions did a poor job of correlating with the full-length gene. Thus, while it is tempting to apply traditional cutoff levels derived for full-length sequences to these shorter sequences, it is not advisable. Analysis of beta-diversity metrics showed that each of these factors can have a significant impact on the comparison of community membership and structure. Taken together, these results

  9. Ultra-high Density SNParray in Neuroblastoma Molecular Diagnostics

    Directory of Open Access Journals (Sweden)

    Inge M. Ambros

    2014-08-01

    Full Text Available Neuroblastoma serves as a paradigm for applying tumor genomic data for determining patient prognosis and thus for treatment allocation. MYCN status, i.e. amplified vs. non-amplified, was one of the very first biomarkers in oncology to discriminate aggressive from less aggressive or even favorable clinical courses of neuroblastoma. However, MYCN amplification is by far not the only genetic change associated with unfavorable clinical courses: so called segmental chromosomal aberrations, i.e. gains or losses of chromosomal fragments, can also indicate tumor aggressiveness. The clinical use of these genomic aberrations has, however, been hampered for many years by methodical and interpretational problems. Only after reaching worldwide consensus on markers, methodology, and data interpretation, information on SCAs has recently been implemented in clinical studies. Now, a number of collaborative studies within COG, GPOH and SIOPEN use genomic information to stratify therapy for patients with localized and metastatic disease. Recently, new types of DNA based aberrations influencing the clinical behavior of neuroblastomas have been described. Deletions or mutations of genes like ATRX and a phenomenon referred to as chromothripsis are all assumed to correlate with an unfavorable clinical behavior. However, these genomic aberrations need to be scrutinized in larger studies applying the most appropriate techniques. Single nucleotide polymorphism (SNP arrays have proven successful in deciphering genomic aberrations of cancer cells; these techniques, however, are usually not applied in the daily routine. Here, we present an ultra-high density (UHD SNParray technique which is, because of its high specificity and sensitivity and the combined copy number and allele information, highly appropriate for the genomic diagnosis of neuroblastoma and other malignancies.

  10. High density microelectronics package using low temperature cofirable ceramics

    International Nuclear Information System (INIS)

    Fu, S.-L.; Hsi, C.-S.; Chen, L.-S.; Lin, W. K.

    1997-01-01

    Low Temperature Cofired Ceramics (LTCC) is a relative new thick film process and has many engineering and manufacturing advantages over both the sequential thick film process and high temperature cofired ceramic modules. Because of low firing temperature, low sheet resistance metal conductors, commercial thick film resistors, and thick film capacitors can be buried in or printed on the substrates. A 3-D multilayer ceramic substrate can be prepared via laminating and co-firing process. The packing density of the LTCC substrates can be increased by this 3-D packing technology. At Kaohsiung Polytechnic Institute (KPI), a LTCC substrate system has been developed for high density packaging applications, which had buried surface capacitors and resistors. The developed cordierite-glass ceramic substrate, which has similar thermal expansion as silicon chip, is a promising material for microelectronic packaging. When the substrates were sintered at temperatures between 850-900 degree centigrade, a relative density higher than 96 % can be obtained. The substrate had a dielectric constant between 5.5 and 6.5. Ruthenium-based resistor pastes were used for resistors purposes. The resistors fabricated in/on the LTCC substrates were strongly depended on the microstructures developed in the resistor films. Surface resistors were laser trimmed in order to obtain specific values for the resistors. Material with composition Pb(Fe 2/3 W 1/3 ) x (Fe l/2 Nb l/2 ) y Ti 2 O 3 was used as dielectric material of the capacitor in the substrate. The material can be sintered at temperatures between 850-930 degree centigrade, and has dielectric constant as high as 26000. After cofiring, good adhesion between dielectric and substrate layers was obtained. Combing the buried resistors and capacitors together with the lamination of LTCC layer, a 3-dimensional multilayered ceramic package was fabricated. (author)

  11. Ignition and burn in contaminated DT fuel at high densities

    International Nuclear Information System (INIS)

    Pasley, J.

    2010-01-01

    Complete text of publication follows. Radiation hydrodynamics simulations have been performed to quantify the effect of contamination upon the ignition threshold in DT at high densities. A detailed thermonuclear burn model, with multi-group multispecies ions, is incorporated alongside a multigroup diffusion approximation for thermal radiation transport. The code used is the research version of the HYADES 1D code. Acceptable levels of contamination are identified for a range of contaminant ion species. A range of different contaminant spatial distribution within the fuel are explored: i) in which the contamination is uniformly distributed throughout the fuel; ii) in which the impurity ions are confined to the hotspot, or iii) where contamination is restricted to a particular region of the hotspot (either centrally, near the surface, or at an intermediate location). Initially the fuel has a constant density with the hotspot located centrally. The overall radius of the fuel is chosen to be sufficiently large that it has no significant effect upon the success or failure of ignition. The evolution of the system is then simulated until ignition either establishes widespread thermonuclear burning, or a failure to ignite is observed. The critical ρr for ignition is found by iteration on the hotspot radius. We show that varying the spatial distribution of the contaminant within the ignition spot has little effect, so long as the total mass of contaminant is held the same. As expected, high-Z contamination is far more detrimental than that by low-Z ions. Discussion of the findings in the context of re-entrant cone-guided fast ignition is presented, in addition to a theoretical interpretation of the results.

  12. Degradation of high density lipoprotein in cultured rat luteal cells

    International Nuclear Information System (INIS)

    Rajan, V.P.; Menon, K.M.J.

    1986-01-01

    In rat ovary luteal cells, degradation of high density lipoprotein (HDL) to tricholoracetic acid (TCA)-soluble products accounts for only a fraction of the HDL-derived cholesterol used for steroidogenesis. In this study the authors have investigated the fate of 125 I]HDL bound to cultured luteal cells using pulse-chase technique. Luteal cell cultures were pulse labeled with [ 125 I]HDL 3 and reincubated in the absence of HDL. By 24 h about 50% of the initallay bound radioactivity was released into the medium, of which 60-65% could be precipitated with 10% TCA. Gel filtration of the chase incubation medium on 10% agarose showed that the amount of TCA-soluble radioactivity was nearly completely accounted for by a sharp peak in the low molecular weight region which was identified as 96% monoiodotyrosine by paper chromatography. The TCA-precipitable radioactivity was nearly completely accounted for by a sharp peak in the low molecular weight region which was identified as 96% monoiodotyrosine by paper chromatography. The TCA-precipitable radioactivity eluted over a wide range of molecular weights (15,000-80,000), and there was very little intact HDL present. Electrophoresis of the chase medium showed that component of the TCA-precipitable portion had mobility similar to apo AI. Lysosomal inhibitors of receptor-mediated endocytosis had no effect on the composition or quantity of radioactivity released during chase incubation. The results show that HDL 3 binding to luteal cells is followed by complete degradation of the lipoprotein, although the TCA-soluble part does not reflect the extent of degradation

  13. Surface interactions involved in flashover with high density electronegative gases.

    Energy Technology Data Exchange (ETDEWEB)

    Hodge, Keith Conquest; Warne, Larry Kevin; Jorgenson, Roy Eberhardt; Wallace, Zachariah Red; Lehr, Jane Marie

    2010-01-01

    This report examines the interactions involved with flashover along a surface in high density electronegative gases. The focus is on fast ionization processes rather than the later time ionic drift or thermalization of the discharge. A kinetic simulation of the gas and surface is used to examine electron multiplication and includes gas collision, excitation and ionization, and attachment processes, gas photoionization and surface photoemission processes, as well as surface attachment. These rates are then used in a 1.5D fluid ionization wave (streamer) model to study streamer propagation with and without the surface in air and in SF6. The 1.5D model therefore includes rates for all these processes. To get a better estimate for the behavior of the radius we have studied radial expansion of the streamer in air and in SF6. The focus of the modeling is on voltage and field level changes (with and without a surface) rather than secondary effects, such as, velocities or changes in discharge path. An experiment has been set up to carry out measurements of threshold voltages, streamer velocities, and other discharge characteristics. This setup includes both electrical and photographic diagnostics (streak and framing cameras). We have observed little change in critical field levels (where avalanche multiplication sets in) in the gas alone versus with the surface. Comparisons between model calculations and experimental measurements are in agreement with this. We have examined streamer sustaining fields (field which maintains ionization wave propagation) in the gas and on the surface. Agreement of the gas levels with available literature is good and agreement between experiment and calculation is good also. Model calculations do not indicate much difference between the gas alone versus the surface levels. Experiments have identified differences in velocity between streamers on the surface and in the gas alone (the surface values being larger).

  14. High density microelectronics package using low temperature cofirable ceramics

    Energy Technology Data Exchange (ETDEWEB)

    Fu, S -L; Hsi, C -S; Chen, L -S; Lin, W K [Kaoshiung Polytechnic Institute Ta-Hsu, Kaoshiung (China)

    1998-12-31

    Low Temperature Cofired Ceramics (LTCC) is a relative new thick film process and has many engineering and manufacturing advantages over both the sequential thick film process and high temperature cofired ceramic modules. Because of low firing temperature, low sheet resistance metal conductors, commercial thick film resistors, and thick film capacitors can be buried in or printed on the substrates. A 3-D multilayer ceramic substrate can be prepared via laminating and co-firing process. The packing density of the LTCC substrates can be increased by this 3-D packing technology. At Kaohsiung Polytechnic Institute (KPI), a LTCC substrate system has been developed for high density packaging applications, which had buried surface capacitors and resistors. The developed cordierite-glass ceramic substrate, which has similar thermal expansion as silicon chip, is a promising material for microelectronic packaging. When the substrates were sintered at temperatures between 850-900 degree centigrade, a relative density higher than 96 % can be obtained. The substrate had a dielectric constant between 5.5 and 6.5. Ruthenium-based resistor pastes were used for resistors purposes. The resistors fabricated in/on the LTCC substrates were strongly depended on the microstructures developed in the resistor films. Surface resistors were laser trimmed in order to obtain specific values for the resistors. Material with composition Pb(Fe{sub 2/3}W{sub 1/3}){sub x}(Fe{sub l/2}Nb{sub l/2}){sub y}Ti{sub 2}O{sub 3} was used as dielectric material of the capacitor in the substrate. The material can be sintered at temperatures between 850-930 degree centigrade, and has dielectric constant as high as 26000. After cofiring, good adhesion between dielectric and substrate layers was obtained. Combing the buried resistors and capacitors together with the lamination of LTCC layer, a 3-dimensional multilayered ceramic package was fabricated. (author)

  15. Renewable carbohydrates are a potential high-density hydrogen carrier

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Y.-H. Percival [Biological Systems Engineering Department, 210-A Seitz Hall, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061 (United States); Institute for Critical Technology and Applied Sciences (ICTAS), Virginia Polytechnic Institute and State University, Blacksburg, VA 24061 (United States); DOE BioEnergy Science Center (BESC), Oak Ridge, TN 37831 (United States)

    2010-10-15

    The possibility of using renewable biomass carbohydrates as a potential high-density hydrogen carrier is discussed here. Gravimetric density of polysaccharides is 14.8 H{sub 2} mass% where water can be recycled from PEM fuel cells or 8.33% H{sub 2} mass% without water recycling; volumetric densities of polysaccharides are >100 kg of H{sup 2}/m{sup 3}. Renewable carbohydrates (e.g., cellulosic materials and starch) are less expensive based on GJ than are other hydrogen carriers, such as hydrocarbons, biodiesel, methanol, ethanol, and ammonia. Biotransformation of carbohydrates to hydrogen by cell-free synthetic (enzymatic) pathway biotransformation (SyPaB) has numerous advantages, such as high product yield (12 H{sub 2}/glucose unit), 100% selectivity, high energy conversion efficiency (122%, based on combustion energy), high-purity hydrogen generated, mild reaction conditions, low-cost of bioreactor, few safety concerns, and nearly no toxicity hazards. Although SyPaB may suffer from current low reaction rates, numerous approaches for accelerating hydrogen production rates are proposed and discussed. Potential applications of carbohydrate-based hydrogen/electricity generation would include hydrogen bioreactors, home-size electricity generators, sugar batteries for portable electronics, sugar-powered passenger vehicles, and so on. Developments in thermostable enzymes as standardized building blocks for cell-free SyPaB projects, use of stable and low-cost biomimetic NAD cofactors, and accelerating reaction rates are among the top research and development priorities. International collaborations are urgently needed to solve the above obstacles within a short time. (author)

  16. Pharmacologic management of isolated low high-density lipoprotein syndrome.

    Science.gov (United States)

    Bermúdez, Valmore; Cano, Raquel; Cano, Clímaco; Bermúdez, Fernando; Arraiz, Nailet; Acosta, Luis; Finol, Freddy; Pabón, María Rebeca; Amell, Anilsa; Reyna, Nadia; Hidalgo, Joaquin; Kendall, Paúl; Manuel, Velasco; Hernández, Rafael

    2008-01-01

    High-density lipoprotein (HDL) cholesterol is a heterogeneous group of lipoproteins exhibiting a variety of properties like prostacyclin production stimulation, decrease in platelet aggregation, endothelial cell apoptosis inhibition, and low-density lipoprotein oxidation blockade. Epidemiologic studies have shown an inverse relation between HDL cholesterol levels and cardiovascular risk. Low HDL cholesterol is associated with increased risk for myocardial infarction, stroke, sudden death, peripheral artery disease, and postangioplasty restenosis. In contrast, high HDL levels are associated with longevity and protection against atherosclerotic disease development. Given the evolving epidemic of obesity, diabetes mellitus, and metabolic syndrome, the prevalence of low HDL will continue to rise. In the United States, low HDL is present in 35% of men, 15% of women, and approximately 63% of patients with coronary artery disease. Data extracted from the Framingham study highlight that 1-mg increase in HDL levels decreases by 2% to 3% the risk of cardiovascular disease. There is no doubt regarding clinical importance about isolated low HDL, but relatively few clinicians consider a direct therapeutic intervention of this dyslipidemia. In this sense, lifestyle measures should be the first-line strategy to manage low HDL levels. On the other hand, pharmacologic options include niacin, fibrates, and statins. Fibrates appear to reduce risk preferentially in patients with low HDL with metabolic syndrome, whereas statins reduce risk across all levels of HDL. Torcetrapib, a cholesteryl esters transfer protein inhibitor, represented a hope to raise this lipoprotein; however, all clinical trials on this drug had ceased after ILLUMINATE, RADIANCE and ERASE trials had recorded an increase in mortality, rates of myocardial infarction, angina, and heart failure. In the near future, drugs as beta-glucans, Apo-A1 mimetic peptides, and ACAT inhibitors, are the new promises to treat this

  17. Neutron shielding properties of a new high-density concrete

    International Nuclear Information System (INIS)

    Lorente, A.; Gallego, E.; Vega Carrillo, H.R.; Mendez, R.

    2008-01-01

    The neutron shielding properties of a new high-density concrete (commercially available under the name Hormirad TM , developed in Spain by the company CT-RAD) have been characterized both experimentally and by Monte Carlo calculations. The shielding properties of this concrete against photons were previously studied and the material is being used to build bunkers, mazes and doors in medical accelerator facilities with good overall results. In this work, the objective was to characterize the material behaviour against neutrons, as well as to test alternative mixings including boron compounds in an effort to improve neutron shielding efficiency. With that purpose, Hormirad TM slabs of different thicknesses were exposed to an 241 Am-Be neutron source under controlled conditions in the neutron measurements laboratory of the Nuclear Engineering Department at UPM. The original mix, which includes a high fraction of magnetite, was then modified by adding different proportions of anhydrous borax (Na 2 B 4 O 7 ). In order to have a reference against common concrete used to shield medical accelerator facilities, the same experiment was repeated with ordinary (HA-25) concrete slabs. In parallel to the experiments, Monte Carlo calculations of the experiments were performed with MCNP5. The experimental results agree reasonably well with the Monte Carlo calculations. Therefore, the first and equilibrium tenth-value layers have been determined for the different types of concrete tested. The results show an advantageous behaviour of the Hormirad TM concrete, in terms of neutron attenuation against real thickness of the shielding. Borated concretes seem less practical since they did not show better neutron attenuation with respect to real thickness and their structural properties are worse. The neutron attenuation properties of Hormirad TM for typical neutron spectra in clinical LINAC accelerators rooms have been also characterized by Monte Carlo calculation. (author)

  18. Deposition and characterisation of copper for high density interconnects

    International Nuclear Information System (INIS)

    McCusker, N.

    1999-09-01

    Copper has been deposited by sputtering and investigated for application as high density interconnects, with a view to maximising its performance and reliability. A sputter deposition process using gettering has been developed, which produces consistently pure, low resistivity films. A relationship between film thickness and resistivity has been explained by studying the grain growth process in copper films using atomic force microscopy. The Maydas-Shatzkes model has been used to separate the contributions of grain boundary and surface scattering to thin film resistivity, in copper and gold. Stress and texture in copper film have been studied. Annealing has been used to promote grain growth and texture development. Electromigration has been studied in copper and aluminium interconnects using a multi-line accelerated test set-up. A difference in failure distributions and void morphologies has been explained by an entirely different damage mechanism. The importance of surface/interface migration in electromigration damage of copper lines has been established and explained using a grain boundary-grooving model. A tantalum overlayer was found to extend the lifetime of copper lines. A composite sputtering target has been used to deposit copper/zirconium alloy films. The composition of the alloys was studied by Rutherford backscattering, Auger and secondary neutral mass spectrometry. The alloy films had an improved electromigration lifetime. A surface controlled mechanism is proposed to explain the advantage. A metal oxide semiconductor (MOS) capacitor technique is used to investigate barrier reliability. Tungsten is shown to be an effective diffusion barrier for copper, up to 700 deg. C. (author)

  19. Modelling high density phenomena in hydrogen fibre Z-pinches

    International Nuclear Information System (INIS)

    Chittenden, J.P.

    1990-09-01

    The application of hydrogen fibre Z-pinches to the study of the radiative collapse phenomenon is studied computationally. Two areas of difficulty, the formation of a fully ionized pinch from a cryogenic fibre and the processes leading to collapse termination, are addressed in detail. A zero-D model based on the energy equation highlights the importance of particle end losses and changes in the Coulomb logarithm upon collapse initiation and termination. A 1-D Lagrangian resistive MHD code shows the importance of the changing radial profile shapes, particularly in delaying collapse termination. A 1-D, three fluid MHD code is developed to model the ionization of the fibre by thermal conduction from a high temperature surface corona to the cold core. Rate equations for collisional ionization, 3-body recombination and equilibration are solved in tandem with fluid equations for the electrons, ions and neutrals. Continuum lowering is found to assist ionization at the corona-core interface. The high density plasma phenomena responsible for radiative collapse termination are identified as the self-trapping of radiation and free electron degeneracy. A radiation transport model and computational analogues for the effects of degeneracy upon the equation of state, transport coefficients and opacity are implemented in the 1-D, single fluid model. As opacity increases the emergent spectrum is observed to become increasingly Planckian and a fall off in radiative cooling at small radii and low frequencies occurs giving rise to collapse termination. Electron degeneracy terminates radiative collapse by supplementing the radial pressure gradient until the electromagnetic pinch force is balanced. Collapse termination is found to be a hybrid process of opacity and degeneracy effects across a wide range of line densities with opacity dominant at large line densities but with electron degeneracy becoming increasingly important at lower line densities. (author)

  20. Biomimetic High-Density Lipoproteins from a Gold Nanoparticle Template

    Science.gov (United States)

    Luthi, Andrea Jane

    For hundreds of years the field of chemistry has looked to nature for inspiration and insight to develop novel solutions for the treatment of human diseases. The ability of chemists to identify, mimic, and modifiy small molecules found in nature has led to the discovery and development of many important therapeutics. Chemistry on the nanoscale has made it possible to mimic natural, macromolecular structures that may also be useful for understanding and treating diseases. One example of such a structure is high-density lipoprotein (HDL). The goal of this work is to use a gold nanoparticle (Au NP) as a template to synthesize functional mimics of HDL and characterize their structure and function. Chapter 1 details the structure and function of natural HDL and how chemistry on the nanoscale provides new strategies for mimicking HDL. This Chapter also describes the first examples of using nanoparticles to mimic HDL. Chapter 2 reports the synthesis and characterization of biomimetic HDL using different sizes of Au NPs and different surface chemistries and how these variables can be used to tailor the properties of biomimetic HDL. From these studies the optimal strategy for synthesizing biomimetic HDL was determined. In Chapter 3, the optimization of the synthesis of biomimetic HDL is discussed as well as a full characterization of its structure. In addition, the work in this chapter shows that biomimetic HDL can be synthesized on a large scale without alterations to its structure or function. Chapter 4 focuses on understanding the pathways by which biomimetic HDL accepts cholesterol from macrophage cells. The results of these studies demonstrate that biomimetic HDL is able to accept cholesterol by both active and passive pathways of cholesterol efflux. In Chapter 5 the preliminary results of in vivo studies to characterize the pharmacokinetics and pharmacodynamics of biomimetic HDL are presented. These studies suggest that biomimetic HDL traffics through tissues prone to

  1. Microbial diversity and activity in the Nematostella vectensis holobiont: insights from 16S rRNA gene sequencing, isolate genomes, and a pilot-scale survey of gene expression

    OpenAIRE

    Har, Jia Y.; Helbig, Tim; Lim, Ju H.; Fernando, Samodha C.; Reitzel, Adam M.; Penn, Kevin; Thompson, Janelle R.

    2015-01-01

    We have characterized the molecular and genomic diversity of the microbiota of the starlet sea anemone Nematostella vectensis, a cnidarian model for comparative developmental and functional biology and a year-round inhabitant of temperate salt marshes. Molecular phylogenetic analysis of 16S rRNA gene clone libraries revealed four ribotypes associated with N. vectensis at multiple locations and times. These associates include two novel ribotypes within the ε-Proteobacterial order Campylobacter...

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

    Science.gov (United States)

    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.

  3. Evidence for a close phylogenetic relationship between Melissococcus pluton, the causative agent of European foulbrood disease, and the genus Enterococcus.

    Science.gov (United States)

    Cai, J; Collins, M D

    1994-04-01

    The 16S rRNA gene sequence of Melissococcus pluton, the causative agent of European foulbrood disease, was determined in order to investigate the phylogenetic relationships between this organism and other low-G + C-content gram-positive bacteria. A comparative sequence analysis revealed that M. pluton is a close phylogenetic relative of the genus Enterococcus.

  4. Linking phylogenetic identities of bacteria to starch fermentation in an in vitro model of the large intestine by RNA-based stable isotope probing.

    Science.gov (United States)

    Kovatcheva-Datchary, Petia; Egert, Markus; Maathuis, Annet; Rajilić-Stojanović, Mirjana; de Graaf, Albert A; Smidt, Hauke; de Vos, Willem M; Venema, Koen

    2009-04-01

    Carbohydrates, including starches, are an important energy source for humans, and are known for their interactions with the microbiota in the digestive tract. Largely, those interactions are thought to promote human health. Using 16S ribosomal RNA (rRNA)-based stable isotope probing (SIP), we identified starch-fermenting bacteria under human colon-like conditions. To the microbiota of the TIM-2 in vitro model of the human colon 7.4 g l(-1) of [U-(13)C]-starch was added. RNA extracted from lumen samples after 0 (control), 2, 4 and 8 h was subjected to density-gradient ultracentrifugation. Terminal-restriction fragment length polymorphism (T-RFLP) fingerprinting and phylogenetic analyses of the labelled and unlabelled 16S rRNA suggested populations related to Ruminococcus bromii, Prevotella spp. and Eubacterium rectale to be involved in starch metabolism. Additionally, 16S rRNA related to that of Bifidobacterium adolescentis was abundant in all analysed fractions. While this might be due to the enrichment of high-GC RNA in high-density fractions, it could also indicate an active role in starch fermentation. Comparison of the T-RFLP fingerprints of experiments performed with labelled and unlabelled starch revealed Ruminococcus bromii as the primary degrader in starch fermentation in the studied model, as it was found to solely predominate in the labelled fractions. LC-MS analyses of the lumen and dialysate samples showed that, for both experiments, starch fermentation primarily yielded acetate, butyrate and propionate. Integration of molecular and metabolite data suggests metabolic cross-feeding in the system, where populations related to Ruminococcus bromii are the primary starch degrader, while those related to Prevotella spp., Bifidobacterium adolescentis and Eubacterium rectale might be further involved in the trophic chain.

  5. Testing the potential of a ribosomal 16S marker for DNA metabarcoding of insects

    Directory of Open Access Journals (Sweden)

    Vasco Elbrecht

    2016-04-01

    Full Text Available Cytochrome c oxidase I (COI is a powerful marker for DNA barcoding of animals, with good taxonomic resolution and a large reference database. However, when used for DNA metabarcoding, estimation of taxa abundances and species detection are limited due to primer bias caused by highly variable primer binding sites across the COI gene. Therefore, we explored the ability of the 16S ribosomal DNA gene as an alternative metabarcoding marker for species level assessments. Ten bulk samples, each containing equal amounts of tissue from 52 freshwater invertebrate taxa, were sequenced with the Illumina NextSeq 500 system. The 16S primers amplified three more insect species than the Folmer COI primers and amplified more equally, probably due to decreased primer bias. Estimation of biomass might be less biased with 16S than with COI, although variation in read abundances of two orders of magnitudes is still observed. According to these results, the marker choice depends on the scientific question. If the goal is to obtain a taxonomic identification at the species level, then COI is more appropriate due to established reference databases and known taxonomic resolution of this marker, knowing that a greater proportion of insects will be missed using COI Folmer primers. If the goal is to obtain a more comprehensive survey the 16S marker, which requires building a local reference database, or optimised degenerated COI primers could be more appropriate.

  6. Intrinsic challenges in ancient microbiome reconstruction using 16S rRNA gene amplification

    NARCIS (Netherlands)

    Ziesemer, K.A.; Mann, A.E.; Sankaranarayanan, K.; Schroeder, H.; Ozga, A.T.; Brandt, B.W.; Zaura, E.; Waters-Rist, A.; Hoogland, M.; Salazar-García, D.C.; Aldenderfer, M.; Speller, C.; Hendy, J.; Weston, D.A.; MacDonald, S.J.; Thomas, G.H.; Collins, M.J.; Lewis, C.M.; Hofman, C.; Warinner, C.

    2015-01-01

    To date, characterization of ancient oral (dental calculus) and gut (coprolite) microbiota has been primarily accomplished through a metataxonomic approach involving targeted amplification of one or more variable regions in the 16S rRNA gene. Specifically, the V3 region (E. coli 341-534) of this

  7. Detection and characterization of Pasteuria 16S rRNA gene sequences from nematodes and soils.

    Science.gov (United States)

    Duan, Y P; Castro, H F; Hewlett, T E; White, J H; Ogram, A V

    2003-01-01

    Various bacterial species in the genus Pasteuria have great potential as biocontrol agents against plant-parasitic nematodes, although study of this important genus is hampered by the current inability to cultivate Pasteuria species outside their host. To aid in the study of this genus, an extensive 16S rRNA gene sequence phylogeny was constructed and this information was used to develop cultivation-independent methods for detection of Pasteuria in soils and nematodes. Thirty new clones of Pasteuria 16S rRNA genes were obtained directly from nematodes and soil samples. These were sequenced and used to construct an extensive phylogeny of this genus. These sequences were divided into two deeply branching clades within the low-G + C, Gram-positive division; some sequences appear to represent novel species within the genus Pasteuria. In addition, a surprising degree of 16S rRNA gene sequence diversity was observed within what had previously been designated a single strain of Pasteuria penetrans (P-20). PCR primers specific to Pasteuria 16S rRNA for detection of Pasteuria in soils were also designed and evaluated. Detection limits for soil DNA were 100-10,000 Pasteuria endospores (g soil)(-1).

  8. Comparison of ViTEK 2, MALDI-TOF and Partial Sequencing of 16S ...

    African Journals Online (AJOL)

    All the strains were susceptible to Vancomycin, Linezolid and Rifampicin while they were all resistant to Penicillin, Fusidic acid, and Trimethoprim. Brevibacterium epidermidis were generally resistant to Erythromycin and Clindamycin while B. iodinum and B. oceani were susceptible. Conclusion - 16S rRNA identification is ...

  9. Problem-Based Test: Functional Analysis of Mutant 16S rRNAs

    Science.gov (United States)

    Szeberenyi, Jozsef

    2010-01-01

    Terms to be familiar with before you start to solve the test: ribosome, ribosomal subunits, antibiotics, point mutation, 16S, 5S, and 23S rRNA, Shine-Dalgarno sequence, mRNA, tRNA, palindrome, hairpin, restriction endonuclease, fMet-tRNA, peptidyl transferase, initiation, elongation, termination of translation, expression plasmid, transformation,…

  10. Prosthetic joint infection due to Lysobacter thermophilus diagnosed by 16S rRNA gene sequencing

    OpenAIRE

    B Dhawan; S Sebastian; R Malhotra; A Kapil; D Gautam

    2016-01-01

    We report the first case of prosthetic joint infection caused by Lysobacter thermophilus which was identified by 16S rRNA gene sequencing. Removal of prosthesis followed by antibiotic treatment resulted in good clinical outcome. This case illustrates the use of molecular diagnostics to detect uncommon organisms in suspected prosthetic infections.

  11. Prosthetic joint infection due to Lysobacter thermophilus diagnosed by 16S rRNA gene sequencing

    Directory of Open Access Journals (Sweden)

    B Dhawan

    2016-01-01

    Full Text Available We report the first case of prosthetic joint infection caused by Lysobacter thermophilus which was identified by 16S rRNA gene sequencing. Removal of prosthesis followed by antibiotic treatment resulted in good clinical outcome. This case illustrates the use of molecular diagnostics to detect uncommon organisms in suspected prosthetic infections.

  12. Characterization of hydrocortisone bioconversion and 16S RNA gene in Synechococcus nidulans cultures.

    Science.gov (United States)

    Rasoul-Amini, S; Ghasemi, Y; Morowvat, M H; Ghoshoon, M B; Raee, M J; Mosavi-Azam, S B; Montazeri-Najafabady, N; Nouri, F; Parvizi, R; Negintaji, N; Khoubani, S

    2010-01-01

    A unicellular cyanobacterium, Synechococcus nidulans (Pringsheim) Komárek, was isolated from paddy-fields and applied in the biotransformation experiment of hydrocortisone (1). This strain has not been previously tested for steroid bioconversion. Fermentation was carried out in BG-11 medium supplemented with 0.05% substrate at 25 degrees C for 14 days of incubation. The obtained products were chromatographically purified followed by their characterization using spectroscopic methods. 11beta,17beta-dihydroxyandrost-4-en-3-one (2), 11beta-hydroxyandrost-4-en-3,17-dione (3), and androst-4-ene-3,17-dione (4) were the main bioproducts in the hydrocortisone bioconversion. The observed bioreaction characteristics were the side chain degradation of the substrate to prepare compounds (2) and (3) following the 11beta-dehydroxylation for accumulation of the compound (4). Time course study showed the accumulation of the product (2) from the second day of the fermentation and compounds (3) and (4) from the third day. All the metabolites reached their maximum concentration in seven days. Cyanobacterial 16S rRNA gene was also amplified by PCR. Sequences were amplified using the universal prokaryotic primers which amplify a approximately 400-bp region of the 16S rRNA gene. PCR products were sequenced to confirm their authenticity as 16S rRNA gene of cyanobacteria. The result of PCR blasted with other sequenced cyanobacteria in NCBI showed 99% identity to the 16S small subunit rRNA of seven Synechococcus species.

  13. Human endothelial progenitor cells internalize high-density lipoprotein.

    Directory of Open Access Journals (Sweden)

    Kaemisa Srisen

    Full Text Available Endothelial progenitor cells (EPCs originate either directly from hematopoietic stem cells or from a subpopulation of monocytes. Controversial views about intracellular lipid traffic prompted us to analyze the uptake of human high density lipoprotein (HDL, and HDL-cholesterol in human monocytic EPCs. Fluorescence and electron microscopy were used to investigate distribution and intracellular trafficking of HDL and its associated cholesterol using fluorescent surrogates (bodipy-cholesterol and bodipy-cholesteryl oleate, cytochemical labels and fluorochromes including horseradish peroxidase and Alexa Fluor® 568. Uptake and intracellular transport of HDL were demonstrated after internalization periods from 0.5 to 4 hours. In case of HDL-Alexa Fluor® 568, bodipy-cholesterol and bodipy-cholesteryl oleate, a photooxidation method was carried out. HDL-specific reaction products were present in invaginations of the plasma membrane at each time of treatment within endocytic vesicles, in multivesicular bodies and at longer periods of uptake, also in lysosomes. Some HDL-positive endosomes were arranged in form of "strings of pearl"- like structures. HDL-positive multivesicular bodies exhibited intensive staining of limiting and vesicular membranes. Multivesicular bodies of HDL-Alexa Fluor® 568-treated EPCs showed multilamellar intra-vacuolar membranes. At all periods of treatment, labeled endocytic vesicles and organelles were apparent close to the cell surface and in perinuclear areas around the Golgi apparatus. No HDL-related particles could be demonstrated close to its cisterns. Electron tomographic reconstructions showed an accumulation of HDL-containing endosomes close to the trans-Golgi-network. HDL-derived bodipy-cholesterol was localized in endosomal vesicles, multivesicular bodies, lysosomes and in many of the stacked Golgi cisternae and the trans-Golgi-network Internalized HDL-derived bodipy-cholesteryl oleate was channeled into the lysosomal

  14. High density internal transport barriers for burning plasma operation

    Energy Technology Data Exchange (ETDEWEB)

    Ridolfini, V Pericoli [Associazione EURATOM-ENEA sulla Fusione, CR Frascati, Rome (Italy); Barbato, E [Associazione EURATOM-ENEA sulla Fusione, CR Frascati, Rome (Italy); Buratti, P [Associazione EURATOM-ENEA sulla Fusione, CR Frascati, Rome (Italy)] (and others)

    2005-12-15

    A tokamak plasma with internal transport barriers (ITBs) is the best candidate for a steady ITER operation, since the high energy confinement allows working at plasma currents (I{sub p}) lower than the reference scenario. To build and sustain an ITB at the ITER high density ({>=}10{sup 20} m{sup -3}) and largely dominant electron (e{sup -}) heating is not trivial in most existing tokamaks. FTU can instead meet both requests, thanks to its radiofrequency heating systems, lower hybrid (LH, up to 1.9 MW) and electron cyclotron (EC up to 1.2 MW). By the combined use of them, ITBs are obtained up to peak densities n{sub e0} > 1.3 x 10{sup 20} m{sup -3}, with central e{sup -} temperatures T{sub e0} {approx} 5.5 keV, and are sustained for as long as the heating pulse is applied (>35 confinement times, {tau}{sub E}). At n{sub e0} {approx} 0.8 x 10{sup 20} m{sup -3} T{sub e0} can be larger than 11 keV. Almost full current drive (CD) and an overall good steadiness is attained within about one {tau}{sub E}, 20 times faster than the ohmic current relaxation time. The ITB extends over a central region with an almost flat or slightly reversed q profile and q{sub min} {approx} 1.3 that is fully sustained by off-axis lower hybrid current drive. Consequent to this is the beneficial good alignment of the bootstrap current, generated by the ITB large pressure gradients, with the LH driven current. Reflectometry shows a clear change in the turbulence close to the ITB radius, consistent with the reduced e{sup -} transport. Ions (i{sup +}) are significantly heated via collisions, but thermal equilibrium with electrons cannot be attained since the e{sup -}-i{sup +} equipartition time is always 4-5 times longer than {tau}{sub E}. No degradation of the overall ion transport, rather a reduction of the i{sup +} heat diffusivity, is observed inside the ITB. The global confinement has been improved up to 1.6 times over the scaling predictions. The ITB radius can be controlled by adjusting the

  15. 16S pan-bacterial PCR can accurately identify patients with ventilator-associated pneumonia.

    Science.gov (United States)

    Conway Morris, Andrew; Gadsby, Naomi; McKenna, James P; Hellyer, Thomas P; Dark, Paul; Singh, Suveer; Walsh, Timothy S; McAuley, Danny F; Templeton, Kate; Simpson, A John; McMullan, Ronan

    2017-11-01

    Ventilator-associated pneumonia (VAP) remains a challenge to intensive care units, with secure diagnosis relying on microbiological cultures that take up to 72 hours to provide a result. We sought to derive and validate a novel, real-time 16S rRNA gene PCR for rapid exclusion of VAP. Bronchoalveolar lavage (BAL) was obtained from two independent cohorts of patients with suspected VAP. Patients were recruited in a 2-centre derivation cohort and a 12-centre confirmation cohort. Confirmed VAP was defined as growth of >10 4 colony forming units/ml on semiquantitative culture and compared with a 16S PCR assay. Samples were tested from 67 patients in the derivation cohort, 10 (15%) of whom had confirmed VAP. Using cycles to cross threshold (C t ) values as the result of the 16S PCR test, the area under the receiver operating characteristic (ROC) curve (AUROC) was 0.94 (95% CI 0.86 to 1.0, p<0.0001). Samples from 92 patients were available from the confirmation cohort, 26 (28%) of whom had confirmed VAP. The AUROC for C t in this cohort was 0.89 (95% CI 0.83 to 0.95, p<0.0001). This study has derived and assessed the diagnostic accuracy of a novel application for 16S PCR. This suggests that 16S PCR in BAL could be used as a rapid test in suspected VAP and may allow better stewardship of antibiotics. VAPRAPID trial ref NCT01972425. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/.

  16. High density plasma heating in the Tokamak à configuration variable

    International Nuclear Information System (INIS)

    Curchod, L.

    2011-04-01

    The Tokamak à Configuration Variable (TCV) is a medium size magnetic confinement thermonuclear fusion experiment designed for the study of the plasma performances as a function of its shape. It is equipped with a high power and highly flexible electron cyclotron heating (ECH) and current drive (ECCD) system. Up to 3 MW of 2 nd harmonic EC power in ordinary (O 2 ) or extraordinary (X 2 ) polarization can be injected from TCV low-field side via six independently steerable launchers. In addition, up to 1.5 MW of 3 rd harmonic EC power (X 3 ) can be launched along the EC resonance from the top of TCV vacuum vessel. At high density, standard ECH and ECCD are prevented by the appearance of a cutoff layer screening the access to the EC resonance at the plasma center. As a consequence, less than 50% of TCV density operational domain is accessible to X 2 and X 3 ECH. The electron Bernstein waves (EBW) have been proposed to overcome this limitation. EBW is an electrostatic mode propagating beyond the plasma cutoff without upper density limit. Since it cannot propagate in vacuum, it has to be excited by mode conversion of EC waves in the plasma. Efficient electron Bernstein waves heating (EBH) and current drive (EBCD) were previously performed in several fusion devices, in particular in the W7-AS stellarator and in the MAST spherical tokamak. In TCV, the conditions for an efficient O-X-B mode conversion (i.e. a steep density gradient at the O 2 plasma cutoff) are met at the edge of high confinement (H-mode) plasmas characterized by the appearance of a pedestal in the electron temperature and density profiles. TCV experiments have demonstrated the first EBW coupling to overdense plasmas in a medium aspect-ratio tokamak via O-X-B mode conversion. This thesis work focuses on several aspects of ECH and EBH in low and high density plasmas. Firstly, the experimental optimum angles for the O-X-B mode conversion is successfully compared to the full-wave mode conversion calculation

  17. Phylogenetic analysis of methanogens from the bovine rumen

    Directory of Open Access Journals (Sweden)

    Forster Robert J

    2001-05-01

    Full Text Available Abstract Background Interest in methanogens from ruminants has resulted from the role of methane in global warming and from the fact that cattle typically lose 6 % of ingested energy as methane. Several species of methanogens have been isolated from ruminants. However they are difficult to culture, few have been consistently found in high numbers, and it is likely that major species of rumen methanogens are yet to be identified. Results Total DNA from clarified bovine rumen fluid was amplified using primers specific for Archaeal 16S rRNA gene sequences (rDNA. Phylogenetic analysis of 41 rDNA sequences identified three clusters of methanogens. The largest cluster contained two distinct subclusters with rDNA sequences similar to Methanobrevibacter ruminantium 16S rDNA. A second cluster contained sequences related to 16S rDNA from Methanosphaera stadtmanae, an organism not previously described in the rumen. The third cluster contained rDNA sequences that may form a novel group of rumen methanogens. Conclusions The current set of 16S rRNA hybridization probes targeting methanogenic Archaea does not cover the phylogenetic diversity present in the rumen and possibly other gastro-intestinal tract environments. New probes and quantitative PCR assays are needed to determine the distribution of the newly identified methanogen clusters in rumen microbial communities.

  18. A renaissance for the pioneering 16S rRNA gene

    Energy Technology Data Exchange (ETDEWEB)

    Tringe, Susannah; Hugenholtz, Philip

    2008-09-07

    Culture-independent molecular surveys using the 16S rRNA gene have become a mainstay for characterizing microbial community structure over the last quarter century. More recently this approach has been overshadowed by metagenomics, which provides a global overview of a community's functional potential rather than just an inventory of its inhabitants. However, the pioneering 16S rRNA gene is making a comeback in its own right thanks to a number of methodological advancements including higher resolution (more sequences), analysis of multiple related samples (e.g. spatial and temporal series) and improved metadata and use of metadata. The standard conclusion that microbial ecosystems are remarkably complex and diverse is now being replaced by detailed insights into microbial ecology and evolution based only on this one historically important marker gene.

  19. A renaissance for the pioneering 16S rRNA gene.

    Science.gov (United States)

    Tringe, Susannah G; Hugenholtz, Philip

    2008-10-01

    Culture-independent molecular surveys using the 16S rRNA gene have become a mainstay for characterizing microbial community structure over the past quarter century. More recently this approach has been overshadowed by metagenomics, which provides a global overview of a community's functional potential rather than just an inventory of its inhabitants. However, the pioneering 16S rRNA gene is making a comeback in its own right thanks to a number of methodological advancements including higher resolution (more sequences), analysis of multiple related samples (e.g. spatial and temporal series) and improved metadata, and use of metadata. The standard conclusion that microbial ecosystems are remarkably complex and diverse is now being replaced by detailed insights into microbial ecology and evolution based only on this one historically important marker gene.

  20. Greengenes: Chimera-checked 16S rRNA gene database and workbenchcompatible in ARB

    Energy Technology Data Exchange (ETDEWEB)

    DeSantis, T.Z.; Hugenholtz, P.; Larsen, N.; Rojas, M.; Brodie,E.L; Keller, K.; Huber, T.; Dalevi, D.; Hu, P.; Andersen, G.L.

    2006-02-01

    A 16S rRNA gene database (http://greengenes.lbl.gov) addresses limitations of public repositories by providing chimera-screening, standard alignments and taxonomic classification using multiple published taxonomies. It was revealed that incongruent taxonomic nomenclature exists among curators even at the phylum-level. Putative chimeras were identified in 3% of environmental sequences and 0.2% of records derived from isolates. Environmental sequences were classified into 100 phylum-level lineages within the Archaea and Bacteria.

  1. [Characterization of Black and Dichothrix Cyanobacteria Based on the 16S Ribosomal RNA Gene Sequence

    Science.gov (United States)

    Ortega, Maya

    2010-01-01

    My project focuses on characterizing different cyanobacteria in thrombolitic mats found on the island of Highborn Cay, Bahamas. Thrombolites are interesting ecosystems because of the ability of bacteria in these mats to remove carbon dioxide from the atmosphere and mineralize it as calcium carbonate. In the future they may be used as models to develop carbon sequestration technologies, which could be used as part of regenerative life systems in space. These thrombolitic communities are also significant because of their similarities to early communities of life on Earth. I targeted two cyanobacteria in my research, Dichothrix spp. and whatever black is, since they are believed to be important to carbon sequestration in these thrombolitic mats. The goal of my summer research project was to molecularly identify these two cyanobacteria. DNA was isolated from each organism through mat dissections and DNA extractions. I ran Polymerase Chain Reactions (PCR) to amplify the 16S ribosomal RNA (rRNA) gene in each cyanobacteria. This specific gene is found in almost all bacteria and is highly conserved, meaning any changes in the sequence are most likely due to evolution. As a result, the 16S rRNA gene can be used for bacterial identification of different species based on the sequence of their 16S rRNA gene. Since the exact sequence of the Dichothrix gene was unknown, I designed different primers that flanked the gene based on the known sequences from other taxonomically similar cyanobacteria. Once the 16S rRNA gene was amplified, I cloned the gene into specialized Escherichia coli cells and sent the gene products for sequencing. Once the sequence is obtained, it will be added to a genetic database for future reference to and classification of other Dichothrix sp.

  2. Deteksi Keragaman Spesies Bakteri Metanogen Rumen Sapi Menggunakan Kloning Gen 16s Rrna dan Sekuensing

    OpenAIRE

    Noor, Shoffiana; Pramono, Hendro; Aziz, Saefuddin

    2014-01-01

    Ruminants produce methane gas which contributes to enhanced greenhouse effect in the atmosphere. Cattle issued the highest methane during the fermentation of feed in the rumen. Methane gas produced by methanogen bacteria in carbohydrates anaerobic fermentation. Methanogen bacteria are difficult to obtain diversity information because difficult cultured. One technique can be used is molecular rRNA 16S gene cloning and sequencing. This study was aims to determine the species diversity of methan...

  3. Phylogenetic Trees From Sequences

    Science.gov (United States)

    Ryvkin, Paul; Wang, Li-San

    In this chapter, we review important concepts and approaches for phylogeny reconstruction from sequence data.We first cover some basic definitions and properties of phylogenetics, and briefly explain how scientists model sequence evolution and measure sequence divergence. We then discuss three major approaches for phylogenetic reconstruction: distance-based phylogenetic reconstruction, maximum parsimony, and maximum likelihood. In the third part of the chapter, we review how multiple phylogenies are compared by consensus methods and how to assess confidence using bootstrapping. At the end of the chapter are two sections that list popular software packages and additional reading.

  4. Culture-Negative Endocarditis Diagnosed Using 16S DNA Polymerase Chain Reaction

    Directory of Open Access Journals (Sweden)

    Stephen Duffett

    2012-01-01

    Full Text Available 16S DNA polymerase chain reaction (PCR is a molecular amplification technique that can be used to identify bacterial pathogens in culture-negative endocarditis. Bacterial DNA can be isolated from surgically excised valve tissue or from blood collected in EDTA vials. Use of this technique is particularly helpful in identifying the bacterial pathogen in cases of culture-negative endocarditis. A case involving a 48-year-old man who presented with severe aortic regurgitation and a four-month prodrome of low-grade fever is reported. Blood and valve tissue cultures following valve replacement were negative. A valve tissue sample was sent for investigation with 16S DNA PCR, which successfully identified Streptococcus salivarius and was interpreted as the true diagnosis. A review of the literature suggests that 16S DNA PCR from valve tissue is a more sensitive diagnostic test than culture. It is also extremely specific, based on a sequence match of at least 500 base pairs.

  5. How conserved are the conserved 16S-rRNA regions?

    Directory of Open Access Journals (Sweden)

    Marcel Martinez-Porchas

    2017-02-01

    Full Text Available The 16S rRNA gene has been used as master key for studying prokaryotic diversity in almost every environment. Despite the claim of several researchers to have the best universal primers, the reality is that no primer has been demonstrated to be truly universal. This suggests that conserved regions of the gene may not be as conserved as expected. The aim of this study was to evaluate the conservation degree of the so-called conserved regions flanking the hypervariable regions of the 16S rRNA gene. Data contained in SILVA database (release 123 were used for the study. Primers reported as matches of each conserved region were assembled to form contigs; sequences sizing 12 nucleotides (12-mers were extracted from these contigs and searched into the entire set of SILVA sequences. Frequency analysis shown that extreme regions, 1 and 10, registered the lowest frequencies. 12-mer frequencies revealed segments of contigs that were not as conserved as expected (≤90%. Fragments corresponding to the primer contigs 3, 4, 5b and 6a were recovered from all sequences in SILVA database. Nucleotide frequency analysis in each consensus demonstrated that only a small fraction of these so-called conserved regions is truly conserved in non-redundant sequences. It could be concluded that conserved regions of the 16S rRNA gene exhibit considerable variation that has to be considered when using this gene as biomarker.

  6. Intrinsic challenges in ancient microbiome reconstruction using 16S rRNA gene amplification.

    Science.gov (United States)

    Ziesemer, Kirsten A; Mann, Allison E; Sankaranarayanan, Krithivasan; Schroeder, Hannes; Ozga, Andrew T; Brandt, Bernd W; Zaura, Egija; Waters-Rist, Andrea; Hoogland, Menno; Salazar-García, Domingo C; Aldenderfer, Mark; Speller, Camilla; Hendy, Jessica; Weston, Darlene A; MacDonald, Sandy J; Thomas, Gavin H; Collins, Matthew J; Lewis, Cecil M; Hofman, Corinne; Warinner, Christina

    2015-11-13

    To date, characterization of ancient oral (dental calculus) and gut (coprolite) microbiota has been primarily accomplished through a metataxonomic approach involving targeted amplification of one or more variable regions in the 16S rRNA gene. Specifically, the V3 region (E. coli 341-534) of this gene has been suggested as an excellent candidate for ancient DNA amplification and microbial community reconstruction. However, in practice this metataxonomic approach often produces highly skewed taxonomic frequency data. In this study, we use non-targeted (shotgun metagenomics) sequencing methods to better understand skewed microbial profiles observed in four ancient dental calculus specimens previously analyzed by amplicon sequencing. Through comparisons of microbial taxonomic counts from paired amplicon (V3 U341F/534R) and shotgun sequencing datasets, we demonstrate that extensive length polymorphisms in the V3 region are a consistent and major cause of differential amplification leading to taxonomic bias in ancient microbiome reconstructions based on amplicon sequencing. We conclude that systematic amplification bias confounds attempts to accurately reconstruct microbiome taxonomic profiles from 16S rRNA V3 amplicon data generated using universal primers. Because in silico analysis indicates that alternative 16S rRNA hypervariable regions will present similar challenges, we advocate for the use of a shotgun metagenomics approach in ancient microbiome reconstructions.

  7. 211At-Rh(16-S4-diol) complex as a precursor for astatine radiopharmaceuticals

    International Nuclear Information System (INIS)

    Pruszynski, M.; Bilewicz, A.

    2006-01-01

    211 At is one of the most promising radionuclides in α-radioimmunotherapy (α-RIT). Unfortunately, biomolecules labeled by direct electrophilic astatination are unstable due to the rapid loss of 211 At under both in vitro and in vivo conditions. The present paper describes the results of our studies on attaching At - to the rhodium(III) complex with thioether ligand: 1,5,9,13-etrathiacyclohexadecane-3,11-diol (16-S4-diol). Rh 3+ was chosen as a moderately soft metal cation which should form very strong bonds with soft At - anions, but first of all because of the kinetic inertness of low spin rhodium(III) d 6 complexes. The 16-S4-diol ligand was selected due to formation of stable complexes with Rh 3+ . The experiments related to optimization of the reaction conditions were performed with the 131 I, basing on a chemical similarity of I - to At - . The experiments with 211 At were then carried out under the conditions found optimal for I - . The preliminary results are promising, and indicate a possibility for astatination of biomolecules by using the 211 At-Rh(16-S4-diol) complex

  8. Nested polymerase chain reaction (PCR) targeting 16S rDNA for bacterial identification in empyema.

    Science.gov (United States)

    Prasad, Rajniti; Kumari, Chhaya; Das, B K; Nath, Gopal

    2014-05-01

    Empyema in children causes significant morbidity and mortality. However, identification of organisms is a major concern. To detect bacterial pathogens in pus specimens of children with empyema by 16S rDNA nested polymerase chain reaction (PCR) and correlate it with culture and sensitivity. Sixty-six children admitted to the paediatric ward with a diagnosis of empyema were enrolled prospectively. Aspirated pus was subjected to cytochemical examination, culture and sensitivity, and nested PCR targeting 16S rDNA using a universal eubacterial primer. Mean (SD) age was 5·8 (1·8) years (range 1-13). Analysis of aspirated pus demonstrated total leucocyte count >1000×10(6)/L, elevated protein (≧20 g/L) and decreased glucose (≤2·2 mmol/L) in 80·3%, 98·5% and 100%, respectively. Gram-positive cocci were detected in 29 (43·9%) and Gram-negative bacilli in two patients. Nested PCR for the presence of bacterial pathogens was positive in 50·0%, compared with 36·3% for culture. 16S rDNA PCR improves rates of detection of bacteria in pleural fluid, and can detect bacterial species in a single assay as well as identifying unusual and unexpected causal agents.

  9. 16S rRNA gene-based association study identified microbial taxa associated with pork intramuscular fat content in feces and cecum lumen.

    Science.gov (United States)

    Fang, Shaoming; Xiong, Xingwei; Su, Ying; Huang, Lusheng; Chen, Congying

    2017-07-19

    Intramuscular fat (IMF) that deposits among muscle fibers or within muscle cells is an important meat quality trait in pigs. Previous studies observed the effects of dietary nutrients and additives on improving the pork IMF. Gut microbiome plays an important role in host metabolism and energy harvest. Whether gut microbiota exerts effect on IMF remains unknown. In this study, we investigated the microbial community structure of 500 samples from porcine cecum and feces using high-throughput 16S rRNA gene sequencing. We found that phylogenetic composition and potential function capacity of microbiome varied between two types of samples. Bacteria wide association study identified 119 OTUs significantly associated with IMF in the two types of samples (FDR microbiome associated with IMF might be caused by the IMF-associated microbial taxa. This study firstly evaluated the contribution of gut microbiome to porcine IMF content. The results presented a potential capacity for improving IMF through modulating gut microbiota.

  10. Identification of Raoultella terrigena as a Rare Causative Agent of Subungual Abscess Based on 16S rRNA and Housekeeping Gene Sequencing

    Directory of Open Access Journals (Sweden)

    Yu Wang

    2016-01-01

    Full Text Available A 63-year-old-man was admitted to our hospital with severe subungual abscess. Bacteria were isolated from pus samples, and an inconsistent identification was shown by VITEK 2 system and MALDI-TOF mass spectrometry as Raoultella planticola and Raoultella terrigena, respectively. Molecular identification by 16S rRNA sequencing suggested that the isolate is R. terrigena, and this was further demonstrated by sequencing three housekeeping genes (rpoB, gyrA, and parC with phylogenetic analysis. To our knowledge, this is the first report of subungual abscess caused by R. terrigena, a rare case of human infection due to soil bacterium. Our study highlights the technique importance on this pathogen identification.

  11. Conservative fragments in bacterial 16S rRNA genes and primer design for 16S ribosomal DNA amplicons in metagenomic studies

    KAUST Repository

    Wang, Yong

    2009-10-09

    Bacterial 16S ribosomal DNA (rDNA) amplicons have been widely used in the classification of uncultured bacteria inhabiting environmental niches. Primers targeting conservative regions of the rDNAs are used to generate amplicons of variant regions that are informative in taxonomic assignment. One problem is that the percentage coverage and application scope of the primers used in previous studies are largely unknown. In this study, conservative fragments of available rDNA sequences were first mined and then used to search for candidate primers within the fragments by measuring the coverage rate defined as the percentage of bacterial sequences containing the target. Thirty predicted primers with a high coverage rate (>90%) were identified, which were basically located in the same conservative regions as known primers in previous reports, whereas 30% of the known primers were associated with a coverage rate of <90%. The application scope of the primers was also examined by calculating the percentages of failed detections in bacterial phyla. Primers A519-539, E969- 983, E1063-1081, U515 and E517, are highly recommended because of their high coverage in almost all phyla. As expected, the three predominant phyla, Firmicutes, Gemmatimonadetes and Proteobacteria, are best covered by the predicted primers. The primers recommended in this report shall facilitate a comprehensive and reliable survey of bacterial diversity in metagenomic studies. © 2009 Wang, Qian.

  12. Compensated readout for high-density MOS-gated memristor crossbar array

    KAUST Repository

    Zidan, Mohammed A.

    2015-01-01

    Leakage current is one of the main challenges facing high-density MOS-gated memristor arrays. In this study, we show that leakage current ruins the memory readout process for high-density arrays, and analyze the tradeoff between the array density and its power consumption. We propose a novel readout technique and its underlying circuitry, which is able to compensate for the transistor leakage-current effect in the high-density gated memristor array.

  13. Towards high-density matter with relativistic heavy-ion collisions

    International Nuclear Information System (INIS)

    Nagamiya, Shoji.

    1990-04-01

    Recent progress in nucleus-nucleus collisions at BNL and CERN suggests a hint that the formation of high-density nuclear matter could be possible with relativistic heavy-ion beams. What is the maximum density that can be achieved by heavy-ion collisions? Are there data which show evidence or hints on the formation of high density matter? Why is the research of high-density interesting? How about the future possibilities on this subject? These points are discussed. (author)

  14. Differential detection of type II methanotrophic bacteria in acidic peatlands using newly developed 16S rRNA-targeted fluorescent oligonucleotide probes.

    Science.gov (United States)

    Dedysh, Svetlana N; Dunfield, Peter F; Derakshani, Manigee; Stubner, Stephan; Heyer, Jürgen; Liesack, Werner

    2003-04-01

    Abstract Based on an extensive 16S rRNA sequence database for type II methanotrophic bacteria, a set of 16S rRNA-targeted oligonucleotide probes was developed for differential detection of specific phylogenetic groups of these bacteria by fluorescence in situ hybridisation (FISH). This set of oligonucleotides included a genus-specific probe for Methylocystis (Mcyst-1432) and three species-specific probes for Methylosinus sporium (Msins-647), Methylosinus trichosporium (Msint-1268) and the recently described acidophilic methanotroph Methylocapsa acidiphila (Mcaps-1032). These novel probes were applied to further characterise the type II methanotroph community that was detected in an acidic Sphagnum peat from West Siberia in a previous study (Dedysh et al. (2001) Appl. Environ. Microbiol. 67, 4850-4857). The largest detectable population of indigenous methanotrophs simultaneously hybridised with a group-specific probe targeting all currently known Methylosinus/Methylocystis spp. (M-450), with a genus-specific probe for Methylocystis spp. (Mcyst-1432), and with an additional probe (Mcyst-1261) that had been designed to target a defined phylogenetic subgroup of Methylocystis spp. The same subgroup of Methylocystis was also detected in acidic peat sampled from Sphagnum-dominated wetland in northern Germany. The population size of this peat-inhabiting Methylocystis subgroup was 2.0+/-0.1x10(6) cells g(-1) (wet weight) of peat from Siberia and 5.5+/-0.5x10(6) cells g(-1) of peat from northern Germany. This represented 60 and 95%, respectively, of the total number of methanotroph cells detected by FISH in these two wetland sites. Other major methanotroph populations were M. acidiphila and Methylocella palustris. Type I methanotrophs accounted for not more than 1% of total methanotroph cells. Neither M. trichosporium nor M. sporium were detected in acidic Sphagnum peat.

  15. High Channel Count, High Density Microphone Arrays for Wind Tunnel Environments, Phase I

    Data.gov (United States)

    National Aeronautics and Space Administration — The Interdisciplinary Consulting Corporation (IC2) proposes the development of high channel count, high density, reduced cost per channel, directional microphone...

  16. Sequencing of 16S rRNA gene for id ntification of Sta h lococcus ...

    African Journals Online (AJOL)

    Asdmin

    2014-01-15

    Jan 15, 2014 ... as the type strains of a species of genus Trichoderma based on phylogenetic tree analysis together with the 18S rRNA gene sequence search in Ribosomal Database Project, small subunit rRNA and large subunit rRNA databases. The sequence was deposited in GenBank with the accession numbers.

  17. Bacterial community structure in High-Arctic snow and freshwater as revealed by pyrosequencing of 16S rRNA genes and cultivation

    Directory of Open Access Journals (Sweden)

    Annette K. Møller

    2013-04-01

    Full Text Available The bacterial community structures in High-Arctic snow over sea ice and an ice-covered freshwater lake were examined by pyrosequencing of 16S rRNA genes and 16S rRNA gene sequencing of cultivated isolates. Both the pyrosequence and cultivation data indicated that the phylogenetic composition of the microbial assemblages was different within the snow layers and between snow and freshwater. The highest diversity was seen in snow. In the middle and top snow layers, Proteobacteria, Bacteroidetes and Cyanobacteria dominated, although Actinobacteria and Firmicutes were relatively abundant also. High numbers of chloroplasts were also observed. In the deepest snow layer, large percentages of Firmicutes and Fusobacteria were seen. In freshwater, Bacteroidetes, Actinobacteria and Verrucomicrobia were the most abundant phyla while relatively few Proteobacteria and Cyanobacteria were present. Possibly, light intensity controlled the distribution of the Cyanobacteria and algae in the snow while carbon and nitrogen fixed by these autotrophs in turn fed the heterotrophic bacteria. In the lake, a probable lower light input relative to snow resulted in low numbers of Cyanobacteria and chloroplasts and, hence, limited input of organic carbon and nitrogen to the heterotrophic bacteria. Thus, differences in the physicochemical conditions may play an important role in the processes leading to distinctive bacterial community structures in High-Arctic snow and freshwater.

  18. Analysis of 16S rRNA and mxaF genes revealing insights into Methylobacterium niche-specific plant association

    Science.gov (United States)

    Dourado, Manuella Nóbrega; Andreote, Fernando Dini; Dini-Andreote, Francisco; Conti, Raphael; Araújo, Janete Magali; Araújo, Welington Luiz

    2012-01-01

    The genus Methylobacterium comprises pink-pigmented facultative methylotrophic (PPFM) bacteria, known to be an important plant-associated bacterial group. Species of this group, described as plant-nodulating, have the dual capacity of producing cytokinin and enzymes, such as pectinase and cellulase, involved in systemic resistance induction and nitrogen fixation under specific plant environmental conditions. The aim hereby was to evaluate the phylogenetic distribution of Methylobacterium spp. isolates from different host plants. Thus, a comparative analysis between sequences from structural (16S rRNA) and functional mxaF (which codifies for a subunit of the enzyme methanol dehydrogenase) ubiquitous genes, was undertaken. Notably, some Methylobacterium spp. isolates are generalists through colonizing more than one host plant, whereas others are exclusively found in certain specific plant-species. Congruency between phylogeny and specific host inhabitance was higher in the mxaF gene than in the 16S rRNA, a possible indication of function-based selection in this niche. Therefore, in a first stage, plant colonization by Methylobacterium spp. could represent generalist behavior, possibly related to microbial competition and adaptation to a plant environment. Otherwise, niche-specific colonization is apparently impelled by the host plant. PMID:22481887

  19. Analysis of 16S rRNA and mxaF genes reveling insights into Methylobacterium niche-specific plant association

    Directory of Open Access Journals (Sweden)

    Manuella Nóbrega Dourado

    2012-01-01

    Full Text Available The genus Methylobacterium comprises pink-pigmented facultative methylotrophic (PPFM bacteria, known to be an important plant-associated bacterial group. Species of this group, described as plant-nodulating, have the dual capacity of producing cytokinin and enzymes, such as pectinase and cellulase, involved in systemic resistance induction and nitrogen fixation under specific plant environmental conditions. The aim hereby was to evaluate the phylogenetic distribution of Methylobacterium spp. isolates from different host plants. Thus, a comparative analysis between sequences from structural (16S rRNA and functional mxaF (which codifies for a subunit of the enzyme methanol dehydrogenase ubiquitous genes, was undertaken. Notably, some Methylobacterium spp. isolates are generalists through colonizing more than one host plant, whereas others are exclusively found in certain specific plant-species. Congruency between phylogeny and specific host inhabitance was higher in the mxaF gene than in the 16S rRNA, a possible indication of function-based selection in this niche. Therefore, in a first stage, plant colonization by Methylobacterium spp. could represent generalist behavior, possibly related to microbial competition and adaptation to a plant environment. Otherwise, niche-specific colonization is apparently impelled by the host plant.

  20. Analysis of 16S rRNA and mxaF genes revealing insights into Methylobacterium niche-specific plant association.

    Science.gov (United States)

    Dourado, Manuella Nóbrega; Andreote, Fernando Dini; Dini-Andreote, Francisco; Conti, Raphael; Araújo, Janete Magali; Araújo, Welington Luiz

    2012-01-01

    The genus Methylobacterium comprises pink-pigmented facultative methylotrophic (PPFM) bacteria, known to be an important plant-associated bacterial group. Species of this group, described as plant-nodulating, have the dual capacity of producing cytokinin and enzymes, such as pectinase and cellulase, involved in systemic resistance induction and nitrogen fixation under specific plant environmental conditions. The aim hereby was to evaluate the phylogenetic distribution of Methylobacterium spp. isolates from different host plants. Thus, a comparative analysis between sequences from structural (16S rRNA) and functional mxaF (which codifies for a subunit of the enzyme methanol dehydrogenase) ubiquitous genes, was undertaken. Notably, some Methylobacterium spp. isolates are generalists through colonizing more than one host plant, whereas others are exclusively found in certain specific plant-species. Congruency between phylogeny and specific host inhabitance was higher in the mxaF gene than in the 16S rRNA, a possible indication of function-based selection in this niche. Therefore, in a first stage, plant colonization by Methylobacterium spp. could represent generalist behavior, possibly related to microbial competition and adaptation to a plant environment. Otherwise, niche-specific colonization is apparently impelled by the host plant.

  1. Bacterial communities in haloalkaliphilic sulfate-reducing bioreactors under different electron donors revealed by 16S rRNA MiSeq sequencing

    Energy Technology Data Exchange (ETDEWEB)

    Zhou, Jiemin [National Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, P.O. Box 353, Beijing 100190 (China); University of Chinese Academy of Sciences, Beijing 100049 (China); Zhou, Xuemei; Li, Yuguang [101 Institute, Ministry of Civil Affairs, Beijing 100070 (China); Xing, Jianmin, E-mail: jmxing@ipe.ac.cn [National Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, P.O. Box 353, Beijing 100190 (China)

    2015-09-15

    Highlights: • Bacterial communities of haloalkaliphilic bioreactors were investigated. • MiSeq was first used in analysis of communities of haloalkaliphilic bioreactors. • Electron donors had significant effect on bacterial communities. - Abstract: Biological technology used to treat flue gas is useful to replace conventional treatment, but there is sulfide inhibition. However, no sulfide toxicity effect was observed in haloalkaliphilic bioreactors. The performance of the ethanol-fed bioreactor was better than that of lactate-, glucose-, and formate-fed bioreactor, respectively. To support this result strongly, Illumina MiSeq paired-end sequencing of 16S rRNA gene was applied to investigate the bacterial communities. A total of 389,971 effective sequences were obtained and all of them were assigned to 10,220 operational taxonomic units (OTUs) at a 97% similarity. Bacterial communities in the glucose-fed bioreactor showed the greatest richness and evenness. The highest relative abundance of sulfate-reducing bacteria (SRB) was found in the ethanol-fed bioreactor, which can explain why the performance of the ethanol-fed bioreactor was the best. Different types of SRB, sulfur-oxidizing bacteria, and sulfur-reducing bacteria were detected, indicating that sulfur may be cycled among these microorganisms. Because high-throughput 16S rRNA gene paired-end sequencing has improved resolution of bacterial community analysis, many rare microorganisms were detected, such as Halanaerobium, Halothiobacillus, Desulfonatronum, Syntrophobacter, and Fusibacter. 16S rRNA gene sequencing of these bacteria would provide more functional and phylogenetic information about the bacterial communities.

  2. Enterohemorrhagic Escherichia coli O157 in milk and dairy products from Libya: Isolation and molecular identification by partial sequencing of 16S rDNA

    Directory of Open Access Journals (Sweden)

    Aboubaker M. Garbaj

    2016-11-01

    Full Text Available Aim: The aim of this work was to isolate and molecularly identify enterohemorrhagic Escherichia coli (EHEC O157 in milk and dairy products in Libya, in addition; to clear the accuracy of cultural and biochemical identification as compared with molecular identification by partial sequencing of 16S rDNA for the existing isolates. Materials and Methods: A total of 108 samples of raw milk (cow, she-camel, and goat and locally made dairy products (fermented cow’s milk, Maasora, Ricotta and ice cream were collected from some regions (Janzour, Tripoli, Kremiya, Tajoura and Tobruk in Libya. Samples were subjected to microbiological analysis for isolation of E. coli that was detected by conventional cultural and molecular method using polymerase chain reaction and partial sequencing of 16S rDNA. Results: Out of 108 samples, only 27 isolates were found to be EHEC O157 based on their cultural characteristics (Tellurite-Cefixime-Sorbitol MacConkey that include 3 isolates from cow’s milk (11%, 3 isolates from she-camel’s milk (11%, two isolates from goat’s milk (7.4% and 7 isolates from fermented raw milk samples (26%, isolates from fresh locally made soft cheeses (Maasora and Ricotta were 9 (33% and 3 (11%, respectively, while none of the ice cream samples revealed any growth. However, out of these 27 isolates, only 11 were confirmed to be E. coli by partial sequencing of 16S rDNA and E. coli O157 Latex agglutination test. Phylogenetic analysis revealed that majority of local E. coli isolates were related to E. coli O157:H7 FRIK944 strain. Conclusion: These results can be used for further studies on EHEC O157 as an emerging foodborne pathogen and its role in human infection in Libya.

  3. Clinical identification of bacteria in human chronic wound infections: culturing vs. 16S ribosomal DNA sequencing

    Directory of Open Access Journals (Sweden)

    Rhoads Daniel D

    2012-11-01

    Full Text Available Abstract Background Chronic wounds affect millions of people and cost billions of dollars in the United States each year. These wounds harbor polymicrobial biofilm communities, which can be difficult to elucidate using culturing methods. Clinical molecular microbiological methods are increasingly being employed to investigate the microbiota of chronic infections, including wounds, as part of standard patient care. However, molecular testing is more sensitive than culturing, which results in markedly different results being reported to clinicians. This study compares the results of aerobic culturing and molecular testing (culture-free 16S ribosomal DNA sequencing, and it examines the relative abundance score that is generated by the molecular test and the usefulness of the relative abundance score in predicting the likelihood that the same organism would be detected by culture. Methods Parallel samples from 51 chronic wounds were studied using aerobic culturing and 16S DNA sequencing for the identification of bacteria. Results One hundred forty-five (145 unique genera were identified using molecular methods, and 68 of these genera were aerotolerant. Fourteen (14 unique genera were identified using aerobic culture methods. One-third (31/92 of the cultures were determined to be Staphylococcus aureus, Pseudomonas aeruginosa, and Enterococcus faecalis with higher relative abundance scores were more likely to be detected by culture as demonstrated with regression modeling. Conclusion Discordance between molecular and culture testing is often observed. However, culture-free 16S ribosomal DNA sequencing and its relative abundance score can provide clinicians with insight into which bacteria are most abundant in a sample and which are most likely to be detected by culture.

  4. Globicatella sanguinis bacteraemia identified by partial 16S rRNA gene sequencing

    DEFF Research Database (Denmark)

    Abdul-Redha, Rawaa Jalil; Balslew, Ulla; Christensen, Jens Jørgen

    2007-01-01

    Globicatella sanguinis is a gram-positive coccus, resembling non-haemolytic streptococci. The organism has been isolated infrequently from normally sterile sites of humans. Three isolates obtained by blood culture could not be identified by Rapid 32 ID Strep, but partial sequencing of the 16S r......RNA gene revealed the identity of the isolated bacteria, and supplementary biochemical tests confirmed the species identification. The cases histories illustrate the dilemma of finding relevant, newly recognized, opportunistic pathogens and the identification achievement (s) that can be obtained by using...

  5. Global Perspectives on Activated Sludge Community Composition analyzed using 16S rRNA amplicon sequencing

    DEFF Research Database (Denmark)

    Nierychlo, Marta; Saunders, Aaron Marc; Albertsen, Mads

    communities, and in this study activated sludge sampled from 32 Wastewater Treatment Plants (WWTPs) around the world was described and compared. The top abundant bacteria in the global activated sludge ecosystem were found and the core population shared by multiple samples was investigated. The results......Activated sludge is the most commonly applied bioprocess throughout the world for wastewater treatment. Microorganisms are key to the process, yet our knowledge of their identity and function is still limited. High-througput16S rRNA amplicon sequencing can reliably characterize microbial...

  6. Low voltage electroosmotic pump for high density integration into microfabricated fluidic systems

    NARCIS (Netherlands)

    Heuck, F.C.A.; Staufer, U.

    2011-01-01

    A low voltage electroosmotic (eo) pump suitable for high density integration into microfabricated fluidic systems has been developed. The high density integration of the eo pump required a small footprint as well as a specific on-chip design to ventilate the electrolyzed gases emerging at the

  7. The phylogenetic likelihood library.

    Science.gov (United States)

    Flouri, T; Izquierdo-Carrasco, F; Darriba, D; Aberer, A J; Nguyen, L-T; Minh, B Q; Von Haeseler, A; Stamatakis, A

    2015-03-01

    We introduce the Phylogenetic Likelihood Library (PLL), a highly optimized application programming interface for developing likelihood-based phylogenetic inference and postanalysis software. The PLL implements appropriate data structures and functions that allow users to quickly implement common, error-prone, and labor-intensive tasks, such as likelihood calculations, model parameter as well as branch length optimization, and tree space exploration. The highly optimized and parallelized implementation of the phylogenetic likelihood function and a thorough documentation provide a framework for rapid development of scalable parallel phylogenetic software. By example of two likelihood-based phylogenetic codes we show that the PLL improves the sequential performance of current software by a factor of 2-10 while requiring only 1 month of programming time for integration. We show that, when numerical scaling for preventing floating point underflow is enabled, the double precision likelihood calculations in the PLL are up to 1.9 times faster than those in BEAGLE. On an empirical DNA dataset with 2000 taxa the AVX version of PLL is 4 times faster than BEAGLE (scaling enabled and required). The PLL is available at http://www.libpll.org under the GNU General Public License (GPL). © The Author(s) 2014. Published by Oxford University Press, on behalf of the Society of Systematic Biologists.

  8. Accuracy of taxonomy prediction for 16S rRNA and fungal ITS sequences

    Directory of Open Access Journals (Sweden)

    Robert C. Edgar

    2018-04-01

    Full Text Available Prediction of taxonomy for marker gene sequences such as 16S ribosomal RNA (rRNA is a fundamental task in microbiology. Most experimentally observed sequences are diverged from reference sequences of authoritatively named organisms, creating a challenge for prediction methods. I assessed the accuracy of several algorithms using cross-validation by identity, a new benchmark strategy which explicitly models the variation in distances between query sequences and the closest entry in a reference database. When the accuracy of genus predictions was averaged over a representative range of identities with the reference database (100%, 99%, 97%, 95% and 90%, all tested methods had ≤50% accuracy on the currently-popular V4 region of 16S rRNA. Accuracy was found to fall rapidly with identity; for example, better methods were found to have V4 genus prediction accuracy of ∼100% at 100% identity but ∼50% at 97% identity. The relationship between identity and taxonomy was quantified as the probability that a rank is the lowest shared by a pair of sequences with a given pair-wise identity. With the V4 region, 95% identity was found to be a twilight zone where taxonomy is highly ambiguous because the probabilities that the lowest shared rank between pairs of sequences is genus, family, order or class are approximately equal.

  9. Caracterização de rizóbios indicados para produção de inoculantes por meio de sequenciamento parcial do 16S rRNA Characterization of rhizobia indicated for inoculant production using 16S rRNA partial sequencing

    Directory of Open Access Journals (Sweden)

    Bethânia Figueiredo Barbosa de Toledo

    2009-04-01

    Full Text Available O objetivo deste trabalho foi confrontar as sequências parciais do gene 16S rRNA de estirpes padrão de rizóbios com as de estirpes recomendadas para a produção de inoculantes no Brasil, com vistas à verificação da confiabilidade do sequenciamento parcial desse gene para a identificação rápida de estirpes. Foram realizados sequenciamentos através de reação em cadeia da polimerase (PCR com iniciadores relativos à região codificadora do gene 16S rRNA entre as bactérias estudadas. Os resultados foram analisados pela consulta de similaridade de nucleotídeos aos do "Basic Local Alignment Search Tool" (Blastn e por meio da interpretação de árvores filogenéticas geradas usando ferramentas de bioinformática. A classificação taxonômica das estirpes Semia recomendadas para inoculação de leguminosas com base em propriedades morfológicas e especificidade hospedeira não foi confirmada em todas as estirpes. A maioria das estirpes estudadas, consultadas no Blastn, é consistente com a classificação proposta pela construção de árvores filogenéticas das sequências destas estirpes, com base na similaridade pelo sequenciamento parcial do gene considerado.The aim of this work was to compare the partial sequences of 16S rRNA gene of rhizobia strain patterns already classified with strains recommended for the production of inoculants in Brazil, in order to verify the reliability of partial sequencing of the gene for the purpose of rapid identification of strains. Polymerase Chain Reaction (PCR sequencing using primers on the coding region of the 16S rRNA gene among the bacteria studied was conducted. The results were analyzed by consulting the nucleotides' similarity based on Basic Local Alignment Search Tool (Blastn and by interpreting the phylogenetic trees generated by bioinformatic tools. The taxonomic classification of Semia strains recommended for legume inoculation based on morphological properties and host specificity was

  10. Phylogenetic diversity and biodiversity indices on phylogenetic networks.

    Science.gov (United States)

    Wicke, Kristina; Fischer, Mareike

    2018-04-01

    In biodiversity conservation it is often necessary to prioritize the species to conserve. Existing approaches to prioritization, e.g. the Fair Proportion Index and the Shapley Value, are based on phylogenetic trees and rank species according to their contribution to overall phylogenetic diversity. However, in many cases evolution is not treelike and thus, phylogenetic networks have been developed as a generalization of phylogenetic trees, allowing for the representation of non-treelike evolutionary events, such as hybridization. Here, we extend the concepts of phylogenetic diversity and phylogenetic diversity indices from phylogenetic trees to phylogenetic networks. On the one hand, we consider the treelike content of a phylogenetic network, e.g. the (multi)set of phylogenetic trees displayed by a network and the so-called lowest stable ancestor tree associated with it. On the other hand, we derive the phylogenetic diversity of subsets of taxa and biodiversity indices directly from the internal structure of the network. We consider both approaches that are independent of so-called inheritance probabilities as well as approaches that explicitly incorporate these probabilities. Furthermore, we introduce our software package NetDiversity, which is implemented in Perl and allows for the calculation of all generalized measures of phylogenetic diversity and generalized phylogenetic diversity indices established in this note that are independent of inheritance probabilities. We apply our methods to a phylogenetic network representing the evolutionary relationships among swordtails and platyfishes (Xiphophorus: Poeciliidae), a group of species characterized by widespread hybridization. Copyright © 2018 Elsevier Inc. All rights reserved.

  11. Phylogenetic congruence and ecological coherence in terrestrial Thaumarchaeota.

    Science.gov (United States)

    Oton, Eduard Vico; Quince, Christopher; Nicol, Graeme W; Prosser, James I; Gubry-Rangin, Cécile

    2016-01-01

    Thaumarchaeota form a ubiquitously distributed archaeal phylum, comprising both the ammonia-oxidising archaea (AOA) and other archaeal groups in which ammonia oxidation has not been demonstrated (including Group 1.1c and Group 1.3). The ecology of AOA in terrestrial environments has been extensively studied using either a functional gene, encoding ammonia monooxygenase subunit A (amoA) or 16S ribosomal RNA (rRNA) genes, which show phylogenetic coherence with respect to soil pH. To test phylogenetic congruence between these two markers and to determine ecological coherence in all Thaumarchaeota, we performed high-throughput sequencing of 16S rRNA and amoA genes in 46 UK soils presenting 29 available contextual soil characteristics. Adaptation to pH and organic matter content reflected strong ecological coherence at various levels of taxonomic resolution for Thaumarchaeota (AOA and non-AOA), whereas nitrogen, total mineralisable nitrogen and zinc concentration were also important factors associated with AOA thaumarchaeotal community distribution. Other significant associations with environmental factors were also detected for amoA and 16S rRNA genes, reflecting different diversity characteristics between these two markers. Nonetheless, there was significant statistical congruence between the markers at fine phylogenetic resolution, supporting the hypothesis of low horizontal gene transfer between Thaumarchaeota. Group 1.1c Thaumarchaeota were also widely distributed, with two clusters predominating, particularly in environments with higher moisture content and organic matter, whereas a similar ecological pattern was observed for Group 1.3 Thaumarchaeota. The ecological and phylogenetic congruence identified is fundamental to understand better the life strategies, evolutionary history and ecosystem function of the Thaumarchaeota.

  12. Phylogenetic analysis of several Thermus strains from Rehai of Tengchong, Yunnan, China.

    Science.gov (United States)

    Lin, Lianbing; Zhang, Jie; Wei, Yunlin; Chen, Chaoyin; Peng, Qian

    2005-10-01

    Several Thermus strains were isolated from 10 hot springs of the Rehai geothermal area in Tengchong, Yunnan province. The diversity of Thermus strains was examined by sequencing the 16S rRNA genes and comparing their sequences. Phylogenetic analysis showed that the 16S rDNA sequences from the Rehai geothermal isolates form four branches in the phylogenetic tree and had greater than 95.9% similarity in the phylogroup. Secondary structure comparison also indicated that the 16S rRNA from the Rehai geothermal isolates have unique secondary structure characteristics in helix 6, helix 9, and helix 10 (reference to Escherichia coli). This research is the first attempt to reveal the diversity of Thermus strains that are distributed in the Rehai geothermal area.

  13. Rapid identification of probiotic Lactobacillus species by multiplex PCR using species-specific primers based on the region extending from 16S rRNA through 23S rRNA.

    Science.gov (United States)

    Kwon, Hyuk-Sang; Yang, Eun-Hee; Yeon, Seung-Woo; Kang, Byoung-Hwa; Kim, Tae-Yong

    2004-10-15

    This study aimed to develop a novel multiplex polymerase chain reaction (PCR) primer set for the identification of seven probiotic Lactobacillus species such as Lactobacillus acidophilus, Lactobacillus delbrueckii, Lactobacillus casei, Lactobacillus gasseri, Lactobacillus plantarum, Lactobacillus reuteri and Lactobacillus rhamnosus. The primer set, comprising of seven specific and two conserved primers, was derived from the integrated sequences of 16S and 23S rRNA genes and their rRNA intergenic spacer region of each species. It was able to identify the seven target species with 93.6% accuracy, which exceeds that of the general biochemical methods. The phylogenetic analyses, using 16S rDNA sequences of the probiotic isolates, also provided further support that the results from the multiplex PCR assay were trustworthy. Taken together, we suggest that the multiplex primer set is an efficient tool for simple, rapid and reliable identification of seven Lactobacillus species.

  14. Reconstruction of phylogenetic trees of prokaryotes using maximal common intervals.

    Science.gov (United States)

    Heydari, Mahdi; Marashi, Sayed-Amir; Tusserkani, Ruzbeh; Sadeghi, Mehdi

    2014-10-01

    One of the fundamental problems in bioinformatics is phylogenetic tree reconstruction, which can be used for classifying living organisms into different taxonomic clades. The classical approach to this problem is based on a marker such as 16S ribosomal RNA. Since evolutionary events like genomic rearrangements are not included in reconstructions of phylogenetic trees based on single genes, much effort has been made to find other characteristics for phylogenetic reconstruction in recent years. With the increasing availability of completely sequenced genomes, gene order can be considered as a new solution for this problem. In the present work, we applied maximal common intervals (MCIs) in two or more genomes to infer their distance and to reconstruct their evolutionary relationship. Additionally, measures based on uncommon segments (UCS's), i.e., those genomic segments which are not detected as part of any of the MCIs, are also used for phylogenetic tree reconstruction. We applied these two types of measures for reconstructing the phylogenetic tree of 63 prokaryotes with known COG (clusters of orthologous groups) families. Similarity between the MCI-based (resp. UCS-based) reconstructed phylogenetic trees and the phylogenetic tree obtained from NCBI taxonomy browser is as high as 93.1% (resp. 94.9%). We show that in the case of this diverse dataset of prokaryotes, tree reconstruction based on MCI and UCS outperforms most of the currently available methods based on gene orders, including breakpoint distance and DCJ. We additionally tested our new measures on a dataset of 13 closely-related bacteria from the genus Prochlorococcus. In this case, distances like rearrangement distance, breakpoint distance and DCJ proved to be useful, while our new measures are still appropriate for phylogenetic reconstruction. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

  15. Phylogenetic diversity of archaeal 16S rRNA and ammonia monooxygenase genes from tropical estuarine sediments on the central west coast of India

    Digital Repository Service at National Institute of Oceanography (India)

    Singh, S.K.; Verma, P.; Ramaiah, N.; Anil, A.C.; Shouche, Y.S.

    of Euryarchaeota. Our results indicate that archaeal diversity in tropical estuarine sediments is influenced by the mangrove vegetation bordering the lower stretches of both estuaries. Higher diversity may be related to elevated land drainage during the monsoon...

  16. A Universal Phylogenetic Tree.

    Science.gov (United States)

    Offner, Susan

    2001-01-01

    Presents a universal phylogenetic tree suitable for use in high school and college-level biology classrooms. Illustrates the antiquity of life and that all life is related, even if it dates back 3.5 billion years. Reflects important evolutionary relationships and provides an exciting way to learn about the history of life. (SAH)

  17. Use of direct gradient analysis to uncover biological hypotheses in 16s survey data and beyond.

    Science.gov (United States)

    Erb-Downward, John R; Sadighi Akha, Amir A; Wang, Juan; Shen, Ning; He, Bei; Martinez, Fernando J; Gyetko, Margaret R; Curtis, Jeffrey L; Huffnagle, Gary B

    2012-01-01

    This study investigated the use of direct gradient analysis of bacterial 16S pyrosequencing surveys to identify relevant bacterial community signals in the midst of a "noisy" background, and to facilitate hypothesis-testing both within and beyond the realm of ecological surveys. The results, utilizing 3 different real world data sets, demonstrate the utility of adding direct gradient analysis to any analysis that draws conclusions from indirect methods such as Principal Component Analysis (PCA) and Principal Coordinates Analysis (PCoA). Direct gradient analysis produces testable models, and can identify significant patterns in the midst of noisy data. Additionally, we demonstrate that direct gradient analysis can be used with other kinds of multivariate data sets, such as flow cytometric data, to identify differentially expressed populations. The results of this study demonstrate the utility of direct gradient analysis in microbial ecology and in other areas of research where large multivariate data sets are involved.

  18. V-1 nuclear power plant standby RPP-16S computer software

    International Nuclear Information System (INIS)

    Suchy, R.

    1988-01-01

    The software structure of the function of program modules of the RPP-16S standby computer which is part of the information system of the V-1 Bohunice nuclear power plant are described. The multitasking AMOS operational system is used for the organization of programs in the computer. The program modules are classified in five groups by function, i.e., in modules for the periodical collection of values and for the measurement of process quantities for both nuclear power plant units; for the primary processing of the values; for the monitoring of exceedance of preset limits; for unit operators' communication with the computer. The fifth group consists of users program modules. The standby computer software was tested in the actual operating conditions of the V-1 power plant. The results showed it operated correctly; minor shortcomings were removed. (Z.M.). 1 fig

  19. Kaon Condensation in Neutron Stars and High Density Behaviour of Nuclear Symmetry Energy

    International Nuclear Information System (INIS)

    Kubis, S.; Kutschera, M.

    1999-01-01

    We study the influence of a high density behaviour of the nuclear symmetry energy on a kaon condensation in neutron stars. We find that the symmetry energy typical for several realistic nuclear potentials, which decreases at high densities, inhibits kaon condensation for weaker kaon-nucleon couplings at any density. There exists a threshold coupling above which the kaon condensate forms at densities exceeding some critical value. This is in contrast to the case of rising symmetry energy, as e.g. for relativistic mean field models, when the kaon condensate can form for any coupling at a sufficiently high density. Properties of the condensate are also different in both cases. (author)

  20. Kaon Condensation in Neutron Stars and High Density Behaviour of Nuclear Symmetry Energy

    International Nuclear Information System (INIS)

    Kubis, S.; Kutschera, M.

    1999-04-01

    We study the influence of a high density behaviour of the nuclear symmetry energy on a kaon condensation in neutron stars. We find that the symmetry energy typical for several realistic nuclear potentials, which decreases at high densities, inhibits kaon condensation for weaker kaon-nucleon couplings at any density. There exists a threshold coupling above which the kaon condensate forms at densities exceeding some critical value. This is in contrast to the case of rising symmetry energy, as e.g. for relativistic mean field models, when the kaon condensate can form for any coupling at a sufficiently high density. Properties of the condensate are also different in both cases

  1. Improvements in gastric diagnosis by using high density contrast media with low viscosity

    International Nuclear Information System (INIS)

    Toischer, H.P.

    1983-01-01

    In a retrospective clinical study, 150 unselected double contrast examinations of the stomach using conventional contrast media (100 g/100 ml barium sulphate) were compared with a similar number of examinations using a high density contrast medium of flow viscosity (250 g/100 ml barium sulphate). The high density contrast medium was distinctly better for demonstrating detail of the gastric mucosa. The uneveness of coating and instability of the older high density contrast media was observed in 15.5% of cases and, in no instance, did this make it impossible to reach a diagnosis. (orig.) [de

  2. The high density and high βpol disruption mechanism on TFTR

    International Nuclear Information System (INIS)

    Fredrickson, E.D.; Manickam, J.; McGuire, K.M.; Monticello, D.; Nagayama, Y.; Park, W.; Taylor, G.

    1992-01-01

    Studies of disruptions on TFTR have been extended to include high density disruptions as well as the high β pol disruptions. The data strongly suggests that the (m,n)=(1,1) mode plays an important role in both types of disruptions. Further, for the first time, it is unambiguously shown, using a fast electron cyclotron emission (ECE) instrument for the electron temperature profile measurements, that the (m,n)=(1,1) precursor to the high density disruptions has a 'cold bubble' structure. The precursor to the major disruption at high density resembles the 'vacuum bubble' model of disruptions first proposed by Kadomtsev and Pogutse. (author) 2 refs., 2 figs

  3. [Identification and phylogenetic analysis of one strain of Lactobacillus delbrueckii subsp. bulgaricus separated from yoghourt].

    Science.gov (United States)

    Wang, Chuan; Zhang, Chaowu; Pei, Xiaofang; Liu, Hengchuan

    2007-11-01

    For being further applied and studied, one strain of Lactobacillus delbrueckii subsp. bulgaricus (wch9901) separated from yoghourt which had been identified by phenotype characteristic analysis was identified by 16S rDNA and phylogenetic analyzed. The 16S rDNA of wch9901 was amplified with the genomic DNA of wch9901 as template, and the conservative sequences of the 16S rDNA as primers. Inserted 16S rDNA amplified into clonal vector pGEM-T under the function of T4 DNA ligase to construct recombined plasmid pGEM-wch9901 16S rDNA. The recombined plasmid was identified by restriction enzyme digestion, and the eligible plasmid was presented to sequencing company for DNA sequencing. Nucleic acid sequence was blast in GenBank and phylogenetic tree was constructed using neighbor-joining method of distance methods by Mega3.1 soft. Results of blastn showed that the homology of 16S rDNA of wch9901 with the 16S rDNA of Lactobacillus delbrueckii subsp. bulgaricus strains was higher than 96%. On the phylogenetic tree, wch9901 formed a separate branch and located between Lactobacillus delbrueckii subsp. bulgaricus LGM2 evolution branch and another evolution branch which was composed of Lactobacillus delbrueckii subsp. bulgaricus DL2 evolution cluster and Lactobacillus delbrueckii subsp. bulgaricus JSQ evolution cluster. The distance between wch9901 evolution branch and Lactobacillus delbrueckii subsp. bulgaricus LGM2 evolution branch was the closest. wch9901 belonged to Lactobacillus delbrueckii subsp. bulgaricus. wch9901 showed the closest evolution relationship to Lactobacillus delbrueckii subsp. bulgaricus LGM2.

  4. Partial Sequencing of 16S rRNA Gene of Selected Staphylococcus aureus Isolates and its Antibiotic Resistance

    Directory of Open Access Journals (Sweden)

    Harsi Dewantari Kusumaningrum

    2016-08-01

    Full Text Available The choice of primer used in 16S rRNA sequencing for identification of Staphylococcus species found in food is important. This study aimed to characterize Staphylococcus aureus isolates by partial sequencing based on 16S rRNA gene employing primers 16sF, 63F or 1387R. The isolates were isolated from milk, egg dishes and chicken dishes and selected based on the presence of sea gene that responsible for formation of enterotoxin-A. Antibiotic susceptibility of the isolates towards six antibiotics was also tested. The use of 16sF resulted generally in higher identity percentage and query coverage compared to the sequencing by 63F or 1387R. BLAST results of all isolates, sequenced by 16sF, showed 99% homology to complete genome of four S. aureus strains, with different characteristics on enterotoxin production and antibiotic resistance. Considering that all isolates were carrying sea gene, indicated by the occurence of 120 bp amplicon after PCR amplification using primer SEA1/SEA2,  the isolates were most in agreeing to S. aureus subsp. aureus ST288. This study indicated that 4 out of 8 selected isolates were resistant towards streptomycin. The 16S rRNA gene sequencing using 16sF is useful for identification of S. aureus. However, additional analysis such as PCR employing specific gene target, should give a valuable supplementary information, when specific characteristic is expected.

  5. Detection of Horizontal Gene Transfers from Phylogenetic Comparisons

    Science.gov (United States)

    Pylro, Victor Satler; Vespoli, Luciano de Souza; Duarte, Gabriela Frois; Yotoko, Karla Suemy Clemente

    2012-01-01

    Bacterial phylogenies have become one of the most important challenges for microbial ecology. This field started in the mid-1970s with the aim of using the sequence of the small subunit ribosomal RNA (16S) tool to infer bacterial phylogenies. Phylogenetic hypotheses based on other sequences usually give conflicting topologies that reveal different evolutionary histories, which in some cases may be the result of horizontal gene transfer events. Currently, one of the major goals of molecular biology is to understand the role that horizontal gene transfer plays in species adaptation and evolution. In this work, we compared the phylogenetic tree based on 16S with the tree based on dszC, a gene involved in the cleavage of carbon-sulfur bonds. Bacteria of several genera perform this survival task when living in environments lacking free mineral sulfur. The biochemical pathway of the desulphurization process was extensively studied due to its economic importance, since this step is expensive and indispensable in fuel production. Our results clearly show that horizontal gene transfer events could be detected using common phylogenetic methods with gene sequences obtained from public sequence databases. PMID:22675653

  6. Assessing the functional properties of high-density lipoproteins : an emerging concept in cardiovascular research

    NARCIS (Netherlands)

    Triolo, Michela; Annema, Wijtske; Dullaart, Robin P. F.; Tietge, Uwe J. F.

    Although plasma concentrations of high-density lipoprotein (HDL) cholesterol correlate inversely with the incidence of atherosclerotic cardiovascular disease, results from recent epidemiological, genetic and pharmacological intervention studies resulted in a shift of concept. Rather than HDL

  7. Human plasma phospholipid transfer protein increases the antiatherogenic potential of high density lipoproteins in transgenic mice

    NARCIS (Netherlands)

    M.J. van Haperen (Rien); A. van Tol (Arie); P. Vermeulen; M. Jauhiainen; T. van Gent (Teus); P.M. van den Berg (Paul); S. Ehnholm (Sonja); A.W.M. van der Kamp (Arthur); M.P.G. de Crom (Rini); F.G. Grosveld (Frank)

    2000-01-01

    textabstractPlasma phospholipid transfer protein (PLTP) transfers phospholipids between lipoprotein particles and alters high density lipoprotein (HDL) subfraction patterns in vitro, but its physiological function is poorly understood. Transgenic mice that overexpress

  8. High-density lipoproteins and adrenal steroidogenesis : A population-based study

    NARCIS (Netherlands)

    Buitenwerf, Edward; Kerstens, Michiel N.; Links, Thera P.; Kema, Ido P.; Dullaart, Robin P. F.

    BACKGROUND: Cholesterol trafficked within plasma lipoproteins, in particular high-density lipoproteins (HDL), may represent an important source of cholesterol that is required for adrenal steroidogenesis. Based on a urinary gas chromatography method, compromised adrenal function has been suggested

  9. Moderate doses of alcoholic beverages with dinner and postprandial high density lipoprotein composition

    NARCIS (Netherlands)

    Hendriks, H.F.J.; Veenstra, J.; Tol, A. van; Groener, J.E.M.; Schaafsma, G.

    1998-01-01

    Moderate alcohol consumption is associated with a reduced risk of coronary heart disease. In this study, postprandial changes in plasma lipids, high-density lipoprotein (HDL) composition and cholesteryl ester transfer protein (CETP) and lecithin: cholesterol acyltransferase (LCAT) activity levels

  10. High-density polymer microarrays: identifying synthetic polymers that control human embryonic stem cell growth.

    Science.gov (United States)

    Hansen, Anne; Mjoseng, Heidi K; Zhang, Rong; Kalloudis, Michail; Koutsos, Vasileios; de Sousa, Paul A; Bradley, Mark

    2014-06-01

    The fabrication of high-density polymer microarray is described, allowing the simultaneous and efficient evaluation of more than 7000 different polymers in a single-cellular-based screen. These high-density polymer arrays are applied in the search for synthetic substrates for hESCs culture. Up-scaling of the identified hit polymers enables long-term cellular cultivation and promoted successful stem-cell maintenance. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  11. Evaluating Approaches to Rendering Braille Text on a High-Density Pin Display.

    Science.gov (United States)

    Morash, Valerie S; Russomanno, Alexander; Gillespie, R Brent; OModhrain, Sile

    2017-10-13

    Refreshable displays for tactile graphics are typically composed of pins that have smaller diameters and spacing than standard braille dots. We investigated configurations of high-density pins to form braille text on such displays using non-refreshable stimuli produced with a 3D printer. Normal dot braille (diameter 1.5 mm) was compared to high-density dot braille (diameter 0.75 mm) wherein each normal dot was rendered by high-density simulated pins alone or in a cluster of pins configured in a diamond, X, or square; and to "blobs" that could result from covering normal braille and high-density multi-pin configurations with a thin membrane. Twelve blind participants read MNREAD sentences displayed in these conditions. For high-density simulated pins, single pins were as quickly and easily read as normal braille, but diamond, X, and square multi-pin configurations were slower and/or harder to read than normal braille. We therefore conclude that as long as center-to-center dot spacing and dot placement is maintained, the dot diameter may be open to variability for rendering braille on a high density tactile display.

  12. Clinical significance of diminution of high-density areas in basal cisterns following acute aneurysmal bleeding

    International Nuclear Information System (INIS)

    Matsuzaki, Takayuki; Takeda, Rihei; Nakagawara, Jyoji; Sato, Shigeru; Fujiwara, Hidetoshi

    1983-01-01

    We analyzed the sequential changes in the high density in basal cisterns in the acute stage of aneurysmal bleeding. We could recognize Group 3 (clot or thick layer), according to Fisher's classification, in 66.3% of the intracranial aneurysms at admission (83 cases). In the early stage of an intracranial aneurysm, a subarachnoid hemorrhage (SAH) was detected in all the patients on CT. We evaluated 40 cases of Group 3 sequentially on CT. This investigation showed that 55% of the Grade I--Ii group, 27.3% of the Grade III group, and 11.1% of the Grade IV--V group changed to Group 2(thin or diffuse pattern) in approximately 20 hours on the average. As for the correlation between the high density in basal cisterns and the neurological condition (Hunt and Hess), we found a neurological improvement in the decreased-high-density group. The unchanged- high-density group showed deterioration. Compared with the decreased-high-density group, the unchanged group showed a greater increase in the CVI (Cerebro Ventricular Index). RI ( 111 In) cisternography also showed a disturbance of the CSF circulation. To lower the vasospasm it is important to decrease the high density in an early stage by carrying out CSF. It was considered to be prognostic when a CT scan was performed within 24 hours after SAH. (author)

  13. Potential formation and confinement in high density plasma on the GAMMA 10 tandem mirror

    International Nuclear Information System (INIS)

    Yatsu, K.

    2002-01-01

    After the attainment of doubling of the density due to the potential confinement, GAMMA 10 experiments have been directed to realization of a high density plasma and also to study dependence of the confining potential and confinement time on the plasma density. These problems are important to understand the physics of potential formation in tandem mirrors and also for the development of a tandem mirror reactor. We reported high density plasma production by using an ion cyclotron range of frequency heating at a high harmonic frequency in the last IAEA Conference. However, the diamagnetic signal of the high density plasma decreased when electron cyclotron resonance heating (ECRH) was applied due to some instabilities. Recently, the high density plasma production was much improved by adjusting the spacing of the conducting plates installed in the anchor transition regions, which enabled us to produce a high density plasma without degradation of the diamagnetic signal with ECRH and also to study the density dependence. In this paper we report production of a high density plasma and dependence of the confining potential and the confinement time on the density. (author)

  14. Molecular Characterization of the 16S rRNA Gene of Phytoplasmas Detected in Two Leafhopper Species Associated with Alfalfa Plants Infected with Witches' Broom in Oman

    Directory of Open Access Journals (Sweden)

    A.J. Khan

    2003-12-01

    Full Text Available Two leafhopper species, Austroagallia avicula and Empoasca sp., were consistently found in alfalfa fields infected with witches’ broom phytoplasma (OmanAlfWB in the Al-Batinah, Dakhliya, North and South Sharqiya, Muscat, and Al-Bureimi regions of the Sultanate of Oman. Phytoplasmas from both leafhoppers were detected by specific polymerase chain reaction (PCR amplification of the 16S rRNA gene and the spacer region in direct PCR using P1/P7 primer pairs. Comparative RFLP profiles of the amplified rRNA gene and the spacer region from leafhopper phytoplasmas and from 20 phytoplasma controls yielded patterns referable to phytoplasmas belonging to the peanut witches’ broom group (16SrII group. In particular, extensive RFLP analyses with the endonucleases HpaII, Tru9I, Tsp509I, and RsaI indicated that the phytoplasmas in A. avicula and Empoasca sp. were identical but showed some differences from OmanAlfWB; however, RFLP patterns obtained with TaqI showed the OmanAlfWB and the phytoplasmas from the two leafhoppers to be identical. Direct PCR products amplified from phytoplasma leafhopper DNA using the P1/P7 primer pair were cloned and sequenced yielding 1758 bp and 1755 bp products from A. avicula and Empoasca sp. respectively; the homology of these sequences with OmanAlfWB and papaya yellow crinkle phytoplasmas was more than 98%. A phylogenetic tree based on the 16S rRNA gene and spacer region sequences from 44 phytoplasmas revealed that the phytoplasmas from the leafhoppers clustered with OmanAlfWB, papaya yellow crinkle, and gerbera phyllody phytoplasmas, all belonging to 16SrII group, but were distinct from lime witches’ broom phytoplasma, the most commonly found phytoplasma in the Sultanate of Oman.

  15. Characterization of 16S rRNA Processing with Pre-30S Subunit Assembly Intermediates from E. coli.

    Science.gov (United States)

    Smith, Brian A; Gupta, Neha; Denny, Kevin; Culver, Gloria M

    2018-06-08

    Ribosomal RNA (rRNA) is a major component of ribosomes and is fundamental to the process of translation. In bacteria, 16S rRNA is a component of the small ribosomal subunit and plays a critical role in mRNA decoding. rRNA maturation entails the removal of intervening spacer sequences contained within the pre-rRNA transcript by nucleolytic enzymes. Enzymatic activities involved in maturation of the 5'-end of 16S rRNA have been identified, but those involved in 3'-end maturation of 16S rRNA are more enigmatic. Here, we investigate molecular details of 16S rRNA maturation using purified in vivo-formed small subunit (SSU) assembly intermediates (pre-SSUs) from wild-type Escherichia coli that contain precursor 16S rRNA (17S rRNA). Upon incubation of pre-SSUs with E. coli S100 cell extracts or purified enzymes implicated in 16S rRNA processing, the 17S rRNA is processed into additional intermediates and mature 16S rRNA. These results illustrate that exonucleases RNase R, RNase II, PNPase, and RNase PH can process the 3'-end of pre-SSUs in vitro. However, the endonuclease YbeY did not exhibit nucleolytic activity with pre-SSUs under these conditions. Furthermore, these data demonstrate that multiple pathways facilitate 16S rRNA maturation with pre-SSUs in vitro, with the dominant pathways entailing complete processing of the 5'-end of 17S rRNA prior to 3'-end maturation or partial processing of the 5'-end with concomitant processing of the 3'-end. These results reveal the multifaceted nature of SSU biogenesis and suggest that E. coli may be able to escape inactivation of any one enzyme by using an existing complementary pathway. Copyright © 2018 Elsevier Ltd. All rights reserved.

  16. Comparison of 16S ribosomal RNA gene sequence analysis and conventional culture in the environmental survey of a hospital

    OpenAIRE

    Manaka, Akihiro; Tokue, Yutaka; Murakami, Masami

    2017-01-01

    Background Nosocomial infection is one of the most common complications within health care facilities. Certain studies have reported outbreaks resulting from contaminated hospital environments. Although the identification of bacteria in the environment can readily be achieved using culturing methods, these methods detect live bacteria. Sequencing of the 16S ribosomal RNA (16S rRNA) gene is recognized to be effective for bacterial identification. In this study, we surveyed wards where drug-res...

  17. Phylogeny of 54 representative strains of species in the family Pasteurellaceae as determined by comparison of 16S rRNA sequences.

    Science.gov (United States)

    Dewhirst, F E; Paster, B J; Olsen, I; Fraser, G J

    1992-03-01

    Virtually complete 16S rRNA sequences were determined for 54 representative strains of species in the family Pasteurellaceae. Of these strains, 15 were Pasteurella, 16 were Actinobacillus, and 23 were Haemophilus. A phylogenetic tree was constructed based on sequence similarity, using the Neighbor-Joining method. Fifty-three of the strains fell within four large clusters. The first cluster included the type strains of Haemophilus influenzae, H. aegyptius, H. aphrophilus, H. haemolyticus, H. paraphrophilus, H. segnis, and Actinobacillus actinomycetemcomitans. This cluster also contained A. actinomycetemcomitans FDC Y4, ATCC 29522, ATCC 29523, and ATCC 29524 and H. aphrophilus NCTC 7901. The second cluster included the type strains of A. seminis and Pasteurella aerogenes and H. somnus OVCG 43826. The third cluster was composed of the type strains of Pasteurella multocida, P. anatis, P. avium, P. canis, P. dagmatis, P. gallinarum, P. langaa, P. stomatis, P. volantium, H. haemoglobinophilus, H. parasuis, H. paracuniculus, H. paragallinarum, and A. capsulatus. This cluster also contained Pasteurella species A CCUG 18782, Pasteurella species B CCUG 19974, Haemophilus taxon C CAPM 5111, H. parasuis type 5 Nagasaki, P. volantium (H. parainfluenzae) NCTC 4101, and P. trehalosi NCTC 10624. The fourth cluster included the type strains of Actinobacillus lignieresii, A. equuli, A. pleuropneumoniae, A. suis, A. ureae, H. parahaemolyticus, H. parainfluenzae, H. paraphrohaemolyticus, H. ducreyi, and P. haemolytica. This cluster also contained Actinobacillus species strain CCUG 19799 (Bisgaard taxon 11), A. suis ATCC 15557, H. ducreyi ATCC 27722 and HD 35000, Haemophilus minor group strain 202, and H. parainfluenzae ATCC 29242. The type strain of P. pneumotropica branched alone to form a fifth group. The branching of the Pasteurellaceae family tree was quite complex. The four major clusters contained multiple subclusters. The clusters contained both rapidly and slowly evolving

  18. Identification by 16S rRNA Gene Sequencing of Lactobacillus salivarius Bacteremic Cholecystitis

    Science.gov (United States)

    Woo, Patrick C. Y.; Fung, Ami M. Y.; Lau, Susanna K. P.; Yuen, Kwok-Yung

    2002-01-01

    An anaerobic, nonsporulating, gram-positive bacterium was isolated from blood and bile pus cultures of a 70-year-old man with bacteremic acute cholecystitis. The API 20A system showed that it was 70% Actinomyces naeslundii and 30% Bifidobacterium species, whereas the Vitek ANI system and the ATB ID32A Expression system showed that it was “unidentified.” The 16S rRNA gene of the strain was amplified and sequenced. There were 3 base differences between the nucleotide sequence of the isolate and that of Lactobacillus salivarius subsp. salivarius or L. salivarius subsp. salicinius, indicating that the isolate was a strain of L. salivarius. The patient responded to cholecystectomy and a 2-week course of antibiotic treatment. Identification of the organism in the present study was important because the duration of antibiotic therapy would have been entirely different depending on the organism. If the bacterium had been identified as Actinomyces, penicillin for 6 months would have been the regimen of choice. However, it was Lactobacillus, and a 2-week course of antibiotic was sufficient. PMID:11773128

  19. ESPRIT: estimating species richness using large collections of 16S rRNA pyrosequences.

    Science.gov (United States)

    Sun, Yijun; Cai, Yunpeng; Liu, Li; Yu, Fahong; Farrell, Michael L; McKendree, William; Farmerie, William

    2009-06-01

    Recent metagenomics studies of environmental samples suggested that microbial communities are much more diverse than previously reported, and deep sequencing will significantly increase the estimate of total species diversity. Massively parallel pyrosequencing technology enables ultra-deep sequencing of complex microbial populations rapidly and inexpensively. However, computational methods for analyzing large collections of 16S ribosomal sequences are limited. We proposed a new algorithm, referred to as ESPRIT, which addresses several computational issues with prior methods. We developed two versions of ESPRIT, one for personal computers (PCs) and one for computer clusters (CCs). The PC version is used for small- and medium-scale data sets and can process several tens of thousands of sequences within a few minutes, while the CC version is for large-scale problems and is able to analyze several hundreds of thousands of reads within one day. Large-scale experiments are presented that clearly demonstrate the effectiveness of the newly proposed algorithm. The source code and user guide are freely available at http://www.biotech.ufl.edu/people/sun/esprit.html.

  20. Prokaryotic community profiling of local algae wastewaters using advanced 16S rRNA gene sequencing.

    Science.gov (United States)

    Limayem, Alya; Micciche, Andrew; Nayak, Bina; Mohapatra, Shyam

    2018-01-01

    Algae biomass-fed wastewaters are a promising source of lipid and bioenergy manufacture, revealing substantial end-product investment returns. However, wastewaters would contain lytic pathogens carrying drug resistance detrimental to algae yield and environmental safety. This study was conducted to simultaneously decipher through high-throughput advanced Illumina 16S ribosomal RNA (rRNA) gene sequencing, the cultivable and uncultivable bacterial community profile found in a single sample that was directly recovered from the local wastewater systems. Samples were collected from two previously documented sources including anaerobically digested (AD) municipal wastewater and swine wastewater with algae namely Chlorella spp. in addition to control samples, swine wastewater, and municipal wastewater without algae. Results indicated the presence of a significant level of Bacteria in all samples with an average of approximately 95.49% followed by Archaea 2.34%, in local wastewaters designed for algae cultivation. Taxonomic genus identification indicated the presence of Calothrix, Pseudomonas, and Clostridium as the most prevalent strains in both local municipal and swine wastewater samples containing algae with an average of 17.37, 12.19, and 7.84%, respectively. Interestingly, swine wastewater without algae displayed the lowest level of Pseudomonas strains algae indicates potential coexistence between these strains and algae microenvironment, suggesting further investigations. This finding was particularly relevant for the earlier documented adverse effects of some nosocomial Pseudomonas strains on algae growth and their multidrug resistance potential, requiring the development of targeted bioremediation with regard to the beneficial flora.

  1. Molecular Analysis of Methanogen Richness in Landfill and Marshland Targeting 16S rDNA Sequences.

    Science.gov (United States)

    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.

  2. Molecular Analysis of Methanogen Richness in Landfill and Marshland Targeting 16S rDNA Sequences

    Directory of Open Access Journals (Sweden)

    Shailendra Yadav

    2015-01-01

    Full Text Available 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.

  3. 16S rRNA-based detection of oral pathogens in coronary atherosclerotic plaque

    Directory of Open Access Journals (Sweden)

    Mahendra Jaideep

    2010-01-01

    Full Text Available Background: Atherosclerosis develops as a response of the vessel wall to injury. Chronic bacterial infections have been associated with an increased risk for atherosclerosis and coronary artery disease. The ability of oral pathogens to colonize in coronary atheromatous plaque is well known. Aim: The aim of this study was to detect the presence of Treponema denticola, Porphyromonas gingivalis and Campylobacter rectus in the subgingival and atherosclerotic plaques of patients with coronary artery disease. Materials and Methods: Fifty-one patients in the age group of 40-80 years with coronary artery disease were selected for the study. DNA was extracted from the plaque samples. The specific primers for T. denticola, C. rectus and P. gingivalis were used to amplify a part of the 16S rRNA gene by polymerase chain reaction. Statistical Analysis Used: Chi-square analysis, correlation coefficient and prevalence percentage of the microorganisms were carried out for the analysis. Results: Of the 51 patients, T. denticola, C. rectus and P. gingivalis were detected in 49.01%, 21.51% and 45.10% of the atherosclerotic plaque samples. Conclusions: Our study revealed the presence of bacterial DNA of the oral pathogenic microorganisms in coronary atherosclerotic plaques. The presence of the bacterial DNA in the coronary atherosclerotic plaques in significant proportion may suggest the possible relationship between periodontal bacterial infection and genesis of coronary atherosclerosis.

  4. Comparative molecular analysis of Herbaspirillum strains by RAPD, RFLP, and 16S rDNA sequencing

    Directory of Open Access Journals (Sweden)

    Soares-Ramos Juliana R.L.

    2003-01-01

    Full Text Available Herbaspirillum spp. are endophytic diazotrophic bacteria associated with important agricultural crops. In this work, we analyzed six strains of H. seropedicae (Z78, M2, ZA69, ZA95, Z152, and Z67 and one strain of H. rubrisubalbicans (M4 by restriction fragment length polymorphism (RFLP using HindIII or DraI restriction endonucleases, random amplified polymorphic DNA (RAPD, and partial sequencing of 16S rDNA. The results of these analyses ascribed the strains studied to three distinct groups: group I, consisting of M2 and M4; group II, of ZA69; and group III, of ZA95, Z78, Z67, and Z152. RAPD fingerprinting showed a higher variability than the other methods, and each strain had a unique electrophoretic pattern with five of the six primers used. Interestingly, H. seropedicae M2 was found by all analyses to be genetically very close to H. rubrisubalbicans M4. Our results show that RAPD can distinguish between all Herbaspirillum strains tested.

  5. Investigation of the koala (Phascolarctos cinereus) hindgut microbiome via 16S pyrosequencing.

    Science.gov (United States)

    Barker, Christopher J; Gillett, Amber; Polkinghorne, Adam; Timms, Peter

    2013-12-27

    As a dietary source, the foliage of Eucalyptus spp. is low in available protein and carbohydrate while containing polyphenolic compounds that interfere with enzymatic digestion. To overcome this, the koala (Phascolarctos cinereus) has evolved a range of anatomical and physiological adaptations to assist with digestion and absorption of nutrients from this food source. Microbial fermentation of partially digested eucalyptus leaves is thought to be critical in this process, however, little is known about the composition and diversity of microorganisms that are associated with digestive health in this native species. In this study, we performed 16S rRNA gene pyrosequencing of caecum, colon and faecal pellet samples from two wild, free ranging, Queensland koalas. Our results reveal a highly complex and diverse ecosystem with considerable intra-individual variation. Although samples were dominated by sequences from the Bacteroidetes and Firmicutes phyla there was considerable variation at the genus level. This study is the first non-culture based microbiota analysis, using 454-amplicon pyrosequencing, and provides preliminary data to expand our understanding of the koala hindgut. Copyright © 2013 Elsevier B.V. All rights reserved.

  6. Visualizing phylogenetic tree landscapes.

    Science.gov (United States)

    Wilgenbusch, James C; Huang, Wen; Gallivan, Kyle A

    2017-02-02

    Genomic-scale sequence alignments are increasingly used to infer phylogenies in order to better understand the processes and patterns of evolution. Different partitions within these new alignments (e.g., genes, codon positions, and structural features) often favor hundreds if not thousands of competing phylogenies. Summarizing and comparing phylogenies obtained from multi-source data sets using current consensus tree methods discards valuable information and can disguise potential methodological problems. Discovery of efficient and accurate dimensionality reduction methods used to display at once in 2- or 3- dimensions the relationship among these competing phylogenies will help practitioners diagnose the limits of current evolutionary models and potential problems with phylogenetic reconstruction methods when analyzing large multi-source data sets. We introduce several dimensionality reduction methods to visualize in 2- and 3-dimensions the relationship among competing phylogenies obtained from gene partitions found in three mid- to large-size mitochondrial genome alignments. We test the performance of these dimensionality reduction methods by applying several goodness-of-fit measures. The intrinsic dimensionality of each data set is also estimated to determine whether projections in 2- and 3-dimensions can be expected to reveal meaningful relationships among trees from different data partitions. Several new approaches to aid in the comparison of different phylogenetic landscapes are presented. Curvilinear Components Analysis (CCA) and a stochastic gradient decent (SGD) optimization method give the best representation of the original tree-to-tree distance matrix for each of the three- mitochondrial genome alignments and greatly outperformed the method currently used to visualize tree landscapes. The CCA + SGD method converged at least as fast as previously applied methods for visualizing tree landscapes. We demonstrate for all three mtDNA alignments that 3D

  7. Liver lipase and high-density lipoprotein. Lipoprotein changes after incubation of human serum with rat liver lipase.

    Science.gov (United States)

    Groot, P H; Scheek, L M; Jansen, H

    1983-05-16

    Human sera were incubated with rat liver lipase after inactivation of lecithin:cholesterol acyltransferase, and the changes in serum lipoprotein composition were measured. In the presence of liver lipase serum triacylglycerol and phosphatidylcholine were hydrolyzed. The main changes in the concentrations of these lipids were found in the high-density lipoprotein fraction. Subfractionation of high-density lipoprotein by rate-zonal ultracentrifugation showed a prominent decrease in all constituents of high-density lipoprotein2, a smaller decrease in the 'light' high-density lipoprotein3 and an increase in the 'heavy' high-density lipoprotein3. These data support a concept in which liver lipase is involved in high-density lipoprotein2 phospholipid and triacylglycerol catabolism and suggest that as a result of this action high-density lipoprotein2 is converted into high-density lipoprotein3.

  8. 16S-ARDRA and MALDI-TOF mass spectrometry as tools for identification of Lactobacillus bacteria isolated from poultry.

    Science.gov (United States)

    Dec, Marta; Puchalski, Andrzej; Urban-Chmiel, Renata; Wernicki, Andrzej

    2016-06-13

    The objective of our study is to evaluate the potential use of Amplified 16S Ribosomal DNA Restriction Analysis (16S-ARDRA) and MALDI-TOF mass spectrometry (MS) as methods for species identification of Lactobacillus strains in poultry. A total of 80 Lactobacillus strains isolated from the cloaca of chicken, geese and turkeys were identified to the species level by MALDI-TOF MS (on-plate extraction method) and 16S-ARDRA. The two techniques produced comparable classification results, some of which were additionally confirmed by sequencing of 16S rDNA. MALDI-TOF MS enabled rapid species identification but produced more than one reliable identification result for 16.25 % of examined strains (mainly of the species L. johnsonii). For 30 % of isolates intermediate log(scores) of 1.70-1.99 were obtained, indicating correct genus identification but only presumptive species identification. The 16S-ARDRA protocol was based on digestion of 16S rDNA with the restriction enzymes MseI, HinfI, MboI and AluI. This technique was able to distinguish 17 of the 19 Lactobacillus reference species tested and enabled identification of all 80 wild isolates. L. salivarius dominated among the 15 recognized species, followed by L. johnsonii and L. ingluviei. The MALDI-TOF MS and 16S-ARDRA assays are valuable tools for the identification of avian lactobacilli to the species level. MALDI-TOF MS is a fast, simple and cost-effective technique, and despite generating a high percentage of results with a log(score) Lactobacillus bacteria from different habitats.

  9. International interlaboratory study comparing single organism 16S rRNA gene sequencing data: Beyond consensus sequence comparisons

    Science.gov (United States)

    Olson, Nathan D.; Lund, Steven P.; Zook, Justin M.; Rojas-Cornejo, Fabiola; Beck, Brian; Foy, Carole; Huggett, Jim; Whale, Alexandra S.; Sui, Zhiwei; Baoutina, Anna; Dobeson, Michael; Partis, Lina; Morrow, Jayne B.

    2015-01-01

    This study presents the results from an interlaboratory sequencing study for which we developed a novel high-resolution method for comparing data from different sequencing platforms for a multi-copy, paralogous gene. The combination of PCR amplification and 16S ribosomal RNA gene (16S rRNA) sequencing has revolutionized bacteriology by enabling rapid identification, frequently without the need for culture. To assess variability between laboratories in sequencing 16S rRNA, six laboratories sequenced the gene encoding the 16S rRNA from Escherichia coli O157:H7 strain EDL933 and Listeria monocytogenes serovar 4b strain NCTC11994. Participants performed sequencing methods and protocols available in their laboratories: Sanger sequencing, Roche 454 pyrosequencing®, or Ion Torrent PGM®. The sequencing data were evaluated on three levels: (1) identity of biologically conserved position, (2) ratio of 16S rRNA gene copies featuring identified variants, and (3) the collection of variant combinations in a set of 16S rRNA gene copies. The same set of biologically conserved positions was identified for each sequencing method. Analytical methods using Bayesian and maximum likelihood statistics were developed to estimate variant copy ratios, which describe the ratio of nucleotides at each identified biologically variable position, as well as the likely set of variant combinations present in 16S rRNA gene copies. Our results indicate that estimated variant copy ratios at biologically variable positions were only reproducible for high throughput sequencing methods. Furthermore, the likely variant combination set was only reproducible with increased sequencing depth and longer read lengths. We also demonstrate novel methods for evaluating variable positions when comparing multi-copy gene sequence data from multiple laboratories generated using multiple sequencing technologies. PMID:27077030

  10. International interlaboratory study comparing single organism 16S rRNA gene sequencing data: Beyond consensus sequence comparisons

    Directory of Open Access Journals (Sweden)

    Nathan D. Olson

    2015-03-01

    Full Text Available This study presents the results from an interlaboratory sequencing study for which we developed a novel high-resolution method for comparing data from different sequencing platforms for a multi-copy, paralogous gene. The combination of PCR amplification and 16S ribosomal RNA gene (16S rRNA sequencing has revolutionized bacteriology by enabling rapid identification, frequently without the need for culture. To assess variability between laboratories in sequencing 16S rRNA, six laboratories sequenced the gene encoding the 16S rRNA from Escherichia coli O157:H7 strain EDL933 and Listeria monocytogenes serovar 4b strain NCTC11994. Participants performed sequencing methods and protocols available in their laboratories: Sanger sequencing, Roche 454 pyrosequencing®, or Ion Torrent PGM®. The sequencing data were evaluated on three levels: (1 identity of biologically conserved position, (2 ratio of 16S rRNA gene copies featuring identified variants, and (3 the collection of variant combinations in a set of 16S rRNA gene copies. The same set of biologically conserved positions was identified for each sequencing method. Analytical methods using Bayesian and maximum likelihood statistics were developed to estimate variant copy ratios, which describe the ratio of nucleotides at each identified biologically variable position, as well as the likely set of variant combinations present in 16S rRNA gene copies. Our results indicate that estimated variant copy ratios at biologically variable positions were only reproducible for high throughput sequencing methods. Furthermore, the likely variant combination set was only reproducible with increased sequencing depth and longer read lengths. We also demonstrate novel methods for evaluating variable positions when comparing multi-copy gene sequence data from multiple laboratories generated using multiple sequencing technologies.

  11. Sputum microbiota in tuberculosis as revealed by 16S rRNA pyrosequencing.

    Directory of Open Access Journals (Sweden)

    Man Kit Cheung

    Full Text Available BACKGROUND: Tuberculosis (TB remains a global threat in the 21st century. Traditional studies of the disease are focused on the single pathogen Mycobacterium tuberculosis. Recent studies have revealed associations of some diseases with an imbalance in the microbial community. Characterization of the TB microbiota could allow a better understanding of the disease. METHODOLOGY/PRINCIPAL FINDINGS: Here, the sputum microbiota in TB infection was examined by using 16S rRNA pyrosequencing. A total of 829,873 high-quality sequencing reads were generated from 22 TB and 14 control sputum samples. Firmicutes, Proteobacteria, Bacteroidetes, Actinobacteria, and Fusobacteria were the five major bacterial phyla recovered, which together composed over 98% of the microbial community. Proteobacteria and Bacteroidetes were more represented in the TB samples and Firmicutes was more predominant in the controls. Sixteen major bacterial genera were recovered. Streptococcus, Neisseria and Prevotella were the most predominant genera, which were dominated by several operational taxonomic units grouped at a 97% similarity level. Actinomyces, Fusobacterium, Leptotrichia, Prevotella, Streptococcus, and Veillonella were found in all TB samples, possibly representing the core genera in TB sputum microbiota. The less represented genera Mogibacterium, Moryella and Oribacterium were enriched statistically in the TB samples, while a genus belonging to the unclassified Lactobacillales was enriched in the controls. The diversity of microbiota was similar in the TB and control samples. CONCLUSIONS/SIGNIFICANCE: The composition and diversity of sputum microbiota in TB infection was characterized for the first time by using high-throughput pyrosequencing. It lays the framework for examination of potential roles played by the diverse microbiota in TB pathogenesis and progression, and could ultimately facilitate advances in TB treatment.

  12. Sources for sedimentary bacteriohopanepolyols as revealed by 16S rDNA stratigraphy.

    Science.gov (United States)

    Coolen, Marco J L; Talbot, Helen M; Abbas, Ben A; Ward, Christopher; Schouten, Stefan; Volkman, John K; Damsté, Jaap S Sinninghe

    2008-07-01

    Bacteriohopanoids are widespread lipid biomarkers in the sedimentary record. Many aerobic and anaerobic bacteria are potential sources of these lipids which sometimes complicates the use of these biomarkers as proxies for ecological and environmental changes. Therefore, we applied preserved 16S ribosomal RNA genes to identify likely Holocene biological sources of bacteriohopanepolyols (BHPs) in the sulfidic sediments of the permanently stratified postglacial Ace Lake, Antarctica. A suite of intact BHPs were identified, which revealed a variety of structural forms whose composition differed through the sediment core reflecting changes in bacterial populations induced by large changes in lake salinity. Stable isotopic compositions of the hopanols formed from periodic acid-cleaved BHPs, showed that some were substantially depleted in (13)C, indicative of their methanotrophic origin. Using sensitive molecular tools, we found that Type I and II methanotrophic bacteria (respectively Methylomonas and Methylocystis) were unique to the oldest lacustrine sediments (> 9400 years BP), but quantification of fossil DNA revealed that the Type I methanotrophs, including methanotrophs related to methanotrophic gill symbionts of deep-sea cold-seep mussels, were the main precursors of the 35-amino BHPs (i.e. aminopentol, -tetrol and -triols). After isolation of the lake approximately 3000 years ago, one Type I methanotroph of the 'methanotrophic gill symbionts cluster' remained the most obvious source of aminotetrol and -triol. We, furthermore, identified a Synechococcus phylotype related to pelagic freshwater strains in the oldest lacustrine sediments as a putative source of 2-methylbacteriohopanetetrol (2-Me BHT). This combined application of advanced geochemical and paleogenomical tools further refined our knowledge about Holocene biogeochemical processes in Ace Lake.

  13. Beyond 16S rRNA Community Profiling: Intra-Species Diversity in the Gut Microbiota

    Science.gov (United States)

    Ellegaard, Kirsten M.; Engel, Philipp

    2016-01-01

    Interactions with microbes affect many aspects of animal biology, including immune system development, nutrition and health. In vertebrates, the gut microbiota is dominated by a small subset of phyla, but the species composition within these phyla is typically not conserved. Moreover, several recent studies have shown that bacterial species in the gut are composed of a multitude of strains, which frequently co-exist in their host, and may be host-specific. However, since the study of intra-species diversity is challenging, particularly in the setting of complex, host-associated microbial communities, our current understanding of the distribution, evolution and functional relevance of intra-species diversity in the gut is scarce. In order to unravel how genomic diversity translates into phenotypic diversity, community analyses going beyond 16S rRNA profiling, in combination with experimental approaches, are needed. Recently, the honeybee has emerged as a promising model for studying gut bacterial communities, particularly in terms of strain-level diversity. Unlike most other invertebrates, the honeybee gut is colonized by a remarkably consistent and specific core microbiota, which is dominated by only eight bacterial species. As for the vertebrate gut microbiota, these species are composed of highly diverse strains suggesting that similar evolutionary forces shape gut community structures in vertebrates and social insects. In this review, we outline current knowledge on the evolution and functional relevance of strain diversity within the gut microbiota, including recent insights gained from mammals and other animals such as the honeybee. We discuss methodological approaches and propose possible future avenues for studying strain diversity in complex bacterial communities. PMID:27708630

  14. Microbial community in persistent apical periodontitis: a 16S rRNA gene clone library analysis.

    Science.gov (United States)

    Zakaria, M N; Takeshita, T; Shibata, Y; Maeda, H; Wada, N; Akamine, A; Yamashita, Y

    2015-08-01

    To characterize the microbial composition of persistent periapical lesions of root filled teeth using a molecular genetics approach. Apical lesion samples were collected from 12 patients (23-80 years old) who visited the Kyushu University Hospital for apicectomy with persistent periapical lesions associated with root filled teeth. DNA was directly extracted from each sample and the microbial composition was comprehensively analysed using clone library analysis of the 16S rRNA gene. Enterococcus faecalis, Candida albicans and specific fimA genotypes of Porphyromonas gingivalis were confirmed using polymerase chain reaction (PCR) analysis with specific primers. Bacteria were detected in all samples, and the dominant findings were P. gingivalis (19.9%), Fusobacterium nucleatum (11.2%) and Propionibacterium acnes (9%). Bacterial diversity was greater in symptomatic lesions than in asymptomatic ones. In addition, the following bacteria or bacterial combinations were characteristic to symptomatic lesions: Prevotella spp., Treponema spp., Peptostreptococcaceae sp. HOT-113, Olsenella uli, Slackia exigua, Selemonas infelix, P. gingivalis with type IV fimA, and a combination of P. gingivalis, F. nucleatum, and Peptostreptococcaceae sp. HOT-113 and predominance of Streptococcus spp. On the other hand, neither Enterococcus faecalis nor C. albicans were detected in any of the samples. Whilst a diverse bacterial species were observed in the persistent apical lesions, some characteristic patterns of bacterial community were found in the symptomatic lesions. The diverse variation of community indicates that bacterial combinations as a community may cause persistent inflammation in periapical tissues rather than specific bacterial species. © 2014 International Endodontic Journal. Published by John Wiley & Sons Ltd.

  15. Investigating bacterial populations in styrene-degrading biofilters by 16S rDNA tag pyrosequencing.

    Science.gov (United States)

    Portune, Kevin J; Pérez, M Carmen; Álvarez-Hornos, F Javier; Gabaldón, Carmen

    2015-01-01

    Microbial biofilms are essential components in the elimination of pollutants within biofilters, yet still little is known regarding the complex relationships between microbial community structure and biodegradation function within these engineered ecosystems. To further explore this relationship, 16S rDNA tag pyrosequencing was applied to samples taken at four time points from a styrene-degrading biofilter undergoing variable operating conditions. Changes in microbial structure were observed between different stages of biofilter operation, and the level of styrene concentration was revealed to be a critical factor affecting these changes. Bacterial genera Azoarcus and Pseudomonas were among the dominant classified genera in the biofilter. Canonical correspondence analysis (CCA) and correlation analysis revealed that the genera Brevundimonas, Hydrogenophaga, and Achromobacter may play important roles in styrene degradation under increasing styrene concentrations. No significant correlations (P > 0.05) could be detected between biofilter operational/functional parameters and biodiversity measurements, although biological heterogeneity within biofilms and/or technical variability within pyrosequencing may have considerably affected these results. Percentages of selected bacterial taxonomic groups detected by fluorescence in situ hybridization (FISH) were compared to results from pyrosequencing in order to assess the effectiveness and limitations of each method for identifying each microbial taxon. Comparison of results revealed discrepancies between the two methods in the detected percentages of numerous taxonomic groups. Biases and technical limitations of both FISH and pyrosequencing, such as the binding of FISH probes to non-target microbial groups and lack of classification of sequences for defined taxonomic groups from pyrosequencing, may partially explain some differences between the two methods.

  16. Fast phylogenetic DNA barcoding

    DEFF Research Database (Denmark)

    Terkelsen, Kasper Munch; Boomsma, Wouter Krogh; Willerslev, Eske

    2008-01-01

    We present a heuristic approach to the DNA assignment problem based on phylogenetic inferences using constrained neighbour joining and non-parametric bootstrapping. We show that this method performs as well as the more computationally intensive full Bayesian approach in an analysis of 500 insect...... DNA sequences obtained from GenBank. We also analyse a previously published dataset of environmental DNA sequences from soil from New Zealand and Siberia, and use these data to illustrate the fact that statistical approaches to the DNA assignment problem allow for more appropriate criteria...... for determining the taxonomic level at which a particular DNA sequence can be assigned....

  17. A novel method for the fabrication of a high-density carbon nanotube microelectrode array

    Directory of Open Access Journals (Sweden)

    Adam Khalifa

    2015-09-01

    Full Text Available We present a novel method for fabricating a high-density carbon nanotube microelectrode array (MEA chip. Vertically aligned carbon nanotubes (VACNTs were synthesized by microwave plasma-enhanced chemical vapor deposition and thermal chemical vapor deposition. The device was characterized using electrochemical experiments such as cyclic voltammetry, impedance spectroscopy and potential transient measurements. Through-silicon vias (TSVs were fabricated and partially filled with polycrystalline silicon to allow electrical connection from the high-density electrodes to a stimulator microchip. In response to the demand for higher resolution implants, we have developed a unique process to obtain a high-density electrode array by making the microelectrodes smaller in size and designing new ways of routing the electrodes to current sources. Keywords: Microelectrode array, Neural implant, Carbon nanotubes, Through-silicon via interconnects, Microfabrication

  18. Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons

    Science.gov (United States)

    Haas, Brian J.; Gevers, Dirk; Earl, Ashlee M.; Feldgarden, Mike; Ward, Doyle V.; Giannoukos, Georgia; Ciulla, Dawn; Tabbaa, Diana; Highlander, Sarah K.; Sodergren, Erica; Methé, Barbara; DeSantis, Todd Z.; Petrosino, Joseph F.; Knight, Rob; Birren, Bruce W.

    2011-01-01

    Bacterial diversity among environmental samples is commonly assessed with PCR-amplified 16S rRNA gene (16S) sequences. Perceived diversity, however, can be influenced by sample preparation, primer selection, and formation of chimeric 16S amplification products. Chimeras are hybrid products between multiple parent sequences that can be falsely interpreted as novel organisms, thus inflating apparent diversity. We developed a new chimera detection tool called Chimera Slayer (CS). CS detects chimeras with greater sensitivity than previous methods, performs well on short sequences such as those produced by the 454 Life Sciences (Roche) Genome Sequencer, and can scale to large data sets. By benchmarking CS performance against sequences derived from a controlled DNA mixture of known organisms and a simulated chimera set, we provide insights into the factors that affect chimera formation such as sequence abundance, the extent of similarity between 16S genes, and PCR conditions. Chimeras were found to reproducibly form among independent amplifications and contributed to false perceptions of sample diversity and the false identification of novel taxa, with less-abundant species exhibiting chimera rates exceeding 70%. Shotgun metagenomic sequences of our mock community appear to be devoid of 16S chimeras, supporting a role for shotgun metagenomics in validating novel organisms discovered in targeted sequence surveys. PMID:21212162

  19. Comparative evaluation of prokaryotic 16S rDNA clone libraries and SSCP in groundwater samples.

    Science.gov (United States)

    Larentis, Michael; Alfreider, Albin

    2011-06-01

    A comparison of ribosomal RNA sequence analysis methods based on clone libraries and single-strand conformational polymorphism technique (SSCP) was performed with groundwater samples obtained between 523-555 meters below surface. The coverage of analyzed clones by phylotype-richness estimates was between 88-100%, confirming that the clone libraries were adequately examined. Analysis of individual bands retrieved from SSCP gels identified 1-6 different taxonomic units per band, suggesting that a single SSCP band does often represent more than one single prokaryotic species. The prokaryotic diversity obtained by both methods showed an overall difference of 42-80%. In comparison to SSCP, clone libraries underestimated the phylogenetic diversity and only 36-66% of the phylotypes observed with SSCP were also detected with the clone libraries. An exception was a sample where the SSCP analysis of Archaea identified only half of the phylotypes retrieved by the clone library. Overall, this study suggests that the clone library and the SSCP approach do not provide an identical picture of the prokaryotic diversity in groundwater samples. The results clearly show that the SSCP method, although this approach is prone to generate methodological artifacts, was able to detect significantly more phylotypes than microbial community analysis based on clone libraries. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  20. Molecular taxonomy of cupped oysters (Crassostrea, Saccostrea, and Striostrea) in Thailand based on COI, 16S, and 18S rDNA polymorphism.

    Science.gov (United States)

    Klinbunga, S; Khamnamtong, B; Puanglarp, N; Jarayabhand, P; Yoosukh, W; Menasveta, P

    2005-01-01

    Genetic diversity of oysters Crassostrea belcheri (Sowerby, 1871), C. iredalei (Faustino, 1932), Saccostrea cucullata (Born, 1778), S. forskali (Gmelin, 1791), and Striostrea (Parastriostrea) mytiloides (Lamarck, 1819) (Ostreoida, Mollusca) was analyzed by polymerase chain reaction - restriction fragment length polymorphism (PCR-RFLP) of 16S ribosomal DNA with AcsI, AluI, DdeI, DraI, RsaI, and TaqI, 18S ribosomal DNA with HinfI, and cytochrome oxidase subunit I with AcsI, DdeI and MboI. A total of 54 composite haplotypes were observed. Species-diagnostic markers were specifically found in C. belcheri, C. iredalei, and S. cucullata, but not in S. forskali and Striostrea mytiloides, which shared common composite haplotypes. Neighbor-joining trees constructed from genetic distances between pairs of composite haplotypes and species indicated large genetic differences between Crassostrea and Saccostrea (including Striostrea mytiloides), but closer relationships were observed within each genus. Four groups of unidentified oysters (Crassostrea sp. and Saccostrea sp. groups 1, 2, and 3) were also genetically analyzed. Fixed RFLP markers were found in Crassostrea sp. and Saccostrea sp. group 2, but not in Saccostrea sp. groups 1 and 3. Phylogenetic and genetic heterogeneity analyses indicated that Crassostrea sp. and Saccostrea sp. group 2 should be considered as newly unidentified oyster species in Thailand.

  1. High-Density Chemical Intercalation of Zero-Valent Copper into Bi 2 Se 3 Nanoribbons

    KAUST Repository

    Koski, Kristie J.; Cha, Judy J.; Reed, Bryan W.; Wessells, Colin D.; Kong, Desheng; Cui, Yi

    2012-01-01

    A major goal of intercalation chemistry is to intercalate high densities of guest species without disrupting the host lattice. Many intercalant concentrations, however, are limited by the charge of the guest species. Here we have developed a general solution-based chemical method for intercalating extraordinarily high densities of zero-valent copper metal into layered Bi 2Se 3 nanoribbons. Up to 60 atom % copper (Cu 7.5Bi 2Se 3) can be intercalated with no disruption to the host lattice using a solution disproportionation redox reaction. © 2012 American Chemical Society.

  2. Reprocessing ability of high density fuels for research and test reactors

    International Nuclear Information System (INIS)

    Gay, A.; Belieres, M.

    1997-01-01

    The development of a new high density fuel is becoming a key issue for Research Reactors operators. Such a new fuel should be a Low Enrichment Uranium (LEU) fuel with a high density, to improve present in core performances. It must be compatible with the reprocessing in an industrial plant to provide a steady back-end solution. Within the framework of a work group CEA/CERCA/COGEMA on new fuel development for Research Reactors, COGEMA has performed an evaluation of the reprocessing ability of some fuel dispersants selected as good candidates. The results will allow US to classify these fuel dispersants from a reprocessing ability point of view. (author)

  3. Slow crack growth in post-consumer recycled high-density polyethylene

    OpenAIRE

    Sciammarella, Cesar A.; Yang, Y.

    2015-01-01

    An experimental study of slow crack growth behavior of post-consumer recycled high-density polyethylene blended with virgin high-density polyethylene copolymer has been done. The study has been performed under constant load and in baths of distilled water at 40, 60, 80°C. The specimen used is notched with side grooves. The test results of crack growth have been analyzed using linear fracture mechanics and the rate process theory. The results show that the resistance to crack growth increases ...

  4. High-Density Chemical Intercalation of Zero-Valent Copper into Bi 2 Se 3 Nanoribbons

    KAUST Repository

    Koski, Kristie J.

    2012-05-09

    A major goal of intercalation chemistry is to intercalate high densities of guest species without disrupting the host lattice. Many intercalant concentrations, however, are limited by the charge of the guest species. Here we have developed a general solution-based chemical method for intercalating extraordinarily high densities of zero-valent copper metal into layered Bi 2Se 3 nanoribbons. Up to 60 atom % copper (Cu 7.5Bi 2Se 3) can be intercalated with no disruption to the host lattice using a solution disproportionation redox reaction. © 2012 American Chemical Society.

  5. Properties of high-density matter in the electroweak symmetric phase

    International Nuclear Information System (INIS)

    Chandra, D.; Goyal, A.

    1992-01-01

    We examine the bulk properties of matter at high densities and finite temperatures in the phase where electroweak symmetry is exact and fermions are massless, by taking the strong interactions into account perturbatively to lowest order in the quark-gluon chromodynamic coupling constant α c . We also discuss the possibility of a phase transition of strange quark matter into this high-density matter in the electroweak symmetric phase at densities likely to be present in the core of dense neutron stars or collapsing stars. Finally, we study the properties of finite-size chunks of this matter by taking surface effects into account and give an estimate of the surface tension

  6. Phylogenetic trees in bioinformatics

    Energy Technology Data Exchange (ETDEWEB)

    Burr, Tom L [Los Alamos National Laboratory

    2008-01-01

    Genetic data is often used to infer evolutionary relationships among a collection of viruses, bacteria, animal or plant species, or other operational taxonomic units (OTU). A phylogenetic tree depicts such relationships and provides a visual representation of the estimated branching order of the OTUs. Tree estimation is unique for several reasons, including: the types of data used to represent each OTU; the use ofprobabilistic nucleotide substitution models; the inference goals involving both tree topology and branch length, and the huge number of possible trees for a given sample of a very modest number of OTUs, which implies that fmding the best tree(s) to describe the genetic data for each OTU is computationally demanding. Bioinformatics is too large a field to review here. We focus on that aspect of bioinformatics that includes study of similarities in genetic data from multiple OTUs. Although research questions are diverse, a common underlying challenge is to estimate the evolutionary history of the OTUs. Therefore, this paper reviews the role of phylogenetic tree estimation in bioinformatics, available methods and software, and identifies areas for additional research and development.

  7. Comparative analysis of vaginal microbiota sampling using 16S rRNA gene analysis.

    Science.gov (United States)

    Virtanen, Seppo; Kalliala, Ilkka; Nieminen, Pekka; Salonen, Anne

    2017-01-01

    Molecular methods such as next-generation sequencing are actively being employed to characterize the vaginal microbiota in health and disease. Previous studies have focused on characterizing the biological variation in the microbiota, and less is known about how factors related to sampling contribute to the results. Our aim was to investigate the impact of a sampling device and anatomical sampling site on the quantitative and qualitative outcomes relevant for vaginal microbiota research. We sampled 10 Finnish women representing diverse clinical characteristics with flocked swabs, the Evalyn® self-sampling device, sterile plastic spatulas and a cervical brush that were used to collect samples from fornix, vaginal wall and cervix. Samples were compared on DNA and protein yield, bacterial load, and microbiota diversity and species composition based on Illumina MiSeq sequencing of the 16S rRNA gene. We quantified the relative contributions of sampling variables versus intrinsic variables in the overall microbiota variation, and evaluated the microbiota profiles using several commonly employed metrics such as alpha and beta diversity as well as abundance of major bacterial genera and species. The total DNA yield was strongly dependent on the sampling device and to a lesser extent on the anatomical site of sampling. The sampling strategy did not affect the protein yield or the bacterial load. All tested sampling methods produced highly comparable microbiota profiles based on MiSeq sequencing. The sampling method explained only 2% (p-value = 0.89) of the overall microbiota variation, markedly surpassed by intrinsic factors such as clinical status (microscopy for bacterial vaginosis 53%, p = 0.0001), bleeding (19%, p = 0.0001), and the variation between subjects (11%, p-value 0.0001). The results indicate that different sampling strategies yield comparable vaginal microbiota composition and diversity. Hence, past and future vaginal microbiota studies employing different

  8. Comparative studies of vertebrate scavenger receptor class B type 1: a high-density lipoprotein binding protein

    Directory of Open Access Journals (Sweden)

    Holmes RS

    2012-06-01

    the average of gene expression. Phylogenetic analyses examined the relationships and potential evolutionary origins of the vertebrate SCARB1 gene with vertebrate SCARB2 and vertebrate and invertebrate SCARB3 (CD36 genes. These suggested that SCARB1 originated in a vertebrate ancestral genome from a gene duplication event of an ancestral invertebrate CD36 gene.Keywords: vertebrates, amino acid sequence, SCARB1, evolution, high-density lipoprotein receptor

  9. Systematics of Plant-Pathogenic and Related Streptomyces Species Based on Phylogenetic Analyses of Multiple Gene Loci

    Science.gov (United States)

    The 10 species of Streptomyces implicated as the etiological agents in scab disease of potatoes or soft rot disease of sweet potatoes are distributed among 7 different phylogenetic clades in analyses based on 16S rRNA gene sequences, but high sequence similarity of this gene among Streptomyces speci...

  10. Phylogenetic tree based on complete genomes using fractal and correlation analyses without sequence alignment

    Directory of Open Access Journals (Sweden)

    Zu-Guo Yu

    2006-06-01

    Full Text Available The complete genomes of living organisms have provided much information on their phylogenetic relationships. Similarly, the complete genomes of chloroplasts have helped resolve the evolution of this organelle in photosynthetic eukaryotes. In this review, we describe two algorithms to construct phylogenetic trees based on the theories of fractals and dynamic language using complete genomes. These algorithms were developed by our research group in the past few years. Our distance-based phylogenetic tree of 109 prokaryotes and eukaryotes agrees with the biologists' "tree of life" based on the 16S-like rRNA genes in a majority of basic branchings and most lower taxa. Our phylogenetic analysis also shows that the chloroplast genomes are separated into two major clades corresponding to chlorophytes s.l. and rhodophytes s.l. The interrelationships among the chloroplasts are largely in agreement with the current understanding on chloroplast evolution.

  11. Defining reference sequences for Nocardia species by similarity and clustering analyses of 16S rRNA gene sequence data.

    Directory of Open Access Journals (Sweden)

    Manal Helal

    Full Text Available BACKGROUND: The intra- and inter-species genetic diversity of bacteria and the absence of 'reference', or the most representative, sequences of individual species present a significant challenge for sequence-based identification. The aims of this study were to determine the utility, and compare the performance of several clustering and classification algorithms to identify the species of 364 sequences of 16S rRNA gene with a defined species in GenBank, and 110 sequences of 16S rRNA gene with no defined species, all within the genus Nocardia. METHODS: A total of 364 16S rRNA gene sequences of Nocardia species were studied. In addition, 110 16S rRNA gene sequences assigned only to the Nocardia genus level at the time of submission to GenBank were used for machine learning classification experiments. Different clustering algorithms were compared with a novel algorithm or the linear mapping (LM of the distance matrix. Principal Components Analysis was used for the dimensionality reduction and visualization. RESULTS: The LM algorithm achieved the highest performance and classified the set of 364 16S rRNA sequences into 80 clusters, the majority of which (83.52% corresponded with the original species. The most representative 16S rRNA sequences for individual Nocardia species have been identified as 'centroids' in respective clusters from which the distances to all other sequences were minimized; 110 16S rRNA gene sequences with identifications recorded only at the genus level were classified using machine learning methods. Simple kNN machine learning demonstrated the highest performance and classified Nocardia species sequences with an accuracy of 92.7% and a mean frequency of 0.578. CONCLUSION: The identification of centroids of 16S rRNA gene sequence clusters using novel distance matrix clustering enables the identification of the most representative sequences for each individual species of Nocardia and allows the quantitation of inter- and intra

  12. Variable Copy Number, Intra-Genomic Heterogeneities and Lateral Transfers of the 16S rRNA Gene in Pseudomonas

    Science.gov (United States)

    Bodilis, Josselin; Nsigue-Meilo, Sandrine; Besaury, Ludovic; Quillet, Laurent

    2012-01-01

    Even though the 16S rRNA gene is the most commonly used taxonomic marker in microbial ecology, its poor resolution is still not fully understood at the intra-genus level. In this work, the number of rRNA gene operons, intra-genomic heterogeneities and lateral transfers were investigated at a fine-scale resolution, throughout the Pseudomonas genus. In addition to nineteen sequenced Pseudomonas strains, we determined the 16S rRNA copy number in four other Pseudomonas strains by Southern hybridization and Pulsed-Field Gel Electrophoresis, and studied the intra-genomic heterogeneities by Denaturing Gradient Gel Electrophoresis and sequencing. Although the variable copy number (from four to seven) seems to be correlated with the evolutionary distance, some close strains in the P. fluorescens lineage showed a different number of 16S rRNA genes, whereas all the strains in the P. aeruginosa lineage displayed the same number of genes (four copies). Further study of the intra-genomic heterogeneities revealed that most of the Pseudomonas strains (15 out of 19 strains) had at least two different 16S rRNA alleles. A great difference (5 or 19 nucleotides, essentially grouped near the V1 hypervariable region) was observed only in two sequenced strains. In one of our strains studied (MFY30 strain), we found a difference of 12 nucleotides (grouped in the V3 hypervariable region) between copies of the 16S rRNA gene. Finally, occurrence of partial lateral transfers of the 16S rRNA gene was further investigated in 1803 full-length sequences of Pseudomonas available in the databases. Remarkably, we found that the two most variable regions (the V1 and V3 hypervariable regions) had probably been laterally transferred from another evolutionary distant Pseudomonas strain for at least 48.3 and 41.6% of the 16S rRNA sequences, respectively. In conclusion, we strongly recommend removing these regions of the 16S rRNA gene during the intra-genus diversity studies. PMID:22545126

  13. 16S rRNA gene sequencing as a tool to study microbial populations in foods and process environments

    DEFF Research Database (Denmark)

    Buschhardt, Tasja; Hansen, Tina Beck; Bahl, Martin Iain

    2015-01-01

    communities in meat and the meat process environment with special focus on the Enterobacteriaceae family as a subpopulation comprising enteropathogens including Salmonella. Samples were analyzed by a nested PCR approach combined with MiSeq® Illumina®16S DNA sequencing and standardized culture methods as cross...... reference. Results: Taxonomic assignments and abundances of sequences in the total community and in the Enterobacteriaceae subpopulation were affected by the 16S rRNA gene variable region, DNA extraction methods, and polymerases chosen. However, community compositions were very reproducible when the same...

  14. Genetic classification and distinguishing of Staphylococcus species based on different partial gap, 16S rRNA, hsp60, rpoB, sodA, and tuf gene sequences.

    Science.gov (United States)

    Ghebremedhin, B; Layer, F; König, W; König, B

    2008-03-01

    The analysis of 16S rRNA gene sequences has been the technique generally used to study the evolution and taxonomy of staphylococci. However, the results of this method do not correspond to the results of polyphasic taxonomy, and the related species cannot always be distinguished from each other. Thus, new phylogenetic markers for Staphylococcus spp. are needed. We partially sequenced the gap gene (approximately 931 bp), which encodes the glyceraldehyde-3-phosphate dehydrogenase, for 27 Staphylococcus species. The partial sequences had 24.3 to 96% interspecies homology and were useful in the identification of staphylococcal species (F. Layer, B. Ghebremedhin, W. König, and B. König, J. Microbiol. Methods 70:542-549, 2007). The DNA sequence similarities of the partial staphylococcal gap sequences were found to be lower than those of 16S rRNA (approximately 97%), rpoB (approximately 86%), hsp60 (approximately 82%), and sodA (approximately 78%). Phylogenetically derived trees revealed four statistically supported groups: S. hyicus/S. intermedius, S. sciuri, S. haemolyticus/S. simulans, and S. aureus/epidermidis. The branching of S. auricularis, S. cohnii subsp. cohnii, and the heterogeneous S. saprophyticus group, comprising S. saprophyticus subsp. saprophyticus and S. equorum subsp. equorum, was not reliable. Thus, the phylogenetic analysis based on the gap gene sequences revealed similarities between the dendrograms based on other gene sequences (e.g., the S. hyicus/S. intermedius and S. sciuri groups) as well as differences, e.g., the grouping of S. arlettae and S. kloosii in the gap-based tree. From our results, we propose the partial sequencing of the gap gene as an alternative molecular tool for the taxonomical analysis of Staphylococcus species and for decreasing the possibility of misidentification.

  15. Genetic Classification and Distinguishing of Staphylococcus Species Based on Different Partial gap, 16S rRNA, hsp60, rpoB, sodA, and tuf Gene Sequences▿

    Science.gov (United States)

    Ghebremedhin, B.; Layer, F.; König, W.; König, B.

    2008-01-01

    The analysis of 16S rRNA gene sequences has been the technique generally used to study the evolution and taxonomy of staphylococci. However, the results of this method do not correspond to the results of polyphasic taxonomy, and the related species cannot always be distinguished from each other. Thus, new phylogenetic markers for Staphylococcus spp. are needed. We partially sequenced the gap gene (∼931 bp), which encodes the glyceraldehyde-3-phosphate dehydrogenase, for 27 Staphylococcus species. The partial sequences had 24.3 to 96% interspecies homology and were useful in the identification of staphylococcal species (F. Layer, B. Ghebremedhin, W. König, and B. König, J. Microbiol. Methods 70:542-549, 2007). The DNA sequence similarities of the partial staphylococcal gap sequences were found to be lower than those of 16S rRNA (∼97%), rpoB (∼86%), hsp60 (∼82%), and sodA (∼78%). Phylogenetically derived trees revealed four statistically supported groups: S. hyicus/S. intermedius, S. sciuri, S. haemolyticus/S. simulans, and S. aureus/epidermidis. The branching of S. auricularis, S. cohnii subsp. cohnii, and the heterogeneous S. saprophyticus group, comprising S. saprophyticus subsp. saprophyticus and S. equorum subsp. equorum, was not reliable. Thus, the phylogenetic analysis based on the gap gene sequences revealed similarities between the dendrograms based on other gene sequences (e.g., the S. hyicus/S. intermedius and S. sciuri groups) as well as differences, e.g., the grouping of S. arlettae and S. kloosii in the gap-based tree. From our results, we propose the partial sequencing of the gap gene as an alternative molecular tool for the taxonomical analysis of Staphylococcus species and for decreasing the possibility of misidentification. PMID:18174295

  16. Magnetic force microscopy of thin film media for high density magnetic recording

    NARCIS (Netherlands)

    Porthun, Steffen; Porthun, S.; Abelmann, Leon; Lodder, J.C.

    1998-01-01

    This paper discusses various aspect of magnetic force microscopy (MFM) for use in the field of high density magnetic recording. After an introduction of the most important magnetic imaging techniques, an overview is given of the operation and theory of MFM. The developments in instrumentation, MFM

  17. A case of thalamic hemorrhage presenting high density on CT in a long time

    International Nuclear Information System (INIS)

    Hosoya, Takaaki; Takeda, Yoshio; Sugai, Yukio; Umetsu, Akemi; Yamaguchi, Koichi

    1988-01-01

    We presented a thalamic hemorrhage in a 29-year-old woman with idiopathic thrombocytopenic purpura during pregnancy showing a high density lesion at least for 50 days on CT. From beginning of the illness, this condition was considered to continue for 3 months by chronic bleeding or recurrent hemorrhage. (author)

  18. Genetic analysis of long-lived families reveals novel variants influencing high density-lipoprotein cholesterol

    DEFF Research Database (Denmark)

    Feitosa, Mary F; Wojczynski, Mary K; Straka, Robert

    2014-01-01

    The plasma levels of high-density lipoprotein cholesterol (HDL) have an inverse relationship to the risks of atherosclerosis and cardiovascular disease (CVD), and have also been associated with longevity. We sought to identify novel loci for HDL that could potentially provide new insights...

  19. Electrical and mechanical properties of highly elongated high density polyethylene as cryogenic insulation materials

    International Nuclear Information System (INIS)

    Yoshino, Katsumi; Park, Dae-Hee; Miyata, Kiyomi; Yamaoka, Hitoshi; Itoh, Minoru; Ichihara, Syouji.

    1989-01-01

    Electrical and mechanical properties of highly elongated high density polyethylene were investigated in the temperature range between 4.2 K and 400 K from a viewpoint of electrical insulation at low temperature and the following properties have been clarified. (1) The electrical conductivity of samples decreases with increasing draw ratio, and also decreases at cryogenic temperature. (2) Breakdown strength of highly elongated sample is similar to that of non-elongated sample. It is nearby temperature independent below 300 K but at higher temperature it falls steeply. (3) Mechanical breakdown stress and elastic modulus of high density polyethylene increase with increasing draw ratio. Their values at liquid nitrogen temperature are much higher than that at room temperature. On the other hand, strains decreases at liquid nitrogen temperature. (4) Break of the sample develops in the direction of 45deg from the direction of stress both at room temperature and at cryogenic temperature. (5) The characteristic of mechanical breakdown at liquid nitrogen temperature can be explained by a brittleness fracture process. (6) Toughness of high density polyethylene increases with increasing draw ratio until draw ratio of 5, and it decreased, and increase at higher draw ratio. However at extremely high draw ratio of 10 it again increases. These findings clearly indicate that highly elongated high density polyethylene has good electrical and mechanical properties at cryogenic temperature and can be used as the insulating materials at cryogenic temperature. (author)

  20. Residual gas entering high density hydrogen plasma: rarefaction due to rapid heating

    NARCIS (Netherlands)

    N. den Harder,; D.C. Schram,; W. J. Goedheer,; de Blank, H. J.; M. C. M. van de Sanden,; van Rooij, G. J.

    2015-01-01

    The interaction of background molecular hydrogen with magnetized (0.4 T) high density (1–5 × 10 20  m −3 ) low temperature (∼3 eV) hydrogen plasma was inferred from the Fulcher band emission in the linear plasma generator Pilot-PSI. In the plasma center,

  1. Value of information to improve daily operations in high-density logistics

    NARCIS (Netherlands)

    Viet, Nguyen Quoc; Behdani, Behzad; Bloemhof, Jacqueline

    2018-01-01

    Agro-food logistics is increasingly challenged to ensure that a wide variety of high-quality products are always available at retail stores. This paper discusses high-density logistics issues caused by more frequent and smaller orders from retailers. Through a case study of the distribution process

  2. Turbulence at the transition to the high density H-mode in Wendelstein 7-AS plasmas

    DEFF Research Database (Denmark)

    Basse, N.P.; Zoletnik, S.; Baumel, S.

    2003-01-01

    Recently a new improved confinement regime was found in the Wendelstein 7-AS (W7-AS) stellarator (Renner H. et al 1989 Plasma Phys. Control. Fusion 31 1579). The discovery of this high density high confinement mode (HDH-mode) was facilitated by the installation of divertor modules. In this paper,...

  3. High-density EEG coherence analysis using functional units applied to mental fatigue

    NARCIS (Netherlands)

    Caat, Michael ten; Lorist, Monicque M.; Bezdan, Eniko; Roerdink, Jos B.T.M.; Maurits, Natasha M.

    2008-01-01

    Electroencephalography (EEG) coherence provides a quantitative measure of functional brain connectivity which is calculated between pairs of signals as a function of frequency. Without hypotheses, traditional coherence analysis would be cumbersome for high-density EEG which employs a large number of

  4. Usefulness of multi-plane dynamic subtraction CT (MPDS-CT) for intracranial high density lesions

    Energy Technology Data Exchange (ETDEWEB)

    Takagi, Ryo; Kumazaki, Tatsuo [Nippon Medical School, Tokyo (Japan)

    1996-02-01

    We present a new CT technique using the high speed CT scanner in detection and evaluation of temporal and spatial contrast enhancement of intracranial high density lesions. A multi-plane dynamic subtraction CT (MPDS-CT) was performed in 21 patients with intracranial high density lesions. These lesions consisted of 10 brain tumors, 7 intracerebral hemorrhages and 4 vascular malformations (2 untreated, 2 post-embolization). Baseline study was first performed, and 5 sequential planes of covering total high density lesions were selected. After obtaining the 5 sequential CT images as mask images, three series of multi-plane dynamic CT were performed for the same 5 planes with an intravenous bolus injection of contrast medium. MPDS-CT images were reconstructed by subtracting dynamic CT images from the mask ones. MPDS-CT were compared with conventional contrast-enhanced CT. MPDS-CT images showed the definite contrast enhancement of high density brain tumors and vascular malformations which were not clearly identified on conventional contrast-enhanced CT images because of calcified or hemorrhagic lesions and embolic materials, enabling us to eliminate enhanced abnormalities with non-enhanced areas such as unusual intracerebral hemorrhages. MPDS-CT will provide us further accurate and objective information and will be greatly helpful for interpreting pathophysiologic condition. (author).

  5. Should we change our lipid management strategies to focus on non-high-density lipoprotein cholesterol?

    NARCIS (Netherlands)

    Rana, Jamal S.; Boekholdt, S. Matthijs

    2010-01-01

    Purpose of review Despite aggressive low-density lipoprotein cholesterol lowering, patients continue to be at significant risk of cardiovascular events. Assessment of non-high-density lipoprotein cholesterol (non-HDL-C) provides a measure of cholesterol contained in all atherogenic particles. In the

  6. Application of Inkjet Printing in High-Density Pixelated RGB Quantum Dot-Hybrid LEDs

    KAUST Repository

    Haverinen, Hanna; Jabbour, Ghassan E.

    2012-01-01

    to fabricate high-density, pixelated (quarter video graphics array (QVGA) format), monochromatic and RGB quantum dots light-emitting diodes (QDLEDs), where inkjet printing is used to deposit the light-emitting layer of QDs. It shows some of the factors

  7. Los Alamos compact toroid, fast-liner, and high-density Z-pinch programs

    Energy Technology Data Exchange (ETDEWEB)

    Linford, R.K.; Sherwood, A.R.; Hammel, J.E.

    1981-03-01

    The Compact Toroid (CT) and High Density Z-Pinch (HDZP) are two of the plasma configurations presently being studied at Los Alamos. The purpose of these two programs, plus the recently terminated (May 1979) Fast Liner (FL) program, is summarized in this section along with a brief description of the experimental facilities. The remaining sections summarize the recent results and the experimental status.

  8. THE GRAFTING OF MALEIC-ANHYDRIDE ON HIGH-DENSITY POLYETHYLENE IN AN EXTRUDER

    NARCIS (Netherlands)

    GANZEVELD, KJ; JANSSEN, LPBM

    The grafting of maleic anhydride (MAH) on high density polyethylene in a counter-rotating twin screw extruder has been studied. As the reaction kinetics appear to be affected by mass transfer, good micro mixing in the extruder is important. Due to the competing mechanisms of increasing mixing and

  9. High-density lipoprotein modulates glucose metabolism in patients with type 2 diabetes mellitus

    DEFF Research Database (Denmark)

    Drew, Brian G; Duffy, Stephen J; Formosa, Melissa F

    2009-01-01

    BACKGROUND: Low plasma high-density lipoprotein (HDL) is associated with elevated cardiovascular risk and aspects of the metabolic syndrome. We hypothesized that HDL modulates glucose metabolism via elevation of plasma insulin and through activation of the key metabolic regulatory enzyme, AMP...

  10. Self-consistency condition and high-density virial theorem in relativistic many-particle systems

    International Nuclear Information System (INIS)

    Kalman, G.; Canuto, V.; Datta, B.

    1976-01-01

    In order for the thermodynamic and kinetic definitions of the chemical potential and the pressure to lead to identical results a nontrivial self-consistency criterion has to be satisfied. This, in turn, leads to a virial-like theorem in the high-density limit

  11. Scaling of energy confinement and poloidal beta in high density tokamaks

    NARCIS (Netherlands)

    Schram, D.C.; Schüller, F.C.

    1980-01-01

    A semi-empirical analysis of the heat balance of ohmically heated, high density Tokamak plasmas, shows that the observed heat transport can be explained by neoclassical (plateau) ion heat conduction in the central part of the plasma. Experimental values for Te, ß¿e, and tEe and the variation of

  12. Collision frequency of Lennard–Jones fluids at high densities by ...

    Indian Academy of Sciences (India)

    Detailed classical molecular dynamics simulation of transport coefficients and collision frequencies at high densities in rare gases are presented in this paper with a view to investigate the likely cause of discrepancy between theory and experiments. The results, when compared with experiments, showed an ...

  13. The biological properties of iron oxide core high-density lipoprotein in experimental atherosclerosis

    NARCIS (Netherlands)

    Skajaa, Torjus; Cormode, David P.; Jarzyna, Peter A.; Delshad, Amanda; Blachford, Courtney; Barazza, Alessandra; Fisher, Edward A.; Gordon, Ronald E.; Fayad, Zahi A.; Mulder, Willem J. M.

    2011-01-01

    Lipoproteins are a family of plasma nanoparticles responsible for the transportation of lipids throughout the body. High-density lipoprotein (HDL), the smallest of the lipoprotein family, measures 7-13 nm in diameter and consists of a cholesteryl ester and triglyceride core that is covered with a

  14. Nanocrystal core high-density lipoproteins: a multimodality contrast agent platform

    NARCIS (Netherlands)

    Cormode, David P.; Skajaa, Torjus; van Schooneveld, Matti M.; Koole, Rolf; Jarzyna, Peter; Lobatto, Mark E.; Calcagno, Claudia; Barazza, Alessandra; Gordon, Ronald E.; Zanzonico, Pat; Fisher, Edward A.; Fayad, Zahi A.; Mulder, Willem J. M.

    2008-01-01

    High density lipoprotein (HDL) is an important natural nanoparticle that may be modified for biomedical imaging purposes. Here we developed a novel technique to create unique multimodality HDL mimicking nanoparticles by incorporation of gold, iron oxide, or quantum dot nanocrystals for computed

  15. Identifying dielectric and resistive electrode losses in high-density capacitors at radio frequencies

    NARCIS (Netherlands)

    Tiggelman, M.P.J.; Reimann, K.; Liu, J.; Klee, M.; Keur, W.; Mauczock, R.; Schmitz, Jurriaan; Hueting, Raymond Josephus Engelbart

    2008-01-01

    A regression-based technique is presented which distinguishes the dielectric loss from the resistive loss of high density planar capacitors in a very wide bandwidth of 0.1–8 GHz. Moreover, the procedure yields useful results if the capacitor deviates from a lumped element model and indicates when

  16. Guidelines for etching silicon MEMS structures using fluorine high-density plasmas at cryogenic temperatures

    NARCIS (Netherlands)

    de Boer, Meint J.; Gardeniers, Johannes G.E.; Jansen, Henricus V.; Gilde, M.J.; Roelofs, Gerard; Sasserath, Jay N.; Elwenspoek, Michael Curt

    This paper presents guidelines for the deep reactive ion etching (DRIE) of silicon MEMS structures, employing SF6/O2-based high-density plasmas at cryogenic temperatures. Procedures of how to tune the equipment for optimal results with respect to etch rate and profile control are described. Profile

  17. Increased Antioxidant Quality Versus Lower Quantity Of High Density Lipoprotein In Benign Prostatic Hyperplasia

    Directory of Open Access Journals (Sweden)

    Aydin Ozgur

    2015-10-01

    Full Text Available Background: Oxidative stress may be involved in the pathogenesis of every human disease. To understand its possible role in benign prostatic hyperplasia (BPH, we measured the overall oxidative status of patients with BPH and the serum activity of the high density lipoprotein (HDL-related antioxidant enzymes paraoxonase 1 (PON1 and arylesterase (ARE.

  18. Neutron star models with realistic high-density equations of state

    International Nuclear Information System (INIS)

    Malone, R.C.; Johnson, M.B.; Bethe, H.A.

    1975-01-01

    We calculate neutron star models using four realistic high-density models of the equation of state. We conclude that the maximum mass of a neutron star is unlikely to exceed 2 M/sub sun/. All of the realistic models are consistent with current estimates of the moment of inertia of the Crab pulsar

  19. Amorphous silicon rich silicon nitride optical waveguides for high density integrated optics

    DEFF Research Database (Denmark)

    Philipp, Hugh T.; Andersen, Karin Nordström; Svendsen, Winnie Edith

    2004-01-01

    Amorphous silicon rich silicon nitride optical waveguides clad in silica are presented as a high-index contrast platform for high density integrated optics. Performance of different cross-sectional geometries have been measured and are presented with regards to bending loss and insertion loss...

  20. Structure and properties of simple molecular systems at very high density

    International Nuclear Information System (INIS)

    LeSar, R.

    1989-01-01

    The use of computer simulations in the study of molecular systems at very high density is reviewed. Applications to the thermodynamics of dense fluid nitrogen and phase transitions in solid oxygen are presented. The effects of changes in the atomic electronic structure on the equation of state of very dense helium are discussed. 19 refs., 2 figs

  1. Spin polarization in high density quark matter under a strong external magnetic field

    DEFF Research Database (Denmark)

    Tsue, Yasuhiko; Da Providência, João; Providência, Constança

    2016-01-01

    In high density quark matter under a strong external magnetic field, possible phases are investigated by using the two-flavor Nambu-Jona-Lasinio (NJL) model with tensor-type four-point interaction between quarks, as well as the axial-vector-type four-point interaction. In the tensor-type interact...

  2. Interplay between spin polarization and color superconductivity in high density quark matter

    DEFF Research Database (Denmark)

    Tsue, Yasuhiko; da Providência, João; Providência, Constança

    2013-01-01

    Here, it is suggested that a four-point interaction of the tensor type may lead to spin polarization in quark matter at high density. It is found that the two-flavor superconducting phase and the spin polarized phase correspond to distinct local minima of a certain generalized thermodynamical pot...

  3. Effect of resin variables on the creep behavior of high density hardwood composite panels

    Science.gov (United States)

    R.C. Tang; Jianhua Pu; C.Y Hse

    1993-01-01

    The flexural creep behavior of oriented strandboards (OSB) fabricated with mixed high, density hardwood flakes was investigated. Three types of adhesives, liquid phenolic-formaldehyde (LPF), melamine modified urea-formaldehyde (MUF), and LPF (face)/MUF (core) were chosen in this investigation. The resin contents (RC) used were 3.5 percent and 5.0 percent. The flakes...

  4. Incompletely resolved phylogenetic trees inflate estimates of phylogenetic conservatism.

    Science.gov (United States)

    Davies, T Jonathan; Kraft, Nathan J B; Salamin, Nicolas; Wolkovich, Elizabeth M

    2012-02-01

    The tendency for more closely related species to share similar traits and ecological strategies can be explained by their longer shared evolutionary histories and represents phylogenetic conservatism. How strongly species traits co-vary with phylogeny can significantly impact how we analyze cross-species data and can influence our interpretation of assembly rules in the rapidly expanding field of community phylogenetics. Phylogenetic conservatism is typically quantified by analyzing the distribution of species values on the phylogenetic tree that connects them. Many phylogenetic approaches, however, assume a completely sampled phylogeny: while we have good estimates of deeper phylogenetic relationships for many species-rich groups, such as birds and flowering plants, we often lack information on more recent interspecific relationships (i.e., within a genus). A common solution has been to represent these relationships as polytomies on trees using taxonomy as a guide. Here we show that such trees can dramatically inflate estimates of phylogenetic conservatism quantified using S. P. Blomberg et al.'s K statistic. Using simulations, we show that even randomly generated traits can appear to be phylogenetically conserved on poorly resolved trees. We provide a simple rarefaction-based solution that can reliably retrieve unbiased estimates of K, and we illustrate our method using data on first flowering times from Thoreau's woods (Concord, Massachusetts, USA).

  5. Transforming phylogenetic networks: Moving beyond tree space

    OpenAIRE

    Huber, Katharina T.; Moulton, Vincent; Wu, Taoyang

    2016-01-01

    Phylogenetic networks are a generalization of phylogenetic trees that are used to represent reticulate evolution. Unrooted phylogenetic networks form a special class of such networks, which naturally generalize unrooted phylogenetic trees. In this paper we define two operations on unrooted phylogenetic networks, one of which is a generalization of the well-known nearest-neighbor interchange (NNI) operation on phylogenetic trees. We show that any unrooted phylogenetic network can be transforme...

  6. DNA sequencing reveals limited heterogeneity in the 16S rRNA gene from the rrnB operon among five Mycoplasma hominis isolates

    DEFF Research Database (Denmark)

    Mygind, T; Birkelund, Svend; Christiansen, Gunna

    1998-01-01

    To investigate the intraspecies heterogeneity within the 16S rRNA gene of Mycoplasma hominis, five isolates with diverse antigenic profiles, variable/identical P120 hypervariable domains, and different 16S rRNA gene RFLP patterns were analysed. The 16S rRNA gene from the rrnB operon was amplified...

  7. Production of an economic high-density concrete for shielding megavoltage radiotherapy rooms and nuclear reactors

    International Nuclear Information System (INIS)

    Mortazavi, S. M. J.; Mosleh-Shirazi, M. A.; Maheri, M. R.; Haji-pour, A.; Yousefnia, H.; Zolghadri, S.

    2007-01-01

    In megavoltage radiotherapy rooms, ordinary concrete is usually used due to its low construction costs, although higher density concrete are sometimes used, as well. The use of high-density concrete decreases the required thickness of the concrete barrier; hence, its disadvantage is its high cost. In a nuclear reactor, neutron radiation is the most difficult to shield. A method for production of economic high-density concrete witt, appropriate engineering properties would be very useful. Materials and Methods: Galena (Pb S) mineral was used to produce of a high-density concrete. Galena can be found in many parts of Iran. Two types of concrete mixes were produced. The water-to-concrete (w/c) ratios of the reference and galena concrete mixes were 0.53 and 0.25, respectively. To measure the gamma radiation attenuation of Galena concrete samples, they were exposed to a narrow beam of gamma rays emitted from a cobalt-60 therapy unit. Results: The Galena mineral used in this study had a density of 7400 kg/m 3 . The concrete samples had a density of 4800 kg/m 3 . The measured half value layer thickness of the Galena concrete samples for cobalt 60 gamma rays was much less than that of ordinary concrete (2.6 cm compared to 6.0 cm). Furthermore, the galena concrete samples had significantly higher compressive strength (500 kg/cm 2 compared to 300 kg/cm 2 ). Conclusion: The Galena concrete samples made in our laboratories had showed good shielding/engineering properties in comparison with all samples made by using high-density materials other than depleted uranium. Based on the preliminary results, Galena concrete is maybe a suitable option where high-density concrete is required in megavoltage radiotherapy rooms as well as nuclear reactors

  8. Evaluating the microbial diversity of an in vitro model of the human large intestine by phylogenetic microarray analysis

    NARCIS (Netherlands)

    Rajilic-Stojanovic, M.; Maathuis, A.; Heilig, G.H.J.; Venema, K.; Vos, de W.M.; Smidt, H.

    2010-01-01

    A high-density phylogenetic microarray targeting small subunit rRNA (SSU rRNA) sequences of over 1000 microbial phylotypes of the human gastrointestinal tract, the HITChip, was used to assess the impact of faecal inoculum preparation and operation conditions on an in vitro model of the human large

  9. Campylobacter jejuni, an uncommon cause of splenic abscess diagnosed by 16S rRNA gene sequencing

    Directory of Open Access Journals (Sweden)

    Piseth Seng

    2014-12-01

    Full Text Available Splenic abscess is a rare disease that primarily occurs in patients with splenic trauma, endocarditis, sickle cell anemia, or other diseases that compromise the immune system. This report describes a culture-negative splenic abscess in an immunocompetent patient caused by Campylobacter jejuni, as determined by 16S rRNA gene sequencing.

  10. Assessing Cat Flea Microbiomes in Northern and Southern California by 16S rRNA Next-Generation Sequencing.

    Science.gov (United States)

    Vasconcelos, Elton J R; Billeter, Sarah A; Jett, Lindsey A; Meinersmann, Richard J; Barr, Margaret C; Diniz, Pedro P V P; Oakley, Brian B

    2018-06-12

    Flea-borne diseases (FBDs) impact both human and animal health worldwide. Because adult fleas are obligately hematophagous and can harbor potential pathogens, fleas act as ectoparasites of vertebrates, as well as zoonotic disease vectors. Cat fleas (Ctenocephalides felis) are important vectors of two zoonotic bacterial genera listed as priority pathogens by the National Institute of Allergy and Infectious Diseases (NIAID-USA): Bartonella spp. and Rickettsia spp., causative agents of bartonelloses and rickettsioses, respectively. In this study, we introduce the first microbiome analysis of C. felis samples from California, determining the presence and abundance of relevant pathogenic genera by characterizing the cat flea microbiome through 16S rRNA next-generation sequencing (16S-NGS). Samples from both northern (NoCal) and southern (SoCal) California were assessed to expand current knowledge regarding FBDs in the state. We identified Rickettsia and Bartonella, as well as the endosymbiont Wolbachia, as the most abundant genera, followed by less abundant taxa. In comparison to our previous study screening Californian cat fleas for rickettsiae using PCR/digestion/sequencing of the ompB gene, the 16S-NGS approach applied herein showed a 95% level of agreement in detecting Rickettsia spp. There was no overall difference in microbiome diversity between NoCal and SoCal samples. Bacterial taxa identified by 16S-NGS in this study may help to improve epidemiological investigations, pathogen surveillance efforts, and clinical diagnostics of FBDs in California and elsewhere.

  11. 16S rRNA amplicon sequencing identifies microbiota associated with oral cancer, Human Papilloma Virus infection and surgical treatment

    NARCIS (Netherlands)

    Guerrero-Preston, Rafael; Godoy-Vitorino, Filipa; Jedlicka, Anne; Rodriguez-Hilario, Arnold; Gonzalez, Herminio; Bondy, Jessica; Lawson, Fahcina; Folawiyo, Oluwasina; Michailidi, Christina; Dziedzic, Amanda; Thangavel, Rajagowthamee; Hadar, Tal; Noordhuis, Maartje G.; Westra, William; Koch, Wayne; Sidransky, David

    2016-01-01

    Systemic inflammatory events and localized disease, mediated by the microbiome, may be measured in saliva as head and neck squamous cell carcinoma (HNSCC) diagnostic and prognostic biomonitors. We used a 16S rRNA V3-V5 marker gene approach to compare the saliva microbiome in DNA isolated from

  12. Methyltransferase That Modifies Guanine 966 of the 16 S rRNA: FUNCTIONAL IDENTIFICATION AND TERTIARY STRUCTURE*

    Science.gov (United States)

    Lesnyak, Dmitry V.; Osipiuk, Jerzy; Skarina, Tatiana; Sergiev, Petr V.; Bogdanov, Alexey A.; Edwards, Aled; Savchenko, Alexei; Joachimiak, Andrzej; Dontsova, Olga A.

    2010-01-01

    N2-Methylguanine 966 is located in the loop of Escherichia coli 16 S rRNA helix 31, forming a part of the P-site tRNA-binding pocket. We found yhhF to be a gene encoding for m2G966 specific 16 S rRNA methyltransferase. Disruption of the yhhF gene by kanamycin resistance marker leads to a loss of modification at G966. The modification could be rescued by expression of recombinant protein from the plasmid carrying the yhhF gene. Moreover, purified m2G966 methyltransferase, in the presence of S-adenosylomethionine (AdoMet), is able to methylate 30 S ribosomal subunits that were purified from yhhF knock-out strain in vitro. The methylation is specific for G966 base of the 16 S rRNA. The m2G966 methyltransferase was crystallized, and its structure has been determined and refined to 2.05 Å. The structure closely resembles RsmC rRNA methyltransferase, specific for m2G1207 of the 16 S rRNA. Structural comparisons and analysis of the enzyme active site suggest modes for binding AdoMet and rRNA to m2G966 methyltransferase. Based on the experimental data and current nomenclature the protein expressed from the yhhF gene was renamed to RsmD. A model for interaction of RsmD with ribosome has been proposed. PMID:17189261

  13. Methyltransferase that modifies guanine 966 of the 16 S rRNA: functional identification and tertiary structure.

    Science.gov (United States)

    Lesnyak, Dmitry V; Osipiuk, Jerzy; Skarina, Tatiana; Sergiev, Petr V; Bogdanov, Alexey A; Edwards, Aled; Savchenko, Alexei; Joachimiak, Andrzej; Dontsova, Olga A

    2007-02-23

    N(2)-Methylguanine 966 is located in the loop of Escherichia coli 16 S rRNA helix 31, forming a part of the P-site tRNA-binding pocket. We found yhhF to be a gene encoding for m(2)G966 specific 16 S rRNA methyltransferase. Disruption of the yhhF gene by kanamycin resistance marker leads to a loss of modification at G966. The modification could be rescued by expression of recombinant protein from the plasmid carrying the yhhF gene. Moreover, purified m(2)G966 methyltransferase, in the presence of S-adenosylomethionine (AdoMet), is able to methylate 30 S ribosomal subunits that were purified from yhhF knock-out strain in vitro. The methylation is specific for G966 base of the 16 S rRNA. The m(2)G966 methyltransferase was crystallized, and its structure has been determined and refined to 2.05A(.) The structure closely resembles RsmC rRNA methyltransferase, specific for m(2)G1207 of the 16 S rRNA. Structural comparisons and analysis of the enzyme active site suggest modes for binding AdoMet and rRNA to m(2)G966 methyltransferase. Based on the experimental data and current nomenclature the protein expressed from the yhhF gene was renamed to RsmD. A model for interaction of RsmD with ribosome has been proposed.

  14. Optimisation of 16S rDNA amplicon sequencing protocols for microbial community profiling of anaerobic digesters

    DEFF Research Database (Denmark)

    Kirkegaard, Rasmus Hansen; McIlroy, Simon Jon; Larsen, Poul

    A reliable and reproducible method for identification and quantification of the microorganisms involved in biogas production is important for the study and understanding of the microbial communities responsible for the function of anaerobic digester systems. DNA based identification using 16S rRN...

  15. A Web-Hosted R Workflow to Simplify and Automate the Analysis of 16S NGS Data

    Science.gov (United States)

    Next-Generation Sequencing (NGS) produces large data sets that include tens-of-thousands of sequence reads per sample. For analysis of bacterial diversity, 16S NGS sequences are typically analyzed in a workflow that containing best-of-breed bioinformatics packages that may levera...

  16. Obtaining representative community profiles of anaerobic digesters through optimisation of 16S rRNA amplicon sequencing protocols

    DEFF Research Database (Denmark)

    Kirkegaard, Rasmus Hansen; McIlroy, Simon Jon; Karst, Søren Michael

    A reliable and reproducible method for identification and quantification of the microorganisms involved in biogas production is important for the study and understanding of the microbial communities responsible for the function of anaerobic digester systems. DNA based identification using 16S r...

  17. Unexpected Diagnosis of Cerebral Toxoplasmosis by 16S and D2 Large-Subunit Ribosomal DNA PCR and Sequencing

    DEFF Research Database (Denmark)

    Kruse, Alexandra Yasmin Collin; Kvich, Lasse Andersson; Eickhardt-Dalbøge, Steffen Robert

    2015-01-01

    The protozoan parasite Toxoplasma gondii causes severe opportunistic infections. Here, we report an unexpected diagnosis of cerebral toxoplasmosis. T. gondii was diagnosed by 16S and D2 large-subunit (LSU) ribosomal DNA (rDNA) sequencing of a cerebral biopsy specimen and confirmed by T. gondii...

  18. Direct 16S rRNA gene sequencing of polymicrobial culture-negative samples with analysis of mixed chromatograms

    DEFF Research Database (Denmark)

    Hartmeyer, Gitte N; Justesen, Ulrik S

    2010-01-01

    Two cases involving polymicrobial culture-negative samples were investigated by 16S rRNA gene sequencing, with analysis of mixed chromatograms. Fusobacterium necrophorum, Prevotella intermedia and Streptococcus constellatus were identified from pleural fluid in a patient with Lemierre's syndrome...

  19. 16S rRNA gene sequencing in routine identification of anaerobic bacteria isolated from blood cultures

    DEFF Research Database (Denmark)

    Justesen, Ulrik Stenz; Skov, Marianne Nielsine; Knudsen, Elisa

    2010-01-01

    A comparison between conventional identification and 16S rRNA gene sequencing of anaerobic bacteria isolated from blood cultures in a routine setting was performed (n = 127). With sequencing, 89% were identified to the species level, versus 52% with conventional identification. The times...

  20. TaxCollector: Modifying Current 16S rRNA Databases for the Rapid Classification at Six Taxonomic Levels

    Directory of Open Access Journals (Sweden)

    Eric W. Triplett

    2010-07-01

    Full Text Available The high level of conservation of 16S ribosomal RNA gene (16S rRNA in all Prokaryotes makes this gene an ideal tool for the rapid identification and classification of these microorganisms. Databases such as the Ribosomal Database Project II (RDP-II and the Greengenes Project offer access to sets of ribosomal RNA sequence databases useful in identification of microbes in a culture-independent analysis of microbial communities. However, these databases do not contain all of the taxonomic levels attached to the published names of the bacterial and archaeal sequences. TaxCollector is a set of scripts developed in Python language that attaches taxonomic information to all 16S rRNA sequences in the RDP-II and Greengenes databases. These modified databases are referred to as TaxCollector databases, which when used in conjunction with BLAST allow for rapid classification of sequences from any environmental or clinical source at six different taxonomic levels, from domain to species. The TaxCollector database prepared from the RDP-II database is an important component of a new 16S rRNA pipeline called PANGEA. The usefulness of TaxCollector databases is demonstrated with two very different datasets obtained using samples from a clinical setting and an agricultural soil. The six TaxCollector scripts are freely available on http://taxcollector.sourceforge.net and on http://www.microgator.org.

  1. Comparison of gull-specific assays targeting 16S rRNA gene of Catellicoccus marimammalium and Streptococcus spp.

    Science.gov (United States)

    Gulls have been implicated as a source of fecal contamination in inland and coastal waters. Only one gull-specific assay is currently available (i.e., gull2 qPCR assay). This assay is based on the 16S rRNA gene of Catellicocclls marimammalium and has showed a high level of host-s...

  2. Ultrafast Approximation for Phylogenetic Bootstrap

    NARCIS (Netherlands)

    Bui Quang Minh, [No Value; Nguyen, Thi; von Haeseler, Arndt

    Nonparametric bootstrap has been a widely used tool in phylogenetic analysis to assess the clade support of phylogenetic trees. However, with the rapidly growing amount of data, this task remains a computational bottleneck. Recently, approximation methods such as the RAxML rapid bootstrap (RBS) and

  3. A format for phylogenetic placements.

    Directory of Open Access Journals (Sweden)

    Frederick A Matsen

    Full Text Available We have developed a unified format for phylogenetic placements, that is, mappings of environmental sequence data (e.g., short reads into a phylogenetic tree. We are motivated to do so by the growing number of tools for computing and post-processing phylogenetic placements, and the lack of an established standard for storing them. The format is lightweight, versatile, extensible, and is based on the JSON format, which can be parsed by most modern programming languages. Our format is already implemented in several tools for computing and post-processing parsimony- and likelihood-based phylogenetic placements and has worked well in practice. We believe that establishing a standard format for analyzing read placements at this early stage will lead to a more efficient development of powerful and portable post-analysis tools for the growing applications of phylogenetic placement.

  4. The use of 16s rDNA methods in soil microbial ecology Uso de métodos 16S rDNA em ecologia microbiana do solo

    Directory of Open Access Journals (Sweden)

    Andrew Macrae

    2000-06-01

    Full Text Available New and exciting molecular methods, many using the 16S small sub-unit ribosomal nucleic acid molecule, are opening the microbial "black box" in soil. These studies have added much to our knowledge of microbial diversity in soils, and are beginning to advance our understanding of the relationship between this diversity and its function in soil processes. Over the next few years, the knowledge gained from molecular studies will, we hope, lead to improvements in sustainable land management and sustainable exploitation of soil genetic resources. As we enter the third millenium, it is appropriate to review the application of 16S rDNA methods to soil microbiology. This review examines 16S ribosomal DNA (rDNA methods and their application to soil. It mentions their limits and suggests how they may be applied in the future.Novas e excitantes técnicas moleculares muitas usando a fração 16S da subunidade menor da molécula de ácido nucleico ribossomal, estão abrindo a "caixa-preta" da microbiologia do solo. Esses estudos têm acrescentado muito ao nosso conhecimento acerca da diversidade microbiana no solo, e começam a avançar nosso entendimento sobre a relação entre essa diversidade a sua função nos processos no solo. Ao longo dos próximos anos, o conhecimento obtido a partir de técnicas moleculares irão, esperamos, levar a melhoramentos do manejo de áreas sustentáveis da exploração dos recursos genéticos do solo. Com a chegada do terceiro milênio, é apropriado revermos a aplicação das técnicas da fração 16S do rDNA em microbiologia de solo. Esta revisão examina aplicações das técnicas da fração 16S do DNA (RNA no solo, menciona seus limites e sugere como elas poderão ser usadas no futuro.

  5. High density plasma productions by hydrogen storage electrode in the Tohoku University Heliac

    International Nuclear Information System (INIS)

    Utoh, H.; Takahashi, H.; Tanaka, Y.; Takenaga, M.; Ogawa, M.; Shinde, J.; Iwazaki, K.; Shinto, K.; Kitajima, S.; Sasao, M.; Nishimura, K.; Inagaki, S.

    2005-01-01

    In the Tohoku University Heliac (TU-Heliac), the influence of a radial electric field on improved modes has been investigated by an electrode biasing. In both positive and negative biasing experiments by the stainless steel (SUS) electrode (cold-electron or ion collection), the improvement of plasma confinement was clearly observed. Furthermore, by negative biasing with a hot cathode (electron injection), the radial electric fields can be actively controlled as a consequence of the control of the electrode current I E . By using the electrode made of a hydrogen storage metal, for example Titanium (Ti) or Vanadium (V), the following possibility can be expected: (1) ions accelerated from the positive biased electrode allow the simulation for the orbit loss of high-energy particles, (2) the electrons/neutral- particles injected from the negative biased electrode provide the production of the high- density plasma, if hydrogen are successfully stored in the electrode. In this present work, several methods were tried as the treatment for hydrogen storage. In the case of the Ti electrode biased positively after the treatment, the improvement of plasma confinement was observed in He plasma, which were same as the experimental results of the SUS electrode. However, in the electron density profiles inside the electrode position there was difference between the biased plasma by the Ti electrode and that by the SUS electrode. In some of Ar discharges biased negatively with the Ti electrode after the treatment, the electron density and the line intensity of H α increased about 10 times of those before biasing. This phenomenon has not been observed in the Ar plasma biased by the SUS electrode. This result suggested that the Ti electrode injected electrons/neutral-hydrogen into the plasma. This high-density plasma productions were observed only 1 ∼ 3 times in the one treatment for hydrogen storage. By using a Vanadium (V) electrode, productions of the high-density plasma

  6. Phylogenetic molecular function annotation

    International Nuclear Information System (INIS)

    Engelhardt, Barbara E; Jordan, Michael I; Repo, Susanna T; Brenner, Steven E

    2009-01-01

    It is now easier to discover thousands of protein sequences in a new microbial genome than it is to biochemically characterize the specific activity of a single protein of unknown function. The molecular functions of protein sequences have typically been predicted using homology-based computational methods, which rely on the principle that homologous proteins share a similar function. However, some protein families include groups of proteins with different molecular functions. A phylogenetic approach for predicting molecular function (sometimes called 'phylogenomics') is an effective means to predict protein molecular function. These methods incorporate functional evidence from all members of a family that have functional characterizations using the evolutionary history of the protein family to make robust predictions for the uncharacterized proteins. However, they are often difficult to apply on a genome-wide scale because of the time-consuming step of reconstructing the phylogenies of each protein to be annotated. Our automated approach for function annotation using phylogeny, the SIFTER (Statistical Inference of Function Through Evolutionary Relationships) methodology, uses a statistical graphical model to compute the probabilities of molecular functions for unannotated proteins. Our benchmark tests showed that SIFTER provides accurate functional predictions on various protein families, outperforming other available methods.

  7. Phylogenetic characterization of two echinoid species of the southeastern Mediterranean, off Egypt

    Directory of Open Access Journals (Sweden)

    Taha Soliman

    2015-12-01

    Full Text Available In this study we investigated the phylogenetics of two sea urchin species, Arbacia lixula and Paracentrotus lividus from the Mediterranean Sea. Specimens were collected from the east coast of Alexandria City, Egypt. Pigmentation examination showed four sympatric color morphotypes (black, purple, reddish brown, and olive green. Mitochondrial DNA was extracted from specimens and mitochondrial cytochrome oxidase subunit I (COI and 16S ribosomal RNA (16S were sequenced. The results showed that all black specimens constituted the species A. lixula. All other colors belonged to P. lividus, with no apparent differentiation between color morphotypes. Moreover, P. lividus showed high haplotype diversity (COI; H = 0.9500 and 16S; H = 0.8580 and low values of nucleotide diversity (COI; π = 0.0075 and 16S; π = 0.0049, indicating a high degree of polymorphism within this species. This study represents the first attempt at DNA barcoding of echinoid species in the southeast Mediterranean off the Egyptian coast, and will provide a base for future phylogenetic analyses.

  8. Workshop on High Power ICH Antenna Designs for High Density Tokamaks

    Science.gov (United States)

    Aamodt, R. E.

    1990-02-01

    A workshop in high power ICH antenna designs for high density tokamaks was held to: (1) review the data base relevant to the high power heating of high density tokamaks; (2) identify the important issues which need to be addressed in order to ensure the success of the ICRF programs on CIT and Alcator C-MOD; and (3) recommend approaches for resolving the issues in a timely realistic manner. Some specific performance goals for the antenna system define a successful design effort. Simply stated these goals are: couple the specified power per antenna into the desired ion species; produce no more than an acceptable level of RF auxiliary power induced impurities; and have a mechanical structure which safely survives the thermal, mechanical and radiation stresses in the relevant environment. These goals are intimately coupled and difficult tradeoffs between scientific and engineering constraints have to be made.

  9. Workshop on high power ICH antenna designs for high density tokamaks

    International Nuclear Information System (INIS)

    Aamodt, R.E.

    1990-01-01

    A workshop in high power ICH antenna designs for high density tokamaks was held in Boulder, Colorado on January 31 through February 2, 1990. The purposes of the workshop were to: (1) review the data base relevant to the high power heating of high density tokamaks; (2) identify the important issues which need to be addressed in order to ensure the success of the ICRF programs on CIT and Alcator C-MOD; and (3) recommend approaches for resolving the issues in a timely realistic manner. Some specific performance goals for the antenna system define a successful design effort. Simply stated these goals are: couple the specified power per antenna into the desired ion species; produce no more than an acceptable level of rf auxiliary power induced impurities; and have a mechanical structure which safely survives the thermal, mechanical and radiation stresses in the relevant environment. These goals are intimately coupled and difficult tradeoffs between scientific and engineering constraints have to be made

  10. A complete life cycle assessment of high density polyethylene plastic bottle

    Science.gov (United States)

    Treenate, P.; Limphitakphong, N.; Chavalparit, O.

    2017-07-01

    This study was aimed to determine environmental performances of a lubricant oil bottle made from high density polyethylene and to develop potential measures for reducing its impacts. A complete life cycle assessment was carried out to understand a whole effect on the environment from acquiring, processing, using, and disposing the product. Two scenarios of disposal phase; recycle and incineration: were examined to quantify a lesser degree on environmental impact. The results illustrated that major impacts of the two scenarios were at the same categories with the highest contributor of raw material acquisition and pre-processing. However, all impacts in case of recycling provided a lower point than that in case of incineration, except mineral extraction. Finally, feasible measures for reducing the environmental impact of high density polyethylene plastic bottle were proposed in accordance with 3Rs concept.

  11. High-density near-field optical disc recording using phase change media and polycarbonate substrate

    Science.gov (United States)

    Shinoda, Masataka; Saito, Kimihiro; Ishimoto, Tsutomu; Kondo, Takao; Nakaoki, Ariyoshi; Furuki, Motohiro; Takeda, Minoru; Akiyama, Yuji; Shimouma, Takashi; Yamamoto, Masanobu

    2004-09-01

    We developed a high density near field optical recording disc system with a solid immersion lens and two laser sources. In order to realize the near field optical recording, we used a phase change recording media and a molded polycarbonate substrate. The near field optical pick-up consists of a solid immersion lens with numerical aperture of 1.84. The clear eye pattern of 90.2 GB capacity (160nm track pitch and 62 nm per bit) was observed. The jitter using a limit equalizer was 10.0 % without cross-talk. The bit error rate using an adaptive PRML with 8 taps was 3.7e-6 without cross-talk. We confirmed that the near field optical disc system is a promising technology for a next generation high density optical disc system.

  12. Evaluation of electrical crosstalk in high-density photodiode arrays for X-ray imaging applications

    International Nuclear Information System (INIS)

    Ji Fan; Juntunen, Mikko; Hietanen, Iiro

    2009-01-01

    Electrical crosstalk is one of the important parameters in the photodiode array detector for X-ray imaging applications, and it becomes more important when the density of the photodiode array becomes higher. This paper presents the design of the high-density photodiode array with 250 μm pitch and 50 μm gap. The electrical crosstalk of the demonstrated samples is evaluated and compared with different electrode configurations: cathode bias mode and anode bias mode. The measurement results show good electrical crosstalk, ∼0.23%, in cathode bias mode regardless of the bias voltage, and slightly decreased or increased electrical crosstalk in anode bias mode. Moreover, the quantum efficiency is also evaluated from the same samples, and it behaves similar to the electrical crosstalk. Finally, some design guidance of the high-density photodiode array is given based on the discussion.

  13. ChemicalVia: a CERN-patented technology for use in high-density circuits

    CERN Multimedia

    Patrice Loïez

    2003-01-01

    High-density multilayer printed circuits such as those pictured here are found in miniaturized modern equipment from video cameras to mobile phones. Adjacent layers in these circuits are electrically connected by microvias, consisting of a small-diameter hole (usually 50 µm) with a thin metal-deposited surface covering their cylindrical walls to ensure local conductivity between the two layers. ChemicalVia is a new method, patented by CERN, to make microvias on high-density multilayer printed circuits using chemicals rather than complex laser, plasma or photoimaging technology. The process is compatible with all standard printed-circuit assembly lines, and has the advantages of low initial investment and reduced manufacturing costs. http://www.cern.ch/ttdatabase

  14. Density measurements of small amounts of high-density solids by a floatation method

    International Nuclear Information System (INIS)

    Akabori, Mitsuo; Shiba, Koreyuki

    1984-09-01

    A floatation method for determining the density of small amounts of high-density solids is described. The use of a float combined with an appropriate floatation liquid allows us to measure the density of high-density substances in small amounts. Using the sample of 0.1 g in weight, the floatation liquid of 3.0 g cm -3 in density and the float of 1.5 g cm -3 in apparent density, the sample densities of 5, 10 and 20 g cm -3 are determined to an accuracy better than +-0.002, +-0.01 and +-0.05 g cm -3 , respectively that correspond to about +-1 x 10 -5 cm 3 in volume. By means of appropriate degassing treatments, the densities of (Th,U)O 2 pellets of --0.1 g in weight and --9.55 g cm -3 in density were determined with an accuracy better than +-0.05 %. (author)

  15. High density lipoproteins as indicators of endothelial dysfunction in children with diadetes type I

    Directory of Open Access Journals (Sweden)

    Lobanova S.M.

    2011-12-01

    Full Text Available The aim of the investigation was to study the level of blood high density lipoproteins (HDL in the groups of children with different course of diadetes type I in order to find out the dependence of course and complications of diabetes on that level. Materials and methods: Blood high density lipoprotein (HDL levels were investigated in children and adolescents with diadetes type I, depending on the duration of diadetes type I, age, stage of sexual development, the stage of diabetic nephropathy and levels of plasma endothelin-1 (E-1. Results: Decrease in HDL level with increasing duration of diadetes type I in prepubertate patients, higher indices of HDL cholesterol were determined in girls, especially with impaired puberty. HDL cholesterol was higher in diabetic nephropathy at the stage of proteinuria and high level of blood endothelin-1. Conclusion: The revealed changes were considered to cause deregulation of vascular endothelium as a manifestation of the initial stages of endothelial dysfunction

  16. Equation-of-state for fluids at high densities-hydrogen isotope measurements and thermodynamic derivations

    International Nuclear Information System (INIS)

    Liebenberg, D.H.; Mills, R.L.; Bronson, J.C.

    1977-01-01

    Hydrogen isotopes play an important role in energy technologies, in particular, the compression to high densities for initiation of controlled thermonuclear fusion energy. At high densities the properties of the compressed hydrogen isotopes depart drastically from ideal thermodynamic predictions. The measurement of accurate data including the author's own recent measurements of n-H 2 and n-D 2 in the range 75 to 300 K and 0.2 to 2.0 GPa (2 to 20 kbar) is reviewed. An equation-of-state of the Benedict type is fit to these data with a double-process least-squares computer program. The results are reviewed and compared with existing data and with a variety of theoretical work reported for fluid hydrogens. A new heuristic correlation is presented for simplicity in predicting volumes and sound velocity at high pressures. 9 figures, 1 table

  17. The use of high-density concretes in radiotherapy treatment room design

    International Nuclear Information System (INIS)

    Facure, A.; Silva, A.X.

    2007-01-01

    With the modernization of radiotherapic centers, medical linear accelerators are largely replacing 60 Co teletherapy units. In many cases, the same vault housing the 60 Co teletherapy unit is reused for the linear accelerator and, when space is at a premium, high-density concrete (3.0-5.0 g/cm 3 ) is employed to provide shielding against the primary, scatter and leakage radiation. This work presents a study based on Monte Carlo simulations of transmission of some clinical photon spectra (of 4-10 MV accelerators) through some types of high-density concretes, normally used in the construction of radiotherapy bunkers. From the simulations, the initial and subsequent tenth-value layers (TVL) for these materials, taking into account realistic clinical photon spectra, are presented, for primary radiation

  18. High-density 3D graphene-based monolith and related materials, methods, and devices

    Energy Technology Data Exchange (ETDEWEB)

    Worsley, Marcus A.; Baumann, Theodore F.; Biener, Juergen; Charnvanichborikarn, Supakit; Kucheyev, Sergei; Montalvo, Elizabeth; Shin, Swanee; Tylski, Elijah

    2017-03-21

    A composition comprising at least one high-density graphene-based monolith, said monolith comprising a three-dimensional structure of graphene sheets crosslinked by covalent carbon bonds and having a density of at least 0.1 g/cm.sup.3. Also provided is a method comprising: preparing a reaction mixture comprising a suspension and at least one catalyst, said suspension selected from a graphene oxide (GO) suspension and a carbon nanotube suspension; curing the reaction mixture to produce a wet gel; drying the wet gel to produce a dry gel, said drying step is substantially free of supercritical drying and freeze drying; and pyrolyzing the dry gel to produce a high-density graphene-based monolith. Exceptional combinations of properties are achieved including high conductive and mechanical properties.

  19. High-density carbon ablator ignition path with low-density gas-filled rugby hohlraum

    International Nuclear Information System (INIS)

    Amendt, Peter; Ho, Darwin D.; Jones, Ogden S.

    2015-01-01

    A recent low gas-fill density (0.6 mg/cc 4 He) cylindrical hohlraum experiment on the National Ignition Facility has shown high laser-coupling efficiency (>96%), reduced phenomenological laser drive corrections, and improved high-density carbon capsule implosion symmetry [Jones et al., Bull. Am. Phys. Soc. 59(15), 66 (2014)]. In this Letter, an ignition design using a large rugby-shaped hohlraum [Amendt et al., Phys. Plasmas 21, 112703 (2014)] for high energetics efficiency and symmetry control with the same low gas-fill density (0.6 mg/cc 4 He) is developed as a potentially robust platform for demonstrating thermonuclear burn. The companion high-density carbon capsule for this hohlraum design is driven by an adiabat-shaped [Betti et al., Phys. Plasmas 9, 2277 (2002)] 4-shock drive profile for robust high gain (>10) 1-D ignition performance and large margin to 2-D perturbation growth

  20. High-density carbon ablator ignition path with low-density gas-filled rugby hohlraum

    Science.gov (United States)

    Amendt, Peter; Ho, Darwin D.; Jones, Ogden S.

    2015-04-01

    A recent low gas-fill density (0.6 mg/cc 4He) cylindrical hohlraum experiment on the National Ignition Facility has shown high laser-coupling efficiency (>96%), reduced phenomenological laser drive corrections, and improved high-density carbon capsule implosion symmetry [Jones et al., Bull. Am. Phys. Soc. 59(15), 66 (2014)]. In this Letter, an ignition design using a large rugby-shaped hohlraum [Amendt et al., Phys. Plasmas 21, 112703 (2014)] for high energetics efficiency and symmetry control with the same low gas-fill density (0.6 mg/cc 4He) is developed as a potentially robust platform for demonstrating thermonuclear burn. The companion high-density carbon capsule for this hohlraum design is driven by an adiabat-shaped [Betti et al., Phys. Plasmas 9, 2277 (2002)] 4-shock drive profile for robust high gain (>10) 1-D ignition performance and large margin to 2-D perturbation growth.

  1. High-density carbon ablator ignition path with low-density gas-filled rugby hohlraum

    Energy Technology Data Exchange (ETDEWEB)

    Amendt, Peter; Ho, Darwin D.; Jones, Ogden S. [Lawrence Livermore National Laboratory, Livermore, California 94551 (United States)

    2015-04-15

    A recent low gas-fill density (0.6 mg/cc {sup 4}He) cylindrical hohlraum experiment on the National Ignition Facility has shown high laser-coupling efficiency (>96%), reduced phenomenological laser drive corrections, and improved high-density carbon capsule implosion symmetry [Jones et al., Bull. Am. Phys. Soc. 59(15), 66 (2014)]. In this Letter, an ignition design using a large rugby-shaped hohlraum [Amendt et al., Phys. Plasmas 21, 112703 (2014)] for high energetics efficiency and symmetry control with the same low gas-fill density (0.6 mg/cc {sup 4}He) is developed as a potentially robust platform for demonstrating thermonuclear burn. The companion high-density carbon capsule for this hohlraum design is driven by an adiabat-shaped [Betti et al., Phys. Plasmas 9, 2277 (2002)] 4-shock drive profile for robust high gain (>10) 1-D ignition performance and large margin to 2-D perturbation growth.

  2. OSCAR experiment high-density network data report: Event 3 - April 16-17, 1981

    Energy Technology Data Exchange (ETDEWEB)

    Dana, M.T.; Easter, R.C.; Thorp, J.M.

    1984-12-01

    The OSCAR (Oxidation and Scavenging Characteristics of April Rains) experiment, conducted during April 1981, was a cooperative field investigation of wet removal in cyclonic storm systems. The high-density component of OSCAR was located in northeast Indiana and included sequential precipitation chemistry measurements on a 100 by 100 km network, as well as airborne air chemistry and cloud chemistry measurements, surface air chemistry measurements, and supporting meteorological measurements. Four separate storm events were studied during the experiment. This report summarizes data taken by Pacific Northwest Laboratory (PNL) during the third storm event, April 16-17. The report contains the high-density network precipitation chemistry data, air chemistry and cloud chemistry data from the PNL aircraft, and meteorological data for the event, including standard National Weather Service products and radar and rawindsonde data from the network. 4 references, 76 figures, 6 tables.

  3. Thermal Experimental Analysis for Dielectric Characterization of High Density Polyethylene Nanocomposites

    Directory of Open Access Journals (Sweden)

    Ahmed Thabet Mohamed

    2016-01-01

    Full Text Available The importance of nanoparticles in controlling physical properties of polymeric nanocomposite materials leads us to study effects of these nanoparticles on electric and dielectric properties of polymers in industry In this research, the dielectric behaviour of High-Density Polyethylene (HDPE nanocomposites materials that filled with nanoparticles of clay or fumed silica has been investigated at various frequencies (10 Hz-1 kHz and temperatures (20-60°C. Dielectric spectroscopy has been used to characterize ionic conduction, then, the effects of nanoparticles concentration on the dielectric losses and capacitive charge of the new nanocomposites can be stated. Capacitive charge and loss tangent in high density polyethylene nanocomposites are measured by dielectric spectroscopy. Different dielectric behaviour has been observed depending on type and concentration of nanoparticles under variant thermal conditions.

  4. High density FTA plates serve as efficient long-term sample storage for HLA genotyping.

    Science.gov (United States)

    Lange, V; Arndt, K; Schwarzelt, C; Boehme, I; Giani, A S; Schmidt, A H; Ehninger, G; Wassmuth, R

    2014-02-01

    Storage of dried blood spots (DBS) on high-density FTA(®) plates could constitute an appealing alternative to frozen storage. However, it remains controversial whether DBS are suitable for high-resolution sequencing of human leukocyte antigen (HLA) alleles. Therefore, we extracted DNA from DBS that had been stored for up to 4 years, using six different methods. We identified those extraction methods that recovered sufficient high-quality DNA for reliable high-resolution HLA sequencing. Further, we confirmed that frozen whole blood samples that had been stored for several years can be transferred to filter paper without compromising HLA genotyping upon extraction. Concluding, DNA derived from high-density FTA(®) plates is suitable for high-resolution HLA sequencing, provided that appropriate extraction protocols are employed. © 2014 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  5. Fueling with edge recycling to high-density in DIII-D

    Energy Technology Data Exchange (ETDEWEB)

    Leonard, A.W., E-mail: leonard@fusion.gat.com [General Atomics, P.O. Box 85608, San Diego, CA 92186-5608 (United States); Elder, J.D. [University of Toronto Institute of Aerospace Studies, Toronto, Canada M3H 5T6 (Canada); Canik, J.M. [Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, TN 37831 (United States); Groebner, R.J.; Osborne, T.H. [General Atomics, P.O. Box 85608, San Diego, CA 92186-5608 (United States)

    2013-07-15

    Pedestal fueling through edge recycling is examined with the interpretive OEDGE code for high-density discharges in DIII-D. A high current, high-density discharge is found to have a similar radial ion flux profile through the pedestal to a lower current, lower density discharge. The higher density discharge, however, has a greater density gradient indicating a pedestal particle diffusion coefficient that scales near linear with 1/I{sub p}. The time dependence of density profile is taken into account in the analysis of a discharge with low frequency ELMs. The time-dependent analysis indicates that the inferred neutral ionization source is inadequate to account for the increase in the density profile between ELMs, implying an inward density convection, or density pinch, near the top of the pedestal.

  6. High density high performance plasma with internal diffusion barrier in Large Helical Device

    International Nuclear Information System (INIS)

    Sakamoto, R.; Kobayashi, M.; Miyazawa, J.

    2008-10-01

    A attractive high density plasma operational regime, namely an internal diffusion barrier (IDB), has been discovered in the intrinsic helical divertor configuration on the Large Helical Device (LHD). The IDB which enables core plasma to access a high density/high pressure regime has been developed. It is revealed that the IDB is reproducibly formed by pellet fueling in the magnetic configurations shifted outward in major radius. Attainable central plasma density exceeds 1x10 21 m -3 . Central pressure reaches 1.5 times atmospheric pressure and the central β value becomes fairly high even at high magnetic field, i.e. β(0)=5.5% at B t =2.57 T. (author)

  7. Implosion characteristics of deuterium--tritium pellets surrounded by high-density shells

    International Nuclear Information System (INIS)

    Fraley, G.S.

    1976-09-01

    The effect of high-density shells on deuterium-tritium pellets imploded by laser energy deposition or other means is investigated. Attention is centered on the inner parts of the pellet where hydrodynamics is the dominant mechanism. The implosions can then be characterized by a pressure boundary condition. Numerical solutions of the implosions are carried out over a wide range of parameters both for solid pellets and pellets with a central void

  8. Rheo-optical Raman study of microscopic deformation in high-density polyethylene under hot drawing

    OpenAIRE

    Kida, Takumitsu; Hiejima, Yusuke; Nitta, Koh-hei

    2015-01-01

    In situ observation of the microscopic structural changes in high-density polyethylene during hot drawing was performed by incorporating a temperature-controlled tensile machine into a Raman spectroscopy apparatus. It was found that the load sharing and molecular orientation during elongation drastically changed at 50°C. The microscopic stress of the crystalline chains decreased with increasing temperature and diminished around 50°C. Moreover, the orientation of the crystalline chains was gre...

  9. The speed of passionate love, as a subliminal prime: A high-density electrical neuroimaging stud

    OpenAIRE

    Cacioppo Stephanie; Grafton Scott T.; Bianchi-Demicheli F

    2012-01-01

    In line with the psychological model of self expansion recent neuroimaging evidence shows an overlap between the brain network mediating passionate love and that involved in self representation. Nevertheless little remains known about the temporal dynamics of these brain areas. To address this question we recorded brain activity from 20 healthy participants using high density electrophysiological recordings while participants were performing a cognitive priming paradigm known to activate the ...

  10. Single-Step Fabrication of High-Density Microdroplet Arrays of Low-Surface-Tension Liquids.

    Science.gov (United States)

    Feng, Wenqian; Li, Linxian; Du, Xin; Welle, Alexander; Levkin, Pavel A

    2016-04-01

    A facile approach for surface patterning that enables single-step fabrication of high-density arrays of low-surface-tension organic-liquid microdroplets is described. This approach enables miniaturized and parallel high-throughput screenings in organic solvents, formation of homogeneous arrays of hydrophobic nanoparticles, polymer micropads of specific shapes, and polymer microlens arrays. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  11. High-Density Renewable Fuels Based on the Selective Dimerization of Pinenes

    Science.gov (United States)

    2009-01-01

    RJ-5, significant ring strain contributing to a high heat of combustion (Table 1). Bulk agricultural waste products, such as cellulose and lignin , are...compact structures and reactive olefin functionalities, these molecules have sig- nificant potential as feedstocks for high-density renewable fuels.2b,7...potential to have heating values exceeding that of JP-10. Given the favorable potential net heat of combustion for these pinene dimers, reactivity

  12. Cooling of high-density and power electronics by means of heat pipes

    International Nuclear Information System (INIS)

    Hubbeling, L.

    1980-06-01

    This report describes how heat pipes can be used for cooling modern electronic equipment, with numerous advantages over air-cooled systems. A brief review of heat-pipe properties is given, with a detailed description of a functioning prototype. This is a single-width CAMAC unit containing high-density electronic circuits cooled by three heat pipes, and allowing a dissipation of over 120 W instead of the normal maximum of 20 W. (orig.)

  13. High-density lipoproteins inhibit urate crystal-induced inflammation in mice

    OpenAIRE

    Scanu Anna; Luisetto Roberto; Oliviero Francesca; Gruaz Lyssia; Sfriso Paolo; Burger Danielle; Punzi Leonardo

    2015-01-01

    Objectives To investigate the effects and mechanisms of action of high density lipoproteins (HDL) in monosodium urate (MSU) crystal induced inflammation—that is gouty inflammation in vivo. Methods Air pouches raised on the backs of mice were injected with MSU crystals or tumour necrosis factor (TNF) in the presence or absence of HDL and/or interleukin (IL) 1 receptor antagonist (IL 1Ra) for 3 h. Leucocyte count and neutrophil percentage in pouch fluids were measured using a haemocytometer an...

  14. High Density Silver Nanowire Arrays using Self-ordered Anodic Aluminum Oxide (AAO) Membrane

    OpenAIRE

    Han, Young-Hwan

    2008-01-01

    High density silver nanowire arrays were synthesized through the self-ordered Anodic Aluminum Oxide (AAO) template. The pore size in the AAO membrane was confirmed by processing the widening porosity with a honeycomb structure with cross sections of 20nm, 50nm, and 100nm, by SEM. Pore numbers by unit area were consistent; only pore size changed. The synthesized silver nanowire, which was crystallized, was dense in the cross sections of the amorphous AAO membrane. The synthesized silver nanowi...

  15. Practical high-density shielding materials for medical linear accelerator rooms

    International Nuclear Information System (INIS)

    Barish, R.J.

    1990-01-01

    High-energy linear accelerators are replacing lower energy units in radiation therapy centers. Radiation protection requirements necessitate expensive reconstruction of existing treatment rooms to accommodate these new machines. We describe two shielding materials: one made by embedding small pieces of scrap steel in cement, and the other made with cast iron in cement. Both materials produce high-density barriers at low cost using standard construction methods

  16. Banks-Casher-type relation for the BCS gap at high density

    OpenAIRE

    Kanazawa, Takuya; Wettig, Tilo; Yamamoto, Naoki

    2012-01-01

    We derive a new Banks-Casher-type relation which relates the density of complex Dirac eigenvalues at the origin to the BCS gap of quarks at high density. Our relation is applicable to QCD and QCD-like theories without a sign problem, such as two-color QCD and adjoint QCD with baryon chemical potential, and QCD with isospin chemical potential. It provides us with a method to measure the BCS gap through the Dirac spectrum on the lattice.

  17. Detection of an electron beam in a high density plasma via an electrostatic probe

    Science.gov (United States)

    Majeski, Stephen; Yoo, Jongsoo; Zweben, Stewart; Yamada, Masaaki; Ji, Hantao

    2017-10-01

    The perturbation in floating potential by an electron beam is detected by a 1D floating potential probe array to evaluate the use of an electron beam for magnetic field line mapping in the Magnetic Reconnection Experiment (MRX) plasma. The MRX plasma is relatively high density (1013 cm-3) and low temperature (5 eV). Beam electrons are emitted from a tungsten filament and are accelerated by a 200 V potential across the sheath. They stream along the magnetic field lines towards the probe array. The spatial electron beam density profile is assumed to be a Gaussian along the radial axis of MRX and the effective beam width is determined from the radial profile of the floating potential. The magnitude of the perturbation is in agreement with theoretical predictions and the location of the perturbation is also in agreement with field line mapping. In addition, no significant broadening of the electron beam is observed after propagation for tens of centimeters through the high density plasma. These results demonstrate that this method of field line mapping is, in principle, feasible in high density plasmas. This work is supported by the DOE Contract No. DE-AC0209CH11466.

  18. Effect of mix proportion of high density concrete on compressive strength, density and radiation absorption

    International Nuclear Information System (INIS)

    Noor Azreen Masenwat; Mohamad Pauzi Ismail; Suhairy Sani; Ismail Mustapha; Nasharuddin Isa; Mohamad Haniza Mahmud; Mohammad Shahrizan Samsu

    2014-01-01

    To prevent radiation leaks at nuclear reactors, high-density concrete is used as an absorbent material for radiation from spreading into the environment. High-density concrete is a mixture of cement, sand, aggregate (usually high-density minerals) and water. In this research, hematite stone is used because of its mineral density higher than the granite used in conventional concrete mixing. Mix concrete in this study were divided into part 1 and part 2. In part 1, the concrete mixture is designed with the same ratio of 1: 2: 4 but differentiated in terms of water-cement ratio (0.60, 0.65, 0.70, 0.75, 0.80 ). Whereas, in part 2, the concrete mixture is designed to vary the ratio of 1: 1: 2, 1: 1.5: 3, 1: 2: 3, 1: 3: 6, 1: 2: 6 with water-cement ratio (0.7, 0.8, 0.85, 0.9). In each section, the division has also performed in a mixture of sand and fine sand hematite. Then, the physical characteristics of the density and the compressive strength of the mixture of part 1 and part 2 is measured. Comparisons were also made in terms of absorption of radiation by Cs-137 and Co-60 source for each mix. This paper describes and discusses the relationship between the concrete mixture ratio, the relationship with the water-cement ratio, compressive strength, density, different mixture of sand and fine sand hematite. (author)

  19. Low-enriched uranium high-density target project. Compendium report

    Energy Technology Data Exchange (ETDEWEB)

    Vandegrift, George; Brown, M. Alex; Jerden, James L.; Gelis, Artem V.; Stepinski, Dominique C.; Wiedmeyer, Stanley; Youker, Amanda; Hebden, Andrew; Solbrekken, G; Allen, C; Robertson., D; El-Gizawy, Sherif; Govindarajan, Srisharan; Hoyer, Annemarie; Makarewicz, Philip; Harris, Jacob; Graybill, Brian; Gunn, Andy; Berlin, James; Bryan, Chris; Sherman, Steven; Hobbs, Randy; Griffin, F. P.; Chandler, David; Hurt, C. J.; Williams, Paul; Creasy, John; Tjader, Barak; McFall, Danielle; Longmire, Hollie

    2016-09-01

    At present, most 99Mo is produced in research, test, or isotope production reactors by irradiation of highly enriched uranium targets. To achieve the denser form of uranium needed for switching from high to low enriched uranium (LEU), targets in the form of a metal foil (~125-150 µm thick) are being developed. The LEU High Density Target Project successfully demonstrated several iterations of an LEU-fission-based Mo-99 technology that has the potential to provide the world’s supply of Mo-99, should major producers choose to utilize the technology. Over 50 annular high density targets have been successfully tested, and the assembly and disassembly of targets have been improved and optimized. Two target front-end processes (acidic and electrochemical) have been scaled up and demonstrated to allow for the high-density target technology to mate up to the existing producer technology for target processing. In the event that a new target processing line is started, the chemical processing of the targets is greatly simplified. Extensive modeling and safety analysis has been conducted, and the target has been qualified to be inserted into the High Flux Isotope Reactor, which is considered above and beyond the requirements for the typical use of this target due to high fluence and irradiation duration.

  20. Synthesis of high density aviation fuel with cyclopentanol derived from lignocellulose

    Science.gov (United States)

    Sheng, Xueru; Li, Ning; Li, Guangyi; Wang, Wentao; Yang, Jinfan; Cong, Yu; Wang, Aiqin; Wang, Xiaodong; Zhang, Tao

    2015-03-01

    For the first time, renewable high density aviation fuels were synthesized at high overall yield (95.6%) by the Guerbet reaction of cyclopentanol which can be derived from lignocellulose, followed by the hydrodeoxygenation (HDO). The solvent-free Guerbet reaction of cyclopentanol was carried out under the co-catalysis of solid bases and Raney metals. Among the investigated catalyst systems, the combinations of magnesium-aluminium hydrotalcite (MgAl-HT) and Raney Ni (or Raney Co) exhibited the best performances. Over them, high carbon yield (96.7%) of C10 and C15 oxygenates was achieved. The Guerbet reaction products were further hydrodeoxygenated to bi(cyclopentane) and tri(cyclopentane) over a series of Ni catalysts. These alkanes have high densities (0.86 g mL-1 and 0.91 g mL-1) and can be used as high density aviation fuels or additives to bio-jet fuel. Among the investigated HDO catalysts, the 35 wt.% Ni-SiO2-DP prepared by deposition-precipitation method exhibited the highest activity.

  1. Seismic and structural analysis of high density/consolidated spent fuel storage racks

    International Nuclear Information System (INIS)

    Shah, S.J.; Biddle, J.R.; Bennett, S.M.; Schechter, C.B.; Harstead, G.A.; Kopecky, B.

    1995-01-01

    In many nuclear power plants, existing storage racks are being replaced with high-density racks to accommodate the increasing inventory of spent fuel. In the hypothetical design considered here, the high-density arrangement of fuel assemblies, or consolidated fuel canisters, is accomplished through the use of borated stainless steel (BSS) plates acting as neutron absorbers. The high-density fuel racks are simply supported by the pool floor with no structural connections to adjacent racks or to the pool walls or floor. Therefore, the racks are free standing and may slide and tip. Several time history, nonlinear, seismic analyses are required to account for variations in the coefficient of friction, rack loading configuration, ad the type of the seismic event. This paper presents several of the mathematical models usually used. The models include features to allow sliding and tipping of the racks and to represent the hydrodynamic coupling which can occur between fuel assemblies and rack cells, between adjacent racks, and between the racks and the reinforced concrete walls. A detailed model representing a single rack is used to evaluate the 3-D loading effects. This model is a controlling case for the stress analysis. A 2-D multi-rack model representing a row of racks between the spent fuel pool walls is used to evaluate the change in gaps between racks. The racks are analyzed for the fuel loading conditions of consolidated, full, empty, and half-loaded with fuel assemblies

  2. X-ray CT high-density artefact suppression in the presence of bones

    Energy Technology Data Exchange (ETDEWEB)

    Wei Jikun [School of Health Sciences, 550 Stadium Mall Drive, West Lafayette, IN 47907-2051 (United States); Chen Laigao [BioImaging Center of Emphasis, Pfizer Global Research and Development, 2800 Plymouth RD, Ann Arbor, MI 48105 (United States); Sandison, George A [School of Health Sciences, 550 Stadium Mall Drive, West Lafayette, IN 47907-2051 (United States); Liang Yun [Department of Radiology, Indiana University Medical School, Indianapolis, IN 46202 (United States); Xu, Lisa X [School of Mechanical Engineering, 585 Purdue Mall, West Lafayette, IN 47907-2040 (United States)

    2004-12-21

    This paper presents a novel method of reducing x-ray CT high-density artefacts generated by metal objects when abundant bone structures are present in the region of interest. This method has an advantage over previously proposed methods since it heavily suppresses the metal artefacts without introducing extra bone artefacts. The method of suppression requires that bone pixels are isolated and segmented by thresholding. Then artificial CT numbers are assigned to the bone pixels so that their projection profiles are smooth and thus can be properly simulated by a polynomial interpolation. The projection profile of the metal object is then removed to fully suppress the artefacts. The resulting processed profile is fed to a reconstruction routine and the previously preserved bone pixels added back. The new method utilizes two important features of the CT image with metal artefacts: (a) metal and bone pixels are not severely affected by the high-density artefacts and (b) the high-density artefacts can be located in specific projection channels in the profile domain, although they are spread out in the image domain. This suppression method solves the problem of CT image artefacts arising from metal objects in the body. It has the potential to greatly improve diagnostic CT imaging in the presence of these objects and treatment planning that utilizes CT for patients with metal applicators (e.g., brachytherapy for cervix cancer and prostate cryotherapy)

  3. Genetic search for an optimal power flow solution from a high density cluster

    Energy Technology Data Exchange (ETDEWEB)

    Amarnath, R.V. [Hi-Tech College of Engineering and Technology, Hyderabad (India); Ramana, N.V. [JNTU College of Engineering, Jagityala (India)

    2008-07-01

    This paper proposed a novel method to solve optimal power flow (OPF) problems. The method is based on a genetic algorithm (GA) search from a High Density Cluster (GAHDC). The algorithm of the proposed method includes 3 stages, notably (1) a suboptimal solution is obtained via a conventional analytical method, (2) a high density cluster, which consists of other suboptimal data points from the first stage, is formed using a density-based cluster algorithm, and (3) a genetic algorithm based search is carried out for the exact optimal solution from a low population sized, high density cluster. The final optimal solution thoroughly satisfies the well defined fitness function. A standard IEEE 30-bus test system was considered for the simulation study. Numerical results were presented and compared with the results of other approaches. It was concluded that although there is not much difference in numerical values, the proposed method has the advantage of minimal computational effort and reduced CPU time. As such, the method would be suitable for online applications such as the present Optimal Power Flow problem. 24 refs., 2 tabs., 4 figs.

  4. Departure mechanisms for host search on high-density patches by the Meteorus pulchricornis.

    Science.gov (United States)

    Sheng, Sheng; Feng, Sufang; Meng, Ling; Li, Baoping

    2014-01-01

    Less attention has been paid to the parasitoid-host system in which the host occurs in considerably high density with a hierarchical patch structure in studies on time allocation strategies of parasitoids. This study used the parasitoid Meteorus pulchricornis (Wesmael) (Hymenoptera: Braconidae) and the Oriental leafworm, Spodoptera litura (Fabricius) (Lepidoptera: Noctuidae) as the parasitoids-host model system to investigate patch-leaving mechanisms as affected by the high-host density, hierarchical patch structure, and foraging behaviors on both former and current patches. The results showed that three out of eight covariates tested had significant effects on the patch-leaving tendency, including the host density, ovipositor insertion, and host rejection on the current patch. The parasitoid paid more visits to the patch with high-density hosts. While the patch with higher host densities decreased the leaving tendency, the spatial distribution of hosts examined had no effect on the leaving tendency. Both oviposition and host rejection decreased the patch-leaving tendency. The variables associated with the former patch, such as the host density and number of ovipositor insertions, however, did not have an effect on the leaving tendency. Our study suggested that M. pulchricornis females may use an incremental mechanism to exploit high-density patches to the fullest. © The Author 2014. Published by Oxford University Press on behalf of the Entomological Society of America.

  5. X-ray CT high-density artefact suppression in the presence of bones

    International Nuclear Information System (INIS)

    Wei Jikun; Chen Laigao; Sandison, George A; Liang Yun; Xu, Lisa X

    2004-01-01

    This paper presents a novel method of reducing x-ray CT high-density artefacts generated by metal objects when abundant bone structures are present in the region of interest. This method has an advantage over previously proposed methods since it heavily suppresses the metal artefacts without introducing extra bone artefacts. The method of suppression requires that bone pixels are isolated and segmented by thresholding. Then artificial CT numbers are assigned to the bone pixels so that their projection profiles are smooth and thus can be properly simulated by a polynomial interpolation. The projection profile of the metal object is then removed to fully suppress the artefacts. The resulting processed profile is fed to a reconstruction routine and the previously preserved bone pixels added back. The new method utilizes two important features of the CT image with metal artefacts: (a) metal and bone pixels are not severely affected by the high-density artefacts and (b) the high-density artefacts can be located in specific projection channels in the profile domain, although they are spread out in the image domain. This suppression method solves the problem of CT image artefacts arising from metal objects in the body. It has the potential to greatly improve diagnostic CT imaging in the presence of these objects and treatment planning that utilizes CT for patients with metal applicators (e.g., brachytherapy for cervix cancer and prostate cryotherapy)

  6. phangorn: phylogenetic analysis in R.

    Science.gov (United States)

    Schliep, Klaus Peter

    2011-02-15

    phangorn is a package for phylogenetic reconstruction and analysis in the R language. Previously it was only possible to estimate phylogenetic trees with distance methods in R. phangorn, now offers the possibility of reconstructing phylogenies with distance based methods, maximum parsimony or maximum likelihood (ML) and performing Hadamard conjugation. Extending the general ML framework, this package provides the possibility of estimating mixture and partition models. Furthermore, phangorn offers several functions for comparing trees, phylogenetic models or splits, simulating character data and performing congruence analyses. phangorn can be obtained through the CRAN homepage http://cran.r-project.org/web/packages/phangorn/index.html. phangorn is licensed under GPL 2.

  7. On Nakhleh's metric for reduced phylogenetic networks

    OpenAIRE

    Cardona, Gabriel; Llabrés, Mercè; Rosselló, Francesc; Valiente Feruglio, Gabriel Alejandro

    2009-01-01

    We prove that Nakhleh’s metric for reduced phylogenetic networks is also a metric on the classes of tree-child phylogenetic networks, semibinary tree-sibling time consistent phylogenetic networks, and multilabeled phylogenetic trees. We also prove that it separates distinguishable phylogenetic networks. In this way, it becomes the strongest dissimilarity measure for phylogenetic networks available so far. Furthermore, we propose a generalization of that metric that separates arbitrary phyl...

  8. Phylogenetic comparative methods on phylogenetic networks with reticulations.

    Science.gov (United States)

    Bastide, Paul; Solís-Lemus, Claudia; Kriebel, Ricardo; Sparks, K William; Ané, Cécile

    2018-04-25

    The goal of Phylogenetic Comparative Methods (PCMs) is to study the distribution of quantitative traits among related species. The observed traits are often seen as the result of a Brownian Motion (BM) along the branches of a phylogenetic tree. Reticulation events such as hybridization, gene flow or horizontal gene transfer, can substantially affect a species' traits, but are not modeled by a tree. Phylogenetic networks have been designed to represent reticulate evolution. As they become available for downstream analyses, new models of trait evolution are needed, applicable to networks. One natural extension of the BM is to use a weighted average model for the trait of a hybrid, at a reticulation point. We develop here an efficient recursive algorithm to compute the phylogenetic variance matrix of a trait on a network, in only one preorder traversal of the network. We then extend the standard PCM tools to this new framework, including phylogenetic regression with covariates (or phylogenetic ANOVA), ancestral trait reconstruction, and Pagel's λ test of phylogenetic signal. The trait of a hybrid is sometimes outside of the range of its two parents, for instance because of hybrid vigor or hybrid depression. These two phenomena are rather commonly observed in present-day hybrids. Transgressive evolution can be modeled as a shift in the trait value following a reticulation point. We develop a general framework to handle such shifts, and take advantage of the phylogenetic regression view of the problem to design statistical tests for ancestral transgressive evolution in the evolutionary history of a group of species. We study the power of these tests in several scenarios, and show that recent events have indeed the strongest impact on the trait distribution of present-day taxa. We apply those methods to a dataset of Xiphophorus fishes, to confirm and complete previous analysis in this group. All the methods developed here are available in the Julia package PhyloNetworks.

  9. Evaluation of an analytic linear Boltzmann transport equation solver for high-density inhomogeneities

    Energy Technology Data Exchange (ETDEWEB)

    Lloyd, S. A. M.; Ansbacher, W. [Department of Physics and Astronomy, University of Victoria, Victoria, British Columbia V8W 3P6 (Canada); Department of Physics and Astronomy, University of Victoria, Victoria, British Columbia V8W 3P6 (Canada) and Department of Medical Physics, British Columbia Cancer Agency-Vancouver Island Centre, Victoria, British Columbia V8R 6V5 (Canada)

    2013-01-15

    Purpose: Acuros external beam (Acuros XB) is a novel dose calculation algorithm implemented through the ECLIPSE treatment planning system. The algorithm finds a deterministic solution to the linear Boltzmann transport equation, the same equation commonly solved stochastically by Monte Carlo methods. This work is an evaluation of Acuros XB, by comparison with Monte Carlo, for dose calculation applications involving high-density materials. Existing non-Monte Carlo clinical dose calculation algorithms, such as the analytic anisotropic algorithm (AAA), do not accurately model dose perturbations due to increased electron scatter within high-density volumes. Methods: Acuros XB, AAA, and EGSnrc based Monte Carlo are used to calculate dose distributions from 18 MV and 6 MV photon beams delivered to a cubic water phantom containing a rectangular high density (4.0-8.0 g/cm{sup 3}) volume at its center. The algorithms are also used to recalculate a clinical prostate treatment plan involving a unilateral hip prosthesis, originally evaluated using AAA. These results are compared graphically and numerically using gamma-index analysis. Radio-chromic film measurements are presented to augment Monte Carlo and Acuros XB dose perturbation data. Results: Using a 2% and 1 mm gamma-analysis, between 91.3% and 96.8% of Acuros XB dose voxels containing greater than 50% the normalized dose were in agreement with Monte Carlo data for virtual phantoms involving 18 MV and 6 MV photons, stainless steel and titanium alloy implants and for on-axis and oblique field delivery. A similar gamma-analysis of AAA against Monte Carlo data showed between 80.8% and 87.3% agreement. Comparing Acuros XB and AAA evaluations of a clinical prostate patient plan involving a unilateral hip prosthesis, Acuros XB showed good overall agreement with Monte Carlo while AAA underestimated dose on the upstream medial surface of the prosthesis due to electron scatter from the high-density material. Film measurements

  10. Pressure-induced magnetic collapse and metallization of TlF e1.6S e2

    Science.gov (United States)

    Naumov, P. G.; Filsinger, K.; Shylin, S. I.; Barkalov, O. I.; Ksenofontov, V.; Qi, Y.; Palasyuk, T.; Schnelle, W.; Medvedev, S. A.; Greenblatt, M.; Felser, C.

    2017-08-01

    The crystal structure, magnetic ordering, and electrical resistivity of TlF e1.6S e2 were studied at high pressures. Below ˜7 GPa , TlF e1.6S e2 is an antiferromagnetically ordered semiconductor with a ThC r2S i2 -type structure. The insulator-to-metal transformation observed at a pressure of ˜7 GPa is accompanied by a loss of magnetic ordering and an isostructural phase transition. In the pressure range ˜7.5 -11 GPa a remarkable downturn in resistivity, which resembles a superconducting transition, is observed below 15 K. We discuss this feature as the possible onset of superconductivity originating from a phase separation in a small fraction of the sample in the vicinity of the magnetic transition.

  11. Flow Cytometry-Assisted Cloning of Specific Sequence Motifs from Complex 16S rRNA Gene Libraries

    DEFF Research Database (Denmark)

    Nielsen, Jeppe Lund; Schramm, Andreas; Bernhard, Anne E.

    2004-01-01

    for Systems Biology,3 Seattle, Washington, and Department of Ecological Microbiology, University of Bayreuth, Bayreuth, Germany2 A flow cytometry method was developed for rapid screening and recovery of cloned DNA containing common sequence motifs. This approach, termed fluorescence-activated cell sorting......  FLOW CYTOMETRY-ASSISTED CLONING OF SPECIFIC SEQUENCE MOTIFS FROM COMPLEX 16S RRNA GENE LIBRARIES Jeppe L. Nielsen,1 Andreas Schramm,1,2 Anne E. Bernhard,1 Gerrit J. van den Engh,3 and David A. Stahl1* Department of Civil and Environmental Engineering, University of Washington,1 and Institute......-assisted cloning, was used to recover sequences affiliated with a unique lineage within the Bacteroidetes not abundant in a clone library of environmental 16S rRNA genes.  ...

  12. Peptostreptococcus micros in primary endodontic infections as detected by 16S rDNA-based polymerase chain reaction.

    Science.gov (United States)

    Siqueira, José F; Rôças, Isabela N; Andrade, Arnaldo F B; de Uzeda, Milton

    2003-02-01

    A 16S rDNA-based polymerase chain reaction (PCR) method was used to detect Peptostreptococcus micros in primary root canal infections. Samples were collected from 50 teeth having carious lesions, necrotic pulps, and different forms of periradicular diseases. DNA extracted from the samples was amplified using the PCR assay, which yielded a specific fragment of P. micros 16S rDNA. P. micros was detected in 6 of 22 root canals associated with asymptomatic chronic periradicular lesions (27.3%), 2 of 8 teeth with acute apical periodontitis (25%), and 6 of 20 cases of acute periradicular abscess (30%). In general, P. micros was found in 14 of 50 cases (28%). There was no correlation between the presence of P. micros and the occurrence of symptoms. Findings suggested that P. micros can be involved in the pathogenesis of different forms of periradicular lesions.

  13. Salinity inhibits post transcriptional processing of chloroplast 16S rRNA in shoot cultures of jojoba (Simmondsia chinesis).

    Science.gov (United States)

    Mizrahi-Aviv, Ela; Mills, David; Benzioni, Aliza; Bar-Zvi, Dudy

    2005-03-01

    Chloroplast metabolism is rapidly affected by salt stress. Photosynthesis is one of the first processes known to be affected by salinity. Here, we report that salinity inhibits chloroplast post-transcriptional RNA processing. A differentially expressed 680-bp cDNA, containing the 3' sequence of 16S rRNA, transcribed intergenic spacer, exon 1 and intron of tRNA(Ile), was isolated by differential display reverse transcriptase PCR from salt-grown jojoba (Simmondsia chinesis) shoot cultures. Northern blot analysis indicated that although most rRNA appears to be fully processed, partially processed chloroplast 16S rRNA accumulates in salt-grown cultures. Thus, salinity appears to decrease the processing of the rrn transcript. The possible effect of this decreased processing on physiological processes is, as yet, unknown.

  14. Differential contributions of specimen types, culturing, and 16S rRNA sequencing in diagnosis of prosthetic joint infections

    DEFF Research Database (Denmark)

    Larsen, Lone Heimann; Khalid, Vesal; Xu, Yijuan

    2018-01-01

    to variations in specimen sampling. In this prospective, multidisciplinary study of hip or knee prosthetic failures, we assessed the contributions of different specimen types, extended culture incubations, and 16S rRNA sequencing for diagnosing prosthetic joint infections (PJI). Project specimens included joint...... fluid (JF), bone biopsy specimens (BB), soft-tissue biopsy specimens (STB), and swabs (SW) from the prosthesis, collected in situ, and sonication fluid collected from prosthetic components (PC). Specimens were cultured for 6 (conventional) or 14 days, and 16S rRNA sequencing was performed at study...... completion. Of the 156 patients enrolled, 111 underwent 114 surgical revisions (cases) due to indications of either PJI (n = 43) or AF (n = 71). Conventional tissue biopsy cultures confirmed PJI in 28/43 (65%) cases and refuted AF in 3/71 (4%) cases; one case was not evaluable. Based on these results, minor...

  15. Dominant obligate anaerobes revealed in lower respiratory tract infection in horses by 16S rRNA gene sequencing.

    Science.gov (United States)

    Kinoshita, Yuta; Niwa, Hidekazu; Katayama, Yoshinari; Hariu, Kazuhisa

    2014-04-01

    Obligate anaerobes are important etiological agents in pneumonia or pleuropneumonia in horses, because they are isolated more commonly from ill horses that have died or been euthanized than from those that survive. We performed bacterial identification and antimicrobial susceptibility testing for obligate anaerobes to establish effective antimicrobial therapy. We used 16S rRNA gene sequencing to identify 58 obligate anaerobes and compared the results with those from a phenotypic identification kit. The identification results of 16S rRNA gene sequencing were more reliable than those of the commercial kit. We concluded that genera Bacteroides and Prevotella-especially B. fragilis and P. heparinolytica-are dominant anaerobes in lower respiratory tract infection in horses; these organisms were susceptible to metronidazole, imipenem and clindamycin.

  16. Differential contributions of specimen types, culturing, and 16S rRNA sequencing in diagnosis of prosthetic joint infections

    DEFF Research Database (Denmark)

    Larsen, Lone Heimann; Khalid, Vesal; Xu, Yijuan

    2018-01-01

    Prosthetic joint failure is mainly caused by infection, aseptic failure (AF), and mechanical problems. Infection detection has been improved with modified culture methods and molecular diagnostics. However, comparisons between modified and conventional microbiology methods are difficult due...... to variations in specimen sampling. In this prospective, multidisciplinary study of hip or knee prosthetic failures, we assessed the contributions of different specimen types, extended culture incubations, and 16S rRNA sequencing for diagnosing prosthetic joint infections (PJI). Project specimens included joint...... fluid (JF), bone biopsy specimens (BB), soft-tissue biopsy specimens (STB), and swabs (SW) from the prosthesis, collected in situ, and sonication fluid collected from prosthetic components (PC). Specimens were cultured for 6 (conventional) or 14 days, and 16S rRNA sequencing was performed at study...

  17. Spatio-temporal dynamics of sulfate-reducing bacteria in extreme environment of Rogoznica Lake revealed by 16S rRNA analysis

    Science.gov (United States)

    Čanković, Milan; Petrić, Ines; Marguš, Marija; Ciglenečki, Irena

    2017-08-01

    Highly eutrophic and euxinic seawater system of Rogoznica Lake (Croatia) was used as a study site for investigation of distribution, diversity and abundance of sulfate-reducing bacteria (SRB) during stratified conditions in the summer and winter season, by targeting 6 phylogenetic subgroups of SRB. 16S rRNA gene sequences indicated that community cannot be directly related to cultured SRB species but rather that Rogoznica Lake harbors habitat-specific SRB populations associated to bacteria belonging to δ-Proteobacteria with few Firmicutes and Verrucomicrobium-related populations. Clear spatial-temporal shifts in the SRB community structure were observed. Results implied existence of distinct SRB populations between the water column and sediment, as well as higher diversity of the SRB occupying water layer then the ones found in the sediment. Likewise, seasonal variations in populations were observed. While SRB community was more diverse in the winter compared to the summer season in the water layer, situation was opposite in the sediment. Water layer communities seem to be more susceptible to changes of physico-chemical parameters, while those in the sediment have prorogated response to these changes. Results indicate that SRB diversity is still highly underestimated in natural environments, especially in specific habitats such as Rogoznica Lake. Presented data show a complex SRB diversity and distribution supporting the idea that habitat-specific SRB communities are important part of the anaerobic food chain in degradation of organic matter as well as cycling of sulfur and carbon species in the Lake and similar anoxic environment.

  18. Molecular analysis of 16S rRNA genes identifies potentially periodontal pathogenic bacteria and archaea in the plaque of partially erupted third molars.

    Science.gov (United States)

    Mansfield, J M; Campbell, J H; Bhandari, A R; Jesionowski, A M; Vickerman, M M

    2012-07-01

    Small subunit rRNA sequencing and phylogenetic analysis were used to identify cultivable and uncultivable microorganisms present in the dental plaque of symptomatic and asymptomatic partially erupted third molars to determine the prevalence of putative periodontal pathogens in pericoronal sites. Template DNA prepared from subgingival plaque collected from partially erupted symptomatic and asymptomatic mandibular third molars and healthy incisors was used in polymerase chain reaction with broad-range oligonucleotide primers to amplify 16S rRNA bacterial and archaeal genes. Amplicons were cloned, sequenced, and compared with known nucleotide sequences in online databases to identify the microorganisms present. Two thousand three hundred two clones from the plaque of 12 patients carried bacterial sequences from 63 genera belonging to 11 phyla, including members of the uncultivable TM7, SR1, and Chloroflexi, and difficult-to-cultivate Synergistetes and Spirochaetes. Dialister invisus, Filifactor alocis, Fusobacterium nucleatum, Porphyromonas endodontalis, Prevotella denticola, Tannerella forsythia, and Treponema denticola, which have been associated with periodontal disease, were found in significantly greater abundance in pericoronal compared with incisor sites. Dialister invisus and F nucleatum were found in greater abundance in sites exhibiting clinical symptoms. The archaeal species, Methanobrevibacter oralis, which has been associated with severe periodontitis, was found in 3 symptomatic patients. These findings have provided new insights into the complex microbiota of pericoronitis. Several bacterial and archaeal species implicated in periodontal disease were recovered in greater incidence and abundance from the plaque of partially erupted third molars compared with incisors, supporting the hypothesis that the pericoronal region may provide a favored niche for periodontal pathogens in otherwise healthy mouths. Copyright © 2012 American Association of Oral and

  19. FILOGENETIK POPULASI UDANG JERBUNG (Fenneropenaeus merguiensis de Man DI INDONESIA BERDASARKAN SEKUENS 16S-rRNA DNA MITOKONDRIA

    Directory of Open Access Journals (Sweden)

    Eni Kusrini

    2016-11-01

    Full Text Available Penelitian ini dilakukan untuk mengetahui hubungan kekerabatan stok udang jerbung Indonesia sebagai informasi dasar bagi program pemuliaan. Udang jerbung uji berasal dari Pantai Bengkulu, Selat Sunda (Banten, Pantai Cilacap (Jawa Tengah, Selat Lombok (NTB, dan Pontianak (Kalimantan Barat. Amplifikasi PCR dan sekuensing daerah 16S-rRNA DNA mitokondria dilakukan menggunakan primer 5’-CGCCTGTTTAAC-AAAAACAT-3’ dan 5’-CCGGTCTGAACTCAGATCATGT-3’. Hasil analisis homologi susunan nukleotida 16S-rRNA DNA mitokondria menunjukkan bahwa udang jerbung yang digunakan dalam penelitian merupakan Fenneropenaeus merguiensis. Hasil analisis kekerabatan menunjukkan bahwa 5 populasi udang jerbung uji dapat dibagi menjadi 2 kelompok besar, yaitu kelompok Kalimantan Barat dan kelompok Bengkulu-Banten-Jawa Tengah-NTB. Populasi udang jerbung Kalimantan dan Bengkulu masing-masing memiliki sekuens spesifik, yaitu ACTGACT dan C-GAC di terminal 5. Sekuens tersebut mungkin dapat digunakan sebagai penanda dalam program pemuliaan udang jerbung Indonesia. The experiment was conducted to understand the family relationship of banana prawn in Indonesia and to provide basic information for breeding program. Prawns were obtained from Bengkulu Coast, Sunda Strait (Banten, Cilacap Coast (Central Java, Lombok Strait (West Nusa Tenggara, Pontianak Coast (West Kalimantan. PCR amplification and sequencing of 16S-rRNA mitochondrial DNA region were performed using 5’-CGCCTGTTTAAC-AAAAACAT-3’ and 5’-CCGGTCTGAACTCAGATCATGT-3’. Analysis of homology sequences of 16S-rRNA mtDNA showed that banana prawn used in this study was Fenneropenaeus merguiensis. Result of family relationship analysis indicated that five populations of banana prawn can be divided into two groups, i.e. West Kalimantan and Bengkulu-Banten-Central Java-NTB groups. Banana prawns from West Kalimantan and Bengkulu have specific sequences at 5’ terminal, ACTGACT and C-GAC, respectively. Those sequences can

  20. Microbial Diversity of Bovine Mastitic Milk as Described by Pyrosequencing of Metagenomic 16s rDNA

    OpenAIRE

    Oikonomou, Georgios; Machado, Vinicius Silva; Santisteban, Carlos; Schukken, Ynte Hein; Bicalho, Rodrigo Carvalho

    2012-01-01

    Dairy cow mastitis is an important disease in the dairy industry. Different microbial species have been identified as causative agents in mastitis, and are traditionally diagnosed by bacterial culture. The objective of this study was to use metagenomic pyrosequencing of bacterial 16S rRNA genes to investigate bacterial DNA diversity in milk samples of mastitic and healthy dairy cows and compare the results with those obtained by classical bacterial culture. One hundred and thirty-six milk sam...

  1. A comprehensive evaluation of the sl1p pipeline for 16S rRNA gene sequencing analysis.

    Science.gov (United States)

    Whelan, Fiona J; Surette, Michael G

    2017-08-14

    Advances in next-generation sequencing technologies have allowed for detailed, molecular-based studies of microbial communities such as the human gut, soil, and ocean waters. Sequencing of the 16S rRNA gene, specific to prokaryotes, using universal PCR primers has become a common approach to studying the composition of these microbiota. However, the bioinformatic processing of the resulting millions of DNA sequences can be challenging, and a standardized protocol would aid in reproducible analyses. The short-read library 16S rRNA gene sequencing pipeline (sl1p, pronounced "slip") was designed with the purpose of mitigating this lack of reproducibility by combining pre-existing tools into a computational pipeline. This pipeline automates the processing of raw 16S rRNA gene sequencing data to create human-readable tables, graphs, and figures to make the collected data more readily accessible. Data generated from mock communities were compared using eight OTU clustering algorithms, two taxon assignment approaches, and three 16S rRNA gene reference databases. While all of these algorithms and options are available to sl1p users, through testing with human-associated mock communities, AbundantOTU+, the RDP Classifier, and the Greengenes 2011 reference database were chosen as sl1p's defaults based on their ability to best represent the known input communities. sl1p promotes reproducible research by providing a comprehensive log file, and reduces the computational knowledge needed by the user to process next-generation sequencing data. sl1p is freely available at https://bitbucket.org/fwhelan/sl1p .

  2. Assessing hog lagoon waste contamination in the Cape Fear Watershed using Bacteroidetes 16S rRNA gene pyrosequencing.

    Science.gov (United States)

    Arfken, Ann M; Song, Bongkeun; Mallin, Michael A

    2015-09-01

    Hog lagoons can be major sources of waste and nutrient contamination to watersheds adjacent to pig farms. Fecal source tracking methods targeting Bacteroidetes 16S rRNA genes in pig fecal matter may underestimate or fail to detect hog lagoon contamination in riverine environments. In order to detect hog lagoon wastewater contamination in the Cape Fear Watershed, where a large number of hog farms are present, we conducted pyrosequencing analyses of Bacteroidetes 16S rRNA genes in hog lagoon waste and identified new hog lagoon-specific marker sequences. Additional pyrosequencing analyses of Bacteroidetes 16S rRNA genes were conducted with surface water samples collected at 4 sites during 5 months in the Cape Fear Watershed. Using an operational taxonomic unit (OTU) identity cutoff value of 97 %, these newly identified hog lagoon markers were found in 3 of the river samples, while only 1 sample contained the pig fecal marker. In the sample containing the pig fecal marker, there was a relatively high percentage (14.1 %) of the hog lagoon markers and a low pig fecal marker relative abundance of 0.4 % in the Bacteroidetes 16S rRNA gene sequences. This suggests that hog lagoon contamination must be somewhat significant in order for pig fecal markers to be detected, and low levels of hog lagoon contamination cannot be detected targeting only pig-specific fecal markers. Thus, new hog lagoon markers have a better detection capacity for lagoon waste contamination, and in conjunction with a pig fecal marker, provide a more comprehensive and accurate detection of hog lagoon waste contamination in susceptible watersheds.

  3. Analysis of 16S rRNA amplicon sequencing options on the Roche/454 next-generation titanium sequencing platform.

    Directory of Open Access Journals (Sweden)

    Hideyuki Tamaki

    Full Text Available BACKGROUND: 16S rRNA gene pyrosequencing approach has revolutionized studies in microbial ecology. While primer selection and short read length can affect the resulting microbial community profile, little is known about the influence of pyrosequencing methods on the sequencing throughput and the outcome of microbial community analyses. The aim of this study is to compare differences in output, ease, and cost among three different amplicon pyrosequencing methods for the Roche/454 Titanium platform METHODOLOGY/PRINCIPAL FINDINGS: The following three pyrosequencing methods for 16S rRNA genes were selected in this study: Method-1 (standard method is the recommended method for bi-directional sequencing using the LIB-A kit; Method-2 is a new option designed in this study for unidirectional sequencing with the LIB-A kit; and Method-3 uses the LIB-L kit for unidirectional sequencing. In our comparison among these three methods using 10 different environmental samples, Method-2 and Method-3 produced 1.5-1.6 times more useable reads than the standard method (Method-1, after quality-based trimming, and did not compromise the outcome of microbial community analyses. Specifically, Method-3 is the most cost-effective unidirectional amplicon sequencing method as it provided the most reads and required the least effort in consumables management. CONCLUSIONS: Our findings clearly demonstrated that alternative pyrosequencing methods for 16S rRNA genes could drastically affect sequencing output (e.g. number of reads before and after trimming but have little effect on the outcomes of microbial community analysis. This finding is important for both researchers and sequencing facilities utilizing 16S rRNA gene pyrosequencing for microbial ecological studies.

  4. Metagenomic Analysis of Slovak Bryndza Cheese Using Next-Generation 16S rDNA Amplicon Sequencing

    Directory of Open Access Journals (Sweden)

    Planý Matej

    2016-06-01

    Full Text Available Knowledge about diversity and taxonomic structure of the microbial population present in traditional fermented foods plays a key role in starter culture selection, safety improvement and quality enhancement of the end product. Aim of this study was to investigate microbial consortia composition in Slovak bryndza cheese. For this purpose, we used culture-independent approach based on 16S rDNA amplicon sequencing using next generation sequencing platform. Results obtained by the analysis of three commercial (produced on industrial scale in winter season and one traditional (artisanal, most valued, produced in May Slovak bryndza cheese sample were compared. A diverse prokaryotic microflora composed mostly of the genera Lactococcus, Streptococcus, Lactobacillus, and Enterococcus was identified. Lactococcus lactis subsp. lactis and Lactococcus lactis subsp. cremoris were the dominant taxons in all tested samples. Second most abundant species, detected in all bryndza cheeses, were Lactococcus fujiensis and Lactococcus taiwanensis, independently by two different approaches, using different reference 16S rRNA genes databases (Greengenes and NCBI respectively. They have been detected in bryndza cheese samples in substantial amount for the first time. The narrowest microbial diversity was observed in a sample made with a starter culture from pasteurised milk. Metagenomic analysis by high-throughput sequencing using 16S rRNA genes seems to be a powerful tool for studying the structure of the microbial population in cheeses.

  5. The Comparison of Biochemical and Sequencing 16S rDNA Gene Methods to Identify Nontuberculous Mycobacteria

    Directory of Open Access Journals (Sweden)

    Shafipour1, M.

    2014-11-01

    Full Text Available The identification of Mycobacteria in the species level has great medical importance. Biochemical tests are laborious and time-consuming, so new techniques could be used to identify the species. This research aimed to the comparison of biochemical and sequencing 16S rDNA gene methods to identify nontuberculous Mycobacteria in patients suspected to tuberculosis in Golestan province which is the most prevalent region of tuberculosis in Iran. Among 3336 patients suspected to tuberculosis referred to hospitals and health care centres in Golestan province during 2010-2011, 319 (9.56% culture positive cases were collected. Identification of species by using biochemical tests was done. On the samples recognized as nontuberculous Mycobacteria, after DNA extraction by boiling, 16S rDNA PCR was done and their sequencing were identified by NCBI BLAST. Of the 319 positive samples in Golestan Province, 300 cases were M.tuberculosis and 19 cases (5.01% were identified as nontuberculous Mycobacteria by biochemical tests. 15 out of 19 nontuberculous Mycobacteria were identified by PCR and sequencing method as similar by biochemical methods (similarity rate: 78.9%. But after PCR, 1 case known as M.simiae by biochemical test was identified as M. lentiflavum and 3 other cases were identified as Nocardia. Biochemical methods corresponded to the 16S rDNA PCR and sequencing in 78.9% of cases. However, in identification of M. lentiflavum and Nocaria sp. the molecular method is better than biochemical methods.

  6. Point estimates in phylogenetic reconstructions

    OpenAIRE

    Benner, Philipp; Bacak, Miroslav; Bourguignon, Pierre-Yves

    2013-01-01

    Motivation: The construction of statistics for summarizing posterior samples returned by a Bayesian phylogenetic study has so far been hindered by the poor geometric insights available into the space of phylogenetic trees, and ad hoc methods such as the derivation of a consensus tree makeup for the ill-definition of the usual concepts of posterior mean, while bootstrap methods mitigate the absence of a sound concept of variance. Yielding satisfactory results with sufficiently concentrated pos...

  7. Paenibacillus larvae 16S-23S rDNA intergenic transcribed spacer (ITS) regions: DNA fingerprinting and characterization.

    Science.gov (United States)

    Dingman, Douglas W

    2012-07-01

    Paenibacillus larvae is the causative agent of American foulbrood in honey bee (Apis mellifera) larvae. PCR amplification of the 16S-23S ribosomal DNA (rDNA) intergenic transcribed spacer (ITS) regions, and agarose gel electrophoresis of the amplified DNA, was performed using genomic DNA collected from 134 P. larvae strains isolated in Connecticut, six Northern Regional Research Laboratory stock strains, four strains isolated in Argentina, and one strain isolated in Chile. Following electrophoresis of amplified DNA, all isolates exhibited a common migratory profile (i.e., ITS-PCR fingerprint pattern) of six DNA bands. This profile represented a unique ITS-PCR DNA fingerprint that was useful as a fast, simple, and accurate procedure for identification of P. larvae. Digestion of ITS-PCR amplified DNA, using mung bean nuclease prior to electrophoresis, characterized only three of the six electrophoresis bands as homoduplex DNA and indicating three true ITS regions. These three ITS regions, DNA migratory band sizes of 915, 1010, and 1474 bp, signify a minimum of three types of rrn operons within P. larvae. DNA sequence analysis of ITS region DNA, using P. larvae NRRL B-3553, identified the 3' terminal nucleotides of the 16S rRNA gene, 5' terminal nucleotides of the 23S rRNA gene, and the complete DNA sequences of the 5S rRNA, tRNA(ala), and tRNA(ile) genes. Gene organization within the three rrn operon types was 16S-23S, 16S-tRNA(ala)-23S, and l6S-5S-tRNA(ile)-tRNA(ala)-23S and these operons were named rrnA, rrnF, and rrnG, respectively. The 23S rRNA gene was shown by I-CeuI digestion and pulsed-field gel electrophoresis of genomic DNA to be present as seven copies. This was suggestive of seven rrn operon copies within the P. larvae genome. Investigation of the 16S-23S rDNA regions of this bacterium has aided the development of a diagnostic procedure and has helped genomic mapping investigations via characterization of the ITS regions. Copyright © 2012 Elsevier Inc

  8. Development of an Analysis Pipeline Characterizing Multiple Hypervariable Regions of 16S rRNA Using Mock Samples.

    Directory of Open Access Journals (Sweden)

    Jennifer J Barb

    Full Text Available There is much speculation on which hypervariable region provides the highest bacterial specificity in 16S rRNA sequencing. The optimum solution to prevent bias and to obtain a comprehensive view of complex bacterial communities would be to sequence the entire 16S rRNA gene; however, this is not possible with second generation standard library design and short-read next-generation sequencing technology.This paper examines a new process using seven hypervariable or V regions of the 16S rRNA (six amplicons: V2, V3, V4, V6-7, V8, and V9 processed simultaneously on the Ion Torrent Personal Genome Machine (Life Technologies, Grand Island, NY. Four mock samples were amplified using the 16S Ion Metagenomics Kit™ (Life Technologies and their sequencing data is subjected to a novel analytical pipeline.Results are presented at family and genus level. The Kullback-Leibler divergence (DKL, a measure of the departure of the computed from the nominal bacterial distribution in the mock samples, was used to infer which region performed best at the family and genus levels. Three different hypervariable regions, V2, V4, and V6-7, produced the lowest divergence compared to the known mock sample. The V9 region gave the highest (worst average DKL while the V4 gave the lowest (best average DKL. In addition to having a high DKL, the V9 region in both the forward and reverse directions performed the worst finding only 17% and 53% of the known family level and 12% and 47% of the genus level bacteria, while results from the forward and reverse V4 region identified all 17 family level bacteria.The results of our analysis have shown that our sequencing methods using 6 hypervariable regions of the 16S rRNA and subsequent analysis is valid. This method also allowed for the assessment of how well each of the variable regions might perform simultaneously. Our findings will provide the basis for future work intended to assess microbial abundance at different time points

  9. Molecular Phylogenetic Classification of Streptomycetes Isolated from the Rhizosphere of Tropical Legume (Paraserianthes falcataria (L. Nielsen

    Directory of Open Access Journals (Sweden)

    LANGKAH SEMBIRING

    2009-09-01

    Full Text Available Intrageneric diversity of 556 streptomycetes isolated from the rhizosphere of tropical legume was determined by using molecular taxonomic method based on 16S rDNA. A total of 46 isolates were taken to represent 37 colour groups of the isolates. 16S rDNA were amplified and subsequently sequenced and the sequences data were aligned with streptomycete sequences retrieved from the ribosomal data base project (RDP data. Phylogenetic trees were generated by using the PHYLIP software package and the matrix of nucleotide similarity and nucleotide difference were generated by using PHYDIT software. The results confirmed and extended the value of 16S rDNA sequencing in streptomycete systematic. The 16S rDNA sequence data showed that most of the tested colour group representatives formed new centers of taxonomic variation within the genus Streptomyces. The generic assignment of these organisms was underpinned by 16S rDNA sequence data which also suggested that most of the strains represented new centers of taxonomic variation. The taxonomic data indicate that diverse populations of streptomycetes are associated with the roots of tropical legume (P. falcataria. Therefore, the combination of selective isolation and molecular taxonomic procedures used in this study provide a powerful way of uncovering new centers of taxonomic variation within the genus Streptomyces.

  10. Use of a high density lead glass tubing projection chamber in positron emission tomography and in high energy physics

    International Nuclear Information System (INIS)

    Conti, M.; Guerra, A.D.; Habel, R.; Mulera, T.; Perez-Mendez, V.; Schwartz, G.

    1985-10-01

    We describe the principle of operation of a high density Projection Chamber, in which the converter/radiator and drift field shaping structures are combined in the form of high density (5 to 6 g/cm 3 ) lead glass tubing. The main applications of this type of detector to Medical Physics (Positron Emission Tomography) and High Energy Physics (Electromagnetic Calorimetry) are discussed

  11. Combined analysis of six lipoprotein lipase genetic variants on triglycerides, high-density lipoprotein, and ischemic heart disease

    DEFF Research Database (Denmark)

    Wittrup, Hans H; Andersen, Rolf V; Tybjaerg-Hansen, Anne

    2006-01-01

    Genetic variants in lipoprotein lipase may affect triglycerides, high-density lipoprotein (HDL), and risk of ischemic heart disease (IHD).......Genetic variants in lipoprotein lipase may affect triglycerides, high-density lipoprotein (HDL), and risk of ischemic heart disease (IHD)....

  12. Phylogenetic lineages in Pseudocercospora.

    Science.gov (United States)

    Crous, P W; Braun, U; Hunter, G C; Wingfield, M J; Verkley, G J M; Shin, H-D; Nakashima, C; Groenewald, J Z

    2013-06-30

    Pseudocercospora is a large cosmopolitan genus of plant pathogenic fungi that are commonly associated with leaf and fruit spots as well as blights on a wide range of plant hosts. They occur in arid as well as wet environments and in a wide range of climates including cool temperate, sub-tropical and tropical regions. Pseudocercospora is now treated as a genus in its own right, although formerly recognised as either an anamorphic state of Mycosphaerella or having mycosphaerella-like teleomorphs. The aim of this study was to sequence the partial 28S nuclear ribosomal RNA gene of a selected set of isolates to resolve phylogenetic generic limits within the Pseudocercospora complex. From these data, 14 clades are recognised, six of which cluster in Mycosphaerellaceae. Pseudocercospora s. str. represents a distinct clade, sister to Passalora eucalypti, and a clade representing the genera Scolecostigmina, Trochophora and Pallidocercospora gen. nov., taxa formerly accommodated in the Mycosphaerella heimii complex and characterised by smooth, pale brown conidia, as well as the formation of red crystals in agar media. Other clades in Mycosphaerellaceae include Sonderhenia, Microcyclosporella, and Paracercospora. Pseudocercosporella resides in a large clade along with Phloeospora, Miuraea, Cercospora and Septoria. Additional clades represent Dissoconiaceae, Teratosphaeriaceae, Cladosporiaceae, and the genera Xenostigmina, Strelitziana, Cyphellophora and Thedgonia. The genus Phaeomycocentrospora is introduced to accommodate Mycocentrospora cantuariensis, primarily distinguished from Pseudocercospora based on its hyaline hyphae, broad conidiogenous loci and hila. Host specificity was considered for 146 species of Pseudocercospora occurring on 115 host genera from 33 countries. Partial nucleotide sequence data for three gene loci, ITS, EF-1α, and ACT suggest that the majority of these species are host specific. Species identified on the basis of host, symptomatology and general

  13. Microbial diversity and activity in the Nematostella vectensis holobiont: insights from 16S rRNA gene sequencing, isolate genomes, and a pilot-scale survey of gene expression

    Directory of Open Access Journals (Sweden)

    Jia Yi Har

    2015-09-01

    Full Text Available We have characterized the molecular and genomic diversity of the microbiota of the starlet sea anemone Nematostella vectensis, a cnidarian model for comparative developmental and functional biology and a year-round inhabitant of temperate salt marshes. Molecular phylogenetic analysis of 16S rRNA gene clone libraries revealed four ribotypes associated with N. vectensis at multiple locations and times. These associates include two novel ribotypes within the ε-Proteobacterial order Campylobacterales and the Spirochetes, respectively, each sharing 99% 16S rRNA identity with Endozoicomonas elysicola and Pseudomonas oleovorans, respectively. Species-specific PCR revealed that these populations persisted in N. vectensis asexually propagated under laboratory conditions. cDNA indicated expression of the Campylobacterales and Endozoicomonas 16S rRNA in anemones from Sippewissett Marsh, MA. A collection of bacteria from laboratory raised N. vectensis was dominated by isolates from P. oleovorans and Rhizobium radiobacter. Isolates from field-collected anemones revealed an association with Limnobacter and Stappia isolates. Genomic DNA sequencing was carried out on 10 cultured bacterial isolates representing field- and laboratory-associates, i.e. Limnobacter spp., Stappia spp., P. oleovorans and R. radiobacter. Genomes contained multiple genes identified as virulence (host-association factors while S. stellulata and L. thiooxidans genomes revealed pathways for mixotrophic sulfur oxidation. A pilot metatranscriptome of laboratory-raised N. vectensis was compared to the isolate genomes and indicated expression of ORFs from L. thiooxidans with predicted functions of motility, nutrient scavenging (Fe and P, polyhydroxyalkanoate synthesis for carbon storage, and selective permeability (porins. We hypothesize that such activities may mediate acclimation and persistence of bacteria in N. vectensis.

  14. Microbial diversity and activity in the Nematostella vectensis holobiont: insights from 16S rRNA gene sequencing, isolate genomes, and a pilot-scale survey of gene expression.

    Science.gov (United States)

    Har, Jia Y; Helbig, Tim; Lim, Ju H; Fernando, Samodha C; Reitzel, Adam M; Penn, Kevin; Thompson, Janelle R

    2015-01-01

    We have characterized the molecular and genomic diversity of the microbiota of the starlet sea anemone Nematostella vectensis, a cnidarian model for comparative developmental and functional biology and a year-round inhabitant of temperate salt marshes. Molecular phylogenetic analysis of 16S rRNA gene clone libraries revealed four ribotypes associated with N. vectensis at multiple locations and times. These associates include two novel ribotypes within the ε-Proteobacterial order Campylobacterales and the Spirochetes, respectively, each sharing 99% 16S rRNA identity with Endozoicomonas elysicola and Pseudomonas oleovorans, respectively. Species-specific PCR revealed that these populations persisted in N. vectensis asexually propagated under laboratory conditions. cDNA indicated expression of the Campylobacterales and Endozoicomonas 16S rRNA in anemones from Sippewissett Marsh, MA. A collection of bacteria from laboratory raised N. vectensis was dominated by isolates from P. oleovorans and Rhizobium radiobacter. Isolates from field-collected anemones revealed an association with Limnobacter and Stappia isolates. Genomic DNA sequencing was carried out on 10 cultured bacterial isolates representing field- and laboratory-associates, i.e., Limnobacter spp., Stappia spp., P. oleovorans and R. radiobacter. Genomes contained multiple genes identified as virulence (host-association) factors while S. stellulata and L. thiooxidans genomes revealed pathways for mixotrophic sulfur oxidation. A pilot metatranscriptome of laboratory-raised N. vectensis was compared to the isolate genomes and indicated expression of ORFs from L. thiooxidans with predicted functions of motility, nutrient scavenging (Fe and P), polyhydroxyalkanoate synthesis for carbon storage, and selective permeability (porins). We hypothesize that such activities may mediate acclimation and persistence of bacteria in a N. vectensis holobiont defined by both internal and external gradients of chemicals and

  15. Novel Bacteriocinogenic Lactobacillus plantarum Strains and Their Differentiation by Sequence Analysis of 16S rDNA, 16S-23S and 23S-5S Intergenic Spacer Regions and Randomly Amplified Polymorphic DNA Analysis

    Directory of Open Access Journals (Sweden)

    Morteza Shojaei Moghadam

    2010-01-01

    Full Text Available Six strains of bacteriocinogenic Lactobacillus plantarum (TL1, RG11, RS5, UL4, RG14 and RI11 isolated from Malaysian foods were investigated for their structural bacteriocin genes. A new combination of plantaricin EF and plantaricin W bacteriocin structural genes was successfully amplified from all studied strains, suggesting that they were novel bacteriocin-producing L. plantarum strains. A four-base pair variable region was detected in the short 16S-23S intergenic spacer regions of the studied strains by a comparative analysis with 17 L. plantarum strains deposited in the GenBank, implying they were new genotypes. The studied L. plantarum strains were subsequently differentiated into four groups on the basis of the detected four-base pair variable region of the short 16S-23S intergenic spacer region. Further analysis of the DNA sequence of 23S-5S intergenic spacer region revealed only one type of 23S-5S intergenic spacer region present in the studied strains, indicating it was highly conserved among the studied L. plantarum strains. Three randomly amplified polymorphic DNA experiments using three different combinations of arbitrary primers successfully differentiated the studied L. plantarum strains from each other, confirming they were different strains. In conclusion, the studied L. plantarum strains were shown to be novel bacteriocin producers and high level of strain discrimination could be achieved with a combination of randomly amplified polymorphic DNA analysis and the analysis of the variable region of short 16S-23S intergenic spacer region present in L. plantarum strains.

  16. Pruning for crop regulation in high density guava (Psidium guajava L.) plantation

    Energy Technology Data Exchange (ETDEWEB)

    Thakre, M.; Lal, S.; Uniyal, S.; Goswami, A.K. Prakash. P.

    2016-11-01

    High density management and crop regulation are two important aspects in guava (Psidium guajava L.) production. Therefore, to find out the economic way of managing high density planting and crop regulation, the present work was carried out on 6-year-old guava trees of cv. Pant Prabhat under double-hedge row system of planting during 2009-10 and 2010-11. Seven different forms of pruning [FBT: flower bud thinning by hand, FBTT: flower bud thinning by hand followed by removal of terminal one leaf pair, RLFO: removal of leaves and flower buds by hand, retaining one leaf pair at the top, RLF: removal of all leaves and flowers by hand, OLPS: one leaf pair shoot pruning, FSP: full shoot pruning, OLPF: one leaf pair pruning of fruited shoots only] were studied along with control (C).Minimum annual increase in tree volume (6.764 m3) was recorded with the treatment OLPF, which was 2.31 times less than the control (15.682 m3). Highest yield during winter season (55.30 kg/tree) and total yield (59.87 kg/tree) was obtained from treatment OLPF. One leaf pair pruning of fruited shoots only (OLPF) was also found profitable among other treatments by recording cost:benefit ratio of 1:2.96. This treatment also recorded the highest return distributed in rainy as well as in winter season. On the basis of findings it can be concluded that one leaf pair pruning of fruited shoots only is suitable for profitable high density management as well as crop regulation of guava in farmer friendly manner. (Author)

  17. Pruning for crop regulation in high density guava (Psidium guajava L. plantation

    Directory of Open Access Journals (Sweden)

    Madhubala Thakre

    2016-06-01

    Full Text Available High density management and crop regulation are two important aspects in guava (Psidium guajava L. production. Therefore, to find out the economic way of managing high density planting and crop regulation, the present work was carried out on 6-year-old guava trees of cv. Pant Prabhat under double-hedge row system of planting during 2009-10 and 2010-11. Seven different forms of pruning [FBT: flower bud thinning by hand, FBTT: flower bud thinning by hand followed by removal of terminal one leaf pair, RLFO: removal of leaves and flower buds by hand, retaining one leaf pair at the top, RLF: removal of all leaves and flowers by hand, OLPS: one leaf pair shoot pruning, FSP: full shoot pruning, OLPF: one leaf pair pruning of fruited shoots only] were studied along with control (C.Minimum annual increase in tree volume (6.764 m3 was recorded with the treatment OLPF, which was 2.31 times less than the control (15.682 m3. Highest yield during winter season (55.30 kg/tree and total yield (59.87 kg/tree was obtained from treatment OLPF. One leaf pair pruning of fruited shoots only (OLPF was also found profitable among other treatments by recording cost:benefit ratio of 1:2.96. This treatment also recorded the highest return distributed in rainy as well as in winter season. On the basis of findings it can be concluded that one leaf pair pruning of fruited shoots only is suitable for profitable high density management as well as crop regulation of guava in farmer friendly manner.

  18. A study of HANARO core conversion using high density U-Mo fuel

    International Nuclear Information System (INIS)

    Lee, K.H.; Lee, C.S.; Lee, B.C.; Park, S.J.; Kim, H.; Kim, C.K.

    2002-01-01

    Currently, HANARO is using 3.15gU/cc U3Si/Al as a driver fuel. HANARO has seven vertical irradiation holes in the core region. Three of them including a central trap are located in the inner region of the core and mainly being used for material irradiation tests. Four of them are located in the reflector tank but cooled by primary coolant. They are used for fuel irradiation tests or radioisotope development tests. For minimum core modification using high density U-Mo fuels, no dimension change is assumed in the current fuel rods and the cladding thickness remains the same in this study. The high density U-Mo fuel will have up to about twice the linear uranium loading of a current HANARO driver fuel. Using this high density fuel 8 fuel sites can be replaced with irradiation sites. Three kinds of conceptual cores are considered using 5 gU/cc U-7Mo/Al and 16 gU/cc U-7Mo. The increase of the linear heat generation rate due to the decrease of total fuel length can be overcome by more uniform radial and axial power distribution using different uranium densities and different fuel meat diameters are introduced into those cores. The new core has 4.54 times larger surface-to-volume ratio than the reference core. The core uranium loading, linear heat generation rate, excess reactivity, and control rod worth as well as the neutron spectra are analysed for each core. (author)

  19. Hydrological impact of high-density small dams in a humid catchment, Southeast China

    Science.gov (United States)

    Lu, W.; Lei, H.; Yang, D.

    2017-12-01

    The Jiulong River basin is a humid catchment with a drainage area of 14,741 km2; however, it has over 1000 hydropower stations within it. Such catchment with high-density small dams is scarce in China. Yet few is known about the impact of high-density small dams on streamflow changes. To what extent the large number of dams alters the hydrologic patterns is a fundamental scientific issue for water resources management, flood control, and aquatic ecological environment protection. Firstly, trend and change point analyses are applied to determine the characteristics of inter-annual streamflow. Based on the detected change point, the study period is divided into two study periods, the ``natural'' and ``disturbed'' periods. Then, a geomorphology-based hydrological model (GBHM) and the fixing-changing method are adopted to evaluate the relative contributions of climate variations and damming to the changes in streamflow at each temporal scale (i.e., from daily, monthly to annual). Based on the simulated natural streamflow, the impact of dam construction on hydrologic alteration and aquatic ecological environment will be evaluated. The hydrologic signatures that will be investigated include flood peak, seasonality of streamflow, and the inter-annual variability of streamflow. In particular, the impacts of damming on aquatic ecological environment will be investigated using eco-flow metrics and indicators of hydrologic alteration (IHA) which contains 33 individual streamflow statistics that are closely related to aquatic ecosystem. The results of this study expect to provide a reference for reservoir operation considering both ecological and economic benefits of such operations in the catchment with high-density dams.

  20. Nuclear matter at high density: Phase transitions, multiquark states, and supernova outbursts

    International Nuclear Information System (INIS)

    Krivoruchenko, M. I.; Nadyozhin, D. K.; Rasinkova, T. L.; Simonov, Yu. A.; Trusov, M. A.; Yudin, A. V.

    2011-01-01

    Phase transition from hadronic matter to quark-gluon matter is discussed for various regimes of temperature and baryon number density. For small and medium densities, the phase transition is accurately described in the framework of the Field Correlation Method, whereas at high density predictions are less certain and leave room for the phenomenological models. We study formation of multiquark states (MQS) at zero temperature and high density. Relevant MQS components of the nuclear matter can be described using a previously developed formalism of the quark compound bags (QCB). Partialwave analysis of nucleon-nucleon scattering indicates the existence of 6QS which manifest themselves as poles of P matrix. In the framework of the QCB model, we formulate a self-consistent system of coupled equations for the nucleon and 6QS propagators in nuclear matter and the G matrix. The approach provides a link between high-density nuclear matter with the MQS components and the cumulative effect observed in reactions on the nuclei, which requires the admixture of MQS in the wave functions of nuclei kinematically. 6QS determines the natural scale of the density for a possible phase transition into theMQS phase of nuclear matter. Such a phase transition can lead to dynamic instability of newly born protoneutron stars and dramatically affect the dynamics of supernovae. Numerical simulations show that the phase transition may be a good remedy for the triggering supernova explosions in the spherically symmetric supernovamodels. A specific signature of the phase transition is an additional neutrino peak in the neutrino light curve. For a Galactic core-collapse supernova, such a peak could be resolved by the present neutrino detectors. The possibility of extracting the parameters of the phase of transition from observation of the neutrino signal is discussed also.